[med-svn] r9264 - in trunk/packages/exonerate/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Thu Jan 12 10:59:00 UTC 2012
Author: tille
Date: 2012-01-12 10:58:59 +0000 (Thu, 12 Jan 2012)
New Revision: 9264
Removed:
trunk/packages/exonerate/trunk/debian/patches/autoreconf.patch
Modified:
trunk/packages/exonerate/trunk/debian/changelog
Log:
Drop unneeded patch
Modified: trunk/packages/exonerate/trunk/debian/changelog
===================================================================
--- trunk/packages/exonerate/trunk/debian/changelog 2012-01-12 10:27:58 UTC (rev 9263)
+++ trunk/packages/exonerate/trunk/debian/changelog 2012-01-12 10:58:59 UTC (rev 9264)
@@ -1,3 +1,10 @@
+exonerate (2.2.0-6) unstable; urgency=low
+
+ * debian/patches/autoreconf.patch: Removed because not needed
+ when using dh-autoreconf
+
+ -- Andreas Tille <tille at debian.org> Thu, 12 Jan 2012 11:29:32 +0100
+
exonerate (2.2.0-5) unstable; urgency=low
* Rather use dh-autoreconf as advised in another patch from
Deleted: trunk/packages/exonerate/trunk/debian/patches/autoreconf.patch
===================================================================
--- trunk/packages/exonerate/trunk/debian/patches/autoreconf.patch 2012-01-12 10:27:58 UTC (rev 9263)
+++ trunk/packages/exonerate/trunk/debian/patches/autoreconf.patch 2012-01-12 10:58:59 UTC (rev 9264)
@@ -1,29372 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Date: Mon, 12 Dec 2011 13:13:02 +0100
-Description: Exonerate was build using aclocal-1.4 which was not supported
- any more in Debian. The patch was created using `autoreconf` to update
- automake tools
-diff -ubrN exonerate-2.2.0.orig/aclocal.m4 exonerate-2.2.0/aclocal.m4
---- exonerate-2.2.0.orig/aclocal.m4 2008-10-17 12:04:50.000000000 +0200
-+++ exonerate-2.2.0/aclocal.m4 2011-12-12 13:32:51.000000000 +0100
-@@ -1,1042 +1,791 @@
--dnl aclocal.m4 generated automatically by aclocal 1.4-p6
-+# generated automatically by aclocal 1.11.1 -*- Autoconf -*-
-
--dnl Copyright (C) 1994, 1995-8, 1999, 2001 Free Software Foundation, Inc.
--dnl This file is free software; the Free Software Foundation
--dnl gives unlimited permission to copy and/or distribute it,
--dnl with or without modifications, as long as this notice is preserved.
--
--dnl This program is distributed in the hope that it will be useful,
--dnl but WITHOUT ANY WARRANTY, to the extent permitted by law; without
--dnl even the implied warranty of MERCHANTABILITY or FITNESS FOR A
--dnl PARTICULAR PURPOSE.
--
--# lib-prefix.m4 serial 5 (gettext-0.15)
--dnl Copyright (C) 2001-2005 Free Software Foundation, Inc.
--dnl This file is free software; the Free Software Foundation
--dnl gives unlimited permission to copy and/or distribute it,
--dnl with or without modifications, as long as this notice is preserved.
--
--dnl From Bruno Haible.
--
--dnl AC_LIB_ARG_WITH is synonymous to AC_ARG_WITH in autoconf-2.13, and
--dnl similar to AC_ARG_WITH in autoconf 2.52...2.57 except that is doesn't
--dnl require excessive bracketing.
--ifdef([AC_HELP_STRING],
--[AC_DEFUN([AC_LIB_ARG_WITH], [AC_ARG_WITH([$1],[[$2]],[$3],[$4])])],
--[AC_DEFUN([AC_][LIB_ARG_WITH], [AC_ARG_WITH([$1],[$2],[$3],[$4])])])
--
--dnl AC_LIB_PREFIX adds to the CPPFLAGS and LDFLAGS the flags that are needed
--dnl to access previously installed libraries. The basic assumption is that
--dnl a user will want packages to use other packages he previously installed
--dnl with the same --prefix option.
--dnl This macro is not needed if only AC_LIB_LINKFLAGS is used to locate
--dnl libraries, but is otherwise very convenient.
--AC_DEFUN([AC_LIB_PREFIX],
--[
-- AC_BEFORE([$0], [AC_LIB_LINKFLAGS])
-- AC_REQUIRE([AC_PROG_CC])
-- AC_REQUIRE([AC_CANONICAL_HOST])
-- AC_REQUIRE([AC_LIB_PREPARE_MULTILIB])
-- AC_REQUIRE([AC_LIB_PREPARE_PREFIX])
-- dnl By default, look in $includedir and $libdir.
-- use_additional=yes
-- AC_LIB_WITH_FINAL_PREFIX([
-- eval additional_includedir=\"$includedir\"
-- eval additional_libdir=\"$libdir\"
-- ])
-- AC_LIB_ARG_WITH([lib-prefix],
--[ --with-lib-prefix[=DIR] search for libraries in DIR/include and DIR/lib
-- --without-lib-prefix don't search for libraries in includedir and libdir],
--[
-- if test "X$withval" = "Xno"; then
-- use_additional=no
-- else
-- if test "X$withval" = "X"; then
-- AC_LIB_WITH_FINAL_PREFIX([
-- eval additional_includedir=\"$includedir\"
-- eval additional_libdir=\"$libdir\"
-- ])
-- else
-- additional_includedir="$withval/include"
-- additional_libdir="$withval/$acl_libdirstem"
-- fi
-- fi
--])
-- if test $use_additional = yes; then
-- dnl Potentially add $additional_includedir to $CPPFLAGS.
-- dnl But don't add it
-- dnl 1. if it's the standard /usr/include,
-- dnl 2. if it's already present in $CPPFLAGS,
-- dnl 3. if it's /usr/local/include and we are using GCC on Linux,
-- dnl 4. if it doesn't exist as a directory.
-- if test "X$additional_includedir" != "X/usr/include"; then
-- haveit=
-- for x in $CPPFLAGS; do
-- AC_LIB_WITH_FINAL_PREFIX([eval x=\"$x\"])
-- if test "X$x" = "X-I$additional_includedir"; then
-- haveit=yes
-- break
-- fi
-- done
-- if test -z "$haveit"; then
-- if test "X$additional_includedir" = "X/usr/local/include"; then
-- if test -n "$GCC"; then
-- case $host_os in
-- linux* | gnu* | k*bsd*-gnu) haveit=yes;;
-- esac
-- fi
-- fi
-- if test -z "$haveit"; then
-- if test -d "$additional_includedir"; then
-- dnl Really add $additional_includedir to $CPPFLAGS.
-- CPPFLAGS="${CPPFLAGS}${CPPFLAGS:+ }-I$additional_includedir"
-- fi
-- fi
-- fi
-- fi
-- dnl Potentially add $additional_libdir to $LDFLAGS.
-- dnl But don't add it
-- dnl 1. if it's the standard /usr/lib,
-- dnl 2. if it's already present in $LDFLAGS,
-- dnl 3. if it's /usr/local/lib and we are using GCC on Linux,
-- dnl 4. if it doesn't exist as a directory.
-- if test "X$additional_libdir" != "X/usr/$acl_libdirstem"; then
-- haveit=
-- for x in $LDFLAGS; do
-- AC_LIB_WITH_FINAL_PREFIX([eval x=\"$x\"])
-- if test "X$x" = "X-L$additional_libdir"; then
-- haveit=yes
-- break
-- fi
-- done
-- if test -z "$haveit"; then
-- if test "X$additional_libdir" = "X/usr/local/$acl_libdirstem"; then
-- if test -n "$GCC"; then
-- case $host_os in
-- linux*) haveit=yes;;
-- esac
-- fi
-- fi
-- if test -z "$haveit"; then
-- if test -d "$additional_libdir"; then
-- dnl Really add $additional_libdir to $LDFLAGS.
-- LDFLAGS="${LDFLAGS}${LDFLAGS:+ }-L$additional_libdir"
-- fi
-- fi
-- fi
-- fi
-- fi
--])
-+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
-+# 2005, 2006, 2007, 2008, 2009 Free Software Foundation, Inc.
-+# This file is free software; the Free Software Foundation
-+# gives unlimited permission to copy and/or distribute it,
-+# with or without modifications, as long as this notice is preserved.
-
--dnl AC_LIB_PREPARE_PREFIX creates variables acl_final_prefix,
--dnl acl_final_exec_prefix, containing the values to which $prefix and
--dnl $exec_prefix will expand at the end of the configure script.
--AC_DEFUN([AC_LIB_PREPARE_PREFIX],
--[
-- dnl Unfortunately, prefix and exec_prefix get only finally determined
-- dnl at the end of configure.
-- if test "X$prefix" = "XNONE"; then
-- acl_final_prefix="$ac_default_prefix"
-- else
-- acl_final_prefix="$prefix"
-- fi
-- if test "X$exec_prefix" = "XNONE"; then
-- acl_final_exec_prefix='${prefix}'
-- else
-- acl_final_exec_prefix="$exec_prefix"
-- fi
-- acl_save_prefix="$prefix"
-- prefix="$acl_final_prefix"
-- eval acl_final_exec_prefix=\"$acl_final_exec_prefix\"
-- prefix="$acl_save_prefix"
--])
-+# This program is distributed in the hope that it will be useful,
-+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
-+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-+# PARTICULAR PURPOSE.
-+
-+m4_ifndef([AC_AUTOCONF_VERSION],
-+ [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
-+m4_if(m4_defn([AC_AUTOCONF_VERSION]), [2.68],,
-+[m4_warning([this file was generated for autoconf 2.68.
-+You have another version of autoconf. It may work, but is not guaranteed to.
-+If you have problems, you may need to regenerate the build system entirely.
-+To do so, use the procedure documented by the package, typically `autoreconf'.])])
-
--dnl AC_LIB_WITH_FINAL_PREFIX([statement]) evaluates statement, with the
--dnl variables prefix and exec_prefix bound to the values they will have
--dnl at the end of the configure script.
--AC_DEFUN([AC_LIB_WITH_FINAL_PREFIX],
--[
-- acl_save_prefix="$prefix"
-- prefix="$acl_final_prefix"
-- acl_save_exec_prefix="$exec_prefix"
-- exec_prefix="$acl_final_exec_prefix"
-- $1
-- exec_prefix="$acl_save_exec_prefix"
-- prefix="$acl_save_prefix"
--])
-+# Copyright (C) 2002, 2003, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
-+#
-+# This file is free software; the Free Software Foundation
-+# gives unlimited permission to copy and/or distribute it,
-+# with or without modifications, as long as this notice is preserved.
-
--dnl AC_LIB_PREPARE_MULTILIB creates a variable acl_libdirstem, containing
--dnl the basename of the libdir, either "lib" or "lib64".
--AC_DEFUN([AC_LIB_PREPARE_MULTILIB],
--[
-- dnl There is no formal standard regarding lib and lib64. The current
-- dnl practice is that on a system supporting 32-bit and 64-bit instruction
-- dnl sets or ABIs, 64-bit libraries go under $prefix/lib64 and 32-bit
-- dnl libraries go under $prefix/lib. We determine the compiler's default
-- dnl mode by looking at the compiler's library search path. If at least
-- dnl of its elements ends in /lib64 or points to a directory whose absolute
-- dnl pathname ends in /lib64, we assume a 64-bit ABI. Otherwise we use the
-- dnl default, namely "lib".
-- acl_libdirstem=lib
-- searchpath=`(LC_ALL=C $CC -print-search-dirs) 2>/dev/null | sed -n -e 's,^libraries: ,,p' | sed -e 's,^=,,'`
-- if test -n "$searchpath"; then
-- acl_save_IFS="${IFS= }"; IFS=":"
-- for searchdir in $searchpath; do
-- if test -d "$searchdir"; then
-- case "$searchdir" in
-- */lib64/ | */lib64 ) acl_libdirstem=lib64 ;;
-- *) searchdir=`cd "$searchdir" && pwd`
-- case "$searchdir" in
-- */lib64 ) acl_libdirstem=lib64 ;;
-- esac ;;
-- esac
-- fi
-- done
-- IFS="$acl_save_IFS"
-- fi
-+# AM_AUTOMAKE_VERSION(VERSION)
-+# ----------------------------
-+# Automake X.Y traces this macro to ensure aclocal.m4 has been
-+# generated from the m4 files accompanying Automake X.Y.
-+# (This private macro should not be called outside this file.)
-+AC_DEFUN([AM_AUTOMAKE_VERSION],
-+[am__api_version='1.11'
-+dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to
-+dnl require some minimum version. Point them to the right macro.
-+m4_if([$1], [1.11.1], [],
-+ [AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl
- ])
-
--# lib-link.m4 serial 9 (gettext-0.16)
--dnl Copyright (C) 2001-2006 Free Software Foundation, Inc.
--dnl This file is free software; the Free Software Foundation
--dnl gives unlimited permission to copy and/or distribute it,
--dnl with or without modifications, as long as this notice is preserved.
--
--dnl From Bruno Haible.
--
--AC_PREREQ(2.50)
--
--dnl AC_LIB_LINKFLAGS(name [, dependencies]) searches for libname and
--dnl the libraries corresponding to explicit and implicit dependencies.
--dnl Sets and AC_SUBSTs the LIB${NAME} and LTLIB${NAME} variables and
--dnl augments the CPPFLAGS variable.
--AC_DEFUN([AC_LIB_LINKFLAGS],
--[
-- AC_REQUIRE([AC_LIB_PREPARE_PREFIX])
-- AC_REQUIRE([AC_LIB_RPATH])
-- define([Name],[translit([$1],[./-], [___])])
-- define([NAME],[translit([$1],[abcdefghijklmnopqrstuvwxyz./-],
-- [ABCDEFGHIJKLMNOPQRSTUVWXYZ___])])
-- AC_CACHE_CHECK([how to link with lib[]$1], [ac_cv_lib[]Name[]_libs], [
-- AC_LIB_LINKFLAGS_BODY([$1], [$2])
-- ac_cv_lib[]Name[]_libs="$LIB[]NAME"
-- ac_cv_lib[]Name[]_ltlibs="$LTLIB[]NAME"
-- ac_cv_lib[]Name[]_cppflags="$INC[]NAME"
-- ])
-- LIB[]NAME="$ac_cv_lib[]Name[]_libs"
-- LTLIB[]NAME="$ac_cv_lib[]Name[]_ltlibs"
-- INC[]NAME="$ac_cv_lib[]Name[]_cppflags"
-- AC_LIB_APPENDTOVAR([CPPFLAGS], [$INC]NAME)
-- AC_SUBST([LIB]NAME)
-- AC_SUBST([LTLIB]NAME)
-- dnl Also set HAVE_LIB[]NAME so that AC_LIB_HAVE_LINKFLAGS can reuse the
-- dnl results of this search when this library appears as a dependency.
-- HAVE_LIB[]NAME=yes
-- undefine([Name])
-- undefine([NAME])
--])
-+# _AM_AUTOCONF_VERSION(VERSION)
-+# -----------------------------
-+# aclocal traces this macro to find the Autoconf version.
-+# This is a private macro too. Using m4_define simplifies
-+# the logic in aclocal, which can simply ignore this definition.
-+m4_define([_AM_AUTOCONF_VERSION], [])
-
--dnl AC_LIB_HAVE_LINKFLAGS(name, dependencies, includes, testcode)
--dnl searches for libname and the libraries corresponding to explicit and
--dnl implicit dependencies, together with the specified include files and
--dnl the ability to compile and link the specified testcode. If found, it
--dnl sets and AC_SUBSTs HAVE_LIB${NAME}=yes and the LIB${NAME} and
--dnl LTLIB${NAME} variables and augments the CPPFLAGS variable, and
--dnl #defines HAVE_LIB${NAME} to 1. Otherwise, it sets and AC_SUBSTs
--dnl HAVE_LIB${NAME}=no and LIB${NAME} and LTLIB${NAME} to empty.
--AC_DEFUN([AC_LIB_HAVE_LINKFLAGS],
--[
-- AC_REQUIRE([AC_LIB_PREPARE_PREFIX])
-- AC_REQUIRE([AC_LIB_RPATH])
-- define([Name],[translit([$1],[./-], [___])])
-- define([NAME],[translit([$1],[abcdefghijklmnopqrstuvwxyz./-],
-- [ABCDEFGHIJKLMNOPQRSTUVWXYZ___])])
--
-- dnl Search for lib[]Name and define LIB[]NAME, LTLIB[]NAME and INC[]NAME
-- dnl accordingly.
-- AC_LIB_LINKFLAGS_BODY([$1], [$2])
--
-- dnl Add $INC[]NAME to CPPFLAGS before performing the following checks,
-- dnl because if the user has installed lib[]Name and not disabled its use
-- dnl via --without-lib[]Name-prefix, he wants to use it.
-- ac_save_CPPFLAGS="$CPPFLAGS"
-- AC_LIB_APPENDTOVAR([CPPFLAGS], [$INC]NAME)
--
-- AC_CACHE_CHECK([for lib[]$1], [ac_cv_lib[]Name], [
-- ac_save_LIBS="$LIBS"
-- LIBS="$LIBS $LIB[]NAME"
-- AC_TRY_LINK([$3], [$4], [ac_cv_lib[]Name=yes], [ac_cv_lib[]Name=no])
-- LIBS="$ac_save_LIBS"
-- ])
-- if test "$ac_cv_lib[]Name" = yes; then
-- HAVE_LIB[]NAME=yes
-- AC_DEFINE([HAVE_LIB]NAME, 1, [Define if you have the $1 library.])
-- AC_MSG_CHECKING([how to link with lib[]$1])
-- AC_MSG_RESULT([$LIB[]NAME])
-- else
-- HAVE_LIB[]NAME=no
-- dnl If $LIB[]NAME didn't lead to a usable library, we don't need
-- dnl $INC[]NAME either.
-- CPPFLAGS="$ac_save_CPPFLAGS"
-- LIB[]NAME=
-- LTLIB[]NAME=
-- fi
-- AC_SUBST([HAVE_LIB]NAME)
-- AC_SUBST([LIB]NAME)
-- AC_SUBST([LTLIB]NAME)
-- undefine([Name])
-- undefine([NAME])
--])
-+# AM_SET_CURRENT_AUTOMAKE_VERSION
-+# -------------------------------
-+# Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced.
-+# This function is AC_REQUIREd by AM_INIT_AUTOMAKE.
-+AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
-+[AM_AUTOMAKE_VERSION([1.11.1])dnl
-+m4_ifndef([AC_AUTOCONF_VERSION],
-+ [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
-+_AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
-
--dnl Determine the platform dependent parameters needed to use rpath:
--dnl libext, shlibext, hardcode_libdir_flag_spec, hardcode_libdir_separator,
--dnl hardcode_direct, hardcode_minus_L.
--AC_DEFUN([AC_LIB_RPATH],
--[
-- dnl Tell automake >= 1.10 to complain if config.rpath is missing.
-- m4_ifdef([AC_REQUIRE_AUX_FILE], [AC_REQUIRE_AUX_FILE([config.rpath])])
-- AC_REQUIRE([AC_PROG_CC]) dnl we use $CC, $GCC, $LDFLAGS
-- AC_REQUIRE([AC_LIB_PROG_LD]) dnl we use $LD, $with_gnu_ld
-- AC_REQUIRE([AC_CANONICAL_HOST]) dnl we use $host
-- AC_REQUIRE([AC_CONFIG_AUX_DIR_DEFAULT]) dnl we use $ac_aux_dir
-- AC_CACHE_CHECK([for shared library run path origin], acl_cv_rpath, [
-- CC="$CC" GCC="$GCC" LDFLAGS="$LDFLAGS" LD="$LD" with_gnu_ld="$with_gnu_ld" \
-- ${CONFIG_SHELL-/bin/sh} "$ac_aux_dir/config.rpath" "$host" > conftest.sh
-- . ./conftest.sh
-- rm -f ./conftest.sh
-- acl_cv_rpath=done
-- ])
-- wl="$acl_cv_wl"
-- libext="$acl_cv_libext"
-- shlibext="$acl_cv_shlibext"
-- hardcode_libdir_flag_spec="$acl_cv_hardcode_libdir_flag_spec"
-- hardcode_libdir_separator="$acl_cv_hardcode_libdir_separator"
-- hardcode_direct="$acl_cv_hardcode_direct"
-- hardcode_minus_L="$acl_cv_hardcode_minus_L"
-- dnl Determine whether the user wants rpath handling at all.
-- AC_ARG_ENABLE(rpath,
-- [ --disable-rpath do not hardcode runtime library paths],
-- :, enable_rpath=yes)
--])
-+# AM_AUX_DIR_EXPAND -*- Autoconf -*-
-
--dnl AC_LIB_LINKFLAGS_BODY(name [, dependencies]) searches for libname and
--dnl the libraries corresponding to explicit and implicit dependencies.
--dnl Sets the LIB${NAME}, LTLIB${NAME} and INC${NAME} variables.
--AC_DEFUN([AC_LIB_LINKFLAGS_BODY],
--[
-- AC_REQUIRE([AC_LIB_PREPARE_MULTILIB])
-- define([NAME],[translit([$1],[abcdefghijklmnopqrstuvwxyz./-],
-- [ABCDEFGHIJKLMNOPQRSTUVWXYZ___])])
-- dnl By default, look in $includedir and $libdir.
-- use_additional=yes
-- AC_LIB_WITH_FINAL_PREFIX([
-- eval additional_includedir=\"$includedir\"
-- eval additional_libdir=\"$libdir\"
-- ])
-- AC_LIB_ARG_WITH([lib$1-prefix],
--[ --with-lib$1-prefix[=DIR] search for lib$1 in DIR/include and DIR/lib
-- --without-lib$1-prefix don't search for lib$1 in includedir and libdir],
--[
-- if test "X$withval" = "Xno"; then
-- use_additional=no
-- else
-- if test "X$withval" = "X"; then
-- AC_LIB_WITH_FINAL_PREFIX([
-- eval additional_includedir=\"$includedir\"
-- eval additional_libdir=\"$libdir\"
-- ])
-- else
-- additional_includedir="$withval/include"
-- additional_libdir="$withval/$acl_libdirstem"
-- fi
-- fi
-+# Copyright (C) 2001, 2003, 2005 Free Software Foundation, Inc.
-+#
-+# This file is free software; the Free Software Foundation
-+# gives unlimited permission to copy and/or distribute it,
-+# with or without modifications, as long as this notice is preserved.
-+
-+# For projects using AC_CONFIG_AUX_DIR([foo]), Autoconf sets
-+# $ac_aux_dir to `$srcdir/foo'. In other projects, it is set to
-+# `$srcdir', `$srcdir/..', or `$srcdir/../..'.
-+#
-+# Of course, Automake must honor this variable whenever it calls a
-+# tool from the auxiliary directory. The problem is that $srcdir (and
-+# therefore $ac_aux_dir as well) can be either absolute or relative,
-+# depending on how configure is run. This is pretty annoying, since
-+# it makes $ac_aux_dir quite unusable in subdirectories: in the top
-+# source directory, any form will work fine, but in subdirectories a
-+# relative path needs to be adjusted first.
-+#
-+# $ac_aux_dir/missing
-+# fails when called from a subdirectory if $ac_aux_dir is relative
-+# $top_srcdir/$ac_aux_dir/missing
-+# fails if $ac_aux_dir is absolute,
-+# fails when called from a subdirectory in a VPATH build with
-+# a relative $ac_aux_dir
-+#
-+# The reason of the latter failure is that $top_srcdir and $ac_aux_dir
-+# are both prefixed by $srcdir. In an in-source build this is usually
-+# harmless because $srcdir is `.', but things will broke when you
-+# start a VPATH build or use an absolute $srcdir.
-+#
-+# So we could use something similar to $top_srcdir/$ac_aux_dir/missing,
-+# iff we strip the leading $srcdir from $ac_aux_dir. That would be:
-+# am_aux_dir='\$(top_srcdir)/'`expr "$ac_aux_dir" : "$srcdir//*\(.*\)"`
-+# and then we would define $MISSING as
-+# MISSING="\${SHELL} $am_aux_dir/missing"
-+# This will work as long as MISSING is not called from configure, because
-+# unfortunately $(top_srcdir) has no meaning in configure.
-+# However there are other variables, like CC, which are often used in
-+# configure, and could therefore not use this "fixed" $ac_aux_dir.
-+#
-+# Another solution, used here, is to always expand $ac_aux_dir to an
-+# absolute PATH. The drawback is that using absolute paths prevent a
-+# configured tree to be moved without reconfiguration.
-+
-+AC_DEFUN([AM_AUX_DIR_EXPAND],
-+[dnl Rely on autoconf to set up CDPATH properly.
-+AC_PREREQ([2.50])dnl
-+# expand $ac_aux_dir to an absolute path
-+am_aux_dir=`cd $ac_aux_dir && pwd`
- ])
-- dnl Search the library and its dependencies in $additional_libdir and
-- dnl $LDFLAGS. Using breadth-first-seach.
-- LIB[]NAME=
-- LTLIB[]NAME=
-- INC[]NAME=
-- rpathdirs=
-- ltrpathdirs=
-- names_already_handled=
-- names_next_round='$1 $2'
-- while test -n "$names_next_round"; do
-- names_this_round="$names_next_round"
-- names_next_round=
-- for name in $names_this_round; do
-- already_handled=
-- for n in $names_already_handled; do
-- if test "$n" = "$name"; then
-- already_handled=yes
-- break
-- fi
-- done
-- if test -z "$already_handled"; then
-- names_already_handled="$names_already_handled $name"
-- dnl See if it was already located by an earlier AC_LIB_LINKFLAGS
-- dnl or AC_LIB_HAVE_LINKFLAGS call.
-- uppername=`echo "$name" | sed -e 'y|abcdefghijklmnopqrstuvwxyz./-|ABCDEFGHIJKLMNOPQRSTUVWXYZ___|'`
-- eval value=\"\$HAVE_LIB$uppername\"
-- if test -n "$value"; then
-- if test "$value" = yes; then
-- eval value=\"\$LIB$uppername\"
-- test -z "$value" || LIB[]NAME="${LIB[]NAME}${LIB[]NAME:+ }$value"
-- eval value=\"\$LTLIB$uppername\"
-- test -z "$value" || LTLIB[]NAME="${LTLIB[]NAME}${LTLIB[]NAME:+ }$value"
-- else
-- dnl An earlier call to AC_LIB_HAVE_LINKFLAGS has determined
-- dnl that this library doesn't exist. So just drop it.
-- :
-- fi
-- else
-- dnl Search the library lib$name in $additional_libdir and $LDFLAGS
-- dnl and the already constructed $LIBNAME/$LTLIBNAME.
-- found_dir=
-- found_la=
-- found_so=
-- found_a=
-- if test $use_additional = yes; then
-- if test -n "$shlibext" \
-- && { test -f "$additional_libdir/lib$name.$shlibext" \
-- || { test "$shlibext" = dll \
-- && test -f "$additional_libdir/lib$name.dll.a"; }; }; then
-- found_dir="$additional_libdir"
-- if test -f "$additional_libdir/lib$name.$shlibext"; then
-- found_so="$additional_libdir/lib$name.$shlibext"
-- else
-- found_so="$additional_libdir/lib$name.dll.a"
-- fi
-- if test -f "$additional_libdir/lib$name.la"; then
-- found_la="$additional_libdir/lib$name.la"
-- fi
-- else
-- if test -f "$additional_libdir/lib$name.$libext"; then
-- found_dir="$additional_libdir"
-- found_a="$additional_libdir/lib$name.$libext"
-- if test -f "$additional_libdir/lib$name.la"; then
-- found_la="$additional_libdir/lib$name.la"
-- fi
-- fi
-- fi
-- fi
-- if test "X$found_dir" = "X"; then
-- for x in $LDFLAGS $LTLIB[]NAME; do
-- AC_LIB_WITH_FINAL_PREFIX([eval x=\"$x\"])
-- case "$x" in
-- -L*)
-- dir=`echo "X$x" | sed -e 's/^X-L//'`
-- if test -n "$shlibext" \
-- && { test -f "$dir/lib$name.$shlibext" \
-- || { test "$shlibext" = dll \
-- && test -f "$dir/lib$name.dll.a"; }; }; then
-- found_dir="$dir"
-- if test -f "$dir/lib$name.$shlibext"; then
-- found_so="$dir/lib$name.$shlibext"
-- else
-- found_so="$dir/lib$name.dll.a"
-- fi
-- if test -f "$dir/lib$name.la"; then
-- found_la="$dir/lib$name.la"
-- fi
-- else
-- if test -f "$dir/lib$name.$libext"; then
-- found_dir="$dir"
-- found_a="$dir/lib$name.$libext"
-- if test -f "$dir/lib$name.la"; then
-- found_la="$dir/lib$name.la"
-- fi
-- fi
-- fi
-+
-+# AM_CONDITIONAL -*- Autoconf -*-
-+
-+# Copyright (C) 1997, 2000, 2001, 2003, 2004, 2005, 2006, 2008
-+# Free Software Foundation, Inc.
-+#
-+# This file is free software; the Free Software Foundation
-+# gives unlimited permission to copy and/or distribute it,
-+# with or without modifications, as long as this notice is preserved.
-+
-+# serial 9
-+
-+# AM_CONDITIONAL(NAME, SHELL-CONDITION)
-+# -------------------------------------
-+# Define a conditional.
-+AC_DEFUN([AM_CONDITIONAL],
-+[AC_PREREQ(2.52)dnl
-+ ifelse([$1], [TRUE], [AC_FATAL([$0: invalid condition: $1])],
-+ [$1], [FALSE], [AC_FATAL([$0: invalid condition: $1])])dnl
-+AC_SUBST([$1_TRUE])dnl
-+AC_SUBST([$1_FALSE])dnl
-+_AM_SUBST_NOTMAKE([$1_TRUE])dnl
-+_AM_SUBST_NOTMAKE([$1_FALSE])dnl
-+m4_define([_AM_COND_VALUE_$1], [$2])dnl
-+if $2; then
-+ $1_TRUE=
-+ $1_FALSE='#'
-+else
-+ $1_TRUE='#'
-+ $1_FALSE=
-+fi
-+AC_CONFIG_COMMANDS_PRE(
-+[if test -z "${$1_TRUE}" && test -z "${$1_FALSE}"; then
-+ AC_MSG_ERROR([[conditional "$1" was never defined.
-+Usually this means the macro was only invoked conditionally.]])
-+fi])])
-+
-+# Copyright (C) 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2009
-+# Free Software Foundation, Inc.
-+#
-+# This file is free software; the Free Software Foundation
-+# gives unlimited permission to copy and/or distribute it,
-+# with or without modifications, as long as this notice is preserved.
-+
-+# serial 10
-+
-+# There are a few dirty hacks below to avoid letting `AC_PROG_CC' be
-+# written in clear, in which case automake, when reading aclocal.m4,
-+# will think it sees a *use*, and therefore will trigger all it's
-+# C support machinery. Also note that it means that autoscan, seeing
-+# CC etc. in the Makefile, will ask for an AC_PROG_CC use...
-+
-+
-+# _AM_DEPENDENCIES(NAME)
-+# ----------------------
-+# See how the compiler implements dependency checking.
-+# NAME is "CC", "CXX", "GCJ", or "OBJC".
-+# We try a few techniques and use that to set a single cache variable.
-+#
-+# We don't AC_REQUIRE the corresponding AC_PROG_CC since the latter was
-+# modified to invoke _AM_DEPENDENCIES(CC); we would have a circular
-+# dependency, and given that the user is not expected to run this macro,
-+# just rely on AC_PROG_CC.
-+AC_DEFUN([_AM_DEPENDENCIES],
-+[AC_REQUIRE([AM_SET_DEPDIR])dnl
-+AC_REQUIRE([AM_OUTPUT_DEPENDENCY_COMMANDS])dnl
-+AC_REQUIRE([AM_MAKE_INCLUDE])dnl
-+AC_REQUIRE([AM_DEP_TRACK])dnl
-+
-+ifelse([$1], CC, [depcc="$CC" am_compiler_list=],
-+ [$1], CXX, [depcc="$CXX" am_compiler_list=],
-+ [$1], OBJC, [depcc="$OBJC" am_compiler_list='gcc3 gcc'],
-+ [$1], UPC, [depcc="$UPC" am_compiler_list=],
-+ [$1], GCJ, [depcc="$GCJ" am_compiler_list='gcc3 gcc'],
-+ [depcc="$$1" am_compiler_list=])
-+
-+AC_CACHE_CHECK([dependency style of $depcc],
-+ [am_cv_$1_dependencies_compiler_type],
-+[if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
-+ # We make a subdir and do the tests there. Otherwise we can end up
-+ # making bogus files that we don't know about and never remove. For
-+ # instance it was reported that on HP-UX the gcc test will end up
-+ # making a dummy file named `D' -- because `-MD' means `put the output
-+ # in D'.
-+ mkdir conftest.dir
-+ # Copy depcomp to subdir because otherwise we won't find it if we're
-+ # using a relative directory.
-+ cp "$am_depcomp" conftest.dir
-+ cd conftest.dir
-+ # We will build objects and dependencies in a subdirectory because
-+ # it helps to detect inapplicable dependency modes. For instance
-+ # both Tru64's cc and ICC support -MD to output dependencies as a
-+ # side effect of compilation, but ICC will put the dependencies in
-+ # the current directory while Tru64 will put them in the object
-+ # directory.
-+ mkdir sub
-+
-+ am_cv_$1_dependencies_compiler_type=none
-+ if test "$am_compiler_list" = ""; then
-+ am_compiler_list=`sed -n ['s/^#*\([a-zA-Z0-9]*\))$/\1/p'] < ./depcomp`
-+ fi
-+ am__universal=false
-+ m4_case([$1], [CC],
-+ [case " $depcc " in #(
-+ *\ -arch\ *\ -arch\ *) am__universal=true ;;
-+ esac],
-+ [CXX],
-+ [case " $depcc " in #(
-+ *\ -arch\ *\ -arch\ *) am__universal=true ;;
-+ esac])
-+
-+ for depmode in $am_compiler_list; do
-+ # Setup a source with many dependencies, because some compilers
-+ # like to wrap large dependency lists on column 80 (with \), and
-+ # we should not choose a depcomp mode which is confused by this.
-+ #
-+ # We need to recreate these files for each test, as the compiler may
-+ # overwrite some of them when testing with obscure command lines.
-+ # This happens at least with the AIX C compiler.
-+ : > sub/conftest.c
-+ for i in 1 2 3 4 5 6; do
-+ echo '#include "conftst'$i'.h"' >> sub/conftest.c
-+ # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
-+ # Solaris 8's {/usr,}/bin/sh.
-+ touch sub/conftst$i.h
-+ done
-+ echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
-+
-+ # We check with `-c' and `-o' for the sake of the "dashmstdout"
-+ # mode. It turns out that the SunPro C++ compiler does not properly
-+ # handle `-M -o', and we need to detect this. Also, some Intel
-+ # versions had trouble with output in subdirs
-+ am__obj=sub/conftest.${OBJEXT-o}
-+ am__minus_obj="-o $am__obj"
-+ case $depmode in
-+ gcc)
-+ # This depmode causes a compiler race in universal mode.
-+ test "$am__universal" = false || continue
- ;;
-- esac
-- if test "X$found_dir" != "X"; then
-- break
-- fi
-- done
-- fi
-- if test "X$found_dir" != "X"; then
-- dnl Found the library.
-- LTLIB[]NAME="${LTLIB[]NAME}${LTLIB[]NAME:+ }-L$found_dir -l$name"
-- if test "X$found_so" != "X"; then
-- dnl Linking with a shared library. We attempt to hardcode its
-- dnl directory into the executable's runpath, unless it's the
-- dnl standard /usr/lib.
-- if test "$enable_rpath" = no || test "X$found_dir" = "X/usr/$acl_libdirstem"; then
-- dnl No hardcoding is needed.
-- LIB[]NAME="${LIB[]NAME}${LIB[]NAME:+ }$found_so"
-+ nosideeffect)
-+ # after this tag, mechanisms are not by side-effect, so they'll
-+ # only be used when explicitly requested
-+ if test "x$enable_dependency_tracking" = xyes; then
-+ continue
- else
-- dnl Use an explicit option to hardcode DIR into the resulting
-- dnl binary.
-- dnl Potentially add DIR to ltrpathdirs.
-- dnl The ltrpathdirs will be appended to $LTLIBNAME at the end.
-- haveit=
-- for x in $ltrpathdirs; do
-- if test "X$x" = "X$found_dir"; then
-- haveit=yes
- break
- fi
-- done
-- if test -z "$haveit"; then
-- ltrpathdirs="$ltrpathdirs $found_dir"
-- fi
-- dnl The hardcoding into $LIBNAME is system dependent.
-- if test "$hardcode_direct" = yes; then
-- dnl Using DIR/libNAME.so during linking hardcodes DIR into the
-- dnl resulting binary.
-- LIB[]NAME="${LIB[]NAME}${LIB[]NAME:+ }$found_so"
-- else
-- if test -n "$hardcode_libdir_flag_spec" && test "$hardcode_minus_L" = no; then
-- dnl Use an explicit option to hardcode DIR into the resulting
-- dnl binary.
-- LIB[]NAME="${LIB[]NAME}${LIB[]NAME:+ }$found_so"
-- dnl Potentially add DIR to rpathdirs.
-- dnl The rpathdirs will be appended to $LIBNAME at the end.
-- haveit=
-- for x in $rpathdirs; do
-- if test "X$x" = "X$found_dir"; then
-- haveit=yes
-- break
-- fi
-- done
-- if test -z "$haveit"; then
-- rpathdirs="$rpathdirs $found_dir"
-- fi
-- else
-- dnl Rely on "-L$found_dir".
-- dnl But don't add it if it's already contained in the LDFLAGS
-- dnl or the already constructed $LIBNAME
-- haveit=
-- for x in $LDFLAGS $LIB[]NAME; do
-- AC_LIB_WITH_FINAL_PREFIX([eval x=\"$x\"])
-- if test "X$x" = "X-L$found_dir"; then
-- haveit=yes
-- break
-- fi
-- done
-- if test -z "$haveit"; then
-- LIB[]NAME="${LIB[]NAME}${LIB[]NAME:+ }-L$found_dir"
-- fi
-- if test "$hardcode_minus_L" != no; then
-- dnl FIXME: Not sure whether we should use
-- dnl "-L$found_dir -l$name" or "-L$found_dir $found_so"
-- dnl here.
-- LIB[]NAME="${LIB[]NAME}${LIB[]NAME:+ }$found_so"
-- else
-- dnl We cannot use $hardcode_runpath_var and LD_RUN_PATH
-- dnl here, because this doesn't fit in flags passed to the
-- dnl compiler. So give up. No hardcoding. This affects only
-- dnl very old systems.
-- dnl FIXME: Not sure whether we should use
-- dnl "-L$found_dir -l$name" or "-L$found_dir $found_so"
-- dnl here.
-- LIB[]NAME="${LIB[]NAME}${LIB[]NAME:+ }-l$name"
-- fi
-- fi
-- fi
-- fi
-- else
-- if test "X$found_a" != "X"; then
-- dnl Linking with a static library.
-- LIB[]NAME="${LIB[]NAME}${LIB[]NAME:+ }$found_a"
-- else
-- dnl We shouldn't come here, but anyway it's good to have a
-- dnl fallback.
-- LIB[]NAME="${LIB[]NAME}${LIB[]NAME:+ }-L$found_dir -l$name"
-- fi
-- fi
-- dnl Assume the include files are nearby.
-- additional_includedir=
-- case "$found_dir" in
-- */$acl_libdirstem | */$acl_libdirstem/)
-- basedir=`echo "X$found_dir" | sed -e 's,^X,,' -e "s,/$acl_libdirstem/"'*$,,'`
-- additional_includedir="$basedir/include"
- ;;
-- esac
-- if test "X$additional_includedir" != "X"; then
-- dnl Potentially add $additional_includedir to $INCNAME.
-- dnl But don't add it
-- dnl 1. if it's the standard /usr/include,
-- dnl 2. if it's /usr/local/include and we are using GCC on Linux,
-- dnl 3. if it's already present in $CPPFLAGS or the already
-- dnl constructed $INCNAME,
-- dnl 4. if it doesn't exist as a directory.
-- if test "X$additional_includedir" != "X/usr/include"; then
-- haveit=
-- if test "X$additional_includedir" = "X/usr/local/include"; then
-- if test -n "$GCC"; then
-- case $host_os in
-- linux* | gnu* | k*bsd*-gnu) haveit=yes;;
-- esac
-- fi
-- fi
-- if test -z "$haveit"; then
-- for x in $CPPFLAGS $INC[]NAME; do
-- AC_LIB_WITH_FINAL_PREFIX([eval x=\"$x\"])
-- if test "X$x" = "X-I$additional_includedir"; then
-- haveit=yes
-- break
-- fi
-- done
-- if test -z "$haveit"; then
-- if test -d "$additional_includedir"; then
-- dnl Really add $additional_includedir to $INCNAME.
-- INC[]NAME="${INC[]NAME}${INC[]NAME:+ }-I$additional_includedir"
-- fi
-- fi
-- fi
-- fi
-- fi
-- dnl Look for dependencies.
-- if test -n "$found_la"; then
-- dnl Read the .la file. It defines the variables
-- dnl dlname, library_names, old_library, dependency_libs, current,
-- dnl age, revision, installed, dlopen, dlpreopen, libdir.
-- save_libdir="$libdir"
-- case "$found_la" in
-- */* | *\\*) . "$found_la" ;;
-- *) . "./$found_la" ;;
-- esac
-- libdir="$save_libdir"
-- dnl We use only dependency_libs.
-- for dep in $dependency_libs; do
-- case "$dep" in
-- -L*)
-- additional_libdir=`echo "X$dep" | sed -e 's/^X-L//'`
-- dnl Potentially add $additional_libdir to $LIBNAME and $LTLIBNAME.
-- dnl But don't add it
-- dnl 1. if it's the standard /usr/lib,
-- dnl 2. if it's /usr/local/lib and we are using GCC on Linux,
-- dnl 3. if it's already present in $LDFLAGS or the already
-- dnl constructed $LIBNAME,
-- dnl 4. if it doesn't exist as a directory.
-- if test "X$additional_libdir" != "X/usr/$acl_libdirstem"; then
-- haveit=
-- if test "X$additional_libdir" = "X/usr/local/$acl_libdirstem"; then
-- if test -n "$GCC"; then
-- case $host_os in
-- linux* | gnu* | k*bsd*-gnu) haveit=yes;;
-- esac
-- fi
-- fi
-- if test -z "$haveit"; then
-- haveit=
-- for x in $LDFLAGS $LIB[]NAME; do
-- AC_LIB_WITH_FINAL_PREFIX([eval x=\"$x\"])
-- if test "X$x" = "X-L$additional_libdir"; then
-- haveit=yes
-- break
-- fi
-- done
-- if test -z "$haveit"; then
-- if test -d "$additional_libdir"; then
-- dnl Really add $additional_libdir to $LIBNAME.
-- LIB[]NAME="${LIB[]NAME}${LIB[]NAME:+ }-L$additional_libdir"
-- fi
-- fi
-- haveit=
-- for x in $LDFLAGS $LTLIB[]NAME; do
-- AC_LIB_WITH_FINAL_PREFIX([eval x=\"$x\"])
-- if test "X$x" = "X-L$additional_libdir"; then
-- haveit=yes
-- break
-- fi
-- done
-- if test -z "$haveit"; then
-- if test -d "$additional_libdir"; then
-- dnl Really add $additional_libdir to $LTLIBNAME.
-- LTLIB[]NAME="${LTLIB[]NAME}${LTLIB[]NAME:+ }-L$additional_libdir"
-- fi
-- fi
-- fi
-- fi
-- ;;
-- -R*)
-- dir=`echo "X$dep" | sed -e 's/^X-R//'`
-- if test "$enable_rpath" != no; then
-- dnl Potentially add DIR to rpathdirs.
-- dnl The rpathdirs will be appended to $LIBNAME at the end.
-- haveit=
-- for x in $rpathdirs; do
-- if test "X$x" = "X$dir"; then
-- haveit=yes
-- break
-- fi
-- done
-- if test -z "$haveit"; then
-- rpathdirs="$rpathdirs $dir"
-- fi
-- dnl Potentially add DIR to ltrpathdirs.
-- dnl The ltrpathdirs will be appended to $LTLIBNAME at the end.
-- haveit=
-- for x in $ltrpathdirs; do
-- if test "X$x" = "X$dir"; then
-- haveit=yes
-- break
-- fi
-- done
-- if test -z "$haveit"; then
-- ltrpathdirs="$ltrpathdirs $dir"
-- fi
-- fi
-- ;;
-- -l*)
-- dnl Handle this in the next round.
-- names_next_round="$names_next_round "`echo "X$dep" | sed -e 's/^X-l//'`
-- ;;
-- *.la)
-- dnl Handle this in the next round. Throw away the .la's
-- dnl directory; it is already contained in a preceding -L
-- dnl option.
-- names_next_round="$names_next_round "`echo "X$dep" | sed -e 's,^X.*/,,' -e 's,^lib,,' -e 's,\.la$,,'`
-- ;;
-- *)
-- dnl Most likely an immediate library name.
-- LIB[]NAME="${LIB[]NAME}${LIB[]NAME:+ }$dep"
-- LTLIB[]NAME="${LTLIB[]NAME}${LTLIB[]NAME:+ }$dep"
-+ msvisualcpp | msvcmsys)
-+ # This compiler won't grok `-c -o', but also, the minuso test has
-+ # not run yet. These depmodes are late enough in the game, and
-+ # so weak that their functioning should not be impacted.
-+ am__obj=conftest.${OBJEXT-o}
-+ am__minus_obj=
- ;;
-+ none) break ;;
- esac
-- done
-- fi
-- else
-- dnl Didn't find the library; assume it is in the system directories
-- dnl known to the linker and runtime loader. (All the system
-- dnl directories known to the linker should also be known to the
-- dnl runtime loader, otherwise the system is severely misconfigured.)
-- LIB[]NAME="${LIB[]NAME}${LIB[]NAME:+ }-l$name"
-- LTLIB[]NAME="${LTLIB[]NAME}${LTLIB[]NAME:+ }-l$name"
-- fi
-- fi
-- fi
-- done
-- done
-- if test "X$rpathdirs" != "X"; then
-- if test -n "$hardcode_libdir_separator"; then
-- dnl Weird platform: only the last -rpath option counts, the user must
-- dnl pass all path elements in one option. We can arrange that for a
-- dnl single library, but not when more than one $LIBNAMEs are used.
-- alldirs=
-- for found_dir in $rpathdirs; do
-- alldirs="${alldirs}${alldirs:+$hardcode_libdir_separator}$found_dir"
-- done
-- dnl Note: hardcode_libdir_flag_spec uses $libdir and $wl.
-- acl_save_libdir="$libdir"
-- libdir="$alldirs"
-- eval flag=\"$hardcode_libdir_flag_spec\"
-- libdir="$acl_save_libdir"
-- LIB[]NAME="${LIB[]NAME}${LIB[]NAME:+ }$flag"
-- else
-- dnl The -rpath options are cumulative.
-- for found_dir in $rpathdirs; do
-- acl_save_libdir="$libdir"
-- libdir="$found_dir"
-- eval flag=\"$hardcode_libdir_flag_spec\"
-- libdir="$acl_save_libdir"
-- LIB[]NAME="${LIB[]NAME}${LIB[]NAME:+ }$flag"
-- done
-+ if depmode=$depmode \
-+ source=sub/conftest.c object=$am__obj \
-+ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
-+ $SHELL ./depcomp $depcc -c $am__minus_obj sub/conftest.c \
-+ >/dev/null 2>conftest.err &&
-+ grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 &&
-+ grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
-+ grep $am__obj sub/conftest.Po > /dev/null 2>&1 &&
-+ ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
-+ # icc doesn't choke on unknown options, it will just issue warnings
-+ # or remarks (even with -Werror). So we grep stderr for any message
-+ # that says an option was ignored or not supported.
-+ # When given -MP, icc 7.0 and 7.1 complain thusly:
-+ # icc: Command line warning: ignoring option '-M'; no argument required
-+ # The diagnosis changed in icc 8.0:
-+ # icc: Command line remark: option '-MP' not supported
-+ if (grep 'ignoring option' conftest.err ||
-+ grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
-+ am_cv_$1_dependencies_compiler_type=$depmode
-+ break
- fi
- fi
-- if test "X$ltrpathdirs" != "X"; then
-- dnl When using libtool, the option that works for both libraries and
-- dnl executables is -R. The -R options are cumulative.
-- for found_dir in $ltrpathdirs; do
-- LTLIB[]NAME="${LTLIB[]NAME}${LTLIB[]NAME:+ }-R$found_dir"
- done
-- fi
-+
-+ cd ..
-+ rm -rf conftest.dir
-+else
-+ am_cv_$1_dependencies_compiler_type=none
-+fi
-+])
-+AC_SUBST([$1DEPMODE], [depmode=$am_cv_$1_dependencies_compiler_type])
-+AM_CONDITIONAL([am__fastdep$1], [
-+ test "x$enable_dependency_tracking" != xno \
-+ && test "$am_cv_$1_dependencies_compiler_type" = gcc3])
- ])
-
--dnl AC_LIB_APPENDTOVAR(VAR, CONTENTS) appends the elements of CONTENTS to VAR,
--dnl unless already present in VAR.
--dnl Works only for CPPFLAGS, not for LIB* variables because that sometimes
--dnl contains two or three consecutive elements that belong together.
--AC_DEFUN([AC_LIB_APPENDTOVAR],
--[
-- for element in [$2]; do
-- haveit=
-- for x in $[$1]; do
-- AC_LIB_WITH_FINAL_PREFIX([eval x=\"$x\"])
-- if test "X$x" = "X$element"; then
-- haveit=yes
-- break
-- fi
-- done
-- if test -z "$haveit"; then
-- [$1]="${[$1]}${[$1]:+ }$element"
-- fi
-- done
-+
-+# AM_SET_DEPDIR
-+# -------------
-+# Choose a directory name for dependency files.
-+# This macro is AC_REQUIREd in _AM_DEPENDENCIES
-+AC_DEFUN([AM_SET_DEPDIR],
-+[AC_REQUIRE([AM_SET_LEADING_DOT])dnl
-+AC_SUBST([DEPDIR], ["${am__leading_dot}deps"])dnl
- ])
-
--dnl For those cases where a variable contains several -L and -l options
--dnl referring to unknown libraries and directories, this macro determines the
--dnl necessary additional linker options for the runtime path.
--dnl AC_LIB_LINKFLAGS_FROM_LIBS([LDADDVAR], [LIBSVALUE], [USE-LIBTOOL])
--dnl sets LDADDVAR to linker options needed together with LIBSVALUE.
--dnl If USE-LIBTOOL evaluates to non-empty, linking with libtool is assumed,
--dnl otherwise linking without libtool is assumed.
--AC_DEFUN([AC_LIB_LINKFLAGS_FROM_LIBS],
--[
-- AC_REQUIRE([AC_LIB_RPATH])
-- AC_REQUIRE([AC_LIB_PREPARE_MULTILIB])
-- $1=
-- if test "$enable_rpath" != no; then
-- if test -n "$hardcode_libdir_flag_spec" && test "$hardcode_minus_L" = no; then
-- dnl Use an explicit option to hardcode directories into the resulting
-- dnl binary.
-- rpathdirs=
-- next=
-- for opt in $2; do
-- if test -n "$next"; then
-- dir="$next"
-- dnl No need to hardcode the standard /usr/lib.
-- if test "X$dir" != "X/usr/$acl_libdirstem"; then
-- rpathdirs="$rpathdirs $dir"
-- fi
-- next=
-- else
-- case $opt in
-- -L) next=yes ;;
-- -L*) dir=`echo "X$opt" | sed -e 's,^X-L,,'`
-- dnl No need to hardcode the standard /usr/lib.
-- if test "X$dir" != "X/usr/$acl_libdirstem"; then
-- rpathdirs="$rpathdirs $dir"
-- fi
-- next= ;;
-- *) next= ;;
-- esac
-- fi
-- done
-- if test "X$rpathdirs" != "X"; then
-- if test -n ""$3""; then
-- dnl libtool is used for linking. Use -R options.
-- for dir in $rpathdirs; do
-- $1="${$1}${$1:+ }-R$dir"
-- done
-- else
-- dnl The linker is used for linking directly.
-- if test -n "$hardcode_libdir_separator"; then
-- dnl Weird platform: only the last -rpath option counts, the user
-- dnl must pass all path elements in one option.
-- alldirs=
-- for dir in $rpathdirs; do
-- alldirs="${alldirs}${alldirs:+$hardcode_libdir_separator}$dir"
-- done
-- acl_save_libdir="$libdir"
-- libdir="$alldirs"
-- eval flag=\"$hardcode_libdir_flag_spec\"
-- libdir="$acl_save_libdir"
-- $1="$flag"
-- else
-- dnl The -rpath options are cumulative.
-- for dir in $rpathdirs; do
-- acl_save_libdir="$libdir"
-- libdir="$dir"
-- eval flag=\"$hardcode_libdir_flag_spec\"
-- libdir="$acl_save_libdir"
-- $1="${$1}${$1:+ }$flag"
-- done
-- fi
-- fi
-- fi
-- fi
-- fi
-- AC_SUBST([$1])
-+
-+# AM_DEP_TRACK
-+# ------------
-+AC_DEFUN([AM_DEP_TRACK],
-+[AC_ARG_ENABLE(dependency-tracking,
-+[ --disable-dependency-tracking speeds up one-time build
-+ --enable-dependency-tracking do not reject slow dependency extractors])
-+if test "x$enable_dependency_tracking" != xno; then
-+ am_depcomp="$ac_aux_dir/depcomp"
-+ AMDEPBACKSLASH='\'
-+fi
-+AM_CONDITIONAL([AMDEP], [test "x$enable_dependency_tracking" != xno])
-+AC_SUBST([AMDEPBACKSLASH])dnl
-+_AM_SUBST_NOTMAKE([AMDEPBACKSLASH])dnl
- ])
-
--# lib-ld.m4 serial 3 (gettext-0.13)
--dnl Copyright (C) 1996-2003 Free Software Foundation, Inc.
--dnl This file is free software; the Free Software Foundation
--dnl gives unlimited permission to copy and/or distribute it,
--dnl with or without modifications, as long as this notice is preserved.
--
--dnl Subroutines of libtool.m4,
--dnl with replacements s/AC_/AC_LIB/ and s/lt_cv/acl_cv/ to avoid collision
--dnl with libtool.m4.
--
--dnl From libtool-1.4. Sets the variable with_gnu_ld to yes or no.
--AC_DEFUN([AC_LIB_PROG_LD_GNU],
--[AC_CACHE_CHECK([if the linker ($LD) is GNU ld], acl_cv_prog_gnu_ld,
--[# I'd rather use --version here, but apparently some GNU ld's only accept -v.
--case `$LD -v 2>&1 </dev/null` in
--*GNU* | *'with BFD'*)
-- acl_cv_prog_gnu_ld=yes ;;
--*)
-- acl_cv_prog_gnu_ld=no ;;
--esac])
--with_gnu_ld=$acl_cv_prog_gnu_ld
-+# Generate code to set up dependency tracking. -*- Autoconf -*-
-+
-+# Copyright (C) 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2008
-+# Free Software Foundation, Inc.
-+#
-+# This file is free software; the Free Software Foundation
-+# gives unlimited permission to copy and/or distribute it,
-+# with or without modifications, as long as this notice is preserved.
-+
-+#serial 5
-+
-+# _AM_OUTPUT_DEPENDENCY_COMMANDS
-+# ------------------------------
-+AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS],
-+[{
-+ # Autoconf 2.62 quotes --file arguments for eval, but not when files
-+ # are listed without --file. Let's play safe and only enable the eval
-+ # if we detect the quoting.
-+ case $CONFIG_FILES in
-+ *\'*) eval set x "$CONFIG_FILES" ;;
-+ *) set x $CONFIG_FILES ;;
-+ esac
-+ shift
-+ for mf
-+ do
-+ # Strip MF so we end up with the name of the file.
-+ mf=`echo "$mf" | sed -e 's/:.*$//'`
-+ # Check whether this is an Automake generated Makefile or not.
-+ # We used to match only the files named `Makefile.in', but
-+ # some people rename them; so instead we look at the file content.
-+ # Grep'ing the first line is not enough: some people post-process
-+ # each Makefile.in and add a new line on top of each file to say so.
-+ # Grep'ing the whole file is not good either: AIX grep has a line
-+ # limit of 2048, but all sed's we know have understand at least 4000.
-+ if sed -n 's,^#.*generated by automake.*,X,p' "$mf" | grep X >/dev/null 2>&1; then
-+ dirpart=`AS_DIRNAME("$mf")`
-+ else
-+ continue
-+ fi
-+ # Extract the definition of DEPDIR, am__include, and am__quote
-+ # from the Makefile without running `make'.
-+ DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
-+ test -z "$DEPDIR" && continue
-+ am__include=`sed -n 's/^am__include = //p' < "$mf"`
-+ test -z "am__include" && continue
-+ am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
-+ # When using ansi2knr, U may be empty or an underscore; expand it
-+ U=`sed -n 's/^U = //p' < "$mf"`
-+ # Find all dependency output files, they are included files with
-+ # $(DEPDIR) in their names. We invoke sed twice because it is the
-+ # simplest approach to changing $(DEPDIR) to its actual value in the
-+ # expansion.
-+ for file in `sed -n "
-+ s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
-+ sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
-+ # Make sure the directory exists.
-+ test -f "$dirpart/$file" && continue
-+ fdir=`AS_DIRNAME(["$file"])`
-+ AS_MKDIR_P([$dirpart/$fdir])
-+ # echo "creating $dirpart/$file"
-+ echo '# dummy' > "$dirpart/$file"
-+ done
-+ done
-+}
-+])# _AM_OUTPUT_DEPENDENCY_COMMANDS
-+
-+
-+# AM_OUTPUT_DEPENDENCY_COMMANDS
-+# -----------------------------
-+# This macro should only be invoked once -- use via AC_REQUIRE.
-+#
-+# This code is only required when automatic dependency tracking
-+# is enabled. FIXME. This creates each `.P' file that we will
-+# need in order to bootstrap the dependency handling code.
-+AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
-+[AC_CONFIG_COMMANDS([depfiles],
-+ [test x"$AMDEP_TRUE" != x"" || _AM_OUTPUT_DEPENDENCY_COMMANDS],
-+ [AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"])
- ])
-
--dnl From libtool-1.4. Sets the variable LD.
--AC_DEFUN([AC_LIB_PROG_LD],
--[AC_ARG_WITH(gnu-ld,
--[ --with-gnu-ld assume the C compiler uses GNU ld [default=no]],
--test "$withval" = no || with_gnu_ld=yes, with_gnu_ld=no)
--AC_REQUIRE([AC_PROG_CC])dnl
--AC_REQUIRE([AC_CANONICAL_HOST])dnl
--# Prepare PATH_SEPARATOR.
--# The user is always right.
--if test "${PATH_SEPARATOR+set}" != set; then
-- echo "#! /bin/sh" >conf$$.sh
-- echo "exit 0" >>conf$$.sh
-- chmod +x conf$$.sh
-- if (PATH="/nonexistent;."; conf$$.sh) >/dev/null 2>&1; then
-- PATH_SEPARATOR=';'
-+# Do all the work for Automake. -*- Autoconf -*-
-+
-+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
-+# 2005, 2006, 2008, 2009 Free Software Foundation, Inc.
-+#
-+# This file is free software; the Free Software Foundation
-+# gives unlimited permission to copy and/or distribute it,
-+# with or without modifications, as long as this notice is preserved.
-+
-+# serial 16
-+
-+# This macro actually does too much. Some checks are only needed if
-+# your package does certain things. But this isn't really a big deal.
-+
-+# AM_INIT_AUTOMAKE(PACKAGE, VERSION, [NO-DEFINE])
-+# AM_INIT_AUTOMAKE([OPTIONS])
-+# -----------------------------------------------
-+# The call with PACKAGE and VERSION arguments is the old style
-+# call (pre autoconf-2.50), which is being phased out. PACKAGE
-+# and VERSION should now be passed to AC_INIT and removed from
-+# the call to AM_INIT_AUTOMAKE.
-+# We support both call styles for the transition. After
-+# the next Automake release, Autoconf can make the AC_INIT
-+# arguments mandatory, and then we can depend on a new Autoconf
-+# release and drop the old call support.
-+AC_DEFUN([AM_INIT_AUTOMAKE],
-+[AC_PREREQ([2.62])dnl
-+dnl Autoconf wants to disallow AM_ names. We explicitly allow
-+dnl the ones we care about.
-+m4_pattern_allow([^AM_[A-Z]+FLAGS$])dnl
-+AC_REQUIRE([AM_SET_CURRENT_AUTOMAKE_VERSION])dnl
-+AC_REQUIRE([AC_PROG_INSTALL])dnl
-+if test "`cd $srcdir && pwd`" != "`pwd`"; then
-+ # Use -I$(srcdir) only when $(srcdir) != ., so that make's output
-+ # is not polluted with repeated "-I."
-+ AC_SUBST([am__isrc], [' -I$(srcdir)'])_AM_SUBST_NOTMAKE([am__isrc])dnl
-+ # test to see if srcdir already configured
-+ if test -f $srcdir/config.status; then
-+ AC_MSG_ERROR([source directory already configured; run "make distclean" there first])
-+ fi
-+fi
-+
-+# test whether we have cygpath
-+if test -z "$CYGPATH_W"; then
-+ if (cygpath --version) >/dev/null 2>/dev/null; then
-+ CYGPATH_W='cygpath -w'
- else
-- PATH_SEPARATOR=:
-+ CYGPATH_W=echo
- fi
-- rm -f conf$$.sh
- fi
--ac_prog=ld
--if test "$GCC" = yes; then
-- # Check if gcc -print-prog-name=ld gives a path.
-- AC_MSG_CHECKING([for ld used by GCC])
-- case $host in
-- *-*-mingw*)
-- # gcc leaves a trailing carriage return which upsets mingw
-- ac_prog=`($CC -print-prog-name=ld) 2>&5 | tr -d '\015'` ;;
-- *)
-- ac_prog=`($CC -print-prog-name=ld) 2>&5` ;;
-+AC_SUBST([CYGPATH_W])
-+
-+# Define the identity of the package.
-+dnl Distinguish between old-style and new-style calls.
-+m4_ifval([$2],
-+[m4_ifval([$3], [_AM_SET_OPTION([no-define])])dnl
-+ AC_SUBST([PACKAGE], [$1])dnl
-+ AC_SUBST([VERSION], [$2])],
-+[_AM_SET_OPTIONS([$1])dnl
-+dnl Diagnose old-style AC_INIT with new-style AM_AUTOMAKE_INIT.
-+m4_if(m4_ifdef([AC_PACKAGE_NAME], 1)m4_ifdef([AC_PACKAGE_VERSION], 1), 11,,
-+ [m4_fatal([AC_INIT should be called with package and version arguments])])dnl
-+ AC_SUBST([PACKAGE], ['AC_PACKAGE_TARNAME'])dnl
-+ AC_SUBST([VERSION], ['AC_PACKAGE_VERSION'])])dnl
-+
-+_AM_IF_OPTION([no-define],,
-+[AC_DEFINE_UNQUOTED(PACKAGE, "$PACKAGE", [Name of package])
-+ AC_DEFINE_UNQUOTED(VERSION, "$VERSION", [Version number of package])])dnl
-+
-+# Some tools Automake needs.
-+AC_REQUIRE([AM_SANITY_CHECK])dnl
-+AC_REQUIRE([AC_ARG_PROGRAM])dnl
-+AM_MISSING_PROG(ACLOCAL, aclocal-${am__api_version})
-+AM_MISSING_PROG(AUTOCONF, autoconf)
-+AM_MISSING_PROG(AUTOMAKE, automake-${am__api_version})
-+AM_MISSING_PROG(AUTOHEADER, autoheader)
-+AM_MISSING_PROG(MAKEINFO, makeinfo)
-+AC_REQUIRE([AM_PROG_INSTALL_SH])dnl
-+AC_REQUIRE([AM_PROG_INSTALL_STRIP])dnl
-+AC_REQUIRE([AM_PROG_MKDIR_P])dnl
-+# We need awk for the "check" target. The system "awk" is bad on
-+# some platforms.
-+AC_REQUIRE([AC_PROG_AWK])dnl
-+AC_REQUIRE([AC_PROG_MAKE_SET])dnl
-+AC_REQUIRE([AM_SET_LEADING_DOT])dnl
-+_AM_IF_OPTION([tar-ustar], [_AM_PROG_TAR([ustar])],
-+ [_AM_IF_OPTION([tar-pax], [_AM_PROG_TAR([pax])],
-+ [_AM_PROG_TAR([v7])])])
-+_AM_IF_OPTION([no-dependencies],,
-+[AC_PROVIDE_IFELSE([AC_PROG_CC],
-+ [_AM_DEPENDENCIES(CC)],
-+ [define([AC_PROG_CC],
-+ defn([AC_PROG_CC])[_AM_DEPENDENCIES(CC)])])dnl
-+AC_PROVIDE_IFELSE([AC_PROG_CXX],
-+ [_AM_DEPENDENCIES(CXX)],
-+ [define([AC_PROG_CXX],
-+ defn([AC_PROG_CXX])[_AM_DEPENDENCIES(CXX)])])dnl
-+AC_PROVIDE_IFELSE([AC_PROG_OBJC],
-+ [_AM_DEPENDENCIES(OBJC)],
-+ [define([AC_PROG_OBJC],
-+ defn([AC_PROG_OBJC])[_AM_DEPENDENCIES(OBJC)])])dnl
-+])
-+_AM_IF_OPTION([silent-rules], [AC_REQUIRE([AM_SILENT_RULES])])dnl
-+dnl The `parallel-tests' driver may need to know about EXEEXT, so add the
-+dnl `am__EXEEXT' conditional if _AM_COMPILER_EXEEXT was seen. This macro
-+dnl is hooked onto _AC_COMPILER_EXEEXT early, see below.
-+AC_CONFIG_COMMANDS_PRE(dnl
-+[m4_provide_if([_AM_COMPILER_EXEEXT],
-+ [AM_CONDITIONAL([am__EXEEXT], [test -n "$EXEEXT"])])])dnl
-+])
-+
-+dnl Hook into `_AC_COMPILER_EXEEXT' early to learn its expansion. Do not
-+dnl add the conditional right here, as _AC_COMPILER_EXEEXT may be further
-+dnl mangled by Autoconf and run in a shell conditional statement.
-+m4_define([_AC_COMPILER_EXEEXT],
-+m4_defn([_AC_COMPILER_EXEEXT])[m4_provide([_AM_COMPILER_EXEEXT])])
-+
-+
-+# When config.status generates a header, we must update the stamp-h file.
-+# This file resides in the same directory as the config header
-+# that is generated. The stamp files are numbered to have different names.
-+
-+# Autoconf calls _AC_AM_CONFIG_HEADER_HOOK (when defined) in the
-+# loop where config.status creates the headers, so we can generate
-+# our stamp files there.
-+AC_DEFUN([_AC_AM_CONFIG_HEADER_HOOK],
-+[# Compute $1's index in $config_headers.
-+_am_arg=$1
-+_am_stamp_count=1
-+for _am_header in $config_headers :; do
-+ case $_am_header in
-+ $_am_arg | $_am_arg:* )
-+ break ;;
-+ * )
-+ _am_stamp_count=`expr $_am_stamp_count + 1` ;;
- esac
-- case $ac_prog in
-- # Accept absolute paths.
-- [[\\/]* | [A-Za-z]:[\\/]*)]
-- [re_direlt='/[^/][^/]*/\.\./']
-- # Canonicalize the path of ld
-- ac_prog=`echo $ac_prog| sed 's%\\\\%/%g'`
-- while echo $ac_prog | grep "$re_direlt" > /dev/null 2>&1; do
-- ac_prog=`echo $ac_prog| sed "s%$re_direlt%/%"`
-- done
-- test -z "$LD" && LD="$ac_prog"
-- ;;
-- "")
-- # If it fails, then pretend we aren't using GCC.
-- ac_prog=ld
-- ;;
-+done
-+echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_count])
-+
-+# Copyright (C) 2001, 2003, 2005, 2008 Free Software Foundation, Inc.
-+#
-+# This file is free software; the Free Software Foundation
-+# gives unlimited permission to copy and/or distribute it,
-+# with or without modifications, as long as this notice is preserved.
-+
-+# AM_PROG_INSTALL_SH
-+# ------------------
-+# Define $install_sh.
-+AC_DEFUN([AM_PROG_INSTALL_SH],
-+[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
-+if test x"${install_sh}" != xset; then
-+ case $am_aux_dir in
-+ *\ * | *\ *)
-+ install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
- *)
-- # If it is relative, then search for the first ld in PATH.
-- with_gnu_ld=unknown
-- ;;
-+ install_sh="\${SHELL} $am_aux_dir/install-sh"
- esac
--elif test "$with_gnu_ld" = yes; then
-- AC_MSG_CHECKING([for GNU ld])
-+fi
-+AC_SUBST(install_sh)])
-+
-+# Copyright (C) 2003, 2005 Free Software Foundation, Inc.
-+#
-+# This file is free software; the Free Software Foundation
-+# gives unlimited permission to copy and/or distribute it,
-+# with or without modifications, as long as this notice is preserved.
-+
-+# serial 2
-+
-+# Check whether the underlying file-system supports filenames
-+# with a leading dot. For instance MS-DOS doesn't.
-+AC_DEFUN([AM_SET_LEADING_DOT],
-+[rm -rf .tst 2>/dev/null
-+mkdir .tst 2>/dev/null
-+if test -d .tst; then
-+ am__leading_dot=.
- else
-- AC_MSG_CHECKING([for non-GNU ld])
-+ am__leading_dot=_
- fi
--AC_CACHE_VAL(acl_cv_path_LD,
--[if test -z "$LD"; then
-- IFS="${IFS= }"; ac_save_ifs="$IFS"; IFS="${IFS}${PATH_SEPARATOR-:}"
-- for ac_dir in $PATH; do
-- test -z "$ac_dir" && ac_dir=.
-- if test -f "$ac_dir/$ac_prog" || test -f "$ac_dir/$ac_prog$ac_exeext"; then
-- acl_cv_path_LD="$ac_dir/$ac_prog"
-- # Check to see if the program is GNU ld. I'd rather use --version,
-- # but apparently some GNU ld's only accept -v.
-- # Break only if it was the GNU/non-GNU ld that we prefer.
-- case `"$acl_cv_path_LD" -v 2>&1 < /dev/null` in
-- *GNU* | *'with BFD'*)
-- test "$with_gnu_ld" != no && break ;;
-- *)
-- test "$with_gnu_ld" != yes && break ;;
-+rmdir .tst 2>/dev/null
-+AC_SUBST([am__leading_dot])])
-+
-+# Check to see how 'make' treats includes. -*- Autoconf -*-
-+
-+# Copyright (C) 2001, 2002, 2003, 2005, 2009 Free Software Foundation, Inc.
-+#
-+# This file is free software; the Free Software Foundation
-+# gives unlimited permission to copy and/or distribute it,
-+# with or without modifications, as long as this notice is preserved.
-+
-+# serial 4
-+
-+# AM_MAKE_INCLUDE()
-+# -----------------
-+# Check to see how make treats includes.
-+AC_DEFUN([AM_MAKE_INCLUDE],
-+[am_make=${MAKE-make}
-+cat > confinc << 'END'
-+am__doit:
-+ @echo this is the am__doit target
-+.PHONY: am__doit
-+END
-+# If we don't find an include directive, just comment out the code.
-+AC_MSG_CHECKING([for style of include used by $am_make])
-+am__include="#"
-+am__quote=
-+_am_result=none
-+# First try GNU make style include.
-+echo "include confinc" > confmf
-+# Ignore all kinds of additional output from `make'.
-+case `$am_make -s -f confmf 2> /dev/null` in #(
-+*the\ am__doit\ target*)
-+ am__include=include
-+ am__quote=
-+ _am_result=GNU
-+ ;;
-+esac
-+# Now try BSD make style include.
-+if test "$am__include" = "#"; then
-+ echo '.include "confinc"' > confmf
-+ case `$am_make -s -f confmf 2> /dev/null` in #(
-+ *the\ am__doit\ target*)
-+ am__include=.include
-+ am__quote="\""
-+ _am_result=BSD
-+ ;;
- esac
-- fi
-- done
-- IFS="$ac_save_ifs"
--else
-- acl_cv_path_LD="$LD" # Let the user override the test with a path.
--fi])
--LD="$acl_cv_path_LD"
--if test -n "$LD"; then
-- AC_MSG_RESULT($LD)
--else
-- AC_MSG_RESULT(no)
- fi
--test -z "$LD" && AC_MSG_ERROR([no acceptable ld found in \$PATH])
--AC_LIB_PROG_LD_GNU
-+AC_SUBST([am__include])
-+AC_SUBST([am__quote])
-+AC_MSG_RESULT([$_am_result])
-+rm -f confinc confmf
- ])
-
--# Do all the work for Automake. This macro actually does too much --
--# some checks are only needed if your package does certain things.
--# But this isn't really a big deal.
-+# Fake the existence of programs that GNU maintainers use. -*- Autoconf -*-
-
--# serial 1
-+# Copyright (C) 1997, 1999, 2000, 2001, 2003, 2004, 2005, 2008
-+# Free Software Foundation, Inc.
-+#
-+# This file is free software; the Free Software Foundation
-+# gives unlimited permission to copy and/or distribute it,
-+# with or without modifications, as long as this notice is preserved.
-
--dnl Usage:
--dnl AM_INIT_AUTOMAKE(package,version, [no-define])
-+# serial 6
-
--AC_DEFUN([AM_INIT_AUTOMAKE],
--[AC_REQUIRE([AM_SET_CURRENT_AUTOMAKE_VERSION])dnl
--AC_REQUIRE([AC_PROG_INSTALL])
--PACKAGE=[$1]
--AC_SUBST(PACKAGE)
--VERSION=[$2]
--AC_SUBST(VERSION)
--dnl test to see if srcdir already configured
--if test "`cd $srcdir && pwd`" != "`pwd`" && test -f $srcdir/config.status; then
-- AC_MSG_ERROR([source directory already configured; run "make distclean" there first])
--fi
--ifelse([$3],,
--AC_DEFINE_UNQUOTED(PACKAGE, "$PACKAGE", [Name of package])
--AC_DEFINE_UNQUOTED(VERSION, "$VERSION", [Version number of package]))
--AC_REQUIRE([AM_SANITY_CHECK])
--AC_REQUIRE([AC_ARG_PROGRAM])
--dnl FIXME This is truly gross.
--missing_dir=`cd $ac_aux_dir && pwd`
--AM_MISSING_PROG(ACLOCAL, aclocal-${am__api_version}, $missing_dir)
--AM_MISSING_PROG(AUTOCONF, autoconf, $missing_dir)
--AM_MISSING_PROG(AUTOMAKE, automake-${am__api_version}, $missing_dir)
--AM_MISSING_PROG(AUTOHEADER, autoheader, $missing_dir)
--AM_MISSING_PROG(MAKEINFO, makeinfo, $missing_dir)
--AC_REQUIRE([AC_PROG_MAKE_SET])])
--
--# Copyright 2002 Free Software Foundation, Inc.
--
--# This program is free software; you can redistribute it and/or modify
--# it under the terms of the GNU General Public License as published by
--# the Free Software Foundation; either version 2, or (at your option)
--# any later version.
-+# AM_MISSING_PROG(NAME, PROGRAM)
-+# ------------------------------
-+AC_DEFUN([AM_MISSING_PROG],
-+[AC_REQUIRE([AM_MISSING_HAS_RUN])
-+$1=${$1-"${am_missing_run}$2"}
-+AC_SUBST($1)])
-
--# This program is distributed in the hope that it will be useful,
--# but WITHOUT ANY WARRANTY; without even the implied warranty of
--# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
--# GNU General Public License for more details.
--
--# You should have received a copy of the GNU General Public License
--# along with this program; if not, write to the Free Software
--# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
-
--# AM_AUTOMAKE_VERSION(VERSION)
--# ----------------------------
--# Automake X.Y traces this macro to ensure aclocal.m4 has been
--# generated from the m4 files accompanying Automake X.Y.
--AC_DEFUN([AM_AUTOMAKE_VERSION],[am__api_version="1.4"])
-+# AM_MISSING_HAS_RUN
-+# ------------------
-+# Define MISSING if not defined so far and test if it supports --run.
-+# If it does, set am_missing_run to use it, otherwise, to nothing.
-+AC_DEFUN([AM_MISSING_HAS_RUN],
-+[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
-+AC_REQUIRE_AUX_FILE([missing])dnl
-+if test x"${MISSING+set}" != xset; then
-+ case $am_aux_dir in
-+ *\ * | *\ *)
-+ MISSING="\${SHELL} \"$am_aux_dir/missing\"" ;;
-+ *)
-+ MISSING="\${SHELL} $am_aux_dir/missing" ;;
-+ esac
-+fi
-+# Use eval to expand $SHELL
-+if eval "$MISSING --run true"; then
-+ am_missing_run="$MISSING --run "
-+else
-+ am_missing_run=
-+ AC_MSG_WARN([`missing' script is too old or missing])
-+fi
-+])
-
--# AM_SET_CURRENT_AUTOMAKE_VERSION
--# -------------------------------
--# Call AM_AUTOMAKE_VERSION so it can be traced.
--# This function is AC_REQUIREd by AC_INIT_AUTOMAKE.
--AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
-- [AM_AUTOMAKE_VERSION([1.4-p6])])
-+# Copyright (C) 2003, 2004, 2005, 2006 Free Software Foundation, Inc.
-+#
-+# This file is free software; the Free Software Foundation
-+# gives unlimited permission to copy and/or distribute it,
-+# with or without modifications, as long as this notice is preserved.
-+
-+# AM_PROG_MKDIR_P
-+# ---------------
-+# Check for `mkdir -p'.
-+AC_DEFUN([AM_PROG_MKDIR_P],
-+[AC_PREREQ([2.60])dnl
-+AC_REQUIRE([AC_PROG_MKDIR_P])dnl
-+dnl Automake 1.8 to 1.9.6 used to define mkdir_p. We now use MKDIR_P,
-+dnl while keeping a definition of mkdir_p for backward compatibility.
-+dnl @MKDIR_P@ is magic: AC_OUTPUT adjusts its value for each Makefile.
-+dnl However we cannot define mkdir_p as $(MKDIR_P) for the sake of
-+dnl Makefile.ins that do not define MKDIR_P, so we do our own
-+dnl adjustment using top_builddir (which is defined more often than
-+dnl MKDIR_P).
-+AC_SUBST([mkdir_p], ["$MKDIR_P"])dnl
-+case $mkdir_p in
-+ [[\\/$]]* | ?:[[\\/]]*) ;;
-+ */*) mkdir_p="\$(top_builddir)/$mkdir_p" ;;
-+esac
-+])
-
-+# Helper functions for option handling. -*- Autoconf -*-
-+
-+# Copyright (C) 2001, 2002, 2003, 2005, 2008 Free Software Foundation, Inc.
- #
--# Check to make sure that the build environment is sane.
-+# This file is free software; the Free Software Foundation
-+# gives unlimited permission to copy and/or distribute it,
-+# with or without modifications, as long as this notice is preserved.
-+
-+# serial 4
-+
-+# _AM_MANGLE_OPTION(NAME)
-+# -----------------------
-+AC_DEFUN([_AM_MANGLE_OPTION],
-+[[_AM_OPTION_]m4_bpatsubst($1, [[^a-zA-Z0-9_]], [_])])
-+
-+# _AM_SET_OPTION(NAME)
-+# ------------------------------
-+# Set option NAME. Presently that only means defining a flag for this option.
-+AC_DEFUN([_AM_SET_OPTION],
-+[m4_define(_AM_MANGLE_OPTION([$1]), 1)])
-+
-+# _AM_SET_OPTIONS(OPTIONS)
-+# ----------------------------------
-+# OPTIONS is a space-separated list of Automake options.
-+AC_DEFUN([_AM_SET_OPTIONS],
-+[m4_foreach_w([_AM_Option], [$1], [_AM_SET_OPTION(_AM_Option)])])
-+
-+# _AM_IF_OPTION(OPTION, IF-SET, [IF-NOT-SET])
-+# -------------------------------------------
-+# Execute IF-SET if OPTION is set, IF-NOT-SET otherwise.
-+AC_DEFUN([_AM_IF_OPTION],
-+[m4_ifset(_AM_MANGLE_OPTION([$1]), [$2], [$3])])
-+
-+# Check to make sure that the build environment is sane. -*- Autoconf -*-
-+
-+# Copyright (C) 1996, 1997, 2000, 2001, 2003, 2005, 2008
-+# Free Software Foundation, Inc.
- #
-+# This file is free software; the Free Software Foundation
-+# gives unlimited permission to copy and/or distribute it,
-+# with or without modifications, as long as this notice is preserved.
-+
-+# serial 5
-
-+# AM_SANITY_CHECK
-+# ---------------
- AC_DEFUN([AM_SANITY_CHECK],
- [AC_MSG_CHECKING([whether build environment is sane])
- # Just in case
- sleep 1
--echo timestamp > conftestfile
-+echo timestamp > conftest.file
-+# Reject unsafe characters in $srcdir or the absolute working directory
-+# name. Accept space and tab only in the latter.
-+am_lf='
-+'
-+case `pwd` in
-+ *[[\\\"\#\$\&\'\`$am_lf]]*)
-+ AC_MSG_ERROR([unsafe absolute working directory name]);;
-+esac
-+case $srcdir in
-+ *[[\\\"\#\$\&\'\`$am_lf\ \ ]]*)
-+ AC_MSG_ERROR([unsafe srcdir value: `$srcdir']);;
-+esac
-+
- # Do `set' in a subshell so we don't clobber the current shell's
- # arguments. Must try -L first in case configure is actually a
- # symlink; some systems play weird games with the mod time of symlinks
- # (eg FreeBSD returns the mod time of the symlink's containing
- # directory).
- if (
-- set X `ls -Lt $srcdir/configure conftestfile 2> /dev/null`
-- if test "[$]*" = "X"; then
-+ set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
-+ if test "$[*]" = "X"; then
- # -L didn't work.
-- set X `ls -t $srcdir/configure conftestfile`
-+ set X `ls -t "$srcdir/configure" conftest.file`
- fi
-- if test "[$]*" != "X $srcdir/configure conftestfile" \
-- && test "[$]*" != "X conftestfile $srcdir/configure"; then
-+ rm -f conftest.file
-+ if test "$[*]" != "X $srcdir/configure conftest.file" \
-+ && test "$[*]" != "X conftest.file $srcdir/configure"; then
-
- # If neither matched, then we have a broken ls. This can happen
- # if, for instance, CONFIG_SHELL is bash and it inherits a
-@@ -1046,7 +795,7 @@
- alias in your environment])
- fi
-
-- test "[$]2" = conftestfile
-+ test "$[2]" = conftest.file
- )
- then
- # Ok.
-@@ -1055,22 +804,148 @@
- AC_MSG_ERROR([newly created file is older than distributed files!
- Check your system clock])
- fi
--rm -f conftest*
- AC_MSG_RESULT(yes)])
-
--dnl AM_MISSING_PROG(NAME, PROGRAM, DIRECTORY)
--dnl The program must properly implement --version.
--AC_DEFUN([AM_MISSING_PROG],
--[AC_MSG_CHECKING(for working $2)
--# Run test in a subshell; some versions of sh will print an error if
--# an executable is not found, even if stderr is redirected.
--# Redirect stdin to placate older versions of autoconf. Sigh.
--if ($2 --version) < /dev/null > /dev/null 2>&1; then
-- $1=$2
-- AC_MSG_RESULT(found)
--else
-- $1="$3/missing $2"
-- AC_MSG_RESULT(missing)
-+# Copyright (C) 2001, 2003, 2005 Free Software Foundation, Inc.
-+#
-+# This file is free software; the Free Software Foundation
-+# gives unlimited permission to copy and/or distribute it,
-+# with or without modifications, as long as this notice is preserved.
-+
-+# AM_PROG_INSTALL_STRIP
-+# ---------------------
-+# One issue with vendor `install' (even GNU) is that you can't
-+# specify the program used to strip binaries. This is especially
-+# annoying in cross-compiling environments, where the build's strip
-+# is unlikely to handle the host's binaries.
-+# Fortunately install-sh will honor a STRIPPROG variable, so we
-+# always use install-sh in `make install-strip', and initialize
-+# STRIPPROG with the value of the STRIP variable (set by the user).
-+AC_DEFUN([AM_PROG_INSTALL_STRIP],
-+[AC_REQUIRE([AM_PROG_INSTALL_SH])dnl
-+# Installed binaries are usually stripped using `strip' when the user
-+# run `make install-strip'. However `strip' might not be the right
-+# tool to use in cross-compilation environments, therefore Automake
-+# will honor the `STRIP' environment variable to overrule this program.
-+dnl Don't test for $cross_compiling = yes, because it might be `maybe'.
-+if test "$cross_compiling" != no; then
-+ AC_CHECK_TOOL([STRIP], [strip], :)
- fi
--AC_SUBST($1)])
-+INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
-+AC_SUBST([INSTALL_STRIP_PROGRAM])])
-+
-+# Copyright (C) 2006, 2008 Free Software Foundation, Inc.
-+#
-+# This file is free software; the Free Software Foundation
-+# gives unlimited permission to copy and/or distribute it,
-+# with or without modifications, as long as this notice is preserved.
-+
-+# serial 2
-+
-+# _AM_SUBST_NOTMAKE(VARIABLE)
-+# ---------------------------
-+# Prevent Automake from outputting VARIABLE = @VARIABLE@ in Makefile.in.
-+# This macro is traced by Automake.
-+AC_DEFUN([_AM_SUBST_NOTMAKE])
-+
-+# AM_SUBST_NOTMAKE(VARIABLE)
-+# ---------------------------
-+# Public sister of _AM_SUBST_NOTMAKE.
-+AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)])
-+
-+# Check how to create a tarball. -*- Autoconf -*-
-+
-+# Copyright (C) 2004, 2005 Free Software Foundation, Inc.
-+#
-+# This file is free software; the Free Software Foundation
-+# gives unlimited permission to copy and/or distribute it,
-+# with or without modifications, as long as this notice is preserved.
-+
-+# serial 2
-+
-+# _AM_PROG_TAR(FORMAT)
-+# --------------------
-+# Check how to create a tarball in format FORMAT.
-+# FORMAT should be one of `v7', `ustar', or `pax'.
-+#
-+# Substitute a variable $(am__tar) that is a command
-+# writing to stdout a FORMAT-tarball containing the directory
-+# $tardir.
-+# tardir=directory && $(am__tar) > result.tar
-+#
-+# Substitute a variable $(am__untar) that extract such
-+# a tarball read from stdin.
-+# $(am__untar) < result.tar
-+AC_DEFUN([_AM_PROG_TAR],
-+[# Always define AMTAR for backward compatibility.
-+AM_MISSING_PROG([AMTAR], [tar])
-+m4_if([$1], [v7],
-+ [am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -'],
-+ [m4_case([$1], [ustar],, [pax],,
-+ [m4_fatal([Unknown tar format])])
-+AC_MSG_CHECKING([how to create a $1 tar archive])
-+# Loop over all known methods to create a tar archive until one works.
-+_am_tools='gnutar m4_if([$1], [ustar], [plaintar]) pax cpio none'
-+_am_tools=${am_cv_prog_tar_$1-$_am_tools}
-+# Do not fold the above two line into one, because Tru64 sh and
-+# Solaris sh will not grok spaces in the rhs of `-'.
-+for _am_tool in $_am_tools
-+do
-+ case $_am_tool in
-+ gnutar)
-+ for _am_tar in tar gnutar gtar;
-+ do
-+ AM_RUN_LOG([$_am_tar --version]) && break
-+ done
-+ am__tar="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$$tardir"'
-+ am__tar_="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$tardir"'
-+ am__untar="$_am_tar -xf -"
-+ ;;
-+ plaintar)
-+ # Must skip GNU tar: if it does not support --format= it doesn't create
-+ # ustar tarball either.
-+ (tar --version) >/dev/null 2>&1 && continue
-+ am__tar='tar chf - "$$tardir"'
-+ am__tar_='tar chf - "$tardir"'
-+ am__untar='tar xf -'
-+ ;;
-+ pax)
-+ am__tar='pax -L -x $1 -w "$$tardir"'
-+ am__tar_='pax -L -x $1 -w "$tardir"'
-+ am__untar='pax -r'
-+ ;;
-+ cpio)
-+ am__tar='find "$$tardir" -print | cpio -o -H $1 -L'
-+ am__tar_='find "$tardir" -print | cpio -o -H $1 -L'
-+ am__untar='cpio -i -H $1 -d'
-+ ;;
-+ none)
-+ am__tar=false
-+ am__tar_=false
-+ am__untar=false
-+ ;;
-+ esac
-+
-+ # If the value was cached, stop now. We just wanted to have am__tar
-+ # and am__untar set.
-+ test -n "${am_cv_prog_tar_$1}" && break
-+
-+ # tar/untar a dummy directory, and stop if the command works
-+ rm -rf conftest.dir
-+ mkdir conftest.dir
-+ echo GrepMe > conftest.dir/file
-+ AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar])
-+ rm -rf conftest.dir
-+ if test -s conftest.tar; then
-+ AM_RUN_LOG([$am__untar <conftest.tar])
-+ grep GrepMe conftest.dir/file >/dev/null 2>&1 && break
-+ fi
-+done
-+rm -rf conftest.dir
-+
-+AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool])
-+AC_MSG_RESULT([$am_cv_prog_tar_$1])])
-+AC_SUBST([am__tar])
-+AC_SUBST([am__untar])
-+]) # _AM_PROG_TAR
-
-diff -ubrN exonerate-2.2.0.orig/configure exonerate-2.2.0/configure
---- exonerate-2.2.0.orig/configure 2008-10-17 12:04:52.000000000 +0200
-+++ exonerate-2.2.0/configure 2011-12-12 13:32:51.000000000 +0100
-@@ -1,60 +1,83 @@
- #! /bin/sh
- # Guess values for system-dependent variables and create Makefiles.
--# Generated by GNU Autoconf 2.61.
-+# Generated by GNU Autoconf 2.68.
-+#
- #
- # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
--# 2002, 2003, 2004, 2005, 2006 Free Software Foundation, Inc.
-+# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free Software
-+# Foundation, Inc.
-+#
-+#
- # This configure script is free software; the Free Software Foundation
- # gives unlimited permission to copy, distribute and modify it.
--## --------------------- ##
-+## -------------------- ##
- ## M4sh Initialization. ##
--## --------------------- ##
-+## -------------------- ##
-
- # Be more Bourne compatible
- DUALCASE=1; export DUALCASE # for MKS sh
--if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
-+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
- emulate sh
- NULLCMD=:
-- # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
-+ # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
- # is contrary to our usage. Disable this feature.
- alias -g '${1+"$@"}'='"$@"'
- setopt NO_GLOB_SUBST
- else
-- case `(set -o) 2>/dev/null` in
-- *posix*) set -o posix ;;
-+ case `(set -o) 2>/dev/null` in #(
-+ *posix*) :
-+ set -o posix ;; #(
-+ *) :
-+ ;;
- esac
--
- fi
-
-
--
--
--# PATH needs CR
--# Avoid depending upon Character Ranges.
--as_cr_letters='abcdefghijklmnopqrstuvwxyz'
--as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
--as_cr_Letters=$as_cr_letters$as_cr_LETTERS
--as_cr_digits='0123456789'
--as_cr_alnum=$as_cr_Letters$as_cr_digits
--
--# The user is always right.
--if test "${PATH_SEPARATOR+set}" != set; then
-- echo "#! /bin/sh" >conf$$.sh
-- echo "exit 0" >>conf$$.sh
-- chmod +x conf$$.sh
-- if (PATH="/nonexistent;."; conf$$.sh) >/dev/null 2>&1; then
-- PATH_SEPARATOR=';'
-+as_nl='
-+'
-+export as_nl
-+# Printing a long string crashes Solaris 7 /usr/bin/printf.
-+as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
-+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
-+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
-+# Prefer a ksh shell builtin over an external printf program on Solaris,
-+# but without wasting forks for bash or zsh.
-+if test -z "$BASH_VERSION$ZSH_VERSION" \
-+ && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
-+ as_echo='print -r --'
-+ as_echo_n='print -rn --'
-+elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
-+ as_echo='printf %s\n'
-+ as_echo_n='printf %s'
-+else
-+ if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
-+ as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
-+ as_echo_n='/usr/ucb/echo -n'
- else
-- PATH_SEPARATOR=:
-+ as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
-+ as_echo_n_body='eval
-+ arg=$1;
-+ case $arg in #(
-+ *"$as_nl"*)
-+ expr "X$arg" : "X\\(.*\\)$as_nl";
-+ arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
-+ esac;
-+ expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl"
-+ '
-+ export as_echo_n_body
-+ as_echo_n='sh -c $as_echo_n_body as_echo'
- fi
-- rm -f conf$$.sh
-+ export as_echo_body
-+ as_echo='sh -c $as_echo_body as_echo'
- fi
-
--# Support unset when possible.
--if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then
-- as_unset=unset
--else
-- as_unset=false
-+# The user is always right.
-+if test "${PATH_SEPARATOR+set}" != set; then
-+ PATH_SEPARATOR=:
-+ (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
-+ (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
-+ PATH_SEPARATOR=';'
-+ }
- fi
-
-
-@@ -63,12 +86,11 @@
- # there to prevent editors from complaining about space-tab.
- # (If _AS_PATH_WALK were called with IFS unset, it would disable word
- # splitting by setting IFS to empty value.)
--as_nl='
--'
- IFS=" "" $as_nl"
-
- # Find who we are. Look in the path if we contain no directory separator.
--case $0 in
-+as_myself=
-+case $0 in #((
- *[\\/]* ) as_myself=$0 ;;
- *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
- for as_dir in $PATH
-@@ -76,7 +98,7 @@
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
- test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
--done
-+ done
- IFS=$as_save_IFS
-
- ;;
-@@ -87,354 +109,328 @@
- as_myself=$0
- fi
- if test ! -f "$as_myself"; then
-- echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
-- { (exit 1); exit 1; }
-+ $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
-+ exit 1
- fi
-
--# Work around bugs in pre-3.0 UWIN ksh.
--for as_var in ENV MAIL MAILPATH
--do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
-+# Unset variables that we do not need and which cause bugs (e.g. in
-+# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1"
-+# suppresses any "Segmentation fault" message there. '((' could
-+# trigger a bug in pdksh 5.2.14.
-+for as_var in BASH_ENV ENV MAIL MAILPATH
-+do eval test x\${$as_var+set} = xset \
-+ && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
- done
- PS1='$ '
- PS2='> '
- PS4='+ '
-
- # NLS nuisances.
--for as_var in \
-- LANG LANGUAGE LC_ADDRESS LC_ALL LC_COLLATE LC_CTYPE LC_IDENTIFICATION \
-- LC_MEASUREMENT LC_MESSAGES LC_MONETARY LC_NAME LC_NUMERIC LC_PAPER \
-- LC_TELEPHONE LC_TIME
--do
-- if (set +x; test -z "`(eval $as_var=C; export $as_var) 2>&1`"); then
-- eval $as_var=C; export $as_var
-- else
-- ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
-- fi
--done
--
--# Required to use basename.
--if expr a : '\(a\)' >/dev/null 2>&1 &&
-- test "X`expr 00001 : '.*\(...\)'`" = X001; then
-- as_expr=expr
--else
-- as_expr=false
--fi
--
--if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
-- as_basename=basename
--else
-- as_basename=false
--fi
--
--
--# Name of the executable.
--as_me=`$as_basename -- "$0" ||
--$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
-- X"$0" : 'X\(//\)$' \| \
-- X"$0" : 'X\(/\)' \| . 2>/dev/null ||
--echo X/"$0" |
-- sed '/^.*\/\([^/][^/]*\)\/*$/{
-- s//\1/
-- q
-- }
-- /^X\/\(\/\/\)$/{
-- s//\1/
-- q
-- }
-- /^X\/\(\/\).*/{
-- s//\1/
-- q
-- }
-- s/.*/./; q'`
-+LC_ALL=C
-+export LC_ALL
-+LANGUAGE=C
-+export LANGUAGE
-
- # CDPATH.
--$as_unset CDPATH
--
-+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
-
- if test "x$CONFIG_SHELL" = x; then
-- if (eval ":") 2>/dev/null; then
-- as_have_required=yes
-+ as_bourne_compatible="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then :
-+ emulate sh
-+ NULLCMD=:
-+ # Pre-4.2 versions of Zsh do word splitting on \${1+\"\$@\"}, which
-+ # is contrary to our usage. Disable this feature.
-+ alias -g '\${1+\"\$@\"}'='\"\$@\"'
-+ setopt NO_GLOB_SUBST
- else
-- as_have_required=no
-+ case \`(set -o) 2>/dev/null\` in #(
-+ *posix*) :
-+ set -o posix ;; #(
-+ *) :
-+ ;;
-+esac
- fi
--
-- if test $as_have_required = yes && (eval ":
--(as_func_return () {
-- (exit \$1)
--}
--as_func_success () {
-- as_func_return 0
--}
--as_func_failure () {
-- as_func_return 1
--}
--as_func_ret_success () {
-- return 0
--}
--as_func_ret_failure () {
-- return 1
--}
-+"
-+ as_required="as_fn_return () { (exit \$1); }
-+as_fn_success () { as_fn_return 0; }
-+as_fn_failure () { as_fn_return 1; }
-+as_fn_ret_success () { return 0; }
-+as_fn_ret_failure () { return 1; }
-
- exitcode=0
--if as_func_success; then
-- :
--else
-- exitcode=1
-- echo as_func_success failed.
--fi
--
--if as_func_failure; then
-- exitcode=1
-- echo as_func_failure succeeded.
--fi
--
--if as_func_ret_success; then
-- :
--else
-- exitcode=1
-- echo as_func_ret_success failed.
--fi
--
--if as_func_ret_failure; then
-- exitcode=1
-- echo as_func_ret_failure succeeded.
--fi
--
--if ( set x; as_func_ret_success y && test x = \"\$1\" ); then
-- :
-+as_fn_success || { exitcode=1; echo as_fn_success failed.; }
-+as_fn_failure && { exitcode=1; echo as_fn_failure succeeded.; }
-+as_fn_ret_success || { exitcode=1; echo as_fn_ret_success failed.; }
-+as_fn_ret_failure && { exitcode=1; echo as_fn_ret_failure succeeded.; }
-+if ( set x; as_fn_ret_success y && test x = \"\$1\" ); then :
-+
-+else
-+ exitcode=1; echo positional parameters were not saved.
-+fi
-+test x\$exitcode = x0 || exit 1"
-+ as_suggested=" as_lineno_1=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_1a=\$LINENO
-+ as_lineno_2=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_2a=\$LINENO
-+ eval 'test \"x\$as_lineno_1'\$as_run'\" != \"x\$as_lineno_2'\$as_run'\" &&
-+ test \"x\`expr \$as_lineno_1'\$as_run' + 1\`\" = \"x\$as_lineno_2'\$as_run'\"' || exit 1
-+test \$(( 1 + 1 )) = 2 || exit 1"
-+ if (eval "$as_required") 2>/dev/null; then :
-+ as_have_required=yes
- else
-- exitcode=1
-- echo positional parameters were not saved.
-+ as_have_required=no
- fi
-+ if test x$as_have_required = xyes && (eval "$as_suggested") 2>/dev/null; then :
-
--test \$exitcode = 0) || { (exit 1); exit 1; }
--
--(
-- as_lineno_1=\$LINENO
-- as_lineno_2=\$LINENO
-- test \"x\$as_lineno_1\" != \"x\$as_lineno_2\" &&
-- test \"x\`expr \$as_lineno_1 + 1\`\" = \"x\$as_lineno_2\") || { (exit 1); exit 1; }
--") 2> /dev/null; then
-- :
- else
-- as_candidate_shells=
- as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-+as_found=false
- for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH
- do
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
-- case $as_dir in
-+ as_found=:
-+ case $as_dir in #(
- /*)
- for as_base in sh bash ksh sh5; do
-- as_candidate_shells="$as_candidate_shells $as_dir/$as_base"
-- done;;
-- esac
--done
--IFS=$as_save_IFS
--
--
-- for as_shell in $as_candidate_shells $SHELL; do
- # Try only shells that exist, to save several forks.
-+ as_shell=$as_dir/$as_base
- if { test -f "$as_shell" || test -f "$as_shell.exe"; } &&
-- { ("$as_shell") 2> /dev/null <<\_ASEOF
--if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
-- emulate sh
-- NULLCMD=:
-- # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
-- # is contrary to our usage. Disable this feature.
-- alias -g '${1+"$@"}'='"$@"'
-- setopt NO_GLOB_SUBST
--else
-- case `(set -o) 2>/dev/null` in
-- *posix*) set -o posix ;;
--esac
--
-+ { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$as_shell"; } 2>/dev/null; then :
-+ CONFIG_SHELL=$as_shell as_have_required=yes
-+ if { $as_echo "$as_bourne_compatible""$as_suggested" | as_run=a "$as_shell"; } 2>/dev/null; then :
-+ break 2
- fi
--
--
--:
--_ASEOF
--}; then
-- CONFIG_SHELL=$as_shell
-- as_have_required=yes
-- if { "$as_shell" 2> /dev/null <<\_ASEOF
--if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
-- emulate sh
-- NULLCMD=:
-- # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
-- # is contrary to our usage. Disable this feature.
-- alias -g '${1+"$@"}'='"$@"'
-- setopt NO_GLOB_SUBST
--else
-- case `(set -o) 2>/dev/null` in
-- *posix*) set -o posix ;;
--esac
--
- fi
-+ done;;
-+ esac
-+ as_found=false
-+done
-+$as_found || { if { test -f "$SHELL" || test -f "$SHELL.exe"; } &&
-+ { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$SHELL"; } 2>/dev/null; then :
-+ CONFIG_SHELL=$SHELL as_have_required=yes
-+fi; }
-+IFS=$as_save_IFS
-
-
--:
--(as_func_return () {
-- (exit $1)
--}
--as_func_success () {
-- as_func_return 0
--}
--as_func_failure () {
-- as_func_return 1
--}
--as_func_ret_success () {
-- return 0
--}
--as_func_ret_failure () {
-- return 1
--}
--
--exitcode=0
--if as_func_success; then
-- :
--else
-- exitcode=1
-- echo as_func_success failed.
--fi
--
--if as_func_failure; then
-- exitcode=1
-- echo as_func_failure succeeded.
-+ if test "x$CONFIG_SHELL" != x; then :
-+ # We cannot yet assume a decent shell, so we have to provide a
-+ # neutralization value for shells without unset; and this also
-+ # works around shells that cannot unset nonexistent variables.
-+ # Preserve -v and -x to the replacement shell.
-+ BASH_ENV=/dev/null
-+ ENV=/dev/null
-+ (unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
-+ export CONFIG_SHELL
-+ case $- in # ((((
-+ *v*x* | *x*v* ) as_opts=-vx ;;
-+ *v* ) as_opts=-v ;;
-+ *x* ) as_opts=-x ;;
-+ * ) as_opts= ;;
-+ esac
-+ exec "$CONFIG_SHELL" $as_opts "$as_myself" ${1+"$@"}
- fi
-
--if as_func_ret_success; then
-- :
--else
-- exitcode=1
-- echo as_func_ret_success failed.
-+ if test x$as_have_required = xno; then :
-+ $as_echo "$0: This script requires a shell more modern than all"
-+ $as_echo "$0: the shells that I found on your system."
-+ if test x${ZSH_VERSION+set} = xset ; then
-+ $as_echo "$0: In particular, zsh $ZSH_VERSION has bugs and should"
-+ $as_echo "$0: be upgraded to zsh 4.3.4 or later."
-+ else
-+ $as_echo "$0: Please tell bug-autoconf at gnu.org about your system,
-+$0: including any error possibly output before this
-+$0: message. Then install a modern shell, or manually run
-+$0: the script under such a shell if you do have one."
-+ fi
-+ exit 1
- fi
--
--if as_func_ret_failure; then
-- exitcode=1
-- echo as_func_ret_failure succeeded.
- fi
--
--if ( set x; as_func_ret_success y && test x = "$1" ); then
-- :
--else
-- exitcode=1
-- echo positional parameters were not saved.
- fi
-+SHELL=${CONFIG_SHELL-/bin/sh}
-+export SHELL
-+# Unset more variables known to interfere with behavior of common tools.
-+CLICOLOR_FORCE= GREP_OPTIONS=
-+unset CLICOLOR_FORCE GREP_OPTIONS
-
--test $exitcode = 0) || { (exit 1); exit 1; }
--
--(
-- as_lineno_1=$LINENO
-- as_lineno_2=$LINENO
-- test "x$as_lineno_1" != "x$as_lineno_2" &&
-- test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2") || { (exit 1); exit 1; }
--
--_ASEOF
--}; then
-- break
--fi
-+## --------------------- ##
-+## M4sh Shell Functions. ##
-+## --------------------- ##
-+# as_fn_unset VAR
-+# ---------------
-+# Portably unset VAR.
-+as_fn_unset ()
-+{
-+ { eval $1=; unset $1;}
-+}
-+as_unset=as_fn_unset
-
--fi
-+# as_fn_set_status STATUS
-+# -----------------------
-+# Set $? to STATUS, without forking.
-+as_fn_set_status ()
-+{
-+ return $1
-+} # as_fn_set_status
-
-- done
-+# as_fn_exit STATUS
-+# -----------------
-+# Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
-+as_fn_exit ()
-+{
-+ set +e
-+ as_fn_set_status $1
-+ exit $1
-+} # as_fn_exit
-+
-+# as_fn_mkdir_p
-+# -------------
-+# Create "$as_dir" as a directory, including parents if necessary.
-+as_fn_mkdir_p ()
-+{
-
-- if test "x$CONFIG_SHELL" != x; then
-- for as_var in BASH_ENV ENV
-- do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
-+ case $as_dir in #(
-+ -*) as_dir=./$as_dir;;
-+ esac
-+ test -d "$as_dir" || eval $as_mkdir_p || {
-+ as_dirs=
-+ while :; do
-+ case $as_dir in #(
-+ *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
-+ *) as_qdir=$as_dir;;
-+ esac
-+ as_dirs="'$as_qdir' $as_dirs"
-+ as_dir=`$as_dirname -- "$as_dir" ||
-+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
-+ X"$as_dir" : 'X\(//\)[^/]' \| \
-+ X"$as_dir" : 'X\(//\)$' \| \
-+ X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
-+$as_echo X"$as_dir" |
-+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
-+ s//\1/
-+ q
-+ }
-+ /^X\(\/\/\)[^/].*/{
-+ s//\1/
-+ q
-+ }
-+ /^X\(\/\/\)$/{
-+ s//\1/
-+ q
-+ }
-+ /^X\(\/\).*/{
-+ s//\1/
-+ q
-+ }
-+ s/.*/./; q'`
-+ test -d "$as_dir" && break
- done
-- export CONFIG_SHELL
-- exec "$CONFIG_SHELL" "$as_myself" ${1+"$@"}
--fi
--
--
-- if test $as_have_required = no; then
-- echo This script requires a shell more modern than all the
-- echo shells that I found on your system. Please install a
-- echo modern shell, or manually run the script under such a
-- echo shell if you do have one.
-- { (exit 1); exit 1; }
--fi
--
-+ test -z "$as_dirs" || eval "mkdir $as_dirs"
-+ } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
-
--fi
-
--fi
-+} # as_fn_mkdir_p
-+# as_fn_append VAR VALUE
-+# ----------------------
-+# Append the text in VALUE to the end of the definition contained in VAR. Take
-+# advantage of any shell optimizations that allow amortized linear growth over
-+# repeated appends, instead of the typical quadratic growth present in naive
-+# implementations.
-+if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
-+ eval 'as_fn_append ()
-+ {
-+ eval $1+=\$2
-+ }'
-+else
-+ as_fn_append ()
-+ {
-+ eval $1=\$$1\$2
-+ }
-+fi # as_fn_append
-
-+# as_fn_arith ARG...
-+# ------------------
-+# Perform arithmetic evaluation on the ARGs, and store the result in the
-+# global $as_val. Take advantage of shells that can avoid forks. The arguments
-+# must be portable across $(()) and expr.
-+if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
-+ eval 'as_fn_arith ()
-+ {
-+ as_val=$(( $* ))
-+ }'
-+else
-+ as_fn_arith ()
-+ {
-+ as_val=`expr "$@" || test $? -eq 1`
-+ }
-+fi # as_fn_arith
-
-
--(eval "as_func_return () {
-- (exit \$1)
--}
--as_func_success () {
-- as_func_return 0
--}
--as_func_failure () {
-- as_func_return 1
--}
--as_func_ret_success () {
-- return 0
--}
--as_func_ret_failure () {
-- return 1
--}
-+# as_fn_error STATUS ERROR [LINENO LOG_FD]
-+# ----------------------------------------
-+# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
-+# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
-+# script with STATUS, using 1 if that was 0.
-+as_fn_error ()
-+{
-+ as_status=$1; test $as_status -eq 0 && as_status=1
-+ if test "$4"; then
-+ as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
-+ $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
-+ fi
-+ $as_echo "$as_me: error: $2" >&2
-+ as_fn_exit $as_status
-+} # as_fn_error
-
--exitcode=0
--if as_func_success; then
-- :
-+if expr a : '\(a\)' >/dev/null 2>&1 &&
-+ test "X`expr 00001 : '.*\(...\)'`" = X001; then
-+ as_expr=expr
- else
-- exitcode=1
-- echo as_func_success failed.
--fi
--
--if as_func_failure; then
-- exitcode=1
-- echo as_func_failure succeeded.
-+ as_expr=false
- fi
-
--if as_func_ret_success; then
-- :
-+if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
-+ as_basename=basename
- else
-- exitcode=1
-- echo as_func_ret_success failed.
--fi
--
--if as_func_ret_failure; then
-- exitcode=1
-- echo as_func_ret_failure succeeded.
-+ as_basename=false
- fi
-
--if ( set x; as_func_ret_success y && test x = \"\$1\" ); then
-- :
-+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
-+ as_dirname=dirname
- else
-- exitcode=1
-- echo positional parameters were not saved.
-+ as_dirname=false
- fi
-
--test \$exitcode = 0") || {
-- echo No shell found that supports shell functions.
-- echo Please tell autoconf at gnu.org about your system,
-- echo including any error possibly output before this
-- echo message
--}
-+as_me=`$as_basename -- "$0" ||
-+$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
-+ X"$0" : 'X\(//\)$' \| \
-+ X"$0" : 'X\(/\)' \| . 2>/dev/null ||
-+$as_echo X/"$0" |
-+ sed '/^.*\/\([^/][^/]*\)\/*$/{
-+ s//\1/
-+ q
-+ }
-+ /^X\/\(\/\/\)$/{
-+ s//\1/
-+ q
-+ }
-+ /^X\/\(\/\).*/{
-+ s//\1/
-+ q
-+ }
-+ s/.*/./; q'`
-
-+# Avoid depending upon Character Ranges.
-+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
-+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
-+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
-+as_cr_digits='0123456789'
-+as_cr_alnum=$as_cr_Letters$as_cr_digits
-
-
-- as_lineno_1=$LINENO
-- as_lineno_2=$LINENO
-- test "x$as_lineno_1" != "x$as_lineno_2" &&
-- test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || {
--
-- # Create $as_me.lineno as a copy of $as_myself, but with $LINENO
-- # uniformly replaced by the line number. The first 'sed' inserts a
-- # line-number line after each line using $LINENO; the second 'sed'
-- # does the real work. The second script uses 'N' to pair each
-- # line-number line with the line containing $LINENO, and appends
-- # trailing '-' during substitution so that $LINENO is not a special
-- # case at line end.
-- # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the
-- # scripts with optimization help from Paolo Bonzini. Blame Lee
-- # E. McMahon (1931-1989) for sed's syntax. :-)
-+ as_lineno_1=$LINENO as_lineno_1a=$LINENO
-+ as_lineno_2=$LINENO as_lineno_2a=$LINENO
-+ eval 'test "x$as_lineno_1'$as_run'" != "x$as_lineno_2'$as_run'" &&
-+ test "x`expr $as_lineno_1'$as_run' + 1`" = "x$as_lineno_2'$as_run'"' || {
-+ # Blame Lee E. McMahon (1931-1989) for sed's syntax. :-)
- sed -n '
- p
- /[$]LINENO/=
-@@ -451,8 +447,7 @@
- s/-\n.*//
- ' >$as_me.lineno &&
- chmod +x "$as_me.lineno" ||
-- { echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2
-- { (exit 1); exit 1; }; }
-+ { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; }
-
- # Don't try to exec as it changes $[0], causing all sort of problems
- # (the dirname of $[0] is not the place where we might find the
-@@ -460,42 +455,30 @@
- . "./$as_me.lineno"
- # Exit status is that of the last command.
- exit
--}
--
--
--if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
-- as_dirname=dirname
--else
-- as_dirname=false
--fi
-+}
-
- ECHO_C= ECHO_N= ECHO_T=
--case `echo -n x` in
-+case `echo -n x` in #(((((
- -n*)
-- case `echo 'x\c'` in
-+ case `echo 'xy\c'` in
- *c*) ECHO_T=' ';; # ECHO_T is single tab character.
-- *) ECHO_C='\c';;
-+ xy) ECHO_C='\c';;
-+ *) echo `echo ksh88 bug on AIX 6.1` > /dev/null
-+ ECHO_T=' ';;
- esac;;
- *)
- ECHO_N='-n';;
- esac
-
--if expr a : '\(a\)' >/dev/null 2>&1 &&
-- test "X`expr 00001 : '.*\(...\)'`" = X001; then
-- as_expr=expr
--else
-- as_expr=false
--fi
--
- rm -f conf$$ conf$$.exe conf$$.file
- if test -d conf$$.dir; then
- rm -f conf$$.dir/conf$$.file
- else
- rm -f conf$$.dir
-- mkdir conf$$.dir
-+ mkdir conf$$.dir 2>/dev/null
- fi
--echo >conf$$.file
--if ln -s conf$$.file conf$$ 2>/dev/null; then
-+if (echo >conf$$.file) 2>/dev/null; then
-+ if ln -s conf$$.file conf$$ 2>/dev/null; then
- as_ln_s='ln -s'
- # ... but there are two gotchas:
- # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
-@@ -503,8 +486,11 @@
- # In both cases, we have to default to `cp -p'.
- ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
- as_ln_s='cp -p'
--elif ln conf$$.file conf$$ 2>/dev/null; then
-+ elif ln conf$$.file conf$$ 2>/dev/null; then
- as_ln_s=ln
-+ else
-+ as_ln_s='cp -p'
-+ fi
- else
- as_ln_s='cp -p'
- fi
-@@ -512,7 +498,7 @@
- rmdir conf$$.dir 2>/dev/null
-
- if mkdir -p . 2>/dev/null; then
-- as_mkdir_p=:
-+ as_mkdir_p='mkdir -p "$as_dir"'
- else
- test -d ./-p && rmdir ./-p
- as_mkdir_p=false
-@@ -531,10 +517,10 @@
- if test -d "$1"; then
- test -d "$1/.";
- else
-- case $1 in
-+ case $1 in #(
- -*)set "./$1";;
- esac;
-- case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in
-+ case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #((
- ???[sx]*):;;*)false;;esac;fi
- '\'' sh
- '
-@@ -548,11 +534,11 @@
- as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
-
-
--
--exec 7<&0 </dev/null 6>&1
-+test -n "$DJDIR" || exec 7<&0 </dev/null
-+exec 6>&1
-
- # Name of the host.
--# hostname on some systems (SVR3.2, Linux) returns a bogus exit status,
-+# hostname on some systems (SVR3.2, old GNU/Linux) returns a bogus exit status,
- # so uname gets run too.
- ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q`
-
-@@ -567,7 +553,6 @@
- subdirs=
- MFLAGS=
- MAKEFLAGS=
--SHELL=${CONFIG_SHELL-/bin/sh}
-
- # Identity of this package.
- PACKAGE_NAME=
-@@ -575,6 +560,7 @@
- PACKAGE_VERSION=
- PACKAGE_STRING=
- PACKAGE_BUGREPORT=
-+PACKAGE_URL=
-
- ac_unique_file="src/sequence/sequence.c"
- # Factoring default headers for most tests.
-@@ -613,84 +599,121 @@
- # include <unistd.h>
- #endif"
-
--ac_subst_vars='SHELL
--PATH_SEPARATOR
--PACKAGE_NAME
--PACKAGE_TARNAME
--PACKAGE_VERSION
--PACKAGE_STRING
--PACKAGE_BUGREPORT
--exec_prefix
--prefix
--program_transform_name
--bindir
--sbindir
--libexecdir
--datarootdir
--datadir
--sysconfdir
--sharedstatedir
--localstatedir
--includedir
--oldincludedir
--docdir
--infodir
--htmldir
--dvidir
--pdfdir
--psdir
--libdir
--localedir
--mandir
--DEFS
--ECHO_C
--ECHO_N
--ECHO_T
--LIBS
--build_alias
--host_alias
--target_alias
--INSTALL_PROGRAM
--INSTALL_SCRIPT
--INSTALL_DATA
--PACKAGE
--VERSION
--ACLOCAL
--AUTOCONF
--AUTOMAKE
--AUTOHEADER
--MAKEINFO
--SET_MAKE
--CC
--CFLAGS
--LDFLAGS
--CPPFLAGS
--ac_ct_CC
--EXEEXT
--OBJEXT
--CPP
--GREP
--EGREP
--build
--build_cpu
--build_vendor
--build_os
--host
--host_cpu
--host_vendor
--host_os
--source_root_dir
--PKG_CONFIG
--GLIB_CONFIG
--glib_libs
--glib_cflags
--codegen_extra_sources
--codegen_extra_ldadd
--installed_util_list
--use_pthreads
-+ac_subst_vars='am__EXEEXT_FALSE
-+am__EXEEXT_TRUE
-+LTLIBOBJS
- LIBOBJS
--LTLIBOBJS'
-+use_pthreads
-+installed_util_list
-+codegen_extra_ldadd
-+codegen_extra_sources
-+glib_cflags
-+glib_libs
-+GLIB_CONFIG
-+PKG_CONFIG
-+source_root_dir
-+host_os
-+host_vendor
-+host_cpu
-+host
-+build_os
-+build_vendor
-+build_cpu
-+build
-+EGREP
-+GREP
-+CPP
-+am__fastdepCC_FALSE
-+am__fastdepCC_TRUE
-+CCDEPMODE
-+AMDEPBACKSLASH
-+AMDEP_FALSE
-+AMDEP_TRUE
-+am__quote
-+am__include
-+DEPDIR
-+OBJEXT
-+EXEEXT
-+ac_ct_CC
-+CPPFLAGS
-+LDFLAGS
-+CFLAGS
-+CC
-+am__untar
-+am__tar
-+AMTAR
-+am__leading_dot
-+SET_MAKE
-+AWK
-+mkdir_p
-+MKDIR_P
-+INSTALL_STRIP_PROGRAM
-+STRIP
-+install_sh
-+MAKEINFO
-+AUTOHEADER
-+AUTOMAKE
-+AUTOCONF
-+ACLOCAL
-+VERSION
-+PACKAGE
-+CYGPATH_W
-+am__isrc
-+INSTALL_DATA
-+INSTALL_SCRIPT
-+INSTALL_PROGRAM
-+target_alias
-+host_alias
-+build_alias
-+LIBS
-+ECHO_T
-+ECHO_N
-+ECHO_C
-+DEFS
-+mandir
-+localedir
-+libdir
-+psdir
-+pdfdir
-+dvidir
-+htmldir
-+infodir
-+docdir
-+oldincludedir
-+includedir
-+localstatedir
-+sharedstatedir
-+sysconfdir
-+datadir
-+datarootdir
-+libexecdir
-+sbindir
-+bindir
-+program_transform_name
-+prefix
-+exec_prefix
-+PACKAGE_URL
-+PACKAGE_BUGREPORT
-+PACKAGE_STRING
-+PACKAGE_VERSION
-+PACKAGE_TARNAME
-+PACKAGE_NAME
-+PATH_SEPARATOR
-+SHELL'
- ac_subst_files=''
-+ac_user_opts='
-+enable_option_checking
-+enable_dependency_tracking
-+enable_glib2
-+enable_assert
-+enable_paranoia
-+enable_gprof
-+enable_gcov
-+enable_largefile
-+enable_compiledmodels
-+enable_utilities
-+enable_pthreads
-+'
- ac_precious_vars='build_alias
- host_alias
- target_alias
-@@ -705,6 +728,8 @@
- # Initialize some variables set by options.
- ac_init_help=
- ac_init_version=false
-+ac_unrecognized_opts=
-+ac_unrecognized_sep=
- # The variables have the same names as the options, with
- # dashes changed to underlines.
- cache_file=/dev/null
-@@ -760,7 +785,8 @@
- fi
-
- case $ac_option in
-- *=*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;
-+ *=?*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;
-+ *=) ac_optarg= ;;
- *) ac_optarg=yes ;;
- esac
-
-@@ -803,13 +829,20 @@
- datarootdir=$ac_optarg ;;
-
- -disable-* | --disable-*)
-- ac_feature=`expr "x$ac_option" : 'x-*disable-\(.*\)'`
-+ ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'`
- # Reject names that are not valid shell variable names.
-- expr "x$ac_feature" : ".*[^-._$as_cr_alnum]" >/dev/null &&
-- { echo "$as_me: error: invalid feature name: $ac_feature" >&2
-- { (exit 1); exit 1; }; }
-- ac_feature=`echo $ac_feature | sed 's/[-.]/_/g'`
-- eval enable_$ac_feature=no ;;
-+ expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
-+ as_fn_error $? "invalid feature name: $ac_useropt"
-+ ac_useropt_orig=$ac_useropt
-+ ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
-+ case $ac_user_opts in
-+ *"
-+"enable_$ac_useropt"
-+"*) ;;
-+ *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--disable-$ac_useropt_orig"
-+ ac_unrecognized_sep=', ';;
-+ esac
-+ eval enable_$ac_useropt=no ;;
-
- -docdir | --docdir | --docdi | --doc | --do)
- ac_prev=docdir ;;
-@@ -822,13 +855,20 @@
- dvidir=$ac_optarg ;;
-
- -enable-* | --enable-*)
-- ac_feature=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'`
-+ ac_useropt=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'`
- # Reject names that are not valid shell variable names.
-- expr "x$ac_feature" : ".*[^-._$as_cr_alnum]" >/dev/null &&
-- { echo "$as_me: error: invalid feature name: $ac_feature" >&2
-- { (exit 1); exit 1; }; }
-- ac_feature=`echo $ac_feature | sed 's/[-.]/_/g'`
-- eval enable_$ac_feature=\$ac_optarg ;;
-+ expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
-+ as_fn_error $? "invalid feature name: $ac_useropt"
-+ ac_useropt_orig=$ac_useropt
-+ ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
-+ case $ac_user_opts in
-+ *"
-+"enable_$ac_useropt"
-+"*) ;;
-+ *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--enable-$ac_useropt_orig"
-+ ac_unrecognized_sep=', ';;
-+ esac
-+ eval enable_$ac_useropt=\$ac_optarg ;;
-
- -exec-prefix | --exec_prefix | --exec-prefix | --exec-prefi \
- | --exec-pref | --exec-pre | --exec-pr | --exec-p | --exec- \
-@@ -1019,22 +1059,36 @@
- ac_init_version=: ;;
-
- -with-* | --with-*)
-- ac_package=`expr "x$ac_option" : 'x-*with-\([^=]*\)'`
-+ ac_useropt=`expr "x$ac_option" : 'x-*with-\([^=]*\)'`
- # Reject names that are not valid shell variable names.
-- expr "x$ac_package" : ".*[^-._$as_cr_alnum]" >/dev/null &&
-- { echo "$as_me: error: invalid package name: $ac_package" >&2
-- { (exit 1); exit 1; }; }
-- ac_package=`echo $ac_package | sed 's/[-.]/_/g'`
-- eval with_$ac_package=\$ac_optarg ;;
-+ expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
-+ as_fn_error $? "invalid package name: $ac_useropt"
-+ ac_useropt_orig=$ac_useropt
-+ ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
-+ case $ac_user_opts in
-+ *"
-+"with_$ac_useropt"
-+"*) ;;
-+ *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--with-$ac_useropt_orig"
-+ ac_unrecognized_sep=', ';;
-+ esac
-+ eval with_$ac_useropt=\$ac_optarg ;;
-
- -without-* | --without-*)
-- ac_package=`expr "x$ac_option" : 'x-*without-\(.*\)'`
-+ ac_useropt=`expr "x$ac_option" : 'x-*without-\(.*\)'`
- # Reject names that are not valid shell variable names.
-- expr "x$ac_package" : ".*[^-._$as_cr_alnum]" >/dev/null &&
-- { echo "$as_me: error: invalid package name: $ac_package" >&2
-- { (exit 1); exit 1; }; }
-- ac_package=`echo $ac_package | sed 's/[-.]/_/g'`
-- eval with_$ac_package=no ;;
-+ expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
-+ as_fn_error $? "invalid package name: $ac_useropt"
-+ ac_useropt_orig=$ac_useropt
-+ ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
-+ case $ac_user_opts in
-+ *"
-+"with_$ac_useropt"
-+"*) ;;
-+ *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--without-$ac_useropt_orig"
-+ ac_unrecognized_sep=', ';;
-+ esac
-+ eval with_$ac_useropt=no ;;
-
- --x)
- # Obsolete; use --with-x.
-@@ -1054,26 +1108,26 @@
- | --x-librar=* | --x-libra=* | --x-libr=* | --x-lib=* | --x-li=* | --x-l=*)
- x_libraries=$ac_optarg ;;
-
-- -*) { echo "$as_me: error: unrecognized option: $ac_option
--Try \`$0 --help' for more information." >&2
-- { (exit 1); exit 1; }; }
-+ -*) as_fn_error $? "unrecognized option: \`$ac_option'
-+Try \`$0 --help' for more information"
- ;;
-
- *=*)
- ac_envvar=`expr "x$ac_option" : 'x\([^=]*\)='`
- # Reject names that are not valid shell variable names.
-- expr "x$ac_envvar" : ".*[^_$as_cr_alnum]" >/dev/null &&
-- { echo "$as_me: error: invalid variable name: $ac_envvar" >&2
-- { (exit 1); exit 1; }; }
-+ case $ac_envvar in #(
-+ '' | [0-9]* | *[!_$as_cr_alnum]* )
-+ as_fn_error $? "invalid variable name: \`$ac_envvar'" ;;
-+ esac
- eval $ac_envvar=\$ac_optarg
- export $ac_envvar ;;
-
- *)
- # FIXME: should be removed in autoconf 3.0.
-- echo "$as_me: WARNING: you should use --build, --host, --target" >&2
-+ $as_echo "$as_me: WARNING: you should use --build, --host, --target" >&2
- expr "x$ac_option" : ".*[^-._$as_cr_alnum]" >/dev/null &&
-- echo "$as_me: WARNING: invalid host type: $ac_option" >&2
-- : ${build_alias=$ac_option} ${host_alias=$ac_option} ${target_alias=$ac_option}
-+ $as_echo "$as_me: WARNING: invalid host type: $ac_option" >&2
-+ : "${build_alias=$ac_option} ${host_alias=$ac_option} ${target_alias=$ac_option}"
- ;;
-
- esac
-@@ -1081,23 +1135,36 @@
-
- if test -n "$ac_prev"; then
- ac_option=--`echo $ac_prev | sed 's/_/-/g'`
-- { echo "$as_me: error: missing argument to $ac_option" >&2
-- { (exit 1); exit 1; }; }
-+ as_fn_error $? "missing argument to $ac_option"
-+fi
-+
-+if test -n "$ac_unrecognized_opts"; then
-+ case $enable_option_checking in
-+ no) ;;
-+ fatal) as_fn_error $? "unrecognized options: $ac_unrecognized_opts" ;;
-+ *) $as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2 ;;
-+ esac
- fi
-
--# Be sure to have absolute directory names.
-+# Check all directory arguments for consistency.
- for ac_var in exec_prefix prefix bindir sbindir libexecdir datarootdir \
- datadir sysconfdir sharedstatedir localstatedir includedir \
- oldincludedir docdir infodir htmldir dvidir pdfdir psdir \
- libdir localedir mandir
- do
- eval ac_val=\$$ac_var
-+ # Remove trailing slashes.
-+ case $ac_val in
-+ */ )
-+ ac_val=`expr "X$ac_val" : 'X\(.*[^/]\)' \| "X$ac_val" : 'X\(.*\)'`
-+ eval $ac_var=\$ac_val;;
-+ esac
-+ # Be sure to have absolute directory names.
- case $ac_val in
- [\\/$]* | ?:[\\/]* ) continue;;
- NONE | '' ) case $ac_var in *prefix ) continue;; esac;;
- esac
-- { echo "$as_me: error: expected an absolute directory name for --$ac_var: $ac_val" >&2
-- { (exit 1); exit 1; }; }
-+ as_fn_error $? "expected an absolute directory name for --$ac_var: $ac_val"
- done
-
- # There might be people who depend on the old broken behavior: `$host'
-@@ -1111,8 +1178,8 @@
- if test "x$host_alias" != x; then
- if test "x$build_alias" = x; then
- cross_compiling=maybe
-- echo "$as_me: WARNING: If you wanted to set the --build type, don't use --host.
-- If a cross compiler is detected then cross compile mode will be used." >&2
-+ $as_echo "$as_me: WARNING: if you wanted to set the --build type, don't use --host.
-+ If a cross compiler is detected then cross compile mode will be used" >&2
- elif test "x$build_alias" != "x$host_alias"; then
- cross_compiling=yes
- fi
-@@ -1127,23 +1194,21 @@
- ac_pwd=`pwd` && test -n "$ac_pwd" &&
- ac_ls_di=`ls -di .` &&
- ac_pwd_ls_di=`cd "$ac_pwd" && ls -di .` ||
-- { echo "$as_me: error: Working directory cannot be determined" >&2
-- { (exit 1); exit 1; }; }
-+ as_fn_error $? "working directory cannot be determined"
- test "X$ac_ls_di" = "X$ac_pwd_ls_di" ||
-- { echo "$as_me: error: pwd does not report name of working directory" >&2
-- { (exit 1); exit 1; }; }
-+ as_fn_error $? "pwd does not report name of working directory"
-
-
- # Find the source files, if location was not specified.
- if test -z "$srcdir"; then
- ac_srcdir_defaulted=yes
- # Try the directory containing this script, then the parent directory.
-- ac_confdir=`$as_dirname -- "$0" ||
--$as_expr X"$0" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
-- X"$0" : 'X\(//\)[^/]' \| \
-- X"$0" : 'X\(//\)$' \| \
-- X"$0" : 'X\(/\)' \| . 2>/dev/null ||
--echo X"$0" |
-+ ac_confdir=`$as_dirname -- "$as_myself" ||
-+$as_expr X"$as_myself" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
-+ X"$as_myself" : 'X\(//\)[^/]' \| \
-+ X"$as_myself" : 'X\(//\)$' \| \
-+ X"$as_myself" : 'X\(/\)' \| . 2>/dev/null ||
-+$as_echo X"$as_myself" |
- sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
- s//\1/
- q
-@@ -1170,13 +1235,11 @@
- fi
- if test ! -r "$srcdir/$ac_unique_file"; then
- test "$ac_srcdir_defaulted" = yes && srcdir="$ac_confdir or .."
-- { echo "$as_me: error: cannot find sources ($ac_unique_file) in $srcdir" >&2
-- { (exit 1); exit 1; }; }
-+ as_fn_error $? "cannot find sources ($ac_unique_file) in $srcdir"
- fi
- ac_msg="sources are in $srcdir, but \`cd $srcdir' does not work"
- ac_abs_confdir=`(
-- cd "$srcdir" && test -r "./$ac_unique_file" || { echo "$as_me: error: $ac_msg" >&2
-- { (exit 1); exit 1; }; }
-+ cd "$srcdir" && test -r "./$ac_unique_file" || as_fn_error $? "$ac_msg"
- pwd)`
- # When building in place, set srcdir=.
- if test "$ac_abs_confdir" = "$ac_pwd"; then
-@@ -1216,7 +1279,7 @@
- --help=short display options specific to this package
- --help=recursive display the short help of all the included packages
- -V, --version display version information and exit
-- -q, --quiet, --silent do not print \`checking...' messages
-+ -q, --quiet, --silent do not print \`checking ...' messages
- --cache-file=FILE cache test results in FILE [disabled]
- -C, --config-cache alias for \`--cache-file=config.cache'
- -n, --no-create do not create output files
-@@ -1275,8 +1338,11 @@
- cat <<\_ACEOF
-
- Optional Features:
-+ --disable-option-checking ignore unrecognized --enable/--with options
- --disable-FEATURE do not include FEATURE (same as --enable-FEATURE=no)
- --enable-FEATURE[=ARG] include FEATURE [ARG=yes]
-+ --disable-dependency-tracking speeds up one-time build
-+ --enable-dependency-tracking do not reject slow dependency extractors
-
- --enable-glib2 Use glib2 library
- --disable-glib2 Do not glib2 (use glib1 instead)
-@@ -1311,13 +1377,14 @@
- LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries in a
- nonstandard directory <lib dir>
- LIBS libraries to pass to the linker, e.g. -l<library>
-- CPPFLAGS C/C++/Objective C preprocessor flags, e.g. -I<include dir> if
-+ CPPFLAGS (Objective) C/C++ preprocessor flags, e.g. -I<include dir> if
- you have headers in a nonstandard directory <include dir>
- CPP C preprocessor
-
- Use these variables to override the choices made by `configure' or to help
- it to find libraries and programs with nonstandard names/locations.
-
-+Report bugs to the package provider.
- _ACEOF
- ac_status=$?
- fi
-@@ -1325,15 +1392,17 @@
- if test "$ac_init_help" = "recursive"; then
- # If there are subdirs, report their specific --help.
- for ac_dir in : $ac_subdirs_all; do test "x$ac_dir" = x: && continue
-- test -d "$ac_dir" || continue
-+ test -d "$ac_dir" ||
-+ { cd "$srcdir" && ac_pwd=`pwd` && srcdir=. && test -d "$ac_dir"; } ||
-+ continue
- ac_builddir=.
-
- case "$ac_dir" in
- .) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
- *)
-- ac_dir_suffix=/`echo "$ac_dir" | sed 's,^\.[\\/],,'`
-+ ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'`
- # A ".." for each directory in $ac_dir_suffix.
-- ac_top_builddir_sub=`echo "$ac_dir_suffix" | sed 's,/[^\\/]*,/..,g;s,/,,'`
-+ ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
- case $ac_top_builddir_sub in
- "") ac_top_builddir_sub=. ac_top_build_prefix= ;;
- *) ac_top_build_prefix=$ac_top_builddir_sub/ ;;
-@@ -1369,7 +1438,7 @@
- echo &&
- $SHELL "$ac_srcdir/configure" --help=recursive
- else
-- echo "$as_me: WARNING: no configuration information is in $ac_dir" >&2
-+ $as_echo "$as_me: WARNING: no configuration information is in $ac_dir" >&2
- fi || ac_status=$?
- cd "$ac_pwd" || { ac_status=$?; break; }
- done
-@@ -1379,21 +1448,259 @@
- if $ac_init_version; then
- cat <<\_ACEOF
- configure
--generated by GNU Autoconf 2.61
-+generated by GNU Autoconf 2.68
-
--Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
--2002, 2003, 2004, 2005, 2006 Free Software Foundation, Inc.
-+Copyright (C) 2010 Free Software Foundation, Inc.
- This configure script is free software; the Free Software Foundation
- gives unlimited permission to copy, distribute and modify it.
- _ACEOF
- exit
- fi
-+
-+## ------------------------ ##
-+## Autoconf initialization. ##
-+## ------------------------ ##
-+
-+# ac_fn_c_try_compile LINENO
-+# --------------------------
-+# Try to compile conftest.$ac_ext, and return whether this succeeded.
-+ac_fn_c_try_compile ()
-+{
-+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
-+ rm -f conftest.$ac_objext
-+ if { { ac_try="$ac_compile"
-+case "(($ac_try" in
-+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-+ *) ac_try_echo=$ac_try;;
-+esac
-+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-+$as_echo "$ac_try_echo"; } >&5
-+ (eval "$ac_compile") 2>conftest.err
-+ ac_status=$?
-+ if test -s conftest.err; then
-+ grep -v '^ *+' conftest.err >conftest.er1
-+ cat conftest.er1 >&5
-+ mv -f conftest.er1 conftest.err
-+ fi
-+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
-+ test $ac_status = 0; } && {
-+ test -z "$ac_c_werror_flag" ||
-+ test ! -s conftest.err
-+ } && test -s conftest.$ac_objext; then :
-+ ac_retval=0
-+else
-+ $as_echo "$as_me: failed program was:" >&5
-+sed 's/^/| /' conftest.$ac_ext >&5
-+
-+ ac_retval=1
-+fi
-+ eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
-+ as_fn_set_status $ac_retval
-+
-+} # ac_fn_c_try_compile
-+
-+# ac_fn_c_try_cpp LINENO
-+# ----------------------
-+# Try to preprocess conftest.$ac_ext, and return whether this succeeded.
-+ac_fn_c_try_cpp ()
-+{
-+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
-+ if { { ac_try="$ac_cpp conftest.$ac_ext"
-+case "(($ac_try" in
-+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-+ *) ac_try_echo=$ac_try;;
-+esac
-+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-+$as_echo "$ac_try_echo"; } >&5
-+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.err
-+ ac_status=$?
-+ if test -s conftest.err; then
-+ grep -v '^ *+' conftest.err >conftest.er1
-+ cat conftest.er1 >&5
-+ mv -f conftest.er1 conftest.err
-+ fi
-+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
-+ test $ac_status = 0; } > conftest.i && {
-+ test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
-+ test ! -s conftest.err
-+ }; then :
-+ ac_retval=0
-+else
-+ $as_echo "$as_me: failed program was:" >&5
-+sed 's/^/| /' conftest.$ac_ext >&5
-+
-+ ac_retval=1
-+fi
-+ eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
-+ as_fn_set_status $ac_retval
-+
-+} # ac_fn_c_try_cpp
-+
-+# ac_fn_c_try_run LINENO
-+# ----------------------
-+# Try to link conftest.$ac_ext, and return whether this succeeded. Assumes
-+# that executables *can* be run.
-+ac_fn_c_try_run ()
-+{
-+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
-+ if { { ac_try="$ac_link"
-+case "(($ac_try" in
-+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-+ *) ac_try_echo=$ac_try;;
-+esac
-+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-+$as_echo "$ac_try_echo"; } >&5
-+ (eval "$ac_link") 2>&5
-+ ac_status=$?
-+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
-+ test $ac_status = 0; } && { ac_try='./conftest$ac_exeext'
-+ { { case "(($ac_try" in
-+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-+ *) ac_try_echo=$ac_try;;
-+esac
-+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-+$as_echo "$ac_try_echo"; } >&5
-+ (eval "$ac_try") 2>&5
-+ ac_status=$?
-+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
-+ test $ac_status = 0; }; }; then :
-+ ac_retval=0
-+else
-+ $as_echo "$as_me: program exited with status $ac_status" >&5
-+ $as_echo "$as_me: failed program was:" >&5
-+sed 's/^/| /' conftest.$ac_ext >&5
-+
-+ ac_retval=$ac_status
-+fi
-+ rm -rf conftest.dSYM conftest_ipa8_conftest.oo
-+ eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
-+ as_fn_set_status $ac_retval
-+
-+} # ac_fn_c_try_run
-+
-+# ac_fn_c_check_header_mongrel LINENO HEADER VAR INCLUDES
-+# -------------------------------------------------------
-+# Tests whether HEADER exists, giving a warning if it cannot be compiled using
-+# the include files in INCLUDES and setting the cache variable VAR
-+# accordingly.
-+ac_fn_c_check_header_mongrel ()
-+{
-+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
-+ if eval \${$3+:} false; then :
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
-+$as_echo_n "checking for $2... " >&6; }
-+if eval \${$3+:} false; then :
-+ $as_echo_n "(cached) " >&6
-+fi
-+eval ac_res=\$$3
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
-+$as_echo "$ac_res" >&6; }
-+else
-+ # Is the header compilable?
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking $2 usability" >&5
-+$as_echo_n "checking $2 usability... " >&6; }
-+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-+/* end confdefs.h. */
-+$4
-+#include <$2>
-+_ACEOF
-+if ac_fn_c_try_compile "$LINENO"; then :
-+ ac_header_compiler=yes
-+else
-+ ac_header_compiler=no
-+fi
-+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_header_compiler" >&5
-+$as_echo "$ac_header_compiler" >&6; }
-+
-+# Is the header present?
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking $2 presence" >&5
-+$as_echo_n "checking $2 presence... " >&6; }
-+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-+/* end confdefs.h. */
-+#include <$2>
-+_ACEOF
-+if ac_fn_c_try_cpp "$LINENO"; then :
-+ ac_header_preproc=yes
-+else
-+ ac_header_preproc=no
-+fi
-+rm -f conftest.err conftest.i conftest.$ac_ext
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_header_preproc" >&5
-+$as_echo "$ac_header_preproc" >&6; }
-+
-+# So? What about this header?
-+case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in #((
-+ yes:no: )
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: accepted by the compiler, rejected by the preprocessor!" >&5
-+$as_echo "$as_me: WARNING: $2: accepted by the compiler, rejected by the preprocessor!" >&2;}
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: proceeding with the compiler's result" >&5
-+$as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;}
-+ ;;
-+ no:yes:* )
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: present but cannot be compiled" >&5
-+$as_echo "$as_me: WARNING: $2: present but cannot be compiled" >&2;}
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: check for missing prerequisite headers?" >&5
-+$as_echo "$as_me: WARNING: $2: check for missing prerequisite headers?" >&2;}
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: see the Autoconf documentation" >&5
-+$as_echo "$as_me: WARNING: $2: see the Autoconf documentation" >&2;}
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: section \"Present But Cannot Be Compiled\"" >&5
-+$as_echo "$as_me: WARNING: $2: section \"Present But Cannot Be Compiled\"" >&2;}
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: proceeding with the compiler's result" >&5
-+$as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;}
-+ ;;
-+esac
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
-+$as_echo_n "checking for $2... " >&6; }
-+if eval \${$3+:} false; then :
-+ $as_echo_n "(cached) " >&6
-+else
-+ eval "$3=\$ac_header_compiler"
-+fi
-+eval ac_res=\$$3
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
-+$as_echo "$ac_res" >&6; }
-+fi
-+ eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
-+
-+} # ac_fn_c_check_header_mongrel
-+
-+# ac_fn_c_check_header_compile LINENO HEADER VAR INCLUDES
-+# -------------------------------------------------------
-+# Tests whether HEADER exists and can be compiled using the include files in
-+# INCLUDES, setting the cache variable VAR accordingly.
-+ac_fn_c_check_header_compile ()
-+{
-+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
-+$as_echo_n "checking for $2... " >&6; }
-+if eval \${$3+:} false; then :
-+ $as_echo_n "(cached) " >&6
-+else
-+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-+/* end confdefs.h. */
-+$4
-+#include <$2>
-+_ACEOF
-+if ac_fn_c_try_compile "$LINENO"; then :
-+ eval "$3=yes"
-+else
-+ eval "$3=no"
-+fi
-+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-+fi
-+eval ac_res=\$$3
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
-+$as_echo "$ac_res" >&6; }
-+ eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
-+
-+} # ac_fn_c_check_header_compile
- cat >config.log <<_ACEOF
- This file contains any messages produced by compilers while
- running configure, to aid debugging if configure makes a mistake.
-
- It was created by $as_me, which was
--generated by GNU Autoconf 2.61. Invocation command line was
-+generated by GNU Autoconf 2.68. Invocation command line was
-
- $ $0 $@
-
-@@ -1429,8 +1736,8 @@
- do
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
-- echo "PATH: $as_dir"
--done
-+ $as_echo "PATH: $as_dir"
-+ done
- IFS=$as_save_IFS
-
- } >&5
-@@ -1464,12 +1771,12 @@
- | -silent | --silent | --silen | --sile | --sil)
- continue ;;
- *\'*)
-- ac_arg=`echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
-+ ac_arg=`$as_echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
- esac
- case $ac_pass in
-- 1) ac_configure_args0="$ac_configure_args0 '$ac_arg'" ;;
-+ 1) as_fn_append ac_configure_args0 " '$ac_arg'" ;;
- 2)
-- ac_configure_args1="$ac_configure_args1 '$ac_arg'"
-+ as_fn_append ac_configure_args1 " '$ac_arg'"
- if test $ac_must_keep_next = true; then
- ac_must_keep_next=false # Got value, back to normal.
- else
-@@ -1485,13 +1792,13 @@
- -* ) ac_must_keep_next=true ;;
- esac
- fi
-- ac_configure_args="$ac_configure_args '$ac_arg'"
-+ as_fn_append ac_configure_args " '$ac_arg'"
- ;;
- esac
- done
- done
--$as_unset ac_configure_args0 || test "${ac_configure_args0+set}" != set || { ac_configure_args0=; export ac_configure_args0; }
--$as_unset ac_configure_args1 || test "${ac_configure_args1+set}" != set || { ac_configure_args1=; export ac_configure_args1; }
-+{ ac_configure_args0=; unset ac_configure_args0;}
-+{ ac_configure_args1=; unset ac_configure_args1;}
-
- # When interrupted or exit'd, cleanup temporary files, and complete
- # config.log. We remove comments because anyway the quotes in there
-@@ -1503,11 +1810,9 @@
- {
- echo
-
-- cat <<\_ASBOX
--## ---------------- ##
-+ $as_echo "## ---------------- ##
- ## Cache variables. ##
--## ---------------- ##
--_ASBOX
-+## ---------------- ##"
- echo
- # The following way of writing the cache mishandles newlines in values,
- (
-@@ -1516,12 +1821,13 @@
- case $ac_val in #(
- *${as_nl}*)
- case $ac_var in #(
-- *_cv_*) { echo "$as_me:$LINENO: WARNING: Cache variable $ac_var contains a newline." >&5
--echo "$as_me: WARNING: Cache variable $ac_var contains a newline." >&2;} ;;
-+ *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5
-+$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
- esac
- case $ac_var in #(
- _ | IFS | as_nl) ;; #(
-- *) $as_unset $ac_var ;;
-+ BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
-+ *) { eval $ac_var=; unset $ac_var;} ;;
- esac ;;
- esac
- done
-@@ -1540,128 +1846,136 @@
- )
- echo
-
-- cat <<\_ASBOX
--## ----------------- ##
-+ $as_echo "## ----------------- ##
- ## Output variables. ##
--## ----------------- ##
--_ASBOX
-+## ----------------- ##"
- echo
- for ac_var in $ac_subst_vars
- do
- eval ac_val=\$$ac_var
- case $ac_val in
-- *\'\''*) ac_val=`echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
-+ *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
- esac
-- echo "$ac_var='\''$ac_val'\''"
-+ $as_echo "$ac_var='\''$ac_val'\''"
- done | sort
- echo
-
- if test -n "$ac_subst_files"; then
-- cat <<\_ASBOX
--## ------------------- ##
-+ $as_echo "## ------------------- ##
- ## File substitutions. ##
--## ------------------- ##
--_ASBOX
-+## ------------------- ##"
- echo
- for ac_var in $ac_subst_files
- do
- eval ac_val=\$$ac_var
- case $ac_val in
-- *\'\''*) ac_val=`echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
-+ *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
- esac
-- echo "$ac_var='\''$ac_val'\''"
-+ $as_echo "$ac_var='\''$ac_val'\''"
- done | sort
- echo
- fi
-
- if test -s confdefs.h; then
-- cat <<\_ASBOX
--## ----------- ##
-+ $as_echo "## ----------- ##
- ## confdefs.h. ##
--## ----------- ##
--_ASBOX
-+## ----------- ##"
- echo
- cat confdefs.h
- echo
- fi
- test "$ac_signal" != 0 &&
-- echo "$as_me: caught signal $ac_signal"
-- echo "$as_me: exit $exit_status"
-+ $as_echo "$as_me: caught signal $ac_signal"
-+ $as_echo "$as_me: exit $exit_status"
- } >&5
- rm -f core *.core core.conftest.* &&
- rm -f -r conftest* confdefs* conf$$* $ac_clean_files &&
- exit $exit_status
- ' 0
- for ac_signal in 1 2 13 15; do
-- trap 'ac_signal='$ac_signal'; { (exit 1); exit 1; }' $ac_signal
-+ trap 'ac_signal='$ac_signal'; as_fn_exit 1' $ac_signal
- done
- ac_signal=0
-
- # confdefs.h avoids OS command line length limits that DEFS can exceed.
- rm -f -r conftest* confdefs.h
-
-+$as_echo "/* confdefs.h */" > confdefs.h
-+
- # Predefined preprocessor variables.
-
- cat >>confdefs.h <<_ACEOF
- #define PACKAGE_NAME "$PACKAGE_NAME"
- _ACEOF
-
--
- cat >>confdefs.h <<_ACEOF
- #define PACKAGE_TARNAME "$PACKAGE_TARNAME"
- _ACEOF
-
--
- cat >>confdefs.h <<_ACEOF
- #define PACKAGE_VERSION "$PACKAGE_VERSION"
- _ACEOF
-
--
- cat >>confdefs.h <<_ACEOF
- #define PACKAGE_STRING "$PACKAGE_STRING"
- _ACEOF
-
--
- cat >>confdefs.h <<_ACEOF
- #define PACKAGE_BUGREPORT "$PACKAGE_BUGREPORT"
- _ACEOF
-
-+cat >>confdefs.h <<_ACEOF
-+#define PACKAGE_URL "$PACKAGE_URL"
-+_ACEOF
-+
-
- # Let the site file select an alternate cache file if it wants to.
--# Prefer explicitly selected file to automatically selected ones.
-+# Prefer an explicitly selected file to automatically selected ones.
-+ac_site_file1=NONE
-+ac_site_file2=NONE
- if test -n "$CONFIG_SITE"; then
-- set x "$CONFIG_SITE"
-+ # We do not want a PATH search for config.site.
-+ case $CONFIG_SITE in #((
-+ -*) ac_site_file1=./$CONFIG_SITE;;
-+ */*) ac_site_file1=$CONFIG_SITE;;
-+ *) ac_site_file1=./$CONFIG_SITE;;
-+ esac
- elif test "x$prefix" != xNONE; then
-- set x "$prefix/share/config.site" "$prefix/etc/config.site"
-+ ac_site_file1=$prefix/share/config.site
-+ ac_site_file2=$prefix/etc/config.site
- else
-- set x "$ac_default_prefix/share/config.site" \
-- "$ac_default_prefix/etc/config.site"
-+ ac_site_file1=$ac_default_prefix/share/config.site
-+ ac_site_file2=$ac_default_prefix/etc/config.site
- fi
--shift
--for ac_site_file
-+for ac_site_file in "$ac_site_file1" "$ac_site_file2"
- do
-- if test -r "$ac_site_file"; then
-- { echo "$as_me:$LINENO: loading site script $ac_site_file" >&5
--echo "$as_me: loading site script $ac_site_file" >&6;}
-+ test "x$ac_site_file" = xNONE && continue
-+ if test /dev/null != "$ac_site_file" && test -r "$ac_site_file"; then
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: loading site script $ac_site_file" >&5
-+$as_echo "$as_me: loading site script $ac_site_file" >&6;}
- sed 's/^/| /' "$ac_site_file" >&5
-- . "$ac_site_file"
-+ . "$ac_site_file" \
-+ || { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
-+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-+as_fn_error $? "failed to load site script $ac_site_file
-+See \`config.log' for more details" "$LINENO" 5; }
- fi
- done
-
- if test -r "$cache_file"; then
-- # Some versions of bash will fail to source /dev/null (special
-- # files actually), so we avoid doing that.
-- if test -f "$cache_file"; then
-- { echo "$as_me:$LINENO: loading cache $cache_file" >&5
--echo "$as_me: loading cache $cache_file" >&6;}
-+ # Some versions of bash will fail to source /dev/null (special files
-+ # actually), so we avoid doing that. DJGPP emulates it as a regular file.
-+ if test /dev/null != "$cache_file" && test -f "$cache_file"; then
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: loading cache $cache_file" >&5
-+$as_echo "$as_me: loading cache $cache_file" >&6;}
- case $cache_file in
- [\\/]* | ?:[\\/]* ) . "$cache_file";;
- *) . "./$cache_file";;
- esac
- fi
- else
-- { echo "$as_me:$LINENO: creating cache $cache_file" >&5
--echo "$as_me: creating cache $cache_file" >&6;}
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: creating cache $cache_file" >&5
-+$as_echo "$as_me: creating cache $cache_file" >&6;}
- >$cache_file
- fi
-
-@@ -1675,60 +1989,56 @@
- eval ac_new_val=\$ac_env_${ac_var}_value
- case $ac_old_set,$ac_new_set in
- set,)
-- { echo "$as_me:$LINENO: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5
--echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;}
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5
-+$as_echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;}
- ac_cache_corrupted=: ;;
- ,set)
-- { echo "$as_me:$LINENO: error: \`$ac_var' was not set in the previous run" >&5
--echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;}
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was not set in the previous run" >&5
-+$as_echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;}
- ac_cache_corrupted=: ;;
- ,);;
- *)
- if test "x$ac_old_val" != "x$ac_new_val"; then
-- { echo "$as_me:$LINENO: error: \`$ac_var' has changed since the previous run:" >&5
--echo "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;}
-- { echo "$as_me:$LINENO: former value: $ac_old_val" >&5
--echo "$as_me: former value: $ac_old_val" >&2;}
-- { echo "$as_me:$LINENO: current value: $ac_new_val" >&5
--echo "$as_me: current value: $ac_new_val" >&2;}
-+ # differences in whitespace do not lead to failure.
-+ ac_old_val_w=`echo x $ac_old_val`
-+ ac_new_val_w=`echo x $ac_new_val`
-+ if test "$ac_old_val_w" != "$ac_new_val_w"; then
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' has changed since the previous run:" >&5
-+$as_echo "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;}
- ac_cache_corrupted=:
-+ else
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5
-+$as_echo "$as_me: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&2;}
-+ eval $ac_var=\$ac_old_val
-+ fi
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: former value: \`$ac_old_val'" >&5
-+$as_echo "$as_me: former value: \`$ac_old_val'" >&2;}
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: current value: \`$ac_new_val'" >&5
-+$as_echo "$as_me: current value: \`$ac_new_val'" >&2;}
- fi;;
- esac
- # Pass precious variables to config.status.
- if test "$ac_new_set" = set; then
- case $ac_new_val in
-- *\'*) ac_arg=$ac_var=`echo "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;;
-+ *\'*) ac_arg=$ac_var=`$as_echo "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;;
- *) ac_arg=$ac_var=$ac_new_val ;;
- esac
- case " $ac_configure_args " in
- *" '$ac_arg' "*) ;; # Avoid dups. Use of quotes ensures accuracy.
-- *) ac_configure_args="$ac_configure_args '$ac_arg'" ;;
-+ *) as_fn_append ac_configure_args " '$ac_arg'" ;;
- esac
- fi
- done
- if $ac_cache_corrupted; then
-- { echo "$as_me:$LINENO: error: changes in the environment can compromise the build" >&5
--echo "$as_me: error: changes in the environment can compromise the build" >&2;}
-- { { echo "$as_me:$LINENO: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&5
--echo "$as_me: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&2;}
-- { (exit 1); exit 1; }; }
--fi
--
--
--
--
--
--
--
--
--
--
--
--
--
--
--
--
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
-+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5
-+$as_echo "$as_me: error: changes in the environment can compromise the build" >&2;}
-+ as_fn_error $? "run \`make distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5
-+fi
-+## -------------------- ##
-+## Main body of script. ##
-+## -------------------- ##
-
- ac_ext=c
- ac_cpp='$CPP $CPPFLAGS'
-@@ -1737,7 +2047,8 @@
- ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-
--am__api_version="1.4"
-+am__api_version='1.11'
-+
- ac_aux_dir=
- for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do
- if test -f "$ac_dir/install-sh"; then
-@@ -1755,9 +2066,7 @@
- fi
- done
- if test -z "$ac_aux_dir"; then
-- { { echo "$as_me:$LINENO: error: cannot find install-sh or install.sh in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" >&5
--echo "$as_me: error: cannot find install-sh or install.sh in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" >&2;}
-- { (exit 1); exit 1; }; }
-+ as_fn_error $? "cannot find install-sh, install.sh, or shtool in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" "$LINENO" 5
- fi
-
- # These three variables are undocumented and unsupported,
-@@ -1782,11 +2091,12 @@
- # SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff"
- # OS/2's system install, which has a completely different semantic
- # ./install, which can be erroneously created by make from ./install.sh.
--{ echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5
--echo $ECHO_N "checking for a BSD-compatible install... $ECHO_C" >&6; }
-+# Reject install programs that cannot install multiple files.
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a BSD-compatible install" >&5
-+$as_echo_n "checking for a BSD-compatible install... " >&6; }
- if test -z "$INSTALL"; then
--if test "${ac_cv_path_install+set}" = set; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
-+if ${ac_cv_path_install+:} false; then :
-+ $as_echo_n "(cached) " >&6
- else
- as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
- for as_dir in $PATH
-@@ -1794,10 +2104,10 @@
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
- # Account for people who put trailing slashes in PATH elements.
--case $as_dir/ in
-- ./ | .// | /cC/* | \
-+case $as_dir/ in #((
-+ ./ | .// | /[cC]/* | \
- /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \
-- ?:\\/os2\\/install\\/* | ?:\\/OS2\\/INSTALL\\/* | \
-+ ?:[\\/]os2[\\/]install[\\/]* | ?:[\\/]OS2[\\/]INSTALL[\\/]* | \
- /usr/ucb/* ) ;;
- *)
- # OSF1 and SCO ODT 3.0 have their own names for install.
-@@ -1815,17 +2125,29 @@
- # program-specific install script used by HP pwplus--don't use.
- :
- else
-+ rm -rf conftest.one conftest.two conftest.dir
-+ echo one > conftest.one
-+ echo two > conftest.two
-+ mkdir conftest.dir
-+ if "$as_dir/$ac_prog$ac_exec_ext" -c conftest.one conftest.two "`pwd`/conftest.dir" &&
-+ test -s conftest.one && test -s conftest.two &&
-+ test -s conftest.dir/conftest.one &&
-+ test -s conftest.dir/conftest.two
-+ then
- ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c"
- break 3
- fi
- fi
-+ fi
- done
- done
- ;;
- esac
--done
-+
-+ done
- IFS=$as_save_IFS
-
-+rm -rf conftest.one conftest.two conftest.dir
-
- fi
- if test "${ac_cv_path_install+set}" = set; then
-@@ -1838,8 +2160,8 @@
- INSTALL=$ac_install_sh
- fi
- fi
--{ echo "$as_me:$LINENO: result: $INSTALL" >&5
--echo "${ECHO_T}$INSTALL" >&6; }
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $INSTALL" >&5
-+$as_echo "$INSTALL" >&6; }
-
- # Use test -z because SunOS4 sh mishandles braces in ${var-val}.
- # It thinks the first close brace ends the variable substitution.
-@@ -1849,76 +2171,300 @@
-
- test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644'
-
--{ echo "$as_me:$LINENO: checking whether build environment is sane" >&5
--echo $ECHO_N "checking whether build environment is sane... $ECHO_C" >&6; }
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether build environment is sane" >&5
-+$as_echo_n "checking whether build environment is sane... " >&6; }
- # Just in case
- sleep 1
--echo timestamp > conftestfile
-+echo timestamp > conftest.file
-+# Reject unsafe characters in $srcdir or the absolute working directory
-+# name. Accept space and tab only in the latter.
-+am_lf='
-+'
-+case `pwd` in
-+ *[\\\"\#\$\&\'\`$am_lf]*)
-+ as_fn_error $? "unsafe absolute working directory name" "$LINENO" 5;;
-+esac
-+case $srcdir in
-+ *[\\\"\#\$\&\'\`$am_lf\ \ ]*)
-+ as_fn_error $? "unsafe srcdir value: \`$srcdir'" "$LINENO" 5;;
-+esac
-+
- # Do `set' in a subshell so we don't clobber the current shell's
- # arguments. Must try -L first in case configure is actually a
- # symlink; some systems play weird games with the mod time of symlinks
- # (eg FreeBSD returns the mod time of the symlink's containing
- # directory).
- if (
-- set X `ls -Lt $srcdir/configure conftestfile 2> /dev/null`
-+ set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
- if test "$*" = "X"; then
- # -L didn't work.
-- set X `ls -t $srcdir/configure conftestfile`
-+ set X `ls -t "$srcdir/configure" conftest.file`
- fi
-- if test "$*" != "X $srcdir/configure conftestfile" \
-- && test "$*" != "X conftestfile $srcdir/configure"; then
-+ rm -f conftest.file
-+ if test "$*" != "X $srcdir/configure conftest.file" \
-+ && test "$*" != "X conftest.file $srcdir/configure"; then
-
- # If neither matched, then we have a broken ls. This can happen
- # if, for instance, CONFIG_SHELL is bash and it inherits a
- # broken ls alias from the environment. This has actually
- # happened. Such a system could not be considered "sane".
-- { { echo "$as_me:$LINENO: error: ls -t appears to fail. Make sure there is not a broken
--alias in your environment" >&5
--echo "$as_me: error: ls -t appears to fail. Make sure there is not a broken
--alias in your environment" >&2;}
-- { (exit 1); exit 1; }; }
-+ as_fn_error $? "ls -t appears to fail. Make sure there is not a broken
-+alias in your environment" "$LINENO" 5
- fi
-
-- test "$2" = conftestfile
-+ test "$2" = conftest.file
- )
- then
- # Ok.
- :
- else
-- { { echo "$as_me:$LINENO: error: newly created file is older than distributed files!
--Check your system clock" >&5
--echo "$as_me: error: newly created file is older than distributed files!
--Check your system clock" >&2;}
-- { (exit 1); exit 1; }; }
-+ as_fn_error $? "newly created file is older than distributed files!
-+Check your system clock" "$LINENO" 5
- fi
--rm -f conftest*
--{ echo "$as_me:$LINENO: result: yes" >&5
--echo "${ECHO_T}yes" >&6; }
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
-+$as_echo "yes" >&6; }
- test "$program_prefix" != NONE &&
- program_transform_name="s&^&$program_prefix&;$program_transform_name"
- # Use a double $ so make ignores it.
- test "$program_suffix" != NONE &&
- program_transform_name="s&\$&$program_suffix&;$program_transform_name"
--# Double any \ or $. echo might interpret backslashes.
-+# Double any \ or $.
- # By default was `s,x,x', remove it if useless.
--cat <<\_ACEOF >conftest.sed
--s/[\\$]/&&/g;s/;s,x,x,$//
--_ACEOF
--program_transform_name=`echo $program_transform_name | sed -f conftest.sed`
--rm -f conftest.sed
-+ac_script='s/[\\$]/&&/g;s/;s,x,x,$//'
-+program_transform_name=`$as_echo "$program_transform_name" | sed "$ac_script"`
-+
-+# expand $ac_aux_dir to an absolute path
-+am_aux_dir=`cd $ac_aux_dir && pwd`
-+
-+if test x"${MISSING+set}" != xset; then
-+ case $am_aux_dir in
-+ *\ * | *\ *)
-+ MISSING="\${SHELL} \"$am_aux_dir/missing\"" ;;
-+ *)
-+ MISSING="\${SHELL} $am_aux_dir/missing" ;;
-+ esac
-+fi
-+# Use eval to expand $SHELL
-+if eval "$MISSING --run true"; then
-+ am_missing_run="$MISSING --run "
-+else
-+ am_missing_run=
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \`missing' script is too old or missing" >&5
-+$as_echo "$as_me: WARNING: \`missing' script is too old or missing" >&2;}
-+fi
-+
-+if test x"${install_sh}" != xset; then
-+ case $am_aux_dir in
-+ *\ * | *\ *)
-+ install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
-+ *)
-+ install_sh="\${SHELL} $am_aux_dir/install-sh"
-+ esac
-+fi
-+
-+# Installed binaries are usually stripped using `strip' when the user
-+# run `make install-strip'. However `strip' might not be the right
-+# tool to use in cross-compilation environments, therefore Automake
-+# will honor the `STRIP' environment variable to overrule this program.
-+if test "$cross_compiling" != no; then
-+ if test -n "$ac_tool_prefix"; then
-+ # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args.
-+set dummy ${ac_tool_prefix}strip; ac_word=$2
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
-+$as_echo_n "checking for $ac_word... " >&6; }
-+if ${ac_cv_prog_STRIP+:} false; then :
-+ $as_echo_n "(cached) " >&6
-+else
-+ if test -n "$STRIP"; then
-+ ac_cv_prog_STRIP="$STRIP" # Let the user override the test.
-+else
-+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-+for as_dir in $PATH
-+do
-+ IFS=$as_save_IFS
-+ test -z "$as_dir" && as_dir=.
-+ for ac_exec_ext in '' $ac_executable_extensions; do
-+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
-+ ac_cv_prog_STRIP="${ac_tool_prefix}strip"
-+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
-+ break 2
-+ fi
-+done
-+ done
-+IFS=$as_save_IFS
-+
-+fi
-+fi
-+STRIP=$ac_cv_prog_STRIP
-+if test -n "$STRIP"; then
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $STRIP" >&5
-+$as_echo "$STRIP" >&6; }
-+else
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-+$as_echo "no" >&6; }
-+fi
-+
-+
-+fi
-+if test -z "$ac_cv_prog_STRIP"; then
-+ ac_ct_STRIP=$STRIP
-+ # Extract the first word of "strip", so it can be a program name with args.
-+set dummy strip; ac_word=$2
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
-+$as_echo_n "checking for $ac_word... " >&6; }
-+if ${ac_cv_prog_ac_ct_STRIP+:} false; then :
-+ $as_echo_n "(cached) " >&6
-+else
-+ if test -n "$ac_ct_STRIP"; then
-+ ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test.
-+else
-+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-+for as_dir in $PATH
-+do
-+ IFS=$as_save_IFS
-+ test -z "$as_dir" && as_dir=.
-+ for ac_exec_ext in '' $ac_executable_extensions; do
-+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
-+ ac_cv_prog_ac_ct_STRIP="strip"
-+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
-+ break 2
-+ fi
-+done
-+ done
-+IFS=$as_save_IFS
-+
-+fi
-+fi
-+ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP
-+if test -n "$ac_ct_STRIP"; then
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_STRIP" >&5
-+$as_echo "$ac_ct_STRIP" >&6; }
-+else
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-+$as_echo "no" >&6; }
-+fi
-+
-+ if test "x$ac_ct_STRIP" = x; then
-+ STRIP=":"
-+ else
-+ case $cross_compiling:$ac_tool_warned in
-+yes:)
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
-+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
-+ac_tool_warned=yes ;;
-+esac
-+ STRIP=$ac_ct_STRIP
-+ fi
-+else
-+ STRIP="$ac_cv_prog_STRIP"
-+fi
-+
-+fi
-+INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
-+
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a thread-safe mkdir -p" >&5
-+$as_echo_n "checking for a thread-safe mkdir -p... " >&6; }
-+if test -z "$MKDIR_P"; then
-+ if ${ac_cv_path_mkdir+:} false; then :
-+ $as_echo_n "(cached) " >&6
-+else
-+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-+for as_dir in $PATH$PATH_SEPARATOR/opt/sfw/bin
-+do
-+ IFS=$as_save_IFS
-+ test -z "$as_dir" && as_dir=.
-+ for ac_prog in mkdir gmkdir; do
-+ for ac_exec_ext in '' $ac_executable_extensions; do
-+ { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; } || continue
-+ case `"$as_dir/$ac_prog$ac_exec_ext" --version 2>&1` in #(
-+ 'mkdir (GNU coreutils) '* | \
-+ 'mkdir (coreutils) '* | \
-+ 'mkdir (fileutils) '4.1*)
-+ ac_cv_path_mkdir=$as_dir/$ac_prog$ac_exec_ext
-+ break 3;;
-+ esac
-+ done
-+ done
-+ done
-+IFS=$as_save_IFS
-+
-+fi
-+
-+ test -d ./--version && rmdir ./--version
-+ if test "${ac_cv_path_mkdir+set}" = set; then
-+ MKDIR_P="$ac_cv_path_mkdir -p"
-+ else
-+ # As a last resort, use the slow shell script. Don't cache a
-+ # value for MKDIR_P within a source directory, because that will
-+ # break other packages using the cache if that directory is
-+ # removed, or if the value is a relative name.
-+ MKDIR_P="$ac_install_sh -d"
-+ fi
-+fi
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $MKDIR_P" >&5
-+$as_echo "$MKDIR_P" >&6; }
-+
-+mkdir_p="$MKDIR_P"
-+case $mkdir_p in
-+ [\\/$]* | ?:[\\/]*) ;;
-+ */*) mkdir_p="\$(top_builddir)/$mkdir_p" ;;
-+esac
-+
-+for ac_prog in gawk mawk nawk awk
-+do
-+ # Extract the first word of "$ac_prog", so it can be a program name with args.
-+set dummy $ac_prog; ac_word=$2
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
-+$as_echo_n "checking for $ac_word... " >&6; }
-+if ${ac_cv_prog_AWK+:} false; then :
-+ $as_echo_n "(cached) " >&6
-+else
-+ if test -n "$AWK"; then
-+ ac_cv_prog_AWK="$AWK" # Let the user override the test.
-+else
-+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-+for as_dir in $PATH
-+do
-+ IFS=$as_save_IFS
-+ test -z "$as_dir" && as_dir=.
-+ for ac_exec_ext in '' $ac_executable_extensions; do
-+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
-+ ac_cv_prog_AWK="$ac_prog"
-+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
-+ break 2
-+ fi
-+done
-+ done
-+IFS=$as_save_IFS
-+
-+fi
-+fi
-+AWK=$ac_cv_prog_AWK
-+if test -n "$AWK"; then
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AWK" >&5
-+$as_echo "$AWK" >&6; }
-+else
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-+$as_echo "no" >&6; }
-+fi
-+
-+
-+ test -n "$AWK" && break
-+done
-
--{ echo "$as_me:$LINENO: checking whether ${MAKE-make} sets \$(MAKE)" >&5
--echo $ECHO_N "checking whether ${MAKE-make} sets \$(MAKE)... $ECHO_C" >&6; }
--set x ${MAKE-make}; ac_make=`echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'`
--if { as_var=ac_cv_prog_make_${ac_make}_set; eval "test \"\${$as_var+set}\" = set"; }; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ${MAKE-make} sets \$(MAKE)" >&5
-+$as_echo_n "checking whether ${MAKE-make} sets \$(MAKE)... " >&6; }
-+set x ${MAKE-make}
-+ac_make=`$as_echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'`
-+if eval \${ac_cv_prog_make_${ac_make}_set+:} false; then :
-+ $as_echo_n "(cached) " >&6
- else
- cat >conftest.make <<\_ACEOF
- SHELL = /bin/sh
- all:
- @echo '@@@%%%=$(MAKE)=@@@%%%'
- _ACEOF
--# GNU make sometimes prints "make[1]: Entering...", which would confuse us.
-+# GNU make sometimes prints "make[1]: Entering ...", which would confuse us.
- case `${MAKE-make} -f conftest.make 2>/dev/null` in
- *@@@%%%=?*=@@@%%%*)
- eval ac_cv_prog_make_${ac_make}_set=yes;;
-@@ -1928,26 +2474,49 @@
- rm -f conftest.make
- fi
- if eval test \$ac_cv_prog_make_${ac_make}_set = yes; then
-- { echo "$as_me:$LINENO: result: yes" >&5
--echo "${ECHO_T}yes" >&6; }
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
-+$as_echo "yes" >&6; }
- SET_MAKE=
- else
-- { echo "$as_me:$LINENO: result: no" >&5
--echo "${ECHO_T}no" >&6; }
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-+$as_echo "no" >&6; }
- SET_MAKE="MAKE=${MAKE-make}"
- fi
-
-+rm -rf .tst 2>/dev/null
-+mkdir .tst 2>/dev/null
-+if test -d .tst; then
-+ am__leading_dot=.
-+else
-+ am__leading_dot=_
-+fi
-+rmdir .tst 2>/dev/null
-
--PACKAGE=exonerate
--
--VERSION=2.2.0
-+if test "`cd $srcdir && pwd`" != "`pwd`"; then
-+ # Use -I$(srcdir) only when $(srcdir) != ., so that make's output
-+ # is not polluted with repeated "-I."
-+ am__isrc=' -I$(srcdir)'
-+ # test to see if srcdir already configured
-+ if test -f $srcdir/config.status; then
-+ as_fn_error $? "source directory already configured; run \"make distclean\" there first" "$LINENO" 5
-+ fi
-+fi
-
--if test "`cd $srcdir && pwd`" != "`pwd`" && test -f $srcdir/config.status; then
-- { { echo "$as_me:$LINENO: error: source directory already configured; run \"make distclean\" there first" >&5
--echo "$as_me: error: source directory already configured; run \"make distclean\" there first" >&2;}
-- { (exit 1); exit 1; }; }
-+# test whether we have cygpath
-+if test -z "$CYGPATH_W"; then
-+ if (cygpath --version) >/dev/null 2>/dev/null; then
-+ CYGPATH_W='cygpath -w'
-+ else
-+ CYGPATH_W=echo
-+ fi
- fi
-
-+
-+# Define the identity of the package.
-+ PACKAGE=exonerate
-+ VERSION=2.2.0
-+
-+
- cat >>confdefs.h <<_ACEOF
- #define PACKAGE "$PACKAGE"
- _ACEOF
-@@ -1957,83 +2526,32 @@
- #define VERSION "$VERSION"
- _ACEOF
-
-+# Some tools Automake needs.
-+
-+ACLOCAL=${ACLOCAL-"${am_missing_run}aclocal-${am__api_version}"}
-+
-+
-+AUTOCONF=${AUTOCONF-"${am_missing_run}autoconf"}
-+
-+
-+AUTOMAKE=${AUTOMAKE-"${am_missing_run}automake-${am__api_version}"}
-+
-+
-+AUTOHEADER=${AUTOHEADER-"${am_missing_run}autoheader"}
-+
-+
-+MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"}
-+
-+# We need awk for the "check" target. The system "awk" is bad on
-+# some platforms.
-+# Always define AMTAR for backward compatibility.
-+
-+AMTAR=${AMTAR-"${am_missing_run}tar"}
-+
-+am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -'
-+
-
-
--missing_dir=`cd $ac_aux_dir && pwd`
--{ echo "$as_me:$LINENO: checking for working aclocal-${am__api_version}" >&5
--echo $ECHO_N "checking for working aclocal-${am__api_version}... $ECHO_C" >&6; }
--# Run test in a subshell; some versions of sh will print an error if
--# an executable is not found, even if stderr is redirected.
--# Redirect stdin to placate older versions of autoconf. Sigh.
--if (aclocal-${am__api_version} --version) < /dev/null > /dev/null 2>&1; then
-- ACLOCAL=aclocal-${am__api_version}
-- { echo "$as_me:$LINENO: result: found" >&5
--echo "${ECHO_T}found" >&6; }
--else
-- ACLOCAL="$missing_dir/missing aclocal-${am__api_version}"
-- { echo "$as_me:$LINENO: result: missing" >&5
--echo "${ECHO_T}missing" >&6; }
--fi
--
--{ echo "$as_me:$LINENO: checking for working autoconf" >&5
--echo $ECHO_N "checking for working autoconf... $ECHO_C" >&6; }
--# Run test in a subshell; some versions of sh will print an error if
--# an executable is not found, even if stderr is redirected.
--# Redirect stdin to placate older versions of autoconf. Sigh.
--if (autoconf --version) < /dev/null > /dev/null 2>&1; then
-- AUTOCONF=autoconf
-- { echo "$as_me:$LINENO: result: found" >&5
--echo "${ECHO_T}found" >&6; }
--else
-- AUTOCONF="$missing_dir/missing autoconf"
-- { echo "$as_me:$LINENO: result: missing" >&5
--echo "${ECHO_T}missing" >&6; }
--fi
--
--{ echo "$as_me:$LINENO: checking for working automake-${am__api_version}" >&5
--echo $ECHO_N "checking for working automake-${am__api_version}... $ECHO_C" >&6; }
--# Run test in a subshell; some versions of sh will print an error if
--# an executable is not found, even if stderr is redirected.
--# Redirect stdin to placate older versions of autoconf. Sigh.
--if (automake-${am__api_version} --version) < /dev/null > /dev/null 2>&1; then
-- AUTOMAKE=automake-${am__api_version}
-- { echo "$as_me:$LINENO: result: found" >&5
--echo "${ECHO_T}found" >&6; }
--else
-- AUTOMAKE="$missing_dir/missing automake-${am__api_version}"
-- { echo "$as_me:$LINENO: result: missing" >&5
--echo "${ECHO_T}missing" >&6; }
--fi
--
--{ echo "$as_me:$LINENO: checking for working autoheader" >&5
--echo $ECHO_N "checking for working autoheader... $ECHO_C" >&6; }
--# Run test in a subshell; some versions of sh will print an error if
--# an executable is not found, even if stderr is redirected.
--# Redirect stdin to placate older versions of autoconf. Sigh.
--if (autoheader --version) < /dev/null > /dev/null 2>&1; then
-- AUTOHEADER=autoheader
-- { echo "$as_me:$LINENO: result: found" >&5
--echo "${ECHO_T}found" >&6; }
--else
-- AUTOHEADER="$missing_dir/missing autoheader"
-- { echo "$as_me:$LINENO: result: missing" >&5
--echo "${ECHO_T}missing" >&6; }
--fi
--
--{ echo "$as_me:$LINENO: checking for working makeinfo" >&5
--echo $ECHO_N "checking for working makeinfo... $ECHO_C" >&6; }
--# Run test in a subshell; some versions of sh will print an error if
--# an executable is not found, even if stderr is redirected.
--# Redirect stdin to placate older versions of autoconf. Sigh.
--if (makeinfo --version) < /dev/null > /dev/null 2>&1; then
-- MAKEINFO=makeinfo
-- { echo "$as_me:$LINENO: result: found" >&5
--echo "${ECHO_T}found" >&6; }
--else
-- MAKEINFO="$missing_dir/missing makeinfo"
-- { echo "$as_me:$LINENO: result: missing" >&5
--echo "${ECHO_T}missing" >&6; }
--fi
-
-
- ac_ext=c
-@@ -2044,10 +2562,10 @@
- if test -n "$ac_tool_prefix"; then
- # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args.
- set dummy ${ac_tool_prefix}gcc; ac_word=$2
--{ echo "$as_me:$LINENO: checking for $ac_word" >&5
--echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
--if test "${ac_cv_prog_CC+set}" = set; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
-+$as_echo_n "checking for $ac_word... " >&6; }
-+if ${ac_cv_prog_CC+:} false; then :
-+ $as_echo_n "(cached) " >&6
- else
- if test -n "$CC"; then
- ac_cv_prog_CC="$CC" # Let the user override the test.
-@@ -2060,22 +2578,22 @@
- for ac_exec_ext in '' $ac_executable_extensions; do
- if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
- ac_cv_prog_CC="${ac_tool_prefix}gcc"
-- echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
-+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
- break 2
- fi
- done
--done
-+ done
- IFS=$as_save_IFS
-
- fi
- fi
- CC=$ac_cv_prog_CC
- if test -n "$CC"; then
-- { echo "$as_me:$LINENO: result: $CC" >&5
--echo "${ECHO_T}$CC" >&6; }
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
-+$as_echo "$CC" >&6; }
- else
-- { echo "$as_me:$LINENO: result: no" >&5
--echo "${ECHO_T}no" >&6; }
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-+$as_echo "no" >&6; }
- fi
-
-
-@@ -2084,10 +2602,10 @@
- ac_ct_CC=$CC
- # Extract the first word of "gcc", so it can be a program name with args.
- set dummy gcc; ac_word=$2
--{ echo "$as_me:$LINENO: checking for $ac_word" >&5
--echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
--if test "${ac_cv_prog_ac_ct_CC+set}" = set; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
-+$as_echo_n "checking for $ac_word... " >&6; }
-+if ${ac_cv_prog_ac_ct_CC+:} false; then :
-+ $as_echo_n "(cached) " >&6
- else
- if test -n "$ac_ct_CC"; then
- ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
-@@ -2100,22 +2618,22 @@
- for ac_exec_ext in '' $ac_executable_extensions; do
- if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
- ac_cv_prog_ac_ct_CC="gcc"
-- echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
-+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
- break 2
- fi
- done
--done
-+ done
- IFS=$as_save_IFS
-
- fi
- fi
- ac_ct_CC=$ac_cv_prog_ac_ct_CC
- if test -n "$ac_ct_CC"; then
-- { echo "$as_me:$LINENO: result: $ac_ct_CC" >&5
--echo "${ECHO_T}$ac_ct_CC" >&6; }
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5
-+$as_echo "$ac_ct_CC" >&6; }
- else
-- { echo "$as_me:$LINENO: result: no" >&5
--echo "${ECHO_T}no" >&6; }
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-+$as_echo "no" >&6; }
- fi
-
- if test "x$ac_ct_CC" = x; then
-@@ -2123,12 +2641,8 @@
- else
- case $cross_compiling:$ac_tool_warned in
- yes:)
--{ echo "$as_me:$LINENO: WARNING: In the future, Autoconf will not detect cross-tools
--whose name does not start with the host triplet. If you think this
--configuration is useful to you, please write to autoconf at gnu.org." >&5
--echo "$as_me: WARNING: In the future, Autoconf will not detect cross-tools
--whose name does not start with the host triplet. If you think this
--configuration is useful to you, please write to autoconf at gnu.org." >&2;}
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
-+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
- ac_tool_warned=yes ;;
- esac
- CC=$ac_ct_CC
-@@ -2141,10 +2655,10 @@
- if test -n "$ac_tool_prefix"; then
- # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args.
- set dummy ${ac_tool_prefix}cc; ac_word=$2
--{ echo "$as_me:$LINENO: checking for $ac_word" >&5
--echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
--if test "${ac_cv_prog_CC+set}" = set; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
-+$as_echo_n "checking for $ac_word... " >&6; }
-+if ${ac_cv_prog_CC+:} false; then :
-+ $as_echo_n "(cached) " >&6
- else
- if test -n "$CC"; then
- ac_cv_prog_CC="$CC" # Let the user override the test.
-@@ -2157,22 +2671,22 @@
- for ac_exec_ext in '' $ac_executable_extensions; do
- if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
- ac_cv_prog_CC="${ac_tool_prefix}cc"
-- echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
-+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
- break 2
- fi
- done
--done
-+ done
- IFS=$as_save_IFS
-
- fi
- fi
- CC=$ac_cv_prog_CC
- if test -n "$CC"; then
-- { echo "$as_me:$LINENO: result: $CC" >&5
--echo "${ECHO_T}$CC" >&6; }
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
-+$as_echo "$CC" >&6; }
- else
-- { echo "$as_me:$LINENO: result: no" >&5
--echo "${ECHO_T}no" >&6; }
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-+$as_echo "no" >&6; }
- fi
-
-
-@@ -2181,10 +2695,10 @@
- if test -z "$CC"; then
- # Extract the first word of "cc", so it can be a program name with args.
- set dummy cc; ac_word=$2
--{ echo "$as_me:$LINENO: checking for $ac_word" >&5
--echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
--if test "${ac_cv_prog_CC+set}" = set; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
-+$as_echo_n "checking for $ac_word... " >&6; }
-+if ${ac_cv_prog_CC+:} false; then :
-+ $as_echo_n "(cached) " >&6
- else
- if test -n "$CC"; then
- ac_cv_prog_CC="$CC" # Let the user override the test.
-@@ -2202,11 +2716,11 @@
- continue
- fi
- ac_cv_prog_CC="cc"
-- echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
-+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
- break 2
- fi
- done
--done
-+ done
- IFS=$as_save_IFS
-
- if test $ac_prog_rejected = yes; then
-@@ -2225,11 +2739,11 @@
- fi
- CC=$ac_cv_prog_CC
- if test -n "$CC"; then
-- { echo "$as_me:$LINENO: result: $CC" >&5
--echo "${ECHO_T}$CC" >&6; }
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
-+$as_echo "$CC" >&6; }
- else
-- { echo "$as_me:$LINENO: result: no" >&5
--echo "${ECHO_T}no" >&6; }
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-+$as_echo "no" >&6; }
- fi
-
-
-@@ -2240,10 +2754,10 @@
- do
- # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
- set dummy $ac_tool_prefix$ac_prog; ac_word=$2
--{ echo "$as_me:$LINENO: checking for $ac_word" >&5
--echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
--if test "${ac_cv_prog_CC+set}" = set; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
-+$as_echo_n "checking for $ac_word... " >&6; }
-+if ${ac_cv_prog_CC+:} false; then :
-+ $as_echo_n "(cached) " >&6
- else
- if test -n "$CC"; then
- ac_cv_prog_CC="$CC" # Let the user override the test.
-@@ -2256,22 +2770,22 @@
- for ac_exec_ext in '' $ac_executable_extensions; do
- if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
- ac_cv_prog_CC="$ac_tool_prefix$ac_prog"
-- echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
-+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
- break 2
- fi
- done
--done
-+ done
- IFS=$as_save_IFS
-
- fi
- fi
- CC=$ac_cv_prog_CC
- if test -n "$CC"; then
-- { echo "$as_me:$LINENO: result: $CC" >&5
--echo "${ECHO_T}$CC" >&6; }
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
-+$as_echo "$CC" >&6; }
- else
-- { echo "$as_me:$LINENO: result: no" >&5
--echo "${ECHO_T}no" >&6; }
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-+$as_echo "no" >&6; }
- fi
-
-
-@@ -2284,10 +2798,10 @@
- do
- # Extract the first word of "$ac_prog", so it can be a program name with args.
- set dummy $ac_prog; ac_word=$2
--{ echo "$as_me:$LINENO: checking for $ac_word" >&5
--echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
--if test "${ac_cv_prog_ac_ct_CC+set}" = set; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
-+$as_echo_n "checking for $ac_word... " >&6; }
-+if ${ac_cv_prog_ac_ct_CC+:} false; then :
-+ $as_echo_n "(cached) " >&6
- else
- if test -n "$ac_ct_CC"; then
- ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
-@@ -2300,22 +2814,22 @@
- for ac_exec_ext in '' $ac_executable_extensions; do
- if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
- ac_cv_prog_ac_ct_CC="$ac_prog"
-- echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
-+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
- break 2
- fi
- done
--done
-+ done
- IFS=$as_save_IFS
-
- fi
- fi
- ac_ct_CC=$ac_cv_prog_ac_ct_CC
- if test -n "$ac_ct_CC"; then
-- { echo "$as_me:$LINENO: result: $ac_ct_CC" >&5
--echo "${ECHO_T}$ac_ct_CC" >&6; }
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5
-+$as_echo "$ac_ct_CC" >&6; }
- else
-- { echo "$as_me:$LINENO: result: no" >&5
--echo "${ECHO_T}no" >&6; }
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-+$as_echo "no" >&6; }
- fi
-
-
-@@ -2327,12 +2841,8 @@
- else
- case $cross_compiling:$ac_tool_warned in
- yes:)
--{ echo "$as_me:$LINENO: WARNING: In the future, Autoconf will not detect cross-tools
--whose name does not start with the host triplet. If you think this
--configuration is useful to you, please write to autoconf at gnu.org." >&5
--echo "$as_me: WARNING: In the future, Autoconf will not detect cross-tools
--whose name does not start with the host triplet. If you think this
--configuration is useful to you, please write to autoconf at gnu.org." >&2;}
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
-+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
- ac_tool_warned=yes ;;
- esac
- CC=$ac_ct_CC
-@@ -2342,51 +2852,37 @@
- fi
-
-
--test -z "$CC" && { { echo "$as_me:$LINENO: error: no acceptable C compiler found in \$PATH
--See \`config.log' for more details." >&5
--echo "$as_me: error: no acceptable C compiler found in \$PATH
--See \`config.log' for more details." >&2;}
-- { (exit 1); exit 1; }; }
-+test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
-+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-+as_fn_error $? "no acceptable C compiler found in \$PATH
-+See \`config.log' for more details" "$LINENO" 5; }
-
- # Provide some information about the compiler.
--echo "$as_me:$LINENO: checking for C compiler version" >&5
--ac_compiler=`set X $ac_compile; echo $2`
--{ (ac_try="$ac_compiler --version >&5"
--case "(($ac_try" in
-- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-- *) ac_try_echo=$ac_try;;
--esac
--eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
-- (eval "$ac_compiler --version >&5") 2>&5
-- ac_status=$?
-- echo "$as_me:$LINENO: \$? = $ac_status" >&5
-- (exit $ac_status); }
--{ (ac_try="$ac_compiler -v >&5"
--case "(($ac_try" in
-- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-- *) ac_try_echo=$ac_try;;
--esac
--eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
-- (eval "$ac_compiler -v >&5") 2>&5
-- ac_status=$?
-- echo "$as_me:$LINENO: \$? = $ac_status" >&5
-- (exit $ac_status); }
--{ (ac_try="$ac_compiler -V >&5"
-+$as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5
-+set X $ac_compile
-+ac_compiler=$2
-+for ac_option in --version -v -V -qversion; do
-+ { { ac_try="$ac_compiler $ac_option >&5"
- case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
- esac
--eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
-- (eval "$ac_compiler -V >&5") 2>&5
-+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-+$as_echo "$ac_try_echo"; } >&5
-+ (eval "$ac_compiler $ac_option >&5") 2>conftest.err
- ac_status=$?
-- echo "$as_me:$LINENO: \$? = $ac_status" >&5
-- (exit $ac_status); }
-+ if test -s conftest.err; then
-+ sed '10a\
-+... rest of stderr output deleted ...
-+ 10q' conftest.err >conftest.er1
-+ cat conftest.er1 >&5
-+ fi
-+ rm -f conftest.er1 conftest.err
-+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
-+ test $ac_status = 0; }
-+done
-
--cat >conftest.$ac_ext <<_ACEOF
--/* confdefs.h. */
--_ACEOF
--cat confdefs.h >>conftest.$ac_ext
--cat >>conftest.$ac_ext <<_ACEOF
-+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
- /* end confdefs.h. */
-
- int
-@@ -2398,42 +2894,38 @@
- }
- _ACEOF
- ac_clean_files_save=$ac_clean_files
--ac_clean_files="$ac_clean_files a.out a.exe b.out"
-+ac_clean_files="$ac_clean_files a.out a.out.dSYM a.exe b.out"
- # Try to create an executable without -o first, disregard a.out.
- # It will help us diagnose broken compilers, and finding out an intuition
- # of exeext.
--{ echo "$as_me:$LINENO: checking for C compiler default output file name" >&5
--echo $ECHO_N "checking for C compiler default output file name... $ECHO_C" >&6; }
--ac_link_default=`echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'`
--#
--# List of possible output files, starting from the most likely.
--# The algorithm is not robust to junk in `.', hence go to wildcards (a.*)
--# only as a last resort. b.out is created by i960 compilers.
--ac_files='a_out.exe a.exe conftest.exe a.out conftest a.* conftest.* b.out'
--#
--# The IRIX 6 linker writes into existing files which may not be
--# executable, retaining their permissions. Remove them first so a
--# subsequent execution test works.
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C compiler works" >&5
-+$as_echo_n "checking whether the C compiler works... " >&6; }
-+ac_link_default=`$as_echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'`
-+
-+# The possible output files:
-+ac_files="a.out conftest.exe conftest a.exe a_out.exe b.out conftest.*"
-+
- ac_rmfiles=
- for ac_file in $ac_files
- do
- case $ac_file in
-- *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.o | *.obj ) ;;
-+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;;
- * ) ac_rmfiles="$ac_rmfiles $ac_file";;
- esac
- done
- rm -f $ac_rmfiles
-
--if { (ac_try="$ac_link_default"
-+if { { ac_try="$ac_link_default"
- case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
- esac
--eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
-+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-+$as_echo "$ac_try_echo"; } >&5
- (eval "$ac_link_default") 2>&5
- ac_status=$?
-- echo "$as_me:$LINENO: \$? = $ac_status" >&5
-- (exit $ac_status); }; then
-+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
-+ test $ac_status = 0; }; then :
- # Autoconf-2.13 could set the ac_cv_exeext variable to `no'.
- # So ignore a value of `no', otherwise this would lead to `EXEEXT = no'
- # in a Makefile. We should not override ac_cv_exeext if it was cached,
-@@ -2443,7 +2935,7 @@
- do
- test -f "$ac_file" || continue
- case $ac_file in
-- *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.o | *.obj )
-+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj )
- ;;
- [ab].out )
- # We found the default executable, but exeext='' is most
-@@ -2469,116 +2961,132 @@
- else
- ac_file=''
- fi
--
--{ echo "$as_me:$LINENO: result: $ac_file" >&5
--echo "${ECHO_T}$ac_file" >&6; }
--if test -z "$ac_file"; then
-- echo "$as_me: failed program was:" >&5
-+if test -z "$ac_file"; then :
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-+$as_echo "no" >&6; }
-+$as_echo "$as_me: failed program was:" >&5
- sed 's/^/| /' conftest.$ac_ext >&5
-
--{ { echo "$as_me:$LINENO: error: C compiler cannot create executables
--See \`config.log' for more details." >&5
--echo "$as_me: error: C compiler cannot create executables
--See \`config.log' for more details." >&2;}
-- { (exit 77); exit 77; }; }
--fi
--
-+{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
-+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-+as_fn_error 77 "C compiler cannot create executables
-+See \`config.log' for more details" "$LINENO" 5; }
-+else
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
-+$as_echo "yes" >&6; }
-+fi
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler default output file name" >&5
-+$as_echo_n "checking for C compiler default output file name... " >&6; }
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_file" >&5
-+$as_echo "$ac_file" >&6; }
- ac_exeext=$ac_cv_exeext
-
-+rm -f -r a.out a.out.dSYM a.exe conftest$ac_cv_exeext b.out
-+ac_clean_files=$ac_clean_files_save
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of executables" >&5
-+$as_echo_n "checking for suffix of executables... " >&6; }
-+if { { ac_try="$ac_link"
-+case "(($ac_try" in
-+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-+ *) ac_try_echo=$ac_try;;
-+esac
-+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-+$as_echo "$ac_try_echo"; } >&5
-+ (eval "$ac_link") 2>&5
-+ ac_status=$?
-+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
-+ test $ac_status = 0; }; then :
-+ # If both `conftest.exe' and `conftest' are `present' (well, observable)
-+# catch `conftest.exe'. For instance with Cygwin, `ls conftest' will
-+# work properly (i.e., refer to `conftest.exe'), while it won't with
-+# `rm'.
-+for ac_file in conftest.exe conftest conftest.*; do
-+ test -f "$ac_file" || continue
-+ case $ac_file in
-+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;;
-+ *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
-+ break;;
-+ * ) break;;
-+ esac
-+done
-+else
-+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
-+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-+as_fn_error $? "cannot compute suffix of executables: cannot compile and link
-+See \`config.log' for more details" "$LINENO" 5; }
-+fi
-+rm -f conftest conftest$ac_cv_exeext
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_exeext" >&5
-+$as_echo "$ac_cv_exeext" >&6; }
-+
-+rm -f conftest.$ac_ext
-+EXEEXT=$ac_cv_exeext
-+ac_exeext=$EXEEXT
-+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-+/* end confdefs.h. */
-+#include <stdio.h>
-+int
-+main ()
-+{
-+FILE *f = fopen ("conftest.out", "w");
-+ return ferror (f) || fclose (f) != 0;
-+
-+ ;
-+ return 0;
-+}
-+_ACEOF
-+ac_clean_files="$ac_clean_files conftest.out"
- # Check that the compiler produces executables we can run. If not, either
- # the compiler is broken, or we cross compile.
--{ echo "$as_me:$LINENO: checking whether the C compiler works" >&5
--echo $ECHO_N "checking whether the C compiler works... $ECHO_C" >&6; }
--# FIXME: These cross compiler hacks should be removed for Autoconf 3.0
--# If not cross compiling, check that we can run a simple program.
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are cross compiling" >&5
-+$as_echo_n "checking whether we are cross compiling... " >&6; }
- if test "$cross_compiling" != yes; then
-- if { ac_try='./$ac_file'
-- { (case "(($ac_try" in
-+ { { ac_try="$ac_link"
-+case "(($ac_try" in
-+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-+ *) ac_try_echo=$ac_try;;
-+esac
-+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-+$as_echo "$ac_try_echo"; } >&5
-+ (eval "$ac_link") 2>&5
-+ ac_status=$?
-+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
-+ test $ac_status = 0; }
-+ if { ac_try='./conftest$ac_cv_exeext'
-+ { { case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
- esac
--eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
-+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-+$as_echo "$ac_try_echo"; } >&5
- (eval "$ac_try") 2>&5
- ac_status=$?
-- echo "$as_me:$LINENO: \$? = $ac_status" >&5
-- (exit $ac_status); }; }; then
-+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
-+ test $ac_status = 0; }; }; then
- cross_compiling=no
- else
- if test "$cross_compiling" = maybe; then
- cross_compiling=yes
- else
-- { { echo "$as_me:$LINENO: error: cannot run C compiled programs.
--If you meant to cross compile, use \`--host'.
--See \`config.log' for more details." >&5
--echo "$as_me: error: cannot run C compiled programs.
-+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
-+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-+as_fn_error $? "cannot run C compiled programs.
- If you meant to cross compile, use \`--host'.
--See \`config.log' for more details." >&2;}
-- { (exit 1); exit 1; }; }
-+See \`config.log' for more details" "$LINENO" 5; }
- fi
- fi
- fi
--{ echo "$as_me:$LINENO: result: yes" >&5
--echo "${ECHO_T}yes" >&6; }
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cross_compiling" >&5
-+$as_echo "$cross_compiling" >&6; }
-
--rm -f a.out a.exe conftest$ac_cv_exeext b.out
-+rm -f conftest.$ac_ext conftest$ac_cv_exeext conftest.out
- ac_clean_files=$ac_clean_files_save
--# Check that the compiler produces executables we can run. If not, either
--# the compiler is broken, or we cross compile.
--{ echo "$as_me:$LINENO: checking whether we are cross compiling" >&5
--echo $ECHO_N "checking whether we are cross compiling... $ECHO_C" >&6; }
--{ echo "$as_me:$LINENO: result: $cross_compiling" >&5
--echo "${ECHO_T}$cross_compiling" >&6; }
--
--{ echo "$as_me:$LINENO: checking for suffix of executables" >&5
--echo $ECHO_N "checking for suffix of executables... $ECHO_C" >&6; }
--if { (ac_try="$ac_link"
--case "(($ac_try" in
-- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-- *) ac_try_echo=$ac_try;;
--esac
--eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
-- (eval "$ac_link") 2>&5
-- ac_status=$?
-- echo "$as_me:$LINENO: \$? = $ac_status" >&5
-- (exit $ac_status); }; then
-- # If both `conftest.exe' and `conftest' are `present' (well, observable)
--# catch `conftest.exe'. For instance with Cygwin, `ls conftest' will
--# work properly (i.e., refer to `conftest.exe'), while it won't with
--# `rm'.
--for ac_file in conftest.exe conftest conftest.*; do
-- test -f "$ac_file" || continue
-- case $ac_file in
-- *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.o | *.obj ) ;;
-- *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
-- break;;
-- * ) break;;
-- esac
--done
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of object files" >&5
-+$as_echo_n "checking for suffix of object files... " >&6; }
-+if ${ac_cv_objext+:} false; then :
-+ $as_echo_n "(cached) " >&6
- else
-- { { echo "$as_me:$LINENO: error: cannot compute suffix of executables: cannot compile and link
--See \`config.log' for more details." >&5
--echo "$as_me: error: cannot compute suffix of executables: cannot compile and link
--See \`config.log' for more details." >&2;}
-- { (exit 1); exit 1; }; }
--fi
--
--rm -f conftest$ac_cv_exeext
--{ echo "$as_me:$LINENO: result: $ac_cv_exeext" >&5
--echo "${ECHO_T}$ac_cv_exeext" >&6; }
--
--rm -f conftest.$ac_ext
--EXEEXT=$ac_cv_exeext
--ac_exeext=$EXEEXT
--{ echo "$as_me:$LINENO: checking for suffix of object files" >&5
--echo $ECHO_N "checking for suffix of object files... $ECHO_C" >&6; }
--if test "${ac_cv_objext+set}" = set; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
--else
-- cat >conftest.$ac_ext <<_ACEOF
--/* confdefs.h. */
--_ACEOF
--cat confdefs.h >>conftest.$ac_ext
--cat >>conftest.$ac_ext <<_ACEOF
-+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
- /* end confdefs.h. */
-
- int
-@@ -2590,51 +3098,46 @@
- }
- _ACEOF
- rm -f conftest.o conftest.obj
--if { (ac_try="$ac_compile"
-+if { { ac_try="$ac_compile"
- case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
- esac
--eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
-+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-+$as_echo "$ac_try_echo"; } >&5
- (eval "$ac_compile") 2>&5
- ac_status=$?
-- echo "$as_me:$LINENO: \$? = $ac_status" >&5
-- (exit $ac_status); }; then
-+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
-+ test $ac_status = 0; }; then :
- for ac_file in conftest.o conftest.obj conftest.*; do
- test -f "$ac_file" || continue;
- case $ac_file in
-- *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf ) ;;
-+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM ) ;;
- *) ac_cv_objext=`expr "$ac_file" : '.*\.\(.*\)'`
- break;;
- esac
- done
- else
-- echo "$as_me: failed program was:" >&5
-+ $as_echo "$as_me: failed program was:" >&5
- sed 's/^/| /' conftest.$ac_ext >&5
-
--{ { echo "$as_me:$LINENO: error: cannot compute suffix of object files: cannot compile
--See \`config.log' for more details." >&5
--echo "$as_me: error: cannot compute suffix of object files: cannot compile
--See \`config.log' for more details." >&2;}
-- { (exit 1); exit 1; }; }
-+{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
-+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-+as_fn_error $? "cannot compute suffix of object files: cannot compile
-+See \`config.log' for more details" "$LINENO" 5; }
- fi
--
- rm -f conftest.$ac_cv_objext conftest.$ac_ext
- fi
--{ echo "$as_me:$LINENO: result: $ac_cv_objext" >&5
--echo "${ECHO_T}$ac_cv_objext" >&6; }
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_objext" >&5
-+$as_echo "$ac_cv_objext" >&6; }
- OBJEXT=$ac_cv_objext
- ac_objext=$OBJEXT
--{ echo "$as_me:$LINENO: checking whether we are using the GNU C compiler" >&5
--echo $ECHO_N "checking whether we are using the GNU C compiler... $ECHO_C" >&6; }
--if test "${ac_cv_c_compiler_gnu+set}" = set; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C compiler" >&5
-+$as_echo_n "checking whether we are using the GNU C compiler... " >&6; }
-+if ${ac_cv_c_compiler_gnu+:} false; then :
-+ $as_echo_n "(cached) " >&6
- else
-- cat >conftest.$ac_ext <<_ACEOF
--/* confdefs.h. */
--_ACEOF
--cat confdefs.h >>conftest.$ac_ext
--cat >>conftest.$ac_ext <<_ACEOF
-+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
- /* end confdefs.h. */
-
- int
-@@ -2648,54 +3151,34 @@
- return 0;
- }
- _ACEOF
--rm -f conftest.$ac_objext
--if { (ac_try="$ac_compile"
--case "(($ac_try" in
-- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-- *) ac_try_echo=$ac_try;;
--esac
--eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
-- (eval "$ac_compile") 2>conftest.er1
-- ac_status=$?
-- grep -v '^ *+' conftest.er1 >conftest.err
-- rm -f conftest.er1
-- cat conftest.err >&5
-- echo "$as_me:$LINENO: \$? = $ac_status" >&5
-- (exit $ac_status); } && {
-- test -z "$ac_c_werror_flag" ||
-- test ! -s conftest.err
-- } && test -s conftest.$ac_objext; then
-+if ac_fn_c_try_compile "$LINENO"; then :
- ac_compiler_gnu=yes
- else
-- echo "$as_me: failed program was:" >&5
--sed 's/^/| /' conftest.$ac_ext >&5
--
- ac_compiler_gnu=no
- fi
--
- rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- ac_cv_c_compiler_gnu=$ac_compiler_gnu
-
- fi
--{ echo "$as_me:$LINENO: result: $ac_cv_c_compiler_gnu" >&5
--echo "${ECHO_T}$ac_cv_c_compiler_gnu" >&6; }
--GCC=`test $ac_compiler_gnu = yes && echo yes`
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_compiler_gnu" >&5
-+$as_echo "$ac_cv_c_compiler_gnu" >&6; }
-+if test $ac_compiler_gnu = yes; then
-+ GCC=yes
-+else
-+ GCC=
-+fi
- ac_test_CFLAGS=${CFLAGS+set}
- ac_save_CFLAGS=$CFLAGS
--{ echo "$as_me:$LINENO: checking whether $CC accepts -g" >&5
--echo $ECHO_N "checking whether $CC accepts -g... $ECHO_C" >&6; }
--if test "${ac_cv_prog_cc_g+set}" = set; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC accepts -g" >&5
-+$as_echo_n "checking whether $CC accepts -g... " >&6; }
-+if ${ac_cv_prog_cc_g+:} false; then :
-+ $as_echo_n "(cached) " >&6
- else
- ac_save_c_werror_flag=$ac_c_werror_flag
- ac_c_werror_flag=yes
- ac_cv_prog_cc_g=no
- CFLAGS="-g"
-- cat >conftest.$ac_ext <<_ACEOF
--/* confdefs.h. */
--_ACEOF
--cat confdefs.h >>conftest.$ac_ext
--cat >>conftest.$ac_ext <<_ACEOF
-+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
- /* end confdefs.h. */
-
- int
-@@ -2706,34 +3189,11 @@
- return 0;
- }
- _ACEOF
--rm -f conftest.$ac_objext
--if { (ac_try="$ac_compile"
--case "(($ac_try" in
-- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-- *) ac_try_echo=$ac_try;;
--esac
--eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
-- (eval "$ac_compile") 2>conftest.er1
-- ac_status=$?
-- grep -v '^ *+' conftest.er1 >conftest.err
-- rm -f conftest.er1
-- cat conftest.err >&5
-- echo "$as_me:$LINENO: \$? = $ac_status" >&5
-- (exit $ac_status); } && {
-- test -z "$ac_c_werror_flag" ||
-- test ! -s conftest.err
-- } && test -s conftest.$ac_objext; then
-+if ac_fn_c_try_compile "$LINENO"; then :
- ac_cv_prog_cc_g=yes
- else
-- echo "$as_me: failed program was:" >&5
--sed 's/^/| /' conftest.$ac_ext >&5
--
- CFLAGS=""
-- cat >conftest.$ac_ext <<_ACEOF
--/* confdefs.h. */
--_ACEOF
--cat confdefs.h >>conftest.$ac_ext
--cat >>conftest.$ac_ext <<_ACEOF
-+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
- /* end confdefs.h. */
-
- int
-@@ -2744,35 +3204,12 @@
- return 0;
- }
- _ACEOF
--rm -f conftest.$ac_objext
--if { (ac_try="$ac_compile"
--case "(($ac_try" in
-- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-- *) ac_try_echo=$ac_try;;
--esac
--eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
-- (eval "$ac_compile") 2>conftest.er1
-- ac_status=$?
-- grep -v '^ *+' conftest.er1 >conftest.err
-- rm -f conftest.er1
-- cat conftest.err >&5
-- echo "$as_me:$LINENO: \$? = $ac_status" >&5
-- (exit $ac_status); } && {
-- test -z "$ac_c_werror_flag" ||
-- test ! -s conftest.err
-- } && test -s conftest.$ac_objext; then
-- :
--else
-- echo "$as_me: failed program was:" >&5
--sed 's/^/| /' conftest.$ac_ext >&5
-+if ac_fn_c_try_compile "$LINENO"; then :
-
-+else
- ac_c_werror_flag=$ac_save_c_werror_flag
- CFLAGS="-g"
-- cat >conftest.$ac_ext <<_ACEOF
--/* confdefs.h. */
--_ACEOF
--cat confdefs.h >>conftest.$ac_ext
--cat >>conftest.$ac_ext <<_ACEOF
-+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
- /* end confdefs.h. */
-
- int
-@@ -2783,42 +3220,18 @@
- return 0;
- }
- _ACEOF
--rm -f conftest.$ac_objext
--if { (ac_try="$ac_compile"
--case "(($ac_try" in
-- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-- *) ac_try_echo=$ac_try;;
--esac
--eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
-- (eval "$ac_compile") 2>conftest.er1
-- ac_status=$?
-- grep -v '^ *+' conftest.er1 >conftest.err
-- rm -f conftest.er1
-- cat conftest.err >&5
-- echo "$as_me:$LINENO: \$? = $ac_status" >&5
-- (exit $ac_status); } && {
-- test -z "$ac_c_werror_flag" ||
-- test ! -s conftest.err
-- } && test -s conftest.$ac_objext; then
-+if ac_fn_c_try_compile "$LINENO"; then :
- ac_cv_prog_cc_g=yes
--else
-- echo "$as_me: failed program was:" >&5
--sed 's/^/| /' conftest.$ac_ext >&5
--
--
- fi
--
- rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- fi
--
- rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- fi
--
- rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- ac_c_werror_flag=$ac_save_c_werror_flag
- fi
--{ echo "$as_me:$LINENO: result: $ac_cv_prog_cc_g" >&5
--echo "${ECHO_T}$ac_cv_prog_cc_g" >&6; }
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_g" >&5
-+$as_echo "$ac_cv_prog_cc_g" >&6; }
- if test "$ac_test_CFLAGS" = set; then
- CFLAGS=$ac_save_CFLAGS
- elif test $ac_cv_prog_cc_g = yes; then
-@@ -2834,18 +3247,14 @@
- CFLAGS=
- fi
- fi
--{ echo "$as_me:$LINENO: checking for $CC option to accept ISO C89" >&5
--echo $ECHO_N "checking for $CC option to accept ISO C89... $ECHO_C" >&6; }
--if test "${ac_cv_prog_cc_c89+set}" = set; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO C89" >&5
-+$as_echo_n "checking for $CC option to accept ISO C89... " >&6; }
-+if ${ac_cv_prog_cc_c89+:} false; then :
-+ $as_echo_n "(cached) " >&6
- else
- ac_cv_prog_cc_c89=no
- ac_save_CC=$CC
--cat >conftest.$ac_ext <<_ACEOF
--/* confdefs.h. */
--_ACEOF
--cat confdefs.h >>conftest.$ac_ext
--cat >>conftest.$ac_ext <<_ACEOF
-+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
- /* end confdefs.h. */
- #include <stdarg.h>
- #include <stdio.h>
-@@ -2902,31 +3311,9 @@
- -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__"
- do
- CC="$ac_save_CC $ac_arg"
-- rm -f conftest.$ac_objext
--if { (ac_try="$ac_compile"
--case "(($ac_try" in
-- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-- *) ac_try_echo=$ac_try;;
--esac
--eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
-- (eval "$ac_compile") 2>conftest.er1
-- ac_status=$?
-- grep -v '^ *+' conftest.er1 >conftest.err
-- rm -f conftest.er1
-- cat conftest.err >&5
-- echo "$as_me:$LINENO: \$? = $ac_status" >&5
-- (exit $ac_status); } && {
-- test -z "$ac_c_werror_flag" ||
-- test ! -s conftest.err
-- } && test -s conftest.$ac_objext; then
-+ if ac_fn_c_try_compile "$LINENO"; then :
- ac_cv_prog_cc_c89=$ac_arg
--else
-- echo "$as_me: failed program was:" >&5
--sed 's/^/| /' conftest.$ac_ext >&5
--
--
- fi
--
- rm -f core conftest.err conftest.$ac_objext
- test "x$ac_cv_prog_cc_c89" != "xno" && break
- done
-@@ -2937,116 +3324,229 @@
- # AC_CACHE_VAL
- case "x$ac_cv_prog_cc_c89" in
- x)
-- { echo "$as_me:$LINENO: result: none needed" >&5
--echo "${ECHO_T}none needed" >&6; } ;;
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5
-+$as_echo "none needed" >&6; } ;;
- xno)
-- { echo "$as_me:$LINENO: result: unsupported" >&5
--echo "${ECHO_T}unsupported" >&6; } ;;
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5
-+$as_echo "unsupported" >&6; } ;;
- *)
- CC="$CC $ac_cv_prog_cc_c89"
-- { echo "$as_me:$LINENO: result: $ac_cv_prog_cc_c89" >&5
--echo "${ECHO_T}$ac_cv_prog_cc_c89" >&6; } ;;
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5
-+$as_echo "$ac_cv_prog_cc_c89" >&6; } ;;
- esac
-+if test "x$ac_cv_prog_cc_c89" != xno; then :
-
-+fi
-
- ac_ext=c
- ac_cpp='$CPP $CPPFLAGS'
- ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
- ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
- ac_compiler_gnu=$ac_cv_c_compiler_gnu
-+DEPDIR="${am__leading_dot}deps"
-
--# Find a good install program. We prefer a C program (faster),
--# so one script is as good as another. But avoid the broken or
--# incompatible versions:
--# SysV /etc/install, /usr/sbin/install
--# SunOS /usr/etc/install
--# IRIX /sbin/install
--# AIX /bin/install
--# AmigaOS /C/install, which installs bootblocks on floppy discs
--# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag
--# AFS /usr/afsws/bin/install, which mishandles nonexistent args
--# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff"
--# OS/2's system install, which has a completely different semantic
--# ./install, which can be erroneously created by make from ./install.sh.
--{ echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5
--echo $ECHO_N "checking for a BSD-compatible install... $ECHO_C" >&6; }
--if test -z "$INSTALL"; then
--if test "${ac_cv_path_install+set}" = set; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
--else
-- as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
--for as_dir in $PATH
--do
-- IFS=$as_save_IFS
-- test -z "$as_dir" && as_dir=.
-- # Account for people who put trailing slashes in PATH elements.
--case $as_dir/ in
-- ./ | .// | /cC/* | \
-- /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \
-- ?:\\/os2\\/install\\/* | ?:\\/OS2\\/INSTALL\\/* | \
-- /usr/ucb/* ) ;;
-- *)
-- # OSF1 and SCO ODT 3.0 have their own names for install.
-- # Don't use installbsd from OSF since it installs stuff as root
-- # by default.
-- for ac_prog in ginstall scoinst install; do
-- for ac_exec_ext in '' $ac_executable_extensions; do
-- if { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; }; then
-- if test $ac_prog = install &&
-- grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
-- # AIX install. It has an incompatible calling convention.
-- :
-- elif test $ac_prog = install &&
-- grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
-- # program-specific install script used by HP pwplus--don't use.
-- :
-- else
-- ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c"
-- break 3
-- fi
-- fi
-- done
-- done
-+ac_config_commands="$ac_config_commands depfiles"
-+
-+
-+am_make=${MAKE-make}
-+cat > confinc << 'END'
-+am__doit:
-+ @echo this is the am__doit target
-+.PHONY: am__doit
-+END
-+# If we don't find an include directive, just comment out the code.
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for style of include used by $am_make" >&5
-+$as_echo_n "checking for style of include used by $am_make... " >&6; }
-+am__include="#"
-+am__quote=
-+_am_result=none
-+# First try GNU make style include.
-+echo "include confinc" > confmf
-+# Ignore all kinds of additional output from `make'.
-+case `$am_make -s -f confmf 2> /dev/null` in #(
-+*the\ am__doit\ target*)
-+ am__include=include
-+ am__quote=
-+ _am_result=GNU
- ;;
- esac
--done
--IFS=$as_save_IFS
-+# Now try BSD make style include.
-+if test "$am__include" = "#"; then
-+ echo '.include "confinc"' > confmf
-+ case `$am_make -s -f confmf 2> /dev/null` in #(
-+ *the\ am__doit\ target*)
-+ am__include=.include
-+ am__quote="\""
-+ _am_result=BSD
-+ ;;
-+ esac
-+fi
-
-
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $_am_result" >&5
-+$as_echo "$_am_result" >&6; }
-+rm -f confinc confmf
-+
-+# Check whether --enable-dependency-tracking was given.
-+if test "${enable_dependency_tracking+set}" = set; then :
-+ enableval=$enable_dependency_tracking;
-+fi
-+
-+if test "x$enable_dependency_tracking" != xno; then
-+ am_depcomp="$ac_aux_dir/depcomp"
-+ AMDEPBACKSLASH='\'
-+fi
-+ if test "x$enable_dependency_tracking" != xno; then
-+ AMDEP_TRUE=
-+ AMDEP_FALSE='#'
-+else
-+ AMDEP_TRUE='#'
-+ AMDEP_FALSE=
- fi
-- if test "${ac_cv_path_install+set}" = set; then
-- INSTALL=$ac_cv_path_install
-+
-+
-+
-+depcc="$CC" am_compiler_list=
-+
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5
-+$as_echo_n "checking dependency style of $depcc... " >&6; }
-+if ${am_cv_CC_dependencies_compiler_type+:} false; then :
-+ $as_echo_n "(cached) " >&6
-+else
-+ if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
-+ # We make a subdir and do the tests there. Otherwise we can end up
-+ # making bogus files that we don't know about and never remove. For
-+ # instance it was reported that on HP-UX the gcc test will end up
-+ # making a dummy file named `D' -- because `-MD' means `put the output
-+ # in D'.
-+ mkdir conftest.dir
-+ # Copy depcomp to subdir because otherwise we won't find it if we're
-+ # using a relative directory.
-+ cp "$am_depcomp" conftest.dir
-+ cd conftest.dir
-+ # We will build objects and dependencies in a subdirectory because
-+ # it helps to detect inapplicable dependency modes. For instance
-+ # both Tru64's cc and ICC support -MD to output dependencies as a
-+ # side effect of compilation, but ICC will put the dependencies in
-+ # the current directory while Tru64 will put them in the object
-+ # directory.
-+ mkdir sub
-+
-+ am_cv_CC_dependencies_compiler_type=none
-+ if test "$am_compiler_list" = ""; then
-+ am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
-+ fi
-+ am__universal=false
-+ case " $depcc " in #(
-+ *\ -arch\ *\ -arch\ *) am__universal=true ;;
-+ esac
-+
-+ for depmode in $am_compiler_list; do
-+ # Setup a source with many dependencies, because some compilers
-+ # like to wrap large dependency lists on column 80 (with \), and
-+ # we should not choose a depcomp mode which is confused by this.
-+ #
-+ # We need to recreate these files for each test, as the compiler may
-+ # overwrite some of them when testing with obscure command lines.
-+ # This happens at least with the AIX C compiler.
-+ : > sub/conftest.c
-+ for i in 1 2 3 4 5 6; do
-+ echo '#include "conftst'$i'.h"' >> sub/conftest.c
-+ # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
-+ # Solaris 8's {/usr,}/bin/sh.
-+ touch sub/conftst$i.h
-+ done
-+ echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
-+
-+ # We check with `-c' and `-o' for the sake of the "dashmstdout"
-+ # mode. It turns out that the SunPro C++ compiler does not properly
-+ # handle `-M -o', and we need to detect this. Also, some Intel
-+ # versions had trouble with output in subdirs
-+ am__obj=sub/conftest.${OBJEXT-o}
-+ am__minus_obj="-o $am__obj"
-+ case $depmode in
-+ gcc)
-+ # This depmode causes a compiler race in universal mode.
-+ test "$am__universal" = false || continue
-+ ;;
-+ nosideeffect)
-+ # after this tag, mechanisms are not by side-effect, so they'll
-+ # only be used when explicitly requested
-+ if test "x$enable_dependency_tracking" = xyes; then
-+ continue
- else
-- # As a last resort, use the slow shell script. Don't cache a
-- # value for INSTALL within a source directory, because that will
-- # break other packages using the cache if that directory is
-- # removed, or if the value is a relative name.
-- INSTALL=$ac_install_sh
-+ break
- fi
-+ ;;
-+ msvisualcpp | msvcmsys)
-+ # This compiler won't grok `-c -o', but also, the minuso test has
-+ # not run yet. These depmodes are late enough in the game, and
-+ # so weak that their functioning should not be impacted.
-+ am__obj=conftest.${OBJEXT-o}
-+ am__minus_obj=
-+ ;;
-+ none) break ;;
-+ esac
-+ if depmode=$depmode \
-+ source=sub/conftest.c object=$am__obj \
-+ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
-+ $SHELL ./depcomp $depcc -c $am__minus_obj sub/conftest.c \
-+ >/dev/null 2>conftest.err &&
-+ grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 &&
-+ grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
-+ grep $am__obj sub/conftest.Po > /dev/null 2>&1 &&
-+ ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
-+ # icc doesn't choke on unknown options, it will just issue warnings
-+ # or remarks (even with -Werror). So we grep stderr for any message
-+ # that says an option was ignored or not supported.
-+ # When given -MP, icc 7.0 and 7.1 complain thusly:
-+ # icc: Command line warning: ignoring option '-M'; no argument required
-+ # The diagnosis changed in icc 8.0:
-+ # icc: Command line remark: option '-MP' not supported
-+ if (grep 'ignoring option' conftest.err ||
-+ grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
-+ am_cv_CC_dependencies_compiler_type=$depmode
-+ break
-+ fi
-+ fi
-+ done
-+
-+ cd ..
-+ rm -rf conftest.dir
-+else
-+ am_cv_CC_dependencies_compiler_type=none
- fi
--{ echo "$as_me:$LINENO: result: $INSTALL" >&5
--echo "${ECHO_T}$INSTALL" >&6; }
-
--# Use test -z because SunOS4 sh mishandles braces in ${var-val}.
--# It thinks the first close brace ends the variable substitution.
--test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}'
-+fi
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CC_dependencies_compiler_type" >&5
-+$as_echo "$am_cv_CC_dependencies_compiler_type" >&6; }
-+CCDEPMODE=depmode=$am_cv_CC_dependencies_compiler_type
-+
-+ if
-+ test "x$enable_dependency_tracking" != xno \
-+ && test "$am_cv_CC_dependencies_compiler_type" = gcc3; then
-+ am__fastdepCC_TRUE=
-+ am__fastdepCC_FALSE='#'
-+else
-+ am__fastdepCC_TRUE='#'
-+ am__fastdepCC_FALSE=
-+fi
-
--test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}'
-
--test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644'
-
--{ echo "$as_me:$LINENO: checking whether ${MAKE-make} sets \$(MAKE)" >&5
--echo $ECHO_N "checking whether ${MAKE-make} sets \$(MAKE)... $ECHO_C" >&6; }
--set x ${MAKE-make}; ac_make=`echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'`
--if { as_var=ac_cv_prog_make_${ac_make}_set; eval "test \"\${$as_var+set}\" = set"; }; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ${MAKE-make} sets \$(MAKE)" >&5
-+$as_echo_n "checking whether ${MAKE-make} sets \$(MAKE)... " >&6; }
-+set x ${MAKE-make}
-+ac_make=`$as_echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'`
-+if eval \${ac_cv_prog_make_${ac_make}_set+:} false; then :
-+ $as_echo_n "(cached) " >&6
- else
- cat >conftest.make <<\_ACEOF
- SHELL = /bin/sh
- all:
- @echo '@@@%%%=$(MAKE)=@@@%%%'
- _ACEOF
--# GNU make sometimes prints "make[1]: Entering...", which would confuse us.
-+# GNU make sometimes prints "make[1]: Entering ...", which would confuse us.
- case `${MAKE-make} -f conftest.make 2>/dev/null` in
- *@@@%%%=?*=@@@%%%*)
- eval ac_cv_prog_make_${ac_make}_set=yes;;
-@@ -3056,12 +3556,12 @@
- rm -f conftest.make
- fi
- if eval test \$ac_cv_prog_make_${ac_make}_set = yes; then
-- { echo "$as_me:$LINENO: result: yes" >&5
--echo "${ECHO_T}yes" >&6; }
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
-+$as_echo "yes" >&6; }
- SET_MAKE=
- else
-- { echo "$as_me:$LINENO: result: no" >&5
--echo "${ECHO_T}no" >&6; }
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-+$as_echo "no" >&6; }
- SET_MAKE="MAKE=${MAKE-make}"
- fi
-
-@@ -3069,16 +3569,12 @@
-
- # OTHER STUFF
-
--{ echo "$as_me:$LINENO: checking for an ANSI C-conforming const" >&5
--echo $ECHO_N "checking for an ANSI C-conforming const... $ECHO_C" >&6; }
--if test "${ac_cv_c_const+set}" = set; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for an ANSI C-conforming const" >&5
-+$as_echo_n "checking for an ANSI C-conforming const... " >&6; }
-+if ${ac_cv_c_const+:} false; then :
-+ $as_echo_n "(cached) " >&6
- else
-- cat >conftest.$ac_ext <<_ACEOF
--/* confdefs.h. */
--_ACEOF
--cat confdefs.h >>conftest.$ac_ext
--cat >>conftest.$ac_ext <<_ACEOF
-+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
- /* end confdefs.h. */
-
- int
-@@ -3138,55 +3634,29 @@
- return 0;
- }
- _ACEOF
--rm -f conftest.$ac_objext
--if { (ac_try="$ac_compile"
--case "(($ac_try" in
-- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-- *) ac_try_echo=$ac_try;;
--esac
--eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
-- (eval "$ac_compile") 2>conftest.er1
-- ac_status=$?
-- grep -v '^ *+' conftest.er1 >conftest.err
-- rm -f conftest.er1
-- cat conftest.err >&5
-- echo "$as_me:$LINENO: \$? = $ac_status" >&5
-- (exit $ac_status); } && {
-- test -z "$ac_c_werror_flag" ||
-- test ! -s conftest.err
-- } && test -s conftest.$ac_objext; then
-+if ac_fn_c_try_compile "$LINENO"; then :
- ac_cv_c_const=yes
- else
-- echo "$as_me: failed program was:" >&5
--sed 's/^/| /' conftest.$ac_ext >&5
--
- ac_cv_c_const=no
- fi
--
- rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- fi
--{ echo "$as_me:$LINENO: result: $ac_cv_c_const" >&5
--echo "${ECHO_T}$ac_cv_c_const" >&6; }
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_const" >&5
-+$as_echo "$ac_cv_c_const" >&6; }
- if test $ac_cv_c_const = no; then
-
--cat >>confdefs.h <<\_ACEOF
--#define const
--_ACEOF
-+$as_echo "#define const /**/" >>confdefs.h
-
- fi
-
--{ echo "$as_me:$LINENO: checking for inline" >&5
--echo $ECHO_N "checking for inline... $ECHO_C" >&6; }
--if test "${ac_cv_c_inline+set}" = set; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for inline" >&5
-+$as_echo_n "checking for inline... " >&6; }
-+if ${ac_cv_c_inline+:} false; then :
-+ $as_echo_n "(cached) " >&6
- else
- ac_cv_c_inline=no
- for ac_kw in inline __inline__ __inline; do
-- cat >conftest.$ac_ext <<_ACEOF
--/* confdefs.h. */
--_ACEOF
--cat confdefs.h >>conftest.$ac_ext
--cat >>conftest.$ac_ext <<_ACEOF
-+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
- /* end confdefs.h. */
- #ifndef __cplusplus
- typedef int foo_t;
-@@ -3195,39 +3665,16 @@
- #endif
-
- _ACEOF
--rm -f conftest.$ac_objext
--if { (ac_try="$ac_compile"
--case "(($ac_try" in
-- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-- *) ac_try_echo=$ac_try;;
--esac
--eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
-- (eval "$ac_compile") 2>conftest.er1
-- ac_status=$?
-- grep -v '^ *+' conftest.er1 >conftest.err
-- rm -f conftest.er1
-- cat conftest.err >&5
-- echo "$as_me:$LINENO: \$? = $ac_status" >&5
-- (exit $ac_status); } && {
-- test -z "$ac_c_werror_flag" ||
-- test ! -s conftest.err
-- } && test -s conftest.$ac_objext; then
-+if ac_fn_c_try_compile "$LINENO"; then :
- ac_cv_c_inline=$ac_kw
--else
-- echo "$as_me: failed program was:" >&5
--sed 's/^/| /' conftest.$ac_ext >&5
--
--
- fi
--
- rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- test "$ac_cv_c_inline" != no && break
- done
-
- fi
--{ echo "$as_me:$LINENO: result: $ac_cv_c_inline" >&5
--echo "${ECHO_T}$ac_cv_c_inline" >&6; }
--
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_inline" >&5
-+$as_echo "$ac_cv_c_inline" >&6; }
-
- case $ac_cv_c_inline in
- inline | yes) ;;
-@@ -3249,15 +3696,15 @@
- ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
- ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
- ac_compiler_gnu=$ac_cv_c_compiler_gnu
--{ echo "$as_me:$LINENO: checking how to run the C preprocessor" >&5
--echo $ECHO_N "checking how to run the C preprocessor... $ECHO_C" >&6; }
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking how to run the C preprocessor" >&5
-+$as_echo_n "checking how to run the C preprocessor... " >&6; }
- # On Suns, sometimes $CPP names a directory.
- if test -n "$CPP" && test -d "$CPP"; then
- CPP=
- fi
- if test -z "$CPP"; then
-- if test "${ac_cv_prog_CPP+set}" = set; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
-+ if ${ac_cv_prog_CPP+:} false; then :
-+ $as_echo_n "(cached) " >&6
- else
- # Double quotes because CPP needs to be expanded
- for CPP in "$CC -E" "$CC -E -traditional-cpp" "/lib/cpp"
-@@ -3271,11 +3718,7 @@
- # <limits.h> exists even on freestanding compilers.
- # On the NeXT, cc -E runs the code through the compiler's parser,
- # not just through cpp. "Syntax error" is here to catch this case.
-- cat >conftest.$ac_ext <<_ACEOF
--/* confdefs.h. */
--_ACEOF
--cat confdefs.h >>conftest.$ac_ext
--cat >>conftest.$ac_ext <<_ACEOF
-+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
- /* end confdefs.h. */
- #ifdef __STDC__
- # include <limits.h>
-@@ -3284,76 +3727,34 @@
- #endif
- Syntax error
- _ACEOF
--if { (ac_try="$ac_cpp conftest.$ac_ext"
--case "(($ac_try" in
-- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-- *) ac_try_echo=$ac_try;;
--esac
--eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
-- (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
-- ac_status=$?
-- grep -v '^ *+' conftest.er1 >conftest.err
-- rm -f conftest.er1
-- cat conftest.err >&5
-- echo "$as_me:$LINENO: \$? = $ac_status" >&5
-- (exit $ac_status); } >/dev/null && {
-- test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
-- test ! -s conftest.err
-- }; then
-- :
--else
-- echo "$as_me: failed program was:" >&5
--sed 's/^/| /' conftest.$ac_ext >&5
-+if ac_fn_c_try_cpp "$LINENO"; then :
-
-+else
- # Broken: fails on valid input.
- continue
- fi
--
--rm -f conftest.err conftest.$ac_ext
-+rm -f conftest.err conftest.i conftest.$ac_ext
-
- # OK, works on sane cases. Now check whether nonexistent headers
- # can be detected and how.
-- cat >conftest.$ac_ext <<_ACEOF
--/* confdefs.h. */
--_ACEOF
--cat confdefs.h >>conftest.$ac_ext
--cat >>conftest.$ac_ext <<_ACEOF
-+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
- /* end confdefs.h. */
- #include <ac_nonexistent.h>
- _ACEOF
--if { (ac_try="$ac_cpp conftest.$ac_ext"
--case "(($ac_try" in
-- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-- *) ac_try_echo=$ac_try;;
--esac
--eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
-- (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
-- ac_status=$?
-- grep -v '^ *+' conftest.er1 >conftest.err
-- rm -f conftest.er1
-- cat conftest.err >&5
-- echo "$as_me:$LINENO: \$? = $ac_status" >&5
-- (exit $ac_status); } >/dev/null && {
-- test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
-- test ! -s conftest.err
-- }; then
-+if ac_fn_c_try_cpp "$LINENO"; then :
- # Broken: success on invalid input.
- continue
- else
-- echo "$as_me: failed program was:" >&5
--sed 's/^/| /' conftest.$ac_ext >&5
--
- # Passes both tests.
- ac_preproc_ok=:
- break
- fi
--
--rm -f conftest.err conftest.$ac_ext
-+rm -f conftest.err conftest.i conftest.$ac_ext
-
- done
- # Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
--rm -f conftest.err conftest.$ac_ext
--if $ac_preproc_ok; then
-+rm -f conftest.i conftest.err conftest.$ac_ext
-+if $ac_preproc_ok; then :
- break
- fi
-
-@@ -3365,8 +3766,8 @@
- else
- ac_cv_prog_CPP=$CPP
- fi
--{ echo "$as_me:$LINENO: result: $CPP" >&5
--echo "${ECHO_T}$CPP" >&6; }
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $CPP" >&5
-+$as_echo "$CPP" >&6; }
- ac_preproc_ok=false
- for ac_c_preproc_warn_flag in '' yes
- do
-@@ -3375,97 +3776,50 @@
- # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
- # <limits.h> exists even on freestanding compilers.
- # On the NeXT, cc -E runs the code through the compiler's parser,
-- # not just through cpp. "Syntax error" is here to catch this case.
-- cat >conftest.$ac_ext <<_ACEOF
--/* confdefs.h. */
--_ACEOF
--cat confdefs.h >>conftest.$ac_ext
--cat >>conftest.$ac_ext <<_ACEOF
--/* end confdefs.h. */
--#ifdef __STDC__
--# include <limits.h>
--#else
--# include <assert.h>
--#endif
-- Syntax error
--_ACEOF
--if { (ac_try="$ac_cpp conftest.$ac_ext"
--case "(($ac_try" in
-- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-- *) ac_try_echo=$ac_try;;
--esac
--eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
-- (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
-- ac_status=$?
-- grep -v '^ *+' conftest.er1 >conftest.err
-- rm -f conftest.er1
-- cat conftest.err >&5
-- echo "$as_me:$LINENO: \$? = $ac_status" >&5
-- (exit $ac_status); } >/dev/null && {
-- test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
-- test ! -s conftest.err
-- }; then
-- :
--else
-- echo "$as_me: failed program was:" >&5
--sed 's/^/| /' conftest.$ac_ext >&5
-+ # not just through cpp. "Syntax error" is here to catch this case.
-+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-+/* end confdefs.h. */
-+#ifdef __STDC__
-+# include <limits.h>
-+#else
-+# include <assert.h>
-+#endif
-+ Syntax error
-+_ACEOF
-+if ac_fn_c_try_cpp "$LINENO"; then :
-
-+else
- # Broken: fails on valid input.
- continue
- fi
--
--rm -f conftest.err conftest.$ac_ext
-+rm -f conftest.err conftest.i conftest.$ac_ext
-
- # OK, works on sane cases. Now check whether nonexistent headers
- # can be detected and how.
-- cat >conftest.$ac_ext <<_ACEOF
--/* confdefs.h. */
--_ACEOF
--cat confdefs.h >>conftest.$ac_ext
--cat >>conftest.$ac_ext <<_ACEOF
-+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
- /* end confdefs.h. */
- #include <ac_nonexistent.h>
- _ACEOF
--if { (ac_try="$ac_cpp conftest.$ac_ext"
--case "(($ac_try" in
-- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-- *) ac_try_echo=$ac_try;;
--esac
--eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
-- (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
-- ac_status=$?
-- grep -v '^ *+' conftest.er1 >conftest.err
-- rm -f conftest.er1
-- cat conftest.err >&5
-- echo "$as_me:$LINENO: \$? = $ac_status" >&5
-- (exit $ac_status); } >/dev/null && {
-- test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
-- test ! -s conftest.err
-- }; then
-+if ac_fn_c_try_cpp "$LINENO"; then :
- # Broken: success on invalid input.
- continue
- else
-- echo "$as_me: failed program was:" >&5
--sed 's/^/| /' conftest.$ac_ext >&5
--
- # Passes both tests.
- ac_preproc_ok=:
- break
- fi
--
--rm -f conftest.err conftest.$ac_ext
-+rm -f conftest.err conftest.i conftest.$ac_ext
-
- done
- # Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
--rm -f conftest.err conftest.$ac_ext
--if $ac_preproc_ok; then
-- :
-+rm -f conftest.i conftest.err conftest.$ac_ext
-+if $ac_preproc_ok; then :
-+
- else
-- { { echo "$as_me:$LINENO: error: C preprocessor \"$CPP\" fails sanity check
--See \`config.log' for more details." >&5
--echo "$as_me: error: C preprocessor \"$CPP\" fails sanity check
--See \`config.log' for more details." >&2;}
-- { (exit 1); exit 1; }; }
-+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
-+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-+as_fn_error $? "C preprocessor \"$CPP\" fails sanity check
-+See \`config.log' for more details" "$LINENO" 5; }
- fi
-
- ac_ext=c
-@@ -3475,20 +3829,15 @@
- ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-
--{ echo "$as_me:$LINENO: checking for grep that handles long lines and -e" >&5
--echo $ECHO_N "checking for grep that handles long lines and -e... $ECHO_C" >&6; }
--if test "${ac_cv_path_GREP+set}" = set; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
--else
-- # Extract the first word of "grep ggrep" to use in msg output
--if test -z "$GREP"; then
--set dummy grep ggrep; ac_prog_name=$2
--if test "${ac_cv_path_GREP+set}" = set; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for grep that handles long lines and -e" >&5
-+$as_echo_n "checking for grep that handles long lines and -e... " >&6; }
-+if ${ac_cv_path_GREP+:} false; then :
-+ $as_echo_n "(cached) " >&6
- else
-+ if test -z "$GREP"; then
- ac_path_GREP_found=false
--# Loop through the user's path and test for each of PROGNAME-LIST
--as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-+ # Loop through the user's path and test for each of PROGNAME-LIST
-+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
- for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin
- do
- IFS=$as_save_IFS
-@@ -3497,23 +3846,23 @@
- for ac_exec_ext in '' $ac_executable_extensions; do
- ac_path_GREP="$as_dir/$ac_prog$ac_exec_ext"
- { test -f "$ac_path_GREP" && $as_test_x "$ac_path_GREP"; } || continue
-- # Check for GNU ac_path_GREP and select it if it is found.
-+# Check for GNU ac_path_GREP and select it if it is found.
- # Check for GNU $ac_path_GREP
- case `"$ac_path_GREP" --version 2>&1` in
- *GNU*)
- ac_cv_path_GREP="$ac_path_GREP" ac_path_GREP_found=:;;
- *)
- ac_count=0
-- echo $ECHO_N "0123456789$ECHO_C" >"conftest.in"
-+ $as_echo_n 0123456789 >"conftest.in"
- while :
- do
- cat "conftest.in" "conftest.in" >"conftest.tmp"
- mv "conftest.tmp" "conftest.in"
- cp "conftest.in" "conftest.nl"
-- echo 'GREP' >> "conftest.nl"
-+ $as_echo 'GREP' >> "conftest.nl"
- "$ac_path_GREP" -e 'GREP$' -e '-(cannot match)-' < "conftest.nl" >"conftest.out" 2>/dev/null || break
- diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
-- ac_count=`expr $ac_count + 1`
-+ as_fn_arith $ac_count + 1 && ac_count=$as_val
- if test $ac_count -gt ${ac_path_GREP_max-0}; then
- # Best one so far, save it but keep looking for a better one
- ac_cv_path_GREP="$ac_path_GREP"
-@@ -3525,52 +3874,36 @@
- rm -f conftest.in conftest.tmp conftest.nl conftest.out;;
- esac
-
--
- $ac_path_GREP_found && break 3
- done
--done
--
--done
-+ done
-+ done
- IFS=$as_save_IFS
--
--
--fi
--
--GREP="$ac_cv_path_GREP"
--if test -z "$GREP"; then
-- { { echo "$as_me:$LINENO: error: no acceptable $ac_prog_name could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&5
--echo "$as_me: error: no acceptable $ac_prog_name could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&2;}
-- { (exit 1); exit 1; }; }
--fi
--
-+ if test -z "$ac_cv_path_GREP"; then
-+ as_fn_error $? "no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
-+ fi
- else
- ac_cv_path_GREP=$GREP
- fi
-
--
- fi
--{ echo "$as_me:$LINENO: result: $ac_cv_path_GREP" >&5
--echo "${ECHO_T}$ac_cv_path_GREP" >&6; }
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_GREP" >&5
-+$as_echo "$ac_cv_path_GREP" >&6; }
- GREP="$ac_cv_path_GREP"
-
-
--{ echo "$as_me:$LINENO: checking for egrep" >&5
--echo $ECHO_N "checking for egrep... $ECHO_C" >&6; }
--if test "${ac_cv_path_EGREP+set}" = set; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for egrep" >&5
-+$as_echo_n "checking for egrep... " >&6; }
-+if ${ac_cv_path_EGREP+:} false; then :
-+ $as_echo_n "(cached) " >&6
- else
- if echo a | $GREP -E '(a|b)' >/dev/null 2>&1
- then ac_cv_path_EGREP="$GREP -E"
- else
-- # Extract the first word of "egrep" to use in msg output
--if test -z "$EGREP"; then
--set dummy egrep; ac_prog_name=$2
--if test "${ac_cv_path_EGREP+set}" = set; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
--else
-+ if test -z "$EGREP"; then
- ac_path_EGREP_found=false
--# Loop through the user's path and test for each of PROGNAME-LIST
--as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-+ # Loop through the user's path and test for each of PROGNAME-LIST
-+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
- for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin
- do
- IFS=$as_save_IFS
-@@ -3579,23 +3912,23 @@
- for ac_exec_ext in '' $ac_executable_extensions; do
- ac_path_EGREP="$as_dir/$ac_prog$ac_exec_ext"
- { test -f "$ac_path_EGREP" && $as_test_x "$ac_path_EGREP"; } || continue
-- # Check for GNU ac_path_EGREP and select it if it is found.
-+# Check for GNU ac_path_EGREP and select it if it is found.
- # Check for GNU $ac_path_EGREP
- case `"$ac_path_EGREP" --version 2>&1` in
- *GNU*)
- ac_cv_path_EGREP="$ac_path_EGREP" ac_path_EGREP_found=:;;
- *)
- ac_count=0
-- echo $ECHO_N "0123456789$ECHO_C" >"conftest.in"
-+ $as_echo_n 0123456789 >"conftest.in"
- while :
- do
- cat "conftest.in" "conftest.in" >"conftest.tmp"
- mv "conftest.tmp" "conftest.in"
- cp "conftest.in" "conftest.nl"
-- echo 'EGREP' >> "conftest.nl"
-+ $as_echo 'EGREP' >> "conftest.nl"
- "$ac_path_EGREP" 'EGREP$' < "conftest.nl" >"conftest.out" 2>/dev/null || break
- diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
-- ac_count=`expr $ac_count + 1`
-+ as_fn_arith $ac_count + 1 && ac_count=$as_val
- if test $ac_count -gt ${ac_path_EGREP_max-0}; then
- # Best one so far, save it but keep looking for a better one
- ac_cv_path_EGREP="$ac_path_EGREP"
-@@ -3607,46 +3940,31 @@
- rm -f conftest.in conftest.tmp conftest.nl conftest.out;;
- esac
-
--
- $ac_path_EGREP_found && break 3
- done
--done
--
--done
-+ done
-+ done
- IFS=$as_save_IFS
--
--
--fi
--
--EGREP="$ac_cv_path_EGREP"
--if test -z "$EGREP"; then
-- { { echo "$as_me:$LINENO: error: no acceptable $ac_prog_name could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&5
--echo "$as_me: error: no acceptable $ac_prog_name could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&2;}
-- { (exit 1); exit 1; }; }
--fi
--
-+ if test -z "$ac_cv_path_EGREP"; then
-+ as_fn_error $? "no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
-+ fi
- else
- ac_cv_path_EGREP=$EGREP
- fi
-
--
- fi
- fi
--{ echo "$as_me:$LINENO: result: $ac_cv_path_EGREP" >&5
--echo "${ECHO_T}$ac_cv_path_EGREP" >&6; }
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_EGREP" >&5
-+$as_echo "$ac_cv_path_EGREP" >&6; }
- EGREP="$ac_cv_path_EGREP"
-
-
--{ echo "$as_me:$LINENO: checking for ANSI C header files" >&5
--echo $ECHO_N "checking for ANSI C header files... $ECHO_C" >&6; }
--if test "${ac_cv_header_stdc+set}" = set; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for ANSI C header files" >&5
-+$as_echo_n "checking for ANSI C header files... " >&6; }
-+if ${ac_cv_header_stdc+:} false; then :
-+ $as_echo_n "(cached) " >&6
- else
-- cat >conftest.$ac_ext <<_ACEOF
--/* confdefs.h. */
--_ACEOF
--cat confdefs.h >>conftest.$ac_ext
--cat >>conftest.$ac_ext <<_ACEOF
-+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
- /* end confdefs.h. */
- #include <stdlib.h>
- #include <stdarg.h>
-@@ -3661,47 +3979,23 @@
- return 0;
- }
- _ACEOF
--rm -f conftest.$ac_objext
--if { (ac_try="$ac_compile"
--case "(($ac_try" in
-- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-- *) ac_try_echo=$ac_try;;
--esac
--eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
-- (eval "$ac_compile") 2>conftest.er1
-- ac_status=$?
-- grep -v '^ *+' conftest.er1 >conftest.err
-- rm -f conftest.er1
-- cat conftest.err >&5
-- echo "$as_me:$LINENO: \$? = $ac_status" >&5
-- (exit $ac_status); } && {
-- test -z "$ac_c_werror_flag" ||
-- test ! -s conftest.err
-- } && test -s conftest.$ac_objext; then
-+if ac_fn_c_try_compile "$LINENO"; then :
- ac_cv_header_stdc=yes
- else
-- echo "$as_me: failed program was:" >&5
--sed 's/^/| /' conftest.$ac_ext >&5
--
- ac_cv_header_stdc=no
- fi
--
- rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-
- if test $ac_cv_header_stdc = yes; then
- # SunOS 4.x string.h does not declare mem*, contrary to ANSI.
-- cat >conftest.$ac_ext <<_ACEOF
--/* confdefs.h. */
--_ACEOF
--cat confdefs.h >>conftest.$ac_ext
--cat >>conftest.$ac_ext <<_ACEOF
-+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
- /* end confdefs.h. */
- #include <string.h>
-
- _ACEOF
- if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
-- $EGREP "memchr" >/dev/null 2>&1; then
-- :
-+ $EGREP "memchr" >/dev/null 2>&1; then :
-+
- else
- ac_cv_header_stdc=no
- fi
-@@ -3711,18 +4005,14 @@
-
- if test $ac_cv_header_stdc = yes; then
- # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI.
-- cat >conftest.$ac_ext <<_ACEOF
--/* confdefs.h. */
--_ACEOF
--cat confdefs.h >>conftest.$ac_ext
--cat >>conftest.$ac_ext <<_ACEOF
-+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
- /* end confdefs.h. */
- #include <stdlib.h>
-
- _ACEOF
- if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
-- $EGREP "free" >/dev/null 2>&1; then
-- :
-+ $EGREP "free" >/dev/null 2>&1; then :
-+
- else
- ac_cv_header_stdc=no
- fi
-@@ -3732,14 +4022,10 @@
-
- if test $ac_cv_header_stdc = yes; then
- # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi.
-- if test "$cross_compiling" = yes; then
-+ if test "$cross_compiling" = yes; then :
- :
- else
-- cat >conftest.$ac_ext <<_ACEOF
--/* confdefs.h. */
--_ACEOF
--cat confdefs.h >>conftest.$ac_ext
--cat >>conftest.$ac_ext <<_ACEOF
-+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
- /* end confdefs.h. */
- #include <ctype.h>
- #include <stdlib.h>
-@@ -3766,113 +4052,35 @@
- return 0;
- }
- _ACEOF
--rm -f conftest$ac_exeext
--if { (ac_try="$ac_link"
--case "(($ac_try" in
-- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-- *) ac_try_echo=$ac_try;;
--esac
--eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
-- (eval "$ac_link") 2>&5
-- ac_status=$?
-- echo "$as_me:$LINENO: \$? = $ac_status" >&5
-- (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
-- { (case "(($ac_try" in
-- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-- *) ac_try_echo=$ac_try;;
--esac
--eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
-- (eval "$ac_try") 2>&5
-- ac_status=$?
-- echo "$as_me:$LINENO: \$? = $ac_status" >&5
-- (exit $ac_status); }; }; then
-- :
--else
-- echo "$as_me: program exited with status $ac_status" >&5
--echo "$as_me: failed program was:" >&5
--sed 's/^/| /' conftest.$ac_ext >&5
-+if ac_fn_c_try_run "$LINENO"; then :
-
--( exit $ac_status )
--ac_cv_header_stdc=no
-+else
-+ ac_cv_header_stdc=no
- fi
--rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
-+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
-+ conftest.$ac_objext conftest.beam conftest.$ac_ext
- fi
-
--
- fi
- fi
--{ echo "$as_me:$LINENO: result: $ac_cv_header_stdc" >&5
--echo "${ECHO_T}$ac_cv_header_stdc" >&6; }
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdc" >&5
-+$as_echo "$ac_cv_header_stdc" >&6; }
- if test $ac_cv_header_stdc = yes; then
-
--cat >>confdefs.h <<\_ACEOF
--#define STDC_HEADERS 1
--_ACEOF
-+$as_echo "#define STDC_HEADERS 1" >>confdefs.h
-
- fi
- # CHECKS FOR stdlib.h stdarg.h string.h and float.h
- # On IRIX 5.3, sys/types and inttypes.h are conflicting.
--
--
--
--
--
--
--
--
--
- for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \
- inttypes.h stdint.h unistd.h
--do
--as_ac_Header=`echo "ac_cv_header_$ac_header" | $as_tr_sh`
--{ echo "$as_me:$LINENO: checking for $ac_header" >&5
--echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6; }
--if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
--else
-- cat >conftest.$ac_ext <<_ACEOF
--/* confdefs.h. */
--_ACEOF
--cat confdefs.h >>conftest.$ac_ext
--cat >>conftest.$ac_ext <<_ACEOF
--/* end confdefs.h. */
--$ac_includes_default
--
--#include <$ac_header>
--_ACEOF
--rm -f conftest.$ac_objext
--if { (ac_try="$ac_compile"
--case "(($ac_try" in
-- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-- *) ac_try_echo=$ac_try;;
--esac
--eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
-- (eval "$ac_compile") 2>conftest.er1
-- ac_status=$?
-- grep -v '^ *+' conftest.er1 >conftest.err
-- rm -f conftest.er1
-- cat conftest.err >&5
-- echo "$as_me:$LINENO: \$? = $ac_status" >&5
-- (exit $ac_status); } && {
-- test -z "$ac_c_werror_flag" ||
-- test ! -s conftest.err
-- } && test -s conftest.$ac_objext; then
-- eval "$as_ac_Header=yes"
--else
-- echo "$as_me: failed program was:" >&5
--sed 's/^/| /' conftest.$ac_ext >&5
--
-- eval "$as_ac_Header=no"
--fi
--
--rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
--fi
--ac_res=`eval echo '${'$as_ac_Header'}'`
-- { echo "$as_me:$LINENO: result: $ac_res" >&5
--echo "${ECHO_T}$ac_res" >&6; }
--if test `eval echo '${'$as_ac_Header'}'` = yes; then
-+do :
-+ as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
-+ac_fn_c_check_header_compile "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default
-+"
-+if eval test \"x\$"$as_ac_Header"\" = x"yes"; then :
- cat >>confdefs.h <<_ACEOF
--#define `echo "HAVE_$ac_header" | $as_tr_cpp` 1
-+#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
- _ACEOF
-
- fi
-@@ -3880,149 +4088,14 @@
- done
-
-
--
--
--
--
--
--
--
--
--
- for ac_header in limits.h errno.h math.h strings.h ctype.h \
- sys/stat.h sys/types.h time.h unistd.h
--do
--as_ac_Header=`echo "ac_cv_header_$ac_header" | $as_tr_sh`
--if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
-- { echo "$as_me:$LINENO: checking for $ac_header" >&5
--echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6; }
--if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
--fi
--ac_res=`eval echo '${'$as_ac_Header'}'`
-- { echo "$as_me:$LINENO: result: $ac_res" >&5
--echo "${ECHO_T}$ac_res" >&6; }
--else
-- # Is the header compilable?
--{ echo "$as_me:$LINENO: checking $ac_header usability" >&5
--echo $ECHO_N "checking $ac_header usability... $ECHO_C" >&6; }
--cat >conftest.$ac_ext <<_ACEOF
--/* confdefs.h. */
--_ACEOF
--cat confdefs.h >>conftest.$ac_ext
--cat >>conftest.$ac_ext <<_ACEOF
--/* end confdefs.h. */
--$ac_includes_default
--#include <$ac_header>
--_ACEOF
--rm -f conftest.$ac_objext
--if { (ac_try="$ac_compile"
--case "(($ac_try" in
-- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-- *) ac_try_echo=$ac_try;;
--esac
--eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
-- (eval "$ac_compile") 2>conftest.er1
-- ac_status=$?
-- grep -v '^ *+' conftest.er1 >conftest.err
-- rm -f conftest.er1
-- cat conftest.err >&5
-- echo "$as_me:$LINENO: \$? = $ac_status" >&5
-- (exit $ac_status); } && {
-- test -z "$ac_c_werror_flag" ||
-- test ! -s conftest.err
-- } && test -s conftest.$ac_objext; then
-- ac_header_compiler=yes
--else
-- echo "$as_me: failed program was:" >&5
--sed 's/^/| /' conftest.$ac_ext >&5
--
-- ac_header_compiler=no
--fi
--
--rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
--{ echo "$as_me:$LINENO: result: $ac_header_compiler" >&5
--echo "${ECHO_T}$ac_header_compiler" >&6; }
--
--# Is the header present?
--{ echo "$as_me:$LINENO: checking $ac_header presence" >&5
--echo $ECHO_N "checking $ac_header presence... $ECHO_C" >&6; }
--cat >conftest.$ac_ext <<_ACEOF
--/* confdefs.h. */
--_ACEOF
--cat confdefs.h >>conftest.$ac_ext
--cat >>conftest.$ac_ext <<_ACEOF
--/* end confdefs.h. */
--#include <$ac_header>
--_ACEOF
--if { (ac_try="$ac_cpp conftest.$ac_ext"
--case "(($ac_try" in
-- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-- *) ac_try_echo=$ac_try;;
--esac
--eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
-- (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
-- ac_status=$?
-- grep -v '^ *+' conftest.er1 >conftest.err
-- rm -f conftest.er1
-- cat conftest.err >&5
-- echo "$as_me:$LINENO: \$? = $ac_status" >&5
-- (exit $ac_status); } >/dev/null && {
-- test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
-- test ! -s conftest.err
-- }; then
-- ac_header_preproc=yes
--else
-- echo "$as_me: failed program was:" >&5
--sed 's/^/| /' conftest.$ac_ext >&5
--
-- ac_header_preproc=no
--fi
--
--rm -f conftest.err conftest.$ac_ext
--{ echo "$as_me:$LINENO: result: $ac_header_preproc" >&5
--echo "${ECHO_T}$ac_header_preproc" >&6; }
--
--# So? What about this header?
--case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in
-- yes:no: )
-- { echo "$as_me:$LINENO: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&5
--echo "$as_me: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&2;}
-- { echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the compiler's result" >&5
--echo "$as_me: WARNING: $ac_header: proceeding with the compiler's result" >&2;}
-- ac_header_preproc=yes
-- ;;
-- no:yes:* )
-- { echo "$as_me:$LINENO: WARNING: $ac_header: present but cannot be compiled" >&5
--echo "$as_me: WARNING: $ac_header: present but cannot be compiled" >&2;}
-- { echo "$as_me:$LINENO: WARNING: $ac_header: check for missing prerequisite headers?" >&5
--echo "$as_me: WARNING: $ac_header: check for missing prerequisite headers?" >&2;}
-- { echo "$as_me:$LINENO: WARNING: $ac_header: see the Autoconf documentation" >&5
--echo "$as_me: WARNING: $ac_header: see the Autoconf documentation" >&2;}
-- { echo "$as_me:$LINENO: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&5
--echo "$as_me: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&2;}
-- { echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the preprocessor's result" >&5
--echo "$as_me: WARNING: $ac_header: proceeding with the preprocessor's result" >&2;}
-- { echo "$as_me:$LINENO: WARNING: $ac_header: in the future, the compiler will take precedence" >&5
--echo "$as_me: WARNING: $ac_header: in the future, the compiler will take precedence" >&2;}
--
-- ;;
--esac
--{ echo "$as_me:$LINENO: checking for $ac_header" >&5
--echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6; }
--if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
--else
-- eval "$as_ac_Header=\$ac_header_preproc"
--fi
--ac_res=`eval echo '${'$as_ac_Header'}'`
-- { echo "$as_me:$LINENO: result: $ac_res" >&5
--echo "${ECHO_T}$ac_res" >&6; }
--
--fi
--if test `eval echo '${'$as_ac_Header'}'` = yes; then
-+do :
-+ as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
-+ac_fn_c_check_header_mongrel "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default"
-+if eval test \"x\$"$as_ac_Header"\" = x"yes"; then :
- cat >>confdefs.h <<_ACEOF
--#define `echo "HAVE_$ac_header" | $as_tr_cpp` 1
-+#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
- _ACEOF
-
- fi
-@@ -4033,35 +4106,27 @@
- # SET host (REQUIRES config.guess AND config.sub)
- # Make sure we can run config.sub.
- $SHELL "$ac_aux_dir/config.sub" sun4 >/dev/null 2>&1 ||
-- { { echo "$as_me:$LINENO: error: cannot run $SHELL $ac_aux_dir/config.sub" >&5
--echo "$as_me: error: cannot run $SHELL $ac_aux_dir/config.sub" >&2;}
-- { (exit 1); exit 1; }; }
--
--{ echo "$as_me:$LINENO: checking build system type" >&5
--echo $ECHO_N "checking build system type... $ECHO_C" >&6; }
--if test "${ac_cv_build+set}" = set; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
-+ as_fn_error $? "cannot run $SHELL $ac_aux_dir/config.sub" "$LINENO" 5
-+
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking build system type" >&5
-+$as_echo_n "checking build system type... " >&6; }
-+if ${ac_cv_build+:} false; then :
-+ $as_echo_n "(cached) " >&6
- else
- ac_build_alias=$build_alias
- test "x$ac_build_alias" = x &&
- ac_build_alias=`$SHELL "$ac_aux_dir/config.guess"`
- test "x$ac_build_alias" = x &&
-- { { echo "$as_me:$LINENO: error: cannot guess build type; you must specify one" >&5
--echo "$as_me: error: cannot guess build type; you must specify one" >&2;}
-- { (exit 1); exit 1; }; }
-+ as_fn_error $? "cannot guess build type; you must specify one" "$LINENO" 5
- ac_cv_build=`$SHELL "$ac_aux_dir/config.sub" $ac_build_alias` ||
-- { { echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $ac_build_alias failed" >&5
--echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $ac_build_alias failed" >&2;}
-- { (exit 1); exit 1; }; }
-+ as_fn_error $? "$SHELL $ac_aux_dir/config.sub $ac_build_alias failed" "$LINENO" 5
-
- fi
--{ echo "$as_me:$LINENO: result: $ac_cv_build" >&5
--echo "${ECHO_T}$ac_cv_build" >&6; }
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_build" >&5
-+$as_echo "$ac_cv_build" >&6; }
- case $ac_cv_build in
- *-*-*) ;;
--*) { { echo "$as_me:$LINENO: error: invalid value of canonical build" >&5
--echo "$as_me: error: invalid value of canonical build" >&2;}
-- { (exit 1); exit 1; }; };;
-+*) as_fn_error $? "invalid value of canonical build" "$LINENO" 5;;
- esac
- build=$ac_cv_build
- ac_save_IFS=$IFS; IFS='-'
-@@ -4077,28 +4142,24 @@
- case $build_os in *\ *) build_os=`echo "$build_os" | sed 's/ /-/g'`;; esac
-
-
--{ echo "$as_me:$LINENO: checking host system type" >&5
--echo $ECHO_N "checking host system type... $ECHO_C" >&6; }
--if test "${ac_cv_host+set}" = set; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking host system type" >&5
-+$as_echo_n "checking host system type... " >&6; }
-+if ${ac_cv_host+:} false; then :
-+ $as_echo_n "(cached) " >&6
- else
- if test "x$host_alias" = x; then
- ac_cv_host=$ac_cv_build
- else
- ac_cv_host=`$SHELL "$ac_aux_dir/config.sub" $host_alias` ||
-- { { echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $host_alias failed" >&5
--echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $host_alias failed" >&2;}
-- { (exit 1); exit 1; }; }
-+ as_fn_error $? "$SHELL $ac_aux_dir/config.sub $host_alias failed" "$LINENO" 5
- fi
-
- fi
--{ echo "$as_me:$LINENO: result: $ac_cv_host" >&5
--echo "${ECHO_T}$ac_cv_host" >&6; }
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_host" >&5
-+$as_echo "$ac_cv_host" >&6; }
- case $ac_cv_host in
- *-*-*) ;;
--*) { { echo "$as_me:$LINENO: error: invalid value of canonical host" >&5
--echo "$as_me: error: invalid value of canonical host" >&2;}
-- { (exit 1); exit 1; }; };;
-+*) as_fn_error $? "invalid value of canonical host" "$LINENO" 5;;
- esac
- host=$ac_cv_host
- ac_save_IFS=$IFS; IFS='-'
-@@ -4163,13 +4224,9 @@
- # CHECK FOR socklen_t
- # THIS IS TO FIX PROBLEMS WHERE socklen_t ISN'T DEFINED (eg. ON OSF)
- #
--{ echo "$as_me:$LINENO: checking for socklen_t" >&5
--echo $ECHO_N "checking for socklen_t... $ECHO_C" >&6; }
--cat >conftest.$ac_ext <<_ACEOF
--/* confdefs.h. */
--_ACEOF
--cat confdefs.h >>conftest.$ac_ext
--cat >>conftest.$ac_ext <<_ACEOF
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for socklen_t" >&5
-+$as_echo_n "checking for socklen_t... " >&6; }
-+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
- /* end confdefs.h. */
- #include <sys/types.h>
- #include <sys/socket.h>
-@@ -4182,34 +4239,11 @@
- return 0;
- }
- _ACEOF
--rm -f conftest.$ac_objext
--if { (ac_try="$ac_compile"
--case "(($ac_try" in
-- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-- *) ac_try_echo=$ac_try;;
--esac
--eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
-- (eval "$ac_compile") 2>conftest.er1
-- ac_status=$?
-- grep -v '^ *+' conftest.er1 >conftest.err
-- rm -f conftest.er1
-- cat conftest.err >&5
-- echo "$as_me:$LINENO: \$? = $ac_status" >&5
-- (exit $ac_status); } && {
-- test -z "$ac_c_werror_flag" ||
-- test ! -s conftest.err
-- } && test -s conftest.$ac_objext; then
-- { echo "$as_me:$LINENO: result: yes" >&5
--echo "${ECHO_T}yes" >&6; }
-+if ac_fn_c_try_compile "$LINENO"; then :
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
-+$as_echo "yes" >&6; }
- else
-- echo "$as_me: failed program was:" >&5
--sed 's/^/| /' conftest.$ac_ext >&5
--
-- cat >conftest.$ac_ext <<_ACEOF
--/* confdefs.h. */
--_ACEOF
--cat confdefs.h >>conftest.$ac_ext
--cat >>conftest.$ac_ext <<_ACEOF
-+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
- /* end confdefs.h. */
- #include <sys/types.h>
- #include <sys/socket.h>
-@@ -4222,45 +4256,20 @@
- return 0;
- }
- _ACEOF
--rm -f conftest.$ac_objext
--if { (ac_try="$ac_compile"
--case "(($ac_try" in
-- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-- *) ac_try_echo=$ac_try;;
--esac
--eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
-- (eval "$ac_compile") 2>conftest.er1
-- ac_status=$?
-- grep -v '^ *+' conftest.er1 >conftest.err
-- rm -f conftest.er1
-- cat conftest.err >&5
-- echo "$as_me:$LINENO: \$? = $ac_status" >&5
-- (exit $ac_status); } && {
-- test -z "$ac_c_werror_flag" ||
-- test ! -s conftest.err
-- } && test -s conftest.$ac_objext; then
-- { echo "$as_me:$LINENO: result: size_t" >&5
--echo "${ECHO_T}size_t" >&6; }
--cat >>confdefs.h <<\_ACEOF
--#define socklen_t size_t
--_ACEOF
-+if ac_fn_c_try_compile "$LINENO"; then :
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: size_t" >&5
-+$as_echo "size_t" >&6; }
-+$as_echo "#define socklen_t size_t" >>confdefs.h
-
- else
-- echo "$as_me: failed program was:" >&5
--sed 's/^/| /' conftest.$ac_ext >&5
-
--
--{ echo "$as_me:$LINENO: result: int" >&5
--echo "${ECHO_T}int" >&6; }
--cat >>confdefs.h <<\_ACEOF
--#define socklen_t int
--_ACEOF
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: int" >&5
-+$as_echo "int" >&6; }
-+$as_echo "#define socklen_t int" >>confdefs.h
-
- fi
--
- rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- fi
--
- rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-
- # ALLOW EITHER GLIB-1 OR GLIB-2 TO BE USED
-@@ -4272,7 +4281,7 @@
- # ANY SUGGESTIONS FOR A BETTER WAY OF DOING THIS WILL BE WELCOME.
- #
- # Check whether --enable-glib2 was given.
--if test "${enable_glib2+set}" = set; then
-+if test "${enable_glib2+set}" = set; then :
- enableval=$enable_glib2; enable_glib2="$enableval"
- else
- enable_glib2=yes
-@@ -4285,10 +4294,10 @@
- # PKG_CHECK_MODULES(GLIB, [glib-2.0], [:], [:])
- # Extract the first word of "pkg-config", so it can be a program name with args.
- set dummy pkg-config; ac_word=$2
--{ echo "$as_me:$LINENO: checking for $ac_word" >&5
--echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
--if test "${ac_cv_path_PKG_CONFIG+set}" = set; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
-+$as_echo_n "checking for $ac_word... " >&6; }
-+if ${ac_cv_path_PKG_CONFIG+:} false; then :
-+ $as_echo_n "(cached) " >&6
- else
- case $PKG_CONFIG in
- [\\/]* | ?:[\\/]*)
-@@ -4303,11 +4312,11 @@
- for ac_exec_ext in '' $ac_executable_extensions; do
- if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
- ac_cv_path_PKG_CONFIG="$as_dir/$ac_word$ac_exec_ext"
-- echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
-+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
- break 2
- fi
- done
--done
-+ done
- IFS=$as_save_IFS
-
- test -z "$ac_cv_path_PKG_CONFIG" && ac_cv_path_PKG_CONFIG="no"
-@@ -4316,11 +4325,11 @@
- fi
- PKG_CONFIG=$ac_cv_path_PKG_CONFIG
- if test -n "$PKG_CONFIG"; then
-- { echo "$as_me:$LINENO: result: $PKG_CONFIG" >&5
--echo "${ECHO_T}$PKG_CONFIG" >&6; }
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $PKG_CONFIG" >&5
-+$as_echo "$PKG_CONFIG" >&6; }
- else
-- { echo "$as_me:$LINENO: result: no" >&5
--echo "${ECHO_T}no" >&6; }
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-+$as_echo "no" >&6; }
- fi
-
-
-@@ -4340,10 +4349,10 @@
- # AC_MSG_ERROR(Cannot find GLIB1: Is glib-config in path?))
- # Extract the first word of "glib-config", so it can be a program name with args.
- set dummy glib-config; ac_word=$2
--{ echo "$as_me:$LINENO: checking for $ac_word" >&5
--echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
--if test "${ac_cv_path_GLIB_CONFIG+set}" = set; then
-- echo $ECHO_N "(cached) $ECHO_C" >&6
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
-+$as_echo_n "checking for $ac_word... " >&6; }
-+if ${ac_cv_path_GLIB_CONFIG+:} false; then :
-+ $as_echo_n "(cached) " >&6
- else
- case $GLIB_CONFIG in
- [\\/]* | ?:[\\/]*)
-@@ -4358,11 +4367,11 @@
- for ac_exec_ext in '' $ac_executable_extensions; do
- if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
- ac_cv_path_GLIB_CONFIG="$as_dir/$ac_word$ac_exec_ext"
-- echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
-+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
- break 2
- fi
- done
--done
-+ done
- IFS=$as_save_IFS
-
- test -z "$ac_cv_path_GLIB_CONFIG" && ac_cv_path_GLIB_CONFIG="no"
-@@ -4371,11 +4380,11 @@
- fi
- GLIB_CONFIG=$ac_cv_path_GLIB_CONFIG
- if test -n "$GLIB_CONFIG"; then
-- { echo "$as_me:$LINENO: result: $GLIB_CONFIG" >&5
--echo "${ECHO_T}$GLIB_CONFIG" >&6; }
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $GLIB_CONFIG" >&5
-+$as_echo "$GLIB_CONFIG" >&6; }
- else
-- { echo "$as_me:$LINENO: result: no" >&5
--echo "${ECHO_T}no" >&6; }
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-+$as_echo "no" >&6; }
- fi
-
-
-@@ -4398,7 +4407,7 @@
- # ALLOW ASSERTIONS TO BE TURNED ON OR OFF
- # THIS ALSO ACTIVATES DEBUGGING OR OPTIMISATION COMPILE OPTIONS
- # Check whether --enable-assert was given.
--if test "${enable_assert+set}" = set; then
-+if test "${enable_assert+set}" = set; then :
- enableval=$enable_assert; enable_assert="$enableval"
- else
- enable_assert=no
-@@ -4422,7 +4431,7 @@
-
- # ALLOW PARANOID CODE CHECKING TO BE TURNED ON OR OFF
- # Check whether --enable-paranoia was given.
--if test "${enable_paranoia+set}" = set; then
-+if test "${enable_paranoia+set}" = set; then :
- enableval=$enable_paranoia; enable_paranoia="$enableval"
- else
- enable_paranoia=no
-@@ -4445,7 +4454,7 @@
-
- # ALLOW PROFILING WITH GPROF
- # Check whether --enable-gprof was given.
--if test "${enable_gprof+set}" = set; then
-+if test "${enable_gprof+set}" = set; then :
- enableval=$enable_gprof; enable_gprof="$enableval"
- else
- enable_gprof=no
-@@ -4467,7 +4476,7 @@
-
- # ALLOW COVERAGE TESTING WITH GCOV
- # Check whether --enable-gcov was given.
--if test "${enable_gcov+set}" = set; then
-+if test "${enable_gcov+set}" = set; then :
- enableval=$enable_gcov; enable_gcof="$enableval"
- else
- enable_gcov=no
-@@ -4487,7 +4496,7 @@
-
- # FORCE LARGEFILE SUPPORT FOR 32 BIT SYSTEMS
- # Check whether --enable-largefile was given.
--if test "${enable_largefile+set}" = set; then
-+if test "${enable_largefile+set}" = set; then :
- enableval=$enable_largefile; enable_largefile="$enableval"
- else
- enable_largefile=yes
-@@ -4506,7 +4515,7 @@
-
- # ALLOW USE OF COMPILED MODELS
- # Check whether --enable-compiledmodels was given.
--if test "${enable_compiledmodels+set}" = set; then
-+if test "${enable_compiledmodels+set}" = set; then :
- enableval=$enable_compiledmodels; enable_compiledmodels="$enableval"
- else
- enable_compiledmodels=yes
-@@ -4533,7 +4542,7 @@
-
- # ALLOW INSTALLATION OF UTILITIES
- # Check whether --enable-utilities was given.
--if test "${enable_utilities+set}" = set; then
-+if test "${enable_utilities+set}" = set; then :
- enableval=$enable_utilities; enable_utilities="$enableval"
- else
- enable_utilities=yes
-@@ -4560,7 +4569,7 @@
-
- # ALLOW DISABLING OF PTHREADS
- # Check whether --enable-pthreads was given.
--if test "${enable_pthreads+set}" = set; then
-+if test "${enable_pthreads+set}" = set; then :
- enableval=$enable_pthreads; enable_pthreads="$enableval"
- else
- enable_pthreads=yes
-@@ -4610,12 +4619,13 @@
- case $ac_val in #(
- *${as_nl}*)
- case $ac_var in #(
-- *_cv_*) { echo "$as_me:$LINENO: WARNING: Cache variable $ac_var contains a newline." >&5
--echo "$as_me: WARNING: Cache variable $ac_var contains a newline." >&2;} ;;
-+ *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5
-+$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
- esac
- case $ac_var in #(
- _ | IFS | as_nl) ;; #(
-- *) $as_unset $ac_var ;;
-+ BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
-+ *) { eval $ac_var=; unset $ac_var;} ;;
- esac ;;
- esac
- done
-@@ -4623,8 +4633,8 @@
- (set) 2>&1 |
- case $as_nl`(ac_space=' '; set) 2>&1` in #(
- *${as_nl}ac_space=\ *)
-- # `set' does not quote correctly, so add quotes (double-quote
-- # substitution turns \\\\ into \\, and sed turns \\ into \).
-+ # `set' does not quote correctly, so add quotes: double-quote
-+ # substitution turns \\\\ into \\, and sed turns \\ into \.
- sed -n \
- "s/'/'\\\\''/g;
- s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p"
-@@ -4646,13 +4656,24 @@
- :end' >>confcache
- if diff "$cache_file" confcache >/dev/null 2>&1; then :; else
- if test -w "$cache_file"; then
-- test "x$cache_file" != "x/dev/null" &&
-- { echo "$as_me:$LINENO: updating cache $cache_file" >&5
--echo "$as_me: updating cache $cache_file" >&6;}
-- cat confcache >$cache_file
-+ if test "x$cache_file" != "x/dev/null"; then
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: updating cache $cache_file" >&5
-+$as_echo "$as_me: updating cache $cache_file" >&6;}
-+ if test ! -f "$cache_file" || test -h "$cache_file"; then
-+ cat confcache >"$cache_file"
-+ else
-+ case $cache_file in #(
-+ */* | ?:*)
-+ mv -f confcache "$cache_file"$$ &&
-+ mv -f "$cache_file"$$ "$cache_file" ;; #(
-+ *)
-+ mv -f confcache "$cache_file" ;;
-+ esac
-+ fi
-+ fi
- else
-- { echo "$as_me:$LINENO: not updating unwritable cache $cache_file" >&5
--echo "$as_me: not updating unwritable cache $cache_file" >&6;}
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: not updating unwritable cache $cache_file" >&5
-+$as_echo "$as_me: not updating unwritable cache $cache_file" >&6;}
- fi
- fi
- rm -f confcache
-@@ -4669,6 +4690,12 @@
- # take arguments), then branch to the quote section. Otherwise,
- # look for a macro that doesn't take arguments.
- ac_script='
-+:mline
-+/\\$/{
-+ N
-+ s,\\\n,,
-+ b mline
-+}
- t clear
- :clear
- s/^[ ]*#[ ]*define[ ][ ]*\([^ (][^ (]*([^)]*)\)[ ]*\(.*\)/-D\1=\2/g
-@@ -4695,27 +4722,46 @@
-
- ac_libobjs=
- ac_ltlibobjs=
-+U=
- for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue
- # 1. Remove the extension, and $U if already installed.
- ac_script='s/\$U\././;s/\.o$//;s/\.obj$//'
-- ac_i=`echo "$ac_i" | sed "$ac_script"`
-+ ac_i=`$as_echo "$ac_i" | sed "$ac_script"`
- # 2. Prepend LIBOBJDIR. When used with automake>=1.10 LIBOBJDIR
- # will be set to the directory where LIBOBJS objects are built.
-- ac_libobjs="$ac_libobjs \${LIBOBJDIR}$ac_i\$U.$ac_objext"
-- ac_ltlibobjs="$ac_ltlibobjs \${LIBOBJDIR}$ac_i"'$U.lo'
-+ as_fn_append ac_libobjs " \${LIBOBJDIR}$ac_i\$U.$ac_objext"
-+ as_fn_append ac_ltlibobjs " \${LIBOBJDIR}$ac_i"'$U.lo'
- done
- LIBOBJS=$ac_libobjs
-
- LTLIBOBJS=$ac_ltlibobjs
-
-
-+ if test -n "$EXEEXT"; then
-+ am__EXEEXT_TRUE=
-+ am__EXEEXT_FALSE='#'
-+else
-+ am__EXEEXT_TRUE='#'
-+ am__EXEEXT_FALSE=
-+fi
-+
-+if test -z "${AMDEP_TRUE}" && test -z "${AMDEP_FALSE}"; then
-+ as_fn_error $? "conditional \"AMDEP\" was never defined.
-+Usually this means the macro was only invoked conditionally." "$LINENO" 5
-+fi
-+if test -z "${am__fastdepCC_TRUE}" && test -z "${am__fastdepCC_FALSE}"; then
-+ as_fn_error $? "conditional \"am__fastdepCC\" was never defined.
-+Usually this means the macro was only invoked conditionally." "$LINENO" 5
-+fi
-
--: ${CONFIG_STATUS=./config.status}
-+: "${CONFIG_STATUS=./config.status}"
-+ac_write_fail=0
- ac_clean_files_save=$ac_clean_files
- ac_clean_files="$ac_clean_files $CONFIG_STATUS"
--{ echo "$as_me:$LINENO: creating $CONFIG_STATUS" >&5
--echo "$as_me: creating $CONFIG_STATUS" >&6;}
--cat >$CONFIG_STATUS <<_ACEOF
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: creating $CONFIG_STATUS" >&5
-+$as_echo "$as_me: creating $CONFIG_STATUS" >&6;}
-+as_write_fail=0
-+cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1
- #! $SHELL
- # Generated by $as_me.
- # Run this file to recreate the current configuration.
-@@ -4725,59 +4771,79 @@
- debug=false
- ac_cs_recheck=false
- ac_cs_silent=false
--SHELL=\${CONFIG_SHELL-$SHELL}
--_ACEOF
-
--cat >>$CONFIG_STATUS <<\_ACEOF
--## --------------------- ##
-+SHELL=\${CONFIG_SHELL-$SHELL}
-+export SHELL
-+_ASEOF
-+cat >>$CONFIG_STATUS <<\_ASEOF || as_write_fail=1
-+## -------------------- ##
- ## M4sh Initialization. ##
--## --------------------- ##
-+## -------------------- ##
-
- # Be more Bourne compatible
- DUALCASE=1; export DUALCASE # for MKS sh
--if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
-+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
- emulate sh
- NULLCMD=:
-- # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
-+ # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
- # is contrary to our usage. Disable this feature.
- alias -g '${1+"$@"}'='"$@"'
- setopt NO_GLOB_SUBST
- else
-- case `(set -o) 2>/dev/null` in
-- *posix*) set -o posix ;;
-+ case `(set -o) 2>/dev/null` in #(
-+ *posix*) :
-+ set -o posix ;; #(
-+ *) :
-+ ;;
- esac
--
- fi
-
-
--
--
--# PATH needs CR
--# Avoid depending upon Character Ranges.
--as_cr_letters='abcdefghijklmnopqrstuvwxyz'
--as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
--as_cr_Letters=$as_cr_letters$as_cr_LETTERS
--as_cr_digits='0123456789'
--as_cr_alnum=$as_cr_Letters$as_cr_digits
--
--# The user is always right.
--if test "${PATH_SEPARATOR+set}" != set; then
-- echo "#! /bin/sh" >conf$$.sh
-- echo "exit 0" >>conf$$.sh
-- chmod +x conf$$.sh
-- if (PATH="/nonexistent;."; conf$$.sh) >/dev/null 2>&1; then
-- PATH_SEPARATOR=';'
-+as_nl='
-+'
-+export as_nl
-+# Printing a long string crashes Solaris 7 /usr/bin/printf.
-+as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
-+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
-+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
-+# Prefer a ksh shell builtin over an external printf program on Solaris,
-+# but without wasting forks for bash or zsh.
-+if test -z "$BASH_VERSION$ZSH_VERSION" \
-+ && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
-+ as_echo='print -r --'
-+ as_echo_n='print -rn --'
-+elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
-+ as_echo='printf %s\n'
-+ as_echo_n='printf %s'
-+else
-+ if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
-+ as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
-+ as_echo_n='/usr/ucb/echo -n'
- else
-- PATH_SEPARATOR=:
-+ as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
-+ as_echo_n_body='eval
-+ arg=$1;
-+ case $arg in #(
-+ *"$as_nl"*)
-+ expr "X$arg" : "X\\(.*\\)$as_nl";
-+ arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
-+ esac;
-+ expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl"
-+ '
-+ export as_echo_n_body
-+ as_echo_n='sh -c $as_echo_n_body as_echo'
- fi
-- rm -f conf$$.sh
-+ export as_echo_body
-+ as_echo='sh -c $as_echo_body as_echo'
- fi
-
--# Support unset when possible.
--if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then
-- as_unset=unset
--else
-- as_unset=false
-+# The user is always right.
-+if test "${PATH_SEPARATOR+set}" != set; then
-+ PATH_SEPARATOR=:
-+ (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
-+ (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
-+ PATH_SEPARATOR=';'
-+ }
- fi
-
-
-@@ -4786,12 +4852,11 @@
- # there to prevent editors from complaining about space-tab.
- # (If _AS_PATH_WALK were called with IFS unset, it would disable word
- # splitting by setting IFS to empty value.)
--as_nl='
--'
- IFS=" "" $as_nl"
-
- # Find who we are. Look in the path if we contain no directory separator.
--case $0 in
-+as_myself=
-+case $0 in #((
- *[\\/]* ) as_myself=$0 ;;
- *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
- for as_dir in $PATH
-@@ -4799,7 +4864,7 @@
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
- test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
--done
-+ done
- IFS=$as_save_IFS
-
- ;;
-@@ -4810,32 +4875,111 @@
- as_myself=$0
- fi
- if test ! -f "$as_myself"; then
-- echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
-- { (exit 1); exit 1; }
-+ $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
-+ exit 1
- fi
-
--# Work around bugs in pre-3.0 UWIN ksh.
--for as_var in ENV MAIL MAILPATH
--do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
-+# Unset variables that we do not need and which cause bugs (e.g. in
-+# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1"
-+# suppresses any "Segmentation fault" message there. '((' could
-+# trigger a bug in pdksh 5.2.14.
-+for as_var in BASH_ENV ENV MAIL MAILPATH
-+do eval test x\${$as_var+set} = xset \
-+ && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
- done
- PS1='$ '
- PS2='> '
- PS4='+ '
-
- # NLS nuisances.
--for as_var in \
-- LANG LANGUAGE LC_ADDRESS LC_ALL LC_COLLATE LC_CTYPE LC_IDENTIFICATION \
-- LC_MEASUREMENT LC_MESSAGES LC_MONETARY LC_NAME LC_NUMERIC LC_PAPER \
-- LC_TELEPHONE LC_TIME
--do
-- if (set +x; test -z "`(eval $as_var=C; export $as_var) 2>&1`"); then
-- eval $as_var=C; export $as_var
-- else
-- ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
-- fi
--done
-+LC_ALL=C
-+export LC_ALL
-+LANGUAGE=C
-+export LANGUAGE
-+
-+# CDPATH.
-+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
-+
-+
-+# as_fn_error STATUS ERROR [LINENO LOG_FD]
-+# ----------------------------------------
-+# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
-+# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
-+# script with STATUS, using 1 if that was 0.
-+as_fn_error ()
-+{
-+ as_status=$1; test $as_status -eq 0 && as_status=1
-+ if test "$4"; then
-+ as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
-+ $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
-+ fi
-+ $as_echo "$as_me: error: $2" >&2
-+ as_fn_exit $as_status
-+} # as_fn_error
-+
-+
-+# as_fn_set_status STATUS
-+# -----------------------
-+# Set $? to STATUS, without forking.
-+as_fn_set_status ()
-+{
-+ return $1
-+} # as_fn_set_status
-+
-+# as_fn_exit STATUS
-+# -----------------
-+# Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
-+as_fn_exit ()
-+{
-+ set +e
-+ as_fn_set_status $1
-+ exit $1
-+} # as_fn_exit
-+
-+# as_fn_unset VAR
-+# ---------------
-+# Portably unset VAR.
-+as_fn_unset ()
-+{
-+ { eval $1=; unset $1;}
-+}
-+as_unset=as_fn_unset
-+# as_fn_append VAR VALUE
-+# ----------------------
-+# Append the text in VALUE to the end of the definition contained in VAR. Take
-+# advantage of any shell optimizations that allow amortized linear growth over
-+# repeated appends, instead of the typical quadratic growth present in naive
-+# implementations.
-+if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
-+ eval 'as_fn_append ()
-+ {
-+ eval $1+=\$2
-+ }'
-+else
-+ as_fn_append ()
-+ {
-+ eval $1=\$$1\$2
-+ }
-+fi # as_fn_append
-+
-+# as_fn_arith ARG...
-+# ------------------
-+# Perform arithmetic evaluation on the ARGs, and store the result in the
-+# global $as_val. Take advantage of shells that can avoid forks. The arguments
-+# must be portable across $(()) and expr.
-+if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
-+ eval 'as_fn_arith ()
-+ {
-+ as_val=$(( $* ))
-+ }'
-+else
-+ as_fn_arith ()
-+ {
-+ as_val=`expr "$@" || test $? -eq 1`
-+ }
-+fi # as_fn_arith
-+
-
--# Required to use basename.
- if expr a : '\(a\)' >/dev/null 2>&1 &&
- test "X`expr 00001 : '.*\(...\)'`" = X001; then
- as_expr=expr
-@@ -4849,13 +4993,17 @@
- as_basename=false
- fi
-
-+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
-+ as_dirname=dirname
-+else
-+ as_dirname=false
-+fi
-
--# Name of the executable.
- as_me=`$as_basename -- "$0" ||
- $as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
- X"$0" : 'X\(//\)$' \| \
- X"$0" : 'X\(/\)' \| . 2>/dev/null ||
--echo X/"$0" |
-+$as_echo X/"$0" |
- sed '/^.*\/\([^/][^/]*\)\/*$/{
- s//\1/
- q
-@@ -4870,87 +5018,35 @@
- }
- s/.*/./; q'`
-
--# CDPATH.
--$as_unset CDPATH
--
--
--
-- as_lineno_1=$LINENO
-- as_lineno_2=$LINENO
-- test "x$as_lineno_1" != "x$as_lineno_2" &&
-- test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || {
--
-- # Create $as_me.lineno as a copy of $as_myself, but with $LINENO
-- # uniformly replaced by the line number. The first 'sed' inserts a
-- # line-number line after each line using $LINENO; the second 'sed'
-- # does the real work. The second script uses 'N' to pair each
-- # line-number line with the line containing $LINENO, and appends
-- # trailing '-' during substitution so that $LINENO is not a special
-- # case at line end.
-- # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the
-- # scripts with optimization help from Paolo Bonzini. Blame Lee
-- # E. McMahon (1931-1989) for sed's syntax. :-)
-- sed -n '
-- p
-- /[$]LINENO/=
-- ' <$as_myself |
-- sed '
-- s/[$]LINENO.*/&-/
-- t lineno
-- b
-- :lineno
-- N
-- :loop
-- s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/
-- t loop
-- s/-\n.*//
-- ' >$as_me.lineno &&
-- chmod +x "$as_me.lineno" ||
-- { echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2
-- { (exit 1); exit 1; }; }
--
-- # Don't try to exec as it changes $[0], causing all sort of problems
-- # (the dirname of $[0] is not the place where we might find the
-- # original and so on. Autoconf is especially sensitive to this).
-- . "./$as_me.lineno"
-- # Exit status is that of the last command.
-- exit
--}
--
--
--if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
-- as_dirname=dirname
--else
-- as_dirname=false
--fi
-+# Avoid depending upon Character Ranges.
-+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
-+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
-+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
-+as_cr_digits='0123456789'
-+as_cr_alnum=$as_cr_Letters$as_cr_digits
-
- ECHO_C= ECHO_N= ECHO_T=
--case `echo -n x` in
-+case `echo -n x` in #(((((
- -n*)
-- case `echo 'x\c'` in
-+ case `echo 'xy\c'` in
- *c*) ECHO_T=' ';; # ECHO_T is single tab character.
-- *) ECHO_C='\c';;
-+ xy) ECHO_C='\c';;
-+ *) echo `echo ksh88 bug on AIX 6.1` > /dev/null
-+ ECHO_T=' ';;
- esac;;
- *)
- ECHO_N='-n';;
- esac
-
--if expr a : '\(a\)' >/dev/null 2>&1 &&
-- test "X`expr 00001 : '.*\(...\)'`" = X001; then
-- as_expr=expr
--else
-- as_expr=false
--fi
--
- rm -f conf$$ conf$$.exe conf$$.file
- if test -d conf$$.dir; then
- rm -f conf$$.dir/conf$$.file
- else
- rm -f conf$$.dir
-- mkdir conf$$.dir
-+ mkdir conf$$.dir 2>/dev/null
- fi
--echo >conf$$.file
--if ln -s conf$$.file conf$$ 2>/dev/null; then
-+if (echo >conf$$.file) 2>/dev/null; then
-+ if ln -s conf$$.file conf$$ 2>/dev/null; then
- as_ln_s='ln -s'
- # ... but there are two gotchas:
- # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
-@@ -4958,16 +5054,67 @@
- # In both cases, we have to default to `cp -p'.
- ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
- as_ln_s='cp -p'
--elif ln conf$$.file conf$$ 2>/dev/null; then
-+ elif ln conf$$.file conf$$ 2>/dev/null; then
- as_ln_s=ln
-+ else
-+ as_ln_s='cp -p'
-+ fi
- else
- as_ln_s='cp -p'
- fi
- rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
- rmdir conf$$.dir 2>/dev/null
-
-+
-+# as_fn_mkdir_p
-+# -------------
-+# Create "$as_dir" as a directory, including parents if necessary.
-+as_fn_mkdir_p ()
-+{
-+
-+ case $as_dir in #(
-+ -*) as_dir=./$as_dir;;
-+ esac
-+ test -d "$as_dir" || eval $as_mkdir_p || {
-+ as_dirs=
-+ while :; do
-+ case $as_dir in #(
-+ *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
-+ *) as_qdir=$as_dir;;
-+ esac
-+ as_dirs="'$as_qdir' $as_dirs"
-+ as_dir=`$as_dirname -- "$as_dir" ||
-+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
-+ X"$as_dir" : 'X\(//\)[^/]' \| \
-+ X"$as_dir" : 'X\(//\)$' \| \
-+ X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
-+$as_echo X"$as_dir" |
-+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
-+ s//\1/
-+ q
-+ }
-+ /^X\(\/\/\)[^/].*/{
-+ s//\1/
-+ q
-+ }
-+ /^X\(\/\/\)$/{
-+ s//\1/
-+ q
-+ }
-+ /^X\(\/\).*/{
-+ s//\1/
-+ q
-+ }
-+ s/.*/./; q'`
-+ test -d "$as_dir" && break
-+ done
-+ test -z "$as_dirs" || eval "mkdir $as_dirs"
-+ } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
-+
-+
-+} # as_fn_mkdir_p
- if mkdir -p . 2>/dev/null; then
-- as_mkdir_p=:
-+ as_mkdir_p='mkdir -p "$as_dir"'
- else
- test -d ./-p && rmdir ./-p
- as_mkdir_p=false
-@@ -4986,10 +5133,10 @@
- if test -d "$1"; then
- test -d "$1/.";
- else
-- case $1 in
-+ case $1 in #(
- -*)set "./$1";;
- esac;
-- case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in
-+ case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #((
- ???[sx]*):;;*)false;;esac;fi
- '\'' sh
- '
-@@ -5004,13 +5151,19 @@
-
-
- exec 6>&1
-+## ----------------------------------- ##
-+## Main body of $CONFIG_STATUS script. ##
-+## ----------------------------------- ##
-+_ASEOF
-+test $as_write_fail = 0 && chmod +x $CONFIG_STATUS || ac_write_fail=1
-
--# Save the log message, to keep $[0] and so on meaningful, and to
-+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
-+# Save the log message, to keep $0 and so on meaningful, and to
- # report actual input values of CONFIG_FILES etc. instead of their
- # values after options handling.
- ac_log="
- This file was extended by $as_me, which was
--generated by GNU Autoconf 2.61. Invocation command line was
-+generated by GNU Autoconf 2.68. Invocation command line was
-
- CONFIG_FILES = $CONFIG_FILES
- CONFIG_HEADERS = $CONFIG_HEADERS
-@@ -5023,22 +5176,32 @@
-
- _ACEOF
-
--cat >>$CONFIG_STATUS <<_ACEOF
-+case $ac_config_files in *"
-+"*) set x $ac_config_files; shift; ac_config_files=$*;;
-+esac
-+
-+
-+
-+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
- # Files that config.status was made for.
- config_files="$ac_config_files"
-+config_commands="$ac_config_commands"
-
- _ACEOF
-
--cat >>$CONFIG_STATUS <<\_ACEOF
-+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
- ac_cs_usage="\
--\`$as_me' instantiates files from templates according to the
--current configuration.
-+\`$as_me' instantiates files and other configuration actions
-+from templates according to the current configuration. Unless the files
-+and actions are specified as TAGs, all are instantiated by default.
-
--Usage: $0 [OPTIONS] [FILE]...
-+Usage: $0 [OPTION]... [TAG]...
-
- -h, --help print this help, then exit
- -V, --version print version number and configuration settings, then exit
-- -q, --quiet do not print progress messages
-+ --config print configuration, then exit
-+ -q, --quiet, --silent
-+ do not print progress messages
- -d, --debug don't remove temporary files
- --recheck update $as_me by reconfiguring in the same conditions
- --file=FILE[:TEMPLATE]
-@@ -5047,36 +5210,47 @@
- Configuration files:
- $config_files
-
--Report bugs to <bug-autoconf at gnu.org>."
-+Configuration commands:
-+$config_commands
-+
-+Report bugs to the package provider."
-
- _ACEOF
--cat >>$CONFIG_STATUS <<_ACEOF
-+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
-+ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
- ac_cs_version="\\
- config.status
--configured by $0, generated by GNU Autoconf 2.61,
-- with options \\"`echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`\\"
-+configured by $0, generated by GNU Autoconf 2.68,
-+ with options \\"\$ac_cs_config\\"
-
--Copyright (C) 2006 Free Software Foundation, Inc.
-+Copyright (C) 2010 Free Software Foundation, Inc.
- This config.status script is free software; the Free Software Foundation
- gives unlimited permission to copy, distribute and modify it."
-
- ac_pwd='$ac_pwd'
- srcdir='$srcdir'
- INSTALL='$INSTALL'
-+MKDIR_P='$MKDIR_P'
-+AWK='$AWK'
-+test -n "\$AWK" || AWK=awk
- _ACEOF
-
--cat >>$CONFIG_STATUS <<\_ACEOF
--# If no file are specified by the user, then we need to provide default
--# value. By we need to know if files were specified by the user.
-+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
-+# The default lists apply if the user does not specify any file.
- ac_need_defaults=:
- while test $# != 0
- do
- case $1 in
-- --*=*)
-+ --*=?*)
- ac_option=`expr "X$1" : 'X\([^=]*\)='`
- ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'`
- ac_shift=:
- ;;
-+ --*=)
-+ ac_option=`expr "X$1" : 'X\([^=]*\)='`
-+ ac_optarg=
-+ ac_shift=:
-+ ;;
- *)
- ac_option=$1
- ac_optarg=$2
-@@ -5089,25 +5263,30 @@
- -recheck | --recheck | --rechec | --reche | --rech | --rec | --re | --r)
- ac_cs_recheck=: ;;
- --version | --versio | --versi | --vers | --ver | --ve | --v | -V )
-- echo "$ac_cs_version"; exit ;;
-+ $as_echo "$ac_cs_version"; exit ;;
-+ --config | --confi | --conf | --con | --co | --c )
-+ $as_echo "$ac_cs_config"; exit ;;
- --debug | --debu | --deb | --de | --d | -d )
- debug=: ;;
- --file | --fil | --fi | --f )
- $ac_shift
-- CONFIG_FILES="$CONFIG_FILES $ac_optarg"
-+ case $ac_optarg in
-+ *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
-+ '') as_fn_error $? "missing file argument" ;;
-+ esac
-+ as_fn_append CONFIG_FILES " '$ac_optarg'"
- ac_need_defaults=false;;
- --he | --h | --help | --hel | -h )
-- echo "$ac_cs_usage"; exit ;;
-+ $as_echo "$ac_cs_usage"; exit ;;
- -q | -quiet | --quiet | --quie | --qui | --qu | --q \
- | -silent | --silent | --silen | --sile | --sil | --si | --s)
- ac_cs_silent=: ;;
-
- # This is an error.
-- -*) { echo "$as_me: error: unrecognized option: $1
--Try \`$0 --help' for more information." >&2
-- { (exit 1); exit 1; }; } ;;
-+ -*) as_fn_error $? "unrecognized option: \`$1'
-+Try \`$0 --help' for more information." ;;
-
-- *) ac_config_targets="$ac_config_targets $1"
-+ *) as_fn_append ac_config_targets " $1"
- ac_need_defaults=false ;;
-
- esac
-@@ -5122,35 +5301,43 @@
- fi
-
- _ACEOF
--cat >>$CONFIG_STATUS <<_ACEOF
-+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
- if \$ac_cs_recheck; then
-- echo "running CONFIG_SHELL=$SHELL $SHELL $0 "$ac_configure_args \$ac_configure_extra_args " --no-create --no-recursion" >&6
-- CONFIG_SHELL=$SHELL
-+ set X '$SHELL' '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion
-+ shift
-+ \$as_echo "running CONFIG_SHELL=$SHELL \$*" >&6
-+ CONFIG_SHELL='$SHELL'
- export CONFIG_SHELL
-- exec $SHELL "$0"$ac_configure_args \$ac_configure_extra_args --no-create --no-recursion
-+ exec "\$@"
- fi
-
- _ACEOF
--cat >>$CONFIG_STATUS <<\_ACEOF
-+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
- exec 5>>config.log
- {
- echo
- sed 'h;s/./-/g;s/^.../## /;s/...$/ ##/;p;x;p;x' <<_ASBOX
- ## Running $as_me. ##
- _ASBOX
-- echo "$ac_log"
-+ $as_echo "$ac_log"
- } >&5
-
- _ACEOF
--cat >>$CONFIG_STATUS <<_ACEOF
-+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
-+#
-+# INIT-COMMANDS
-+#
-+AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"
-+
- _ACEOF
-
--cat >>$CONFIG_STATUS <<\_ACEOF
-+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
-
- # Handling of arguments.
- for ac_config_target in $ac_config_targets
- do
- case $ac_config_target in
-+ "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
- "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
- "doc/Makefile") CONFIG_FILES="$CONFIG_FILES doc/Makefile" ;;
- "doc/man/Makefile") CONFIG_FILES="$CONFIG_FILES doc/man/Makefile" ;;
-@@ -5176,9 +5363,7 @@
- "test/data/cdna/Makefile") CONFIG_FILES="$CONFIG_FILES test/data/cdna/Makefile" ;;
- "test/data/protein/Makefile") CONFIG_FILES="$CONFIG_FILES test/data/protein/Makefile" ;;
-
-- *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5
--echo "$as_me: error: invalid argument: $ac_config_target" >&2;}
-- { (exit 1); exit 1; }; };;
-+ *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5;;
- esac
- done
-
-@@ -5189,6 +5374,7 @@
- # bizarre bug on SunOS 4.1.3.
- if $ac_need_defaults; then
- test "${CONFIG_FILES+set}" = set || CONFIG_FILES=$config_files
-+ test "${CONFIG_COMMANDS+set}" = set || CONFIG_COMMANDS=$config_commands
- fi
-
- # Have a temporary directory for convenience. Make it in the build tree
-@@ -5199,188 +5385,194 @@
- # after its creation but before its name has been assigned to `$tmp'.
- $debug ||
- {
-- tmp=
-+ tmp= ac_tmp=
- trap 'exit_status=$?
-- { test -z "$tmp" || test ! -d "$tmp" || rm -fr "$tmp"; } && exit $exit_status
-+ : "${ac_tmp:=$tmp}"
-+ { test ! -d "$ac_tmp" || rm -fr "$ac_tmp"; } && exit $exit_status
- ' 0
-- trap '{ (exit 1); exit 1; }' 1 2 13 15
-+ trap 'as_fn_exit 1' 1 2 13 15
- }
- # Create a (secure) tmp directory for tmp files.
-
- {
- tmp=`(umask 077 && mktemp -d "./confXXXXXX") 2>/dev/null` &&
-- test -n "$tmp" && test -d "$tmp"
-+ test -d "$tmp"
- } ||
- {
- tmp=./conf$$-$RANDOM
- (umask 077 && mkdir "$tmp")
--} ||
--{
-- echo "$me: cannot create a temporary directory in ." >&2
-- { (exit 1); exit 1; }
--}
--
--#
--# Set up the sed scripts for CONFIG_FILES section.
--#
-+} || as_fn_error $? "cannot create a temporary directory in ." "$LINENO" 5
-+ac_tmp=$tmp
-
--# No need to generate the scripts if there are no CONFIG_FILES.
--# This happens for instance when ./config.status config.h
-+# Set up the scripts for CONFIG_FILES section.
-+# No need to generate them if there are no CONFIG_FILES.
-+# This happens for instance with `./config.status config.h'.
- if test -n "$CONFIG_FILES"; then
-
--_ACEOF
-
-+ac_cr=`echo X | tr X '\015'`
-+# On cygwin, bash can eat \r inside `` if the user requested igncr.
-+# But we know of no other shell where ac_cr would be empty at this
-+# point, so we can use a bashism as a fallback.
-+if test "x$ac_cr" = x; then
-+ eval ac_cr=\$\'\\r\'
-+fi
-+ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' </dev/null 2>/dev/null`
-+if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then
-+ ac_cs_awk_cr='\\r'
-+else
-+ ac_cs_awk_cr=$ac_cr
-+fi
-+
-+echo 'BEGIN {' >"$ac_tmp/subs1.awk" &&
-+_ACEOF
-
-
-+{
-+ echo "cat >conf$$subs.awk <<_ACEOF" &&
-+ echo "$ac_subst_vars" | sed 's/.*/&!$&$ac_delim/' &&
-+ echo "_ACEOF"
-+} >conf$$subs.sh ||
-+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
-+ac_delim_num=`echo "$ac_subst_vars" | grep -c '^'`
- ac_delim='%!_!# '
- for ac_last_try in false false false false false :; do
-- cat >conf$$subs.sed <<_ACEOF
--SHELL!$SHELL$ac_delim
--PATH_SEPARATOR!$PATH_SEPARATOR$ac_delim
--PACKAGE_NAME!$PACKAGE_NAME$ac_delim
--PACKAGE_TARNAME!$PACKAGE_TARNAME$ac_delim
--PACKAGE_VERSION!$PACKAGE_VERSION$ac_delim
--PACKAGE_STRING!$PACKAGE_STRING$ac_delim
--PACKAGE_BUGREPORT!$PACKAGE_BUGREPORT$ac_delim
--exec_prefix!$exec_prefix$ac_delim
--prefix!$prefix$ac_delim
--program_transform_name!$program_transform_name$ac_delim
--bindir!$bindir$ac_delim
--sbindir!$sbindir$ac_delim
--libexecdir!$libexecdir$ac_delim
--datarootdir!$datarootdir$ac_delim
--datadir!$datadir$ac_delim
--sysconfdir!$sysconfdir$ac_delim
--sharedstatedir!$sharedstatedir$ac_delim
--localstatedir!$localstatedir$ac_delim
--includedir!$includedir$ac_delim
--oldincludedir!$oldincludedir$ac_delim
--docdir!$docdir$ac_delim
--infodir!$infodir$ac_delim
--htmldir!$htmldir$ac_delim
--dvidir!$dvidir$ac_delim
--pdfdir!$pdfdir$ac_delim
--psdir!$psdir$ac_delim
--libdir!$libdir$ac_delim
--localedir!$localedir$ac_delim
--mandir!$mandir$ac_delim
--DEFS!$DEFS$ac_delim
--ECHO_C!$ECHO_C$ac_delim
--ECHO_N!$ECHO_N$ac_delim
--ECHO_T!$ECHO_T$ac_delim
--LIBS!$LIBS$ac_delim
--build_alias!$build_alias$ac_delim
--host_alias!$host_alias$ac_delim
--target_alias!$target_alias$ac_delim
--INSTALL_PROGRAM!$INSTALL_PROGRAM$ac_delim
--INSTALL_SCRIPT!$INSTALL_SCRIPT$ac_delim
--INSTALL_DATA!$INSTALL_DATA$ac_delim
--PACKAGE!$PACKAGE$ac_delim
--VERSION!$VERSION$ac_delim
--ACLOCAL!$ACLOCAL$ac_delim
--AUTOCONF!$AUTOCONF$ac_delim
--AUTOMAKE!$AUTOMAKE$ac_delim
--AUTOHEADER!$AUTOHEADER$ac_delim
--MAKEINFO!$MAKEINFO$ac_delim
--SET_MAKE!$SET_MAKE$ac_delim
--CC!$CC$ac_delim
--CFLAGS!$CFLAGS$ac_delim
--LDFLAGS!$LDFLAGS$ac_delim
--CPPFLAGS!$CPPFLAGS$ac_delim
--ac_ct_CC!$ac_ct_CC$ac_delim
--EXEEXT!$EXEEXT$ac_delim
--OBJEXT!$OBJEXT$ac_delim
--CPP!$CPP$ac_delim
--GREP!$GREP$ac_delim
--EGREP!$EGREP$ac_delim
--build!$build$ac_delim
--build_cpu!$build_cpu$ac_delim
--build_vendor!$build_vendor$ac_delim
--build_os!$build_os$ac_delim
--host!$host$ac_delim
--host_cpu!$host_cpu$ac_delim
--host_vendor!$host_vendor$ac_delim
--host_os!$host_os$ac_delim
--source_root_dir!$source_root_dir$ac_delim
--PKG_CONFIG!$PKG_CONFIG$ac_delim
--GLIB_CONFIG!$GLIB_CONFIG$ac_delim
--glib_libs!$glib_libs$ac_delim
--glib_cflags!$glib_cflags$ac_delim
--codegen_extra_sources!$codegen_extra_sources$ac_delim
--codegen_extra_ldadd!$codegen_extra_ldadd$ac_delim
--installed_util_list!$installed_util_list$ac_delim
--use_pthreads!$use_pthreads$ac_delim
--LIBOBJS!$LIBOBJS$ac_delim
--LTLIBOBJS!$LTLIBOBJS$ac_delim
--_ACEOF
-+ . ./conf$$subs.sh ||
-+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
-
-- if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed | grep -c X` = 77; then
-+ ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X`
-+ if test $ac_delim_n = $ac_delim_num; then
- break
- elif $ac_last_try; then
-- { { echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5
--echo "$as_me: error: could not make $CONFIG_STATUS" >&2;}
-- { (exit 1); exit 1; }; }
-+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
- else
- ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
- fi
- done
-+rm -f conf$$subs.sh
-
--ac_eof=`sed -n '/^CEOF[0-9]*$/s/CEOF/0/p' conf$$subs.sed`
--if test -n "$ac_eof"; then
-- ac_eof=`echo "$ac_eof" | sort -nru | sed 1q`
-- ac_eof=`expr $ac_eof + 1`
--fi
--
--cat >>$CONFIG_STATUS <<_ACEOF
--cat >"\$tmp/subs-1.sed" <<\CEOF$ac_eof
--/@[a-zA-Z_][a-zA-Z_0-9]*@/!b end
--_ACEOF
--sed '
--s/[,\\&]/\\&/g; s/@/@|#_!!_#|/g
--s/^/s,@/; s/!/@,|#_!!_#|/
--:n
--t n
--s/'"$ac_delim"'$/,g/; t
--s/$/\\/; p
--N; s/^.*\n//; s/[,\\&]/\\&/g; s/@/@|#_!!_#|/g; b n
--' >>$CONFIG_STATUS <conf$$subs.sed
--rm -f conf$$subs.sed
--cat >>$CONFIG_STATUS <<_ACEOF
--:end
--s/|#_!!_#|//g
--CEOF$ac_eof
-+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
-+cat >>"\$ac_tmp/subs1.awk" <<\\_ACAWK &&
- _ACEOF
-+sed -n '
-+h
-+s/^/S["/; s/!.*/"]=/
-+p
-+g
-+s/^[^!]*!//
-+:repl
-+t repl
-+s/'"$ac_delim"'$//
-+t delim
-+:nl
-+h
-+s/\(.\{148\}\)..*/\1/
-+t more1
-+s/["\\]/\\&/g; s/^/"/; s/$/\\n"\\/
-+p
-+n
-+b repl
-+:more1
-+s/["\\]/\\&/g; s/^/"/; s/$/"\\/
-+p
-+g
-+s/.\{148\}//
-+t nl
-+:delim
-+h
-+s/\(.\{148\}\)..*/\1/
-+t more2
-+s/["\\]/\\&/g; s/^/"/; s/$/"/
-+p
-+b
-+:more2
-+s/["\\]/\\&/g; s/^/"/; s/$/"\\/
-+p
-+g
-+s/.\{148\}//
-+t delim
-+' <conf$$subs.awk | sed '
-+/^[^""]/{
-+ N
-+ s/\n//
-+}
-+' >>$CONFIG_STATUS || ac_write_fail=1
-+rm -f conf$$subs.awk
-+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
-+_ACAWK
-+cat >>"\$ac_tmp/subs1.awk" <<_ACAWK &&
-+ for (key in S) S_is_set[key] = 1
-+ FS = ""
-+
-+}
-+{
-+ line = $ 0
-+ nfields = split(line, field, "@")
-+ substed = 0
-+ len = length(field[1])
-+ for (i = 2; i < nfields; i++) {
-+ key = field[i]
-+ keylen = length(key)
-+ if (S_is_set[key]) {
-+ value = S[key]
-+ line = substr(line, 1, len) "" value "" substr(line, len + keylen + 3)
-+ len += length(value) + length(field[++i])
-+ substed = 1
-+ } else
-+ len += 1 + keylen
-+ }
-+
-+ print line
-+}
-
-+_ACAWK
-+_ACEOF
-+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
-+if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then
-+ sed "s/$ac_cr\$//; s/$ac_cr/$ac_cs_awk_cr/g"
-+else
-+ cat
-+fi < "$ac_tmp/subs1.awk" > "$ac_tmp/subs.awk" \
-+ || as_fn_error $? "could not setup config files machinery" "$LINENO" 5
-+_ACEOF
-
--# VPATH may cause trouble with some makes, so we remove $(srcdir),
--# ${srcdir} and @srcdir@ from VPATH if srcdir is ".", strip leading and
-+# VPATH may cause trouble with some makes, so we remove sole $(srcdir),
-+# ${srcdir} and @srcdir@ entries from VPATH if srcdir is ".", strip leading and
- # trailing colons and then remove the whole line if VPATH becomes empty
- # (actually we leave an empty line to preserve line numbers).
- if test "x$srcdir" = x.; then
-- ac_vpsub='/^[ ]*VPATH[ ]*=/{
--s/:*\$(srcdir):*/:/
--s/:*\${srcdir}:*/:/
--s/:*@srcdir@:*/:/
--s/^\([^=]*=[ ]*\):*/\1/
-+ ac_vpsub='/^[ ]*VPATH[ ]*=[ ]*/{
-+h
-+s///
-+s/^/:/
-+s/[ ]*$/:/
-+s/:\$(srcdir):/:/g
-+s/:\${srcdir}:/:/g
-+s/:@srcdir@:/:/g
-+s/^:*//
- s/:*$//
-+x
-+s/\(=[ ]*\).*/\1/
-+G
-+s/\n//
- s/^[^=]*=[ ]*$//
- }'
- fi
-
--cat >>$CONFIG_STATUS <<\_ACEOF
-+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
- fi # test -n "$CONFIG_FILES"
-
-
--for ac_tag in :F $CONFIG_FILES
-+eval set X " :F $CONFIG_FILES :C $CONFIG_COMMANDS"
-+shift
-+for ac_tag
- do
- case $ac_tag in
- :[FHLC]) ac_mode=$ac_tag; continue;;
- esac
- case $ac_mode$ac_tag in
- :[FHL]*:*);;
-- :L* | :C*:*) { { echo "$as_me:$LINENO: error: Invalid tag $ac_tag." >&5
--echo "$as_me: error: Invalid tag $ac_tag." >&2;}
-- { (exit 1); exit 1; }; };;
-+ :L* | :C*:*) as_fn_error $? "invalid tag \`$ac_tag'" "$LINENO" 5;;
- :[FH]-) ac_tag=-:-;;
- :[FH]*) ac_tag=$ac_tag:$ac_tag.in;;
- esac
-@@ -5399,7 +5591,7 @@
- for ac_f
- do
- case $ac_f in
-- -) ac_f="$tmp/stdin";;
-+ -) ac_f="$ac_tmp/stdin";;
- *) # Look for the file first in the build tree, then in the source tree
- # (if the path is not absolute). The absolute path cannot be DOS-style,
- # because $ac_f cannot contain `:'.
-@@ -5408,26 +5600,34 @@
- [\\/$]*) false;;
- *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";;
- esac ||
-- { { echo "$as_me:$LINENO: error: cannot find input file: $ac_f" >&5
--echo "$as_me: error: cannot find input file: $ac_f" >&2;}
-- { (exit 1); exit 1; }; };;
-+ as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5;;
- esac
-- ac_file_inputs="$ac_file_inputs $ac_f"
-+ case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac
-+ as_fn_append ac_file_inputs " '$ac_f'"
- done
-
- # Let's still pretend it is `configure' which instantiates (i.e., don't
- # use $as_me), people would be surprised to read:
- # /* config.h. Generated by config.status. */
-- configure_input="Generated from "`IFS=:
-- echo $* | sed 's|^[^:]*/||;s|:[^:]*/|, |g'`" by configure."
-+ configure_input='Generated from '`
-+ $as_echo "$*" | sed 's|^[^:]*/||;s|:[^:]*/|, |g'
-+ `' by configure.'
- if test x"$ac_file" != x-; then
- configure_input="$ac_file. $configure_input"
-- { echo "$as_me:$LINENO: creating $ac_file" >&5
--echo "$as_me: creating $ac_file" >&6;}
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: creating $ac_file" >&5
-+$as_echo "$as_me: creating $ac_file" >&6;}
- fi
-+ # Neutralize special characters interpreted by sed in replacement strings.
-+ case $configure_input in #(
-+ *\&* | *\|* | *\\* )
-+ ac_sed_conf_input=`$as_echo "$configure_input" |
-+ sed 's/[\\\\&|]/\\\\&/g'`;; #(
-+ *) ac_sed_conf_input=$configure_input;;
-+ esac
-
- case $ac_tag in
-- *:-:* | *:-) cat >"$tmp/stdin";;
-+ *:-:* | *:-) cat >"$ac_tmp/stdin" \
-+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5 ;;
- esac
- ;;
- esac
-@@ -5437,42 +5637,7 @@
- X"$ac_file" : 'X\(//\)[^/]' \| \
- X"$ac_file" : 'X\(//\)$' \| \
- X"$ac_file" : 'X\(/\)' \| . 2>/dev/null ||
--echo X"$ac_file" |
-- sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
-- s//\1/
-- q
-- }
-- /^X\(\/\/\)[^/].*/{
-- s//\1/
-- q
-- }
-- /^X\(\/\/\)$/{
-- s//\1/
-- q
-- }
-- /^X\(\/\).*/{
-- s//\1/
-- q
-- }
-- s/.*/./; q'`
-- { as_dir="$ac_dir"
-- case $as_dir in #(
-- -*) as_dir=./$as_dir;;
-- esac
-- test -d "$as_dir" || { $as_mkdir_p && mkdir -p "$as_dir"; } || {
-- as_dirs=
-- while :; do
-- case $as_dir in #(
-- *\'*) as_qdir=`echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #(
-- *) as_qdir=$as_dir;;
-- esac
-- as_dirs="'$as_qdir' $as_dirs"
-- as_dir=`$as_dirname -- "$as_dir" ||
--$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
-- X"$as_dir" : 'X\(//\)[^/]' \| \
-- X"$as_dir" : 'X\(//\)$' \| \
-- X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
--echo X"$as_dir" |
-+$as_echo X"$ac_file" |
- sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
- s//\1/
- q
-@@ -5490,20 +5655,15 @@
- q
- }
- s/.*/./; q'`
-- test -d "$as_dir" && break
-- done
-- test -z "$as_dirs" || eval "mkdir $as_dirs"
-- } || test -d "$as_dir" || { { echo "$as_me:$LINENO: error: cannot create directory $as_dir" >&5
--echo "$as_me: error: cannot create directory $as_dir" >&2;}
-- { (exit 1); exit 1; }; }; }
-+ as_dir="$ac_dir"; as_fn_mkdir_p
- ac_builddir=.
-
- case "$ac_dir" in
- .) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
- *)
-- ac_dir_suffix=/`echo "$ac_dir" | sed 's,^\.[\\/],,'`
-+ ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'`
- # A ".." for each directory in $ac_dir_suffix.
-- ac_top_builddir_sub=`echo "$ac_dir_suffix" | sed 's,/[^\\/]*,/..,g;s,/,,'`
-+ ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
- case $ac_top_builddir_sub in
- "") ac_top_builddir_sub=. ac_top_build_prefix= ;;
- *) ac_top_build_prefix=$ac_top_builddir_sub/ ;;
-@@ -5541,14 +5701,19 @@
- [\\/$]* | ?:[\\/]* ) ac_INSTALL=$INSTALL ;;
- *) ac_INSTALL=$ac_top_build_prefix$INSTALL ;;
- esac
-+ ac_MKDIR_P=$MKDIR_P
-+ case $MKDIR_P in
-+ [\\/$]* | ?:[\\/]* ) ;;
-+ */*) ac_MKDIR_P=$ac_top_build_prefix$MKDIR_P ;;
-+ esac
- _ACEOF
-
--cat >>$CONFIG_STATUS <<\_ACEOF
-+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
- # If the template does not know about datarootdir, expand it.
- # FIXME: This hack should be removed a few years after 2.60.
- ac_datarootdir_hack=; ac_datarootdir_seen=
--
--case `sed -n '/datarootdir/ {
-+ac_sed_dataroot='
-+/datarootdir/ {
- p
- q
- }
-@@ -5556,14 +5721,14 @@
- /@docdir@/p
- /@infodir@/p
- /@localedir@/p
--/@mandir@/p
--' $ac_file_inputs` in
-+/@mandir@/p'
-+case `eval "sed -n \"\$ac_sed_dataroot\" $ac_file_inputs"` in
- *datarootdir*) ac_datarootdir_seen=yes;;
- *@datadir@*|*@docdir@*|*@infodir@*|*@localedir@*|*@mandir@*)
-- { echo "$as_me:$LINENO: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5
--echo "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&2;}
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5
-+$as_echo "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&2;}
- _ACEOF
--cat >>$CONFIG_STATUS <<_ACEOF
-+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
- ac_datarootdir_hack='
- s&@datadir@&$datadir&g
- s&@docdir@&$docdir&g
-@@ -5577,15 +5742,16 @@
- # Neutralize VPATH when `$srcdir' = `.'.
- # Shell code in configure.ac might set extrasub.
- # FIXME: do we really want to maintain this feature?
--cat >>$CONFIG_STATUS <<_ACEOF
-- sed "$ac_vpsub
-+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
-+ac_sed_extra="$ac_vpsub
- $extrasub
- _ACEOF
--cat >>$CONFIG_STATUS <<\_ACEOF
-+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
- :t
- /@[a-zA-Z_][a-zA-Z_0-9]*@/!b
--s&@configure_input@&$configure_input&;t t
-+s|@configure_input@|$ac_sed_conf_input|;t t
- s&@top_builddir@&$ac_top_builddir_sub&;t t
-+s&@top_build_prefix@&$ac_top_build_prefix&;t t
- s&@srcdir@&$ac_srcdir&;t t
- s&@abs_srcdir@&$ac_abs_srcdir&;t t
- s&@top_srcdir@&$ac_top_srcdir&;t t
-@@ -5594,36 +5760,144 @@
- s&@abs_builddir@&$ac_abs_builddir&;t t
- s&@abs_top_builddir@&$ac_abs_top_builddir&;t t
- s&@INSTALL@&$ac_INSTALL&;t t
-+s&@MKDIR_P@&$ac_MKDIR_P&;t t
- $ac_datarootdir_hack
--" $ac_file_inputs | sed -f "$tmp/subs-1.sed" >$tmp/out
-+"
-+eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$ac_tmp/subs.awk" \
-+ >$ac_tmp/out || as_fn_error $? "could not create $ac_file" "$LINENO" 5
-
- test -z "$ac_datarootdir_hack$ac_datarootdir_seen" &&
-- { ac_out=`sed -n '/\${datarootdir}/p' "$tmp/out"`; test -n "$ac_out"; } &&
-- { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' "$tmp/out"`; test -z "$ac_out"; } &&
-- { echo "$as_me:$LINENO: WARNING: $ac_file contains a reference to the variable \`datarootdir'
--which seems to be undefined. Please make sure it is defined." >&5
--echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir'
--which seems to be undefined. Please make sure it is defined." >&2;}
-+ { ac_out=`sed -n '/\${datarootdir}/p' "$ac_tmp/out"`; test -n "$ac_out"; } &&
-+ { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' \
-+ "$ac_tmp/out"`; test -z "$ac_out"; } &&
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir'
-+which seems to be undefined. Please make sure it is defined" >&5
-+$as_echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir'
-+which seems to be undefined. Please make sure it is defined" >&2;}
-
-- rm -f "$tmp/stdin"
-+ rm -f "$ac_tmp/stdin"
- case $ac_file in
-- -) cat "$tmp/out"; rm -f "$tmp/out";;
-- *) rm -f "$ac_file"; mv "$tmp/out" $ac_file;;
-- esac
-+ -) cat "$ac_tmp/out" && rm -f "$ac_tmp/out";;
-+ *) rm -f "$ac_file" && mv "$ac_tmp/out" "$ac_file";;
-+ esac \
-+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5
- ;;
-
-
-+ :C) { $as_echo "$as_me:${as_lineno-$LINENO}: executing $ac_file commands" >&5
-+$as_echo "$as_me: executing $ac_file commands" >&6;}
-+ ;;
-+ esac
-+
-
-+ case $ac_file$ac_mode in
-+ "depfiles":C) test x"$AMDEP_TRUE" != x"" || {
-+ # Autoconf 2.62 quotes --file arguments for eval, but not when files
-+ # are listed without --file. Let's play safe and only enable the eval
-+ # if we detect the quoting.
-+ case $CONFIG_FILES in
-+ *\'*) eval set x "$CONFIG_FILES" ;;
-+ *) set x $CONFIG_FILES ;;
- esac
-+ shift
-+ for mf
-+ do
-+ # Strip MF so we end up with the name of the file.
-+ mf=`echo "$mf" | sed -e 's/:.*$//'`
-+ # Check whether this is an Automake generated Makefile or not.
-+ # We used to match only the files named `Makefile.in', but
-+ # some people rename them; so instead we look at the file content.
-+ # Grep'ing the first line is not enough: some people post-process
-+ # each Makefile.in and add a new line on top of each file to say so.
-+ # Grep'ing the whole file is not good either: AIX grep has a line
-+ # limit of 2048, but all sed's we know have understand at least 4000.
-+ if sed -n 's,^#.*generated by automake.*,X,p' "$mf" | grep X >/dev/null 2>&1; then
-+ dirpart=`$as_dirname -- "$mf" ||
-+$as_expr X"$mf" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
-+ X"$mf" : 'X\(//\)[^/]' \| \
-+ X"$mf" : 'X\(//\)$' \| \
-+ X"$mf" : 'X\(/\)' \| . 2>/dev/null ||
-+$as_echo X"$mf" |
-+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
-+ s//\1/
-+ q
-+ }
-+ /^X\(\/\/\)[^/].*/{
-+ s//\1/
-+ q
-+ }
-+ /^X\(\/\/\)$/{
-+ s//\1/
-+ q
-+ }
-+ /^X\(\/\).*/{
-+ s//\1/
-+ q
-+ }
-+ s/.*/./; q'`
-+ else
-+ continue
-+ fi
-+ # Extract the definition of DEPDIR, am__include, and am__quote
-+ # from the Makefile without running `make'.
-+ DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
-+ test -z "$DEPDIR" && continue
-+ am__include=`sed -n 's/^am__include = //p' < "$mf"`
-+ test -z "am__include" && continue
-+ am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
-+ # When using ansi2knr, U may be empty or an underscore; expand it
-+ U=`sed -n 's/^U = //p' < "$mf"`
-+ # Find all dependency output files, they are included files with
-+ # $(DEPDIR) in their names. We invoke sed twice because it is the
-+ # simplest approach to changing $(DEPDIR) to its actual value in the
-+ # expansion.
-+ for file in `sed -n "
-+ s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
-+ sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
-+ # Make sure the directory exists.
-+ test -f "$dirpart/$file" && continue
-+ fdir=`$as_dirname -- "$file" ||
-+$as_expr X"$file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
-+ X"$file" : 'X\(//\)[^/]' \| \
-+ X"$file" : 'X\(//\)$' \| \
-+ X"$file" : 'X\(/\)' \| . 2>/dev/null ||
-+$as_echo X"$file" |
-+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
-+ s//\1/
-+ q
-+ }
-+ /^X\(\/\/\)[^/].*/{
-+ s//\1/
-+ q
-+ }
-+ /^X\(\/\/\)$/{
-+ s//\1/
-+ q
-+ }
-+ /^X\(\/\).*/{
-+ s//\1/
-+ q
-+ }
-+ s/.*/./; q'`
-+ as_dir=$dirpart/$fdir; as_fn_mkdir_p
-+ # echo "creating $dirpart/$file"
-+ echo '# dummy' > "$dirpart/$file"
-+ done
-+ done
-+}
-+ ;;
-
-+ esac
- done # for ac_tag
-
-
--{ (exit 0); exit 0; }
-+as_fn_exit 0
- _ACEOF
--chmod +x $CONFIG_STATUS
- ac_clean_files=$ac_clean_files_save
-
-+test $ac_write_fail = 0 ||
-+ as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5
-+
-
- # configure is writing to config.log, and then calls config.status.
- # config.status does its own redirection, appending to config.log.
-@@ -5643,7 +5917,11 @@
- exec 5>>config.log
- # Use ||, not &&, to avoid exiting from the if with $? = 1, which
- # would make configure fail if this is the last instruction.
-- $ac_cs_success || { (exit 1); exit 1; }
-+ $ac_cs_success || as_fn_exit 1
-+fi
-+if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then
-+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5
-+$as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;}
- fi
-
-
-diff -ubrN exonerate-2.2.0.orig/depcomp exonerate-2.2.0/depcomp
---- exonerate-2.2.0.orig/depcomp 1970-01-01 01:00:00.000000000 +0100
-+++ exonerate-2.2.0/depcomp 2010-01-18 07:28:57.000000000 +0100
-@@ -0,0 +1,630 @@
-+#! /bin/sh
-+# depcomp - compile a program generating dependencies as side-effects
-+
-+scriptversion=2009-04-28.21; # UTC
-+
-+# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007, 2009 Free
-+# Software Foundation, Inc.
-+
-+# This program is free software; you can redistribute it and/or modify
-+# it under the terms of the GNU General Public License as published by
-+# the Free Software Foundation; either version 2, or (at your option)
-+# any later version.
-+
-+# This program is distributed in the hope that it will be useful,
-+# but WITHOUT ANY WARRANTY; without even the implied warranty of
-+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-+# GNU General Public License for more details.
-+
-+# You should have received a copy of the GNU General Public License
-+# along with this program. If not, see <http://www.gnu.org/licenses/>.
-+
-+# As a special exception to the GNU General Public License, if you
-+# distribute this file as part of a program that contains a
-+# configuration script generated by Autoconf, you may include it under
-+# the same distribution terms that you use for the rest of that program.
-+
-+# Originally written by Alexandre Oliva <oliva at dcc.unicamp.br>.
-+
-+case $1 in
-+ '')
-+ echo "$0: No command. Try \`$0 --help' for more information." 1>&2
-+ exit 1;
-+ ;;
-+ -h | --h*)
-+ cat <<\EOF
-+Usage: depcomp [--help] [--version] PROGRAM [ARGS]
-+
-+Run PROGRAMS ARGS to compile a file, generating dependencies
-+as side-effects.
-+
-+Environment variables:
-+ depmode Dependency tracking mode.
-+ source Source file read by `PROGRAMS ARGS'.
-+ object Object file output by `PROGRAMS ARGS'.
-+ DEPDIR directory where to store dependencies.
-+ depfile Dependency file to output.
-+ tmpdepfile Temporary file to use when outputing dependencies.
-+ libtool Whether libtool is used (yes/no).
-+
-+Report bugs to <bug-automake at gnu.org>.
-+EOF
-+ exit $?
-+ ;;
-+ -v | --v*)
-+ echo "depcomp $scriptversion"
-+ exit $?
-+ ;;
-+esac
-+
-+if test -z "$depmode" || test -z "$source" || test -z "$object"; then
-+ echo "depcomp: Variables source, object and depmode must be set" 1>&2
-+ exit 1
-+fi
-+
-+# Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po.
-+depfile=${depfile-`echo "$object" |
-+ sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`}
-+tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`}
-+
-+rm -f "$tmpdepfile"
-+
-+# Some modes work just like other modes, but use different flags. We
-+# parameterize here, but still list the modes in the big case below,
-+# to make depend.m4 easier to write. Note that we *cannot* use a case
-+# here, because this file can only contain one case statement.
-+if test "$depmode" = hp; then
-+ # HP compiler uses -M and no extra arg.
-+ gccflag=-M
-+ depmode=gcc
-+fi
-+
-+if test "$depmode" = dashXmstdout; then
-+ # This is just like dashmstdout with a different argument.
-+ dashmflag=-xM
-+ depmode=dashmstdout
-+fi
-+
-+cygpath_u="cygpath -u -f -"
-+if test "$depmode" = msvcmsys; then
-+ # This is just like msvisualcpp but w/o cygpath translation.
-+ # Just convert the backslash-escaped backslashes to single forward
-+ # slashes to satisfy depend.m4
-+ cygpath_u="sed s,\\\\\\\\,/,g"
-+ depmode=msvisualcpp
-+fi
-+
-+case "$depmode" in
-+gcc3)
-+## gcc 3 implements dependency tracking that does exactly what
-+## we want. Yay! Note: for some reason libtool 1.4 doesn't like
-+## it if -MD -MP comes after the -MF stuff. Hmm.
-+## Unfortunately, FreeBSD c89 acceptance of flags depends upon
-+## the command line argument order; so add the flags where they
-+## appear in depend2.am. Note that the slowdown incurred here
-+## affects only configure: in makefiles, %FASTDEP% shortcuts this.
-+ for arg
-+ do
-+ case $arg in
-+ -c) set fnord "$@" -MT "$object" -MD -MP -MF "$tmpdepfile" "$arg" ;;
-+ *) set fnord "$@" "$arg" ;;
-+ esac
-+ shift # fnord
-+ shift # $arg
-+ done
-+ "$@"
-+ stat=$?
-+ if test $stat -eq 0; then :
-+ else
-+ rm -f "$tmpdepfile"
-+ exit $stat
-+ fi
-+ mv "$tmpdepfile" "$depfile"
-+ ;;
-+
-+gcc)
-+## There are various ways to get dependency output from gcc. Here's
-+## why we pick this rather obscure method:
-+## - Don't want to use -MD because we'd like the dependencies to end
-+## up in a subdir. Having to rename by hand is ugly.
-+## (We might end up doing this anyway to support other compilers.)
-+## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
-+## -MM, not -M (despite what the docs say).
-+## - Using -M directly means running the compiler twice (even worse
-+## than renaming).
-+ if test -z "$gccflag"; then
-+ gccflag=-MD,
-+ fi
-+ "$@" -Wp,"$gccflag$tmpdepfile"
-+ stat=$?
-+ if test $stat -eq 0; then :
-+ else
-+ rm -f "$tmpdepfile"
-+ exit $stat
-+ fi
-+ rm -f "$depfile"
-+ echo "$object : \\" > "$depfile"
-+ alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
-+## The second -e expression handles DOS-style file names with drive letters.
-+ sed -e 's/^[^:]*: / /' \
-+ -e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"
-+## This next piece of magic avoids the `deleted header file' problem.
-+## The problem is that when a header file which appears in a .P file
-+## is deleted, the dependency causes make to die (because there is
-+## typically no way to rebuild the header). We avoid this by adding
-+## dummy dependencies for each header file. Too bad gcc doesn't do
-+## this for us directly.
-+ tr ' ' '
-+' < "$tmpdepfile" |
-+## Some versions of gcc put a space before the `:'. On the theory
-+## that the space means something, we add a space to the output as
-+## well.
-+## Some versions of the HPUX 10.20 sed can't process this invocation
-+## correctly. Breaking it into two sed invocations is a workaround.
-+ sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
-+ rm -f "$tmpdepfile"
-+ ;;
-+
-+hp)
-+ # This case exists only to let depend.m4 do its work. It works by
-+ # looking at the text of this script. This case will never be run,
-+ # since it is checked for above.
-+ exit 1
-+ ;;
-+
-+sgi)
-+ if test "$libtool" = yes; then
-+ "$@" "-Wp,-MDupdate,$tmpdepfile"
-+ else
-+ "$@" -MDupdate "$tmpdepfile"
-+ fi
-+ stat=$?
-+ if test $stat -eq 0; then :
-+ else
-+ rm -f "$tmpdepfile"
-+ exit $stat
-+ fi
-+ rm -f "$depfile"
-+
-+ if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files
-+ echo "$object : \\" > "$depfile"
-+
-+ # Clip off the initial element (the dependent). Don't try to be
-+ # clever and replace this with sed code, as IRIX sed won't handle
-+ # lines with more than a fixed number of characters (4096 in
-+ # IRIX 6.2 sed, 8192 in IRIX 6.5). We also remove comment lines;
-+ # the IRIX cc adds comments like `#:fec' to the end of the
-+ # dependency line.
-+ tr ' ' '
-+' < "$tmpdepfile" \
-+ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \
-+ tr '
-+' ' ' >> "$depfile"
-+ echo >> "$depfile"
-+
-+ # The second pass generates a dummy entry for each header file.
-+ tr ' ' '
-+' < "$tmpdepfile" \
-+ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
-+ >> "$depfile"
-+ else
-+ # The sourcefile does not contain any dependencies, so just
-+ # store a dummy comment line, to avoid errors with the Makefile
-+ # "include basename.Plo" scheme.
-+ echo "#dummy" > "$depfile"
-+ fi
-+ rm -f "$tmpdepfile"
-+ ;;
-+
-+aix)
-+ # The C for AIX Compiler uses -M and outputs the dependencies
-+ # in a .u file. In older versions, this file always lives in the
-+ # current directory. Also, the AIX compiler puts `$object:' at the
-+ # start of each line; $object doesn't have directory information.
-+ # Version 6 uses the directory in both cases.
-+ dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
-+ test "x$dir" = "x$object" && dir=
-+ base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
-+ if test "$libtool" = yes; then
-+ tmpdepfile1=$dir$base.u
-+ tmpdepfile2=$base.u
-+ tmpdepfile3=$dir.libs/$base.u
-+ "$@" -Wc,-M
-+ else
-+ tmpdepfile1=$dir$base.u
-+ tmpdepfile2=$dir$base.u
-+ tmpdepfile3=$dir$base.u
-+ "$@" -M
-+ fi
-+ stat=$?
-+
-+ if test $stat -eq 0; then :
-+ else
-+ rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
-+ exit $stat
-+ fi
-+
-+ for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
-+ do
-+ test -f "$tmpdepfile" && break
-+ done
-+ if test -f "$tmpdepfile"; then
-+ # Each line is of the form `foo.o: dependent.h'.
-+ # Do two passes, one to just change these to
-+ # `$object: dependent.h' and one to simply `dependent.h:'.
-+ sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
-+ # That's a tab and a space in the [].
-+ sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
-+ else
-+ # The sourcefile does not contain any dependencies, so just
-+ # store a dummy comment line, to avoid errors with the Makefile
-+ # "include basename.Plo" scheme.
-+ echo "#dummy" > "$depfile"
-+ fi
-+ rm -f "$tmpdepfile"
-+ ;;
-+
-+icc)
-+ # Intel's C compiler understands `-MD -MF file'. However on
-+ # icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c
-+ # ICC 7.0 will fill foo.d with something like
-+ # foo.o: sub/foo.c
-+ # foo.o: sub/foo.h
-+ # which is wrong. We want:
-+ # sub/foo.o: sub/foo.c
-+ # sub/foo.o: sub/foo.h
-+ # sub/foo.c:
-+ # sub/foo.h:
-+ # ICC 7.1 will output
-+ # foo.o: sub/foo.c sub/foo.h
-+ # and will wrap long lines using \ :
-+ # foo.o: sub/foo.c ... \
-+ # sub/foo.h ... \
-+ # ...
-+
-+ "$@" -MD -MF "$tmpdepfile"
-+ stat=$?
-+ if test $stat -eq 0; then :
-+ else
-+ rm -f "$tmpdepfile"
-+ exit $stat
-+ fi
-+ rm -f "$depfile"
-+ # Each line is of the form `foo.o: dependent.h',
-+ # or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'.
-+ # Do two passes, one to just change these to
-+ # `$object: dependent.h' and one to simply `dependent.h:'.
-+ sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile"
-+ # Some versions of the HPUX 10.20 sed can't process this invocation
-+ # correctly. Breaking it into two sed invocations is a workaround.
-+ sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" |
-+ sed -e 's/$/ :/' >> "$depfile"
-+ rm -f "$tmpdepfile"
-+ ;;
-+
-+hp2)
-+ # The "hp" stanza above does not work with aCC (C++) and HP's ia64
-+ # compilers, which have integrated preprocessors. The correct option
-+ # to use with these is +Maked; it writes dependencies to a file named
-+ # 'foo.d', which lands next to the object file, wherever that
-+ # happens to be.
-+ # Much of this is similar to the tru64 case; see comments there.
-+ dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
-+ test "x$dir" = "x$object" && dir=
-+ base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
-+ if test "$libtool" = yes; then
-+ tmpdepfile1=$dir$base.d
-+ tmpdepfile2=$dir.libs/$base.d
-+ "$@" -Wc,+Maked
-+ else
-+ tmpdepfile1=$dir$base.d
-+ tmpdepfile2=$dir$base.d
-+ "$@" +Maked
-+ fi
-+ stat=$?
-+ if test $stat -eq 0; then :
-+ else
-+ rm -f "$tmpdepfile1" "$tmpdepfile2"
-+ exit $stat
-+ fi
-+
-+ for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2"
-+ do
-+ test -f "$tmpdepfile" && break
-+ done
-+ if test -f "$tmpdepfile"; then
-+ sed -e "s,^.*\.[a-z]*:,$object:," "$tmpdepfile" > "$depfile"
-+ # Add `dependent.h:' lines.
-+ sed -ne '2,${
-+ s/^ *//
-+ s/ \\*$//
-+ s/$/:/
-+ p
-+ }' "$tmpdepfile" >> "$depfile"
-+ else
-+ echo "#dummy" > "$depfile"
-+ fi
-+ rm -f "$tmpdepfile" "$tmpdepfile2"
-+ ;;
-+
-+tru64)
-+ # The Tru64 compiler uses -MD to generate dependencies as a side
-+ # effect. `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'.
-+ # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
-+ # dependencies in `foo.d' instead, so we check for that too.
-+ # Subdirectories are respected.
-+ dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
-+ test "x$dir" = "x$object" && dir=
-+ base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
-+
-+ if test "$libtool" = yes; then
-+ # With Tru64 cc, shared objects can also be used to make a
-+ # static library. This mechanism is used in libtool 1.4 series to
-+ # handle both shared and static libraries in a single compilation.
-+ # With libtool 1.4, dependencies were output in $dir.libs/$base.lo.d.
-+ #
-+ # With libtool 1.5 this exception was removed, and libtool now
-+ # generates 2 separate objects for the 2 libraries. These two
-+ # compilations output dependencies in $dir.libs/$base.o.d and
-+ # in $dir$base.o.d. We have to check for both files, because
-+ # one of the two compilations can be disabled. We should prefer
-+ # $dir$base.o.d over $dir.libs/$base.o.d because the latter is
-+ # automatically cleaned when .libs/ is deleted, while ignoring
-+ # the former would cause a distcleancheck panic.
-+ tmpdepfile1=$dir.libs/$base.lo.d # libtool 1.4
-+ tmpdepfile2=$dir$base.o.d # libtool 1.5
-+ tmpdepfile3=$dir.libs/$base.o.d # libtool 1.5
-+ tmpdepfile4=$dir.libs/$base.d # Compaq CCC V6.2-504
-+ "$@" -Wc,-MD
-+ else
-+ tmpdepfile1=$dir$base.o.d
-+ tmpdepfile2=$dir$base.d
-+ tmpdepfile3=$dir$base.d
-+ tmpdepfile4=$dir$base.d
-+ "$@" -MD
-+ fi
-+
-+ stat=$?
-+ if test $stat -eq 0; then :
-+ else
-+ rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
-+ exit $stat
-+ fi
-+
-+ for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
-+ do
-+ test -f "$tmpdepfile" && break
-+ done
-+ if test -f "$tmpdepfile"; then
-+ sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
-+ # That's a tab and a space in the [].
-+ sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
-+ else
-+ echo "#dummy" > "$depfile"
-+ fi
-+ rm -f "$tmpdepfile"
-+ ;;
-+
-+#nosideeffect)
-+ # This comment above is used by automake to tell side-effect
-+ # dependency tracking mechanisms from slower ones.
-+
-+dashmstdout)
-+ # Important note: in order to support this mode, a compiler *must*
-+ # always write the preprocessed file to stdout, regardless of -o.
-+ "$@" || exit $?
-+
-+ # Remove the call to Libtool.
-+ if test "$libtool" = yes; then
-+ while test "X$1" != 'X--mode=compile'; do
-+ shift
-+ done
-+ shift
-+ fi
-+
-+ # Remove `-o $object'.
-+ IFS=" "
-+ for arg
-+ do
-+ case $arg in
-+ -o)
-+ shift
-+ ;;
-+ $object)
-+ shift
-+ ;;
-+ *)
-+ set fnord "$@" "$arg"
-+ shift # fnord
-+ shift # $arg
-+ ;;
-+ esac
-+ done
-+
-+ test -z "$dashmflag" && dashmflag=-M
-+ # Require at least two characters before searching for `:'
-+ # in the target name. This is to cope with DOS-style filenames:
-+ # a dependency such as `c:/foo/bar' could be seen as target `c' otherwise.
-+ "$@" $dashmflag |
-+ sed 's:^[ ]*[^: ][^:][^:]*\:[ ]*:'"$object"'\: :' > "$tmpdepfile"
-+ rm -f "$depfile"
-+ cat < "$tmpdepfile" > "$depfile"
-+ tr ' ' '
-+' < "$tmpdepfile" | \
-+## Some versions of the HPUX 10.20 sed can't process this invocation
-+## correctly. Breaking it into two sed invocations is a workaround.
-+ sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
-+ rm -f "$tmpdepfile"
-+ ;;
-+
-+dashXmstdout)
-+ # This case only exists to satisfy depend.m4. It is never actually
-+ # run, as this mode is specially recognized in the preamble.
-+ exit 1
-+ ;;
-+
-+makedepend)
-+ "$@" || exit $?
-+ # Remove any Libtool call
-+ if test "$libtool" = yes; then
-+ while test "X$1" != 'X--mode=compile'; do
-+ shift
-+ done
-+ shift
-+ fi
-+ # X makedepend
-+ shift
-+ cleared=no eat=no
-+ for arg
-+ do
-+ case $cleared in
-+ no)
-+ set ""; shift
-+ cleared=yes ;;
-+ esac
-+ if test $eat = yes; then
-+ eat=no
-+ continue
-+ fi
-+ case "$arg" in
-+ -D*|-I*)
-+ set fnord "$@" "$arg"; shift ;;
-+ # Strip any option that makedepend may not understand. Remove
-+ # the object too, otherwise makedepend will parse it as a source file.
-+ -arch)
-+ eat=yes ;;
-+ -*|$object)
-+ ;;
-+ *)
-+ set fnord "$@" "$arg"; shift ;;
-+ esac
-+ done
-+ obj_suffix=`echo "$object" | sed 's/^.*\././'`
-+ touch "$tmpdepfile"
-+ ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"
-+ rm -f "$depfile"
-+ cat < "$tmpdepfile" > "$depfile"
-+ sed '1,2d' "$tmpdepfile" | tr ' ' '
-+' | \
-+## Some versions of the HPUX 10.20 sed can't process this invocation
-+## correctly. Breaking it into two sed invocations is a workaround.
-+ sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
-+ rm -f "$tmpdepfile" "$tmpdepfile".bak
-+ ;;
-+
-+cpp)
-+ # Important note: in order to support this mode, a compiler *must*
-+ # always write the preprocessed file to stdout.
-+ "$@" || exit $?
-+
-+ # Remove the call to Libtool.
-+ if test "$libtool" = yes; then
-+ while test "X$1" != 'X--mode=compile'; do
-+ shift
-+ done
-+ shift
-+ fi
-+
-+ # Remove `-o $object'.
-+ IFS=" "
-+ for arg
-+ do
-+ case $arg in
-+ -o)
-+ shift
-+ ;;
-+ $object)
-+ shift
-+ ;;
-+ *)
-+ set fnord "$@" "$arg"
-+ shift # fnord
-+ shift # $arg
-+ ;;
-+ esac
-+ done
-+
-+ "$@" -E |
-+ sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
-+ -e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' |
-+ sed '$ s: \\$::' > "$tmpdepfile"
-+ rm -f "$depfile"
-+ echo "$object : \\" > "$depfile"
-+ cat < "$tmpdepfile" >> "$depfile"
-+ sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile"
-+ rm -f "$tmpdepfile"
-+ ;;
-+
-+msvisualcpp)
-+ # Important note: in order to support this mode, a compiler *must*
-+ # always write the preprocessed file to stdout.
-+ "$@" || exit $?
-+
-+ # Remove the call to Libtool.
-+ if test "$libtool" = yes; then
-+ while test "X$1" != 'X--mode=compile'; do
-+ shift
-+ done
-+ shift
-+ fi
-+
-+ IFS=" "
-+ for arg
-+ do
-+ case "$arg" in
-+ -o)
-+ shift
-+ ;;
-+ $object)
-+ shift
-+ ;;
-+ "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
-+ set fnord "$@"
-+ shift
-+ shift
-+ ;;
-+ *)
-+ set fnord "$@" "$arg"
-+ shift
-+ shift
-+ ;;
-+ esac
-+ done
-+ "$@" -E 2>/dev/null |
-+ sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::\1:p' | $cygpath_u | sort -u > "$tmpdepfile"
-+ rm -f "$depfile"
-+ echo "$object : \\" > "$depfile"
-+ sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile"
-+ echo " " >> "$depfile"
-+ sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile"
-+ rm -f "$tmpdepfile"
-+ ;;
-+
-+msvcmsys)
-+ # This case exists only to let depend.m4 do its work. It works by
-+ # looking at the text of this script. This case will never be run,
-+ # since it is checked for above.
-+ exit 1
-+ ;;
-+
-+none)
-+ exec "$@"
-+ ;;
-+
-+*)
-+ echo "Unknown depmode $depmode" 1>&2
-+ exit 1
-+ ;;
-+esac
-+
-+exit 0
-+
-+# Local Variables:
-+# mode: shell-script
-+# sh-indentation: 2
-+# eval: (add-hook 'write-file-hooks 'time-stamp)
-+# time-stamp-start: "scriptversion="
-+# time-stamp-format: "%:y-%02m-%02d.%02H"
-+# time-stamp-time-zone: "UTC"
-+# time-stamp-end: "; # UTC"
-+# End:
-diff -ubrN exonerate-2.2.0.orig/doc/Makefile.in exonerate-2.2.0/doc/Makefile.in
---- exonerate-2.2.0.orig/doc/Makefile.in 2008-10-17 12:05:00.000000000 +0200
-+++ exonerate-2.2.0/doc/Makefile.in 2011-12-12 13:33:16.000000000 +0100
-@@ -1,6 +1,9 @@
--# Makefile.in generated automatically by automake 1.4-p6 from Makefile.am
-+# Makefile.in generated by automake 1.11.1 from Makefile.am.
-+# @configure_input@
-
--# Copyright (C) 1994, 1995-8, 1999, 2001 Free Software Foundation, Inc.
-+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
-+# Inc.
- # This Makefile.in is free software; the Free Software Foundation
- # gives unlimited permission to copy and/or distribute it,
- # with or without modifications, as long as this notice is preserved.
-@@ -10,95 +13,216 @@
- # even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- # PARTICULAR PURPOSE.
-
--
--SHELL = @SHELL@
--
--srcdir = @srcdir@
--top_srcdir = @top_srcdir@
-+ at SET_MAKE@
- VPATH = @srcdir@
--prefix = @prefix@
--exec_prefix = @exec_prefix@
--
--bindir = @bindir@
--sbindir = @sbindir@
--libexecdir = @libexecdir@
--datadir = @datadir@
--sysconfdir = @sysconfdir@
--sharedstatedir = @sharedstatedir@
--localstatedir = @localstatedir@
--libdir = @libdir@
--infodir = @infodir@
--mandir = @mandir@
--includedir = @includedir@
--oldincludedir = /usr/include
--
--DESTDIR =
--
- pkgdatadir = $(datadir)/@PACKAGE@
--pkglibdir = $(libdir)/@PACKAGE@
- pkgincludedir = $(includedir)/@PACKAGE@
--
--top_builddir = ..
--
--ACLOCAL = @ACLOCAL@
--AUTOCONF = @AUTOCONF@
--AUTOMAKE = @AUTOMAKE@
--AUTOHEADER = @AUTOHEADER@
--
--INSTALL = @INSTALL@
--INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
--INSTALL_DATA = @INSTALL_DATA@
--INSTALL_SCRIPT = @INSTALL_SCRIPT@
--transform = @program_transform_name@
--
-+pkglibdir = $(libdir)/@PACKAGE@
-+pkglibexecdir = $(libexecdir)/@PACKAGE@
-+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-+install_sh_DATA = $(install_sh) -c -m 644
-+install_sh_PROGRAM = $(install_sh) -c
-+install_sh_SCRIPT = $(install_sh) -c
-+INSTALL_HEADER = $(INSTALL_DATA)
-+transform = $(program_transform_name)
- NORMAL_INSTALL = :
- PRE_INSTALL = :
- POST_INSTALL = :
- NORMAL_UNINSTALL = :
- PRE_UNINSTALL = :
- POST_UNINSTALL = :
--host_alias = @host_alias@
-+build_triplet = @build@
- host_triplet = @host@
-+subdir = doc
-+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
-+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-+am__aclocal_m4_deps = $(top_srcdir)/configure.in
-+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-+ $(ACLOCAL_M4)
-+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
-+CONFIG_CLEAN_FILES =
-+CONFIG_CLEAN_VPATH_FILES =
-+SOURCES =
-+DIST_SOURCES =
-+RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
-+ html-recursive info-recursive install-data-recursive \
-+ install-dvi-recursive install-exec-recursive \
-+ install-html-recursive install-info-recursive \
-+ install-pdf-recursive install-ps-recursive install-recursive \
-+ installcheck-recursive installdirs-recursive pdf-recursive \
-+ ps-recursive uninstall-recursive
-+RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive \
-+ distclean-recursive maintainer-clean-recursive
-+AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
-+ $(RECURSIVE_CLEAN_TARGETS:-recursive=) tags TAGS ctags CTAGS \
-+ distdir
-+ETAGS = etags
-+CTAGS = ctags
-+DIST_SUBDIRS = $(SUBDIRS)
-+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-+am__relativize = \
-+ dir0=`pwd`; \
-+ sed_first='s,^\([^/]*\)/.*$$,\1,'; \
-+ sed_rest='s,^[^/]*/*,,'; \
-+ sed_last='s,^.*/\([^/]*\)$$,\1,'; \
-+ sed_butlast='s,/*[^/]*$$,,'; \
-+ while test -n "$$dir1"; do \
-+ first=`echo "$$dir1" | sed -e "$$sed_first"`; \
-+ if test "$$first" != "."; then \
-+ if test "$$first" = ".."; then \
-+ dir2=`echo "$$dir0" | sed -e "$$sed_last"`/"$$dir2"; \
-+ dir0=`echo "$$dir0" | sed -e "$$sed_butlast"`; \
-+ else \
-+ first2=`echo "$$dir2" | sed -e "$$sed_first"`; \
-+ if test "$$first2" = "$$first"; then \
-+ dir2=`echo "$$dir2" | sed -e "$$sed_rest"`; \
-+ else \
-+ dir2="../$$dir2"; \
-+ fi; \
-+ dir0="$$dir0"/"$$first"; \
-+ fi; \
-+ fi; \
-+ dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \
-+ done; \
-+ reldir="$$dir2"
-+ACLOCAL = @ACLOCAL@
-+AMTAR = @AMTAR@
-+AUTOCONF = @AUTOCONF@
-+AUTOHEADER = @AUTOHEADER@
-+AUTOMAKE = @AUTOMAKE@
-+AWK = @AWK@
- CC = @CC@
-+CCDEPMODE = @CCDEPMODE@
-+CFLAGS = @CFLAGS@
-+CPP = @CPP@
-+CPPFLAGS = @CPPFLAGS@
-+CYGPATH_W = @CYGPATH_W@
-+DEFS = @DEFS@
-+DEPDIR = @DEPDIR@
-+ECHO_C = @ECHO_C@
-+ECHO_N = @ECHO_N@
-+ECHO_T = @ECHO_T@
-+EGREP = @EGREP@
-+EXEEXT = @EXEEXT@
- GLIB_CONFIG = @GLIB_CONFIG@
--HAVE_LIB = @HAVE_LIB@
--LIB = @LIB@
--LTLIB = @LTLIB@
-+GREP = @GREP@
-+INSTALL = @INSTALL@
-+INSTALL_DATA = @INSTALL_DATA@
-+INSTALL_PROGRAM = @INSTALL_PROGRAM@
-+INSTALL_SCRIPT = @INSTALL_SCRIPT@
-+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-+LDFLAGS = @LDFLAGS@
-+LIBOBJS = @LIBOBJS@
-+LIBS = @LIBS@
-+LTLIBOBJS = @LTLIBOBJS@
- MAKEINFO = @MAKEINFO@
-+MKDIR_P = @MKDIR_P@
-+OBJEXT = @OBJEXT@
- PACKAGE = @PACKAGE@
-+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-+PACKAGE_NAME = @PACKAGE_NAME@
-+PACKAGE_STRING = @PACKAGE_STRING@
-+PACKAGE_TARNAME = @PACKAGE_TARNAME@
-+PACKAGE_URL = @PACKAGE_URL@
-+PACKAGE_VERSION = @PACKAGE_VERSION@
-+PATH_SEPARATOR = @PATH_SEPARATOR@
- PKG_CONFIG = @PKG_CONFIG@
-+SET_MAKE = @SET_MAKE@
-+SHELL = @SHELL@
-+STRIP = @STRIP@
- VERSION = @VERSION@
-+abs_builddir = @abs_builddir@
-+abs_srcdir = @abs_srcdir@
-+abs_top_builddir = @abs_top_builddir@
-+abs_top_srcdir = @abs_top_srcdir@
-+ac_ct_CC = @ac_ct_CC@
-+am__include = @am__include@
-+am__leading_dot = @am__leading_dot@
-+am__quote = @am__quote@
-+am__tar = @am__tar@
-+am__untar = @am__untar@
-+bindir = @bindir@
-+build = @build@
-+build_alias = @build_alias@
-+build_cpu = @build_cpu@
-+build_os = @build_os@
-+build_vendor = @build_vendor@
-+builddir = @builddir@
- codegen_extra_ldadd = @codegen_extra_ldadd@
- codegen_extra_sources = @codegen_extra_sources@
-+datadir = @datadir@
- datarootdir = @datarootdir@
-+docdir = @docdir@
-+dvidir = @dvidir@
-+exec_prefix = @exec_prefix@
- glib_cflags = @glib_cflags@
- glib_libs = @glib_libs@
- host = @host@
-+host_alias = @host_alias@
-+host_cpu = @host_cpu@
-+host_os = @host_os@
-+host_vendor = @host_vendor@
-+htmldir = @htmldir@
-+includedir = @includedir@
-+infodir = @infodir@
-+install_sh = @install_sh@
- installed_util_list = @installed_util_list@
-+libdir = @libdir@
-+libexecdir = @libexecdir@
-+localedir = @localedir@
-+localstatedir = @localstatedir@
-+mandir = @mandir@
-+mkdir_p = @mkdir_p@
-+oldincludedir = @oldincludedir@
-+pdfdir = @pdfdir@
-+prefix = @prefix@
-+program_transform_name = @program_transform_name@
-+psdir = @psdir@
-+sbindir = @sbindir@
-+sharedstatedir = @sharedstatedir@
- source_root_dir = @source_root_dir@
-+srcdir = @srcdir@
-+sysconfdir = @sysconfdir@
-+target_alias = @target_alias@
-+top_build_prefix = @top_build_prefix@
-+top_builddir = @top_builddir@
-+top_srcdir = @top_srcdir@
- use_pthreads = @use_pthreads@
--
- SUBDIRS = man
--
- MAINTAINERCLEANFILES = Makefile.in
--mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
--CONFIG_CLEAN_FILES =
--DIST_COMMON = Makefile.am Makefile.in
--
-+all: all-recursive
-
--DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
--
--TAR = tar
--GZIP_ENV = --best
--all: all-redirect
- .SUFFIXES:
--$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4)
-- cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps doc/Makefile
--
-+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
-+ @for dep in $?; do \
-+ case '$(am__configure_deps)' in \
-+ *$$dep*) \
-+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-+ && { if test -f $@; then exit 0; else break; fi; }; \
-+ exit 1;; \
-+ esac; \
-+ done; \
-+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu doc/Makefile'; \
-+ $(am__cd) $(top_srcdir) && \
-+ $(AUTOMAKE) --gnu doc/Makefile
-+.PRECIOUS: Makefile
- Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-- cd $(top_builddir) \
-- && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
--
-+ @case '$?' in \
-+ *config.status*) \
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-+ *) \
-+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-+ esac;
-+
-+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+
-+$(top_srcdir)/configure: $(am__configure_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(am__aclocal_m4_deps):
-
- # This directory's subdirectories are mostly independent; you can cd
- # into them and run `make' without going through this Makefile.
-@@ -106,13 +230,14 @@
- # (1) if the variable is set in `config.status', edit `config.status'
- # (which will cause the Makefiles to be regenerated when you run `make');
- # (2) otherwise, pass the desired values on the `make' command line.
--
-- at SET_MAKE@
--
--all-recursive install-data-recursive install-exec-recursive \
--installdirs-recursive install-recursive uninstall-recursive \
--check-recursive installcheck-recursive info-recursive dvi-recursive:
-- @set fnord $(MAKEFLAGS); amf=$$2; \
-+$(RECURSIVE_TARGETS):
-+ @fail= failcom='exit 1'; \
-+ for f in x $$MAKEFLAGS; do \
-+ case $$f in \
-+ *=* | --[!k]*);; \
-+ *k*) failcom='fail=yes';; \
-+ esac; \
-+ done; \
- dot_seen=no; \
- target=`echo $@ | sed s/-recursive//`; \
- list='$(SUBDIRS)'; for subdir in $$list; do \
-@@ -123,22 +248,32 @@
- else \
- local_target="$$target"; \
- fi; \
-- (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-- || case "$$amf" in *=*) exit 1;; *k*) fail=yes;; *) exit 1;; esac; \
-+ ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-+ || eval $$failcom; \
- done; \
- if test "$$dot_seen" = "no"; then \
- $(MAKE) $(AM_MAKEFLAGS) "$$target-am" || exit 1; \
- fi; test -z "$$fail"
-
--mostlyclean-recursive clean-recursive distclean-recursive \
--maintainer-clean-recursive:
-- @set fnord $(MAKEFLAGS); amf=$$2; \
-+$(RECURSIVE_CLEAN_TARGETS):
-+ @fail= failcom='exit 1'; \
-+ for f in x $$MAKEFLAGS; do \
-+ case $$f in \
-+ *=* | --[!k]*);; \
-+ *k*) failcom='fail=yes';; \
-+ esac; \
-+ done; \
- dot_seen=no; \
-- rev=''; list='$(SUBDIRS)'; for subdir in $$list; do \
-+ case "$@" in \
-+ distclean-* | maintainer-clean-*) list='$(DIST_SUBDIRS)' ;; \
-+ *) list='$(SUBDIRS)' ;; \
-+ esac; \
-+ rev=''; for subdir in $$list; do \
-+ if test "$$subdir" = "."; then :; else \
- rev="$$subdir $$rev"; \
-- test "$$subdir" != "." || dot_seen=yes; \
-+ fi; \
- done; \
-- test "$$dot_seen" = "no" && rev=". $$rev"; \
-+ rev="$$rev ."; \
- target=`echo $@ | sed s/-recursive//`; \
- for subdir in $$rev; do \
- echo "Making $$target in $$subdir"; \
-@@ -147,141 +282,253 @@
- else \
- local_target="$$target"; \
- fi; \
-- (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-- || case "$$amf" in *=*) exit 1;; *k*) fail=yes;; *) exit 1;; esac; \
-+ ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-+ || eval $$failcom; \
- done && test -z "$$fail"
- tags-recursive:
- list='$(SUBDIRS)'; for subdir in $$list; do \
-- test "$$subdir" = . || (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
-+ test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
-+ done
-+ctags-recursive:
-+ list='$(SUBDIRS)'; for subdir in $$list; do \
-+ test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \
- done
-
-+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ mkid -fID $$unique
- tags: TAGS
-
--ID: $(HEADERS) $(SOURCES) $(LISP)
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- here=`pwd` && cd $(srcdir) \
-- && mkid -f$$here/ID $$unique $(LISP)
--
--TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) $(LISP)
-- tags=; \
-+TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ set x; \
- here=`pwd`; \
-+ if ($(ETAGS) --etags-include --version) >/dev/null 2>&1; then \
-+ include_option=--etags-include; \
-+ empty_fix=.; \
-+ else \
-+ include_option=--include; \
-+ empty_fix=; \
-+ fi; \
- list='$(SUBDIRS)'; for subdir in $$list; do \
- if test "$$subdir" = .; then :; else \
-- test -f $$subdir/TAGS && tags="$$tags -i $$here/$$subdir/TAGS"; \
-+ test ! -f $$subdir/TAGS || \
-+ set "$$@" "$$include_option=$$here/$$subdir/TAGS"; \
- fi; \
- done; \
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- test -z "$(ETAGS_ARGS)$$unique$(LISP)$$tags" \
-- || (cd $(srcdir) && etags -o $$here/TAGS $(ETAGS_ARGS) $$tags $$unique $(LISP))
--
--mostlyclean-tags:
--
--clean-tags:
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ shift; \
-+ if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
-+ test -n "$$unique" || unique=$$empty_fix; \
-+ if test $$# -gt 0; then \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ "$$@" $$unique; \
-+ else \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ $$unique; \
-+ fi; \
-+ fi
-+ctags: CTAGS
-+CTAGS: ctags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ test -z "$(CTAGS_ARGS)$$unique" \
-+ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-+ $$unique
-+
-+GTAGS:
-+ here=`$(am__cd) $(top_builddir) && pwd` \
-+ && $(am__cd) $(top_srcdir) \
-+ && gtags -i $(GTAGS_ARGS) "$$here"
-
- distclean-tags:
-- -rm -f TAGS ID
--
--maintainer-clean-tags:
--
--distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
--
--subdir = doc
-+ -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-
- distdir: $(DISTFILES)
-- @for file in $(DISTFILES); do \
-- d=$(srcdir); \
-+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ list='$(DISTFILES)'; \
-+ dist_files=`for file in $$list; do echo $$file; done | \
-+ sed -e "s|^$$srcdirstrip/||;t" \
-+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-+ case $$dist_files in \
-+ */*) $(MKDIR_P) `echo "$$dist_files" | \
-+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-+ sort -u` ;; \
-+ esac; \
-+ for file in $$dist_files; do \
-+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
- if test -d $$d/$$file; then \
-- cp -pr $$d/$$file $(distdir)/$$file; \
-+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-+ if test -d "$(distdir)/$$file"; then \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
- else \
-- test -f $(distdir)/$$file \
-- || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
-- || cp -p $$d/$$file $(distdir)/$$file || :; \
-+ test -f "$(distdir)/$$file" \
-+ || cp -p $$d/$$file "$(distdir)/$$file" \
-+ || exit 1; \
- fi; \
- done
-- for subdir in $(SUBDIRS); do \
-+ @list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
- if test "$$subdir" = .; then :; else \
-- test -d $(distdir)/$$subdir \
-- || mkdir $(distdir)/$$subdir \
-+ test -d "$(distdir)/$$subdir" \
-+ || $(MKDIR_P) "$(distdir)/$$subdir" \
- || exit 1; \
-- chmod 777 $(distdir)/$$subdir; \
-- (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir=../$(top_distdir) distdir=../$(distdir)/$$subdir distdir) \
-+ fi; \
-+ done
-+ @list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
-+ if test "$$subdir" = .; then :; else \
-+ dir1=$$subdir; dir2="$(distdir)/$$subdir"; \
-+ $(am__relativize); \
-+ new_distdir=$$reldir; \
-+ dir1=$$subdir; dir2="$(top_distdir)"; \
-+ $(am__relativize); \
-+ new_top_distdir=$$reldir; \
-+ echo " (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir="$$new_top_distdir" distdir="$$new_distdir" \\"; \
-+ echo " am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)"; \
-+ ($(am__cd) $$subdir && \
-+ $(MAKE) $(AM_MAKEFLAGS) \
-+ top_distdir="$$new_top_distdir" \
-+ distdir="$$new_distdir" \
-+ am__remove_distdir=: \
-+ am__skip_length_check=: \
-+ am__skip_mode_fix=: \
-+ distdir) \
- || exit 1; \
- fi; \
- done
--info-am:
--info: info-recursive
--dvi-am:
--dvi: dvi-recursive
- check-am: all-am
- check: check-recursive
--installcheck-am:
--installcheck: installcheck-recursive
--install-exec-am:
-+all-am: Makefile
-+installdirs: installdirs-recursive
-+installdirs-am:
-+install: install-recursive
- install-exec: install-exec-recursive
--
--install-data-am:
- install-data: install-data-recursive
-+uninstall: uninstall-recursive
-
- install-am: all-am
- @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
--install: install-recursive
--uninstall-am:
--uninstall: uninstall-recursive
--all-am: Makefile
--all-redirect: all-recursive
--install-strip:
-- $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
--installdirs: installdirs-recursive
--installdirs-am:
--
-
-+installcheck: installcheck-recursive
-+install-strip:
-+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-+ `test -z '$(STRIP)' || \
-+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
- mostlyclean-generic:
-
- clean-generic:
-
- distclean-generic:
-- -rm -f Makefile $(CONFIG_CLEAN_FILES)
-- -rm -f config.cache config.log stamp-h stamp-h[0-9]*
-+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
- maintainer-clean-generic:
-+ @echo "This command is intended for maintainers to use"
-+ @echo "it deletes files that may require special tools to rebuild."
- -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
--mostlyclean-am: mostlyclean-tags mostlyclean-generic
-+clean: clean-recursive
-
--mostlyclean: mostlyclean-recursive
-+clean-am: clean-generic mostlyclean-am
-
--clean-am: clean-tags clean-generic mostlyclean-am
-+distclean: distclean-recursive
-+ -rm -f Makefile
-+distclean-am: clean-am distclean-generic distclean-tags
-
--clean: clean-recursive
-+dvi: dvi-recursive
-
--distclean-am: distclean-tags distclean-generic clean-am
-+dvi-am:
-
--distclean: distclean-recursive
-+html: html-recursive
-
--maintainer-clean-am: maintainer-clean-tags maintainer-clean-generic \
-- distclean-am
-- @echo "This command is intended for maintainers to use;"
-- @echo "it deletes files that may require special tools to rebuild."
-+html-am:
-+
-+info: info-recursive
-+
-+info-am:
-+
-+install-data-am:
-+
-+install-dvi: install-dvi-recursive
-+
-+install-dvi-am:
-+
-+install-exec-am:
-+
-+install-html: install-html-recursive
-+
-+install-html-am:
-+
-+install-info: install-info-recursive
-+
-+install-info-am:
-+
-+install-man:
-+
-+install-pdf: install-pdf-recursive
-+
-+install-pdf-am:
-+
-+install-ps: install-ps-recursive
-+
-+install-ps-am:
-+
-+installcheck-am:
-
- maintainer-clean: maintainer-clean-recursive
-+ -rm -f Makefile
-+maintainer-clean-am: distclean-am maintainer-clean-generic
-+
-+mostlyclean: mostlyclean-recursive
-+
-+mostlyclean-am: mostlyclean-generic
-+
-+pdf: pdf-recursive
-+
-+pdf-am:
-+
-+ps: ps-recursive
-+
-+ps-am:
-+
-+uninstall-am:
-+
-+.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) ctags-recursive \
-+ install-am install-strip tags-recursive
-
--.PHONY: install-data-recursive uninstall-data-recursive \
--install-exec-recursive uninstall-exec-recursive installdirs-recursive \
--uninstalldirs-recursive all-recursive check-recursive \
--installcheck-recursive info-recursive dvi-recursive \
--mostlyclean-recursive distclean-recursive clean-recursive \
--maintainer-clean-recursive tags tags-recursive mostlyclean-tags \
--distclean-tags clean-tags maintainer-clean-tags distdir info-am info \
--dvi-am dvi check check-am installcheck-am installcheck install-exec-am \
--install-exec install-data-am install-data install-am install \
--uninstall-am uninstall all-redirect all-am all installdirs-am \
--installdirs mostlyclean-generic distclean-generic clean-generic \
--maintainer-clean-generic clean mostlyclean distclean maintainer-clean
-+.PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
-+ all all-am check check-am clean clean-generic ctags \
-+ ctags-recursive distclean distclean-generic distclean-tags \
-+ distdir dvi dvi-am html html-am info info-am install \
-+ install-am install-data install-data-am install-dvi \
-+ install-dvi-am install-exec install-exec-am install-html \
-+ install-html-am install-info install-info-am install-man \
-+ install-pdf install-pdf-am install-ps install-ps-am \
-+ install-strip installcheck installcheck-am installdirs \
-+ installdirs-am maintainer-clean maintainer-clean-generic \
-+ mostlyclean mostlyclean-generic pdf pdf-am ps ps-am tags \
-+ tags-recursive uninstall uninstall-am
-
-
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -ubrN exonerate-2.2.0.orig/doc/man/Makefile.in exonerate-2.2.0/doc/man/Makefile.in
---- exonerate-2.2.0.orig/doc/man/Makefile.in 2008-10-17 12:05:00.000000000 +0200
-+++ exonerate-2.2.0/doc/man/Makefile.in 2011-12-12 13:33:16.000000000 +0100
-@@ -1,6 +1,9 @@
--# Makefile.in generated automatically by automake 1.4-p6 from Makefile.am
-+# Makefile.in generated by automake 1.11.1 from Makefile.am.
-+# @configure_input@
-
--# Copyright (C) 1994, 1995-8, 1999, 2001 Free Software Foundation, Inc.
-+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
-+# Inc.
- # This Makefile.in is free software; the Free Software Foundation
- # gives unlimited permission to copy and/or distribute it,
- # with or without modifications, as long as this notice is preserved.
-@@ -10,95 +13,216 @@
- # even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- # PARTICULAR PURPOSE.
-
--
--SHELL = @SHELL@
--
--srcdir = @srcdir@
--top_srcdir = @top_srcdir@
-+ at SET_MAKE@
- VPATH = @srcdir@
--prefix = @prefix@
--exec_prefix = @exec_prefix@
--
--bindir = @bindir@
--sbindir = @sbindir@
--libexecdir = @libexecdir@
--datadir = @datadir@
--sysconfdir = @sysconfdir@
--sharedstatedir = @sharedstatedir@
--localstatedir = @localstatedir@
--libdir = @libdir@
--infodir = @infodir@
--mandir = @mandir@
--includedir = @includedir@
--oldincludedir = /usr/include
--
--DESTDIR =
--
- pkgdatadir = $(datadir)/@PACKAGE@
--pkglibdir = $(libdir)/@PACKAGE@
- pkgincludedir = $(includedir)/@PACKAGE@
--
--top_builddir = ../..
--
--ACLOCAL = @ACLOCAL@
--AUTOCONF = @AUTOCONF@
--AUTOMAKE = @AUTOMAKE@
--AUTOHEADER = @AUTOHEADER@
--
--INSTALL = @INSTALL@
--INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
--INSTALL_DATA = @INSTALL_DATA@
--INSTALL_SCRIPT = @INSTALL_SCRIPT@
--transform = @program_transform_name@
--
-+pkglibdir = $(libdir)/@PACKAGE@
-+pkglibexecdir = $(libexecdir)/@PACKAGE@
-+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-+install_sh_DATA = $(install_sh) -c -m 644
-+install_sh_PROGRAM = $(install_sh) -c
-+install_sh_SCRIPT = $(install_sh) -c
-+INSTALL_HEADER = $(INSTALL_DATA)
-+transform = $(program_transform_name)
- NORMAL_INSTALL = :
- PRE_INSTALL = :
- POST_INSTALL = :
- NORMAL_UNINSTALL = :
- PRE_UNINSTALL = :
- POST_UNINSTALL = :
--host_alias = @host_alias@
-+build_triplet = @build@
- host_triplet = @host@
-+subdir = doc/man
-+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
-+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-+am__aclocal_m4_deps = $(top_srcdir)/configure.in
-+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-+ $(ACLOCAL_M4)
-+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
-+CONFIG_CLEAN_FILES =
-+CONFIG_CLEAN_VPATH_FILES =
-+SOURCES =
-+DIST_SOURCES =
-+RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
-+ html-recursive info-recursive install-data-recursive \
-+ install-dvi-recursive install-exec-recursive \
-+ install-html-recursive install-info-recursive \
-+ install-pdf-recursive install-ps-recursive install-recursive \
-+ installcheck-recursive installdirs-recursive pdf-recursive \
-+ ps-recursive uninstall-recursive
-+RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive \
-+ distclean-recursive maintainer-clean-recursive
-+AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
-+ $(RECURSIVE_CLEAN_TARGETS:-recursive=) tags TAGS ctags CTAGS \
-+ distdir
-+ETAGS = etags
-+CTAGS = ctags
-+DIST_SUBDIRS = $(SUBDIRS)
-+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-+am__relativize = \
-+ dir0=`pwd`; \
-+ sed_first='s,^\([^/]*\)/.*$$,\1,'; \
-+ sed_rest='s,^[^/]*/*,,'; \
-+ sed_last='s,^.*/\([^/]*\)$$,\1,'; \
-+ sed_butlast='s,/*[^/]*$$,,'; \
-+ while test -n "$$dir1"; do \
-+ first=`echo "$$dir1" | sed -e "$$sed_first"`; \
-+ if test "$$first" != "."; then \
-+ if test "$$first" = ".."; then \
-+ dir2=`echo "$$dir0" | sed -e "$$sed_last"`/"$$dir2"; \
-+ dir0=`echo "$$dir0" | sed -e "$$sed_butlast"`; \
-+ else \
-+ first2=`echo "$$dir2" | sed -e "$$sed_first"`; \
-+ if test "$$first2" = "$$first"; then \
-+ dir2=`echo "$$dir2" | sed -e "$$sed_rest"`; \
-+ else \
-+ dir2="../$$dir2"; \
-+ fi; \
-+ dir0="$$dir0"/"$$first"; \
-+ fi; \
-+ fi; \
-+ dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \
-+ done; \
-+ reldir="$$dir2"
-+ACLOCAL = @ACLOCAL@
-+AMTAR = @AMTAR@
-+AUTOCONF = @AUTOCONF@
-+AUTOHEADER = @AUTOHEADER@
-+AUTOMAKE = @AUTOMAKE@
-+AWK = @AWK@
- CC = @CC@
-+CCDEPMODE = @CCDEPMODE@
-+CFLAGS = @CFLAGS@
-+CPP = @CPP@
-+CPPFLAGS = @CPPFLAGS@
-+CYGPATH_W = @CYGPATH_W@
-+DEFS = @DEFS@
-+DEPDIR = @DEPDIR@
-+ECHO_C = @ECHO_C@
-+ECHO_N = @ECHO_N@
-+ECHO_T = @ECHO_T@
-+EGREP = @EGREP@
-+EXEEXT = @EXEEXT@
- GLIB_CONFIG = @GLIB_CONFIG@
--HAVE_LIB = @HAVE_LIB@
--LIB = @LIB@
--LTLIB = @LTLIB@
-+GREP = @GREP@
-+INSTALL = @INSTALL@
-+INSTALL_DATA = @INSTALL_DATA@
-+INSTALL_PROGRAM = @INSTALL_PROGRAM@
-+INSTALL_SCRIPT = @INSTALL_SCRIPT@
-+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-+LDFLAGS = @LDFLAGS@
-+LIBOBJS = @LIBOBJS@
-+LIBS = @LIBS@
-+LTLIBOBJS = @LTLIBOBJS@
- MAKEINFO = @MAKEINFO@
-+MKDIR_P = @MKDIR_P@
-+OBJEXT = @OBJEXT@
- PACKAGE = @PACKAGE@
-+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-+PACKAGE_NAME = @PACKAGE_NAME@
-+PACKAGE_STRING = @PACKAGE_STRING@
-+PACKAGE_TARNAME = @PACKAGE_TARNAME@
-+PACKAGE_URL = @PACKAGE_URL@
-+PACKAGE_VERSION = @PACKAGE_VERSION@
-+PATH_SEPARATOR = @PATH_SEPARATOR@
- PKG_CONFIG = @PKG_CONFIG@
-+SET_MAKE = @SET_MAKE@
-+SHELL = @SHELL@
-+STRIP = @STRIP@
- VERSION = @VERSION@
-+abs_builddir = @abs_builddir@
-+abs_srcdir = @abs_srcdir@
-+abs_top_builddir = @abs_top_builddir@
-+abs_top_srcdir = @abs_top_srcdir@
-+ac_ct_CC = @ac_ct_CC@
-+am__include = @am__include@
-+am__leading_dot = @am__leading_dot@
-+am__quote = @am__quote@
-+am__tar = @am__tar@
-+am__untar = @am__untar@
-+bindir = @bindir@
-+build = @build@
-+build_alias = @build_alias@
-+build_cpu = @build_cpu@
-+build_os = @build_os@
-+build_vendor = @build_vendor@
-+builddir = @builddir@
- codegen_extra_ldadd = @codegen_extra_ldadd@
- codegen_extra_sources = @codegen_extra_sources@
-+datadir = @datadir@
- datarootdir = @datarootdir@
-+docdir = @docdir@
-+dvidir = @dvidir@
-+exec_prefix = @exec_prefix@
- glib_cflags = @glib_cflags@
- glib_libs = @glib_libs@
- host = @host@
-+host_alias = @host_alias@
-+host_cpu = @host_cpu@
-+host_os = @host_os@
-+host_vendor = @host_vendor@
-+htmldir = @htmldir@
-+includedir = @includedir@
-+infodir = @infodir@
-+install_sh = @install_sh@
- installed_util_list = @installed_util_list@
-+libdir = @libdir@
-+libexecdir = @libexecdir@
-+localedir = @localedir@
-+localstatedir = @localstatedir@
-+mandir = @mandir@
-+mkdir_p = @mkdir_p@
-+oldincludedir = @oldincludedir@
-+pdfdir = @pdfdir@
-+prefix = @prefix@
-+program_transform_name = @program_transform_name@
-+psdir = @psdir@
-+sbindir = @sbindir@
-+sharedstatedir = @sharedstatedir@
- source_root_dir = @source_root_dir@
-+srcdir = @srcdir@
-+sysconfdir = @sysconfdir@
-+target_alias = @target_alias@
-+top_build_prefix = @top_build_prefix@
-+top_builddir = @top_builddir@
-+top_srcdir = @top_srcdir@
- use_pthreads = @use_pthreads@
--
- SUBDIRS = man1
--
- MAINTAINERCLEANFILES = Makefile.in
--mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
--CONFIG_CLEAN_FILES =
--DIST_COMMON = Makefile.am Makefile.in
--
-+all: all-recursive
-
--DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
--
--TAR = tar
--GZIP_ENV = --best
--all: all-redirect
- .SUFFIXES:
--$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4)
-- cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps doc/man/Makefile
--
-+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
-+ @for dep in $?; do \
-+ case '$(am__configure_deps)' in \
-+ *$$dep*) \
-+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-+ && { if test -f $@; then exit 0; else break; fi; }; \
-+ exit 1;; \
-+ esac; \
-+ done; \
-+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu doc/man/Makefile'; \
-+ $(am__cd) $(top_srcdir) && \
-+ $(AUTOMAKE) --gnu doc/man/Makefile
-+.PRECIOUS: Makefile
- Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-- cd $(top_builddir) \
-- && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
--
-+ @case '$?' in \
-+ *config.status*) \
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-+ *) \
-+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-+ esac;
-+
-+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+
-+$(top_srcdir)/configure: $(am__configure_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(am__aclocal_m4_deps):
-
- # This directory's subdirectories are mostly independent; you can cd
- # into them and run `make' without going through this Makefile.
-@@ -106,13 +230,14 @@
- # (1) if the variable is set in `config.status', edit `config.status'
- # (which will cause the Makefiles to be regenerated when you run `make');
- # (2) otherwise, pass the desired values on the `make' command line.
--
-- at SET_MAKE@
--
--all-recursive install-data-recursive install-exec-recursive \
--installdirs-recursive install-recursive uninstall-recursive \
--check-recursive installcheck-recursive info-recursive dvi-recursive:
-- @set fnord $(MAKEFLAGS); amf=$$2; \
-+$(RECURSIVE_TARGETS):
-+ @fail= failcom='exit 1'; \
-+ for f in x $$MAKEFLAGS; do \
-+ case $$f in \
-+ *=* | --[!k]*);; \
-+ *k*) failcom='fail=yes';; \
-+ esac; \
-+ done; \
- dot_seen=no; \
- target=`echo $@ | sed s/-recursive//`; \
- list='$(SUBDIRS)'; for subdir in $$list; do \
-@@ -123,22 +248,32 @@
- else \
- local_target="$$target"; \
- fi; \
-- (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-- || case "$$amf" in *=*) exit 1;; *k*) fail=yes;; *) exit 1;; esac; \
-+ ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-+ || eval $$failcom; \
- done; \
- if test "$$dot_seen" = "no"; then \
- $(MAKE) $(AM_MAKEFLAGS) "$$target-am" || exit 1; \
- fi; test -z "$$fail"
-
--mostlyclean-recursive clean-recursive distclean-recursive \
--maintainer-clean-recursive:
-- @set fnord $(MAKEFLAGS); amf=$$2; \
-+$(RECURSIVE_CLEAN_TARGETS):
-+ @fail= failcom='exit 1'; \
-+ for f in x $$MAKEFLAGS; do \
-+ case $$f in \
-+ *=* | --[!k]*);; \
-+ *k*) failcom='fail=yes';; \
-+ esac; \
-+ done; \
- dot_seen=no; \
-- rev=''; list='$(SUBDIRS)'; for subdir in $$list; do \
-+ case "$@" in \
-+ distclean-* | maintainer-clean-*) list='$(DIST_SUBDIRS)' ;; \
-+ *) list='$(SUBDIRS)' ;; \
-+ esac; \
-+ rev=''; for subdir in $$list; do \
-+ if test "$$subdir" = "."; then :; else \
- rev="$$subdir $$rev"; \
-- test "$$subdir" != "." || dot_seen=yes; \
-+ fi; \
- done; \
-- test "$$dot_seen" = "no" && rev=". $$rev"; \
-+ rev="$$rev ."; \
- target=`echo $@ | sed s/-recursive//`; \
- for subdir in $$rev; do \
- echo "Making $$target in $$subdir"; \
-@@ -147,141 +282,253 @@
- else \
- local_target="$$target"; \
- fi; \
-- (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-- || case "$$amf" in *=*) exit 1;; *k*) fail=yes;; *) exit 1;; esac; \
-+ ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-+ || eval $$failcom; \
- done && test -z "$$fail"
- tags-recursive:
- list='$(SUBDIRS)'; for subdir in $$list; do \
-- test "$$subdir" = . || (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
-+ test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
-+ done
-+ctags-recursive:
-+ list='$(SUBDIRS)'; for subdir in $$list; do \
-+ test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \
- done
-
-+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ mkid -fID $$unique
- tags: TAGS
-
--ID: $(HEADERS) $(SOURCES) $(LISP)
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- here=`pwd` && cd $(srcdir) \
-- && mkid -f$$here/ID $$unique $(LISP)
--
--TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) $(LISP)
-- tags=; \
-+TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ set x; \
- here=`pwd`; \
-+ if ($(ETAGS) --etags-include --version) >/dev/null 2>&1; then \
-+ include_option=--etags-include; \
-+ empty_fix=.; \
-+ else \
-+ include_option=--include; \
-+ empty_fix=; \
-+ fi; \
- list='$(SUBDIRS)'; for subdir in $$list; do \
- if test "$$subdir" = .; then :; else \
-- test -f $$subdir/TAGS && tags="$$tags -i $$here/$$subdir/TAGS"; \
-+ test ! -f $$subdir/TAGS || \
-+ set "$$@" "$$include_option=$$here/$$subdir/TAGS"; \
- fi; \
- done; \
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- test -z "$(ETAGS_ARGS)$$unique$(LISP)$$tags" \
-- || (cd $(srcdir) && etags -o $$here/TAGS $(ETAGS_ARGS) $$tags $$unique $(LISP))
--
--mostlyclean-tags:
--
--clean-tags:
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ shift; \
-+ if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
-+ test -n "$$unique" || unique=$$empty_fix; \
-+ if test $$# -gt 0; then \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ "$$@" $$unique; \
-+ else \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ $$unique; \
-+ fi; \
-+ fi
-+ctags: CTAGS
-+CTAGS: ctags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ test -z "$(CTAGS_ARGS)$$unique" \
-+ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-+ $$unique
-+
-+GTAGS:
-+ here=`$(am__cd) $(top_builddir) && pwd` \
-+ && $(am__cd) $(top_srcdir) \
-+ && gtags -i $(GTAGS_ARGS) "$$here"
-
- distclean-tags:
-- -rm -f TAGS ID
--
--maintainer-clean-tags:
--
--distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
--
--subdir = doc/man
-+ -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-
- distdir: $(DISTFILES)
-- @for file in $(DISTFILES); do \
-- d=$(srcdir); \
-+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ list='$(DISTFILES)'; \
-+ dist_files=`for file in $$list; do echo $$file; done | \
-+ sed -e "s|^$$srcdirstrip/||;t" \
-+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-+ case $$dist_files in \
-+ */*) $(MKDIR_P) `echo "$$dist_files" | \
-+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-+ sort -u` ;; \
-+ esac; \
-+ for file in $$dist_files; do \
-+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
- if test -d $$d/$$file; then \
-- cp -pr $$d/$$file $(distdir)/$$file; \
-+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-+ if test -d "$(distdir)/$$file"; then \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
- else \
-- test -f $(distdir)/$$file \
-- || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
-- || cp -p $$d/$$file $(distdir)/$$file || :; \
-+ test -f "$(distdir)/$$file" \
-+ || cp -p $$d/$$file "$(distdir)/$$file" \
-+ || exit 1; \
- fi; \
- done
-- for subdir in $(SUBDIRS); do \
-+ @list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
- if test "$$subdir" = .; then :; else \
-- test -d $(distdir)/$$subdir \
-- || mkdir $(distdir)/$$subdir \
-+ test -d "$(distdir)/$$subdir" \
-+ || $(MKDIR_P) "$(distdir)/$$subdir" \
- || exit 1; \
-- chmod 777 $(distdir)/$$subdir; \
-- (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir=../$(top_distdir) distdir=../$(distdir)/$$subdir distdir) \
-+ fi; \
-+ done
-+ @list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
-+ if test "$$subdir" = .; then :; else \
-+ dir1=$$subdir; dir2="$(distdir)/$$subdir"; \
-+ $(am__relativize); \
-+ new_distdir=$$reldir; \
-+ dir1=$$subdir; dir2="$(top_distdir)"; \
-+ $(am__relativize); \
-+ new_top_distdir=$$reldir; \
-+ echo " (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir="$$new_top_distdir" distdir="$$new_distdir" \\"; \
-+ echo " am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)"; \
-+ ($(am__cd) $$subdir && \
-+ $(MAKE) $(AM_MAKEFLAGS) \
-+ top_distdir="$$new_top_distdir" \
-+ distdir="$$new_distdir" \
-+ am__remove_distdir=: \
-+ am__skip_length_check=: \
-+ am__skip_mode_fix=: \
-+ distdir) \
- || exit 1; \
- fi; \
- done
--info-am:
--info: info-recursive
--dvi-am:
--dvi: dvi-recursive
- check-am: all-am
- check: check-recursive
--installcheck-am:
--installcheck: installcheck-recursive
--install-exec-am:
-+all-am: Makefile
-+installdirs: installdirs-recursive
-+installdirs-am:
-+install: install-recursive
- install-exec: install-exec-recursive
--
--install-data-am:
- install-data: install-data-recursive
-+uninstall: uninstall-recursive
-
- install-am: all-am
- @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
--install: install-recursive
--uninstall-am:
--uninstall: uninstall-recursive
--all-am: Makefile
--all-redirect: all-recursive
--install-strip:
-- $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
--installdirs: installdirs-recursive
--installdirs-am:
--
-
-+installcheck: installcheck-recursive
-+install-strip:
-+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-+ `test -z '$(STRIP)' || \
-+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
- mostlyclean-generic:
-
- clean-generic:
-
- distclean-generic:
-- -rm -f Makefile $(CONFIG_CLEAN_FILES)
-- -rm -f config.cache config.log stamp-h stamp-h[0-9]*
-+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
- maintainer-clean-generic:
-+ @echo "This command is intended for maintainers to use"
-+ @echo "it deletes files that may require special tools to rebuild."
- -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
--mostlyclean-am: mostlyclean-tags mostlyclean-generic
-+clean: clean-recursive
-
--mostlyclean: mostlyclean-recursive
-+clean-am: clean-generic mostlyclean-am
-
--clean-am: clean-tags clean-generic mostlyclean-am
-+distclean: distclean-recursive
-+ -rm -f Makefile
-+distclean-am: clean-am distclean-generic distclean-tags
-
--clean: clean-recursive
-+dvi: dvi-recursive
-
--distclean-am: distclean-tags distclean-generic clean-am
-+dvi-am:
-
--distclean: distclean-recursive
-+html: html-recursive
-
--maintainer-clean-am: maintainer-clean-tags maintainer-clean-generic \
-- distclean-am
-- @echo "This command is intended for maintainers to use;"
-- @echo "it deletes files that may require special tools to rebuild."
-+html-am:
-+
-+info: info-recursive
-+
-+info-am:
-+
-+install-data-am:
-+
-+install-dvi: install-dvi-recursive
-+
-+install-dvi-am:
-+
-+install-exec-am:
-+
-+install-html: install-html-recursive
-+
-+install-html-am:
-+
-+install-info: install-info-recursive
-+
-+install-info-am:
-+
-+install-man:
-+
-+install-pdf: install-pdf-recursive
-+
-+install-pdf-am:
-+
-+install-ps: install-ps-recursive
-+
-+install-ps-am:
-+
-+installcheck-am:
-
- maintainer-clean: maintainer-clean-recursive
-+ -rm -f Makefile
-+maintainer-clean-am: distclean-am maintainer-clean-generic
-+
-+mostlyclean: mostlyclean-recursive
-+
-+mostlyclean-am: mostlyclean-generic
-+
-+pdf: pdf-recursive
-+
-+pdf-am:
-+
-+ps: ps-recursive
-+
-+ps-am:
-+
-+uninstall-am:
-+
-+.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) ctags-recursive \
-+ install-am install-strip tags-recursive
-
--.PHONY: install-data-recursive uninstall-data-recursive \
--install-exec-recursive uninstall-exec-recursive installdirs-recursive \
--uninstalldirs-recursive all-recursive check-recursive \
--installcheck-recursive info-recursive dvi-recursive \
--mostlyclean-recursive distclean-recursive clean-recursive \
--maintainer-clean-recursive tags tags-recursive mostlyclean-tags \
--distclean-tags clean-tags maintainer-clean-tags distdir info-am info \
--dvi-am dvi check check-am installcheck-am installcheck install-exec-am \
--install-exec install-data-am install-data install-am install \
--uninstall-am uninstall all-redirect all-am all installdirs-am \
--installdirs mostlyclean-generic distclean-generic clean-generic \
--maintainer-clean-generic clean mostlyclean distclean maintainer-clean
-+.PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
-+ all all-am check check-am clean clean-generic ctags \
-+ ctags-recursive distclean distclean-generic distclean-tags \
-+ distdir dvi dvi-am html html-am info info-am install \
-+ install-am install-data install-data-am install-dvi \
-+ install-dvi-am install-exec install-exec-am install-html \
-+ install-html-am install-info install-info-am install-man \
-+ install-pdf install-pdf-am install-ps install-ps-am \
-+ install-strip installcheck installcheck-am installdirs \
-+ installdirs-am maintainer-clean maintainer-clean-generic \
-+ mostlyclean mostlyclean-generic pdf pdf-am ps ps-am tags \
-+ tags-recursive uninstall uninstall-am
-
-
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -ubrN exonerate-2.2.0.orig/doc/man/man1/Makefile.in exonerate-2.2.0/doc/man/man1/Makefile.in
---- exonerate-2.2.0.orig/doc/man/man1/Makefile.in 2008-10-17 12:05:00.000000000 +0200
-+++ exonerate-2.2.0/doc/man/man1/Makefile.in 2011-12-12 13:33:16.000000000 +0100
-@@ -1,6 +1,9 @@
--# Makefile.in generated automatically by automake 1.4-p6 from Makefile.am
-+# Makefile.in generated by automake 1.11.1 from Makefile.am.
-+# @configure_input@
-
--# Copyright (C) 1994, 1995-8, 1999, 2001 Free Software Foundation, Inc.
-+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
-+# Inc.
- # This Makefile.in is free software; the Free Software Foundation
- # gives unlimited permission to copy and/or distribute it,
- # with or without modifications, as long as this notice is preserved.
-@@ -10,219 +13,403 @@
- # even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- # PARTICULAR PURPOSE.
-
--
--SHELL = @SHELL@
--
--srcdir = @srcdir@
--top_srcdir = @top_srcdir@
-+ at SET_MAKE@
- VPATH = @srcdir@
--prefix = @prefix@
--exec_prefix = @exec_prefix@
--
--bindir = @bindir@
--sbindir = @sbindir@
--libexecdir = @libexecdir@
--datadir = @datadir@
--sysconfdir = @sysconfdir@
--sharedstatedir = @sharedstatedir@
--localstatedir = @localstatedir@
--libdir = @libdir@
--infodir = @infodir@
--mandir = @mandir@
--includedir = @includedir@
--oldincludedir = /usr/include
--
--DESTDIR =
--
- pkgdatadir = $(datadir)/@PACKAGE@
--pkglibdir = $(libdir)/@PACKAGE@
- pkgincludedir = $(includedir)/@PACKAGE@
--
--top_builddir = ../../..
--
--ACLOCAL = @ACLOCAL@
--AUTOCONF = @AUTOCONF@
--AUTOMAKE = @AUTOMAKE@
--AUTOHEADER = @AUTOHEADER@
--
--INSTALL = @INSTALL@
--INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
--INSTALL_DATA = @INSTALL_DATA@
--INSTALL_SCRIPT = @INSTALL_SCRIPT@
--transform = @program_transform_name@
--
-+pkglibdir = $(libdir)/@PACKAGE@
-+pkglibexecdir = $(libexecdir)/@PACKAGE@
-+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-+install_sh_DATA = $(install_sh) -c -m 644
-+install_sh_PROGRAM = $(install_sh) -c
-+install_sh_SCRIPT = $(install_sh) -c
-+INSTALL_HEADER = $(INSTALL_DATA)
-+transform = $(program_transform_name)
- NORMAL_INSTALL = :
- PRE_INSTALL = :
- POST_INSTALL = :
- NORMAL_UNINSTALL = :
- PRE_UNINSTALL = :
- POST_UNINSTALL = :
--host_alias = @host_alias@
-+build_triplet = @build@
- host_triplet = @host@
-+subdir = doc/man/man1
-+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
-+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-+am__aclocal_m4_deps = $(top_srcdir)/configure.in
-+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-+ $(ACLOCAL_M4)
-+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
-+CONFIG_CLEAN_FILES =
-+CONFIG_CLEAN_VPATH_FILES =
-+SOURCES =
-+DIST_SOURCES =
-+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
-+am__vpath_adj = case $$p in \
-+ $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
-+ *) f=$$p;; \
-+ esac;
-+am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
-+am__install_max = 40
-+am__nobase_strip_setup = \
-+ srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
-+am__nobase_strip = \
-+ for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
-+am__nobase_list = $(am__nobase_strip_setup); \
-+ for p in $$list; do echo "$$p $$p"; done | \
-+ sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
-+ $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
-+ if (++n[$$2] == $(am__install_max)) \
-+ { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
-+ END { for (dir in files) print dir, files[dir] }'
-+am__base_list = \
-+ sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
-+ sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
-+man1dir = $(mandir)/man1
-+am__installdirs = "$(DESTDIR)$(man1dir)"
-+NROFF = nroff
-+MANS = $(man_MANS)
-+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-+ACLOCAL = @ACLOCAL@
-+AMTAR = @AMTAR@
-+AUTOCONF = @AUTOCONF@
-+AUTOHEADER = @AUTOHEADER@
-+AUTOMAKE = @AUTOMAKE@
-+AWK = @AWK@
- CC = @CC@
-+CCDEPMODE = @CCDEPMODE@
-+CFLAGS = @CFLAGS@
-+CPP = @CPP@
-+CPPFLAGS = @CPPFLAGS@
-+CYGPATH_W = @CYGPATH_W@
-+DEFS = @DEFS@
-+DEPDIR = @DEPDIR@
-+ECHO_C = @ECHO_C@
-+ECHO_N = @ECHO_N@
-+ECHO_T = @ECHO_T@
-+EGREP = @EGREP@
-+EXEEXT = @EXEEXT@
- GLIB_CONFIG = @GLIB_CONFIG@
--HAVE_LIB = @HAVE_LIB@
--LIB = @LIB@
--LTLIB = @LTLIB@
-+GREP = @GREP@
-+INSTALL = @INSTALL@
-+INSTALL_DATA = @INSTALL_DATA@
-+INSTALL_PROGRAM = @INSTALL_PROGRAM@
-+INSTALL_SCRIPT = @INSTALL_SCRIPT@
-+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-+LDFLAGS = @LDFLAGS@
-+LIBOBJS = @LIBOBJS@
-+LIBS = @LIBS@
-+LTLIBOBJS = @LTLIBOBJS@
- MAKEINFO = @MAKEINFO@
-+MKDIR_P = @MKDIR_P@
-+OBJEXT = @OBJEXT@
- PACKAGE = @PACKAGE@
-+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-+PACKAGE_NAME = @PACKAGE_NAME@
-+PACKAGE_STRING = @PACKAGE_STRING@
-+PACKAGE_TARNAME = @PACKAGE_TARNAME@
-+PACKAGE_URL = @PACKAGE_URL@
-+PACKAGE_VERSION = @PACKAGE_VERSION@
-+PATH_SEPARATOR = @PATH_SEPARATOR@
- PKG_CONFIG = @PKG_CONFIG@
-+SET_MAKE = @SET_MAKE@
-+SHELL = @SHELL@
-+STRIP = @STRIP@
- VERSION = @VERSION@
-+abs_builddir = @abs_builddir@
-+abs_srcdir = @abs_srcdir@
-+abs_top_builddir = @abs_top_builddir@
-+abs_top_srcdir = @abs_top_srcdir@
-+ac_ct_CC = @ac_ct_CC@
-+am__include = @am__include@
-+am__leading_dot = @am__leading_dot@
-+am__quote = @am__quote@
-+am__tar = @am__tar@
-+am__untar = @am__untar@
-+bindir = @bindir@
-+build = @build@
-+build_alias = @build_alias@
-+build_cpu = @build_cpu@
-+build_os = @build_os@
-+build_vendor = @build_vendor@
-+builddir = @builddir@
- codegen_extra_ldadd = @codegen_extra_ldadd@
- codegen_extra_sources = @codegen_extra_sources@
-+datadir = @datadir@
- datarootdir = @datarootdir@
-+docdir = @docdir@
-+dvidir = @dvidir@
-+exec_prefix = @exec_prefix@
- glib_cflags = @glib_cflags@
- glib_libs = @glib_libs@
- host = @host@
-+host_alias = @host_alias@
-+host_cpu = @host_cpu@
-+host_os = @host_os@
-+host_vendor = @host_vendor@
-+htmldir = @htmldir@
-+includedir = @includedir@
-+infodir = @infodir@
-+install_sh = @install_sh@
- installed_util_list = @installed_util_list@
-+libdir = @libdir@
-+libexecdir = @libexecdir@
-+localedir = @localedir@
-+localstatedir = @localstatedir@
-+mandir = @mandir@
-+mkdir_p = @mkdir_p@
-+oldincludedir = @oldincludedir@
-+pdfdir = @pdfdir@
-+prefix = @prefix@
-+program_transform_name = @program_transform_name@
-+psdir = @psdir@
-+sbindir = @sbindir@
-+sharedstatedir = @sharedstatedir@
- source_root_dir = @source_root_dir@
-+srcdir = @srcdir@
-+sysconfdir = @sysconfdir@
-+target_alias = @target_alias@
-+top_build_prefix = @top_build_prefix@
-+top_builddir = @top_builddir@
-+top_srcdir = @top_srcdir@
- use_pthreads = @use_pthreads@
--
- man_MANS = exonerate.1 ipcress.1 exonerate-server.1 fastautils.1
- EXTRA_DIST = $(man_MANS)
--
- MAINTAINERCLEANFILES = Makefile.in
--mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
--CONFIG_CLEAN_FILES =
--man1dir = $(mandir)/man1
--MANS = $(man_MANS)
-+all: all-am
-
--NROFF = nroff
--DIST_COMMON = Makefile.am Makefile.in
--
--
--DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
--
--TAR = tar
--GZIP_ENV = --best
--all: all-redirect
- .SUFFIXES:
--$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4)
-- cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps doc/man/man1/Makefile
--
--Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-- cd $(top_builddir) \
-- && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
--
--
--install-man1:
-- $(mkinstalldirs) $(DESTDIR)$(man1dir)
-- @list='$(man1_MANS)'; \
-- l2='$(man_MANS)'; for i in $$l2; do \
-- case "$$i" in \
-- *.1*) list="$$list $$i" ;; \
-+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
-+ @for dep in $?; do \
-+ case '$(am__configure_deps)' in \
-+ *$$dep*) \
-+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-+ && { if test -f $@; then exit 0; else break; fi; }; \
-+ exit 1;; \
- esac; \
- done; \
-- for i in $$list; do \
-- if test -f $(srcdir)/$$i; then file=$(srcdir)/$$i; \
-- else file=$$i; fi; \
-- ext=`echo $$i | sed -e 's/^.*\\.//'`; \
-- inst=`echo $$i | sed -e 's/\\.[0-9a-z]*$$//'`; \
-- inst=`echo $$inst | sed '$(transform)'`.$$ext; \
-- echo " $(INSTALL_DATA) $$file $(DESTDIR)$(man1dir)/$$inst"; \
-- $(INSTALL_DATA) $$file $(DESTDIR)$(man1dir)/$$inst; \
-- done
-+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu doc/man/man1/Makefile'; \
-+ $(am__cd) $(top_srcdir) && \
-+ $(AUTOMAKE) --gnu doc/man/man1/Makefile
-+.PRECIOUS: Makefile
-+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-+ @case '$?' in \
-+ *config.status*) \
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-+ *) \
-+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-+ esac;
-+
-+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+
-+$(top_srcdir)/configure: $(am__configure_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(am__aclocal_m4_deps):
-+install-man1: $(man_MANS)
-+ @$(NORMAL_INSTALL)
-+ test -z "$(man1dir)" || $(MKDIR_P) "$(DESTDIR)$(man1dir)"
-+ @list=''; test -n "$(man1dir)" || exit 0; \
-+ { for i in $$list; do echo "$$i"; done; \
-+ l2='$(man_MANS)'; for i in $$l2; do echo "$$i"; done | \
-+ sed -n '/\.1[a-z]*$$/p'; \
-+ } | while read p; do \
-+ if test -f $$p; then d=; else d="$(srcdir)/"; fi; \
-+ echo "$$d$$p"; echo "$$p"; \
-+ done | \
-+ sed -e 'n;s,.*/,,;p;h;s,.*\.,,;s,^[^1][0-9a-z]*$$,1,;x' \
-+ -e 's,\.[0-9a-z]*$$,,;$(transform);G;s,\n,.,' | \
-+ sed 'N;N;s,\n, ,g' | { \
-+ list=; while read file base inst; do \
-+ if test "$$base" = "$$inst"; then list="$$list $$file"; else \
-+ echo " $(INSTALL_DATA) '$$file' '$(DESTDIR)$(man1dir)/$$inst'"; \
-+ $(INSTALL_DATA) "$$file" "$(DESTDIR)$(man1dir)/$$inst" || exit $$?; \
-+ fi; \
-+ done; \
-+ for i in $$list; do echo "$$i"; done | $(am__base_list) | \
-+ while read files; do \
-+ test -z "$$files" || { \
-+ echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(man1dir)'"; \
-+ $(INSTALL_DATA) $$files "$(DESTDIR)$(man1dir)" || exit $$?; }; \
-+ done; }
-
- uninstall-man1:
-- @list='$(man1_MANS)'; \
-- l2='$(man_MANS)'; for i in $$l2; do \
-- case "$$i" in \
-- *.1*) list="$$list $$i" ;; \
-- esac; \
-- done; \
-- for i in $$list; do \
-- ext=`echo $$i | sed -e 's/^.*\\.//'`; \
-- inst=`echo $$i | sed -e 's/\\.[0-9a-z]*$$//'`; \
-- inst=`echo $$inst | sed '$(transform)'`.$$ext; \
-- echo " rm -f $(DESTDIR)$(man1dir)/$$inst"; \
-- rm -f $(DESTDIR)$(man1dir)/$$inst; \
-- done
--install-man: $(MANS)
-- @$(NORMAL_INSTALL)
-- $(MAKE) $(AM_MAKEFLAGS) install-man1
--uninstall-man:
- @$(NORMAL_UNINSTALL)
-- $(MAKE) $(AM_MAKEFLAGS) uninstall-man1
-+ @list=''; test -n "$(man1dir)" || exit 0; \
-+ files=`{ for i in $$list; do echo "$$i"; done; \
-+ l2='$(man_MANS)'; for i in $$l2; do echo "$$i"; done | \
-+ sed -n '/\.1[a-z]*$$/p'; \
-+ } | sed -e 's,.*/,,;h;s,.*\.,,;s,^[^1][0-9a-z]*$$,1,;x' \
-+ -e 's,\.[0-9a-z]*$$,,;$(transform);G;s,\n,.,'`; \
-+ test -z "$$files" || { \
-+ echo " ( cd '$(DESTDIR)$(man1dir)' && rm -f" $$files ")"; \
-+ cd "$(DESTDIR)$(man1dir)" && rm -f $$files; }
- tags: TAGS
- TAGS:
-
-+ctags: CTAGS
-+CTAGS:
-
--distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
--
--subdir = doc/man/man1
-
- distdir: $(DISTFILES)
-- @for file in $(DISTFILES); do \
-- d=$(srcdir); \
-+ @list='$(MANS)'; if test -n "$$list"; then \
-+ list=`for p in $$list; do \
-+ if test -f $$p; then d=; else d="$(srcdir)/"; fi; \
-+ if test -f "$$d$$p"; then echo "$$d$$p"; else :; fi; done`; \
-+ if test -n "$$list" && \
-+ grep 'ab help2man is required to generate this page' $$list >/dev/null; then \
-+ echo "error: found man pages containing the \`missing help2man' replacement text:" >&2; \
-+ grep -l 'ab help2man is required to generate this page' $$list | sed 's/^/ /' >&2; \
-+ echo " to fix them, install help2man, remove and regenerate the man pages;" >&2; \
-+ echo " typically \`make maintainer-clean' will remove them" >&2; \
-+ exit 1; \
-+ else :; fi; \
-+ else :; fi
-+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ list='$(DISTFILES)'; \
-+ dist_files=`for file in $$list; do echo $$file; done | \
-+ sed -e "s|^$$srcdirstrip/||;t" \
-+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-+ case $$dist_files in \
-+ */*) $(MKDIR_P) `echo "$$dist_files" | \
-+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-+ sort -u` ;; \
-+ esac; \
-+ for file in $$dist_files; do \
-+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
- if test -d $$d/$$file; then \
-- cp -pr $$d/$$file $(distdir)/$$file; \
-+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-+ if test -d "$(distdir)/$$file"; then \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
- else \
-- test -f $(distdir)/$$file \
-- || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
-- || cp -p $$d/$$file $(distdir)/$$file || :; \
-+ test -f "$(distdir)/$$file" \
-+ || cp -p $$d/$$file "$(distdir)/$$file" \
-+ || exit 1; \
- fi; \
- done
--info-am:
--info: info-am
--dvi-am:
--dvi: dvi-am
- check-am: all-am
- check: check-am
--installcheck-am:
--installcheck: installcheck-am
--install-exec-am:
-+all-am: Makefile $(MANS)
-+installdirs:
-+ for dir in "$(DESTDIR)$(man1dir)"; do \
-+ test -z "$$dir" || $(MKDIR_P) "$$dir"; \
-+ done
-+install: install-am
- install-exec: install-exec-am
--
--install-data-am: install-man
- install-data: install-data-am
-+uninstall: uninstall-am
-
- install-am: all-am
- @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
--install: install-am
--uninstall-am: uninstall-man
--uninstall: uninstall-am
--all-am: Makefile $(MANS)
--all-redirect: all-am
--install-strip:
-- $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
--installdirs:
-- $(mkinstalldirs) $(DESTDIR)$(mandir)/man1
--
-
-+installcheck: installcheck-am
-+install-strip:
-+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-+ `test -z '$(STRIP)' || \
-+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
- mostlyclean-generic:
-
- clean-generic:
-
- distclean-generic:
-- -rm -f Makefile $(CONFIG_CLEAN_FILES)
-- -rm -f config.cache config.log stamp-h stamp-h[0-9]*
-+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
- maintainer-clean-generic:
-+ @echo "This command is intended for maintainers to use"
-+ @echo "it deletes files that may require special tools to rebuild."
- -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
--mostlyclean-am: mostlyclean-generic
--
--mostlyclean: mostlyclean-am
-+clean: clean-am
-
- clean-am: clean-generic mostlyclean-am
-
--clean: clean-am
-+distclean: distclean-am
-+ -rm -f Makefile
-+distclean-am: clean-am distclean-generic
-
--distclean-am: distclean-generic clean-am
-+dvi: dvi-am
-
--distclean: distclean-am
-+dvi-am:
-
--maintainer-clean-am: maintainer-clean-generic distclean-am
-- @echo "This command is intended for maintainers to use;"
-- @echo "it deletes files that may require special tools to rebuild."
-+html: html-am
-+
-+html-am:
-+
-+info: info-am
-+
-+info-am:
-+
-+install-data-am: install-man
-+
-+install-dvi: install-dvi-am
-+
-+install-dvi-am:
-+
-+install-exec-am:
-+
-+install-html: install-html-am
-+
-+install-html-am:
-+
-+install-info: install-info-am
-+
-+install-info-am:
-+
-+install-man: install-man1
-+
-+install-pdf: install-pdf-am
-+
-+install-pdf-am:
-+
-+install-ps: install-ps-am
-+
-+install-ps-am:
-+
-+installcheck-am:
-
- maintainer-clean: maintainer-clean-am
-+ -rm -f Makefile
-+maintainer-clean-am: distclean-am maintainer-clean-generic
-+
-+mostlyclean: mostlyclean-am
-+
-+mostlyclean-am: mostlyclean-generic
-+
-+pdf: pdf-am
-+
-+pdf-am:
-+
-+ps: ps-am
-+
-+ps-am:
-+
-+uninstall-am: uninstall-man
-+
-+uninstall-man: uninstall-man1
-+
-+.MAKE: install-am install-strip
-
--.PHONY: install-man1 uninstall-man1 install-man uninstall-man tags \
--distdir info-am info dvi-am dvi check check-am installcheck-am \
--installcheck install-exec-am install-exec install-data-am install-data \
--install-am install uninstall-am uninstall all-redirect all-am all \
--installdirs mostlyclean-generic distclean-generic clean-generic \
--maintainer-clean-generic clean mostlyclean distclean maintainer-clean
-+.PHONY: all all-am check check-am clean clean-generic distclean \
-+ distclean-generic distdir dvi dvi-am html html-am info info-am \
-+ install install-am install-data install-data-am install-dvi \
-+ install-dvi-am install-exec install-exec-am install-html \
-+ install-html-am install-info install-info-am install-man \
-+ install-man1 install-pdf install-pdf-am install-ps \
-+ install-ps-am install-strip installcheck installcheck-am \
-+ installdirs maintainer-clean maintainer-clean-generic \
-+ mostlyclean mostlyclean-generic pdf pdf-am ps ps-am uninstall \
-+ uninstall-am uninstall-man uninstall-man1
-
-
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -ubrN exonerate-2.2.0.orig/Makefile.in exonerate-2.2.0/Makefile.in
---- exonerate-2.2.0.orig/Makefile.in 2008-10-17 12:04:50.000000000 +0200
-+++ exonerate-2.2.0/Makefile.in 2011-12-12 13:33:17.000000000 +0100
-@@ -1,6 +1,9 @@
--# Makefile.in generated automatically by automake 1.4-p6 from Makefile.am
-+# Makefile.in generated by automake 1.11.1 from Makefile.am.
-+# @configure_input@
-
--# Copyright (C) 1994, 1995-8, 1999, 2001 Free Software Foundation, Inc.
-+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
-+# Inc.
- # This Makefile.in is free software; the Free Software Foundation
- # gives unlimited permission to copy and/or distribute it,
- # with or without modifications, as long as this notice is preserved.
-@@ -10,106 +13,238 @@
- # even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- # PARTICULAR PURPOSE.
-
--
--SHELL = @SHELL@
--
--srcdir = @srcdir@
--top_srcdir = @top_srcdir@
-+ at SET_MAKE@
- VPATH = @srcdir@
--prefix = @prefix@
--exec_prefix = @exec_prefix@
--
--bindir = @bindir@
--sbindir = @sbindir@
--libexecdir = @libexecdir@
--datadir = @datadir@
--sysconfdir = @sysconfdir@
--sharedstatedir = @sharedstatedir@
--localstatedir = @localstatedir@
--libdir = @libdir@
--infodir = @infodir@
--mandir = @mandir@
--includedir = @includedir@
--oldincludedir = /usr/include
--
--DESTDIR =
--
- pkgdatadir = $(datadir)/@PACKAGE@
--pkglibdir = $(libdir)/@PACKAGE@
- pkgincludedir = $(includedir)/@PACKAGE@
--
--top_builddir = .
--
--ACLOCAL = @ACLOCAL@
--AUTOCONF = @AUTOCONF@
--AUTOMAKE = @AUTOMAKE@
--AUTOHEADER = @AUTOHEADER@
--
--INSTALL = @INSTALL@
--INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
--INSTALL_DATA = @INSTALL_DATA@
--INSTALL_SCRIPT = @INSTALL_SCRIPT@
--transform = @program_transform_name@
--
-+pkglibdir = $(libdir)/@PACKAGE@
-+pkglibexecdir = $(libexecdir)/@PACKAGE@
-+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-+install_sh_DATA = $(install_sh) -c -m 644
-+install_sh_PROGRAM = $(install_sh) -c
-+install_sh_SCRIPT = $(install_sh) -c
-+INSTALL_HEADER = $(INSTALL_DATA)
-+transform = $(program_transform_name)
- NORMAL_INSTALL = :
- PRE_INSTALL = :
- POST_INSTALL = :
- NORMAL_UNINSTALL = :
- PRE_UNINSTALL = :
- POST_UNINSTALL = :
--host_alias = @host_alias@
-+build_triplet = @build@
- host_triplet = @host@
-+subdir = .
-+DIST_COMMON = README $(am__configure_deps) $(srcdir)/Makefile.am \
-+ $(srcdir)/Makefile.in $(top_srcdir)/configure AUTHORS COPYING \
-+ ChangeLog INSTALL NEWS TODO config.guess config.sub depcomp \
-+ install-sh missing mkinstalldirs
-+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-+am__aclocal_m4_deps = $(top_srcdir)/configure.in
-+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-+ $(ACLOCAL_M4)
-+am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \
-+ configure.lineno config.status.lineno
-+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
-+CONFIG_CLEAN_FILES =
-+CONFIG_CLEAN_VPATH_FILES =
-+SOURCES =
-+DIST_SOURCES =
-+RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
-+ html-recursive info-recursive install-data-recursive \
-+ install-dvi-recursive install-exec-recursive \
-+ install-html-recursive install-info-recursive \
-+ install-pdf-recursive install-ps-recursive install-recursive \
-+ installcheck-recursive installdirs-recursive pdf-recursive \
-+ ps-recursive uninstall-recursive
-+RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive \
-+ distclean-recursive maintainer-clean-recursive
-+AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
-+ $(RECURSIVE_CLEAN_TARGETS:-recursive=) tags TAGS ctags CTAGS \
-+ distdir dist dist-all distcheck
-+ETAGS = etags
-+CTAGS = ctags
-+DIST_SUBDIRS = $(SUBDIRS)
-+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-+distdir = $(PACKAGE)-$(VERSION)
-+top_distdir = $(distdir)
-+am__remove_distdir = \
-+ { test ! -d "$(distdir)" \
-+ || { find "$(distdir)" -type d ! -perm -200 -exec chmod u+w {} ';' \
-+ && rm -fr "$(distdir)"; }; }
-+am__relativize = \
-+ dir0=`pwd`; \
-+ sed_first='s,^\([^/]*\)/.*$$,\1,'; \
-+ sed_rest='s,^[^/]*/*,,'; \
-+ sed_last='s,^.*/\([^/]*\)$$,\1,'; \
-+ sed_butlast='s,/*[^/]*$$,,'; \
-+ while test -n "$$dir1"; do \
-+ first=`echo "$$dir1" | sed -e "$$sed_first"`; \
-+ if test "$$first" != "."; then \
-+ if test "$$first" = ".."; then \
-+ dir2=`echo "$$dir0" | sed -e "$$sed_last"`/"$$dir2"; \
-+ dir0=`echo "$$dir0" | sed -e "$$sed_butlast"`; \
-+ else \
-+ first2=`echo "$$dir2" | sed -e "$$sed_first"`; \
-+ if test "$$first2" = "$$first"; then \
-+ dir2=`echo "$$dir2" | sed -e "$$sed_rest"`; \
-+ else \
-+ dir2="../$$dir2"; \
-+ fi; \
-+ dir0="$$dir0"/"$$first"; \
-+ fi; \
-+ fi; \
-+ dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \
-+ done; \
-+ reldir="$$dir2"
-+DIST_ARCHIVES = $(distdir).tar.gz
-+GZIP_ENV = --best
-+distuninstallcheck_listfiles = find . -type f -print
-+distcleancheck_listfiles = find . -type f -print
-+ACLOCAL = @ACLOCAL@
-+AMTAR = @AMTAR@
-+AUTOCONF = @AUTOCONF@
-+AUTOHEADER = @AUTOHEADER@
-+AUTOMAKE = @AUTOMAKE@
-+AWK = @AWK@
- CC = @CC@
-+CCDEPMODE = @CCDEPMODE@
-+CFLAGS = @CFLAGS@
-+CPP = @CPP@
-+CPPFLAGS = @CPPFLAGS@
-+CYGPATH_W = @CYGPATH_W@
-+DEFS = @DEFS@
-+DEPDIR = @DEPDIR@
-+ECHO_C = @ECHO_C@
-+ECHO_N = @ECHO_N@
-+ECHO_T = @ECHO_T@
-+EGREP = @EGREP@
-+EXEEXT = @EXEEXT@
- GLIB_CONFIG = @GLIB_CONFIG@
--HAVE_LIB = @HAVE_LIB@
--LIB = @LIB@
--LTLIB = @LTLIB@
-+GREP = @GREP@
-+INSTALL = @INSTALL@
-+INSTALL_DATA = @INSTALL_DATA@
-+INSTALL_PROGRAM = @INSTALL_PROGRAM@
-+INSTALL_SCRIPT = @INSTALL_SCRIPT@
-+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-+LDFLAGS = @LDFLAGS@
-+LIBOBJS = @LIBOBJS@
-+LIBS = @LIBS@
-+LTLIBOBJS = @LTLIBOBJS@
- MAKEINFO = @MAKEINFO@
-+MKDIR_P = @MKDIR_P@
-+OBJEXT = @OBJEXT@
- PACKAGE = @PACKAGE@
-+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-+PACKAGE_NAME = @PACKAGE_NAME@
-+PACKAGE_STRING = @PACKAGE_STRING@
-+PACKAGE_TARNAME = @PACKAGE_TARNAME@
-+PACKAGE_URL = @PACKAGE_URL@
-+PACKAGE_VERSION = @PACKAGE_VERSION@
-+PATH_SEPARATOR = @PATH_SEPARATOR@
- PKG_CONFIG = @PKG_CONFIG@
-+SET_MAKE = @SET_MAKE@
-+SHELL = @SHELL@
-+STRIP = @STRIP@
- VERSION = @VERSION@
-+abs_builddir = @abs_builddir@
-+abs_srcdir = @abs_srcdir@
-+abs_top_builddir = @abs_top_builddir@
-+abs_top_srcdir = @abs_top_srcdir@
-+ac_ct_CC = @ac_ct_CC@
-+am__include = @am__include@
-+am__leading_dot = @am__leading_dot@
-+am__quote = @am__quote@
-+am__tar = @am__tar@
-+am__untar = @am__untar@
-+bindir = @bindir@
-+build = @build@
-+build_alias = @build_alias@
-+build_cpu = @build_cpu@
-+build_os = @build_os@
-+build_vendor = @build_vendor@
-+builddir = @builddir@
- codegen_extra_ldadd = @codegen_extra_ldadd@
- codegen_extra_sources = @codegen_extra_sources@
-+datadir = @datadir@
- datarootdir = @datarootdir@
-+docdir = @docdir@
-+dvidir = @dvidir@
-+exec_prefix = @exec_prefix@
- glib_cflags = @glib_cflags@
- glib_libs = @glib_libs@
- host = @host@
-+host_alias = @host_alias@
-+host_cpu = @host_cpu@
-+host_os = @host_os@
-+host_vendor = @host_vendor@
-+htmldir = @htmldir@
-+includedir = @includedir@
-+infodir = @infodir@
-+install_sh = @install_sh@
- installed_util_list = @installed_util_list@
-+libdir = @libdir@
-+libexecdir = @libexecdir@
-+localedir = @localedir@
-+localstatedir = @localstatedir@
-+mandir = @mandir@
-+mkdir_p = @mkdir_p@
-+oldincludedir = @oldincludedir@
-+pdfdir = @pdfdir@
-+prefix = @prefix@
-+program_transform_name = @program_transform_name@
-+psdir = @psdir@
-+sbindir = @sbindir@
-+sharedstatedir = @sharedstatedir@
- source_root_dir = @source_root_dir@
-+srcdir = @srcdir@
-+sysconfdir = @sysconfdir@
-+target_alias = @target_alias@
-+top_build_prefix = @top_build_prefix@
-+top_builddir = @top_builddir@
-+top_srcdir = @top_srcdir@
- use_pthreads = @use_pthreads@
--
- SUBDIRS = doc src test
-+MAINTAINERCLEANFILES = Makefile.in aclocal.m4 \
-+ config.h.in configure \
-+ tags
-
--MAINTAINERCLEANFILES = Makefile.in aclocal.m4 config.h.in configure tags
--
--ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
--mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
--CONFIG_CLEAN_FILES =
--DIST_COMMON = README AUTHORS COPYING ChangeLog INSTALL Makefile.am \
--Makefile.in NEWS TODO aclocal.m4 config.guess config.sub configure \
--configure.in install-sh missing mkinstalldirs
--
-+all: all-recursive
-
--DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
--
--TAR = tar
--GZIP_ENV = --best
--all: all-redirect
- .SUFFIXES:
--$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4)
-- cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps Makefile
--
-+am--refresh:
-+ @:
-+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
-+ @for dep in $?; do \
-+ case '$(am__configure_deps)' in \
-+ *$$dep*) \
-+ echo ' cd $(srcdir) && $(AUTOMAKE) --gnu'; \
-+ $(am__cd) $(srcdir) && $(AUTOMAKE) --gnu \
-+ && exit 0; \
-+ exit 1;; \
-+ esac; \
-+ done; \
-+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu Makefile'; \
-+ $(am__cd) $(top_srcdir) && \
-+ $(AUTOMAKE) --gnu Makefile
-+.PRECIOUS: Makefile
- Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-- cd $(top_builddir) \
-- && CONFIG_FILES=$@ CONFIG_HEADERS= $(SHELL) ./config.status
--
--$(ACLOCAL_M4): configure.in
-- cd $(srcdir) && $(ACLOCAL)
-+ @case '$?' in \
-+ *config.status*) \
-+ echo ' $(SHELL) ./config.status'; \
-+ $(SHELL) ./config.status;; \
-+ *) \
-+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe)'; \
-+ cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe);; \
-+ esac;
-
--config.status: $(srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
- $(SHELL) ./config.status --recheck
--$(srcdir)/configure: $(srcdir)/configure.in $(ACLOCAL_M4) $(CONFIGURE_DEPENDENCIES)
-- cd $(srcdir) && $(AUTOCONF)
-+
-+$(top_srcdir)/configure: $(am__configure_deps)
-+ $(am__cd) $(srcdir) && $(AUTOCONF)
-+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
-+ $(am__cd) $(srcdir) && $(ACLOCAL) $(ACLOCAL_AMFLAGS)
-+$(am__aclocal_m4_deps):
-
- # This directory's subdirectories are mostly independent; you can cd
- # into them and run `make' without going through this Makefile.
-@@ -117,13 +252,14 @@
- # (1) if the variable is set in `config.status', edit `config.status'
- # (which will cause the Makefiles to be regenerated when you run `make');
- # (2) otherwise, pass the desired values on the `make' command line.
--
-- at SET_MAKE@
--
--all-recursive install-data-recursive install-exec-recursive \
--installdirs-recursive install-recursive uninstall-recursive \
--check-recursive installcheck-recursive info-recursive dvi-recursive:
-- @set fnord $(MAKEFLAGS); amf=$$2; \
-+$(RECURSIVE_TARGETS):
-+ @fail= failcom='exit 1'; \
-+ for f in x $$MAKEFLAGS; do \
-+ case $$f in \
-+ *=* | --[!k]*);; \
-+ *k*) failcom='fail=yes';; \
-+ esac; \
-+ done; \
- dot_seen=no; \
- target=`echo $@ | sed s/-recursive//`; \
- list='$(SUBDIRS)'; for subdir in $$list; do \
-@@ -134,22 +270,32 @@
- else \
- local_target="$$target"; \
- fi; \
-- (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-- || case "$$amf" in *=*) exit 1;; *k*) fail=yes;; *) exit 1;; esac; \
-+ ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-+ || eval $$failcom; \
- done; \
- if test "$$dot_seen" = "no"; then \
- $(MAKE) $(AM_MAKEFLAGS) "$$target-am" || exit 1; \
- fi; test -z "$$fail"
-
--mostlyclean-recursive clean-recursive distclean-recursive \
--maintainer-clean-recursive:
-- @set fnord $(MAKEFLAGS); amf=$$2; \
-+$(RECURSIVE_CLEAN_TARGETS):
-+ @fail= failcom='exit 1'; \
-+ for f in x $$MAKEFLAGS; do \
-+ case $$f in \
-+ *=* | --[!k]*);; \
-+ *k*) failcom='fail=yes';; \
-+ esac; \
-+ done; \
- dot_seen=no; \
-- rev=''; list='$(SUBDIRS)'; for subdir in $$list; do \
-+ case "$@" in \
-+ distclean-* | maintainer-clean-*) list='$(DIST_SUBDIRS)' ;; \
-+ *) list='$(SUBDIRS)' ;; \
-+ esac; \
-+ rev=''; for subdir in $$list; do \
-+ if test "$$subdir" = "."; then :; else \
- rev="$$subdir $$rev"; \
-- test "$$subdir" != "." || dot_seen=yes; \
-+ fi; \
- done; \
-- test "$$dot_seen" = "no" && rev=". $$rev"; \
-+ rev="$$rev ."; \
- target=`echo $@ | sed s/-recursive//`; \
- for subdir in $$rev; do \
- echo "Making $$target in $$subdir"; \
-@@ -158,176 +304,375 @@
- else \
- local_target="$$target"; \
- fi; \
-- (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-- || case "$$amf" in *=*) exit 1;; *k*) fail=yes;; *) exit 1;; esac; \
-+ ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-+ || eval $$failcom; \
- done && test -z "$$fail"
- tags-recursive:
- list='$(SUBDIRS)'; for subdir in $$list; do \
-- test "$$subdir" = . || (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
-+ test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
-+ done
-+ctags-recursive:
-+ list='$(SUBDIRS)'; for subdir in $$list; do \
-+ test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \
- done
-
-+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ mkid -fID $$unique
- tags: TAGS
-
--ID: $(HEADERS) $(SOURCES) $(LISP)
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- here=`pwd` && cd $(srcdir) \
-- && mkid -f$$here/ID $$unique $(LISP)
--
--TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) $(LISP)
-- tags=; \
-+TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ set x; \
- here=`pwd`; \
-+ if ($(ETAGS) --etags-include --version) >/dev/null 2>&1; then \
-+ include_option=--etags-include; \
-+ empty_fix=.; \
-+ else \
-+ include_option=--include; \
-+ empty_fix=; \
-+ fi; \
- list='$(SUBDIRS)'; for subdir in $$list; do \
- if test "$$subdir" = .; then :; else \
-- test -f $$subdir/TAGS && tags="$$tags -i $$here/$$subdir/TAGS"; \
-+ test ! -f $$subdir/TAGS || \
-+ set "$$@" "$$include_option=$$here/$$subdir/TAGS"; \
- fi; \
- done; \
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- test -z "$(ETAGS_ARGS)$$unique$(LISP)$$tags" \
-- || (cd $(srcdir) && etags -o $$here/TAGS $(ETAGS_ARGS) $$tags $$unique $(LISP))
--
--mostlyclean-tags:
--
--clean-tags:
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ shift; \
-+ if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
-+ test -n "$$unique" || unique=$$empty_fix; \
-+ if test $$# -gt 0; then \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ "$$@" $$unique; \
-+ else \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ $$unique; \
-+ fi; \
-+ fi
-+ctags: CTAGS
-+CTAGS: ctags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ test -z "$(CTAGS_ARGS)$$unique" \
-+ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-+ $$unique
-+
-+GTAGS:
-+ here=`$(am__cd) $(top_builddir) && pwd` \
-+ && $(am__cd) $(top_srcdir) \
-+ && gtags -i $(GTAGS_ARGS) "$$here"
-
- distclean-tags:
-- -rm -f TAGS ID
--
--maintainer-clean-tags:
--
--distdir = $(PACKAGE)-$(VERSION)
--top_distdir = $(distdir)
-+ -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-
--# This target untars the dist file and tries a VPATH configuration. Then
--# it guarantees that the distribution is self-contained by making another
--# tarfile.
--distcheck: dist
-- -rm -rf $(distdir)
-- GZIP=$(GZIP_ENV) $(TAR) zxf $(distdir).tar.gz
-- mkdir $(distdir)/=build
-- mkdir $(distdir)/=inst
-- dc_install_base=`cd $(distdir)/=inst && pwd`; \
-- cd $(distdir)/=build \
-- && ../configure --srcdir=.. --prefix=$$dc_install_base \
-- && $(MAKE) $(AM_MAKEFLAGS) \
-- && $(MAKE) $(AM_MAKEFLAGS) dvi \
-- && $(MAKE) $(AM_MAKEFLAGS) check \
-- && $(MAKE) $(AM_MAKEFLAGS) install \
-- && $(MAKE) $(AM_MAKEFLAGS) installcheck \
-- && $(MAKE) $(AM_MAKEFLAGS) dist
-- -rm -rf $(distdir)
-- @banner="$(distdir).tar.gz is ready for distribution"; \
-- dashes=`echo "$$banner" | sed s/./=/g`; \
-- echo "$$dashes"; \
-- echo "$$banner"; \
-- echo "$$dashes"
--dist: distdir
-- -chmod -R a+r $(distdir)
-- GZIP=$(GZIP_ENV) $(TAR) chozf $(distdir).tar.gz $(distdir)
-- -rm -rf $(distdir)
--dist-all: distdir
-- -chmod -R a+r $(distdir)
-- GZIP=$(GZIP_ENV) $(TAR) chozf $(distdir).tar.gz $(distdir)
-- -rm -rf $(distdir)
- distdir: $(DISTFILES)
-- -rm -rf $(distdir)
-- mkdir $(distdir)
-- -chmod 777 $(distdir)
-- @for file in $(DISTFILES); do \
-- d=$(srcdir); \
-+ $(am__remove_distdir)
-+ test -d "$(distdir)" || mkdir "$(distdir)"
-+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ list='$(DISTFILES)'; \
-+ dist_files=`for file in $$list; do echo $$file; done | \
-+ sed -e "s|^$$srcdirstrip/||;t" \
-+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-+ case $$dist_files in \
-+ */*) $(MKDIR_P) `echo "$$dist_files" | \
-+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-+ sort -u` ;; \
-+ esac; \
-+ for file in $$dist_files; do \
-+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
- if test -d $$d/$$file; then \
-- cp -pr $$d/$$file $(distdir)/$$file; \
-+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-+ if test -d "$(distdir)/$$file"; then \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
- else \
-- test -f $(distdir)/$$file \
-- || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
-- || cp -p $$d/$$file $(distdir)/$$file || :; \
-+ test -f "$(distdir)/$$file" \
-+ || cp -p $$d/$$file "$(distdir)/$$file" \
-+ || exit 1; \
- fi; \
- done
-- for subdir in $(SUBDIRS); do \
-+ @list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
- if test "$$subdir" = .; then :; else \
-- test -d $(distdir)/$$subdir \
-- || mkdir $(distdir)/$$subdir \
-+ test -d "$(distdir)/$$subdir" \
-+ || $(MKDIR_P) "$(distdir)/$$subdir" \
- || exit 1; \
-- chmod 777 $(distdir)/$$subdir; \
-- (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir=../$(distdir) distdir=../$(distdir)/$$subdir distdir) \
-+ fi; \
-+ done
-+ @list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
-+ if test "$$subdir" = .; then :; else \
-+ dir1=$$subdir; dir2="$(distdir)/$$subdir"; \
-+ $(am__relativize); \
-+ new_distdir=$$reldir; \
-+ dir1=$$subdir; dir2="$(top_distdir)"; \
-+ $(am__relativize); \
-+ new_top_distdir=$$reldir; \
-+ echo " (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir="$$new_top_distdir" distdir="$$new_distdir" \\"; \
-+ echo " am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)"; \
-+ ($(am__cd) $$subdir && \
-+ $(MAKE) $(AM_MAKEFLAGS) \
-+ top_distdir="$$new_top_distdir" \
-+ distdir="$$new_distdir" \
-+ am__remove_distdir=: \
-+ am__skip_length_check=: \
-+ am__skip_mode_fix=: \
-+ distdir) \
- || exit 1; \
- fi; \
- done
--info-am:
--info: info-recursive
--dvi-am:
--dvi: dvi-recursive
-+ -test -n "$(am__skip_mode_fix)" \
-+ || find "$(distdir)" -type d ! -perm -755 \
-+ -exec chmod u+rwx,go+rx {} \; -o \
-+ ! -type d ! -perm -444 -links 1 -exec chmod a+r {} \; -o \
-+ ! -type d ! -perm -400 -exec chmod a+r {} \; -o \
-+ ! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \
-+ || chmod -R a+r "$(distdir)"
-+dist-gzip: distdir
-+ tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
-+ $(am__remove_distdir)
-+
-+dist-bzip2: distdir
-+ tardir=$(distdir) && $(am__tar) | bzip2 -9 -c >$(distdir).tar.bz2
-+ $(am__remove_distdir)
-+
-+dist-lzma: distdir
-+ tardir=$(distdir) && $(am__tar) | lzma -9 -c >$(distdir).tar.lzma
-+ $(am__remove_distdir)
-+
-+dist-xz: distdir
-+ tardir=$(distdir) && $(am__tar) | xz -c >$(distdir).tar.xz
-+ $(am__remove_distdir)
-+
-+dist-tarZ: distdir
-+ tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z
-+ $(am__remove_distdir)
-+
-+dist-shar: distdir
-+ shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz
-+ $(am__remove_distdir)
-+
-+dist-zip: distdir
-+ -rm -f $(distdir).zip
-+ zip -rq $(distdir).zip $(distdir)
-+ $(am__remove_distdir)
-+
-+dist dist-all: distdir
-+ tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
-+ $(am__remove_distdir)
-+
-+# This target untars the dist file and tries a VPATH configuration. Then
-+# it guarantees that the distribution is self-contained by making another
-+# tarfile.
-+distcheck: dist
-+ case '$(DIST_ARCHIVES)' in \
-+ *.tar.gz*) \
-+ GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\
-+ *.tar.bz2*) \
-+ bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\
-+ *.tar.lzma*) \
-+ lzma -dc $(distdir).tar.lzma | $(am__untar) ;;\
-+ *.tar.xz*) \
-+ xz -dc $(distdir).tar.xz | $(am__untar) ;;\
-+ *.tar.Z*) \
-+ uncompress -c $(distdir).tar.Z | $(am__untar) ;;\
-+ *.shar.gz*) \
-+ GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\
-+ *.zip*) \
-+ unzip $(distdir).zip ;;\
-+ esac
-+ chmod -R a-w $(distdir); chmod a+w $(distdir)
-+ mkdir $(distdir)/_build
-+ mkdir $(distdir)/_inst
-+ chmod a-w $(distdir)
-+ test -d $(distdir)/_build || exit 0; \
-+ dc_install_base=`$(am__cd) $(distdir)/_inst && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \
-+ && dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \
-+ && am__cwd=`pwd` \
-+ && $(am__cd) $(distdir)/_build \
-+ && ../configure --srcdir=.. --prefix="$$dc_install_base" \
-+ $(DISTCHECK_CONFIGURE_FLAGS) \
-+ && $(MAKE) $(AM_MAKEFLAGS) \
-+ && $(MAKE) $(AM_MAKEFLAGS) dvi \
-+ && $(MAKE) $(AM_MAKEFLAGS) check \
-+ && $(MAKE) $(AM_MAKEFLAGS) install \
-+ && $(MAKE) $(AM_MAKEFLAGS) installcheck \
-+ && $(MAKE) $(AM_MAKEFLAGS) uninstall \
-+ && $(MAKE) $(AM_MAKEFLAGS) distuninstallcheck_dir="$$dc_install_base" \
-+ distuninstallcheck \
-+ && chmod -R a-w "$$dc_install_base" \
-+ && ({ \
-+ (cd ../.. && umask 077 && mkdir "$$dc_destdir") \
-+ && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" install \
-+ && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" uninstall \
-+ && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" \
-+ distuninstallcheck_dir="$$dc_destdir" distuninstallcheck; \
-+ } || { rm -rf "$$dc_destdir"; exit 1; }) \
-+ && rm -rf "$$dc_destdir" \
-+ && $(MAKE) $(AM_MAKEFLAGS) dist \
-+ && rm -rf $(DIST_ARCHIVES) \
-+ && $(MAKE) $(AM_MAKEFLAGS) distcleancheck \
-+ && cd "$$am__cwd" \
-+ || exit 1
-+ $(am__remove_distdir)
-+ @(echo "$(distdir) archives ready for distribution: "; \
-+ list='$(DIST_ARCHIVES)'; for i in $$list; do echo $$i; done) | \
-+ sed -e 1h -e 1s/./=/g -e 1p -e 1x -e '$$p' -e '$$x'
-+distuninstallcheck:
-+ @$(am__cd) '$(distuninstallcheck_dir)' \
-+ && test `$(distuninstallcheck_listfiles) | wc -l` -le 1 \
-+ || { echo "ERROR: files left after uninstall:" ; \
-+ if test -n "$(DESTDIR)"; then \
-+ echo " (check DESTDIR support)"; \
-+ fi ; \
-+ $(distuninstallcheck_listfiles) ; \
-+ exit 1; } >&2
-+distcleancheck: distclean
-+ @if test '$(srcdir)' = . ; then \
-+ echo "ERROR: distcleancheck can only run from a VPATH build" ; \
-+ exit 1 ; \
-+ fi
-+ @test `$(distcleancheck_listfiles) | wc -l` -eq 0 \
-+ || { echo "ERROR: files left in build directory after distclean:" ; \
-+ $(distcleancheck_listfiles) ; \
-+ exit 1; } >&2
- check-am: all-am
- check: check-recursive
--installcheck-am:
--installcheck: installcheck-recursive
--install-exec-am:
-+all-am: Makefile
-+installdirs: installdirs-recursive
-+installdirs-am:
-+install: install-recursive
- install-exec: install-exec-recursive
--
--install-data-am:
- install-data: install-data-recursive
-+uninstall: uninstall-recursive
-
- install-am: all-am
- @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
--install: install-recursive
--uninstall-am:
--uninstall: uninstall-recursive
--all-am: Makefile
--all-redirect: all-recursive
--install-strip:
-- $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
--installdirs: installdirs-recursive
--installdirs-am:
--
-
-+installcheck: installcheck-recursive
-+install-strip:
-+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-+ `test -z '$(STRIP)' || \
-+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
- mostlyclean-generic:
-
- clean-generic:
-
- distclean-generic:
-- -rm -f Makefile $(CONFIG_CLEAN_FILES)
-- -rm -f config.cache config.log stamp-h stamp-h[0-9]*
-+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
- maintainer-clean-generic:
-+ @echo "This command is intended for maintainers to use"
-+ @echo "it deletes files that may require special tools to rebuild."
- -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
--mostlyclean-am: mostlyclean-tags mostlyclean-generic
-+clean: clean-recursive
-
--mostlyclean: mostlyclean-recursive
-+clean-am: clean-generic mostlyclean-am
-+
-+distclean: distclean-recursive
-+ -rm -f $(am__CONFIG_DISTCLEAN_FILES)
-+ -rm -f Makefile
-+distclean-am: clean-am distclean-generic distclean-tags
-
--clean-am: clean-tags clean-generic mostlyclean-am
-+dvi: dvi-recursive
-
--clean: clean-recursive
-+dvi-am:
-
--distclean-am: distclean-tags distclean-generic clean-am
-+html: html-recursive
-
--distclean: distclean-recursive
-- -rm -f config.status
-+html-am:
-
--maintainer-clean-am: maintainer-clean-tags maintainer-clean-generic \
-- distclean-am
-- @echo "This command is intended for maintainers to use;"
-- @echo "it deletes files that may require special tools to rebuild."
-+info: info-recursive
-+
-+info-am:
-+
-+install-data-am:
-+
-+install-dvi: install-dvi-recursive
-+
-+install-dvi-am:
-+
-+install-exec-am:
-+
-+install-html: install-html-recursive
-+
-+install-html-am:
-+
-+install-info: install-info-recursive
-+
-+install-info-am:
-+
-+install-man:
-+
-+install-pdf: install-pdf-recursive
-+
-+install-pdf-am:
-+
-+install-ps: install-ps-recursive
-+
-+install-ps-am:
-+
-+installcheck-am:
-
- maintainer-clean: maintainer-clean-recursive
-- -rm -f config.status
-+ -rm -f $(am__CONFIG_DISTCLEAN_FILES)
-+ -rm -rf $(top_srcdir)/autom4te.cache
-+ -rm -f Makefile
-+maintainer-clean-am: distclean-am maintainer-clean-generic
-+
-+mostlyclean: mostlyclean-recursive
-+
-+mostlyclean-am: mostlyclean-generic
-+
-+pdf: pdf-recursive
-+
-+pdf-am:
-+
-+ps: ps-recursive
-+
-+ps-am:
-+
-+uninstall-am:
-+
-+.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) ctags-recursive \
-+ install-am install-strip tags-recursive
-
--.PHONY: install-data-recursive uninstall-data-recursive \
--install-exec-recursive uninstall-exec-recursive installdirs-recursive \
--uninstalldirs-recursive all-recursive check-recursive \
--installcheck-recursive info-recursive dvi-recursive \
--mostlyclean-recursive distclean-recursive clean-recursive \
--maintainer-clean-recursive tags tags-recursive mostlyclean-tags \
--distclean-tags clean-tags maintainer-clean-tags distdir info-am info \
--dvi-am dvi check check-am installcheck-am installcheck install-exec-am \
--install-exec install-data-am install-data install-am install \
--uninstall-am uninstall all-redirect all-am all installdirs-am \
--installdirs mostlyclean-generic distclean-generic clean-generic \
--maintainer-clean-generic clean mostlyclean distclean maintainer-clean
-+.PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
-+ all all-am am--refresh check check-am clean clean-generic \
-+ ctags ctags-recursive dist dist-all dist-bzip2 dist-gzip \
-+ dist-lzma dist-shar dist-tarZ dist-xz dist-zip distcheck \
-+ distclean distclean-generic distclean-tags distcleancheck \
-+ distdir distuninstallcheck dvi dvi-am html html-am info \
-+ info-am install install-am install-data install-data-am \
-+ install-dvi install-dvi-am install-exec install-exec-am \
-+ install-html install-html-am install-info install-info-am \
-+ install-man install-pdf install-pdf-am install-ps \
-+ install-ps-am install-strip installcheck installcheck-am \
-+ installdirs installdirs-am maintainer-clean \
-+ maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
-+ pdf-am ps ps-am tags tags-recursive uninstall uninstall-am
-
-
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -ubrN exonerate-2.2.0.orig/src/bsdp/Makefile.in exonerate-2.2.0/src/bsdp/Makefile.in
---- exonerate-2.2.0.orig/src/bsdp/Makefile.in 2008-10-17 12:04:36.000000000 +0200
-+++ exonerate-2.2.0/src/bsdp/Makefile.in 2011-12-12 13:33:16.000000000 +0100
-@@ -1,6 +1,9 @@
--# Makefile.in generated automatically by automake 1.4-p6 from Makefile.am
-+# Makefile.in generated by automake 1.11.1 from Makefile.am.
-+# @configure_input@
-
--# Copyright (C) 1994, 1995-8, 1999, 2001 Free Software Foundation, Inc.
-+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
-+# Inc.
- # This Makefile.in is free software; the Free Software Foundation
- # gives unlimited permission to copy and/or distribute it,
- # with or without modifications, as long as this notice is preserved.
-@@ -10,393 +13,634 @@
- # even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- # PARTICULAR PURPOSE.
-
-+ at SET_MAKE@
-
--SHELL = @SHELL@
-
--srcdir = @srcdir@
--top_srcdir = @top_srcdir@
- VPATH = @srcdir@
--prefix = @prefix@
--exec_prefix = @exec_prefix@
--
--bindir = @bindir@
--sbindir = @sbindir@
--libexecdir = @libexecdir@
--datadir = @datadir@
--sysconfdir = @sysconfdir@
--sharedstatedir = @sharedstatedir@
--localstatedir = @localstatedir@
--libdir = @libdir@
--infodir = @infodir@
--mandir = @mandir@
--includedir = @includedir@
--oldincludedir = /usr/include
--
--DESTDIR =
--
- pkgdatadir = $(datadir)/@PACKAGE@
--pkglibdir = $(libdir)/@PACKAGE@
- pkgincludedir = $(includedir)/@PACKAGE@
--
--top_builddir = ../..
--
--ACLOCAL = @ACLOCAL@
--AUTOCONF = @AUTOCONF@
--AUTOMAKE = @AUTOMAKE@
--AUTOHEADER = @AUTOHEADER@
--
--INSTALL = @INSTALL@
--INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
--INSTALL_DATA = @INSTALL_DATA@
--INSTALL_SCRIPT = @INSTALL_SCRIPT@
--transform = @program_transform_name@
--
-+pkglibdir = $(libdir)/@PACKAGE@
-+pkglibexecdir = $(libexecdir)/@PACKAGE@
-+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-+install_sh_DATA = $(install_sh) -c -m 644
-+install_sh_PROGRAM = $(install_sh) -c
-+install_sh_SCRIPT = $(install_sh) -c
-+INSTALL_HEADER = $(INSTALL_DATA)
-+transform = $(program_transform_name)
- NORMAL_INSTALL = :
- PRE_INSTALL = :
- POST_INSTALL = :
- NORMAL_UNINSTALL = :
- PRE_UNINSTALL = :
- POST_UNINSTALL = :
--host_alias = @host_alias@
-+build_triplet = @build@
- host_triplet = @host@
-+TESTS = heuristic.test$(EXEEXT) bsdp.test$(EXEEXT) hpair.test$(EXEEXT) \
-+ sar.test$(EXEEXT)
-+noinst_PROGRAMS = $(am__EXEEXT_1)
-+subdir = src/bsdp
-+DIST_COMMON = $(noinst_HEADERS) $(srcdir)/Makefile.am \
-+ $(srcdir)/Makefile.in
-+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-+am__aclocal_m4_deps = $(top_srcdir)/configure.in
-+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-+ $(ACLOCAL_M4)
-+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
-+CONFIG_CLEAN_FILES =
-+CONFIG_CLEAN_VPATH_FILES =
-+am__EXEEXT_1 = heuristic.test$(EXEEXT) bsdp.test$(EXEEXT) \
-+ hpair.test$(EXEEXT) sar.test$(EXEEXT)
-+PROGRAMS = $(noinst_PROGRAMS)
-+am_bsdp_test_OBJECTS = bsdp.test.$(OBJEXT) bsdp.$(OBJEXT)
-+bsdp_test_OBJECTS = $(am_bsdp_test_OBJECTS)
-+bsdp_test_DEPENDENCIES = $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/struct/pqueue.o \
-+ $(top_srcdir)/src/struct/recyclebin.o
-+am_heuristic_test_OBJECTS = heuristic.test.$(OBJEXT) \
-+ heuristic.$(OBJEXT)
-+heuristic_test_OBJECTS = $(am_heuristic_test_OBJECTS)
-+am__DEPENDENCIES_1 = $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o \
-+ $(top_srcdir)/src/sequence/sequence.o \
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/lineparse.o
-+am__DEPENDENCIES_2 = $(top_srcdir)/src/comparison/match.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o \
-+ $(top_srcdir)/src/sequence/submat.o $(C4_OBJ) \
-+ $(am__DEPENDENCIES_1)
-+heuristic_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/rangetree.o $(am__DEPENDENCIES_2)
-+am_hpair_test_OBJECTS = hpair.test.$(OBJEXT) hpair.$(OBJEXT) \
-+ heuristic.$(OBJEXT) bsdp.$(OBJEXT) sar.$(OBJEXT)
-+hpair_test_OBJECTS = $(am_hpair_test_OBJECTS)
-+hpair_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \
-+ $(top_srcdir)/src/struct/pqueue.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/comparison/hspset.o \
-+ $(top_srcdir)/src/comparison/wordhood.o \
-+ $(top_srcdir)/src/struct/rangetree.o $(am__DEPENDENCIES_2)
-+am_sar_test_OBJECTS = sar.test.$(OBJEXT) sar.$(OBJEXT) \
-+ heuristic.$(OBJEXT)
-+sar_test_OBJECTS = $(am_sar_test_OBJECTS)
-+sar_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/rangetree.o $(am__DEPENDENCIES_2)
-+DEFAULT_INCLUDES = -I. at am__isrc@
-+depcomp = $(SHELL) $(top_srcdir)/depcomp
-+am__depfiles_maybe = depfiles
-+am__mv = mv -f
-+COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
-+ $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
-+CCLD = $(CC)
-+LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
-+SOURCES = $(bsdp_test_SOURCES) $(heuristic_test_SOURCES) \
-+ $(hpair_test_SOURCES) $(sar_test_SOURCES)
-+DIST_SOURCES = $(bsdp_test_SOURCES) $(heuristic_test_SOURCES) \
-+ $(hpair_test_SOURCES) $(sar_test_SOURCES)
-+HEADERS = $(noinst_HEADERS)
-+ETAGS = etags
-+CTAGS = ctags
-+am__tty_colors = \
-+red=; grn=; lgn=; blu=; std=
-+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-+ACLOCAL = @ACLOCAL@
-+AMTAR = @AMTAR@
-+AUTOCONF = @AUTOCONF@
-+AUTOHEADER = @AUTOHEADER@
-+AUTOMAKE = @AUTOMAKE@
-+AWK = @AWK@
- CC = @CC@
-+CCDEPMODE = @CCDEPMODE@
-+CFLAGS = @CFLAGS@
-+CPP = @CPP@
-+CPPFLAGS = @CPPFLAGS@
-+CYGPATH_W = @CYGPATH_W@
-+DEFS = @DEFS@
-+DEPDIR = @DEPDIR@
-+ECHO_C = @ECHO_C@
-+ECHO_N = @ECHO_N@
-+ECHO_T = @ECHO_T@
-+EGREP = @EGREP@
-+EXEEXT = @EXEEXT@
- GLIB_CONFIG = @GLIB_CONFIG@
--HAVE_LIB = @HAVE_LIB@
--LIB = @LIB@
--LTLIB = @LTLIB@
-+GREP = @GREP@
-+INSTALL = @INSTALL@
-+INSTALL_DATA = @INSTALL_DATA@
-+INSTALL_PROGRAM = @INSTALL_PROGRAM@
-+INSTALL_SCRIPT = @INSTALL_SCRIPT@
-+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-+LDFLAGS = @LDFLAGS@
-+LIBOBJS = @LIBOBJS@
-+LIBS = @LIBS@
-+LTLIBOBJS = @LTLIBOBJS@
- MAKEINFO = @MAKEINFO@
-+MKDIR_P = @MKDIR_P@
-+OBJEXT = @OBJEXT@
- PACKAGE = @PACKAGE@
-+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-+PACKAGE_NAME = @PACKAGE_NAME@
-+PACKAGE_STRING = @PACKAGE_STRING@
-+PACKAGE_TARNAME = @PACKAGE_TARNAME@
-+PACKAGE_URL = @PACKAGE_URL@
-+PACKAGE_VERSION = @PACKAGE_VERSION@
-+PATH_SEPARATOR = @PATH_SEPARATOR@
- PKG_CONFIG = @PKG_CONFIG@
-+SET_MAKE = @SET_MAKE@
-+SHELL = @SHELL@
-+STRIP = @STRIP@
- VERSION = @VERSION@
-+abs_builddir = @abs_builddir@
-+abs_srcdir = @abs_srcdir@
-+abs_top_builddir = @abs_top_builddir@
-+abs_top_srcdir = @abs_top_srcdir@
-+ac_ct_CC = @ac_ct_CC@
-+am__include = @am__include@
-+am__leading_dot = @am__leading_dot@
-+am__quote = @am__quote@
-+am__tar = @am__tar@
-+am__untar = @am__untar@
-+bindir = @bindir@
-+build = @build@
-+build_alias = @build_alias@
-+build_cpu = @build_cpu@
-+build_os = @build_os@
-+build_vendor = @build_vendor@
-+builddir = @builddir@
- codegen_extra_ldadd = @codegen_extra_ldadd@
- codegen_extra_sources = @codegen_extra_sources@
-+datadir = @datadir@
- datarootdir = @datarootdir@
-+docdir = @docdir@
-+dvidir = @dvidir@
-+exec_prefix = @exec_prefix@
- glib_cflags = @glib_cflags@
- glib_libs = @glib_libs@
- host = @host@
-+host_alias = @host_alias@
-+host_cpu = @host_cpu@
-+host_os = @host_os@
-+host_vendor = @host_vendor@
-+htmldir = @htmldir@
-+includedir = @includedir@
-+infodir = @infodir@
-+install_sh = @install_sh@
- installed_util_list = @installed_util_list@
-+libdir = @libdir@
-+libexecdir = @libexecdir@
-+localedir = @localedir@
-+localstatedir = @localstatedir@
-+mandir = @mandir@
-+mkdir_p = @mkdir_p@
-+oldincludedir = @oldincludedir@
-+pdfdir = @pdfdir@
-+prefix = @prefix@
-+program_transform_name = @program_transform_name@
-+psdir = @psdir@
-+sbindir = @sbindir@
-+sharedstatedir = @sharedstatedir@
- source_root_dir = @source_root_dir@
-+srcdir = @srcdir@
-+sysconfdir = @sysconfdir@
-+target_alias = @target_alias@
-+top_build_prefix = @top_build_prefix@
-+top_builddir = @top_builddir@
-+top_srcdir = @top_srcdir@
- use_pthreads = @use_pthreads@
--
--TESTS = heuristic.test bsdp.test hpair.test sar.test
--
--noinst_PROGRAMS = $(TESTS)
--
--INCLUDES = -I$(top_srcdir)/src/struct -I$(top_srcdir)/src/comparison -I$(top_srcdir)/src/sequence -I$(top_srcdir)/src/general -I$(top_srcdir)/src/c4 -DSOURCE_ROOT_DIR="\"@source_root_dir@\"" -DGLIB_CFLAGS="\"@glib_cflags@\"" -DHOSTTYPE="\"@host@\""
--
-+INCLUDES = -I$(top_srcdir)/src/struct \
-+ -I$(top_srcdir)/src/comparison \
-+ -I$(top_srcdir)/src/sequence \
-+ -I$(top_srcdir)/src/general \
-+ -I$(top_srcdir)/src/c4 \
-+ -DSOURCE_ROOT_DIR="\"@source_root_dir@\"" \
-+ -DGLIB_CFLAGS="\"@glib_cflags@\"" \
-+ -DHOSTTYPE="\"@host@\""
-
- noinst_HEADERS = heuristic.h bsdp.h hpair.h sar.h
--
--SEQUENCE_OBJ = $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o $(top_srcdir)/src/sequence/alphabet.o $(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/sequence/translate.o $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/general/lineparse.o -lm
--
--
--C4_OBJ = $(top_srcdir)/src/c4/c4.o $(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/optimal.o $(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/region.o $(top_srcdir)/src/c4/layout.o $(top_srcdir)/src/c4/viterbi.o $(top_srcdir)/src/c4/subopt.o $(top_srcdir)/src/c4/cgutil.o
--
--
--ALIGNMENT_OBJ = $(top_srcdir)/src/comparison/match.o $(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/sequence/submat.o $(C4_OBJ) $(SEQUENCE_OBJ)
--
-+SEQUENCE_OBJ = $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o \
-+ $(top_srcdir)/src/sequence/sequence.o \
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ -lm
-+
-+C4_OBJ = $(top_srcdir)/src/c4/c4.o \
-+ $(top_srcdir)/src/c4/alignment.o \
-+ $(top_srcdir)/src/c4/optimal.o \
-+ $(top_srcdir)/src/c4/codegen.o \
-+ $(top_srcdir)/src/c4/region.o \
-+ $(top_srcdir)/src/c4/layout.o \
-+ $(top_srcdir)/src/c4/viterbi.o \
-+ $(top_srcdir)/src/c4/subopt.o \
-+ $(top_srcdir)/src/c4/cgutil.o
-+
-+ALIGNMENT_OBJ = $(top_srcdir)/src/comparison/match.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o \
-+ $(top_srcdir)/src/sequence/submat.o \
-+ $(C4_OBJ) $(SEQUENCE_OBJ)
-
- heuristic_test_SOURCES = heuristic.test.c heuristic.c
--heuristic_test_LDADD = $(top_srcdir)/src/struct/slist.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/rangetree.o $(ALIGNMENT_OBJ)
--
-+heuristic_test_LDADD = $(top_srcdir)/src/struct/slist.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/rangetree.o \
-+ $(ALIGNMENT_OBJ)
-
- bsdp_test_SOURCES = bsdp.test.c bsdp.c
--bsdp_test_LDADD = $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o
--
-+bsdp_test_LDADD = $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/struct/pqueue.o \
-+ $(top_srcdir)/src/struct/recyclebin.o
-
- hpair_test_SOURCES = hpair.test.c hpair.c heuristic.c bsdp.c sar.c
--hpair_test_LDADD = $(top_srcdir)/src/struct/slist.o $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/comparison/hspset.o $(top_srcdir)/src/comparison/wordhood.o $(top_srcdir)/src/struct/rangetree.o $(ALIGNMENT_OBJ)
--
-+hpair_test_LDADD = $(top_srcdir)/src/struct/slist.o \
-+ $(top_srcdir)/src/struct/pqueue.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/comparison/hspset.o \
-+ $(top_srcdir)/src/comparison/wordhood.o \
-+ $(top_srcdir)/src/struct/rangetree.o \
-+ $(ALIGNMENT_OBJ)
-
- sar_test_SOURCES = sar.test.c sar.c heuristic.c
--sar_test_LDADD = $(top_srcdir)/src/struct/slist.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/rangetree.o $(ALIGNMENT_OBJ)
-+sar_test_LDADD = $(top_srcdir)/src/struct/slist.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/rangetree.o \
-+ $(ALIGNMENT_OBJ)
-
-
- # Files to clear away
--
- MAINTAINERCLEANFILES = Makefile.in
--mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
--CONFIG_CLEAN_FILES =
--PROGRAMS = $(noinst_PROGRAMS)
-+all: all-am
-
--
--DEFS = @DEFS@ -I. -I$(srcdir)
--CPPFLAGS = @CPPFLAGS@
--LDFLAGS = @LDFLAGS@
--LIBS = @LIBS@
--heuristic_test_OBJECTS = heuristic.test.o heuristic.o
--heuristic_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \
--$(top_srcdir)/src/struct/recyclebin.o \
--$(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/c4/c4.o \
--$(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/optimal.o \
--$(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/region.o \
--$(top_srcdir)/src/c4/layout.o $(top_srcdir)/src/c4/viterbi.o \
--$(top_srcdir)/src/c4/subopt.o $(top_srcdir)/src/c4/cgutil.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--heuristic_test_LDFLAGS =
--bsdp_test_OBJECTS = bsdp.test.o bsdp.o
--bsdp_test_DEPENDENCIES = $(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o
--bsdp_test_LDFLAGS =
--hpair_test_OBJECTS = hpair.test.o hpair.o heuristic.o bsdp.o sar.o
--hpair_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \
--$(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o \
--$(top_srcdir)/src/comparison/hspset.o \
--$(top_srcdir)/src/comparison/wordhood.o \
--$(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/c4/c4.o \
--$(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/optimal.o \
--$(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/region.o \
--$(top_srcdir)/src/c4/layout.o $(top_srcdir)/src/c4/viterbi.o \
--$(top_srcdir)/src/c4/subopt.o $(top_srcdir)/src/c4/cgutil.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--hpair_test_LDFLAGS =
--sar_test_OBJECTS = sar.test.o sar.o heuristic.o
--sar_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \
--$(top_srcdir)/src/struct/recyclebin.o \
--$(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/c4/c4.o \
--$(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/optimal.o \
--$(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/region.o \
--$(top_srcdir)/src/c4/layout.o $(top_srcdir)/src/c4/viterbi.o \
--$(top_srcdir)/src/c4/subopt.o $(top_srcdir)/src/c4/cgutil.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--sar_test_LDFLAGS =
--CFLAGS = @CFLAGS@
--COMPILE = $(CC) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
--CCLD = $(CC)
--LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(LDFLAGS) -o $@
--HEADERS = $(noinst_HEADERS)
--
--DIST_COMMON = Makefile.am Makefile.in
--
--
--DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
--
--TAR = tar
--GZIP_ENV = --best
--SOURCES = $(heuristic_test_SOURCES) $(bsdp_test_SOURCES) $(hpair_test_SOURCES) $(sar_test_SOURCES)
--OBJECTS = $(heuristic_test_OBJECTS) $(bsdp_test_OBJECTS) $(hpair_test_OBJECTS) $(sar_test_OBJECTS)
--
--all: all-redirect
- .SUFFIXES:
--.SUFFIXES: .S .c .o .s
--$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4)
-- cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps src/bsdp/Makefile
--
-+.SUFFIXES: .c .o .obj
-+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
-+ @for dep in $?; do \
-+ case '$(am__configure_deps)' in \
-+ *$$dep*) \
-+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-+ && { if test -f $@; then exit 0; else break; fi; }; \
-+ exit 1;; \
-+ esac; \
-+ done; \
-+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/bsdp/Makefile'; \
-+ $(am__cd) $(top_srcdir) && \
-+ $(AUTOMAKE) --gnu src/bsdp/Makefile
-+.PRECIOUS: Makefile
- Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-- cd $(top_builddir) \
-- && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
--
--
--mostlyclean-noinstPROGRAMS:
-+ @case '$?' in \
-+ *config.status*) \
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-+ *) \
-+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-+ esac;
-+
-+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+
-+$(top_srcdir)/configure: $(am__configure_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(am__aclocal_m4_deps):
-
- clean-noinstPROGRAMS:
- -test -z "$(noinst_PROGRAMS)" || rm -f $(noinst_PROGRAMS)
--
--distclean-noinstPROGRAMS:
--
--maintainer-clean-noinstPROGRAMS:
--
--.c.o:
-- $(COMPILE) -c $<
--
--.s.o:
-- $(COMPILE) -c $<
--
--.S.o:
-- $(COMPILE) -c $<
-+bsdp.test$(EXEEXT): $(bsdp_test_OBJECTS) $(bsdp_test_DEPENDENCIES)
-+ @rm -f bsdp.test$(EXEEXT)
-+ $(LINK) $(bsdp_test_OBJECTS) $(bsdp_test_LDADD) $(LIBS)
-+heuristic.test$(EXEEXT): $(heuristic_test_OBJECTS) $(heuristic_test_DEPENDENCIES)
-+ @rm -f heuristic.test$(EXEEXT)
-+ $(LINK) $(heuristic_test_OBJECTS) $(heuristic_test_LDADD) $(LIBS)
-+hpair.test$(EXEEXT): $(hpair_test_OBJECTS) $(hpair_test_DEPENDENCIES)
-+ @rm -f hpair.test$(EXEEXT)
-+ $(LINK) $(hpair_test_OBJECTS) $(hpair_test_LDADD) $(LIBS)
-+sar.test$(EXEEXT): $(sar_test_OBJECTS) $(sar_test_DEPENDENCIES)
-+ @rm -f sar.test$(EXEEXT)
-+ $(LINK) $(sar_test_OBJECTS) $(sar_test_LDADD) $(LIBS)
-
- mostlyclean-compile:
-- -rm -f *.o core *.core
--
--clean-compile:
-+ -rm -f *.$(OBJEXT)
-
- distclean-compile:
- -rm -f *.tab.c
-
--maintainer-clean-compile:
--
--heuristic.test: $(heuristic_test_OBJECTS) $(heuristic_test_DEPENDENCIES)
-- @rm -f heuristic.test
-- $(LINK) $(heuristic_test_LDFLAGS) $(heuristic_test_OBJECTS) $(heuristic_test_LDADD) $(LIBS)
--
--bsdp.test: $(bsdp_test_OBJECTS) $(bsdp_test_DEPENDENCIES)
-- @rm -f bsdp.test
-- $(LINK) $(bsdp_test_LDFLAGS) $(bsdp_test_OBJECTS) $(bsdp_test_LDADD) $(LIBS)
--
--hpair.test: $(hpair_test_OBJECTS) $(hpair_test_DEPENDENCIES)
-- @rm -f hpair.test
-- $(LINK) $(hpair_test_LDFLAGS) $(hpair_test_OBJECTS) $(hpair_test_LDADD) $(LIBS)
--
--sar.test: $(sar_test_OBJECTS) $(sar_test_DEPENDENCIES)
-- @rm -f sar.test
-- $(LINK) $(sar_test_LDFLAGS) $(sar_test_OBJECTS) $(sar_test_LDADD) $(LIBS)
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/bsdp.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/bsdp.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/heuristic.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/heuristic.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/hpair.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/hpair.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sar.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sar.test.Po at am__quote@
-
-+.c.o:
-+ at am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
-+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-+ at am__fastdepCC_FALSE@ $(COMPILE) -c $<
-+
-+.c.obj:
-+ at am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
-+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-+ at am__fastdepCC_FALSE@ $(COMPILE) -c `$(CYGPATH_W) '$<'`
-+
-+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ mkid -fID $$unique
- tags: TAGS
-
--ID: $(HEADERS) $(SOURCES) $(LISP)
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- here=`pwd` && cd $(srcdir) \
-- && mkid -f$$here/ID $$unique $(LISP)
--
--TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) $(LISP)
-- tags=; \
-+TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ set x; \
- here=`pwd`; \
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- test -z "$(ETAGS_ARGS)$$unique$(LISP)$$tags" \
-- || (cd $(srcdir) && etags -o $$here/TAGS $(ETAGS_ARGS) $$tags $$unique $(LISP))
--
--mostlyclean-tags:
--
--clean-tags:
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ shift; \
-+ if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
-+ test -n "$$unique" || unique=$$empty_fix; \
-+ if test $$# -gt 0; then \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ "$$@" $$unique; \
-+ else \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ $$unique; \
-+ fi; \
-+ fi
-+ctags: CTAGS
-+CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ test -z "$(CTAGS_ARGS)$$unique" \
-+ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-+ $$unique
-+
-+GTAGS:
-+ here=`$(am__cd) $(top_builddir) && pwd` \
-+ && $(am__cd) $(top_srcdir) \
-+ && gtags -i $(GTAGS_ARGS) "$$here"
-
- distclean-tags:
-- -rm -f TAGS ID
-+ -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-
--maintainer-clean-tags:
--
--distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
--
--subdir = src/bsdp
--
--distdir: $(DISTFILES)
-- @for file in $(DISTFILES); do \
-- d=$(srcdir); \
-- if test -d $$d/$$file; then \
-- cp -pr $$d/$$file $(distdir)/$$file; \
-- else \
-- test -f $(distdir)/$$file \
-- || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
-- || cp -p $$d/$$file $(distdir)/$$file || :; \
-- fi; \
-- done
- check-TESTS: $(TESTS)
-- @failed=0; all=0; \
-+ @failed=0; all=0; xfail=0; xpass=0; skip=0; \
- srcdir=$(srcdir); export srcdir; \
-- for tst in $(TESTS); do \
-- if test -f $$tst; then dir=.; \
-- else dir="$(srcdir)"; fi; \
-- if $(TESTS_ENVIRONMENT) $$dir/$$tst; then \
-+ list=' $(TESTS) '; \
-+ $(am__tty_colors); \
-+ if test -n "$$list"; then \
-+ for tst in $$list; do \
-+ if test -f ./$$tst; then dir=./; \
-+ elif test -f $$tst; then dir=; \
-+ else dir="$(srcdir)/"; fi; \
-+ if $(TESTS_ENVIRONMENT) $${dir}$$tst; then \
- all=`expr $$all + 1`; \
-- echo "PASS: $$tst"; \
-+ case " $(XFAIL_TESTS) " in \
-+ *[\ \ ]$$tst[\ \ ]*) \
-+ xpass=`expr $$xpass + 1`; \
-+ failed=`expr $$failed + 1`; \
-+ col=$$red; res=XPASS; \
-+ ;; \
-+ *) \
-+ col=$$grn; res=PASS; \
-+ ;; \
-+ esac; \
- elif test $$? -ne 77; then \
- all=`expr $$all + 1`; \
-+ case " $(XFAIL_TESTS) " in \
-+ *[\ \ ]$$tst[\ \ ]*) \
-+ xfail=`expr $$xfail + 1`; \
-+ col=$$lgn; res=XFAIL; \
-+ ;; \
-+ *) \
- failed=`expr $$failed + 1`; \
-- echo "FAIL: $$tst"; \
-+ col=$$red; res=FAIL; \
-+ ;; \
-+ esac; \
-+ else \
-+ skip=`expr $$skip + 1`; \
-+ col=$$blu; res=SKIP; \
- fi; \
-+ echo "$${col}$$res$${std}: $$tst"; \
- done; \
-+ if test "$$all" -eq 1; then \
-+ tests="test"; \
-+ All=""; \
-+ else \
-+ tests="tests"; \
-+ All="All "; \
-+ fi; \
- if test "$$failed" -eq 0; then \
-- banner="All $$all tests passed"; \
-+ if test "$$xfail" -eq 0; then \
-+ banner="$$All$$all $$tests passed"; \
- else \
-- banner="$$failed of $$all tests failed"; \
-+ if test "$$xfail" -eq 1; then failures=failure; else failures=failures; fi; \
-+ banner="$$All$$all $$tests behaved as expected ($$xfail expected $$failures)"; \
-+ fi; \
-+ else \
-+ if test "$$xpass" -eq 0; then \
-+ banner="$$failed of $$all $$tests failed"; \
-+ else \
-+ if test "$$xpass" -eq 1; then passes=pass; else passes=passes; fi; \
-+ banner="$$failed of $$all $$tests did not behave as expected ($$xpass unexpected $$passes)"; \
-+ fi; \
-+ fi; \
-+ dashes="$$banner"; \
-+ skipped=""; \
-+ if test "$$skip" -ne 0; then \
-+ if test "$$skip" -eq 1; then \
-+ skipped="($$skip test was not run)"; \
-+ else \
-+ skipped="($$skip tests were not run)"; \
-+ fi; \
-+ test `echo "$$skipped" | wc -c` -le `echo "$$banner" | wc -c` || \
-+ dashes="$$skipped"; \
-+ fi; \
-+ report=""; \
-+ if test "$$failed" -ne 0 && test -n "$(PACKAGE_BUGREPORT)"; then \
-+ report="Please report to $(PACKAGE_BUGREPORT)"; \
-+ test `echo "$$report" | wc -c` -le `echo "$$banner" | wc -c` || \
-+ dashes="$$report"; \
-+ fi; \
-+ dashes=`echo "$$dashes" | sed s/./=/g`; \
-+ if test "$$failed" -eq 0; then \
-+ echo "$$grn$$dashes"; \
-+ else \
-+ echo "$$red$$dashes"; \
- fi; \
-- dashes=`echo "$$banner" | sed s/./=/g`; \
-- echo "$$dashes"; \
- echo "$$banner"; \
-- echo "$$dashes"; \
-- test "$$failed" -eq 0
--info-am:
--info: info-am
--dvi-am:
--dvi: dvi-am
-+ test -z "$$skipped" || echo "$$skipped"; \
-+ test -z "$$report" || echo "$$report"; \
-+ echo "$$dashes$$std"; \
-+ test "$$failed" -eq 0; \
-+ else :; fi
-+
-+distdir: $(DISTFILES)
-+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ list='$(DISTFILES)'; \
-+ dist_files=`for file in $$list; do echo $$file; done | \
-+ sed -e "s|^$$srcdirstrip/||;t" \
-+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-+ case $$dist_files in \
-+ */*) $(MKDIR_P) `echo "$$dist_files" | \
-+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-+ sort -u` ;; \
-+ esac; \
-+ for file in $$dist_files; do \
-+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
-+ if test -d $$d/$$file; then \
-+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-+ if test -d "$(distdir)/$$file"; then \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
-+ else \
-+ test -f "$(distdir)/$$file" \
-+ || cp -p $$d/$$file "$(distdir)/$$file" \
-+ || exit 1; \
-+ fi; \
-+ done
- check-am: all-am
- $(MAKE) $(AM_MAKEFLAGS) check-TESTS
- check: check-am
--installcheck-am:
--installcheck: installcheck-am
--install-exec-am:
-+all-am: Makefile $(PROGRAMS) $(HEADERS)
-+installdirs:
-+install: install-am
- install-exec: install-exec-am
--
--install-data-am:
- install-data: install-data-am
-+uninstall: uninstall-am
-
- install-am: all-am
- @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
--install: install-am
--uninstall-am:
--uninstall: uninstall-am
--all-am: Makefile $(PROGRAMS) $(HEADERS)
--all-redirect: all-am
--install-strip:
-- $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
--installdirs:
--
-
-+installcheck: installcheck-am
-+install-strip:
-+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-+ `test -z '$(STRIP)' || \
-+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
- mostlyclean-generic:
-
- clean-generic:
-
- distclean-generic:
-- -rm -f Makefile $(CONFIG_CLEAN_FILES)
-- -rm -f config.cache config.log stamp-h stamp-h[0-9]*
-+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
- maintainer-clean-generic:
-+ @echo "This command is intended for maintainers to use"
-+ @echo "it deletes files that may require special tools to rebuild."
- -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
--mostlyclean-am: mostlyclean-noinstPROGRAMS mostlyclean-compile \
-- mostlyclean-tags mostlyclean-generic
-+clean: clean-am
-
--mostlyclean: mostlyclean-am
-+clean-am: clean-generic clean-noinstPROGRAMS mostlyclean-am
-
--clean-am: clean-noinstPROGRAMS clean-compile clean-tags clean-generic \
-- mostlyclean-am
-+distclean: distclean-am
-+ -rm -rf ./$(DEPDIR)
-+ -rm -f Makefile
-+distclean-am: clean-am distclean-compile distclean-generic \
-+ distclean-tags
-
--clean: clean-am
-+dvi: dvi-am
-
--distclean-am: distclean-noinstPROGRAMS distclean-compile distclean-tags \
-- distclean-generic clean-am
-+dvi-am:
-
--distclean: distclean-am
-+html: html-am
-
--maintainer-clean-am: maintainer-clean-noinstPROGRAMS \
-- maintainer-clean-compile maintainer-clean-tags \
-- maintainer-clean-generic distclean-am
-- @echo "This command is intended for maintainers to use;"
-- @echo "it deletes files that may require special tools to rebuild."
-+html-am:
-+
-+info: info-am
-+
-+info-am:
-+
-+install-data-am:
-+
-+install-dvi: install-dvi-am
-+
-+install-dvi-am:
-+
-+install-exec-am:
-+
-+install-html: install-html-am
-+
-+install-html-am:
-+
-+install-info: install-info-am
-+
-+install-info-am:
-+
-+install-man:
-+
-+install-pdf: install-pdf-am
-+
-+install-pdf-am:
-+
-+install-ps: install-ps-am
-+
-+install-ps-am:
-+
-+installcheck-am:
-
- maintainer-clean: maintainer-clean-am
-+ -rm -rf ./$(DEPDIR)
-+ -rm -f Makefile
-+maintainer-clean-am: distclean-am maintainer-clean-generic
-+
-+mostlyclean: mostlyclean-am
-+
-+mostlyclean-am: mostlyclean-compile mostlyclean-generic
-+
-+pdf: pdf-am
-+
-+pdf-am:
-+
-+ps: ps-am
-+
-+ps-am:
-+
-+uninstall-am:
-+
-+.MAKE: check-am install-am install-strip
-
--.PHONY: mostlyclean-noinstPROGRAMS distclean-noinstPROGRAMS \
--clean-noinstPROGRAMS maintainer-clean-noinstPROGRAMS \
--mostlyclean-compile distclean-compile clean-compile \
--maintainer-clean-compile tags mostlyclean-tags distclean-tags \
--clean-tags maintainer-clean-tags distdir check-TESTS info-am info \
--dvi-am dvi check check-am installcheck-am installcheck install-exec-am \
--install-exec install-data-am install-data install-am install \
--uninstall-am uninstall all-redirect all-am all installdirs \
--mostlyclean-generic distclean-generic clean-generic \
--maintainer-clean-generic clean mostlyclean distclean maintainer-clean
-+.PHONY: CTAGS GTAGS all all-am check check-TESTS check-am clean \
-+ clean-generic clean-noinstPROGRAMS ctags distclean \
-+ distclean-compile distclean-generic distclean-tags distdir dvi \
-+ dvi-am html html-am info info-am install install-am \
-+ install-data install-data-am install-dvi install-dvi-am \
-+ install-exec install-exec-am install-html install-html-am \
-+ install-info install-info-am install-man install-pdf \
-+ install-pdf-am install-ps install-ps-am install-strip \
-+ installcheck installcheck-am installdirs maintainer-clean \
-+ maintainer-clean-generic mostlyclean mostlyclean-compile \
-+ mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
-+ uninstall-am
-
-
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -ubrN exonerate-2.2.0.orig/src/c4/Makefile.in exonerate-2.2.0/src/c4/Makefile.in
---- exonerate-2.2.0.orig/src/c4/Makefile.in 2008-10-17 12:04:36.000000000 +0200
-+++ exonerate-2.2.0/src/c4/Makefile.in 2011-12-12 13:33:16.000000000 +0100
-@@ -1,6 +1,9 @@
--# Makefile.in generated automatically by automake 1.4-p6 from Makefile.am
-+# Makefile.in generated by automake 1.11.1 from Makefile.am.
-+# @configure_input@
-
--# Copyright (C) 1994, 1995-8, 1999, 2001 Free Software Foundation, Inc.
-+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
-+# Inc.
- # This Makefile.in is free software; the Free Software Foundation
- # gives unlimited permission to copy and/or distribute it,
- # with or without modifications, as long as this notice is preserved.
-@@ -10,454 +13,708 @@
- # even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- # PARTICULAR PURPOSE.
-
-+ at SET_MAKE@
-
--SHELL = @SHELL@
-
--srcdir = @srcdir@
--top_srcdir = @top_srcdir@
- VPATH = @srcdir@
--prefix = @prefix@
--exec_prefix = @exec_prefix@
--
--bindir = @bindir@
--sbindir = @sbindir@
--libexecdir = @libexecdir@
--datadir = @datadir@
--sysconfdir = @sysconfdir@
--sharedstatedir = @sharedstatedir@
--localstatedir = @localstatedir@
--libdir = @libdir@
--infodir = @infodir@
--mandir = @mandir@
--includedir = @includedir@
--oldincludedir = /usr/include
--
--DESTDIR =
--
- pkgdatadir = $(datadir)/@PACKAGE@
--pkglibdir = $(libdir)/@PACKAGE@
- pkgincludedir = $(includedir)/@PACKAGE@
--
--top_builddir = ../..
--
--ACLOCAL = @ACLOCAL@
--AUTOCONF = @AUTOCONF@
--AUTOMAKE = @AUTOMAKE@
--AUTOHEADER = @AUTOHEADER@
--
--INSTALL = @INSTALL@
--INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
--INSTALL_DATA = @INSTALL_DATA@
--INSTALL_SCRIPT = @INSTALL_SCRIPT@
--transform = @program_transform_name@
--
-+pkglibdir = $(libdir)/@PACKAGE@
-+pkglibexecdir = $(libexecdir)/@PACKAGE@
-+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-+install_sh_DATA = $(install_sh) -c -m 644
-+install_sh_PROGRAM = $(install_sh) -c
-+install_sh_SCRIPT = $(install_sh) -c
-+INSTALL_HEADER = $(INSTALL_DATA)
-+transform = $(program_transform_name)
- NORMAL_INSTALL = :
- PRE_INSTALL = :
- POST_INSTALL = :
- NORMAL_UNINSTALL = :
- PRE_UNINSTALL = :
- POST_UNINSTALL = :
--host_alias = @host_alias@
-+build_triplet = @build@
- host_triplet = @host@
-+TESTS = region.test$(EXEEXT) c4.test$(EXEEXT) alignment.test$(EXEEXT) \
-+ codegen.test$(EXEEXT) optimal.test$(EXEEXT) \
-+ layout.test$(EXEEXT) viterbi.test$(EXEEXT) opair.test$(EXEEXT) \
-+ subopt.test$(EXEEXT) cgutil.test$(EXEEXT)
-+noinst_PROGRAMS = $(am__EXEEXT_1)
-+subdir = src/c4
-+DIST_COMMON = $(noinst_HEADERS) $(srcdir)/Makefile.am \
-+ $(srcdir)/Makefile.in
-+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-+am__aclocal_m4_deps = $(top_srcdir)/configure.in
-+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-+ $(ACLOCAL_M4)
-+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
-+CONFIG_CLEAN_FILES =
-+CONFIG_CLEAN_VPATH_FILES =
-+am__EXEEXT_1 = region.test$(EXEEXT) c4.test$(EXEEXT) \
-+ alignment.test$(EXEEXT) codegen.test$(EXEEXT) \
-+ optimal.test$(EXEEXT) layout.test$(EXEEXT) \
-+ viterbi.test$(EXEEXT) opair.test$(EXEEXT) subopt.test$(EXEEXT) \
-+ cgutil.test$(EXEEXT)
-+PROGRAMS = $(noinst_PROGRAMS)
-+am_alignment_test_OBJECTS = alignment.test.$(OBJEXT) \
-+ alignment.$(OBJEXT) c4.$(OBJEXT) region.$(OBJEXT)
-+alignment_test_OBJECTS = $(am_alignment_test_OBJECTS)
-+am__DEPENDENCIES_1 = $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o \
-+ $(top_srcdir)/src/sequence/sequence.o \
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/lineparse.o
-+am__DEPENDENCIES_2 = $(top_srcdir)/src/comparison/match.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o \
-+ $(top_srcdir)/src/sequence/submat.o $(am__DEPENDENCIES_1)
-+alignment_test_DEPENDENCIES = $(am__DEPENDENCIES_2)
-+am_c4_test_OBJECTS = c4.test.$(OBJEXT) c4.$(OBJEXT) region.$(OBJEXT)
-+c4_test_OBJECTS = $(am_c4_test_OBJECTS)
-+c4_test_DEPENDENCIES = $(top_srcdir)/src/struct/matrix.o
-+am_cgutil_test_OBJECTS = cgutil.test.$(OBJEXT) cgutil.$(OBJEXT) \
-+ codegen.$(OBJEXT) c4.$(OBJEXT) region.$(OBJEXT)
-+cgutil_test_OBJECTS = $(am_cgutil_test_OBJECTS)
-+cgutil_test_DEPENDENCIES = $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/struct/matrix.o
-+am_codegen_test_OBJECTS = codegen.test.$(OBJEXT) codegen.$(OBJEXT)
-+codegen_test_OBJECTS = $(am_codegen_test_OBJECTS)
-+codegen_test_DEPENDENCIES = $(top_srcdir)/src/general/argument.o
-+am_layout_test_OBJECTS = layout.test.$(OBJEXT) layout.$(OBJEXT)
-+layout_test_OBJECTS = $(am_layout_test_OBJECTS)
-+layout_test_DEPENDENCIES = $(top_srcdir)/src/struct/matrix.o
-+am_opair_test_OBJECTS = opair.test.$(OBJEXT) opair.$(OBJEXT) \
-+ optimal.$(OBJEXT) c4.$(OBJEXT) alignment.$(OBJEXT) \
-+ codegen.$(OBJEXT) region.$(OBJEXT) layout.$(OBJEXT) \
-+ viterbi.$(OBJEXT) subopt.$(OBJEXT) cgutil.$(OBJEXT)
-+opair_test_OBJECTS = $(am_opair_test_OBJECTS)
-+opair_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/rangetree.o $(am__DEPENDENCIES_2)
-+am_optimal_test_OBJECTS = optimal.test.$(OBJEXT) optimal.$(OBJEXT) \
-+ c4.$(OBJEXT) alignment.$(OBJEXT) codegen.$(OBJEXT) \
-+ region.$(OBJEXT) layout.$(OBJEXT) viterbi.$(OBJEXT) \
-+ subopt.$(OBJEXT) cgutil.$(OBJEXT)
-+optimal_test_OBJECTS = $(am_optimal_test_OBJECTS)
-+optimal_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/rangetree.o $(am__DEPENDENCIES_2)
-+am_region_test_OBJECTS = region.test.$(OBJEXT) region.$(OBJEXT)
-+region_test_OBJECTS = $(am_region_test_OBJECTS)
-+region_test_LDADD = $(LDADD)
-+am_subopt_test_OBJECTS = subopt.test.$(OBJEXT) subopt.$(OBJEXT) \
-+ region.$(OBJEXT)
-+subopt_test_OBJECTS = $(am_subopt_test_OBJECTS)
-+subopt_test_DEPENDENCIES = $(top_srcdir)/src/struct/rangetree.o \
-+ $(top_srcdir)/src/struct/recyclebin.o
-+am_viterbi_test_OBJECTS = viterbi.test.$(OBJEXT) viterbi.$(OBJEXT) \
-+ c4.$(OBJEXT) region.$(OBJEXT) alignment.$(OBJEXT) \
-+ codegen.$(OBJEXT) layout.$(OBJEXT) subopt.$(OBJEXT) \
-+ cgutil.$(OBJEXT)
-+viterbi_test_OBJECTS = $(am_viterbi_test_OBJECTS)
-+viterbi_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/rangetree.o $(am__DEPENDENCIES_2)
-+DEFAULT_INCLUDES = -I. at am__isrc@
-+depcomp = $(SHELL) $(top_srcdir)/depcomp
-+am__depfiles_maybe = depfiles
-+am__mv = mv -f
-+COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
-+ $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
-+CCLD = $(CC)
-+LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
-+SOURCES = $(alignment_test_SOURCES) $(c4_test_SOURCES) \
-+ $(cgutil_test_SOURCES) $(codegen_test_SOURCES) \
-+ $(layout_test_SOURCES) $(opair_test_SOURCES) \
-+ $(optimal_test_SOURCES) $(region_test_SOURCES) \
-+ $(subopt_test_SOURCES) $(viterbi_test_SOURCES)
-+DIST_SOURCES = $(alignment_test_SOURCES) $(c4_test_SOURCES) \
-+ $(cgutil_test_SOURCES) $(codegen_test_SOURCES) \
-+ $(layout_test_SOURCES) $(opair_test_SOURCES) \
-+ $(optimal_test_SOURCES) $(region_test_SOURCES) \
-+ $(subopt_test_SOURCES) $(viterbi_test_SOURCES)
-+HEADERS = $(noinst_HEADERS)
-+ETAGS = etags
-+CTAGS = ctags
-+am__tty_colors = \
-+red=; grn=; lgn=; blu=; std=
-+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-+ACLOCAL = @ACLOCAL@
-+AMTAR = @AMTAR@
-+AUTOCONF = @AUTOCONF@
-+AUTOHEADER = @AUTOHEADER@
-+AUTOMAKE = @AUTOMAKE@
-+AWK = @AWK@
- CC = @CC@
-+CCDEPMODE = @CCDEPMODE@
-+CFLAGS = @CFLAGS@
-+CPP = @CPP@
-+CPPFLAGS = @CPPFLAGS@
-+CYGPATH_W = @CYGPATH_W@
-+DEFS = @DEFS@
-+DEPDIR = @DEPDIR@
-+ECHO_C = @ECHO_C@
-+ECHO_N = @ECHO_N@
-+ECHO_T = @ECHO_T@
-+EGREP = @EGREP@
-+EXEEXT = @EXEEXT@
- GLIB_CONFIG = @GLIB_CONFIG@
--HAVE_LIB = @HAVE_LIB@
--LIB = @LIB@
--LTLIB = @LTLIB@
-+GREP = @GREP@
-+INSTALL = @INSTALL@
-+INSTALL_DATA = @INSTALL_DATA@
-+INSTALL_PROGRAM = @INSTALL_PROGRAM@
-+INSTALL_SCRIPT = @INSTALL_SCRIPT@
-+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-+LDFLAGS = @LDFLAGS@
-+LIBOBJS = @LIBOBJS@
-+LIBS = @LIBS@
-+LTLIBOBJS = @LTLIBOBJS@
- MAKEINFO = @MAKEINFO@
-+MKDIR_P = @MKDIR_P@
-+OBJEXT = @OBJEXT@
- PACKAGE = @PACKAGE@
-+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-+PACKAGE_NAME = @PACKAGE_NAME@
-+PACKAGE_STRING = @PACKAGE_STRING@
-+PACKAGE_TARNAME = @PACKAGE_TARNAME@
-+PACKAGE_URL = @PACKAGE_URL@
-+PACKAGE_VERSION = @PACKAGE_VERSION@
-+PATH_SEPARATOR = @PATH_SEPARATOR@
- PKG_CONFIG = @PKG_CONFIG@
-+SET_MAKE = @SET_MAKE@
-+SHELL = @SHELL@
-+STRIP = @STRIP@
- VERSION = @VERSION@
-+abs_builddir = @abs_builddir@
-+abs_srcdir = @abs_srcdir@
-+abs_top_builddir = @abs_top_builddir@
-+abs_top_srcdir = @abs_top_srcdir@
-+ac_ct_CC = @ac_ct_CC@
-+am__include = @am__include@
-+am__leading_dot = @am__leading_dot@
-+am__quote = @am__quote@
-+am__tar = @am__tar@
-+am__untar = @am__untar@
-+bindir = @bindir@
-+build = @build@
-+build_alias = @build_alias@
-+build_cpu = @build_cpu@
-+build_os = @build_os@
-+build_vendor = @build_vendor@
-+builddir = @builddir@
- codegen_extra_ldadd = @codegen_extra_ldadd@
- codegen_extra_sources = @codegen_extra_sources@
-+datadir = @datadir@
- datarootdir = @datarootdir@
-+docdir = @docdir@
-+dvidir = @dvidir@
-+exec_prefix = @exec_prefix@
- glib_cflags = @glib_cflags@
- glib_libs = @glib_libs@
- host = @host@
-+host_alias = @host_alias@
-+host_cpu = @host_cpu@
-+host_os = @host_os@
-+host_vendor = @host_vendor@
-+htmldir = @htmldir@
-+includedir = @includedir@
-+infodir = @infodir@
-+install_sh = @install_sh@
- installed_util_list = @installed_util_list@
-+libdir = @libdir@
-+libexecdir = @libexecdir@
-+localedir = @localedir@
-+localstatedir = @localstatedir@
-+mandir = @mandir@
-+mkdir_p = @mkdir_p@
-+oldincludedir = @oldincludedir@
-+pdfdir = @pdfdir@
-+prefix = @prefix@
-+program_transform_name = @program_transform_name@
-+psdir = @psdir@
-+sbindir = @sbindir@
-+sharedstatedir = @sharedstatedir@
- source_root_dir = @source_root_dir@
-+srcdir = @srcdir@
-+sysconfdir = @sysconfdir@
-+target_alias = @target_alias@
-+top_build_prefix = @top_build_prefix@
-+top_builddir = @top_builddir@
-+top_srcdir = @top_srcdir@
- use_pthreads = @use_pthreads@
--
--TESTS = region.test c4.test alignment.test codegen.test optimal.test layout.test viterbi.test opair.test subopt.test cgutil.test
--
--
--noinst_PROGRAMS = $(TESTS)
--
--INCLUDES = -I$(top_srcdir)/src/struct -I$(top_srcdir)/src/comparison -I$(top_srcdir)/src/sequence -I$(top_srcdir)/src/general -DSOURCE_ROOT_DIR="\"@source_root_dir@\"" -DGLIB_CFLAGS="\"@glib_cflags@\"" -DHOSTTYPE="\"@host@\""
--
--
--noinst_HEADERS = region.h c4.h alignment.h codegen.h optimal.h layout.h viterbi.h opair.h subopt.h cgutil.h
--
-+INCLUDES = -I$(top_srcdir)/src/struct \
-+ -I$(top_srcdir)/src/comparison \
-+ -I$(top_srcdir)/src/sequence \
-+ -I$(top_srcdir)/src/general \
-+ -DSOURCE_ROOT_DIR="\"@source_root_dir@\"" \
-+ -DGLIB_CFLAGS="\"@glib_cflags@\"" \
-+ -DHOSTTYPE="\"@host@\""
-+
-+noinst_HEADERS = region.h c4.h alignment.h codegen.h optimal.h \
-+ layout.h viterbi.h opair.h subopt.h \
-+ cgutil.h
-
- region_test_SOURCES = region.test.c region.c
--
- c4_test_SOURCES = c4.test.c c4.c region.c
- c4_test_LDADD = $(top_srcdir)/src/struct/matrix.o
--
--SEQUENCE_OBJ = $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o $(top_srcdir)/src/sequence/alphabet.o $(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/sequence/translate.o $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/general/lineparse.o -lm
--
--
--ALIGNMENT_OBJ = $(top_srcdir)/src/comparison/match.o $(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/sequence/submat.o $(SEQUENCE_OBJ)
-+SEQUENCE_OBJ = $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o \
-+ $(top_srcdir)/src/sequence/sequence.o \
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ -lm
-+
-+ALIGNMENT_OBJ = $(top_srcdir)/src/comparison/match.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o \
-+ $(top_srcdir)/src/sequence/submat.o \
-+ $(SEQUENCE_OBJ)
-
- alignment_test_SOURCES = alignment.test.c alignment.c c4.c region.c
- alignment_test_LDADD = $(ALIGNMENT_OBJ)
--
- codegen_test_SOURCES = codegen.test.c codegen.c
- codegen_test_LDADD = $(top_srcdir)/src/general/argument.o
--
- cgutil_test_SOURCES = cgutil.test.c cgutil.c codegen.c c4.c region.c
--cgutil_test_LDADD = $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/struct/matrix.o
--
--
--viterbi_test_SOURCES = viterbi.test.c viterbi.c c4.c region.c alignment.c codegen.c layout.c subopt.c cgutil.c
--
--viterbi_test_LDADD = $(top_srcdir)/src/struct/slist.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/rangetree.o $(ALIGNMENT_OBJ)
--
--
--optimal_test_SOURCES = optimal.test.c optimal.c c4.c alignment.c codegen.c region.c layout.c viterbi.c subopt.c cgutil.c
--
--optimal_test_LDADD = $(top_srcdir)/src/struct/slist.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/rangetree.o $(ALIGNMENT_OBJ)
-+cgutil_test_LDADD = $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/struct/matrix.o
-
-+viterbi_test_SOURCES = viterbi.test.c viterbi.c c4.c region.c \
-+ alignment.c codegen.c layout.c subopt.c \
-+ cgutil.c
-+
-+viterbi_test_LDADD = $(top_srcdir)/src/struct/slist.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/rangetree.o \
-+ $(ALIGNMENT_OBJ)
-+
-+optimal_test_SOURCES = optimal.test.c optimal.c c4.c alignment.c \
-+ codegen.c region.c layout.c viterbi.c \
-+ subopt.c cgutil.c
-+
-+optimal_test_LDADD = $(top_srcdir)/src/struct/slist.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/rangetree.o \
-+ $(ALIGNMENT_OBJ)
-
- layout_test_SOURCES = layout.test.c layout.c
- layout_test_LDADD = $(top_srcdir)/src/struct/matrix.o
--
--opair_test_SOURCES = opair.test.c opair.c optimal.c c4.c alignment.c codegen.c region.c layout.c viterbi.c subopt.c cgutil.c
--
--opair_test_LDADD = $(top_srcdir)/src/struct/slist.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/rangetree.o $(ALIGNMENT_OBJ)
--
-+opair_test_SOURCES = opair.test.c opair.c optimal.c c4.c alignment.c \
-+ codegen.c region.c layout.c viterbi.c subopt.c \
-+ cgutil.c
-+
-+opair_test_LDADD = $(top_srcdir)/src/struct/slist.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/rangetree.o \
-+ $(ALIGNMENT_OBJ)
-
- subopt_test_SOURCES = subopt.test.c subopt.c region.c
--subopt_test_LDADD = $(top_srcdir)/src/struct/rangetree.o $(top_srcdir)/src/struct/recyclebin.o
-+subopt_test_LDADD = $(top_srcdir)/src/struct/rangetree.o \
-+ $(top_srcdir)/src/struct/recyclebin.o
-
-
- # Files to clear away
--
- MAINTAINERCLEANFILES = Makefile.in
--mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
--CONFIG_CLEAN_FILES =
--PROGRAMS = $(noinst_PROGRAMS)
--
-+all: all-am
-
--DEFS = @DEFS@ -I. -I$(srcdir)
--CPPFLAGS = @CPPFLAGS@
--LDFLAGS = @LDFLAGS@
--LIBS = @LIBS@
--region_test_OBJECTS = region.test.o region.o
--region_test_LDADD = $(LDADD)
--region_test_DEPENDENCIES =
--region_test_LDFLAGS =
--c4_test_OBJECTS = c4.test.o c4.o region.o
--c4_test_DEPENDENCIES = $(top_srcdir)/src/struct/matrix.o
--c4_test_LDFLAGS =
--alignment_test_OBJECTS = alignment.test.o alignment.o c4.o region.o
--alignment_test_DEPENDENCIES = $(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--alignment_test_LDFLAGS =
--codegen_test_OBJECTS = codegen.test.o codegen.o
--codegen_test_DEPENDENCIES = $(top_srcdir)/src/general/argument.o
--codegen_test_LDFLAGS =
--optimal_test_OBJECTS = optimal.test.o optimal.o c4.o alignment.o \
--codegen.o region.o layout.o viterbi.o subopt.o cgutil.o
--optimal_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \
--$(top_srcdir)/src/struct/recyclebin.o \
--$(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--optimal_test_LDFLAGS =
--layout_test_OBJECTS = layout.test.o layout.o
--layout_test_DEPENDENCIES = $(top_srcdir)/src/struct/matrix.o
--layout_test_LDFLAGS =
--viterbi_test_OBJECTS = viterbi.test.o viterbi.o c4.o region.o \
--alignment.o codegen.o layout.o subopt.o cgutil.o
--viterbi_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \
--$(top_srcdir)/src/struct/recyclebin.o \
--$(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--viterbi_test_LDFLAGS =
--opair_test_OBJECTS = opair.test.o opair.o optimal.o c4.o alignment.o \
--codegen.o region.o layout.o viterbi.o subopt.o cgutil.o
--opair_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \
--$(top_srcdir)/src/struct/recyclebin.o \
--$(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--opair_test_LDFLAGS =
--subopt_test_OBJECTS = subopt.test.o subopt.o region.o
--subopt_test_DEPENDENCIES = $(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/struct/recyclebin.o
--subopt_test_LDFLAGS =
--cgutil_test_OBJECTS = cgutil.test.o cgutil.o codegen.o c4.o region.o
--cgutil_test_DEPENDENCIES = $(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/struct/matrix.o
--cgutil_test_LDFLAGS =
--CFLAGS = @CFLAGS@
--COMPILE = $(CC) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
--CCLD = $(CC)
--LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(LDFLAGS) -o $@
--HEADERS = $(noinst_HEADERS)
--
--DIST_COMMON = Makefile.am Makefile.in
--
--
--DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
--
--TAR = tar
--GZIP_ENV = --best
--SOURCES = $(region_test_SOURCES) $(c4_test_SOURCES) $(alignment_test_SOURCES) $(codegen_test_SOURCES) $(optimal_test_SOURCES) $(layout_test_SOURCES) $(viterbi_test_SOURCES) $(opair_test_SOURCES) $(subopt_test_SOURCES) $(cgutil_test_SOURCES)
--OBJECTS = $(region_test_OBJECTS) $(c4_test_OBJECTS) $(alignment_test_OBJECTS) $(codegen_test_OBJECTS) $(optimal_test_OBJECTS) $(layout_test_OBJECTS) $(viterbi_test_OBJECTS) $(opair_test_OBJECTS) $(subopt_test_OBJECTS) $(cgutil_test_OBJECTS)
--
--all: all-redirect
- .SUFFIXES:
--.SUFFIXES: .S .c .o .s
--$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4)
-- cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps src/c4/Makefile
--
-+.SUFFIXES: .c .o .obj
-+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
-+ @for dep in $?; do \
-+ case '$(am__configure_deps)' in \
-+ *$$dep*) \
-+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-+ && { if test -f $@; then exit 0; else break; fi; }; \
-+ exit 1;; \
-+ esac; \
-+ done; \
-+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/c4/Makefile'; \
-+ $(am__cd) $(top_srcdir) && \
-+ $(AUTOMAKE) --gnu src/c4/Makefile
-+.PRECIOUS: Makefile
- Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-- cd $(top_builddir) \
-- && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
--
--
--mostlyclean-noinstPROGRAMS:
-+ @case '$?' in \
-+ *config.status*) \
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-+ *) \
-+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-+ esac;
-+
-+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+
-+$(top_srcdir)/configure: $(am__configure_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(am__aclocal_m4_deps):
-
- clean-noinstPROGRAMS:
- -test -z "$(noinst_PROGRAMS)" || rm -f $(noinst_PROGRAMS)
--
--distclean-noinstPROGRAMS:
--
--maintainer-clean-noinstPROGRAMS:
--
--.c.o:
-- $(COMPILE) -c $<
--
--.s.o:
-- $(COMPILE) -c $<
--
--.S.o:
-- $(COMPILE) -c $<
-+alignment.test$(EXEEXT): $(alignment_test_OBJECTS) $(alignment_test_DEPENDENCIES)
-+ @rm -f alignment.test$(EXEEXT)
-+ $(LINK) $(alignment_test_OBJECTS) $(alignment_test_LDADD) $(LIBS)
-+c4.test$(EXEEXT): $(c4_test_OBJECTS) $(c4_test_DEPENDENCIES)
-+ @rm -f c4.test$(EXEEXT)
-+ $(LINK) $(c4_test_OBJECTS) $(c4_test_LDADD) $(LIBS)
-+cgutil.test$(EXEEXT): $(cgutil_test_OBJECTS) $(cgutil_test_DEPENDENCIES)
-+ @rm -f cgutil.test$(EXEEXT)
-+ $(LINK) $(cgutil_test_OBJECTS) $(cgutil_test_LDADD) $(LIBS)
-+codegen.test$(EXEEXT): $(codegen_test_OBJECTS) $(codegen_test_DEPENDENCIES)
-+ @rm -f codegen.test$(EXEEXT)
-+ $(LINK) $(codegen_test_OBJECTS) $(codegen_test_LDADD) $(LIBS)
-+layout.test$(EXEEXT): $(layout_test_OBJECTS) $(layout_test_DEPENDENCIES)
-+ @rm -f layout.test$(EXEEXT)
-+ $(LINK) $(layout_test_OBJECTS) $(layout_test_LDADD) $(LIBS)
-+opair.test$(EXEEXT): $(opair_test_OBJECTS) $(opair_test_DEPENDENCIES)
-+ @rm -f opair.test$(EXEEXT)
-+ $(LINK) $(opair_test_OBJECTS) $(opair_test_LDADD) $(LIBS)
-+optimal.test$(EXEEXT): $(optimal_test_OBJECTS) $(optimal_test_DEPENDENCIES)
-+ @rm -f optimal.test$(EXEEXT)
-+ $(LINK) $(optimal_test_OBJECTS) $(optimal_test_LDADD) $(LIBS)
-+region.test$(EXEEXT): $(region_test_OBJECTS) $(region_test_DEPENDENCIES)
-+ @rm -f region.test$(EXEEXT)
-+ $(LINK) $(region_test_OBJECTS) $(region_test_LDADD) $(LIBS)
-+subopt.test$(EXEEXT): $(subopt_test_OBJECTS) $(subopt_test_DEPENDENCIES)
-+ @rm -f subopt.test$(EXEEXT)
-+ $(LINK) $(subopt_test_OBJECTS) $(subopt_test_LDADD) $(LIBS)
-+viterbi.test$(EXEEXT): $(viterbi_test_OBJECTS) $(viterbi_test_DEPENDENCIES)
-+ @rm -f viterbi.test$(EXEEXT)
-+ $(LINK) $(viterbi_test_OBJECTS) $(viterbi_test_LDADD) $(LIBS)
-
- mostlyclean-compile:
-- -rm -f *.o core *.core
--
--clean-compile:
-+ -rm -f *.$(OBJEXT)
-
- distclean-compile:
- -rm -f *.tab.c
-
--maintainer-clean-compile:
--
--region.test: $(region_test_OBJECTS) $(region_test_DEPENDENCIES)
-- @rm -f region.test
-- $(LINK) $(region_test_LDFLAGS) $(region_test_OBJECTS) $(region_test_LDADD) $(LIBS)
--
--c4.test: $(c4_test_OBJECTS) $(c4_test_DEPENDENCIES)
-- @rm -f c4.test
-- $(LINK) $(c4_test_LDFLAGS) $(c4_test_OBJECTS) $(c4_test_LDADD) $(LIBS)
--
--alignment.test: $(alignment_test_OBJECTS) $(alignment_test_DEPENDENCIES)
-- @rm -f alignment.test
-- $(LINK) $(alignment_test_LDFLAGS) $(alignment_test_OBJECTS) $(alignment_test_LDADD) $(LIBS)
--
--codegen.test: $(codegen_test_OBJECTS) $(codegen_test_DEPENDENCIES)
-- @rm -f codegen.test
-- $(LINK) $(codegen_test_LDFLAGS) $(codegen_test_OBJECTS) $(codegen_test_LDADD) $(LIBS)
--
--optimal.test: $(optimal_test_OBJECTS) $(optimal_test_DEPENDENCIES)
-- @rm -f optimal.test
-- $(LINK) $(optimal_test_LDFLAGS) $(optimal_test_OBJECTS) $(optimal_test_LDADD) $(LIBS)
--
--layout.test: $(layout_test_OBJECTS) $(layout_test_DEPENDENCIES)
-- @rm -f layout.test
-- $(LINK) $(layout_test_LDFLAGS) $(layout_test_OBJECTS) $(layout_test_LDADD) $(LIBS)
--
--viterbi.test: $(viterbi_test_OBJECTS) $(viterbi_test_DEPENDENCIES)
-- @rm -f viterbi.test
-- $(LINK) $(viterbi_test_LDFLAGS) $(viterbi_test_OBJECTS) $(viterbi_test_LDADD) $(LIBS)
--
--opair.test: $(opair_test_OBJECTS) $(opair_test_DEPENDENCIES)
-- @rm -f opair.test
-- $(LINK) $(opair_test_LDFLAGS) $(opair_test_OBJECTS) $(opair_test_LDADD) $(LIBS)
--
--subopt.test: $(subopt_test_OBJECTS) $(subopt_test_DEPENDENCIES)
-- @rm -f subopt.test
-- $(LINK) $(subopt_test_LDFLAGS) $(subopt_test_OBJECTS) $(subopt_test_LDADD) $(LIBS)
--
--cgutil.test: $(cgutil_test_OBJECTS) $(cgutil_test_DEPENDENCIES)
-- @rm -f cgutil.test
-- $(LINK) $(cgutil_test_LDFLAGS) $(cgutil_test_OBJECTS) $(cgutil_test_LDADD) $(LIBS)
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/alignment.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/alignment.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/c4.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/c4.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cgutil.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cgutil.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/codegen.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/codegen.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/layout.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/layout.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/opair.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/opair.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/optimal.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/optimal.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/region.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/region.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/subopt.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/subopt.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/viterbi.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/viterbi.test.Po at am__quote@
-
-+.c.o:
-+ at am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
-+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-+ at am__fastdepCC_FALSE@ $(COMPILE) -c $<
-+
-+.c.obj:
-+ at am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
-+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-+ at am__fastdepCC_FALSE@ $(COMPILE) -c `$(CYGPATH_W) '$<'`
-+
-+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ mkid -fID $$unique
- tags: TAGS
-
--ID: $(HEADERS) $(SOURCES) $(LISP)
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- here=`pwd` && cd $(srcdir) \
-- && mkid -f$$here/ID $$unique $(LISP)
--
--TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) $(LISP)
-- tags=; \
-+TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ set x; \
- here=`pwd`; \
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- test -z "$(ETAGS_ARGS)$$unique$(LISP)$$tags" \
-- || (cd $(srcdir) && etags -o $$here/TAGS $(ETAGS_ARGS) $$tags $$unique $(LISP))
--
--mostlyclean-tags:
--
--clean-tags:
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ shift; \
-+ if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
-+ test -n "$$unique" || unique=$$empty_fix; \
-+ if test $$# -gt 0; then \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ "$$@" $$unique; \
-+ else \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ $$unique; \
-+ fi; \
-+ fi
-+ctags: CTAGS
-+CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ test -z "$(CTAGS_ARGS)$$unique" \
-+ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-+ $$unique
-+
-+GTAGS:
-+ here=`$(am__cd) $(top_builddir) && pwd` \
-+ && $(am__cd) $(top_srcdir) \
-+ && gtags -i $(GTAGS_ARGS) "$$here"
-
- distclean-tags:
-- -rm -f TAGS ID
-+ -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-
--maintainer-clean-tags:
--
--distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
--
--subdir = src/c4
--
--distdir: $(DISTFILES)
-- @for file in $(DISTFILES); do \
-- d=$(srcdir); \
-- if test -d $$d/$$file; then \
-- cp -pr $$d/$$file $(distdir)/$$file; \
-- else \
-- test -f $(distdir)/$$file \
-- || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
-- || cp -p $$d/$$file $(distdir)/$$file || :; \
-- fi; \
-- done
- check-TESTS: $(TESTS)
-- @failed=0; all=0; \
-+ @failed=0; all=0; xfail=0; xpass=0; skip=0; \
- srcdir=$(srcdir); export srcdir; \
-- for tst in $(TESTS); do \
-- if test -f $$tst; then dir=.; \
-- else dir="$(srcdir)"; fi; \
-- if $(TESTS_ENVIRONMENT) $$dir/$$tst; then \
-+ list=' $(TESTS) '; \
-+ $(am__tty_colors); \
-+ if test -n "$$list"; then \
-+ for tst in $$list; do \
-+ if test -f ./$$tst; then dir=./; \
-+ elif test -f $$tst; then dir=; \
-+ else dir="$(srcdir)/"; fi; \
-+ if $(TESTS_ENVIRONMENT) $${dir}$$tst; then \
- all=`expr $$all + 1`; \
-- echo "PASS: $$tst"; \
-+ case " $(XFAIL_TESTS) " in \
-+ *[\ \ ]$$tst[\ \ ]*) \
-+ xpass=`expr $$xpass + 1`; \
-+ failed=`expr $$failed + 1`; \
-+ col=$$red; res=XPASS; \
-+ ;; \
-+ *) \
-+ col=$$grn; res=PASS; \
-+ ;; \
-+ esac; \
- elif test $$? -ne 77; then \
- all=`expr $$all + 1`; \
-+ case " $(XFAIL_TESTS) " in \
-+ *[\ \ ]$$tst[\ \ ]*) \
-+ xfail=`expr $$xfail + 1`; \
-+ col=$$lgn; res=XFAIL; \
-+ ;; \
-+ *) \
- failed=`expr $$failed + 1`; \
-- echo "FAIL: $$tst"; \
-+ col=$$red; res=FAIL; \
-+ ;; \
-+ esac; \
-+ else \
-+ skip=`expr $$skip + 1`; \
-+ col=$$blu; res=SKIP; \
- fi; \
-+ echo "$${col}$$res$${std}: $$tst"; \
- done; \
-+ if test "$$all" -eq 1; then \
-+ tests="test"; \
-+ All=""; \
-+ else \
-+ tests="tests"; \
-+ All="All "; \
-+ fi; \
- if test "$$failed" -eq 0; then \
-- banner="All $$all tests passed"; \
-+ if test "$$xfail" -eq 0; then \
-+ banner="$$All$$all $$tests passed"; \
- else \
-- banner="$$failed of $$all tests failed"; \
-+ if test "$$xfail" -eq 1; then failures=failure; else failures=failures; fi; \
-+ banner="$$All$$all $$tests behaved as expected ($$xfail expected $$failures)"; \
-+ fi; \
-+ else \
-+ if test "$$xpass" -eq 0; then \
-+ banner="$$failed of $$all $$tests failed"; \
-+ else \
-+ if test "$$xpass" -eq 1; then passes=pass; else passes=passes; fi; \
-+ banner="$$failed of $$all $$tests did not behave as expected ($$xpass unexpected $$passes)"; \
-+ fi; \
-+ fi; \
-+ dashes="$$banner"; \
-+ skipped=""; \
-+ if test "$$skip" -ne 0; then \
-+ if test "$$skip" -eq 1; then \
-+ skipped="($$skip test was not run)"; \
-+ else \
-+ skipped="($$skip tests were not run)"; \
-+ fi; \
-+ test `echo "$$skipped" | wc -c` -le `echo "$$banner" | wc -c` || \
-+ dashes="$$skipped"; \
-+ fi; \
-+ report=""; \
-+ if test "$$failed" -ne 0 && test -n "$(PACKAGE_BUGREPORT)"; then \
-+ report="Please report to $(PACKAGE_BUGREPORT)"; \
-+ test `echo "$$report" | wc -c` -le `echo "$$banner" | wc -c` || \
-+ dashes="$$report"; \
-+ fi; \
-+ dashes=`echo "$$dashes" | sed s/./=/g`; \
-+ if test "$$failed" -eq 0; then \
-+ echo "$$grn$$dashes"; \
-+ else \
-+ echo "$$red$$dashes"; \
- fi; \
-- dashes=`echo "$$banner" | sed s/./=/g`; \
-- echo "$$dashes"; \
- echo "$$banner"; \
-- echo "$$dashes"; \
-- test "$$failed" -eq 0
--info-am:
--info: info-am
--dvi-am:
--dvi: dvi-am
-+ test -z "$$skipped" || echo "$$skipped"; \
-+ test -z "$$report" || echo "$$report"; \
-+ echo "$$dashes$$std"; \
-+ test "$$failed" -eq 0; \
-+ else :; fi
-+
-+distdir: $(DISTFILES)
-+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ list='$(DISTFILES)'; \
-+ dist_files=`for file in $$list; do echo $$file; done | \
-+ sed -e "s|^$$srcdirstrip/||;t" \
-+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-+ case $$dist_files in \
-+ */*) $(MKDIR_P) `echo "$$dist_files" | \
-+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-+ sort -u` ;; \
-+ esac; \
-+ for file in $$dist_files; do \
-+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
-+ if test -d $$d/$$file; then \
-+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-+ if test -d "$(distdir)/$$file"; then \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
-+ else \
-+ test -f "$(distdir)/$$file" \
-+ || cp -p $$d/$$file "$(distdir)/$$file" \
-+ || exit 1; \
-+ fi; \
-+ done
- check-am: all-am
- $(MAKE) $(AM_MAKEFLAGS) check-TESTS
- check: check-am
--installcheck-am:
--installcheck: installcheck-am
--install-exec-am:
-+all-am: Makefile $(PROGRAMS) $(HEADERS)
-+installdirs:
-+install: install-am
- install-exec: install-exec-am
--
--install-data-am:
- install-data: install-data-am
-+uninstall: uninstall-am
-
- install-am: all-am
- @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
--install: install-am
--uninstall-am:
--uninstall: uninstall-am
--all-am: Makefile $(PROGRAMS) $(HEADERS)
--all-redirect: all-am
--install-strip:
-- $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
--installdirs:
--
-
-+installcheck: installcheck-am
-+install-strip:
-+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-+ `test -z '$(STRIP)' || \
-+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
- mostlyclean-generic:
-
- clean-generic:
-
- distclean-generic:
-- -rm -f Makefile $(CONFIG_CLEAN_FILES)
-- -rm -f config.cache config.log stamp-h stamp-h[0-9]*
-+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
- maintainer-clean-generic:
-+ @echo "This command is intended for maintainers to use"
-+ @echo "it deletes files that may require special tools to rebuild."
- -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
--mostlyclean-am: mostlyclean-noinstPROGRAMS mostlyclean-compile \
-- mostlyclean-tags mostlyclean-generic
-+clean: clean-am
-
--mostlyclean: mostlyclean-am
-+clean-am: clean-generic clean-noinstPROGRAMS mostlyclean-am
-+
-+distclean: distclean-am
-+ -rm -rf ./$(DEPDIR)
-+ -rm -f Makefile
-+distclean-am: clean-am distclean-compile distclean-generic \
-+ distclean-tags
-
--clean-am: clean-noinstPROGRAMS clean-compile clean-tags clean-generic \
-- mostlyclean-am
-+dvi: dvi-am
-
--clean: clean-am
-+dvi-am:
-
--distclean-am: distclean-noinstPROGRAMS distclean-compile distclean-tags \
-- distclean-generic clean-am
-+html: html-am
-
--distclean: distclean-am
-+html-am:
-
--maintainer-clean-am: maintainer-clean-noinstPROGRAMS \
-- maintainer-clean-compile maintainer-clean-tags \
-- maintainer-clean-generic distclean-am
-- @echo "This command is intended for maintainers to use;"
-- @echo "it deletes files that may require special tools to rebuild."
-+info: info-am
-+
-+info-am:
-+
-+install-data-am:
-+
-+install-dvi: install-dvi-am
-+
-+install-dvi-am:
-+
-+install-exec-am:
-+
-+install-html: install-html-am
-+
-+install-html-am:
-+
-+install-info: install-info-am
-+
-+install-info-am:
-+
-+install-man:
-+
-+install-pdf: install-pdf-am
-+
-+install-pdf-am:
-+
-+install-ps: install-ps-am
-+
-+install-ps-am:
-+
-+installcheck-am:
-
- maintainer-clean: maintainer-clean-am
-+ -rm -rf ./$(DEPDIR)
-+ -rm -f Makefile
-+maintainer-clean-am: distclean-am maintainer-clean-generic
-+
-+mostlyclean: mostlyclean-am
-+
-+mostlyclean-am: mostlyclean-compile mostlyclean-generic
-+
-+pdf: pdf-am
-+
-+pdf-am:
-+
-+ps: ps-am
-+
-+ps-am:
-+
-+uninstall-am:
-+
-+.MAKE: check-am install-am install-strip
-
--.PHONY: mostlyclean-noinstPROGRAMS distclean-noinstPROGRAMS \
--clean-noinstPROGRAMS maintainer-clean-noinstPROGRAMS \
--mostlyclean-compile distclean-compile clean-compile \
--maintainer-clean-compile tags mostlyclean-tags distclean-tags \
--clean-tags maintainer-clean-tags distdir check-TESTS info-am info \
--dvi-am dvi check check-am installcheck-am installcheck install-exec-am \
--install-exec install-data-am install-data install-am install \
--uninstall-am uninstall all-redirect all-am all installdirs \
--mostlyclean-generic distclean-generic clean-generic \
--maintainer-clean-generic clean mostlyclean distclean maintainer-clean
-+.PHONY: CTAGS GTAGS all all-am check check-TESTS check-am clean \
-+ clean-generic clean-noinstPROGRAMS ctags distclean \
-+ distclean-compile distclean-generic distclean-tags distdir dvi \
-+ dvi-am html html-am info info-am install install-am \
-+ install-data install-data-am install-dvi install-dvi-am \
-+ install-exec install-exec-am install-html install-html-am \
-+ install-info install-info-am install-man install-pdf \
-+ install-pdf-am install-ps install-ps-am install-strip \
-+ installcheck installcheck-am installdirs maintainer-clean \
-+ maintainer-clean-generic mostlyclean mostlyclean-compile \
-+ mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
-+ uninstall-am
-
-
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -ubrN exonerate-2.2.0.orig/src/comparison/Makefile.in exonerate-2.2.0/src/comparison/Makefile.in
---- exonerate-2.2.0.orig/src/comparison/Makefile.in 2008-10-17 12:04:35.000000000 +0200
-+++ exonerate-2.2.0/src/comparison/Makefile.in 2011-12-12 13:33:16.000000000 +0100
-@@ -1,6 +1,9 @@
--# Makefile.in generated automatically by automake 1.4-p6 from Makefile.am
-+# Makefile.in generated by automake 1.11.1 from Makefile.am.
-+# @configure_input@
-
--# Copyright (C) 1994, 1995-8, 1999, 2001 Free Software Foundation, Inc.
-+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
-+# Inc.
- # This Makefile.in is free software; the Free Software Foundation
- # gives unlimited permission to copy and/or distribute it,
- # with or without modifications, as long as this notice is preserved.
-@@ -10,415 +13,659 @@
- # even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- # PARTICULAR PURPOSE.
-
-+ at SET_MAKE@
-
--SHELL = @SHELL@
-
--srcdir = @srcdir@
--top_srcdir = @top_srcdir@
- VPATH = @srcdir@
--prefix = @prefix@
--exec_prefix = @exec_prefix@
--
--bindir = @bindir@
--sbindir = @sbindir@
--libexecdir = @libexecdir@
--datadir = @datadir@
--sysconfdir = @sysconfdir@
--sharedstatedir = @sharedstatedir@
--localstatedir = @localstatedir@
--libdir = @libdir@
--infodir = @infodir@
--mandir = @mandir@
--includedir = @includedir@
--oldincludedir = /usr/include
--
--DESTDIR =
--
- pkgdatadir = $(datadir)/@PACKAGE@
--pkglibdir = $(libdir)/@PACKAGE@
- pkgincludedir = $(includedir)/@PACKAGE@
--
--top_builddir = ../..
--
--ACLOCAL = @ACLOCAL@
--AUTOCONF = @AUTOCONF@
--AUTOMAKE = @AUTOMAKE@
--AUTOHEADER = @AUTOHEADER@
--
--INSTALL = @INSTALL@
--INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
--INSTALL_DATA = @INSTALL_DATA@
--INSTALL_SCRIPT = @INSTALL_SCRIPT@
--transform = @program_transform_name@
--
-+pkglibdir = $(libdir)/@PACKAGE@
-+pkglibexecdir = $(libexecdir)/@PACKAGE@
-+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-+install_sh_DATA = $(install_sh) -c -m 644
-+install_sh_PROGRAM = $(install_sh) -c
-+install_sh_SCRIPT = $(install_sh) -c
-+INSTALL_HEADER = $(INSTALL_DATA)
-+transform = $(program_transform_name)
- NORMAL_INSTALL = :
- PRE_INSTALL = :
- POST_INSTALL = :
- NORMAL_UNINSTALL = :
- PRE_UNINSTALL = :
- POST_UNINSTALL = :
--host_alias = @host_alias@
-+build_triplet = @build@
- host_triplet = @host@
-+TESTS = wordhood.test$(EXEEXT) hspset.test$(EXEEXT) pcr.test$(EXEEXT) \
-+ comparison.test$(EXEEXT) match.test$(EXEEXT) \
-+ seeder.test$(EXEEXT)
-+noinst_PROGRAMS = $(am__EXEEXT_1)
-+subdir = src/comparison
-+DIST_COMMON = $(noinst_HEADERS) $(srcdir)/Makefile.am \
-+ $(srcdir)/Makefile.in
-+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-+am__aclocal_m4_deps = $(top_srcdir)/configure.in
-+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-+ $(ACLOCAL_M4)
-+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
-+CONFIG_CLEAN_FILES =
-+CONFIG_CLEAN_VPATH_FILES =
-+am__EXEEXT_1 = wordhood.test$(EXEEXT) hspset.test$(EXEEXT) \
-+ pcr.test$(EXEEXT) comparison.test$(EXEEXT) match.test$(EXEEXT) \
-+ seeder.test$(EXEEXT)
-+PROGRAMS = $(noinst_PROGRAMS)
-+am_comparison_test_OBJECTS = comparison.test.$(OBJEXT) \
-+ comparison.$(OBJEXT) hspset.$(OBJEXT) match.$(OBJEXT) \
-+ wordhood.$(OBJEXT)
-+comparison_test_OBJECTS = $(am_comparison_test_OBJECTS)
-+am__DEPENDENCIES_1 = $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o \
-+ $(top_srcdir)/src/sequence/sequence.o \
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/lineparse.o
-+comparison_test_DEPENDENCIES = $(top_srcdir)/src/sequence/submat.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/pqueue.o $(am__DEPENDENCIES_1)
-+am_hspset_test_OBJECTS = hspset.test.$(OBJEXT) hspset.$(OBJEXT) \
-+ match.$(OBJEXT) wordhood.$(OBJEXT)
-+hspset_test_OBJECTS = $(am_hspset_test_OBJECTS)
-+hspset_test_DEPENDENCIES = $(top_srcdir)/src/sequence/submat.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o \
-+ $(top_srcdir)/src/struct/pqueue.o \
-+ $(top_srcdir)/src/struct/recyclebin.o $(am__DEPENDENCIES_1)
-+am_match_test_OBJECTS = match.test.$(OBJEXT) match.$(OBJEXT)
-+match_test_OBJECTS = $(am_match_test_OBJECTS)
-+match_test_DEPENDENCIES = $(top_srcdir)/src/sequence/submat.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o $(am__DEPENDENCIES_1)
-+am_pcr_test_OBJECTS = pcr.test.$(OBJEXT) pcr.$(OBJEXT) \
-+ wordhood.$(OBJEXT)
-+pcr_test_OBJECTS = $(am_pcr_test_OBJECTS)
-+pcr_test_DEPENDENCIES = $(top_srcdir)/src/sequence/submat.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o \
-+ $(top_srcdir)/src/struct/fsm.o \
-+ $(top_srcdir)/src/struct/slist.o \
-+ $(top_srcdir)/src/struct/recyclebin.o $(am__DEPENDENCIES_1)
-+am_seeder_test_OBJECTS = seeder.test.$(OBJEXT) seeder.$(OBJEXT) \
-+ wordhood.$(OBJEXT) hspset.$(OBJEXT) match.$(OBJEXT) \
-+ comparison.$(OBJEXT)
-+seeder_test_OBJECTS = $(am_seeder_test_OBJECTS)
-+seeder_test_DEPENDENCIES = $(top_srcdir)/src/sequence/submat.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/fsm.o $(top_srcdir)/src/struct/vfsm.o \
-+ $(top_srcdir)/src/struct/pqueue.o $(am__DEPENDENCIES_1)
-+am_wordhood_test_OBJECTS = wordhood.test.$(OBJEXT) wordhood.$(OBJEXT)
-+wordhood_test_OBJECTS = $(am_wordhood_test_OBJECTS)
-+wordhood_test_DEPENDENCIES = $(top_srcdir)/src/sequence/submat.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o $(am__DEPENDENCIES_1)
-+DEFAULT_INCLUDES = -I. at am__isrc@
-+depcomp = $(SHELL) $(top_srcdir)/depcomp
-+am__depfiles_maybe = depfiles
-+am__mv = mv -f
-+COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
-+ $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
-+CCLD = $(CC)
-+LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
-+SOURCES = $(comparison_test_SOURCES) $(hspset_test_SOURCES) \
-+ $(match_test_SOURCES) $(pcr_test_SOURCES) \
-+ $(seeder_test_SOURCES) $(wordhood_test_SOURCES)
-+DIST_SOURCES = $(comparison_test_SOURCES) $(hspset_test_SOURCES) \
-+ $(match_test_SOURCES) $(pcr_test_SOURCES) \
-+ $(seeder_test_SOURCES) $(wordhood_test_SOURCES)
-+HEADERS = $(noinst_HEADERS)
-+ETAGS = etags
-+CTAGS = ctags
-+am__tty_colors = \
-+red=; grn=; lgn=; blu=; std=
-+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-+ACLOCAL = @ACLOCAL@
-+AMTAR = @AMTAR@
-+AUTOCONF = @AUTOCONF@
-+AUTOHEADER = @AUTOHEADER@
-+AUTOMAKE = @AUTOMAKE@
-+AWK = @AWK@
- CC = @CC@
-+CCDEPMODE = @CCDEPMODE@
-+CFLAGS = @CFLAGS@
-+CPP = @CPP@
-+CPPFLAGS = @CPPFLAGS@
-+CYGPATH_W = @CYGPATH_W@
-+DEFS = @DEFS@
-+DEPDIR = @DEPDIR@
-+ECHO_C = @ECHO_C@
-+ECHO_N = @ECHO_N@
-+ECHO_T = @ECHO_T@
-+EGREP = @EGREP@
-+EXEEXT = @EXEEXT@
- GLIB_CONFIG = @GLIB_CONFIG@
--HAVE_LIB = @HAVE_LIB@
--LIB = @LIB@
--LTLIB = @LTLIB@
-+GREP = @GREP@
-+INSTALL = @INSTALL@
-+INSTALL_DATA = @INSTALL_DATA@
-+INSTALL_PROGRAM = @INSTALL_PROGRAM@
-+INSTALL_SCRIPT = @INSTALL_SCRIPT@
-+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-+LDFLAGS = @LDFLAGS@
-+LIBOBJS = @LIBOBJS@
-+LIBS = @LIBS@
-+LTLIBOBJS = @LTLIBOBJS@
- MAKEINFO = @MAKEINFO@
-+MKDIR_P = @MKDIR_P@
-+OBJEXT = @OBJEXT@
- PACKAGE = @PACKAGE@
-+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-+PACKAGE_NAME = @PACKAGE_NAME@
-+PACKAGE_STRING = @PACKAGE_STRING@
-+PACKAGE_TARNAME = @PACKAGE_TARNAME@
-+PACKAGE_URL = @PACKAGE_URL@
-+PACKAGE_VERSION = @PACKAGE_VERSION@
-+PATH_SEPARATOR = @PATH_SEPARATOR@
- PKG_CONFIG = @PKG_CONFIG@
-+SET_MAKE = @SET_MAKE@
-+SHELL = @SHELL@
-+STRIP = @STRIP@
- VERSION = @VERSION@
-+abs_builddir = @abs_builddir@
-+abs_srcdir = @abs_srcdir@
-+abs_top_builddir = @abs_top_builddir@
-+abs_top_srcdir = @abs_top_srcdir@
-+ac_ct_CC = @ac_ct_CC@
-+am__include = @am__include@
-+am__leading_dot = @am__leading_dot@
-+am__quote = @am__quote@
-+am__tar = @am__tar@
-+am__untar = @am__untar@
-+bindir = @bindir@
-+build = @build@
-+build_alias = @build_alias@
-+build_cpu = @build_cpu@
-+build_os = @build_os@
-+build_vendor = @build_vendor@
-+builddir = @builddir@
- codegen_extra_ldadd = @codegen_extra_ldadd@
- codegen_extra_sources = @codegen_extra_sources@
-+datadir = @datadir@
- datarootdir = @datarootdir@
-+docdir = @docdir@
-+dvidir = @dvidir@
-+exec_prefix = @exec_prefix@
- glib_cflags = @glib_cflags@
- glib_libs = @glib_libs@
- host = @host@
-+host_alias = @host_alias@
-+host_cpu = @host_cpu@
-+host_os = @host_os@
-+host_vendor = @host_vendor@
-+htmldir = @htmldir@
-+includedir = @includedir@
-+infodir = @infodir@
-+install_sh = @install_sh@
- installed_util_list = @installed_util_list@
-+libdir = @libdir@
-+libexecdir = @libexecdir@
-+localedir = @localedir@
-+localstatedir = @localstatedir@
-+mandir = @mandir@
-+mkdir_p = @mkdir_p@
-+oldincludedir = @oldincludedir@
-+pdfdir = @pdfdir@
-+prefix = @prefix@
-+program_transform_name = @program_transform_name@
-+psdir = @psdir@
-+sbindir = @sbindir@
-+sharedstatedir = @sharedstatedir@
- source_root_dir = @source_root_dir@
-+srcdir = @srcdir@
-+sysconfdir = @sysconfdir@
-+target_alias = @target_alias@
-+top_build_prefix = @top_build_prefix@
-+top_builddir = @top_builddir@
-+top_srcdir = @top_srcdir@
- use_pthreads = @use_pthreads@
--
--TESTS = wordhood.test hspset.test pcr.test comparison.test match.test seeder.test
--
--
--noinst_PROGRAMS = $(TESTS)
--
--INCLUDES = -I$(top_srcdir)/src/sequence -I$(top_srcdir)/src/struct -I$(top_srcdir)/src/general
--
--
--noinst_HEADERS = wordhood.h hspset.h pcr.h comparison.h match.h seeder.h
--
--
--SEQUENCE_OBJ = $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o $(top_srcdir)/src/sequence/alphabet.o $(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/sequence/translate.o $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/general/lineparse.o -lm
-+INCLUDES = -I$(top_srcdir)/src/sequence \
-+ -I$(top_srcdir)/src/struct \
-+ -I$(top_srcdir)/src/general
-+
-+noinst_HEADERS = wordhood.h hspset.h pcr.h \
-+ comparison.h match.h seeder.h
-+
-+SEQUENCE_OBJ = $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o \
-+ $(top_srcdir)/src/sequence/sequence.o \
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ -lm
-
- wordhood_test_SOURCES = wordhood.test.c wordhood.c
--wordhood_test_LDADD = $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o $(SEQUENCE_OBJ)
-+wordhood_test_LDADD = $(top_srcdir)/src/sequence/submat.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o \
-+ $(SEQUENCE_OBJ)
-
- hspset_test_SOURCES = hspset.test.c hspset.c match.c wordhood.c
--hspset_test_LDADD = $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o $(SEQUENCE_OBJ)
--
-+hspset_test_LDADD = $(top_srcdir)/src/sequence/submat.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o \
-+ $(top_srcdir)/src/struct/pqueue.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(SEQUENCE_OBJ)
-
- pcr_test_SOURCES = pcr.test.c pcr.c wordhood.c
--pcr_test_LDADD = $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/struct/fsm.o $(top_srcdir)/src/struct/slist.o $(top_srcdir)/src/struct/recyclebin.o $(SEQUENCE_OBJ)
--
--
--comparison_test_SOURCES = comparison.test.c comparison.c hspset.c match.c wordhood.c
--
--comparison_test_LDADD = $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/pqueue.o $(SEQUENCE_OBJ)
--
-+pcr_test_LDADD = $(top_srcdir)/src/sequence/submat.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o \
-+ $(top_srcdir)/src/struct/fsm.o \
-+ $(top_srcdir)/src/struct/slist.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(SEQUENCE_OBJ)
-+
-+comparison_test_SOURCES = comparison.test.c comparison.c hspset.c \
-+ match.c wordhood.c
-+
-+comparison_test_LDADD = $(top_srcdir)/src/sequence/submat.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/pqueue.o \
-+ $(SEQUENCE_OBJ)
-
- match_test_SOURCES = match.test.c match.c
--match_test_LDADD = $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o $(SEQUENCE_OBJ)
--
--
--seeder_test_SOURCES = seeder.test.c seeder.c wordhood.c hspset.c match.c comparison.c
--
--seeder_test_LDADD = $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/fsm.o $(top_srcdir)/src/struct/vfsm.o $(top_srcdir)/src/struct/pqueue.o $(SEQUENCE_OBJ)
-+match_test_LDADD = $(top_srcdir)/src/sequence/submat.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o \
-+ $(SEQUENCE_OBJ)
-+
-+seeder_test_SOURCES = seeder.test.c seeder.c wordhood.c hspset.c \
-+ match.c comparison.c
-+
-+seeder_test_LDADD = $(top_srcdir)/src/sequence/submat.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/fsm.o \
-+ $(top_srcdir)/src/struct/vfsm.o \
-+ $(top_srcdir)/src/struct/pqueue.o \
-+ $(SEQUENCE_OBJ)
-
-
- # Files to clear away
--
- MAINTAINERCLEANFILES = Makefile.in
--mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
--CONFIG_CLEAN_FILES =
--PROGRAMS = $(noinst_PROGRAMS)
--
--
--DEFS = @DEFS@ -I. -I$(srcdir)
--CPPFLAGS = @CPPFLAGS@
--LDFLAGS = @LDFLAGS@
--LIBS = @LIBS@
--wordhood_test_OBJECTS = wordhood.test.o wordhood.o
--wordhood_test_DEPENDENCIES = $(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--wordhood_test_LDFLAGS =
--hspset_test_OBJECTS = hspset.test.o hspset.o match.o wordhood.o
--hspset_test_DEPENDENCIES = $(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--hspset_test_LDFLAGS =
--pcr_test_OBJECTS = pcr.test.o pcr.o wordhood.o
--pcr_test_DEPENDENCIES = $(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/struct/fsm.o \
--$(top_srcdir)/src/struct/slist.o $(top_srcdir)/src/struct/recyclebin.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--pcr_test_LDFLAGS =
--comparison_test_OBJECTS = comparison.test.o comparison.o hspset.o \
--match.o wordhood.o
--comparison_test_DEPENDENCIES = $(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/pqueue.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--comparison_test_LDFLAGS =
--match_test_OBJECTS = match.test.o match.o
--match_test_DEPENDENCIES = $(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--match_test_LDFLAGS =
--seeder_test_OBJECTS = seeder.test.o seeder.o wordhood.o hspset.o \
--match.o comparison.o
--seeder_test_DEPENDENCIES = $(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/fsm.o \
--$(top_srcdir)/src/struct/vfsm.o $(top_srcdir)/src/struct/pqueue.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--seeder_test_LDFLAGS =
--CFLAGS = @CFLAGS@
--COMPILE = $(CC) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
--CCLD = $(CC)
--LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(LDFLAGS) -o $@
--HEADERS = $(noinst_HEADERS)
--
--DIST_COMMON = Makefile.am Makefile.in
--
-+all: all-am
-
--DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
--
--TAR = tar
--GZIP_ENV = --best
--SOURCES = $(wordhood_test_SOURCES) $(hspset_test_SOURCES) $(pcr_test_SOURCES) $(comparison_test_SOURCES) $(match_test_SOURCES) $(seeder_test_SOURCES)
--OBJECTS = $(wordhood_test_OBJECTS) $(hspset_test_OBJECTS) $(pcr_test_OBJECTS) $(comparison_test_OBJECTS) $(match_test_OBJECTS) $(seeder_test_OBJECTS)
--
--all: all-redirect
- .SUFFIXES:
--.SUFFIXES: .S .c .o .s
--$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4)
-- cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps src/comparison/Makefile
--
-+.SUFFIXES: .c .o .obj
-+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
-+ @for dep in $?; do \
-+ case '$(am__configure_deps)' in \
-+ *$$dep*) \
-+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-+ && { if test -f $@; then exit 0; else break; fi; }; \
-+ exit 1;; \
-+ esac; \
-+ done; \
-+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/comparison/Makefile'; \
-+ $(am__cd) $(top_srcdir) && \
-+ $(AUTOMAKE) --gnu src/comparison/Makefile
-+.PRECIOUS: Makefile
- Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-- cd $(top_builddir) \
-- && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
--
--
--mostlyclean-noinstPROGRAMS:
-+ @case '$?' in \
-+ *config.status*) \
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-+ *) \
-+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-+ esac;
-+
-+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+
-+$(top_srcdir)/configure: $(am__configure_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(am__aclocal_m4_deps):
-
- clean-noinstPROGRAMS:
- -test -z "$(noinst_PROGRAMS)" || rm -f $(noinst_PROGRAMS)
--
--distclean-noinstPROGRAMS:
--
--maintainer-clean-noinstPROGRAMS:
--
--.c.o:
-- $(COMPILE) -c $<
--
--.s.o:
-- $(COMPILE) -c $<
--
--.S.o:
-- $(COMPILE) -c $<
-+comparison.test$(EXEEXT): $(comparison_test_OBJECTS) $(comparison_test_DEPENDENCIES)
-+ @rm -f comparison.test$(EXEEXT)
-+ $(LINK) $(comparison_test_OBJECTS) $(comparison_test_LDADD) $(LIBS)
-+hspset.test$(EXEEXT): $(hspset_test_OBJECTS) $(hspset_test_DEPENDENCIES)
-+ @rm -f hspset.test$(EXEEXT)
-+ $(LINK) $(hspset_test_OBJECTS) $(hspset_test_LDADD) $(LIBS)
-+match.test$(EXEEXT): $(match_test_OBJECTS) $(match_test_DEPENDENCIES)
-+ @rm -f match.test$(EXEEXT)
-+ $(LINK) $(match_test_OBJECTS) $(match_test_LDADD) $(LIBS)
-+pcr.test$(EXEEXT): $(pcr_test_OBJECTS) $(pcr_test_DEPENDENCIES)
-+ @rm -f pcr.test$(EXEEXT)
-+ $(LINK) $(pcr_test_OBJECTS) $(pcr_test_LDADD) $(LIBS)
-+seeder.test$(EXEEXT): $(seeder_test_OBJECTS) $(seeder_test_DEPENDENCIES)
-+ @rm -f seeder.test$(EXEEXT)
-+ $(LINK) $(seeder_test_OBJECTS) $(seeder_test_LDADD) $(LIBS)
-+wordhood.test$(EXEEXT): $(wordhood_test_OBJECTS) $(wordhood_test_DEPENDENCIES)
-+ @rm -f wordhood.test$(EXEEXT)
-+ $(LINK) $(wordhood_test_OBJECTS) $(wordhood_test_LDADD) $(LIBS)
-
- mostlyclean-compile:
-- -rm -f *.o core *.core
--
--clean-compile:
-+ -rm -f *.$(OBJEXT)
-
- distclean-compile:
- -rm -f *.tab.c
-
--maintainer-clean-compile:
--
--wordhood.test: $(wordhood_test_OBJECTS) $(wordhood_test_DEPENDENCIES)
-- @rm -f wordhood.test
-- $(LINK) $(wordhood_test_LDFLAGS) $(wordhood_test_OBJECTS) $(wordhood_test_LDADD) $(LIBS)
--
--hspset.test: $(hspset_test_OBJECTS) $(hspset_test_DEPENDENCIES)
-- @rm -f hspset.test
-- $(LINK) $(hspset_test_LDFLAGS) $(hspset_test_OBJECTS) $(hspset_test_LDADD) $(LIBS)
--
--pcr.test: $(pcr_test_OBJECTS) $(pcr_test_DEPENDENCIES)
-- @rm -f pcr.test
-- $(LINK) $(pcr_test_LDFLAGS) $(pcr_test_OBJECTS) $(pcr_test_LDADD) $(LIBS)
--
--comparison.test: $(comparison_test_OBJECTS) $(comparison_test_DEPENDENCIES)
-- @rm -f comparison.test
-- $(LINK) $(comparison_test_LDFLAGS) $(comparison_test_OBJECTS) $(comparison_test_LDADD) $(LIBS)
--
--match.test: $(match_test_OBJECTS) $(match_test_DEPENDENCIES)
-- @rm -f match.test
-- $(LINK) $(match_test_LDFLAGS) $(match_test_OBJECTS) $(match_test_LDADD) $(LIBS)
--
--seeder.test: $(seeder_test_OBJECTS) $(seeder_test_DEPENDENCIES)
-- @rm -f seeder.test
-- $(LINK) $(seeder_test_LDFLAGS) $(seeder_test_OBJECTS) $(seeder_test_LDADD) $(LIBS)
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/comparison.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/comparison.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/hspset.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/hspset.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/match.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/match.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pcr.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pcr.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/seeder.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/seeder.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/wordhood.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/wordhood.test.Po at am__quote@
-
-+.c.o:
-+ at am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
-+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-+ at am__fastdepCC_FALSE@ $(COMPILE) -c $<
-+
-+.c.obj:
-+ at am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
-+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-+ at am__fastdepCC_FALSE@ $(COMPILE) -c `$(CYGPATH_W) '$<'`
-+
-+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ mkid -fID $$unique
- tags: TAGS
-
--ID: $(HEADERS) $(SOURCES) $(LISP)
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- here=`pwd` && cd $(srcdir) \
-- && mkid -f$$here/ID $$unique $(LISP)
--
--TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) $(LISP)
-- tags=; \
-+TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ set x; \
- here=`pwd`; \
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- test -z "$(ETAGS_ARGS)$$unique$(LISP)$$tags" \
-- || (cd $(srcdir) && etags -o $$here/TAGS $(ETAGS_ARGS) $$tags $$unique $(LISP))
--
--mostlyclean-tags:
--
--clean-tags:
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ shift; \
-+ if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
-+ test -n "$$unique" || unique=$$empty_fix; \
-+ if test $$# -gt 0; then \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ "$$@" $$unique; \
-+ else \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ $$unique; \
-+ fi; \
-+ fi
-+ctags: CTAGS
-+CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ test -z "$(CTAGS_ARGS)$$unique" \
-+ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-+ $$unique
-+
-+GTAGS:
-+ here=`$(am__cd) $(top_builddir) && pwd` \
-+ && $(am__cd) $(top_srcdir) \
-+ && gtags -i $(GTAGS_ARGS) "$$here"
-
- distclean-tags:
-- -rm -f TAGS ID
--
--maintainer-clean-tags:
--
--distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
--
--subdir = src/comparison
-+ -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-
--distdir: $(DISTFILES)
-- @for file in $(DISTFILES); do \
-- d=$(srcdir); \
-- if test -d $$d/$$file; then \
-- cp -pr $$d/$$file $(distdir)/$$file; \
-- else \
-- test -f $(distdir)/$$file \
-- || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
-- || cp -p $$d/$$file $(distdir)/$$file || :; \
-- fi; \
-- done
- check-TESTS: $(TESTS)
-- @failed=0; all=0; \
-+ @failed=0; all=0; xfail=0; xpass=0; skip=0; \
- srcdir=$(srcdir); export srcdir; \
-- for tst in $(TESTS); do \
-- if test -f $$tst; then dir=.; \
-- else dir="$(srcdir)"; fi; \
-- if $(TESTS_ENVIRONMENT) $$dir/$$tst; then \
-+ list=' $(TESTS) '; \
-+ $(am__tty_colors); \
-+ if test -n "$$list"; then \
-+ for tst in $$list; do \
-+ if test -f ./$$tst; then dir=./; \
-+ elif test -f $$tst; then dir=; \
-+ else dir="$(srcdir)/"; fi; \
-+ if $(TESTS_ENVIRONMENT) $${dir}$$tst; then \
- all=`expr $$all + 1`; \
-- echo "PASS: $$tst"; \
-+ case " $(XFAIL_TESTS) " in \
-+ *[\ \ ]$$tst[\ \ ]*) \
-+ xpass=`expr $$xpass + 1`; \
-+ failed=`expr $$failed + 1`; \
-+ col=$$red; res=XPASS; \
-+ ;; \
-+ *) \
-+ col=$$grn; res=PASS; \
-+ ;; \
-+ esac; \
- elif test $$? -ne 77; then \
- all=`expr $$all + 1`; \
-+ case " $(XFAIL_TESTS) " in \
-+ *[\ \ ]$$tst[\ \ ]*) \
-+ xfail=`expr $$xfail + 1`; \
-+ col=$$lgn; res=XFAIL; \
-+ ;; \
-+ *) \
- failed=`expr $$failed + 1`; \
-- echo "FAIL: $$tst"; \
-+ col=$$red; res=FAIL; \
-+ ;; \
-+ esac; \
-+ else \
-+ skip=`expr $$skip + 1`; \
-+ col=$$blu; res=SKIP; \
- fi; \
-+ echo "$${col}$$res$${std}: $$tst"; \
- done; \
-+ if test "$$all" -eq 1; then \
-+ tests="test"; \
-+ All=""; \
-+ else \
-+ tests="tests"; \
-+ All="All "; \
-+ fi; \
-+ if test "$$failed" -eq 0; then \
-+ if test "$$xfail" -eq 0; then \
-+ banner="$$All$$all $$tests passed"; \
-+ else \
-+ if test "$$xfail" -eq 1; then failures=failure; else failures=failures; fi; \
-+ banner="$$All$$all $$tests behaved as expected ($$xfail expected $$failures)"; \
-+ fi; \
-+ else \
-+ if test "$$xpass" -eq 0; then \
-+ banner="$$failed of $$all $$tests failed"; \
-+ else \
-+ if test "$$xpass" -eq 1; then passes=pass; else passes=passes; fi; \
-+ banner="$$failed of $$all $$tests did not behave as expected ($$xpass unexpected $$passes)"; \
-+ fi; \
-+ fi; \
-+ dashes="$$banner"; \
-+ skipped=""; \
-+ if test "$$skip" -ne 0; then \
-+ if test "$$skip" -eq 1; then \
-+ skipped="($$skip test was not run)"; \
-+ else \
-+ skipped="($$skip tests were not run)"; \
-+ fi; \
-+ test `echo "$$skipped" | wc -c` -le `echo "$$banner" | wc -c` || \
-+ dashes="$$skipped"; \
-+ fi; \
-+ report=""; \
-+ if test "$$failed" -ne 0 && test -n "$(PACKAGE_BUGREPORT)"; then \
-+ report="Please report to $(PACKAGE_BUGREPORT)"; \
-+ test `echo "$$report" | wc -c` -le `echo "$$banner" | wc -c` || \
-+ dashes="$$report"; \
-+ fi; \
-+ dashes=`echo "$$dashes" | sed s/./=/g`; \
- if test "$$failed" -eq 0; then \
-- banner="All $$all tests passed"; \
-+ echo "$$grn$$dashes"; \
- else \
-- banner="$$failed of $$all tests failed"; \
-+ echo "$$red$$dashes"; \
- fi; \
-- dashes=`echo "$$banner" | sed s/./=/g`; \
-- echo "$$dashes"; \
- echo "$$banner"; \
-- echo "$$dashes"; \
-- test "$$failed" -eq 0
--info-am:
--info: info-am
--dvi-am:
--dvi: dvi-am
-+ test -z "$$skipped" || echo "$$skipped"; \
-+ test -z "$$report" || echo "$$report"; \
-+ echo "$$dashes$$std"; \
-+ test "$$failed" -eq 0; \
-+ else :; fi
-+
-+distdir: $(DISTFILES)
-+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ list='$(DISTFILES)'; \
-+ dist_files=`for file in $$list; do echo $$file; done | \
-+ sed -e "s|^$$srcdirstrip/||;t" \
-+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-+ case $$dist_files in \
-+ */*) $(MKDIR_P) `echo "$$dist_files" | \
-+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-+ sort -u` ;; \
-+ esac; \
-+ for file in $$dist_files; do \
-+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
-+ if test -d $$d/$$file; then \
-+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-+ if test -d "$(distdir)/$$file"; then \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
-+ else \
-+ test -f "$(distdir)/$$file" \
-+ || cp -p $$d/$$file "$(distdir)/$$file" \
-+ || exit 1; \
-+ fi; \
-+ done
- check-am: all-am
- $(MAKE) $(AM_MAKEFLAGS) check-TESTS
- check: check-am
--installcheck-am:
--installcheck: installcheck-am
--install-exec-am:
-+all-am: Makefile $(PROGRAMS) $(HEADERS)
-+installdirs:
-+install: install-am
- install-exec: install-exec-am
--
--install-data-am:
- install-data: install-data-am
-+uninstall: uninstall-am
-
- install-am: all-am
- @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
--install: install-am
--uninstall-am:
--uninstall: uninstall-am
--all-am: Makefile $(PROGRAMS) $(HEADERS)
--all-redirect: all-am
--install-strip:
-- $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
--installdirs:
--
-
-+installcheck: installcheck-am
-+install-strip:
-+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-+ `test -z '$(STRIP)' || \
-+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
- mostlyclean-generic:
-
- clean-generic:
-
- distclean-generic:
-- -rm -f Makefile $(CONFIG_CLEAN_FILES)
-- -rm -f config.cache config.log stamp-h stamp-h[0-9]*
-+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
- maintainer-clean-generic:
-+ @echo "This command is intended for maintainers to use"
-+ @echo "it deletes files that may require special tools to rebuild."
- -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
--mostlyclean-am: mostlyclean-noinstPROGRAMS mostlyclean-compile \
-- mostlyclean-tags mostlyclean-generic
-+clean: clean-am
-
--mostlyclean: mostlyclean-am
-+clean-am: clean-generic clean-noinstPROGRAMS mostlyclean-am
-
--clean-am: clean-noinstPROGRAMS clean-compile clean-tags clean-generic \
-- mostlyclean-am
-+distclean: distclean-am
-+ -rm -rf ./$(DEPDIR)
-+ -rm -f Makefile
-+distclean-am: clean-am distclean-compile distclean-generic \
-+ distclean-tags
-
--clean: clean-am
-+dvi: dvi-am
-
--distclean-am: distclean-noinstPROGRAMS distclean-compile distclean-tags \
-- distclean-generic clean-am
-+dvi-am:
-
--distclean: distclean-am
-+html: html-am
-
--maintainer-clean-am: maintainer-clean-noinstPROGRAMS \
-- maintainer-clean-compile maintainer-clean-tags \
-- maintainer-clean-generic distclean-am
-- @echo "This command is intended for maintainers to use;"
-- @echo "it deletes files that may require special tools to rebuild."
-+html-am:
-+
-+info: info-am
-+
-+info-am:
-+
-+install-data-am:
-+
-+install-dvi: install-dvi-am
-+
-+install-dvi-am:
-+
-+install-exec-am:
-+
-+install-html: install-html-am
-+
-+install-html-am:
-+
-+install-info: install-info-am
-+
-+install-info-am:
-+
-+install-man:
-+
-+install-pdf: install-pdf-am
-+
-+install-pdf-am:
-+
-+install-ps: install-ps-am
-+
-+install-ps-am:
-+
-+installcheck-am:
-
- maintainer-clean: maintainer-clean-am
-+ -rm -rf ./$(DEPDIR)
-+ -rm -f Makefile
-+maintainer-clean-am: distclean-am maintainer-clean-generic
-+
-+mostlyclean: mostlyclean-am
-+
-+mostlyclean-am: mostlyclean-compile mostlyclean-generic
-+
-+pdf: pdf-am
-+
-+pdf-am:
-+
-+ps: ps-am
-+
-+ps-am:
-+
-+uninstall-am:
-+
-+.MAKE: check-am install-am install-strip
-
--.PHONY: mostlyclean-noinstPROGRAMS distclean-noinstPROGRAMS \
--clean-noinstPROGRAMS maintainer-clean-noinstPROGRAMS \
--mostlyclean-compile distclean-compile clean-compile \
--maintainer-clean-compile tags mostlyclean-tags distclean-tags \
--clean-tags maintainer-clean-tags distdir check-TESTS info-am info \
--dvi-am dvi check check-am installcheck-am installcheck install-exec-am \
--install-exec install-data-am install-data install-am install \
--uninstall-am uninstall all-redirect all-am all installdirs \
--mostlyclean-generic distclean-generic clean-generic \
--maintainer-clean-generic clean mostlyclean distclean maintainer-clean
-+.PHONY: CTAGS GTAGS all all-am check check-TESTS check-am clean \
-+ clean-generic clean-noinstPROGRAMS ctags distclean \
-+ distclean-compile distclean-generic distclean-tags distdir dvi \
-+ dvi-am html html-am info info-am install install-am \
-+ install-data install-data-am install-dvi install-dvi-am \
-+ install-exec install-exec-am install-html install-html-am \
-+ install-info install-info-am install-man install-pdf \
-+ install-pdf-am install-ps install-ps-am install-strip \
-+ installcheck installcheck-am installdirs maintainer-clean \
-+ maintainer-clean-generic mostlyclean mostlyclean-compile \
-+ mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
-+ uninstall-am
-
-
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -ubrN exonerate-2.2.0.orig/src/database/Makefile.in exonerate-2.2.0/src/database/Makefile.in
---- exonerate-2.2.0.orig/src/database/Makefile.in 2008-10-17 12:04:35.000000000 +0200
-+++ exonerate-2.2.0/src/database/Makefile.in 2011-12-12 13:33:16.000000000 +0100
-@@ -1,6 +1,9 @@
--# Makefile.in generated automatically by automake 1.4-p6 from Makefile.am
-+# Makefile.in generated by automake 1.11.1 from Makefile.am.
-+# @configure_input@
-
--# Copyright (C) 1994, 1995-8, 1999, 2001 Free Software Foundation, Inc.
-+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
-+# Inc.
- # This Makefile.in is free software; the Free Software Foundation
- # gives unlimited permission to copy and/or distribute it,
- # with or without modifications, as long as this notice is preserved.
-@@ -10,375 +13,621 @@
- # even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- # PARTICULAR PURPOSE.
-
-+ at SET_MAKE@
-
--SHELL = @SHELL@
-
--srcdir = @srcdir@
--top_srcdir = @top_srcdir@
- VPATH = @srcdir@
--prefix = @prefix@
--exec_prefix = @exec_prefix@
--
--bindir = @bindir@
--sbindir = @sbindir@
--libexecdir = @libexecdir@
--datadir = @datadir@
--sysconfdir = @sysconfdir@
--sharedstatedir = @sharedstatedir@
--localstatedir = @localstatedir@
--libdir = @libdir@
--infodir = @infodir@
--mandir = @mandir@
--includedir = @includedir@
--oldincludedir = /usr/include
--
--DESTDIR =
--
- pkgdatadir = $(datadir)/@PACKAGE@
--pkglibdir = $(libdir)/@PACKAGE@
- pkgincludedir = $(includedir)/@PACKAGE@
--
--top_builddir = ../..
--
--ACLOCAL = @ACLOCAL@
--AUTOCONF = @AUTOCONF@
--AUTOMAKE = @AUTOMAKE@
--AUTOHEADER = @AUTOHEADER@
--
--INSTALL = @INSTALL@
--INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
--INSTALL_DATA = @INSTALL_DATA@
--INSTALL_SCRIPT = @INSTALL_SCRIPT@
--transform = @program_transform_name@
--
-+pkglibdir = $(libdir)/@PACKAGE@
-+pkglibexecdir = $(libexecdir)/@PACKAGE@
-+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-+install_sh_DATA = $(install_sh) -c -m 644
-+install_sh_PROGRAM = $(install_sh) -c
-+install_sh_SCRIPT = $(install_sh) -c
-+INSTALL_HEADER = $(INSTALL_DATA)
-+transform = $(program_transform_name)
- NORMAL_INSTALL = :
- PRE_INSTALL = :
- POST_INSTALL = :
- NORMAL_UNINSTALL = :
- PRE_UNINSTALL = :
- POST_UNINSTALL = :
--host_alias = @host_alias@
-+build_triplet = @build@
- host_triplet = @host@
-+TESTS = fastadb.test$(EXEEXT) fastapipe.test$(EXEEXT) \
-+ dataset.test$(EXEEXT) index.test$(EXEEXT)
-+noinst_PROGRAMS = $(am__EXEEXT_1)
-+subdir = src/database
-+DIST_COMMON = $(noinst_HEADERS) $(srcdir)/Makefile.am \
-+ $(srcdir)/Makefile.in
-+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-+am__aclocal_m4_deps = $(top_srcdir)/configure.in
-+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-+ $(ACLOCAL_M4)
-+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
-+CONFIG_CLEAN_FILES =
-+CONFIG_CLEAN_VPATH_FILES =
-+am__EXEEXT_1 = fastadb.test$(EXEEXT) fastapipe.test$(EXEEXT) \
-+ dataset.test$(EXEEXT) index.test$(EXEEXT)
-+PROGRAMS = $(noinst_PROGRAMS)
-+am_dataset_test_OBJECTS = dataset.test.$(OBJEXT) dataset.$(OBJEXT)
-+dataset_test_OBJECTS = $(am_dataset_test_OBJECTS)
-+am__DEPENDENCIES_1 = $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o \
-+ $(top_srcdir)/src/sequence/sequence.o \
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/lineparse.o
-+dataset_test_DEPENDENCIES = fastadb.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/struct/bitarray.o $(am__DEPENDENCIES_1)
-+am_fastadb_test_OBJECTS = fastadb.test.$(OBJEXT) fastadb.$(OBJEXT)
-+fastadb_test_OBJECTS = $(am_fastadb_test_OBJECTS)
-+fastadb_test_DEPENDENCIES = $(top_srcdir)/src/general/compoundfile.o \
-+ $(am__DEPENDENCIES_1)
-+am_fastapipe_test_OBJECTS = fastapipe.test.$(OBJEXT) \
-+ fastapipe.$(OBJEXT)
-+fastapipe_test_OBJECTS = $(am_fastapipe_test_OBJECTS)
-+fastapipe_test_DEPENDENCIES = fastadb.o \
-+ $(top_srcdir)/src/general/compoundfile.o $(am__DEPENDENCIES_1)
-+am_index_test_OBJECTS = index.test.$(OBJEXT) index.$(OBJEXT)
-+index_test_OBJECTS = $(am_index_test_OBJECTS)
-+index_test_DEPENDENCIES = fastadb.o dataset.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/struct/bitarray.o \
-+ $(top_srcdir)/src/struct/vfsm.o \
-+ $(top_srcdir)/src/struct/pqueue.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/rangetree.o \
-+ $(top_srcdir)/src/struct/splaytree.o \
-+ $(top_srcdir)/src/struct/noitree.o \
-+ $(top_srcdir)/src/comparison/wordhood.o \
-+ $(top_srcdir)/src/comparison/hspset.o \
-+ $(top_srcdir)/src/comparison/match.o \
-+ $(top_srcdir)/src/sequence/submat.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o $(am__DEPENDENCIES_1)
-+DEFAULT_INCLUDES = -I. at am__isrc@
-+depcomp = $(SHELL) $(top_srcdir)/depcomp
-+am__depfiles_maybe = depfiles
-+am__mv = mv -f
-+COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
-+ $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
-+CCLD = $(CC)
-+LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
-+SOURCES = $(dataset_test_SOURCES) $(fastadb_test_SOURCES) \
-+ $(fastapipe_test_SOURCES) $(index_test_SOURCES)
-+DIST_SOURCES = $(dataset_test_SOURCES) $(fastadb_test_SOURCES) \
-+ $(fastapipe_test_SOURCES) $(index_test_SOURCES)
-+HEADERS = $(noinst_HEADERS)
-+ETAGS = etags
-+CTAGS = ctags
-+am__tty_colors = \
-+red=; grn=; lgn=; blu=; std=
-+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-+ACLOCAL = @ACLOCAL@
-+AMTAR = @AMTAR@
-+AUTOCONF = @AUTOCONF@
-+AUTOHEADER = @AUTOHEADER@
-+AUTOMAKE = @AUTOMAKE@
-+AWK = @AWK@
- CC = @CC@
-+CCDEPMODE = @CCDEPMODE@
-+CFLAGS = @CFLAGS@
-+CPP = @CPP@
-+CPPFLAGS = @CPPFLAGS@
-+CYGPATH_W = @CYGPATH_W@
-+DEFS = @DEFS@
-+DEPDIR = @DEPDIR@
-+ECHO_C = @ECHO_C@
-+ECHO_N = @ECHO_N@
-+ECHO_T = @ECHO_T@
-+EGREP = @EGREP@
-+EXEEXT = @EXEEXT@
- GLIB_CONFIG = @GLIB_CONFIG@
--HAVE_LIB = @HAVE_LIB@
--LIB = @LIB@
--LTLIB = @LTLIB@
-+GREP = @GREP@
-+INSTALL = @INSTALL@
-+INSTALL_DATA = @INSTALL_DATA@
-+INSTALL_PROGRAM = @INSTALL_PROGRAM@
-+INSTALL_SCRIPT = @INSTALL_SCRIPT@
-+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-+LDFLAGS = @LDFLAGS@
-+LIBOBJS = @LIBOBJS@
-+LIBS = @LIBS@
-+LTLIBOBJS = @LTLIBOBJS@
- MAKEINFO = @MAKEINFO@
-+MKDIR_P = @MKDIR_P@
-+OBJEXT = @OBJEXT@
- PACKAGE = @PACKAGE@
-+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-+PACKAGE_NAME = @PACKAGE_NAME@
-+PACKAGE_STRING = @PACKAGE_STRING@
-+PACKAGE_TARNAME = @PACKAGE_TARNAME@
-+PACKAGE_URL = @PACKAGE_URL@
-+PACKAGE_VERSION = @PACKAGE_VERSION@
-+PATH_SEPARATOR = @PATH_SEPARATOR@
- PKG_CONFIG = @PKG_CONFIG@
-+SET_MAKE = @SET_MAKE@
-+SHELL = @SHELL@
-+STRIP = @STRIP@
- VERSION = @VERSION@
-+abs_builddir = @abs_builddir@
-+abs_srcdir = @abs_srcdir@
-+abs_top_builddir = @abs_top_builddir@
-+abs_top_srcdir = @abs_top_srcdir@
-+ac_ct_CC = @ac_ct_CC@
-+am__include = @am__include@
-+am__leading_dot = @am__leading_dot@
-+am__quote = @am__quote@
-+am__tar = @am__tar@
-+am__untar = @am__untar@
-+bindir = @bindir@
-+build = @build@
-+build_alias = @build_alias@
-+build_cpu = @build_cpu@
-+build_os = @build_os@
-+build_vendor = @build_vendor@
-+builddir = @builddir@
- codegen_extra_ldadd = @codegen_extra_ldadd@
- codegen_extra_sources = @codegen_extra_sources@
-+datadir = @datadir@
- datarootdir = @datarootdir@
-+docdir = @docdir@
-+dvidir = @dvidir@
-+exec_prefix = @exec_prefix@
- glib_cflags = @glib_cflags@
- glib_libs = @glib_libs@
- host = @host@
-+host_alias = @host_alias@
-+host_cpu = @host_cpu@
-+host_os = @host_os@
-+host_vendor = @host_vendor@
-+htmldir = @htmldir@
-+includedir = @includedir@
-+infodir = @infodir@
-+install_sh = @install_sh@
- installed_util_list = @installed_util_list@
-+libdir = @libdir@
-+libexecdir = @libexecdir@
-+localedir = @localedir@
-+localstatedir = @localstatedir@
-+mandir = @mandir@
-+mkdir_p = @mkdir_p@
-+oldincludedir = @oldincludedir@
-+pdfdir = @pdfdir@
-+prefix = @prefix@
-+program_transform_name = @program_transform_name@
-+psdir = @psdir@
-+sbindir = @sbindir@
-+sharedstatedir = @sharedstatedir@
- source_root_dir = @source_root_dir@
-+srcdir = @srcdir@
-+sysconfdir = @sysconfdir@
-+target_alias = @target_alias@
-+top_build_prefix = @top_build_prefix@
-+top_builddir = @top_builddir@
-+top_srcdir = @top_srcdir@
- use_pthreads = @use_pthreads@
--
--TESTS = fastadb.test fastapipe.test dataset.test index.test
--noinst_PROGRAMS = $(TESTS)
--
--INCLUDES = -I$(top_srcdir)/src/sequence -I$(top_srcdir)/src/struct -I$(top_srcdir)/src/general -I$(top_srcdir)/src/comparison
--
-+INCLUDES = -I$(top_srcdir)/src/sequence \
-+ -I$(top_srcdir)/src/struct \
-+ -I$(top_srcdir)/src/general \
-+ -I$(top_srcdir)/src/comparison
-
- noinst_HEADERS = fastadb.h fastapipe.h dataset.h index.h
--
--SEQUENCE_OBJ = $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o $(top_srcdir)/src/sequence/alphabet.o $(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/sequence/translate.o $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/general/lineparse.o -lm
-+SEQUENCE_OBJ = $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o \
-+ $(top_srcdir)/src/sequence/sequence.o \
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ -lm
-
- fastadb_test_SOURCES = fastadb.test.c fastadb.c
--fastadb_test_LDADD = $(top_srcdir)/src/general/compoundfile.o $(SEQUENCE_OBJ)
--
-+fastadb_test_LDADD = $(top_srcdir)/src/general/compoundfile.o \
-+ $(SEQUENCE_OBJ)
-
- fastapipe_test_SOURCES = fastapipe.test.c fastapipe.c
--fastapipe_test_LDADD = fastadb.o $(top_srcdir)/src/general/compoundfile.o $(SEQUENCE_OBJ)
--
-+fastapipe_test_LDADD = fastadb.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(SEQUENCE_OBJ)
-
- dataset_test_SOURCES = dataset.test.c dataset.c
--dataset_test_LDADD = fastadb.o $(top_srcdir)/src/general/compoundfile.o $(top_srcdir)/src/struct/bitarray.o $(SEQUENCE_OBJ)
--
-+dataset_test_LDADD = fastadb.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/struct/bitarray.o \
-+ $(SEQUENCE_OBJ)
-
- index_test_SOURCES = index.test.c index.c
--index_test_LDADD = fastadb.o dataset.o $(top_srcdir)/src/general/compoundfile.o $(top_srcdir)/src/struct/bitarray.o $(top_srcdir)/src/struct/vfsm.o $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/rangetree.o $(top_srcdir)/src/struct/splaytree.o $(top_srcdir)/src/struct/noitree.o $(top_srcdir)/src/comparison/wordhood.o $(top_srcdir)/src/comparison/hspset.o $(top_srcdir)/src/comparison/match.o $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o $(SEQUENCE_OBJ)
-+index_test_LDADD = fastadb.o dataset.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/struct/bitarray.o \
-+ $(top_srcdir)/src/struct/vfsm.o \
-+ $(top_srcdir)/src/struct/pqueue.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/rangetree.o \
-+ $(top_srcdir)/src/struct/splaytree.o \
-+ $(top_srcdir)/src/struct/noitree.o \
-+ $(top_srcdir)/src/comparison/wordhood.o \
-+ $(top_srcdir)/src/comparison/hspset.o \
-+ $(top_srcdir)/src/comparison/match.o \
-+ $(top_srcdir)/src/sequence/submat.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o \
-+ $(SEQUENCE_OBJ)
-
-
- # Files to clear away
--
- MAINTAINERCLEANFILES = Makefile.in
--mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
--CONFIG_CLEAN_FILES =
--PROGRAMS = $(noinst_PROGRAMS)
--
--
--DEFS = @DEFS@ -I. -I$(srcdir)
--CPPFLAGS = @CPPFLAGS@
--LDFLAGS = @LDFLAGS@
--LIBS = @LIBS@
--fastadb_test_OBJECTS = fastadb.test.o fastadb.o
--fastadb_test_DEPENDENCIES = $(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--fastadb_test_LDFLAGS =
--fastapipe_test_OBJECTS = fastapipe.test.o fastapipe.o
--fastapipe_test_DEPENDENCIES = fastadb.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--fastapipe_test_LDFLAGS =
--dataset_test_OBJECTS = dataset.test.o dataset.o
--dataset_test_DEPENDENCIES = fastadb.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/struct/bitarray.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--dataset_test_LDFLAGS =
--index_test_OBJECTS = index.test.o index.o
--index_test_DEPENDENCIES = fastadb.o dataset.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/struct/bitarray.o $(top_srcdir)/src/struct/vfsm.o \
--$(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o \
--$(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/struct/splaytree.o $(top_srcdir)/src/struct/noitree.o \
--$(top_srcdir)/src/comparison/wordhood.o \
--$(top_srcdir)/src/comparison/hspset.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--index_test_LDFLAGS =
--CFLAGS = @CFLAGS@
--COMPILE = $(CC) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
--CCLD = $(CC)
--LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(LDFLAGS) -o $@
--HEADERS = $(noinst_HEADERS)
--
--DIST_COMMON = Makefile.am Makefile.in
--
-+all: all-am
-
--DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
--
--TAR = tar
--GZIP_ENV = --best
--SOURCES = $(fastadb_test_SOURCES) $(fastapipe_test_SOURCES) $(dataset_test_SOURCES) $(index_test_SOURCES)
--OBJECTS = $(fastadb_test_OBJECTS) $(fastapipe_test_OBJECTS) $(dataset_test_OBJECTS) $(index_test_OBJECTS)
--
--all: all-redirect
- .SUFFIXES:
--.SUFFIXES: .S .c .o .s
--$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4)
-- cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps src/database/Makefile
--
-+.SUFFIXES: .c .o .obj
-+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
-+ @for dep in $?; do \
-+ case '$(am__configure_deps)' in \
-+ *$$dep*) \
-+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-+ && { if test -f $@; then exit 0; else break; fi; }; \
-+ exit 1;; \
-+ esac; \
-+ done; \
-+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/database/Makefile'; \
-+ $(am__cd) $(top_srcdir) && \
-+ $(AUTOMAKE) --gnu src/database/Makefile
-+.PRECIOUS: Makefile
- Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-- cd $(top_builddir) \
-- && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
--
--
--mostlyclean-noinstPROGRAMS:
-+ @case '$?' in \
-+ *config.status*) \
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-+ *) \
-+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-+ esac;
-+
-+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+
-+$(top_srcdir)/configure: $(am__configure_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(am__aclocal_m4_deps):
-
- clean-noinstPROGRAMS:
- -test -z "$(noinst_PROGRAMS)" || rm -f $(noinst_PROGRAMS)
--
--distclean-noinstPROGRAMS:
--
--maintainer-clean-noinstPROGRAMS:
--
--.c.o:
-- $(COMPILE) -c $<
--
--.s.o:
-- $(COMPILE) -c $<
--
--.S.o:
-- $(COMPILE) -c $<
-+dataset.test$(EXEEXT): $(dataset_test_OBJECTS) $(dataset_test_DEPENDENCIES)
-+ @rm -f dataset.test$(EXEEXT)
-+ $(LINK) $(dataset_test_OBJECTS) $(dataset_test_LDADD) $(LIBS)
-+fastadb.test$(EXEEXT): $(fastadb_test_OBJECTS) $(fastadb_test_DEPENDENCIES)
-+ @rm -f fastadb.test$(EXEEXT)
-+ $(LINK) $(fastadb_test_OBJECTS) $(fastadb_test_LDADD) $(LIBS)
-+fastapipe.test$(EXEEXT): $(fastapipe_test_OBJECTS) $(fastapipe_test_DEPENDENCIES)
-+ @rm -f fastapipe.test$(EXEEXT)
-+ $(LINK) $(fastapipe_test_OBJECTS) $(fastapipe_test_LDADD) $(LIBS)
-+index.test$(EXEEXT): $(index_test_OBJECTS) $(index_test_DEPENDENCIES)
-+ @rm -f index.test$(EXEEXT)
-+ $(LINK) $(index_test_OBJECTS) $(index_test_LDADD) $(LIBS)
-
- mostlyclean-compile:
-- -rm -f *.o core *.core
--
--clean-compile:
-+ -rm -f *.$(OBJEXT)
-
- distclean-compile:
- -rm -f *.tab.c
-
--maintainer-clean-compile:
--
--fastadb.test: $(fastadb_test_OBJECTS) $(fastadb_test_DEPENDENCIES)
-- @rm -f fastadb.test
-- $(LINK) $(fastadb_test_LDFLAGS) $(fastadb_test_OBJECTS) $(fastadb_test_LDADD) $(LIBS)
--
--fastapipe.test: $(fastapipe_test_OBJECTS) $(fastapipe_test_DEPENDENCIES)
-- @rm -f fastapipe.test
-- $(LINK) $(fastapipe_test_LDFLAGS) $(fastapipe_test_OBJECTS) $(fastapipe_test_LDADD) $(LIBS)
--
--dataset.test: $(dataset_test_OBJECTS) $(dataset_test_DEPENDENCIES)
-- @rm -f dataset.test
-- $(LINK) $(dataset_test_LDFLAGS) $(dataset_test_OBJECTS) $(dataset_test_LDADD) $(LIBS)
--
--index.test: $(index_test_OBJECTS) $(index_test_DEPENDENCIES)
-- @rm -f index.test
-- $(LINK) $(index_test_LDFLAGS) $(index_test_OBJECTS) $(index_test_LDADD) $(LIBS)
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/dataset.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/dataset.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fastadb.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fastadb.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fastapipe.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fastapipe.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/index.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/index.test.Po at am__quote@
-
-+.c.o:
-+ at am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
-+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-+ at am__fastdepCC_FALSE@ $(COMPILE) -c $<
-+
-+.c.obj:
-+ at am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
-+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-+ at am__fastdepCC_FALSE@ $(COMPILE) -c `$(CYGPATH_W) '$<'`
-+
-+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ mkid -fID $$unique
- tags: TAGS
-
--ID: $(HEADERS) $(SOURCES) $(LISP)
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- here=`pwd` && cd $(srcdir) \
-- && mkid -f$$here/ID $$unique $(LISP)
--
--TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) $(LISP)
-- tags=; \
-+TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ set x; \
- here=`pwd`; \
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- test -z "$(ETAGS_ARGS)$$unique$(LISP)$$tags" \
-- || (cd $(srcdir) && etags -o $$here/TAGS $(ETAGS_ARGS) $$tags $$unique $(LISP))
--
--mostlyclean-tags:
--
--clean-tags:
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ shift; \
-+ if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
-+ test -n "$$unique" || unique=$$empty_fix; \
-+ if test $$# -gt 0; then \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ "$$@" $$unique; \
-+ else \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ $$unique; \
-+ fi; \
-+ fi
-+ctags: CTAGS
-+CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ test -z "$(CTAGS_ARGS)$$unique" \
-+ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-+ $$unique
-+
-+GTAGS:
-+ here=`$(am__cd) $(top_builddir) && pwd` \
-+ && $(am__cd) $(top_srcdir) \
-+ && gtags -i $(GTAGS_ARGS) "$$here"
-
- distclean-tags:
-- -rm -f TAGS ID
-+ -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-
--maintainer-clean-tags:
--
--distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
--
--subdir = src/database
--
--distdir: $(DISTFILES)
-- @for file in $(DISTFILES); do \
-- d=$(srcdir); \
-- if test -d $$d/$$file; then \
-- cp -pr $$d/$$file $(distdir)/$$file; \
-- else \
-- test -f $(distdir)/$$file \
-- || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
-- || cp -p $$d/$$file $(distdir)/$$file || :; \
-- fi; \
-- done
- check-TESTS: $(TESTS)
-- @failed=0; all=0; \
-+ @failed=0; all=0; xfail=0; xpass=0; skip=0; \
- srcdir=$(srcdir); export srcdir; \
-- for tst in $(TESTS); do \
-- if test -f $$tst; then dir=.; \
-- else dir="$(srcdir)"; fi; \
-- if $(TESTS_ENVIRONMENT) $$dir/$$tst; then \
-+ list=' $(TESTS) '; \
-+ $(am__tty_colors); \
-+ if test -n "$$list"; then \
-+ for tst in $$list; do \
-+ if test -f ./$$tst; then dir=./; \
-+ elif test -f $$tst; then dir=; \
-+ else dir="$(srcdir)/"; fi; \
-+ if $(TESTS_ENVIRONMENT) $${dir}$$tst; then \
- all=`expr $$all + 1`; \
-- echo "PASS: $$tst"; \
-+ case " $(XFAIL_TESTS) " in \
-+ *[\ \ ]$$tst[\ \ ]*) \
-+ xpass=`expr $$xpass + 1`; \
-+ failed=`expr $$failed + 1`; \
-+ col=$$red; res=XPASS; \
-+ ;; \
-+ *) \
-+ col=$$grn; res=PASS; \
-+ ;; \
-+ esac; \
- elif test $$? -ne 77; then \
- all=`expr $$all + 1`; \
-+ case " $(XFAIL_TESTS) " in \
-+ *[\ \ ]$$tst[\ \ ]*) \
-+ xfail=`expr $$xfail + 1`; \
-+ col=$$lgn; res=XFAIL; \
-+ ;; \
-+ *) \
- failed=`expr $$failed + 1`; \
-- echo "FAIL: $$tst"; \
-+ col=$$red; res=FAIL; \
-+ ;; \
-+ esac; \
-+ else \
-+ skip=`expr $$skip + 1`; \
-+ col=$$blu; res=SKIP; \
- fi; \
-+ echo "$${col}$$res$${std}: $$tst"; \
- done; \
-+ if test "$$all" -eq 1; then \
-+ tests="test"; \
-+ All=""; \
-+ else \
-+ tests="tests"; \
-+ All="All "; \
-+ fi; \
- if test "$$failed" -eq 0; then \
-- banner="All $$all tests passed"; \
-+ if test "$$xfail" -eq 0; then \
-+ banner="$$All$$all $$tests passed"; \
-+ else \
-+ if test "$$xfail" -eq 1; then failures=failure; else failures=failures; fi; \
-+ banner="$$All$$all $$tests behaved as expected ($$xfail expected $$failures)"; \
-+ fi; \
-+ else \
-+ if test "$$xpass" -eq 0; then \
-+ banner="$$failed of $$all $$tests failed"; \
- else \
-- banner="$$failed of $$all tests failed"; \
-+ if test "$$xpass" -eq 1; then passes=pass; else passes=passes; fi; \
-+ banner="$$failed of $$all $$tests did not behave as expected ($$xpass unexpected $$passes)"; \
-+ fi; \
-+ fi; \
-+ dashes="$$banner"; \
-+ skipped=""; \
-+ if test "$$skip" -ne 0; then \
-+ if test "$$skip" -eq 1; then \
-+ skipped="($$skip test was not run)"; \
-+ else \
-+ skipped="($$skip tests were not run)"; \
-+ fi; \
-+ test `echo "$$skipped" | wc -c` -le `echo "$$banner" | wc -c` || \
-+ dashes="$$skipped"; \
-+ fi; \
-+ report=""; \
-+ if test "$$failed" -ne 0 && test -n "$(PACKAGE_BUGREPORT)"; then \
-+ report="Please report to $(PACKAGE_BUGREPORT)"; \
-+ test `echo "$$report" | wc -c` -le `echo "$$banner" | wc -c` || \
-+ dashes="$$report"; \
-+ fi; \
-+ dashes=`echo "$$dashes" | sed s/./=/g`; \
-+ if test "$$failed" -eq 0; then \
-+ echo "$$grn$$dashes"; \
-+ else \
-+ echo "$$red$$dashes"; \
- fi; \
-- dashes=`echo "$$banner" | sed s/./=/g`; \
-- echo "$$dashes"; \
- echo "$$banner"; \
-- echo "$$dashes"; \
-- test "$$failed" -eq 0
--info-am:
--info: info-am
--dvi-am:
--dvi: dvi-am
-+ test -z "$$skipped" || echo "$$skipped"; \
-+ test -z "$$report" || echo "$$report"; \
-+ echo "$$dashes$$std"; \
-+ test "$$failed" -eq 0; \
-+ else :; fi
-+
-+distdir: $(DISTFILES)
-+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ list='$(DISTFILES)'; \
-+ dist_files=`for file in $$list; do echo $$file; done | \
-+ sed -e "s|^$$srcdirstrip/||;t" \
-+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-+ case $$dist_files in \
-+ */*) $(MKDIR_P) `echo "$$dist_files" | \
-+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-+ sort -u` ;; \
-+ esac; \
-+ for file in $$dist_files; do \
-+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
-+ if test -d $$d/$$file; then \
-+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-+ if test -d "$(distdir)/$$file"; then \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
-+ else \
-+ test -f "$(distdir)/$$file" \
-+ || cp -p $$d/$$file "$(distdir)/$$file" \
-+ || exit 1; \
-+ fi; \
-+ done
- check-am: all-am
- $(MAKE) $(AM_MAKEFLAGS) check-TESTS
- check: check-am
--installcheck-am:
--installcheck: installcheck-am
--install-exec-am:
-+all-am: Makefile $(PROGRAMS) $(HEADERS)
-+installdirs:
-+install: install-am
- install-exec: install-exec-am
--
--install-data-am:
- install-data: install-data-am
-+uninstall: uninstall-am
-
- install-am: all-am
- @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
--install: install-am
--uninstall-am:
--uninstall: uninstall-am
--all-am: Makefile $(PROGRAMS) $(HEADERS)
--all-redirect: all-am
--install-strip:
-- $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
--installdirs:
--
-
-+installcheck: installcheck-am
-+install-strip:
-+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-+ `test -z '$(STRIP)' || \
-+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
- mostlyclean-generic:
-
- clean-generic:
-
- distclean-generic:
-- -rm -f Makefile $(CONFIG_CLEAN_FILES)
-- -rm -f config.cache config.log stamp-h stamp-h[0-9]*
-+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
- maintainer-clean-generic:
-+ @echo "This command is intended for maintainers to use"
-+ @echo "it deletes files that may require special tools to rebuild."
- -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
--mostlyclean-am: mostlyclean-noinstPROGRAMS mostlyclean-compile \
-- mostlyclean-tags mostlyclean-generic
-+clean: clean-am
-
--mostlyclean: mostlyclean-am
-+clean-am: clean-generic clean-noinstPROGRAMS mostlyclean-am
-
--clean-am: clean-noinstPROGRAMS clean-compile clean-tags clean-generic \
-- mostlyclean-am
-+distclean: distclean-am
-+ -rm -rf ./$(DEPDIR)
-+ -rm -f Makefile
-+distclean-am: clean-am distclean-compile distclean-generic \
-+ distclean-tags
-
--clean: clean-am
-+dvi: dvi-am
-
--distclean-am: distclean-noinstPROGRAMS distclean-compile distclean-tags \
-- distclean-generic clean-am
-+dvi-am:
-
--distclean: distclean-am
-+html: html-am
-
--maintainer-clean-am: maintainer-clean-noinstPROGRAMS \
-- maintainer-clean-compile maintainer-clean-tags \
-- maintainer-clean-generic distclean-am
-- @echo "This command is intended for maintainers to use;"
-- @echo "it deletes files that may require special tools to rebuild."
-+html-am:
-+
-+info: info-am
-+
-+info-am:
-+
-+install-data-am:
-+
-+install-dvi: install-dvi-am
-+
-+install-dvi-am:
-+
-+install-exec-am:
-+
-+install-html: install-html-am
-+
-+install-html-am:
-+
-+install-info: install-info-am
-+
-+install-info-am:
-+
-+install-man:
-+
-+install-pdf: install-pdf-am
-+
-+install-pdf-am:
-+
-+install-ps: install-ps-am
-+
-+install-ps-am:
-+
-+installcheck-am:
-
- maintainer-clean: maintainer-clean-am
-+ -rm -rf ./$(DEPDIR)
-+ -rm -f Makefile
-+maintainer-clean-am: distclean-am maintainer-clean-generic
-+
-+mostlyclean: mostlyclean-am
-+
-+mostlyclean-am: mostlyclean-compile mostlyclean-generic
-+
-+pdf: pdf-am
-+
-+pdf-am:
-+
-+ps: ps-am
-+
-+ps-am:
-+
-+uninstall-am:
-+
-+.MAKE: check-am install-am install-strip
-
--.PHONY: mostlyclean-noinstPROGRAMS distclean-noinstPROGRAMS \
--clean-noinstPROGRAMS maintainer-clean-noinstPROGRAMS \
--mostlyclean-compile distclean-compile clean-compile \
--maintainer-clean-compile tags mostlyclean-tags distclean-tags \
--clean-tags maintainer-clean-tags distdir check-TESTS info-am info \
--dvi-am dvi check check-am installcheck-am installcheck install-exec-am \
--install-exec install-data-am install-data install-am install \
--uninstall-am uninstall all-redirect all-am all installdirs \
--mostlyclean-generic distclean-generic clean-generic \
--maintainer-clean-generic clean mostlyclean distclean maintainer-clean
-+.PHONY: CTAGS GTAGS all all-am check check-TESTS check-am clean \
-+ clean-generic clean-noinstPROGRAMS ctags distclean \
-+ distclean-compile distclean-generic distclean-tags distdir dvi \
-+ dvi-am html html-am info info-am install install-am \
-+ install-data install-data-am install-dvi install-dvi-am \
-+ install-exec install-exec-am install-html install-html-am \
-+ install-info install-info-am install-man install-pdf \
-+ install-pdf-am install-ps install-ps-am install-strip \
-+ installcheck installcheck-am installdirs maintainer-clean \
-+ maintainer-clean-generic mostlyclean mostlyclean-compile \
-+ mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
-+ uninstall-am
-
-
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -ubrN exonerate-2.2.0.orig/src/general/Makefile.in exonerate-2.2.0/src/general/Makefile.in
---- exonerate-2.2.0.orig/src/general/Makefile.in 2008-10-17 12:05:01.000000000 +0200
-+++ exonerate-2.2.0/src/general/Makefile.in 2011-12-12 13:33:16.000000000 +0100
-@@ -1,6 +1,9 @@
--# Makefile.in generated automatically by automake 1.4-p6 from Makefile.am
-+# Makefile.in generated by automake 1.11.1 from Makefile.am.
-+# @configure_input@
-
--# Copyright (C) 1994, 1995-8, 1999, 2001 Free Software Foundation, Inc.
-+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
-+# Inc.
- # This Makefile.in is free software; the Free Software Foundation
- # gives unlimited permission to copy and/or distribute it,
- # with or without modifications, as long as this notice is preserved.
-@@ -10,324 +13,555 @@
- # even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- # PARTICULAR PURPOSE.
-
-+ at SET_MAKE@
-
--SHELL = @SHELL@
-
--srcdir = @srcdir@
--top_srcdir = @top_srcdir@
- VPATH = @srcdir@
--prefix = @prefix@
--exec_prefix = @exec_prefix@
--
--bindir = @bindir@
--sbindir = @sbindir@
--libexecdir = @libexecdir@
--datadir = @datadir@
--sysconfdir = @sysconfdir@
--sharedstatedir = @sharedstatedir@
--localstatedir = @localstatedir@
--libdir = @libdir@
--infodir = @infodir@
--mandir = @mandir@
--includedir = @includedir@
--oldincludedir = /usr/include
--
--DESTDIR =
--
- pkgdatadir = $(datadir)/@PACKAGE@
--pkglibdir = $(libdir)/@PACKAGE@
- pkgincludedir = $(includedir)/@PACKAGE@
--
--top_builddir = ../..
--
--ACLOCAL = @ACLOCAL@
--AUTOCONF = @AUTOCONF@
--AUTOMAKE = @AUTOMAKE@
--AUTOHEADER = @AUTOHEADER@
--
--INSTALL = @INSTALL@
--INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
--INSTALL_DATA = @INSTALL_DATA@
--INSTALL_SCRIPT = @INSTALL_SCRIPT@
--transform = @program_transform_name@
--
-+pkglibdir = $(libdir)/@PACKAGE@
-+pkglibexecdir = $(libexecdir)/@PACKAGE@
-+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-+install_sh_DATA = $(install_sh) -c -m 644
-+install_sh_PROGRAM = $(install_sh) -c
-+install_sh_SCRIPT = $(install_sh) -c
-+INSTALL_HEADER = $(INSTALL_DATA)
-+transform = $(program_transform_name)
- NORMAL_INSTALL = :
- PRE_INSTALL = :
- POST_INSTALL = :
- NORMAL_UNINSTALL = :
- PRE_UNINSTALL = :
- POST_UNINSTALL = :
--host_alias = @host_alias@
-+build_triplet = @build@
- host_triplet = @host@
-+TESTS = argument.test$(EXEEXT) lineparse.test$(EXEEXT) \
-+ compoundfile.test$(EXEEXT) socket.test$(EXEEXT)
-+noinst_PROGRAMS = $(am__EXEEXT_1)
-+subdir = src/general
-+DIST_COMMON = $(noinst_HEADERS) $(srcdir)/Makefile.am \
-+ $(srcdir)/Makefile.in
-+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-+am__aclocal_m4_deps = $(top_srcdir)/configure.in
-+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-+ $(ACLOCAL_M4)
-+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
-+CONFIG_CLEAN_FILES =
-+CONFIG_CLEAN_VPATH_FILES =
-+am__EXEEXT_1 = argument.test$(EXEEXT) lineparse.test$(EXEEXT) \
-+ compoundfile.test$(EXEEXT) socket.test$(EXEEXT)
-+PROGRAMS = $(noinst_PROGRAMS)
-+am_argument_test_OBJECTS = argument.test.$(OBJEXT) argument.$(OBJEXT)
-+argument_test_OBJECTS = $(am_argument_test_OBJECTS)
-+argument_test_LDADD = $(LDADD)
-+am_compoundfile_test_OBJECTS = compoundfile.test.$(OBJEXT) \
-+ compoundfile.$(OBJEXT)
-+compoundfile_test_OBJECTS = $(am_compoundfile_test_OBJECTS)
-+compoundfile_test_LDADD = $(LDADD)
-+am_lineparse_test_OBJECTS = lineparse.test.$(OBJEXT) \
-+ lineparse.$(OBJEXT)
-+lineparse_test_OBJECTS = $(am_lineparse_test_OBJECTS)
-+lineparse_test_LDADD = $(LDADD)
-+am_socket_test_OBJECTS = socket.test.$(OBJEXT) socket.$(OBJEXT)
-+socket_test_OBJECTS = $(am_socket_test_OBJECTS)
-+socket_test_LDADD = $(LDADD)
-+DEFAULT_INCLUDES = -I. at am__isrc@
-+depcomp = $(SHELL) $(top_srcdir)/depcomp
-+am__depfiles_maybe = depfiles
-+am__mv = mv -f
-+COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
-+ $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
-+CCLD = $(CC)
-+LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
-+SOURCES = $(argument_test_SOURCES) $(compoundfile_test_SOURCES) \
-+ $(lineparse_test_SOURCES) $(socket_test_SOURCES)
-+DIST_SOURCES = $(argument_test_SOURCES) $(compoundfile_test_SOURCES) \
-+ $(lineparse_test_SOURCES) $(socket_test_SOURCES)
-+HEADERS = $(noinst_HEADERS)
-+ETAGS = etags
-+CTAGS = ctags
-+am__tty_colors = \
-+red=; grn=; lgn=; blu=; std=
-+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-+ACLOCAL = @ACLOCAL@
-+AMTAR = @AMTAR@
-+AUTOCONF = @AUTOCONF@
-+AUTOHEADER = @AUTOHEADER@
-+AUTOMAKE = @AUTOMAKE@
-+AWK = @AWK@
- CC = @CC@
-+CCDEPMODE = @CCDEPMODE@
-+CFLAGS = @CFLAGS@
-+CPP = @CPP@
-+CPPFLAGS = @CPPFLAGS@
-+CYGPATH_W = @CYGPATH_W@
-+DEFS = @DEFS@
-+DEPDIR = @DEPDIR@
-+ECHO_C = @ECHO_C@
-+ECHO_N = @ECHO_N@
-+ECHO_T = @ECHO_T@
-+EGREP = @EGREP@
-+EXEEXT = @EXEEXT@
- GLIB_CONFIG = @GLIB_CONFIG@
--HAVE_LIB = @HAVE_LIB@
--LIB = @LIB@
--LTLIB = @LTLIB@
-+GREP = @GREP@
-+INSTALL = @INSTALL@
-+INSTALL_DATA = @INSTALL_DATA@
-+INSTALL_PROGRAM = @INSTALL_PROGRAM@
-+INSTALL_SCRIPT = @INSTALL_SCRIPT@
-+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-+LDFLAGS = @LDFLAGS@
-+LIBOBJS = @LIBOBJS@
-+LIBS = @LIBS@
-+LTLIBOBJS = @LTLIBOBJS@
- MAKEINFO = @MAKEINFO@
-+MKDIR_P = @MKDIR_P@
-+OBJEXT = @OBJEXT@
- PACKAGE = @PACKAGE@
-+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-+PACKAGE_NAME = @PACKAGE_NAME@
-+PACKAGE_STRING = @PACKAGE_STRING@
-+PACKAGE_TARNAME = @PACKAGE_TARNAME@
-+PACKAGE_URL = @PACKAGE_URL@
-+PACKAGE_VERSION = @PACKAGE_VERSION@
-+PATH_SEPARATOR = @PATH_SEPARATOR@
- PKG_CONFIG = @PKG_CONFIG@
-+SET_MAKE = @SET_MAKE@
-+SHELL = @SHELL@
-+STRIP = @STRIP@
- VERSION = @VERSION@
-+abs_builddir = @abs_builddir@
-+abs_srcdir = @abs_srcdir@
-+abs_top_builddir = @abs_top_builddir@
-+abs_top_srcdir = @abs_top_srcdir@
-+ac_ct_CC = @ac_ct_CC@
-+am__include = @am__include@
-+am__leading_dot = @am__leading_dot@
-+am__quote = @am__quote@
-+am__tar = @am__tar@
-+am__untar = @am__untar@
-+bindir = @bindir@
-+build = @build@
-+build_alias = @build_alias@
-+build_cpu = @build_cpu@
-+build_os = @build_os@
-+build_vendor = @build_vendor@
-+builddir = @builddir@
- codegen_extra_ldadd = @codegen_extra_ldadd@
- codegen_extra_sources = @codegen_extra_sources@
-+datadir = @datadir@
- datarootdir = @datarootdir@
-+docdir = @docdir@
-+dvidir = @dvidir@
-+exec_prefix = @exec_prefix@
- glib_cflags = @glib_cflags@
- glib_libs = @glib_libs@
- host = @host@
-+host_alias = @host_alias@
-+host_cpu = @host_cpu@
-+host_os = @host_os@
-+host_vendor = @host_vendor@
-+htmldir = @htmldir@
-+includedir = @includedir@
-+infodir = @infodir@
-+install_sh = @install_sh@
- installed_util_list = @installed_util_list@
-+libdir = @libdir@
-+libexecdir = @libexecdir@
-+localedir = @localedir@
-+localstatedir = @localstatedir@
-+mandir = @mandir@
-+mkdir_p = @mkdir_p@
-+oldincludedir = @oldincludedir@
-+pdfdir = @pdfdir@
-+prefix = @prefix@
-+program_transform_name = @program_transform_name@
-+psdir = @psdir@
-+sbindir = @sbindir@
-+sharedstatedir = @sharedstatedir@
- source_root_dir = @source_root_dir@
-+srcdir = @srcdir@
-+sysconfdir = @sysconfdir@
-+target_alias = @target_alias@
-+top_build_prefix = @top_build_prefix@
-+top_builddir = @top_builddir@
-+top_srcdir = @top_srcdir@
- use_pthreads = @use_pthreads@
--
--TESTS = argument.test lineparse.test compoundfile.test socket.test
--noinst_PROGRAMS = $(TESTS)
--
- noinst_HEADERS = argument.h lineparse.h compoundfile.h socket.h
--
- INCLUDES = -DSOURCE_ROOT_DIR="\"@source_root_dir@\""
--
- argument_test_SOURCES = argument.test.c argument.c
- lineparse_test_SOURCES = lineparse.test.c lineparse.c
- compoundfile_test_SOURCES = compoundfile.test.c compoundfile.c
- socket_test_SOURCES = socket.test.c socket.c
-
- # Files to clear away
--
- MAINTAINERCLEANFILES = Makefile.in
--mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
--CONFIG_CLEAN_FILES =
--PROGRAMS = $(noinst_PROGRAMS)
--
--
--DEFS = @DEFS@ -I. -I$(srcdir)
--CPPFLAGS = @CPPFLAGS@
--LDFLAGS = @LDFLAGS@
--LIBS = @LIBS@
--argument_test_OBJECTS = argument.test.o argument.o
--argument_test_LDADD = $(LDADD)
--argument_test_DEPENDENCIES =
--argument_test_LDFLAGS =
--lineparse_test_OBJECTS = lineparse.test.o lineparse.o
--lineparse_test_LDADD = $(LDADD)
--lineparse_test_DEPENDENCIES =
--lineparse_test_LDFLAGS =
--compoundfile_test_OBJECTS = compoundfile.test.o compoundfile.o
--compoundfile_test_LDADD = $(LDADD)
--compoundfile_test_DEPENDENCIES =
--compoundfile_test_LDFLAGS =
--socket_test_OBJECTS = socket.test.o socket.o
--socket_test_LDADD = $(LDADD)
--socket_test_DEPENDENCIES =
--socket_test_LDFLAGS =
--CFLAGS = @CFLAGS@
--COMPILE = $(CC) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
--CCLD = $(CC)
--LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(LDFLAGS) -o $@
--HEADERS = $(noinst_HEADERS)
-+all: all-am
-
--DIST_COMMON = Makefile.am Makefile.in
--
--
--DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
--
--TAR = tar
--GZIP_ENV = --best
--SOURCES = $(argument_test_SOURCES) $(lineparse_test_SOURCES) $(compoundfile_test_SOURCES) $(socket_test_SOURCES)
--OBJECTS = $(argument_test_OBJECTS) $(lineparse_test_OBJECTS) $(compoundfile_test_OBJECTS) $(socket_test_OBJECTS)
--
--all: all-redirect
- .SUFFIXES:
--.SUFFIXES: .S .c .o .s
--$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4)
-- cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps src/general/Makefile
--
-+.SUFFIXES: .c .o .obj
-+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
-+ @for dep in $?; do \
-+ case '$(am__configure_deps)' in \
-+ *$$dep*) \
-+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-+ && { if test -f $@; then exit 0; else break; fi; }; \
-+ exit 1;; \
-+ esac; \
-+ done; \
-+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/general/Makefile'; \
-+ $(am__cd) $(top_srcdir) && \
-+ $(AUTOMAKE) --gnu src/general/Makefile
-+.PRECIOUS: Makefile
- Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-- cd $(top_builddir) \
-- && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
--
--
--mostlyclean-noinstPROGRAMS:
-+ @case '$?' in \
-+ *config.status*) \
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-+ *) \
-+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-+ esac;
-+
-+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+
-+$(top_srcdir)/configure: $(am__configure_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(am__aclocal_m4_deps):
-
- clean-noinstPROGRAMS:
- -test -z "$(noinst_PROGRAMS)" || rm -f $(noinst_PROGRAMS)
--
--distclean-noinstPROGRAMS:
--
--maintainer-clean-noinstPROGRAMS:
--
--.c.o:
-- $(COMPILE) -c $<
--
--.s.o:
-- $(COMPILE) -c $<
--
--.S.o:
-- $(COMPILE) -c $<
-+argument.test$(EXEEXT): $(argument_test_OBJECTS) $(argument_test_DEPENDENCIES)
-+ @rm -f argument.test$(EXEEXT)
-+ $(LINK) $(argument_test_OBJECTS) $(argument_test_LDADD) $(LIBS)
-+compoundfile.test$(EXEEXT): $(compoundfile_test_OBJECTS) $(compoundfile_test_DEPENDENCIES)
-+ @rm -f compoundfile.test$(EXEEXT)
-+ $(LINK) $(compoundfile_test_OBJECTS) $(compoundfile_test_LDADD) $(LIBS)
-+lineparse.test$(EXEEXT): $(lineparse_test_OBJECTS) $(lineparse_test_DEPENDENCIES)
-+ @rm -f lineparse.test$(EXEEXT)
-+ $(LINK) $(lineparse_test_OBJECTS) $(lineparse_test_LDADD) $(LIBS)
-+socket.test$(EXEEXT): $(socket_test_OBJECTS) $(socket_test_DEPENDENCIES)
-+ @rm -f socket.test$(EXEEXT)
-+ $(LINK) $(socket_test_OBJECTS) $(socket_test_LDADD) $(LIBS)
-
- mostlyclean-compile:
-- -rm -f *.o core *.core
--
--clean-compile:
-+ -rm -f *.$(OBJEXT)
-
- distclean-compile:
- -rm -f *.tab.c
-
--maintainer-clean-compile:
--
--argument.test: $(argument_test_OBJECTS) $(argument_test_DEPENDENCIES)
-- @rm -f argument.test
-- $(LINK) $(argument_test_LDFLAGS) $(argument_test_OBJECTS) $(argument_test_LDADD) $(LIBS)
--
--lineparse.test: $(lineparse_test_OBJECTS) $(lineparse_test_DEPENDENCIES)
-- @rm -f lineparse.test
-- $(LINK) $(lineparse_test_LDFLAGS) $(lineparse_test_OBJECTS) $(lineparse_test_LDADD) $(LIBS)
--
--compoundfile.test: $(compoundfile_test_OBJECTS) $(compoundfile_test_DEPENDENCIES)
-- @rm -f compoundfile.test
-- $(LINK) $(compoundfile_test_LDFLAGS) $(compoundfile_test_OBJECTS) $(compoundfile_test_LDADD) $(LIBS)
--
--socket.test: $(socket_test_OBJECTS) $(socket_test_DEPENDENCIES)
-- @rm -f socket.test
-- $(LINK) $(socket_test_LDFLAGS) $(socket_test_OBJECTS) $(socket_test_LDADD) $(LIBS)
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/argument.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/argument.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/compoundfile.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/compoundfile.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/lineparse.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/lineparse.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/socket.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/socket.test.Po at am__quote@
-
-+.c.o:
-+ at am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
-+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-+ at am__fastdepCC_FALSE@ $(COMPILE) -c $<
-+
-+.c.obj:
-+ at am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
-+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-+ at am__fastdepCC_FALSE@ $(COMPILE) -c `$(CYGPATH_W) '$<'`
-+
-+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ mkid -fID $$unique
- tags: TAGS
-
--ID: $(HEADERS) $(SOURCES) $(LISP)
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- here=`pwd` && cd $(srcdir) \
-- && mkid -f$$here/ID $$unique $(LISP)
--
--TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) $(LISP)
-- tags=; \
-+TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ set x; \
- here=`pwd`; \
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- test -z "$(ETAGS_ARGS)$$unique$(LISP)$$tags" \
-- || (cd $(srcdir) && etags -o $$here/TAGS $(ETAGS_ARGS) $$tags $$unique $(LISP))
--
--mostlyclean-tags:
--
--clean-tags:
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ shift; \
-+ if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
-+ test -n "$$unique" || unique=$$empty_fix; \
-+ if test $$# -gt 0; then \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ "$$@" $$unique; \
-+ else \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ $$unique; \
-+ fi; \
-+ fi
-+ctags: CTAGS
-+CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ test -z "$(CTAGS_ARGS)$$unique" \
-+ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-+ $$unique
-+
-+GTAGS:
-+ here=`$(am__cd) $(top_builddir) && pwd` \
-+ && $(am__cd) $(top_srcdir) \
-+ && gtags -i $(GTAGS_ARGS) "$$here"
-
- distclean-tags:
-- -rm -f TAGS ID
--
--maintainer-clean-tags:
--
--distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
--
--subdir = src/general
-+ -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-
--distdir: $(DISTFILES)
-- @for file in $(DISTFILES); do \
-- d=$(srcdir); \
-- if test -d $$d/$$file; then \
-- cp -pr $$d/$$file $(distdir)/$$file; \
-- else \
-- test -f $(distdir)/$$file \
-- || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
-- || cp -p $$d/$$file $(distdir)/$$file || :; \
-- fi; \
-- done
- check-TESTS: $(TESTS)
-- @failed=0; all=0; \
-+ @failed=0; all=0; xfail=0; xpass=0; skip=0; \
- srcdir=$(srcdir); export srcdir; \
-- for tst in $(TESTS); do \
-- if test -f $$tst; then dir=.; \
-- else dir="$(srcdir)"; fi; \
-- if $(TESTS_ENVIRONMENT) $$dir/$$tst; then \
-+ list=' $(TESTS) '; \
-+ $(am__tty_colors); \
-+ if test -n "$$list"; then \
-+ for tst in $$list; do \
-+ if test -f ./$$tst; then dir=./; \
-+ elif test -f $$tst; then dir=; \
-+ else dir="$(srcdir)/"; fi; \
-+ if $(TESTS_ENVIRONMENT) $${dir}$$tst; then \
- all=`expr $$all + 1`; \
-- echo "PASS: $$tst"; \
-+ case " $(XFAIL_TESTS) " in \
-+ *[\ \ ]$$tst[\ \ ]*) \
-+ xpass=`expr $$xpass + 1`; \
-+ failed=`expr $$failed + 1`; \
-+ col=$$red; res=XPASS; \
-+ ;; \
-+ *) \
-+ col=$$grn; res=PASS; \
-+ ;; \
-+ esac; \
- elif test $$? -ne 77; then \
- all=`expr $$all + 1`; \
-+ case " $(XFAIL_TESTS) " in \
-+ *[\ \ ]$$tst[\ \ ]*) \
-+ xfail=`expr $$xfail + 1`; \
-+ col=$$lgn; res=XFAIL; \
-+ ;; \
-+ *) \
- failed=`expr $$failed + 1`; \
-- echo "FAIL: $$tst"; \
-+ col=$$red; res=FAIL; \
-+ ;; \
-+ esac; \
-+ else \
-+ skip=`expr $$skip + 1`; \
-+ col=$$blu; res=SKIP; \
- fi; \
-+ echo "$${col}$$res$${std}: $$tst"; \
- done; \
-+ if test "$$all" -eq 1; then \
-+ tests="test"; \
-+ All=""; \
-+ else \
-+ tests="tests"; \
-+ All="All "; \
-+ fi; \
-+ if test "$$failed" -eq 0; then \
-+ if test "$$xfail" -eq 0; then \
-+ banner="$$All$$all $$tests passed"; \
-+ else \
-+ if test "$$xfail" -eq 1; then failures=failure; else failures=failures; fi; \
-+ banner="$$All$$all $$tests behaved as expected ($$xfail expected $$failures)"; \
-+ fi; \
-+ else \
-+ if test "$$xpass" -eq 0; then \
-+ banner="$$failed of $$all $$tests failed"; \
-+ else \
-+ if test "$$xpass" -eq 1; then passes=pass; else passes=passes; fi; \
-+ banner="$$failed of $$all $$tests did not behave as expected ($$xpass unexpected $$passes)"; \
-+ fi; \
-+ fi; \
-+ dashes="$$banner"; \
-+ skipped=""; \
-+ if test "$$skip" -ne 0; then \
-+ if test "$$skip" -eq 1; then \
-+ skipped="($$skip test was not run)"; \
-+ else \
-+ skipped="($$skip tests were not run)"; \
-+ fi; \
-+ test `echo "$$skipped" | wc -c` -le `echo "$$banner" | wc -c` || \
-+ dashes="$$skipped"; \
-+ fi; \
-+ report=""; \
-+ if test "$$failed" -ne 0 && test -n "$(PACKAGE_BUGREPORT)"; then \
-+ report="Please report to $(PACKAGE_BUGREPORT)"; \
-+ test `echo "$$report" | wc -c` -le `echo "$$banner" | wc -c` || \
-+ dashes="$$report"; \
-+ fi; \
-+ dashes=`echo "$$dashes" | sed s/./=/g`; \
- if test "$$failed" -eq 0; then \
-- banner="All $$all tests passed"; \
-+ echo "$$grn$$dashes"; \
- else \
-- banner="$$failed of $$all tests failed"; \
-+ echo "$$red$$dashes"; \
- fi; \
-- dashes=`echo "$$banner" | sed s/./=/g`; \
-- echo "$$dashes"; \
- echo "$$banner"; \
-- echo "$$dashes"; \
-- test "$$failed" -eq 0
--info-am:
--info: info-am
--dvi-am:
--dvi: dvi-am
-+ test -z "$$skipped" || echo "$$skipped"; \
-+ test -z "$$report" || echo "$$report"; \
-+ echo "$$dashes$$std"; \
-+ test "$$failed" -eq 0; \
-+ else :; fi
-+
-+distdir: $(DISTFILES)
-+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ list='$(DISTFILES)'; \
-+ dist_files=`for file in $$list; do echo $$file; done | \
-+ sed -e "s|^$$srcdirstrip/||;t" \
-+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-+ case $$dist_files in \
-+ */*) $(MKDIR_P) `echo "$$dist_files" | \
-+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-+ sort -u` ;; \
-+ esac; \
-+ for file in $$dist_files; do \
-+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
-+ if test -d $$d/$$file; then \
-+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-+ if test -d "$(distdir)/$$file"; then \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
-+ else \
-+ test -f "$(distdir)/$$file" \
-+ || cp -p $$d/$$file "$(distdir)/$$file" \
-+ || exit 1; \
-+ fi; \
-+ done
- check-am: all-am
- $(MAKE) $(AM_MAKEFLAGS) check-TESTS
- check: check-am
--installcheck-am:
--installcheck: installcheck-am
--install-exec-am:
-+all-am: Makefile $(PROGRAMS) $(HEADERS)
-+installdirs:
-+install: install-am
- install-exec: install-exec-am
--
--install-data-am:
- install-data: install-data-am
-+uninstall: uninstall-am
-
- install-am: all-am
- @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
--install: install-am
--uninstall-am:
--uninstall: uninstall-am
--all-am: Makefile $(PROGRAMS) $(HEADERS)
--all-redirect: all-am
--install-strip:
-- $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
--installdirs:
--
-
-+installcheck: installcheck-am
-+install-strip:
-+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-+ `test -z '$(STRIP)' || \
-+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
- mostlyclean-generic:
-
- clean-generic:
-
- distclean-generic:
-- -rm -f Makefile $(CONFIG_CLEAN_FILES)
-- -rm -f config.cache config.log stamp-h stamp-h[0-9]*
-+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
- maintainer-clean-generic:
-+ @echo "This command is intended for maintainers to use"
-+ @echo "it deletes files that may require special tools to rebuild."
- -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
--mostlyclean-am: mostlyclean-noinstPROGRAMS mostlyclean-compile \
-- mostlyclean-tags mostlyclean-generic
-+clean: clean-am
-
--mostlyclean: mostlyclean-am
-+clean-am: clean-generic clean-noinstPROGRAMS mostlyclean-am
-
--clean-am: clean-noinstPROGRAMS clean-compile clean-tags clean-generic \
-- mostlyclean-am
-+distclean: distclean-am
-+ -rm -rf ./$(DEPDIR)
-+ -rm -f Makefile
-+distclean-am: clean-am distclean-compile distclean-generic \
-+ distclean-tags
-
--clean: clean-am
-+dvi: dvi-am
-
--distclean-am: distclean-noinstPROGRAMS distclean-compile distclean-tags \
-- distclean-generic clean-am
-+dvi-am:
-
--distclean: distclean-am
-+html: html-am
-
--maintainer-clean-am: maintainer-clean-noinstPROGRAMS \
-- maintainer-clean-compile maintainer-clean-tags \
-- maintainer-clean-generic distclean-am
-- @echo "This command is intended for maintainers to use;"
-- @echo "it deletes files that may require special tools to rebuild."
-+html-am:
-+
-+info: info-am
-+
-+info-am:
-+
-+install-data-am:
-+
-+install-dvi: install-dvi-am
-+
-+install-dvi-am:
-+
-+install-exec-am:
-+
-+install-html: install-html-am
-+
-+install-html-am:
-+
-+install-info: install-info-am
-+
-+install-info-am:
-+
-+install-man:
-+
-+install-pdf: install-pdf-am
-+
-+install-pdf-am:
-+
-+install-ps: install-ps-am
-+
-+install-ps-am:
-+
-+installcheck-am:
-
- maintainer-clean: maintainer-clean-am
-+ -rm -rf ./$(DEPDIR)
-+ -rm -f Makefile
-+maintainer-clean-am: distclean-am maintainer-clean-generic
-+
-+mostlyclean: mostlyclean-am
-+
-+mostlyclean-am: mostlyclean-compile mostlyclean-generic
-+
-+pdf: pdf-am
-+
-+pdf-am:
-+
-+ps: ps-am
-+
-+ps-am:
-+
-+uninstall-am:
-+
-+.MAKE: check-am install-am install-strip
-
--.PHONY: mostlyclean-noinstPROGRAMS distclean-noinstPROGRAMS \
--clean-noinstPROGRAMS maintainer-clean-noinstPROGRAMS \
--mostlyclean-compile distclean-compile clean-compile \
--maintainer-clean-compile tags mostlyclean-tags distclean-tags \
--clean-tags maintainer-clean-tags distdir check-TESTS info-am info \
--dvi-am dvi check check-am installcheck-am installcheck install-exec-am \
--install-exec install-data-am install-data install-am install \
--uninstall-am uninstall all-redirect all-am all installdirs \
--mostlyclean-generic distclean-generic clean-generic \
--maintainer-clean-generic clean mostlyclean distclean maintainer-clean
-+.PHONY: CTAGS GTAGS all all-am check check-TESTS check-am clean \
-+ clean-generic clean-noinstPROGRAMS ctags distclean \
-+ distclean-compile distclean-generic distclean-tags distdir dvi \
-+ dvi-am html html-am info info-am install install-am \
-+ install-data install-data-am install-dvi install-dvi-am \
-+ install-exec install-exec-am install-html install-html-am \
-+ install-info install-info-am install-man install-pdf \
-+ install-pdf-am install-ps install-ps-am install-strip \
-+ installcheck installcheck-am installdirs maintainer-clean \
-+ maintainer-clean-generic mostlyclean mostlyclean-compile \
-+ mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
-+ uninstall-am
-
-
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -ubrN exonerate-2.2.0.orig/src/hub/Makefile.in exonerate-2.2.0/src/hub/Makefile.in
---- exonerate-2.2.0.orig/src/hub/Makefile.in 2008-10-17 12:04:45.000000000 +0200
-+++ exonerate-2.2.0/src/hub/Makefile.in 2011-12-12 13:33:17.000000000 +0100
-@@ -1,6 +1,9 @@
--# Makefile.in generated automatically by automake 1.4-p6 from Makefile.am
-+# Makefile.in generated by automake 1.11.1 from Makefile.am.
-+# @configure_input@
-
--# Copyright (C) 1994, 1995-8, 1999, 2001 Free Software Foundation, Inc.
-+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
-+# Inc.
- # This Makefile.in is free software; the Free Software Foundation
- # gives unlimited permission to copy and/or distribute it,
- # with or without modifications, as long as this notice is preserved.
-@@ -10,412 +13,715 @@
- # even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- # PARTICULAR PURPOSE.
-
-+ at SET_MAKE@
-
--SHELL = @SHELL@
-
--srcdir = @srcdir@
--top_srcdir = @top_srcdir@
- VPATH = @srcdir@
--prefix = @prefix@
--exec_prefix = @exec_prefix@
--
--bindir = @bindir@
--sbindir = @sbindir@
--libexecdir = @libexecdir@
--datadir = @datadir@
--sysconfdir = @sysconfdir@
--sharedstatedir = @sharedstatedir@
--localstatedir = @localstatedir@
--libdir = @libdir@
--infodir = @infodir@
--mandir = @mandir@
--includedir = @includedir@
--oldincludedir = /usr/include
--
--DESTDIR =
--
- pkgdatadir = $(datadir)/@PACKAGE@
--pkglibdir = $(libdir)/@PACKAGE@
- pkgincludedir = $(includedir)/@PACKAGE@
--
--top_builddir = ../..
--
--ACLOCAL = @ACLOCAL@
--AUTOCONF = @AUTOCONF@
--AUTOMAKE = @AUTOMAKE@
--AUTOHEADER = @AUTOHEADER@
--
--INSTALL = @INSTALL@
--INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
--INSTALL_DATA = @INSTALL_DATA@
--INSTALL_SCRIPT = @INSTALL_SCRIPT@
--transform = @program_transform_name@
--
-+pkglibdir = $(libdir)/@PACKAGE@
-+pkglibexecdir = $(libexecdir)/@PACKAGE@
-+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-+install_sh_DATA = $(install_sh) -c -m 644
-+install_sh_PROGRAM = $(install_sh) -c
-+install_sh_SCRIPT = $(install_sh) -c
-+INSTALL_HEADER = $(INSTALL_DATA)
-+transform = $(program_transform_name)
- NORMAL_INSTALL = :
- PRE_INSTALL = :
- POST_INSTALL = :
- NORMAL_UNINSTALL = :
- PRE_UNINSTALL = :
- POST_UNINSTALL = :
--host_alias = @host_alias@
-+build_triplet = @build@
- host_triplet = @host@
-+TESTS = gam.test$(EXEEXT) analysis.test$(EXEEXT) bsam.test$(EXEEXT)
-+noinst_PROGRAMS = $(am__EXEEXT_1)
-+subdir = src/hub
-+DIST_COMMON = $(noinst_HEADERS) $(srcdir)/Makefile.am \
-+ $(srcdir)/Makefile.in
-+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-+am__aclocal_m4_deps = $(top_srcdir)/configure.in
-+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-+ $(ACLOCAL_M4)
-+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
-+CONFIG_CLEAN_FILES =
-+CONFIG_CLEAN_VPATH_FILES =
-+am__EXEEXT_1 = gam.test$(EXEEXT) analysis.test$(EXEEXT) \
-+ bsam.test$(EXEEXT)
-+PROGRAMS = $(noinst_PROGRAMS)
-+am_analysis_test_OBJECTS = analysis.test.$(OBJEXT) analysis.$(OBJEXT) \
-+ gam.$(OBJEXT) bsam.$(OBJEXT)
-+analysis_test_OBJECTS = $(am_analysis_test_OBJECTS)
-+am__DEPENDENCIES_1 = $(top_srcdir)/src/c4/c4.o \
-+ $(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/cgutil.o \
-+ $(top_srcdir)/src/c4/opair.o $(top_srcdir)/src/c4/alignment.o \
-+ $(top_srcdir)/src/c4/optimal.o $(top_srcdir)/src/c4/viterbi.o \
-+ $(top_srcdir)/src/c4/layout.o $(top_srcdir)/src/c4/region.o \
-+ $(top_srcdir)/src/c4/subopt.o $(top_srcdir)/src/bsdp/bsdp.o \
-+ $(top_srcdir)/src/bsdp/sar.o \
-+ $(top_srcdir)/src/bsdp/heuristic.o \
-+ $(top_srcdir)/src/bsdp/hpair.o \
-+ $(top_srcdir)/src/sdp/boundary.o $(top_srcdir)/src/sdp/sdp.o \
-+ $(top_srcdir)/src/sdp/scheduler.o \
-+ $(top_srcdir)/src/sdp/straceback.o \
-+ $(top_srcdir)/src/sdp/lookahead.o \
-+ $(top_srcdir)/src/struct/matrix.o \
-+ $(top_srcdir)/src/struct/slist.o \
-+ $(top_srcdir)/src/struct/pqueue.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/rangetree.o \
-+ $(top_srcdir)/src/sequence/sequence.o \
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/model/affine.o \
-+ $(top_srcdir)/src/model/est2genome.o \
-+ $(top_srcdir)/src/model/ner.o \
-+ $(top_srcdir)/src/model/protein2dna.o \
-+ $(top_srcdir)/src/model/protein2genome.o \
-+ $(top_srcdir)/src/model/coding2coding.o \
-+ $(top_srcdir)/src/model/coding2genome.o \
-+ $(top_srcdir)/src/model/cdna2genome.o \
-+ $(top_srcdir)/src/model/genome2genome.o \
-+ $(top_srcdir)/src/model/ungapped.o \
-+ $(top_srcdir)/src/model/intron.o \
-+ $(top_srcdir)/src/model/frameshift.o \
-+ $(top_srcdir)/src/model/phase.o \
-+ $(top_srcdir)/src/model/modeltype.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/comparison/match.o \
-+ $(top_srcdir)/src/sequence/submat.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o
-+analysis_test_DEPENDENCIES = $(top_srcdir)/src/comparison/hspset.o \
-+ $(top_srcdir)/src/comparison/wordhood.o \
-+ $(top_srcdir)/src/comparison/seeder.o \
-+ $(top_srcdir)/src/comparison/comparison.o \
-+ $(top_srcdir)/src/database/fastapipe.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/struct/dejavu.o \
-+ $(top_srcdir)/src/struct/fsm.o $(top_srcdir)/src/struct/vfsm.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/general/socket.o $(am__DEPENDENCIES_1)
-+am_bsam_test_OBJECTS = bsam.test.$(OBJEXT) bsam.$(OBJEXT)
-+bsam_test_OBJECTS = $(am_bsam_test_OBJECTS)
-+bsam_test_DEPENDENCIES = $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/comparison/hspset.o \
-+ $(top_srcdir)/src/comparison/comparison.o \
-+ $(top_srcdir)/src/comparison/match.o \
-+ $(top_srcdir)/src/comparison/wordhood.o \
-+ $(top_srcdir)/src/sequence/sequence.o \
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/sequence/submat.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/struct/dejavu.o \
-+ $(top_srcdir)/src/struct/pqueue.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/matrix.o
-+am_gam_test_OBJECTS = gam.test.$(OBJEXT) gam.$(OBJEXT)
-+gam_test_OBJECTS = $(am_gam_test_OBJECTS)
-+gam_test_DEPENDENCIES = $(top_srcdir)/src/comparison/hspset.o \
-+ $(top_srcdir)/src/comparison/comparison.o \
-+ $(top_srcdir)/src/comparison/wordhood.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/general/compoundfile.o $(am__DEPENDENCIES_1)
-+DEFAULT_INCLUDES = -I. at am__isrc@
-+depcomp = $(SHELL) $(top_srcdir)/depcomp
-+am__depfiles_maybe = depfiles
-+am__mv = mv -f
-+COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
-+ $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
-+CCLD = $(CC)
-+LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
-+SOURCES = $(analysis_test_SOURCES) $(bsam_test_SOURCES) \
-+ $(gam_test_SOURCES)
-+DIST_SOURCES = $(analysis_test_SOURCES) $(bsam_test_SOURCES) \
-+ $(gam_test_SOURCES)
-+HEADERS = $(noinst_HEADERS)
-+ETAGS = etags
-+CTAGS = ctags
-+am__tty_colors = \
-+red=; grn=; lgn=; blu=; std=
-+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-+ACLOCAL = @ACLOCAL@
-+AMTAR = @AMTAR@
-+AUTOCONF = @AUTOCONF@
-+AUTOHEADER = @AUTOHEADER@
-+AUTOMAKE = @AUTOMAKE@
-+AWK = @AWK@
- CC = @CC@
-+CCDEPMODE = @CCDEPMODE@
-+CFLAGS = @CFLAGS@
-+CPP = @CPP@
-+CPPFLAGS = @CPPFLAGS@
-+CYGPATH_W = @CYGPATH_W@
-+DEFS = @DEFS@
-+DEPDIR = @DEPDIR@
-+ECHO_C = @ECHO_C@
-+ECHO_N = @ECHO_N@
-+ECHO_T = @ECHO_T@
-+EGREP = @EGREP@
-+EXEEXT = @EXEEXT@
- GLIB_CONFIG = @GLIB_CONFIG@
--HAVE_LIB = @HAVE_LIB@
--LIB = @LIB@
--LTLIB = @LTLIB@
-+GREP = @GREP@
-+INSTALL = @INSTALL@
-+INSTALL_DATA = @INSTALL_DATA@
-+INSTALL_PROGRAM = @INSTALL_PROGRAM@
-+INSTALL_SCRIPT = @INSTALL_SCRIPT@
-+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-+LDFLAGS = @LDFLAGS@
-+LIBOBJS = @LIBOBJS@
-+LIBS = @LIBS@
-+LTLIBOBJS = @LTLIBOBJS@
- MAKEINFO = @MAKEINFO@
-+MKDIR_P = @MKDIR_P@
-+OBJEXT = @OBJEXT@
- PACKAGE = @PACKAGE@
-+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-+PACKAGE_NAME = @PACKAGE_NAME@
-+PACKAGE_STRING = @PACKAGE_STRING@
-+PACKAGE_TARNAME = @PACKAGE_TARNAME@
-+PACKAGE_URL = @PACKAGE_URL@
-+PACKAGE_VERSION = @PACKAGE_VERSION@
-+PATH_SEPARATOR = @PATH_SEPARATOR@
- PKG_CONFIG = @PKG_CONFIG@
-+SET_MAKE = @SET_MAKE@
-+SHELL = @SHELL@
-+STRIP = @STRIP@
- VERSION = @VERSION@
-+abs_builddir = @abs_builddir@
-+abs_srcdir = @abs_srcdir@
-+abs_top_builddir = @abs_top_builddir@
-+abs_top_srcdir = @abs_top_srcdir@
-+ac_ct_CC = @ac_ct_CC@
-+am__include = @am__include@
-+am__leading_dot = @am__leading_dot@
-+am__quote = @am__quote@
-+am__tar = @am__tar@
-+am__untar = @am__untar@
-+bindir = @bindir@
-+build = @build@
-+build_alias = @build_alias@
-+build_cpu = @build_cpu@
-+build_os = @build_os@
-+build_vendor = @build_vendor@
-+builddir = @builddir@
- codegen_extra_ldadd = @codegen_extra_ldadd@
- codegen_extra_sources = @codegen_extra_sources@
-+datadir = @datadir@
- datarootdir = @datarootdir@
-+docdir = @docdir@
-+dvidir = @dvidir@
-+exec_prefix = @exec_prefix@
- glib_cflags = @glib_cflags@
- glib_libs = @glib_libs@
- host = @host@
-+host_alias = @host_alias@
-+host_cpu = @host_cpu@
-+host_os = @host_os@
-+host_vendor = @host_vendor@
-+htmldir = @htmldir@
-+includedir = @includedir@
-+infodir = @infodir@
-+install_sh = @install_sh@
- installed_util_list = @installed_util_list@
-+libdir = @libdir@
-+libexecdir = @libexecdir@
-+localedir = @localedir@
-+localstatedir = @localstatedir@
-+mandir = @mandir@
-+mkdir_p = @mkdir_p@
-+oldincludedir = @oldincludedir@
-+pdfdir = @pdfdir@
-+prefix = @prefix@
-+program_transform_name = @program_transform_name@
-+psdir = @psdir@
-+sbindir = @sbindir@
-+sharedstatedir = @sharedstatedir@
- source_root_dir = @source_root_dir@
-+srcdir = @srcdir@
-+sysconfdir = @sysconfdir@
-+target_alias = @target_alias@
-+top_build_prefix = @top_build_prefix@
-+top_builddir = @top_builddir@
-+top_srcdir = @top_srcdir@
- use_pthreads = @use_pthreads@
--
--TESTS = gam.test analysis.test bsam.test
--noinst_PROGRAMS = $(TESTS)
--
--INCLUDES = -I$(top_srcdir)/src/sequence -I$(top_srcdir)/src/database -I$(top_srcdir)/src/comparison -I$(top_srcdir)/src/struct -I$(top_srcdir)/src/c4 -I$(top_srcdir)/src/bsdp -I$(top_srcdir)/src/sdp -I$(top_srcdir)/src/model -I$(top_srcdir)/src/general -DHOSTTYPE="\"@host@\"" -DSOURCE_ROOT_DIR="\"@source_root_dir@\""
--
-+INCLUDES = -I$(top_srcdir)/src/sequence \
-+ -I$(top_srcdir)/src/database \
-+ -I$(top_srcdir)/src/comparison \
-+ -I$(top_srcdir)/src/struct \
-+ -I$(top_srcdir)/src/c4 \
-+ -I$(top_srcdir)/src/bsdp \
-+ -I$(top_srcdir)/src/sdp \
-+ -I$(top_srcdir)/src/model \
-+ -I$(top_srcdir)/src/general \
-+ -DHOSTTYPE="\"@host@\"" \
-+ -DSOURCE_ROOT_DIR="\"@source_root_dir@\""
-
- noinst_HEADERS = gam.h analysis.h bsam.h
--
--C4_OBJECTS = $(top_srcdir)/src/c4/c4.o $(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/cgutil.o $(top_srcdir)/src/c4/opair.o $(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/optimal.o $(top_srcdir)/src/c4/viterbi.o $(top_srcdir)/src/c4/layout.o $(top_srcdir)/src/c4/region.o $(top_srcdir)/src/c4/subopt.o $(top_srcdir)/src/bsdp/bsdp.o $(top_srcdir)/src/bsdp/sar.o $(top_srcdir)/src/bsdp/heuristic.o $(top_srcdir)/src/bsdp/hpair.o $(top_srcdir)/src/sdp/boundary.o $(top_srcdir)/src/sdp/sdp.o $(top_srcdir)/src/sdp/scheduler.o $(top_srcdir)/src/sdp/straceback.o $(top_srcdir)/src/sdp/lookahead.o $(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/struct/slist.o $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/rangetree.o $(top_srcdir)/src/sequence/sequence.o $(top_srcdir)/src/sequence/alphabet.o $(top_srcdir)/src/sequence/translate.o $(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/model/affine.o $(top_srcdir)/src/model/est2genome.o $(top_srcdir)/src/model/ner.o $(top_srcdir)/src/model/protein2dna.o $(top_srcdir)/src/model/protein2genome.o $(top_srcdir)/src/model/coding2coding.o $(top_srcdir)/src/model/coding2genome.o $(top_srcdir)/src/model/cdna2genome.o $(top_srcdir)/src/model/genome2genome.o $(top_srcdir)/src/model/ungapped.o $(top_srcdir)/src/model/intron.o $(top_srcdir)/src/model/frameshift.o $(top_srcdir)/src/model/phase.o $(top_srcdir)/src/model/modeltype.o $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/general/lineparse.o $(top_srcdir)/src/comparison/match.o $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o -lm
--
-+C4_OBJECTS = $(top_srcdir)/src/c4/c4.o \
-+ $(top_srcdir)/src/c4/codegen.o \
-+ $(top_srcdir)/src/c4/cgutil.o \
-+ $(top_srcdir)/src/c4/opair.o \
-+ $(top_srcdir)/src/c4/alignment.o \
-+ $(top_srcdir)/src/c4/optimal.o \
-+ $(top_srcdir)/src/c4/viterbi.o \
-+ $(top_srcdir)/src/c4/layout.o \
-+ $(top_srcdir)/src/c4/region.o \
-+ $(top_srcdir)/src/c4/subopt.o \
-+ $(top_srcdir)/src/bsdp/bsdp.o \
-+ $(top_srcdir)/src/bsdp/sar.o \
-+ $(top_srcdir)/src/bsdp/heuristic.o \
-+ $(top_srcdir)/src/bsdp/hpair.o \
-+ $(top_srcdir)/src/sdp/boundary.o \
-+ $(top_srcdir)/src/sdp/sdp.o \
-+ $(top_srcdir)/src/sdp/scheduler.o \
-+ $(top_srcdir)/src/sdp/straceback.o \
-+ $(top_srcdir)/src/sdp/lookahead.o \
-+ $(top_srcdir)/src/struct/matrix.o \
-+ $(top_srcdir)/src/struct/slist.o \
-+ $(top_srcdir)/src/struct/pqueue.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/rangetree.o \
-+ $(top_srcdir)/src/sequence/sequence.o \
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/model/affine.o \
-+ $(top_srcdir)/src/model/est2genome.o \
-+ $(top_srcdir)/src/model/ner.o \
-+ $(top_srcdir)/src/model/protein2dna.o \
-+ $(top_srcdir)/src/model/protein2genome.o \
-+ $(top_srcdir)/src/model/coding2coding.o \
-+ $(top_srcdir)/src/model/coding2genome.o \
-+ $(top_srcdir)/src/model/cdna2genome.o \
-+ $(top_srcdir)/src/model/genome2genome.o \
-+ $(top_srcdir)/src/model/ungapped.o \
-+ $(top_srcdir)/src/model/intron.o \
-+ $(top_srcdir)/src/model/frameshift.o \
-+ $(top_srcdir)/src/model/phase.o \
-+ $(top_srcdir)/src/model/modeltype.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/comparison/match.o \
-+ $(top_srcdir)/src/sequence/submat.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o \
-+ -lm
-
- gam_test_SOURCES = gam.test.c gam.c
--gam_test_LDADD = $(top_srcdir)/src/comparison/hspset.o $(top_srcdir)/src/comparison/comparison.o $(top_srcdir)/src/comparison/wordhood.o $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/general/compoundfile.o $(C4_OBJECTS)
--
-+gam_test_LDADD = $(top_srcdir)/src/comparison/hspset.o \
-+ $(top_srcdir)/src/comparison/comparison.o \
-+ $(top_srcdir)/src/comparison/wordhood.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(C4_OBJECTS)
-
- bsam_test_SOURCES = bsam.test.c bsam.c
--bsam_test_LDADD = $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/general/lineparse.o $(top_srcdir)/src/comparison/hspset.o $(top_srcdir)/src/comparison/comparison.o $(top_srcdir)/src/comparison/match.o $(top_srcdir)/src/comparison/wordhood.o $(top_srcdir)/src/sequence/sequence.o $(top_srcdir)/src/sequence/alphabet.o $(top_srcdir)/src/sequence/translate.o $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/struct/dejavu.o $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/matrix.o -lm
-+bsam_test_LDADD = $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/comparison/hspset.o \
-+ $(top_srcdir)/src/comparison/comparison.o \
-+ $(top_srcdir)/src/comparison/match.o \
-+ $(top_srcdir)/src/comparison/wordhood.o \
-+ $(top_srcdir)/src/sequence/sequence.o \
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/sequence/submat.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/struct/dejavu.o \
-+ $(top_srcdir)/src/struct/pqueue.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/matrix.o \
-+ -lm
-
- analysis_test_SOURCES = analysis.test.c analysis.c gam.c bsam.c
--analysis_test_LDADD = $(top_srcdir)/src/comparison/hspset.o $(top_srcdir)/src/comparison/wordhood.o $(top_srcdir)/src/comparison/seeder.o $(top_srcdir)/src/comparison/comparison.o $(top_srcdir)/src/database/fastapipe.o $(top_srcdir)/src/database/fastadb.o $(top_srcdir)/src/struct/dejavu.o $(top_srcdir)/src/struct/fsm.o $(top_srcdir)/src/struct/vfsm.o $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/general/compoundfile.o $(top_srcdir)/src/general/socket.o $(C4_OBJECTS)
-+analysis_test_LDADD = $(top_srcdir)/src/comparison/hspset.o \
-+ $(top_srcdir)/src/comparison/wordhood.o \
-+ $(top_srcdir)/src/comparison/seeder.o \
-+ $(top_srcdir)/src/comparison/comparison.o \
-+ $(top_srcdir)/src/database/fastapipe.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/struct/dejavu.o \
-+ $(top_srcdir)/src/struct/fsm.o \
-+ $(top_srcdir)/src/struct/vfsm.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/general/socket.o \
-+ $(C4_OBJECTS)
-
-
- # Files to clear away
--
- MAINTAINERCLEANFILES = Makefile.in
--mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
--CONFIG_CLEAN_FILES =
--PROGRAMS = $(noinst_PROGRAMS)
--
--
--DEFS = @DEFS@ -I. -I$(srcdir)
--CPPFLAGS = @CPPFLAGS@
--LDFLAGS = @LDFLAGS@
--LIBS = @LIBS@
--gam_test_OBJECTS = gam.test.o gam.o
--gam_test_DEPENDENCIES = $(top_srcdir)/src/comparison/hspset.o \
--$(top_srcdir)/src/comparison/comparison.o \
--$(top_srcdir)/src/comparison/wordhood.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/general/compoundfile.o $(top_srcdir)/src/c4/c4.o \
--$(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/cgutil.o \
--$(top_srcdir)/src/c4/opair.o $(top_srcdir)/src/c4/alignment.o \
--$(top_srcdir)/src/c4/optimal.o $(top_srcdir)/src/c4/viterbi.o \
--$(top_srcdir)/src/c4/layout.o $(top_srcdir)/src/c4/region.o \
--$(top_srcdir)/src/c4/subopt.o $(top_srcdir)/src/bsdp/bsdp.o \
--$(top_srcdir)/src/bsdp/sar.o $(top_srcdir)/src/bsdp/heuristic.o \
--$(top_srcdir)/src/bsdp/hpair.o $(top_srcdir)/src/sdp/boundary.o \
--$(top_srcdir)/src/sdp/sdp.o $(top_srcdir)/src/sdp/scheduler.o \
--$(top_srcdir)/src/sdp/straceback.o $(top_srcdir)/src/sdp/lookahead.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/struct/slist.o \
--$(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o \
--$(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/model/affine.o \
--$(top_srcdir)/src/model/est2genome.o $(top_srcdir)/src/model/ner.o \
--$(top_srcdir)/src/model/protein2dna.o \
--$(top_srcdir)/src/model/protein2genome.o \
--$(top_srcdir)/src/model/coding2coding.o \
--$(top_srcdir)/src/model/coding2genome.o \
--$(top_srcdir)/src/model/cdna2genome.o \
--$(top_srcdir)/src/model/genome2genome.o \
--$(top_srcdir)/src/model/ungapped.o $(top_srcdir)/src/model/intron.o \
--$(top_srcdir)/src/model/frameshift.o $(top_srcdir)/src/model/phase.o \
--$(top_srcdir)/src/model/modeltype.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/sequence/codonsubmat.o
--gam_test_LDFLAGS =
--analysis_test_OBJECTS = analysis.test.o analysis.o gam.o bsam.o
--analysis_test_DEPENDENCIES = $(top_srcdir)/src/comparison/hspset.o \
--$(top_srcdir)/src/comparison/wordhood.o \
--$(top_srcdir)/src/comparison/seeder.o \
--$(top_srcdir)/src/comparison/comparison.o \
--$(top_srcdir)/src/database/fastapipe.o \
--$(top_srcdir)/src/database/fastadb.o $(top_srcdir)/src/struct/dejavu.o \
--$(top_srcdir)/src/struct/fsm.o $(top_srcdir)/src/struct/vfsm.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/general/socket.o $(top_srcdir)/src/c4/c4.o \
--$(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/cgutil.o \
--$(top_srcdir)/src/c4/opair.o $(top_srcdir)/src/c4/alignment.o \
--$(top_srcdir)/src/c4/optimal.o $(top_srcdir)/src/c4/viterbi.o \
--$(top_srcdir)/src/c4/layout.o $(top_srcdir)/src/c4/region.o \
--$(top_srcdir)/src/c4/subopt.o $(top_srcdir)/src/bsdp/bsdp.o \
--$(top_srcdir)/src/bsdp/sar.o $(top_srcdir)/src/bsdp/heuristic.o \
--$(top_srcdir)/src/bsdp/hpair.o $(top_srcdir)/src/sdp/boundary.o \
--$(top_srcdir)/src/sdp/sdp.o $(top_srcdir)/src/sdp/scheduler.o \
--$(top_srcdir)/src/sdp/straceback.o $(top_srcdir)/src/sdp/lookahead.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/struct/slist.o \
--$(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o \
--$(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/model/affine.o \
--$(top_srcdir)/src/model/est2genome.o $(top_srcdir)/src/model/ner.o \
--$(top_srcdir)/src/model/protein2dna.o \
--$(top_srcdir)/src/model/protein2genome.o \
--$(top_srcdir)/src/model/coding2coding.o \
--$(top_srcdir)/src/model/coding2genome.o \
--$(top_srcdir)/src/model/cdna2genome.o \
--$(top_srcdir)/src/model/genome2genome.o \
--$(top_srcdir)/src/model/ungapped.o $(top_srcdir)/src/model/intron.o \
--$(top_srcdir)/src/model/frameshift.o $(top_srcdir)/src/model/phase.o \
--$(top_srcdir)/src/model/modeltype.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/sequence/codonsubmat.o
--analysis_test_LDFLAGS =
--bsam_test_OBJECTS = bsam.test.o bsam.o
--bsam_test_DEPENDENCIES = $(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o \
--$(top_srcdir)/src/comparison/hspset.o \
--$(top_srcdir)/src/comparison/comparison.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/comparison/wordhood.o \
--$(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/struct/dejavu.o \
--$(top_srcdir)/src/struct/pqueue.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/matrix.o
--bsam_test_LDFLAGS =
--CFLAGS = @CFLAGS@
--COMPILE = $(CC) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
--CCLD = $(CC)
--LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(LDFLAGS) -o $@
--HEADERS = $(noinst_HEADERS)
-+all: all-am
-
--DIST_COMMON = Makefile.am Makefile.in
--
--
--DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
--
--TAR = tar
--GZIP_ENV = --best
--SOURCES = $(gam_test_SOURCES) $(analysis_test_SOURCES) $(bsam_test_SOURCES)
--OBJECTS = $(gam_test_OBJECTS) $(analysis_test_OBJECTS) $(bsam_test_OBJECTS)
--
--all: all-redirect
- .SUFFIXES:
--.SUFFIXES: .S .c .o .s
--$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4)
-- cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps src/hub/Makefile
--
-+.SUFFIXES: .c .o .obj
-+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
-+ @for dep in $?; do \
-+ case '$(am__configure_deps)' in \
-+ *$$dep*) \
-+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-+ && { if test -f $@; then exit 0; else break; fi; }; \
-+ exit 1;; \
-+ esac; \
-+ done; \
-+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/hub/Makefile'; \
-+ $(am__cd) $(top_srcdir) && \
-+ $(AUTOMAKE) --gnu src/hub/Makefile
-+.PRECIOUS: Makefile
- Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-- cd $(top_builddir) \
-- && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
--
--
--mostlyclean-noinstPROGRAMS:
-+ @case '$?' in \
-+ *config.status*) \
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-+ *) \
-+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-+ esac;
-+
-+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+
-+$(top_srcdir)/configure: $(am__configure_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(am__aclocal_m4_deps):
-
- clean-noinstPROGRAMS:
- -test -z "$(noinst_PROGRAMS)" || rm -f $(noinst_PROGRAMS)
--
--distclean-noinstPROGRAMS:
--
--maintainer-clean-noinstPROGRAMS:
--
--.c.o:
-- $(COMPILE) -c $<
--
--.s.o:
-- $(COMPILE) -c $<
--
--.S.o:
-- $(COMPILE) -c $<
-+analysis.test$(EXEEXT): $(analysis_test_OBJECTS) $(analysis_test_DEPENDENCIES)
-+ @rm -f analysis.test$(EXEEXT)
-+ $(LINK) $(analysis_test_OBJECTS) $(analysis_test_LDADD) $(LIBS)
-+bsam.test$(EXEEXT): $(bsam_test_OBJECTS) $(bsam_test_DEPENDENCIES)
-+ @rm -f bsam.test$(EXEEXT)
-+ $(LINK) $(bsam_test_OBJECTS) $(bsam_test_LDADD) $(LIBS)
-+gam.test$(EXEEXT): $(gam_test_OBJECTS) $(gam_test_DEPENDENCIES)
-+ @rm -f gam.test$(EXEEXT)
-+ $(LINK) $(gam_test_OBJECTS) $(gam_test_LDADD) $(LIBS)
-
- mostlyclean-compile:
-- -rm -f *.o core *.core
--
--clean-compile:
-+ -rm -f *.$(OBJEXT)
-
- distclean-compile:
- -rm -f *.tab.c
-
--maintainer-clean-compile:
--
--gam.test: $(gam_test_OBJECTS) $(gam_test_DEPENDENCIES)
-- @rm -f gam.test
-- $(LINK) $(gam_test_LDFLAGS) $(gam_test_OBJECTS) $(gam_test_LDADD) $(LIBS)
--
--analysis.test: $(analysis_test_OBJECTS) $(analysis_test_DEPENDENCIES)
-- @rm -f analysis.test
-- $(LINK) $(analysis_test_LDFLAGS) $(analysis_test_OBJECTS) $(analysis_test_LDADD) $(LIBS)
--
--bsam.test: $(bsam_test_OBJECTS) $(bsam_test_DEPENDENCIES)
-- @rm -f bsam.test
-- $(LINK) $(bsam_test_LDFLAGS) $(bsam_test_OBJECTS) $(bsam_test_LDADD) $(LIBS)
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/analysis.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/analysis.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/bsam.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/bsam.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gam.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gam.test.Po at am__quote@
-
-+.c.o:
-+ at am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
-+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-+ at am__fastdepCC_FALSE@ $(COMPILE) -c $<
-+
-+.c.obj:
-+ at am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
-+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-+ at am__fastdepCC_FALSE@ $(COMPILE) -c `$(CYGPATH_W) '$<'`
-+
-+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ mkid -fID $$unique
- tags: TAGS
-
--ID: $(HEADERS) $(SOURCES) $(LISP)
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- here=`pwd` && cd $(srcdir) \
-- && mkid -f$$here/ID $$unique $(LISP)
--
--TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) $(LISP)
-- tags=; \
-+TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ set x; \
- here=`pwd`; \
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- test -z "$(ETAGS_ARGS)$$unique$(LISP)$$tags" \
-- || (cd $(srcdir) && etags -o $$here/TAGS $(ETAGS_ARGS) $$tags $$unique $(LISP))
--
--mostlyclean-tags:
--
--clean-tags:
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ shift; \
-+ if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
-+ test -n "$$unique" || unique=$$empty_fix; \
-+ if test $$# -gt 0; then \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ "$$@" $$unique; \
-+ else \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ $$unique; \
-+ fi; \
-+ fi
-+ctags: CTAGS
-+CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ test -z "$(CTAGS_ARGS)$$unique" \
-+ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-+ $$unique
-+
-+GTAGS:
-+ here=`$(am__cd) $(top_builddir) && pwd` \
-+ && $(am__cd) $(top_srcdir) \
-+ && gtags -i $(GTAGS_ARGS) "$$here"
-
- distclean-tags:
-- -rm -f TAGS ID
--
--maintainer-clean-tags:
--
--distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
--
--subdir = src/hub
-+ -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-
--distdir: $(DISTFILES)
-- @for file in $(DISTFILES); do \
-- d=$(srcdir); \
-- if test -d $$d/$$file; then \
-- cp -pr $$d/$$file $(distdir)/$$file; \
-- else \
-- test -f $(distdir)/$$file \
-- || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
-- || cp -p $$d/$$file $(distdir)/$$file || :; \
-- fi; \
-- done
- check-TESTS: $(TESTS)
-- @failed=0; all=0; \
-+ @failed=0; all=0; xfail=0; xpass=0; skip=0; \
- srcdir=$(srcdir); export srcdir; \
-- for tst in $(TESTS); do \
-- if test -f $$tst; then dir=.; \
-- else dir="$(srcdir)"; fi; \
-- if $(TESTS_ENVIRONMENT) $$dir/$$tst; then \
-+ list=' $(TESTS) '; \
-+ $(am__tty_colors); \
-+ if test -n "$$list"; then \
-+ for tst in $$list; do \
-+ if test -f ./$$tst; then dir=./; \
-+ elif test -f $$tst; then dir=; \
-+ else dir="$(srcdir)/"; fi; \
-+ if $(TESTS_ENVIRONMENT) $${dir}$$tst; then \
- all=`expr $$all + 1`; \
-- echo "PASS: $$tst"; \
-+ case " $(XFAIL_TESTS) " in \
-+ *[\ \ ]$$tst[\ \ ]*) \
-+ xpass=`expr $$xpass + 1`; \
-+ failed=`expr $$failed + 1`; \
-+ col=$$red; res=XPASS; \
-+ ;; \
-+ *) \
-+ col=$$grn; res=PASS; \
-+ ;; \
-+ esac; \
- elif test $$? -ne 77; then \
- all=`expr $$all + 1`; \
-+ case " $(XFAIL_TESTS) " in \
-+ *[\ \ ]$$tst[\ \ ]*) \
-+ xfail=`expr $$xfail + 1`; \
-+ col=$$lgn; res=XFAIL; \
-+ ;; \
-+ *) \
- failed=`expr $$failed + 1`; \
-- echo "FAIL: $$tst"; \
-+ col=$$red; res=FAIL; \
-+ ;; \
-+ esac; \
-+ else \
-+ skip=`expr $$skip + 1`; \
-+ col=$$blu; res=SKIP; \
- fi; \
-+ echo "$${col}$$res$${std}: $$tst"; \
- done; \
-+ if test "$$all" -eq 1; then \
-+ tests="test"; \
-+ All=""; \
-+ else \
-+ tests="tests"; \
-+ All="All "; \
-+ fi; \
-+ if test "$$failed" -eq 0; then \
-+ if test "$$xfail" -eq 0; then \
-+ banner="$$All$$all $$tests passed"; \
-+ else \
-+ if test "$$xfail" -eq 1; then failures=failure; else failures=failures; fi; \
-+ banner="$$All$$all $$tests behaved as expected ($$xfail expected $$failures)"; \
-+ fi; \
-+ else \
-+ if test "$$xpass" -eq 0; then \
-+ banner="$$failed of $$all $$tests failed"; \
-+ else \
-+ if test "$$xpass" -eq 1; then passes=pass; else passes=passes; fi; \
-+ banner="$$failed of $$all $$tests did not behave as expected ($$xpass unexpected $$passes)"; \
-+ fi; \
-+ fi; \
-+ dashes="$$banner"; \
-+ skipped=""; \
-+ if test "$$skip" -ne 0; then \
-+ if test "$$skip" -eq 1; then \
-+ skipped="($$skip test was not run)"; \
-+ else \
-+ skipped="($$skip tests were not run)"; \
-+ fi; \
-+ test `echo "$$skipped" | wc -c` -le `echo "$$banner" | wc -c` || \
-+ dashes="$$skipped"; \
-+ fi; \
-+ report=""; \
-+ if test "$$failed" -ne 0 && test -n "$(PACKAGE_BUGREPORT)"; then \
-+ report="Please report to $(PACKAGE_BUGREPORT)"; \
-+ test `echo "$$report" | wc -c` -le `echo "$$banner" | wc -c` || \
-+ dashes="$$report"; \
-+ fi; \
-+ dashes=`echo "$$dashes" | sed s/./=/g`; \
- if test "$$failed" -eq 0; then \
-- banner="All $$all tests passed"; \
-+ echo "$$grn$$dashes"; \
- else \
-- banner="$$failed of $$all tests failed"; \
-+ echo "$$red$$dashes"; \
- fi; \
-- dashes=`echo "$$banner" | sed s/./=/g`; \
-- echo "$$dashes"; \
- echo "$$banner"; \
-- echo "$$dashes"; \
-- test "$$failed" -eq 0
--info-am:
--info: info-am
--dvi-am:
--dvi: dvi-am
-+ test -z "$$skipped" || echo "$$skipped"; \
-+ test -z "$$report" || echo "$$report"; \
-+ echo "$$dashes$$std"; \
-+ test "$$failed" -eq 0; \
-+ else :; fi
-+
-+distdir: $(DISTFILES)
-+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ list='$(DISTFILES)'; \
-+ dist_files=`for file in $$list; do echo $$file; done | \
-+ sed -e "s|^$$srcdirstrip/||;t" \
-+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-+ case $$dist_files in \
-+ */*) $(MKDIR_P) `echo "$$dist_files" | \
-+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-+ sort -u` ;; \
-+ esac; \
-+ for file in $$dist_files; do \
-+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
-+ if test -d $$d/$$file; then \
-+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-+ if test -d "$(distdir)/$$file"; then \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
-+ else \
-+ test -f "$(distdir)/$$file" \
-+ || cp -p $$d/$$file "$(distdir)/$$file" \
-+ || exit 1; \
-+ fi; \
-+ done
- check-am: all-am
- $(MAKE) $(AM_MAKEFLAGS) check-TESTS
- check: check-am
--installcheck-am:
--installcheck: installcheck-am
--install-exec-am:
-+all-am: Makefile $(PROGRAMS) $(HEADERS)
-+installdirs:
-+install: install-am
- install-exec: install-exec-am
--
--install-data-am:
- install-data: install-data-am
-+uninstall: uninstall-am
-
- install-am: all-am
- @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
--install: install-am
--uninstall-am:
--uninstall: uninstall-am
--all-am: Makefile $(PROGRAMS) $(HEADERS)
--all-redirect: all-am
--install-strip:
-- $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
--installdirs:
--
-
-+installcheck: installcheck-am
-+install-strip:
-+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-+ `test -z '$(STRIP)' || \
-+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
- mostlyclean-generic:
-
- clean-generic:
-
- distclean-generic:
-- -rm -f Makefile $(CONFIG_CLEAN_FILES)
-- -rm -f config.cache config.log stamp-h stamp-h[0-9]*
-+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
- maintainer-clean-generic:
-+ @echo "This command is intended for maintainers to use"
-+ @echo "it deletes files that may require special tools to rebuild."
- -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
--mostlyclean-am: mostlyclean-noinstPROGRAMS mostlyclean-compile \
-- mostlyclean-tags mostlyclean-generic
-+clean: clean-am
-
--mostlyclean: mostlyclean-am
-+clean-am: clean-generic clean-noinstPROGRAMS mostlyclean-am
-
--clean-am: clean-noinstPROGRAMS clean-compile clean-tags clean-generic \
-- mostlyclean-am
-+distclean: distclean-am
-+ -rm -rf ./$(DEPDIR)
-+ -rm -f Makefile
-+distclean-am: clean-am distclean-compile distclean-generic \
-+ distclean-tags
-
--clean: clean-am
-+dvi: dvi-am
-
--distclean-am: distclean-noinstPROGRAMS distclean-compile distclean-tags \
-- distclean-generic clean-am
-+dvi-am:
-
--distclean: distclean-am
-+html: html-am
-
--maintainer-clean-am: maintainer-clean-noinstPROGRAMS \
-- maintainer-clean-compile maintainer-clean-tags \
-- maintainer-clean-generic distclean-am
-- @echo "This command is intended for maintainers to use;"
-- @echo "it deletes files that may require special tools to rebuild."
-+html-am:
-+
-+info: info-am
-+
-+info-am:
-+
-+install-data-am:
-+
-+install-dvi: install-dvi-am
-+
-+install-dvi-am:
-+
-+install-exec-am:
-+
-+install-html: install-html-am
-+
-+install-html-am:
-+
-+install-info: install-info-am
-+
-+install-info-am:
-+
-+install-man:
-+
-+install-pdf: install-pdf-am
-+
-+install-pdf-am:
-+
-+install-ps: install-ps-am
-+
-+install-ps-am:
-+
-+installcheck-am:
-
- maintainer-clean: maintainer-clean-am
-+ -rm -rf ./$(DEPDIR)
-+ -rm -f Makefile
-+maintainer-clean-am: distclean-am maintainer-clean-generic
-+
-+mostlyclean: mostlyclean-am
-+
-+mostlyclean-am: mostlyclean-compile mostlyclean-generic
-+
-+pdf: pdf-am
-+
-+pdf-am:
-+
-+ps: ps-am
-+
-+ps-am:
-+
-+uninstall-am:
-+
-+.MAKE: check-am install-am install-strip
-
--.PHONY: mostlyclean-noinstPROGRAMS distclean-noinstPROGRAMS \
--clean-noinstPROGRAMS maintainer-clean-noinstPROGRAMS \
--mostlyclean-compile distclean-compile clean-compile \
--maintainer-clean-compile tags mostlyclean-tags distclean-tags \
--clean-tags maintainer-clean-tags distdir check-TESTS info-am info \
--dvi-am dvi check check-am installcheck-am installcheck install-exec-am \
--install-exec install-data-am install-data install-am install \
--uninstall-am uninstall all-redirect all-am all installdirs \
--mostlyclean-generic distclean-generic clean-generic \
--maintainer-clean-generic clean mostlyclean distclean maintainer-clean
-+.PHONY: CTAGS GTAGS all all-am check check-TESTS check-am clean \
-+ clean-generic clean-noinstPROGRAMS ctags distclean \
-+ distclean-compile distclean-generic distclean-tags distdir dvi \
-+ dvi-am html html-am info info-am install install-am \
-+ install-data install-data-am install-dvi install-dvi-am \
-+ install-exec install-exec-am install-html install-html-am \
-+ install-info install-info-am install-man install-pdf \
-+ install-pdf-am install-ps install-ps-am install-strip \
-+ installcheck installcheck-am installdirs maintainer-clean \
-+ maintainer-clean-generic mostlyclean mostlyclean-compile \
-+ mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
-+ uninstall-am
-
-
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -ubrN exonerate-2.2.0.orig/src/Makefile.in exonerate-2.2.0/src/Makefile.in
---- exonerate-2.2.0.orig/src/Makefile.in 2008-10-17 12:04:46.000000000 +0200
-+++ exonerate-2.2.0/src/Makefile.in 2011-12-12 13:33:16.000000000 +0100
-@@ -1,6 +1,9 @@
--# Makefile.in generated automatically by automake 1.4-p6 from Makefile.am
-+# Makefile.in generated by automake 1.11.1 from Makefile.am.
-+# @configure_input@
-
--# Copyright (C) 1994, 1995-8, 1999, 2001 Free Software Foundation, Inc.
-+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
-+# Inc.
- # This Makefile.in is free software; the Free Software Foundation
- # gives unlimited permission to copy and/or distribute it,
- # with or without modifications, as long as this notice is preserved.
-@@ -10,96 +13,218 @@
- # even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- # PARTICULAR PURPOSE.
-
--
--SHELL = @SHELL@
--
--srcdir = @srcdir@
--top_srcdir = @top_srcdir@
-+ at SET_MAKE@
- VPATH = @srcdir@
--prefix = @prefix@
--exec_prefix = @exec_prefix@
--
--bindir = @bindir@
--sbindir = @sbindir@
--libexecdir = @libexecdir@
--datadir = @datadir@
--sysconfdir = @sysconfdir@
--sharedstatedir = @sharedstatedir@
--localstatedir = @localstatedir@
--libdir = @libdir@
--infodir = @infodir@
--mandir = @mandir@
--includedir = @includedir@
--oldincludedir = /usr/include
--
--DESTDIR =
--
- pkgdatadir = $(datadir)/@PACKAGE@
--pkglibdir = $(libdir)/@PACKAGE@
- pkgincludedir = $(includedir)/@PACKAGE@
--
--top_builddir = ..
--
--ACLOCAL = @ACLOCAL@
--AUTOCONF = @AUTOCONF@
--AUTOMAKE = @AUTOMAKE@
--AUTOHEADER = @AUTOHEADER@
--
--INSTALL = @INSTALL@
--INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
--INSTALL_DATA = @INSTALL_DATA@
--INSTALL_SCRIPT = @INSTALL_SCRIPT@
--transform = @program_transform_name@
--
-+pkglibdir = $(libdir)/@PACKAGE@
-+pkglibexecdir = $(libexecdir)/@PACKAGE@
-+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-+install_sh_DATA = $(install_sh) -c -m 644
-+install_sh_PROGRAM = $(install_sh) -c
-+install_sh_SCRIPT = $(install_sh) -c
-+INSTALL_HEADER = $(INSTALL_DATA)
-+transform = $(program_transform_name)
- NORMAL_INSTALL = :
- PRE_INSTALL = :
- POST_INSTALL = :
- NORMAL_UNINSTALL = :
- PRE_UNINSTALL = :
- POST_UNINSTALL = :
--host_alias = @host_alias@
-+build_triplet = @build@
- host_triplet = @host@
-+subdir = src
-+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
-+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-+am__aclocal_m4_deps = $(top_srcdir)/configure.in
-+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-+ $(ACLOCAL_M4)
-+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
-+CONFIG_CLEAN_FILES =
-+CONFIG_CLEAN_VPATH_FILES =
-+SOURCES =
-+DIST_SOURCES =
-+RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
-+ html-recursive info-recursive install-data-recursive \
-+ install-dvi-recursive install-exec-recursive \
-+ install-html-recursive install-info-recursive \
-+ install-pdf-recursive install-ps-recursive install-recursive \
-+ installcheck-recursive installdirs-recursive pdf-recursive \
-+ ps-recursive uninstall-recursive
-+RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive \
-+ distclean-recursive maintainer-clean-recursive
-+AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
-+ $(RECURSIVE_CLEAN_TARGETS:-recursive=) tags TAGS ctags CTAGS \
-+ distdir
-+ETAGS = etags
-+CTAGS = ctags
-+DIST_SUBDIRS = $(SUBDIRS)
-+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-+am__relativize = \
-+ dir0=`pwd`; \
-+ sed_first='s,^\([^/]*\)/.*$$,\1,'; \
-+ sed_rest='s,^[^/]*/*,,'; \
-+ sed_last='s,^.*/\([^/]*\)$$,\1,'; \
-+ sed_butlast='s,/*[^/]*$$,,'; \
-+ while test -n "$$dir1"; do \
-+ first=`echo "$$dir1" | sed -e "$$sed_first"`; \
-+ if test "$$first" != "."; then \
-+ if test "$$first" = ".."; then \
-+ dir2=`echo "$$dir0" | sed -e "$$sed_last"`/"$$dir2"; \
-+ dir0=`echo "$$dir0" | sed -e "$$sed_butlast"`; \
-+ else \
-+ first2=`echo "$$dir2" | sed -e "$$sed_first"`; \
-+ if test "$$first2" = "$$first"; then \
-+ dir2=`echo "$$dir2" | sed -e "$$sed_rest"`; \
-+ else \
-+ dir2="../$$dir2"; \
-+ fi; \
-+ dir0="$$dir0"/"$$first"; \
-+ fi; \
-+ fi; \
-+ dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \
-+ done; \
-+ reldir="$$dir2"
-+ACLOCAL = @ACLOCAL@
-+AMTAR = @AMTAR@
-+AUTOCONF = @AUTOCONF@
-+AUTOHEADER = @AUTOHEADER@
-+AUTOMAKE = @AUTOMAKE@
-+AWK = @AWK@
- CC = @CC@
-+CCDEPMODE = @CCDEPMODE@
-+CFLAGS = @CFLAGS@
-+CPP = @CPP@
-+CPPFLAGS = @CPPFLAGS@
-+CYGPATH_W = @CYGPATH_W@
-+DEFS = @DEFS@
-+DEPDIR = @DEPDIR@
-+ECHO_C = @ECHO_C@
-+ECHO_N = @ECHO_N@
-+ECHO_T = @ECHO_T@
-+EGREP = @EGREP@
-+EXEEXT = @EXEEXT@
- GLIB_CONFIG = @GLIB_CONFIG@
--HAVE_LIB = @HAVE_LIB@
--LIB = @LIB@
--LTLIB = @LTLIB@
-+GREP = @GREP@
-+INSTALL = @INSTALL@
-+INSTALL_DATA = @INSTALL_DATA@
-+INSTALL_PROGRAM = @INSTALL_PROGRAM@
-+INSTALL_SCRIPT = @INSTALL_SCRIPT@
-+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-+LDFLAGS = @LDFLAGS@
-+LIBOBJS = @LIBOBJS@
-+LIBS = @LIBS@
-+LTLIBOBJS = @LTLIBOBJS@
- MAKEINFO = @MAKEINFO@
-+MKDIR_P = @MKDIR_P@
-+OBJEXT = @OBJEXT@
- PACKAGE = @PACKAGE@
-+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-+PACKAGE_NAME = @PACKAGE_NAME@
-+PACKAGE_STRING = @PACKAGE_STRING@
-+PACKAGE_TARNAME = @PACKAGE_TARNAME@
-+PACKAGE_URL = @PACKAGE_URL@
-+PACKAGE_VERSION = @PACKAGE_VERSION@
-+PATH_SEPARATOR = @PATH_SEPARATOR@
- PKG_CONFIG = @PKG_CONFIG@
-+SET_MAKE = @SET_MAKE@
-+SHELL = @SHELL@
-+STRIP = @STRIP@
- VERSION = @VERSION@
-+abs_builddir = @abs_builddir@
-+abs_srcdir = @abs_srcdir@
-+abs_top_builddir = @abs_top_builddir@
-+abs_top_srcdir = @abs_top_srcdir@
-+ac_ct_CC = @ac_ct_CC@
-+am__include = @am__include@
-+am__leading_dot = @am__leading_dot@
-+am__quote = @am__quote@
-+am__tar = @am__tar@
-+am__untar = @am__untar@
-+bindir = @bindir@
-+build = @build@
-+build_alias = @build_alias@
-+build_cpu = @build_cpu@
-+build_os = @build_os@
-+build_vendor = @build_vendor@
-+builddir = @builddir@
- codegen_extra_ldadd = @codegen_extra_ldadd@
- codegen_extra_sources = @codegen_extra_sources@
-+datadir = @datadir@
- datarootdir = @datarootdir@
-+docdir = @docdir@
-+dvidir = @dvidir@
-+exec_prefix = @exec_prefix@
- glib_cflags = @glib_cflags@
- glib_libs = @glib_libs@
- host = @host@
-+host_alias = @host_alias@
-+host_cpu = @host_cpu@
-+host_os = @host_os@
-+host_vendor = @host_vendor@
-+htmldir = @htmldir@
-+includedir = @includedir@
-+infodir = @infodir@
-+install_sh = @install_sh@
- installed_util_list = @installed_util_list@
-+libdir = @libdir@
-+libexecdir = @libexecdir@
-+localedir = @localedir@
-+localstatedir = @localstatedir@
-+mandir = @mandir@
-+mkdir_p = @mkdir_p@
-+oldincludedir = @oldincludedir@
-+pdfdir = @pdfdir@
-+prefix = @prefix@
-+program_transform_name = @program_transform_name@
-+psdir = @psdir@
-+sbindir = @sbindir@
-+sharedstatedir = @sharedstatedir@
- source_root_dir = @source_root_dir@
-+srcdir = @srcdir@
-+sysconfdir = @sysconfdir@
-+target_alias = @target_alias@
-+top_build_prefix = @top_build_prefix@
-+top_builddir = @top_builddir@
-+top_srcdir = @top_srcdir@
- use_pthreads = @use_pthreads@
--
--SUBDIRS = struct general sequence comparison database c4 bsdp sdp model hub program util
--
-+SUBDIRS = struct general sequence comparison database \
-+ c4 bsdp sdp model hub program util
-
- MAINTAINERCLEANFILES = Makefile.in
--mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
--CONFIG_CLEAN_FILES =
--DIST_COMMON = Makefile.am Makefile.in
--
-+all: all-recursive
-
--DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
--
--TAR = tar
--GZIP_ENV = --best
--all: all-redirect
- .SUFFIXES:
--$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4)
-- cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps src/Makefile
--
-+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
-+ @for dep in $?; do \
-+ case '$(am__configure_deps)' in \
-+ *$$dep*) \
-+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-+ && { if test -f $@; then exit 0; else break; fi; }; \
-+ exit 1;; \
-+ esac; \
-+ done; \
-+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/Makefile'; \
-+ $(am__cd) $(top_srcdir) && \
-+ $(AUTOMAKE) --gnu src/Makefile
-+.PRECIOUS: Makefile
- Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-- cd $(top_builddir) \
-- && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
--
-+ @case '$?' in \
-+ *config.status*) \
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-+ *) \
-+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-+ esac;
-+
-+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+
-+$(top_srcdir)/configure: $(am__configure_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(am__aclocal_m4_deps):
-
- # This directory's subdirectories are mostly independent; you can cd
- # into them and run `make' without going through this Makefile.
-@@ -107,13 +232,14 @@
- # (1) if the variable is set in `config.status', edit `config.status'
- # (which will cause the Makefiles to be regenerated when you run `make');
- # (2) otherwise, pass the desired values on the `make' command line.
--
-- at SET_MAKE@
--
--all-recursive install-data-recursive install-exec-recursive \
--installdirs-recursive install-recursive uninstall-recursive \
--check-recursive installcheck-recursive info-recursive dvi-recursive:
-- @set fnord $(MAKEFLAGS); amf=$$2; \
-+$(RECURSIVE_TARGETS):
-+ @fail= failcom='exit 1'; \
-+ for f in x $$MAKEFLAGS; do \
-+ case $$f in \
-+ *=* | --[!k]*);; \
-+ *k*) failcom='fail=yes';; \
-+ esac; \
-+ done; \
- dot_seen=no; \
- target=`echo $@ | sed s/-recursive//`; \
- list='$(SUBDIRS)'; for subdir in $$list; do \
-@@ -124,22 +250,32 @@
- else \
- local_target="$$target"; \
- fi; \
-- (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-- || case "$$amf" in *=*) exit 1;; *k*) fail=yes;; *) exit 1;; esac; \
-+ ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-+ || eval $$failcom; \
- done; \
- if test "$$dot_seen" = "no"; then \
- $(MAKE) $(AM_MAKEFLAGS) "$$target-am" || exit 1; \
- fi; test -z "$$fail"
-
--mostlyclean-recursive clean-recursive distclean-recursive \
--maintainer-clean-recursive:
-- @set fnord $(MAKEFLAGS); amf=$$2; \
-+$(RECURSIVE_CLEAN_TARGETS):
-+ @fail= failcom='exit 1'; \
-+ for f in x $$MAKEFLAGS; do \
-+ case $$f in \
-+ *=* | --[!k]*);; \
-+ *k*) failcom='fail=yes';; \
-+ esac; \
-+ done; \
- dot_seen=no; \
-- rev=''; list='$(SUBDIRS)'; for subdir in $$list; do \
-+ case "$@" in \
-+ distclean-* | maintainer-clean-*) list='$(DIST_SUBDIRS)' ;; \
-+ *) list='$(SUBDIRS)' ;; \
-+ esac; \
-+ rev=''; for subdir in $$list; do \
-+ if test "$$subdir" = "."; then :; else \
- rev="$$subdir $$rev"; \
-- test "$$subdir" != "." || dot_seen=yes; \
-+ fi; \
- done; \
-- test "$$dot_seen" = "no" && rev=". $$rev"; \
-+ rev="$$rev ."; \
- target=`echo $@ | sed s/-recursive//`; \
- for subdir in $$rev; do \
- echo "Making $$target in $$subdir"; \
-@@ -148,141 +284,253 @@
- else \
- local_target="$$target"; \
- fi; \
-- (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-- || case "$$amf" in *=*) exit 1;; *k*) fail=yes;; *) exit 1;; esac; \
-+ ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-+ || eval $$failcom; \
- done && test -z "$$fail"
- tags-recursive:
- list='$(SUBDIRS)'; for subdir in $$list; do \
-- test "$$subdir" = . || (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
-+ test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
-+ done
-+ctags-recursive:
-+ list='$(SUBDIRS)'; for subdir in $$list; do \
-+ test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \
- done
-
-+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ mkid -fID $$unique
- tags: TAGS
-
--ID: $(HEADERS) $(SOURCES) $(LISP)
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- here=`pwd` && cd $(srcdir) \
-- && mkid -f$$here/ID $$unique $(LISP)
--
--TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) $(LISP)
-- tags=; \
-+TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ set x; \
- here=`pwd`; \
-+ if ($(ETAGS) --etags-include --version) >/dev/null 2>&1; then \
-+ include_option=--etags-include; \
-+ empty_fix=.; \
-+ else \
-+ include_option=--include; \
-+ empty_fix=; \
-+ fi; \
- list='$(SUBDIRS)'; for subdir in $$list; do \
- if test "$$subdir" = .; then :; else \
-- test -f $$subdir/TAGS && tags="$$tags -i $$here/$$subdir/TAGS"; \
-+ test ! -f $$subdir/TAGS || \
-+ set "$$@" "$$include_option=$$here/$$subdir/TAGS"; \
- fi; \
- done; \
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- test -z "$(ETAGS_ARGS)$$unique$(LISP)$$tags" \
-- || (cd $(srcdir) && etags -o $$here/TAGS $(ETAGS_ARGS) $$tags $$unique $(LISP))
--
--mostlyclean-tags:
--
--clean-tags:
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ shift; \
-+ if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
-+ test -n "$$unique" || unique=$$empty_fix; \
-+ if test $$# -gt 0; then \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ "$$@" $$unique; \
-+ else \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ $$unique; \
-+ fi; \
-+ fi
-+ctags: CTAGS
-+CTAGS: ctags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ test -z "$(CTAGS_ARGS)$$unique" \
-+ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-+ $$unique
-+
-+GTAGS:
-+ here=`$(am__cd) $(top_builddir) && pwd` \
-+ && $(am__cd) $(top_srcdir) \
-+ && gtags -i $(GTAGS_ARGS) "$$here"
-
- distclean-tags:
-- -rm -f TAGS ID
--
--maintainer-clean-tags:
--
--distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
--
--subdir = src
-+ -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-
- distdir: $(DISTFILES)
-- @for file in $(DISTFILES); do \
-- d=$(srcdir); \
-+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ list='$(DISTFILES)'; \
-+ dist_files=`for file in $$list; do echo $$file; done | \
-+ sed -e "s|^$$srcdirstrip/||;t" \
-+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-+ case $$dist_files in \
-+ */*) $(MKDIR_P) `echo "$$dist_files" | \
-+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-+ sort -u` ;; \
-+ esac; \
-+ for file in $$dist_files; do \
-+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
- if test -d $$d/$$file; then \
-- cp -pr $$d/$$file $(distdir)/$$file; \
-+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-+ if test -d "$(distdir)/$$file"; then \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
- else \
-- test -f $(distdir)/$$file \
-- || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
-- || cp -p $$d/$$file $(distdir)/$$file || :; \
-+ test -f "$(distdir)/$$file" \
-+ || cp -p $$d/$$file "$(distdir)/$$file" \
-+ || exit 1; \
- fi; \
- done
-- for subdir in $(SUBDIRS); do \
-+ @list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
- if test "$$subdir" = .; then :; else \
-- test -d $(distdir)/$$subdir \
-- || mkdir $(distdir)/$$subdir \
-+ test -d "$(distdir)/$$subdir" \
-+ || $(MKDIR_P) "$(distdir)/$$subdir" \
- || exit 1; \
-- chmod 777 $(distdir)/$$subdir; \
-- (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir=../$(top_distdir) distdir=../$(distdir)/$$subdir distdir) \
-+ fi; \
-+ done
-+ @list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
-+ if test "$$subdir" = .; then :; else \
-+ dir1=$$subdir; dir2="$(distdir)/$$subdir"; \
-+ $(am__relativize); \
-+ new_distdir=$$reldir; \
-+ dir1=$$subdir; dir2="$(top_distdir)"; \
-+ $(am__relativize); \
-+ new_top_distdir=$$reldir; \
-+ echo " (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir="$$new_top_distdir" distdir="$$new_distdir" \\"; \
-+ echo " am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)"; \
-+ ($(am__cd) $$subdir && \
-+ $(MAKE) $(AM_MAKEFLAGS) \
-+ top_distdir="$$new_top_distdir" \
-+ distdir="$$new_distdir" \
-+ am__remove_distdir=: \
-+ am__skip_length_check=: \
-+ am__skip_mode_fix=: \
-+ distdir) \
- || exit 1; \
- fi; \
- done
--info-am:
--info: info-recursive
--dvi-am:
--dvi: dvi-recursive
- check-am: all-am
- check: check-recursive
--installcheck-am:
--installcheck: installcheck-recursive
--install-exec-am:
-+all-am: Makefile
-+installdirs: installdirs-recursive
-+installdirs-am:
-+install: install-recursive
- install-exec: install-exec-recursive
--
--install-data-am:
- install-data: install-data-recursive
-+uninstall: uninstall-recursive
-
- install-am: all-am
- @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
--install: install-recursive
--uninstall-am:
--uninstall: uninstall-recursive
--all-am: Makefile
--all-redirect: all-recursive
--install-strip:
-- $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
--installdirs: installdirs-recursive
--installdirs-am:
--
-
-+installcheck: installcheck-recursive
-+install-strip:
-+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-+ `test -z '$(STRIP)' || \
-+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
- mostlyclean-generic:
-
- clean-generic:
-
- distclean-generic:
-- -rm -f Makefile $(CONFIG_CLEAN_FILES)
-- -rm -f config.cache config.log stamp-h stamp-h[0-9]*
-+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
- maintainer-clean-generic:
-+ @echo "This command is intended for maintainers to use"
-+ @echo "it deletes files that may require special tools to rebuild."
- -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
--mostlyclean-am: mostlyclean-tags mostlyclean-generic
-+clean: clean-recursive
-
--mostlyclean: mostlyclean-recursive
-+clean-am: clean-generic mostlyclean-am
-
--clean-am: clean-tags clean-generic mostlyclean-am
-+distclean: distclean-recursive
-+ -rm -f Makefile
-+distclean-am: clean-am distclean-generic distclean-tags
-
--clean: clean-recursive
-+dvi: dvi-recursive
-
--distclean-am: distclean-tags distclean-generic clean-am
-+dvi-am:
-
--distclean: distclean-recursive
-+html: html-recursive
-
--maintainer-clean-am: maintainer-clean-tags maintainer-clean-generic \
-- distclean-am
-- @echo "This command is intended for maintainers to use;"
-- @echo "it deletes files that may require special tools to rebuild."
-+html-am:
-+
-+info: info-recursive
-+
-+info-am:
-+
-+install-data-am:
-+
-+install-dvi: install-dvi-recursive
-+
-+install-dvi-am:
-+
-+install-exec-am:
-+
-+install-html: install-html-recursive
-+
-+install-html-am:
-+
-+install-info: install-info-recursive
-+
-+install-info-am:
-+
-+install-man:
-+
-+install-pdf: install-pdf-recursive
-+
-+install-pdf-am:
-+
-+install-ps: install-ps-recursive
-+
-+install-ps-am:
-+
-+installcheck-am:
-
- maintainer-clean: maintainer-clean-recursive
-+ -rm -f Makefile
-+maintainer-clean-am: distclean-am maintainer-clean-generic
-+
-+mostlyclean: mostlyclean-recursive
-+
-+mostlyclean-am: mostlyclean-generic
-+
-+pdf: pdf-recursive
-+
-+pdf-am:
-+
-+ps: ps-recursive
-+
-+ps-am:
-+
-+uninstall-am:
-+
-+.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) ctags-recursive \
-+ install-am install-strip tags-recursive
-
--.PHONY: install-data-recursive uninstall-data-recursive \
--install-exec-recursive uninstall-exec-recursive installdirs-recursive \
--uninstalldirs-recursive all-recursive check-recursive \
--installcheck-recursive info-recursive dvi-recursive \
--mostlyclean-recursive distclean-recursive clean-recursive \
--maintainer-clean-recursive tags tags-recursive mostlyclean-tags \
--distclean-tags clean-tags maintainer-clean-tags distdir info-am info \
--dvi-am dvi check check-am installcheck-am installcheck install-exec-am \
--install-exec install-data-am install-data install-am install \
--uninstall-am uninstall all-redirect all-am all installdirs-am \
--installdirs mostlyclean-generic distclean-generic clean-generic \
--maintainer-clean-generic clean mostlyclean distclean maintainer-clean
-+.PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
-+ all all-am check check-am clean clean-generic ctags \
-+ ctags-recursive distclean distclean-generic distclean-tags \
-+ distdir dvi dvi-am html html-am info info-am install \
-+ install-am install-data install-data-am install-dvi \
-+ install-dvi-am install-exec install-exec-am install-html \
-+ install-html-am install-info install-info-am install-man \
-+ install-pdf install-pdf-am install-ps install-ps-am \
-+ install-strip installcheck installcheck-am installdirs \
-+ installdirs-am maintainer-clean maintainer-clean-generic \
-+ mostlyclean mostlyclean-generic pdf pdf-am ps ps-am tags \
-+ tags-recursive uninstall uninstall-am
-
-
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -ubrN exonerate-2.2.0.orig/src/model/Makefile.in exonerate-2.2.0/src/model/Makefile.in
---- exonerate-2.2.0.orig/src/model/Makefile.in 2008-10-17 12:04:37.000000000 +0200
-+++ exonerate-2.2.0/src/model/Makefile.in 2011-12-12 13:33:17.000000000 +0100
-@@ -1,6 +1,9 @@
--# Makefile.in generated automatically by automake 1.4-p6 from Makefile.am
-+# Makefile.in generated by automake 1.11.1 from Makefile.am.
-+# @configure_input@
-
--# Copyright (C) 1994, 1995-8, 1999, 2001 Free Software Foundation, Inc.
-+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
-+# Inc.
- # This Makefile.in is free software; the Free Software Foundation
- # gives unlimited permission to copy and/or distribute it,
- # with or without modifications, as long as this notice is preserved.
-@@ -10,749 +13,852 @@
- # even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- # PARTICULAR PURPOSE.
-
-+ at SET_MAKE@
-
--SHELL = @SHELL@
-
--srcdir = @srcdir@
--top_srcdir = @top_srcdir@
- VPATH = @srcdir@
--prefix = @prefix@
--exec_prefix = @exec_prefix@
--
--bindir = @bindir@
--sbindir = @sbindir@
--libexecdir = @libexecdir@
--datadir = @datadir@
--sysconfdir = @sysconfdir@
--sharedstatedir = @sharedstatedir@
--localstatedir = @localstatedir@
--libdir = @libdir@
--infodir = @infodir@
--mandir = @mandir@
--includedir = @includedir@
--oldincludedir = /usr/include
--
--DESTDIR =
--
- pkgdatadir = $(datadir)/@PACKAGE@
--pkglibdir = $(libdir)/@PACKAGE@
- pkgincludedir = $(includedir)/@PACKAGE@
--
--top_builddir = ../..
--
--ACLOCAL = @ACLOCAL@
--AUTOCONF = @AUTOCONF@
--AUTOMAKE = @AUTOMAKE@
--AUTOHEADER = @AUTOHEADER@
--
--INSTALL = @INSTALL@
--INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
--INSTALL_DATA = @INSTALL_DATA@
--INSTALL_SCRIPT = @INSTALL_SCRIPT@
--transform = @program_transform_name@
--
-+pkglibdir = $(libdir)/@PACKAGE@
-+pkglibexecdir = $(libexecdir)/@PACKAGE@
-+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-+install_sh_DATA = $(install_sh) -c -m 644
-+install_sh_PROGRAM = $(install_sh) -c
-+install_sh_SCRIPT = $(install_sh) -c
-+INSTALL_HEADER = $(INSTALL_DATA)
-+transform = $(program_transform_name)
- NORMAL_INSTALL = :
- PRE_INSTALL = :
- POST_INSTALL = :
- NORMAL_UNINSTALL = :
- PRE_UNINSTALL = :
- POST_UNINSTALL = :
--host_alias = @host_alias@
-+build_triplet = @build@
- host_triplet = @host@
-+TESTS = edit_distance.test$(EXEEXT) affine.test$(EXEEXT) \
-+ protein2dna.test$(EXEEXT) ner.test$(EXEEXT) \
-+ est2genome.test$(EXEEXT) ungapped.test$(EXEEXT) \
-+ intron.test$(EXEEXT) protein2genome.test$(EXEEXT) \
-+ coding2coding.test$(EXEEXT) frameshift.test$(EXEEXT) \
-+ coding2genome.test$(EXEEXT) cdna2genome.test$(EXEEXT) \
-+ genome2genome.test$(EXEEXT) phase.test$(EXEEXT) \
-+ modeltype.test$(EXEEXT)
-+noinst_PROGRAMS = $(am__EXEEXT_1) bootstrapper$(EXEEXT)
-+subdir = src/model
-+DIST_COMMON = $(noinst_HEADERS) $(srcdir)/Makefile.am \
-+ $(srcdir)/Makefile.in
-+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-+am__aclocal_m4_deps = $(top_srcdir)/configure.in
-+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-+ $(ACLOCAL_M4)
-+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
-+CONFIG_CLEAN_FILES =
-+CONFIG_CLEAN_VPATH_FILES =
-+am__EXEEXT_1 = edit_distance.test$(EXEEXT) affine.test$(EXEEXT) \
-+ protein2dna.test$(EXEEXT) ner.test$(EXEEXT) \
-+ est2genome.test$(EXEEXT) ungapped.test$(EXEEXT) \
-+ intron.test$(EXEEXT) protein2genome.test$(EXEEXT) \
-+ coding2coding.test$(EXEEXT) frameshift.test$(EXEEXT) \
-+ coding2genome.test$(EXEEXT) cdna2genome.test$(EXEEXT) \
-+ genome2genome.test$(EXEEXT) phase.test$(EXEEXT) \
-+ modeltype.test$(EXEEXT)
-+PROGRAMS = $(noinst_PROGRAMS)
-+am_affine_test_OBJECTS = affine.test.$(OBJEXT) affine.$(OBJEXT) \
-+ ungapped.$(OBJEXT)
-+affine_test_OBJECTS = $(am_affine_test_OBJECTS)
-+am__DEPENDENCIES_1 = $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o \
-+ $(top_srcdir)/src/sequence/sequence.o \
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/lineparse.o
-+am__DEPENDENCIES_2 = $(top_srcdir)/src/comparison/match.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o \
-+ $(top_srcdir)/src/sequence/submat.o $(am__DEPENDENCIES_1)
-+am__DEPENDENCIES_3 = $(top_srcdir)/src/struct/slist.o \
-+ $(top_srcdir)/src/struct/rangetree.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/c4/optimal.o $(top_srcdir)/src/c4/viterbi.o \
-+ $(top_srcdir)/src/c4/layout.o $(top_srcdir)/src/c4/codegen.o \
-+ $(top_srcdir)/src/c4/cgutil.o $(top_srcdir)/src/c4/alignment.o \
-+ $(top_srcdir)/src/c4/region.o $(top_srcdir)/src/c4/c4.o \
-+ $(top_srcdir)/src/c4/subopt.o $(am__DEPENDENCIES_2)
-+affine_test_DEPENDENCIES = $(am__DEPENDENCIES_3)
-+am_bootstrapper_OBJECTS = bootstrapper.$(OBJEXT) modeltype.$(OBJEXT) \
-+ ungapped.$(OBJEXT) affine.$(OBJEXT) est2genome.$(OBJEXT) \
-+ ner.$(OBJEXT) protein2dna.$(OBJEXT) protein2genome.$(OBJEXT) \
-+ coding2coding.$(OBJEXT) coding2genome.$(OBJEXT) \
-+ genome2genome.$(OBJEXT) cdna2genome.$(OBJEXT) \
-+ frameshift.$(OBJEXT) intron.$(OBJEXT) phase.$(OBJEXT)
-+bootstrapper_OBJECTS = $(am_bootstrapper_OBJECTS)
-+bootstrapper_DEPENDENCIES = $(top_srcdir)/src/struct/pqueue.o \
-+ $(top_srcdir)/src/comparison/comparison.o \
-+ $(top_srcdir)/src/comparison/hspset.o \
-+ $(top_srcdir)/src/comparison/wordhood.o \
-+ $(top_srcdir)/src/bsdp/heuristic.o $(top_srcdir)/src/sdp/sdp.o \
-+ $(top_srcdir)/src/sdp/scheduler.o \
-+ $(top_srcdir)/src/sdp/straceback.o \
-+ $(top_srcdir)/src/sdp/lookahead.o \
-+ $(top_srcdir)/src/sdp/boundary.o $(am__DEPENDENCIES_3)
-+am_cdna2genome_test_OBJECTS = cdna2genome.test.$(OBJEXT) \
-+ cdna2genome.$(OBJEXT) affine.$(OBJEXT) ungapped.$(OBJEXT) \
-+ frameshift.$(OBJEXT) intron.$(OBJEXT) phase.$(OBJEXT) \
-+ coding2coding.$(OBJEXT) coding2genome.$(OBJEXT) \
-+ est2genome.$(OBJEXT)
-+cdna2genome_test_OBJECTS = $(am_cdna2genome_test_OBJECTS)
-+cdna2genome_test_DEPENDENCIES = $(am__DEPENDENCIES_3)
-+am_coding2coding_test_OBJECTS = coding2coding.test.$(OBJEXT) \
-+ coding2coding.$(OBJEXT) affine.$(OBJEXT) ungapped.$(OBJEXT) \
-+ frameshift.$(OBJEXT)
-+coding2coding_test_OBJECTS = $(am_coding2coding_test_OBJECTS)
-+coding2coding_test_DEPENDENCIES = $(am__DEPENDENCIES_3)
-+am_coding2genome_test_OBJECTS = coding2genome.test.$(OBJEXT) \
-+ coding2genome.$(OBJEXT) coding2coding.$(OBJEXT) \
-+ affine.$(OBJEXT) ungapped.$(OBJEXT) frameshift.$(OBJEXT) \
-+ intron.$(OBJEXT) phase.$(OBJEXT)
-+coding2genome_test_OBJECTS = $(am_coding2genome_test_OBJECTS)
-+coding2genome_test_DEPENDENCIES = $(am__DEPENDENCIES_3)
-+am_edit_distance_test_OBJECTS = edit_distance.test.$(OBJEXT) \
-+ edit_distance.$(OBJEXT)
-+edit_distance_test_OBJECTS = $(am_edit_distance_test_OBJECTS)
-+edit_distance_test_DEPENDENCIES = $(am__DEPENDENCIES_3)
-+am_est2genome_test_OBJECTS = est2genome.test.$(OBJEXT) \
-+ est2genome.$(OBJEXT) affine.$(OBJEXT) ungapped.$(OBJEXT) \
-+ intron.$(OBJEXT)
-+est2genome_test_OBJECTS = $(am_est2genome_test_OBJECTS)
-+est2genome_test_DEPENDENCIES = $(am__DEPENDENCIES_3)
-+am_frameshift_test_OBJECTS = frameshift.test.$(OBJEXT) \
-+ frameshift.$(OBJEXT)
-+frameshift_test_OBJECTS = $(am_frameshift_test_OBJECTS)
-+frameshift_test_DEPENDENCIES = $(am__DEPENDENCIES_3)
-+am_genome2genome_test_OBJECTS = genome2genome.test.$(OBJEXT) \
-+ genome2genome.$(OBJEXT) coding2coding.$(OBJEXT) \
-+ affine.$(OBJEXT) ungapped.$(OBJEXT) frameshift.$(OBJEXT) \
-+ intron.$(OBJEXT) phase.$(OBJEXT) coding2genome.$(OBJEXT) \
-+ cdna2genome.$(OBJEXT) est2genome.$(OBJEXT)
-+genome2genome_test_OBJECTS = $(am_genome2genome_test_OBJECTS)
-+genome2genome_test_DEPENDENCIES = $(am__DEPENDENCIES_3)
-+am_intron_test_OBJECTS = intron.test.$(OBJEXT) intron.$(OBJEXT)
-+intron_test_OBJECTS = $(am_intron_test_OBJECTS)
-+intron_test_DEPENDENCIES = $(am__DEPENDENCIES_3)
-+am_modeltype_test_OBJECTS = modeltype.test.$(OBJEXT) \
-+ modeltype.$(OBJEXT) ungapped.$(OBJEXT) affine.$(OBJEXT) \
-+ est2genome.$(OBJEXT) ner.$(OBJEXT) protein2dna.$(OBJEXT) \
-+ protein2genome.$(OBJEXT) coding2coding.$(OBJEXT) \
-+ coding2genome.$(OBJEXT) genome2genome.$(OBJEXT) \
-+ cdna2genome.$(OBJEXT) frameshift.$(OBJEXT) phase.$(OBJEXT) \
-+ intron.$(OBJEXT)
-+modeltype_test_OBJECTS = $(am_modeltype_test_OBJECTS)
-+modeltype_test_DEPENDENCIES = $(am__DEPENDENCIES_3)
-+am_ner_test_OBJECTS = ner.test.$(OBJEXT) ner.$(OBJEXT) \
-+ affine.$(OBJEXT) ungapped.$(OBJEXT)
-+ner_test_OBJECTS = $(am_ner_test_OBJECTS)
-+ner_test_DEPENDENCIES = $(am__DEPENDENCIES_3)
-+am_phase_test_OBJECTS = phase.test.$(OBJEXT) phase.$(OBJEXT) \
-+ intron.$(OBJEXT)
-+phase_test_OBJECTS = $(am_phase_test_OBJECTS)
-+phase_test_DEPENDENCIES = $(am__DEPENDENCIES_3)
-+am_protein2dna_test_OBJECTS = protein2dna.test.$(OBJEXT) \
-+ protein2dna.$(OBJEXT) affine.$(OBJEXT) ungapped.$(OBJEXT) \
-+ frameshift.$(OBJEXT)
-+protein2dna_test_OBJECTS = $(am_protein2dna_test_OBJECTS)
-+protein2dna_test_DEPENDENCIES = $(am__DEPENDENCIES_3)
-+am_protein2genome_test_OBJECTS = protein2genome.test.$(OBJEXT) \
-+ protein2genome.$(OBJEXT) protein2dna.$(OBJEXT) \
-+ ungapped.$(OBJEXT) intron.$(OBJEXT) affine.$(OBJEXT) \
-+ frameshift.$(OBJEXT) phase.$(OBJEXT)
-+protein2genome_test_OBJECTS = $(am_protein2genome_test_OBJECTS)
-+protein2genome_test_DEPENDENCIES = $(am__DEPENDENCIES_3)
-+am_ungapped_test_OBJECTS = ungapped.test.$(OBJEXT) ungapped.$(OBJEXT)
-+ungapped_test_OBJECTS = $(am_ungapped_test_OBJECTS)
-+ungapped_test_DEPENDENCIES = $(am__DEPENDENCIES_3)
-+DEFAULT_INCLUDES = -I. at am__isrc@
-+depcomp = $(SHELL) $(top_srcdir)/depcomp
-+am__depfiles_maybe = depfiles
-+am__mv = mv -f
-+COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
-+ $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
-+CCLD = $(CC)
-+LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
-+SOURCES = $(affine_test_SOURCES) $(bootstrapper_SOURCES) \
-+ $(cdna2genome_test_SOURCES) $(coding2coding_test_SOURCES) \
-+ $(coding2genome_test_SOURCES) $(edit_distance_test_SOURCES) \
-+ $(est2genome_test_SOURCES) $(frameshift_test_SOURCES) \
-+ $(genome2genome_test_SOURCES) $(intron_test_SOURCES) \
-+ $(modeltype_test_SOURCES) $(ner_test_SOURCES) \
-+ $(phase_test_SOURCES) $(protein2dna_test_SOURCES) \
-+ $(protein2genome_test_SOURCES) $(ungapped_test_SOURCES)
-+DIST_SOURCES = $(affine_test_SOURCES) $(bootstrapper_SOURCES) \
-+ $(cdna2genome_test_SOURCES) $(coding2coding_test_SOURCES) \
-+ $(coding2genome_test_SOURCES) $(edit_distance_test_SOURCES) \
-+ $(est2genome_test_SOURCES) $(frameshift_test_SOURCES) \
-+ $(genome2genome_test_SOURCES) $(intron_test_SOURCES) \
-+ $(modeltype_test_SOURCES) $(ner_test_SOURCES) \
-+ $(phase_test_SOURCES) $(protein2dna_test_SOURCES) \
-+ $(protein2genome_test_SOURCES) $(ungapped_test_SOURCES)
-+HEADERS = $(noinst_HEADERS)
-+ETAGS = etags
-+CTAGS = ctags
-+am__tty_colors = \
-+red=; grn=; lgn=; blu=; std=
-+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-+ACLOCAL = @ACLOCAL@
-+AMTAR = @AMTAR@
-+AUTOCONF = @AUTOCONF@
-+AUTOHEADER = @AUTOHEADER@
-+AUTOMAKE = @AUTOMAKE@
-+AWK = @AWK@
- CC = @CC@
-+CCDEPMODE = @CCDEPMODE@
-+CFLAGS = @CFLAGS@
-+CPP = @CPP@
-+CPPFLAGS = @CPPFLAGS@
-+CYGPATH_W = @CYGPATH_W@
-+DEFS = @DEFS@
-+DEPDIR = @DEPDIR@
-+ECHO_C = @ECHO_C@
-+ECHO_N = @ECHO_N@
-+ECHO_T = @ECHO_T@
-+EGREP = @EGREP@
-+EXEEXT = @EXEEXT@
- GLIB_CONFIG = @GLIB_CONFIG@
--HAVE_LIB = @HAVE_LIB@
--LIB = @LIB@
--LTLIB = @LTLIB@
-+GREP = @GREP@
-+INSTALL = @INSTALL@
-+INSTALL_DATA = @INSTALL_DATA@
-+INSTALL_PROGRAM = @INSTALL_PROGRAM@
-+INSTALL_SCRIPT = @INSTALL_SCRIPT@
-+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-+LDFLAGS = @LDFLAGS@
-+LIBOBJS = @LIBOBJS@
-+LIBS = @LIBS@
-+LTLIBOBJS = @LTLIBOBJS@
- MAKEINFO = @MAKEINFO@
-+MKDIR_P = @MKDIR_P@
-+OBJEXT = @OBJEXT@
- PACKAGE = @PACKAGE@
-+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-+PACKAGE_NAME = @PACKAGE_NAME@
-+PACKAGE_STRING = @PACKAGE_STRING@
-+PACKAGE_TARNAME = @PACKAGE_TARNAME@
-+PACKAGE_URL = @PACKAGE_URL@
-+PACKAGE_VERSION = @PACKAGE_VERSION@
-+PATH_SEPARATOR = @PATH_SEPARATOR@
- PKG_CONFIG = @PKG_CONFIG@
-+SET_MAKE = @SET_MAKE@
-+SHELL = @SHELL@
-+STRIP = @STRIP@
- VERSION = @VERSION@
-+abs_builddir = @abs_builddir@
-+abs_srcdir = @abs_srcdir@
-+abs_top_builddir = @abs_top_builddir@
-+abs_top_srcdir = @abs_top_srcdir@
-+ac_ct_CC = @ac_ct_CC@
-+am__include = @am__include@
-+am__leading_dot = @am__leading_dot@
-+am__quote = @am__quote@
-+am__tar = @am__tar@
-+am__untar = @am__untar@
-+bindir = @bindir@
-+build = @build@
-+build_alias = @build_alias@
-+build_cpu = @build_cpu@
-+build_os = @build_os@
-+build_vendor = @build_vendor@
-+builddir = @builddir@
- codegen_extra_ldadd = @codegen_extra_ldadd@
- codegen_extra_sources = @codegen_extra_sources@
-+datadir = @datadir@
- datarootdir = @datarootdir@
-+docdir = @docdir@
-+dvidir = @dvidir@
-+exec_prefix = @exec_prefix@
- glib_cflags = @glib_cflags@
- glib_libs = @glib_libs@
- host = @host@
-+host_alias = @host_alias@
-+host_cpu = @host_cpu@
-+host_os = @host_os@
-+host_vendor = @host_vendor@
-+htmldir = @htmldir@
-+includedir = @includedir@
-+infodir = @infodir@
-+install_sh = @install_sh@
- installed_util_list = @installed_util_list@
-+libdir = @libdir@
-+libexecdir = @libexecdir@
-+localedir = @localedir@
-+localstatedir = @localstatedir@
-+mandir = @mandir@
-+mkdir_p = @mkdir_p@
-+oldincludedir = @oldincludedir@
-+pdfdir = @pdfdir@
-+prefix = @prefix@
-+program_transform_name = @program_transform_name@
-+psdir = @psdir@
-+sbindir = @sbindir@
-+sharedstatedir = @sharedstatedir@
- source_root_dir = @source_root_dir@
-+srcdir = @srcdir@
-+sysconfdir = @sysconfdir@
-+target_alias = @target_alias@
-+top_build_prefix = @top_build_prefix@
-+top_builddir = @top_builddir@
-+top_srcdir = @top_srcdir@
- use_pthreads = @use_pthreads@
--
--TESTS = edit_distance.test affine.test protein2dna.test ner.test est2genome.test ungapped.test intron.test protein2genome.test coding2coding.test frameshift.test coding2genome.test cdna2genome.test genome2genome.test phase.test modeltype.test
--
--
--noinst_PROGRAMS = $(TESTS) bootstrapper
--
--INCLUDES = -I$(top_srcdir)/src/c4 -I$(top_srcdir)/src/bsdp -I$(top_srcdir)/src/sdp -I$(top_srcdir)/src/sequence -I$(top_srcdir)/src/general -I$(top_srcdir)/src/comparison -I$(top_srcdir)/src/struct -DSOURCE_ROOT_DIR="\"@source_root_dir@\"" -DGLIB_CFLAGS="\"@glib_cflags@\""
--
--
--SEQUENCE_OBJ = $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o $(top_srcdir)/src/sequence/alphabet.o $(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/sequence/translate.o $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/general/lineparse.o -lm
--
--
--ALIGNMENT_OBJ = $(top_srcdir)/src/comparison/match.o $(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/sequence/submat.o $(SEQUENCE_OBJ)
--
--
--C4_OBJECTS = $(top_srcdir)/src/struct/slist.o $(top_srcdir)/src/struct/rangetree.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/c4/optimal.o $(top_srcdir)/src/c4/viterbi.o $(top_srcdir)/src/c4/layout.o $(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/cgutil.o $(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/region.o $(top_srcdir)/src/c4/c4.o $(top_srcdir)/src/c4/subopt.o $(ALIGNMENT_OBJ)
-+INCLUDES = -I$(top_srcdir)/src/c4 \
-+ -I$(top_srcdir)/src/bsdp \
-+ -I$(top_srcdir)/src/sdp \
-+ -I$(top_srcdir)/src/sequence \
-+ -I$(top_srcdir)/src/general \
-+ -I$(top_srcdir)/src/comparison \
-+ -I$(top_srcdir)/src/struct \
-+ -DSOURCE_ROOT_DIR="\"@source_root_dir@\"" \
-+ -DGLIB_CFLAGS="\"@glib_cflags@\""
-+
-+SEQUENCE_OBJ = $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o \
-+ $(top_srcdir)/src/sequence/sequence.o \
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ -lm
-+
-+ALIGNMENT_OBJ = $(top_srcdir)/src/comparison/match.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o \
-+ $(top_srcdir)/src/sequence/submat.o \
-+ $(SEQUENCE_OBJ)
-+
-+C4_OBJECTS = $(top_srcdir)/src/struct/slist.o \
-+ $(top_srcdir)/src/struct/rangetree.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/c4/optimal.o \
-+ $(top_srcdir)/src/c4/viterbi.o \
-+ $(top_srcdir)/src/c4/layout.o \
-+ $(top_srcdir)/src/c4/codegen.o \
-+ $(top_srcdir)/src/c4/cgutil.o \
-+ $(top_srcdir)/src/c4/alignment.o \
-+ $(top_srcdir)/src/c4/region.o \
-+ $(top_srcdir)/src/c4/c4.o \
-+ $(top_srcdir)/src/c4/subopt.o \
-+ $(ALIGNMENT_OBJ)
-
-
- # -lm should be at end of argument list for IRIX
--
--noinst_HEADERS = edit_distance.h affine.h protein2dna.h ner.h est2genome.h ungapped.h intron.h protein2genome.h coding2coding.h frameshift.h coding2genome.h genome2genome.h cdna2genome.h phase.h modeltype.h
--
--
--bootstrapper_SOURCES = bootstrapper.c modeltype.c ungapped.c affine.c est2genome.c ner.c protein2dna.c protein2genome.c coding2coding.c coding2genome.c genome2genome.c cdna2genome.c frameshift.c intron.c phase.c
--
--bootstrapper_LDADD = $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/comparison/comparison.o $(top_srcdir)/src/comparison/hspset.o $(top_srcdir)/src/comparison/wordhood.o $(top_srcdir)/src/bsdp/heuristic.o $(top_srcdir)/src/sdp/sdp.o $(top_srcdir)/src/sdp/scheduler.o $(top_srcdir)/src/sdp/straceback.o $(top_srcdir)/src/sdp/lookahead.o $(top_srcdir)/src/sdp/boundary.o $(C4_OBJECTS)
--
-+noinst_HEADERS = edit_distance.h affine.h protein2dna.h \
-+ ner.h est2genome.h ungapped.h intron.h \
-+ protein2genome.h coding2coding.h frameshift.h \
-+ coding2genome.h genome2genome.h cdna2genome.h \
-+ phase.h modeltype.h
-+
-+bootstrapper_SOURCES = bootstrapper.c modeltype.c \
-+ ungapped.c affine.c est2genome.c ner.c \
-+ protein2dna.c protein2genome.c coding2coding.c \
-+ coding2genome.c genome2genome.c cdna2genome.c \
-+ frameshift.c intron.c phase.c
-+
-+bootstrapper_LDADD = $(top_srcdir)/src/struct/pqueue.o \
-+ $(top_srcdir)/src/comparison/comparison.o \
-+ $(top_srcdir)/src/comparison/hspset.o \
-+ $(top_srcdir)/src/comparison/wordhood.o \
-+ $(top_srcdir)/src/bsdp/heuristic.o \
-+ $(top_srcdir)/src/sdp/sdp.o \
-+ $(top_srcdir)/src/sdp/scheduler.o \
-+ $(top_srcdir)/src/sdp/straceback.o \
-+ $(top_srcdir)/src/sdp/lookahead.o \
-+ $(top_srcdir)/src/sdp/boundary.o \
-+ $(C4_OBJECTS)
-
- edit_distance_test_SOURCES = edit_distance.test.c edit_distance.c
- edit_distance_test_LDADD = $(C4_OBJECTS)
--
- affine_test_SOURCES = affine.test.c affine.c ungapped.c
- affine_test_LDADD = $(C4_OBJECTS)
--
--protein2dna_test_SOURCES = protein2dna.test.c protein2dna.c affine.c ungapped.c frameshift.c
-+protein2dna_test_SOURCES = protein2dna.test.c protein2dna.c \
-+ affine.c ungapped.c frameshift.c
-
- protein2dna_test_LDADD = $(C4_OBJECTS)
--
- ner_test_SOURCES = ner.test.c ner.c affine.c ungapped.c
- ner_test_LDADD = $(C4_OBJECTS)
--
--est2genome_test_SOURCES = est2genome.test.c est2genome.c affine.c ungapped.c intron.c
-+est2genome_test_SOURCES = est2genome.test.c est2genome.c \
-+ affine.c ungapped.c intron.c
-
- est2genome_test_LDADD = $(C4_OBJECTS)
--
- ungapped_test_SOURCES = ungapped.test.c ungapped.c
- ungapped_test_LDADD = $(C4_OBJECTS)
--
- intron_test_SOURCES = intron.test.c intron.c
- intron_test_LDADD = $(C4_OBJECTS)
--
--protein2genome_test_SOURCES = protein2genome.test.c protein2genome.c protein2dna.c ungapped.c intron.c affine.c frameshift.c phase.c
-+protein2genome_test_SOURCES = protein2genome.test.c protein2genome.c \
-+ protein2dna.c ungapped.c intron.c \
-+ affine.c frameshift.c phase.c
-
- protein2genome_test_LDADD = $(C4_OBJECTS)
--
--coding2coding_test_SOURCES = coding2coding.test.c coding2coding.c affine.c ungapped.c frameshift.c
-+coding2coding_test_SOURCES = coding2coding.test.c coding2coding.c \
-+ affine.c ungapped.c frameshift.c
-
- coding2coding_test_LDADD = $(C4_OBJECTS)
--
- frameshift_test_SOURCES = frameshift.test.c frameshift.c
- frameshift_test_LDADD = $(C4_OBJECTS)
--
--coding2genome_test_SOURCES = coding2genome.test.c coding2genome.c coding2coding.c affine.c ungapped.c frameshift.c intron.c phase.c
-+coding2genome_test_SOURCES = coding2genome.test.c coding2genome.c \
-+ coding2coding.c affine.c ungapped.c \
-+ frameshift.c intron.c phase.c
-
- coding2genome_test_LDADD = $(C4_OBJECTS)
--
--cdna2genome_test_SOURCES = cdna2genome.test.c cdna2genome.c affine.c ungapped.c frameshift.c intron.c phase.c coding2coding.c coding2genome.c est2genome.c
-+cdna2genome_test_SOURCES = cdna2genome.test.c cdna2genome.c \
-+ affine.c ungapped.c \
-+ frameshift.c intron.c phase.c \
-+ coding2coding.c coding2genome.c \
-+ est2genome.c
-
- cdna2genome_test_LDADD = $(C4_OBJECTS)
--
--genome2genome_test_SOURCES = genome2genome.test.c genome2genome.c coding2coding.c affine.c ungapped.c frameshift.c intron.c phase.c coding2genome.c cdna2genome.c est2genome.c
-+genome2genome_test_SOURCES = genome2genome.test.c genome2genome.c \
-+ coding2coding.c affine.c ungapped.c \
-+ frameshift.c intron.c phase.c \
-+ coding2genome.c cdna2genome.c \
-+ est2genome.c
-
- genome2genome_test_LDADD = $(C4_OBJECTS)
--
- phase_test_SOURCES = phase.test.c phase.c intron.c
- phase_test_LDADD = $(C4_OBJECTS)
--
--modeltype_test_SOURCES = modeltype.test.c modeltype.c ungapped.c affine.c est2genome.c ner.c protein2dna.c protein2genome.c coding2coding.c coding2genome.c genome2genome.c cdna2genome.c frameshift.c phase.c intron.c
-+modeltype_test_SOURCES = modeltype.test.c modeltype.c \
-+ ungapped.c affine.c est2genome.c ner.c \
-+ protein2dna.c protein2genome.c \
-+ coding2coding.c coding2genome.c \
-+ genome2genome.c cdna2genome.c \
-+ frameshift.c phase.c intron.c
-
- modeltype_test_LDADD = $(C4_OBJECTS)
-
- # Files to clear away
--
- MAINTAINERCLEANFILES = Makefile.in
--mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
--CONFIG_CLEAN_FILES =
--PROGRAMS = $(noinst_PROGRAMS)
--
--
--DEFS = @DEFS@ -I. -I$(srcdir)
--CPPFLAGS = @CPPFLAGS@
--LDFLAGS = @LDFLAGS@
--LIBS = @LIBS@
--edit_distance_test_OBJECTS = edit_distance.test.o edit_distance.o
--edit_distance_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \
--$(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/c4/optimal.o \
--$(top_srcdir)/src/c4/viterbi.o $(top_srcdir)/src/c4/layout.o \
--$(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/cgutil.o \
--$(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/region.o \
--$(top_srcdir)/src/c4/c4.o $(top_srcdir)/src/c4/subopt.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--edit_distance_test_LDFLAGS =
--affine_test_OBJECTS = affine.test.o affine.o ungapped.o
--affine_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \
--$(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/c4/optimal.o \
--$(top_srcdir)/src/c4/viterbi.o $(top_srcdir)/src/c4/layout.o \
--$(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/cgutil.o \
--$(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/region.o \
--$(top_srcdir)/src/c4/c4.o $(top_srcdir)/src/c4/subopt.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--affine_test_LDFLAGS =
--protein2dna_test_OBJECTS = protein2dna.test.o protein2dna.o affine.o \
--ungapped.o frameshift.o
--protein2dna_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \
--$(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/c4/optimal.o \
--$(top_srcdir)/src/c4/viterbi.o $(top_srcdir)/src/c4/layout.o \
--$(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/cgutil.o \
--$(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/region.o \
--$(top_srcdir)/src/c4/c4.o $(top_srcdir)/src/c4/subopt.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--protein2dna_test_LDFLAGS =
--ner_test_OBJECTS = ner.test.o ner.o affine.o ungapped.o
--ner_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \
--$(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/c4/optimal.o \
--$(top_srcdir)/src/c4/viterbi.o $(top_srcdir)/src/c4/layout.o \
--$(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/cgutil.o \
--$(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/region.o \
--$(top_srcdir)/src/c4/c4.o $(top_srcdir)/src/c4/subopt.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--ner_test_LDFLAGS =
--est2genome_test_OBJECTS = est2genome.test.o est2genome.o affine.o \
--ungapped.o intron.o
--est2genome_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \
--$(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/c4/optimal.o \
--$(top_srcdir)/src/c4/viterbi.o $(top_srcdir)/src/c4/layout.o \
--$(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/cgutil.o \
--$(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/region.o \
--$(top_srcdir)/src/c4/c4.o $(top_srcdir)/src/c4/subopt.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--est2genome_test_LDFLAGS =
--ungapped_test_OBJECTS = ungapped.test.o ungapped.o
--ungapped_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \
--$(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/c4/optimal.o \
--$(top_srcdir)/src/c4/viterbi.o $(top_srcdir)/src/c4/layout.o \
--$(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/cgutil.o \
--$(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/region.o \
--$(top_srcdir)/src/c4/c4.o $(top_srcdir)/src/c4/subopt.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--ungapped_test_LDFLAGS =
--intron_test_OBJECTS = intron.test.o intron.o
--intron_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \
--$(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/c4/optimal.o \
--$(top_srcdir)/src/c4/viterbi.o $(top_srcdir)/src/c4/layout.o \
--$(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/cgutil.o \
--$(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/region.o \
--$(top_srcdir)/src/c4/c4.o $(top_srcdir)/src/c4/subopt.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--intron_test_LDFLAGS =
--protein2genome_test_OBJECTS = protein2genome.test.o protein2genome.o \
--protein2dna.o ungapped.o intron.o affine.o frameshift.o phase.o
--protein2genome_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \
--$(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/c4/optimal.o \
--$(top_srcdir)/src/c4/viterbi.o $(top_srcdir)/src/c4/layout.o \
--$(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/cgutil.o \
--$(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/region.o \
--$(top_srcdir)/src/c4/c4.o $(top_srcdir)/src/c4/subopt.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--protein2genome_test_LDFLAGS =
--coding2coding_test_OBJECTS = coding2coding.test.o coding2coding.o \
--affine.o ungapped.o frameshift.o
--coding2coding_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \
--$(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/c4/optimal.o \
--$(top_srcdir)/src/c4/viterbi.o $(top_srcdir)/src/c4/layout.o \
--$(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/cgutil.o \
--$(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/region.o \
--$(top_srcdir)/src/c4/c4.o $(top_srcdir)/src/c4/subopt.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--coding2coding_test_LDFLAGS =
--frameshift_test_OBJECTS = frameshift.test.o frameshift.o
--frameshift_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \
--$(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/c4/optimal.o \
--$(top_srcdir)/src/c4/viterbi.o $(top_srcdir)/src/c4/layout.o \
--$(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/cgutil.o \
--$(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/region.o \
--$(top_srcdir)/src/c4/c4.o $(top_srcdir)/src/c4/subopt.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--frameshift_test_LDFLAGS =
--coding2genome_test_OBJECTS = coding2genome.test.o coding2genome.o \
--coding2coding.o affine.o ungapped.o frameshift.o intron.o phase.o
--coding2genome_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \
--$(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/c4/optimal.o \
--$(top_srcdir)/src/c4/viterbi.o $(top_srcdir)/src/c4/layout.o \
--$(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/cgutil.o \
--$(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/region.o \
--$(top_srcdir)/src/c4/c4.o $(top_srcdir)/src/c4/subopt.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--coding2genome_test_LDFLAGS =
--cdna2genome_test_OBJECTS = cdna2genome.test.o cdna2genome.o affine.o \
--ungapped.o frameshift.o intron.o phase.o coding2coding.o \
--coding2genome.o est2genome.o
--cdna2genome_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \
--$(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/c4/optimal.o \
--$(top_srcdir)/src/c4/viterbi.o $(top_srcdir)/src/c4/layout.o \
--$(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/cgutil.o \
--$(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/region.o \
--$(top_srcdir)/src/c4/c4.o $(top_srcdir)/src/c4/subopt.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--cdna2genome_test_LDFLAGS =
--genome2genome_test_OBJECTS = genome2genome.test.o genome2genome.o \
--coding2coding.o affine.o ungapped.o frameshift.o intron.o phase.o \
--coding2genome.o cdna2genome.o est2genome.o
--genome2genome_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \
--$(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/c4/optimal.o \
--$(top_srcdir)/src/c4/viterbi.o $(top_srcdir)/src/c4/layout.o \
--$(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/cgutil.o \
--$(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/region.o \
--$(top_srcdir)/src/c4/c4.o $(top_srcdir)/src/c4/subopt.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--genome2genome_test_LDFLAGS =
--phase_test_OBJECTS = phase.test.o phase.o intron.o
--phase_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \
--$(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/c4/optimal.o \
--$(top_srcdir)/src/c4/viterbi.o $(top_srcdir)/src/c4/layout.o \
--$(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/cgutil.o \
--$(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/region.o \
--$(top_srcdir)/src/c4/c4.o $(top_srcdir)/src/c4/subopt.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--phase_test_LDFLAGS =
--modeltype_test_OBJECTS = modeltype.test.o modeltype.o ungapped.o \
--affine.o est2genome.o ner.o protein2dna.o protein2genome.o \
--coding2coding.o coding2genome.o genome2genome.o cdna2genome.o \
--frameshift.o phase.o intron.o
--modeltype_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \
--$(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/c4/optimal.o \
--$(top_srcdir)/src/c4/viterbi.o $(top_srcdir)/src/c4/layout.o \
--$(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/cgutil.o \
--$(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/region.o \
--$(top_srcdir)/src/c4/c4.o $(top_srcdir)/src/c4/subopt.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--modeltype_test_LDFLAGS =
--bootstrapper_OBJECTS = bootstrapper.o modeltype.o ungapped.o affine.o \
--est2genome.o ner.o protein2dna.o protein2genome.o coding2coding.o \
--coding2genome.o genome2genome.o cdna2genome.o frameshift.o intron.o \
--phase.o
--bootstrapper_DEPENDENCIES = $(top_srcdir)/src/struct/pqueue.o \
--$(top_srcdir)/src/comparison/comparison.o \
--$(top_srcdir)/src/comparison/hspset.o \
--$(top_srcdir)/src/comparison/wordhood.o \
--$(top_srcdir)/src/bsdp/heuristic.o $(top_srcdir)/src/sdp/sdp.o \
--$(top_srcdir)/src/sdp/scheduler.o $(top_srcdir)/src/sdp/straceback.o \
--$(top_srcdir)/src/sdp/lookahead.o $(top_srcdir)/src/sdp/boundary.o \
--$(top_srcdir)/src/struct/slist.o $(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/c4/optimal.o \
--$(top_srcdir)/src/c4/viterbi.o $(top_srcdir)/src/c4/layout.o \
--$(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/cgutil.o \
--$(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/region.o \
--$(top_srcdir)/src/c4/c4.o $(top_srcdir)/src/c4/subopt.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--bootstrapper_LDFLAGS =
--CFLAGS = @CFLAGS@
--COMPILE = $(CC) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
--CCLD = $(CC)
--LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(LDFLAGS) -o $@
--HEADERS = $(noinst_HEADERS)
--
--DIST_COMMON = Makefile.am Makefile.in
--
--
--DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
-+all: all-am
-
--TAR = tar
--GZIP_ENV = --best
--SOURCES = $(edit_distance_test_SOURCES) $(affine_test_SOURCES) $(protein2dna_test_SOURCES) $(ner_test_SOURCES) $(est2genome_test_SOURCES) $(ungapped_test_SOURCES) $(intron_test_SOURCES) $(protein2genome_test_SOURCES) $(coding2coding_test_SOURCES) $(frameshift_test_SOURCES) $(coding2genome_test_SOURCES) $(cdna2genome_test_SOURCES) $(genome2genome_test_SOURCES) $(phase_test_SOURCES) $(modeltype_test_SOURCES) $(bootstrapper_SOURCES)
--OBJECTS = $(edit_distance_test_OBJECTS) $(affine_test_OBJECTS) $(protein2dna_test_OBJECTS) $(ner_test_OBJECTS) $(est2genome_test_OBJECTS) $(ungapped_test_OBJECTS) $(intron_test_OBJECTS) $(protein2genome_test_OBJECTS) $(coding2coding_test_OBJECTS) $(frameshift_test_OBJECTS) $(coding2genome_test_OBJECTS) $(cdna2genome_test_OBJECTS) $(genome2genome_test_OBJECTS) $(phase_test_OBJECTS) $(modeltype_test_OBJECTS) $(bootstrapper_OBJECTS)
--
--all: all-redirect
- .SUFFIXES:
--.SUFFIXES: .S .c .o .s
--$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4)
-- cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps src/model/Makefile
--
-+.SUFFIXES: .c .o .obj
-+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
-+ @for dep in $?; do \
-+ case '$(am__configure_deps)' in \
-+ *$$dep*) \
-+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-+ && { if test -f $@; then exit 0; else break; fi; }; \
-+ exit 1;; \
-+ esac; \
-+ done; \
-+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/model/Makefile'; \
-+ $(am__cd) $(top_srcdir) && \
-+ $(AUTOMAKE) --gnu src/model/Makefile
-+.PRECIOUS: Makefile
- Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-- cd $(top_builddir) \
-- && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
--
--
--mostlyclean-noinstPROGRAMS:
-+ @case '$?' in \
-+ *config.status*) \
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-+ *) \
-+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-+ esac;
-+
-+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+
-+$(top_srcdir)/configure: $(am__configure_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(am__aclocal_m4_deps):
-
- clean-noinstPROGRAMS:
- -test -z "$(noinst_PROGRAMS)" || rm -f $(noinst_PROGRAMS)
--
--distclean-noinstPROGRAMS:
--
--maintainer-clean-noinstPROGRAMS:
--
--.c.o:
-- $(COMPILE) -c $<
--
--.s.o:
-- $(COMPILE) -c $<
--
--.S.o:
-- $(COMPILE) -c $<
-+affine.test$(EXEEXT): $(affine_test_OBJECTS) $(affine_test_DEPENDENCIES)
-+ @rm -f affine.test$(EXEEXT)
-+ $(LINK) $(affine_test_OBJECTS) $(affine_test_LDADD) $(LIBS)
-+bootstrapper$(EXEEXT): $(bootstrapper_OBJECTS) $(bootstrapper_DEPENDENCIES)
-+ @rm -f bootstrapper$(EXEEXT)
-+ $(LINK) $(bootstrapper_OBJECTS) $(bootstrapper_LDADD) $(LIBS)
-+cdna2genome.test$(EXEEXT): $(cdna2genome_test_OBJECTS) $(cdna2genome_test_DEPENDENCIES)
-+ @rm -f cdna2genome.test$(EXEEXT)
-+ $(LINK) $(cdna2genome_test_OBJECTS) $(cdna2genome_test_LDADD) $(LIBS)
-+coding2coding.test$(EXEEXT): $(coding2coding_test_OBJECTS) $(coding2coding_test_DEPENDENCIES)
-+ @rm -f coding2coding.test$(EXEEXT)
-+ $(LINK) $(coding2coding_test_OBJECTS) $(coding2coding_test_LDADD) $(LIBS)
-+coding2genome.test$(EXEEXT): $(coding2genome_test_OBJECTS) $(coding2genome_test_DEPENDENCIES)
-+ @rm -f coding2genome.test$(EXEEXT)
-+ $(LINK) $(coding2genome_test_OBJECTS) $(coding2genome_test_LDADD) $(LIBS)
-+edit_distance.test$(EXEEXT): $(edit_distance_test_OBJECTS) $(edit_distance_test_DEPENDENCIES)
-+ @rm -f edit_distance.test$(EXEEXT)
-+ $(LINK) $(edit_distance_test_OBJECTS) $(edit_distance_test_LDADD) $(LIBS)
-+est2genome.test$(EXEEXT): $(est2genome_test_OBJECTS) $(est2genome_test_DEPENDENCIES)
-+ @rm -f est2genome.test$(EXEEXT)
-+ $(LINK) $(est2genome_test_OBJECTS) $(est2genome_test_LDADD) $(LIBS)
-+frameshift.test$(EXEEXT): $(frameshift_test_OBJECTS) $(frameshift_test_DEPENDENCIES)
-+ @rm -f frameshift.test$(EXEEXT)
-+ $(LINK) $(frameshift_test_OBJECTS) $(frameshift_test_LDADD) $(LIBS)
-+genome2genome.test$(EXEEXT): $(genome2genome_test_OBJECTS) $(genome2genome_test_DEPENDENCIES)
-+ @rm -f genome2genome.test$(EXEEXT)
-+ $(LINK) $(genome2genome_test_OBJECTS) $(genome2genome_test_LDADD) $(LIBS)
-+intron.test$(EXEEXT): $(intron_test_OBJECTS) $(intron_test_DEPENDENCIES)
-+ @rm -f intron.test$(EXEEXT)
-+ $(LINK) $(intron_test_OBJECTS) $(intron_test_LDADD) $(LIBS)
-+modeltype.test$(EXEEXT): $(modeltype_test_OBJECTS) $(modeltype_test_DEPENDENCIES)
-+ @rm -f modeltype.test$(EXEEXT)
-+ $(LINK) $(modeltype_test_OBJECTS) $(modeltype_test_LDADD) $(LIBS)
-+ner.test$(EXEEXT): $(ner_test_OBJECTS) $(ner_test_DEPENDENCIES)
-+ @rm -f ner.test$(EXEEXT)
-+ $(LINK) $(ner_test_OBJECTS) $(ner_test_LDADD) $(LIBS)
-+phase.test$(EXEEXT): $(phase_test_OBJECTS) $(phase_test_DEPENDENCIES)
-+ @rm -f phase.test$(EXEEXT)
-+ $(LINK) $(phase_test_OBJECTS) $(phase_test_LDADD) $(LIBS)
-+protein2dna.test$(EXEEXT): $(protein2dna_test_OBJECTS) $(protein2dna_test_DEPENDENCIES)
-+ @rm -f protein2dna.test$(EXEEXT)
-+ $(LINK) $(protein2dna_test_OBJECTS) $(protein2dna_test_LDADD) $(LIBS)
-+protein2genome.test$(EXEEXT): $(protein2genome_test_OBJECTS) $(protein2genome_test_DEPENDENCIES)
-+ @rm -f protein2genome.test$(EXEEXT)
-+ $(LINK) $(protein2genome_test_OBJECTS) $(protein2genome_test_LDADD) $(LIBS)
-+ungapped.test$(EXEEXT): $(ungapped_test_OBJECTS) $(ungapped_test_DEPENDENCIES)
-+ @rm -f ungapped.test$(EXEEXT)
-+ $(LINK) $(ungapped_test_OBJECTS) $(ungapped_test_LDADD) $(LIBS)
-
- mostlyclean-compile:
-- -rm -f *.o core *.core
--
--clean-compile:
-+ -rm -f *.$(OBJEXT)
-
- distclean-compile:
- -rm -f *.tab.c
-
--maintainer-clean-compile:
--
--edit_distance.test: $(edit_distance_test_OBJECTS) $(edit_distance_test_DEPENDENCIES)
-- @rm -f edit_distance.test
-- $(LINK) $(edit_distance_test_LDFLAGS) $(edit_distance_test_OBJECTS) $(edit_distance_test_LDADD) $(LIBS)
--
--affine.test: $(affine_test_OBJECTS) $(affine_test_DEPENDENCIES)
-- @rm -f affine.test
-- $(LINK) $(affine_test_LDFLAGS) $(affine_test_OBJECTS) $(affine_test_LDADD) $(LIBS)
--
--protein2dna.test: $(protein2dna_test_OBJECTS) $(protein2dna_test_DEPENDENCIES)
-- @rm -f protein2dna.test
-- $(LINK) $(protein2dna_test_LDFLAGS) $(protein2dna_test_OBJECTS) $(protein2dna_test_LDADD) $(LIBS)
--
--ner.test: $(ner_test_OBJECTS) $(ner_test_DEPENDENCIES)
-- @rm -f ner.test
-- $(LINK) $(ner_test_LDFLAGS) $(ner_test_OBJECTS) $(ner_test_LDADD) $(LIBS)
--
--est2genome.test: $(est2genome_test_OBJECTS) $(est2genome_test_DEPENDENCIES)
-- @rm -f est2genome.test
-- $(LINK) $(est2genome_test_LDFLAGS) $(est2genome_test_OBJECTS) $(est2genome_test_LDADD) $(LIBS)
--
--ungapped.test: $(ungapped_test_OBJECTS) $(ungapped_test_DEPENDENCIES)
-- @rm -f ungapped.test
-- $(LINK) $(ungapped_test_LDFLAGS) $(ungapped_test_OBJECTS) $(ungapped_test_LDADD) $(LIBS)
--
--intron.test: $(intron_test_OBJECTS) $(intron_test_DEPENDENCIES)
-- @rm -f intron.test
-- $(LINK) $(intron_test_LDFLAGS) $(intron_test_OBJECTS) $(intron_test_LDADD) $(LIBS)
--
--protein2genome.test: $(protein2genome_test_OBJECTS) $(protein2genome_test_DEPENDENCIES)
-- @rm -f protein2genome.test
-- $(LINK) $(protein2genome_test_LDFLAGS) $(protein2genome_test_OBJECTS) $(protein2genome_test_LDADD) $(LIBS)
--
--coding2coding.test: $(coding2coding_test_OBJECTS) $(coding2coding_test_DEPENDENCIES)
-- @rm -f coding2coding.test
-- $(LINK) $(coding2coding_test_LDFLAGS) $(coding2coding_test_OBJECTS) $(coding2coding_test_LDADD) $(LIBS)
--
--frameshift.test: $(frameshift_test_OBJECTS) $(frameshift_test_DEPENDENCIES)
-- @rm -f frameshift.test
-- $(LINK) $(frameshift_test_LDFLAGS) $(frameshift_test_OBJECTS) $(frameshift_test_LDADD) $(LIBS)
--
--coding2genome.test: $(coding2genome_test_OBJECTS) $(coding2genome_test_DEPENDENCIES)
-- @rm -f coding2genome.test
-- $(LINK) $(coding2genome_test_LDFLAGS) $(coding2genome_test_OBJECTS) $(coding2genome_test_LDADD) $(LIBS)
--
--cdna2genome.test: $(cdna2genome_test_OBJECTS) $(cdna2genome_test_DEPENDENCIES)
-- @rm -f cdna2genome.test
-- $(LINK) $(cdna2genome_test_LDFLAGS) $(cdna2genome_test_OBJECTS) $(cdna2genome_test_LDADD) $(LIBS)
--
--genome2genome.test: $(genome2genome_test_OBJECTS) $(genome2genome_test_DEPENDENCIES)
-- @rm -f genome2genome.test
-- $(LINK) $(genome2genome_test_LDFLAGS) $(genome2genome_test_OBJECTS) $(genome2genome_test_LDADD) $(LIBS)
--
--phase.test: $(phase_test_OBJECTS) $(phase_test_DEPENDENCIES)
-- @rm -f phase.test
-- $(LINK) $(phase_test_LDFLAGS) $(phase_test_OBJECTS) $(phase_test_LDADD) $(LIBS)
--
--modeltype.test: $(modeltype_test_OBJECTS) $(modeltype_test_DEPENDENCIES)
-- @rm -f modeltype.test
-- $(LINK) $(modeltype_test_LDFLAGS) $(modeltype_test_OBJECTS) $(modeltype_test_LDADD) $(LIBS)
--
--bootstrapper: $(bootstrapper_OBJECTS) $(bootstrapper_DEPENDENCIES)
-- @rm -f bootstrapper
-- $(LINK) $(bootstrapper_LDFLAGS) $(bootstrapper_OBJECTS) $(bootstrapper_LDADD) $(LIBS)
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/affine.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/affine.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/bootstrapper.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cdna2genome.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cdna2genome.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/coding2coding.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/coding2coding.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/coding2genome.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/coding2genome.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/edit_distance.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/edit_distance.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/est2genome.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/est2genome.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/frameshift.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/frameshift.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/genome2genome.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/genome2genome.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/intron.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/intron.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/modeltype.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/modeltype.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/ner.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/ner.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/phase.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/phase.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/protein2dna.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/protein2dna.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/protein2genome.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/protein2genome.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/ungapped.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/ungapped.test.Po at am__quote@
-
-+.c.o:
-+ at am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
-+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-+ at am__fastdepCC_FALSE@ $(COMPILE) -c $<
-+
-+.c.obj:
-+ at am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
-+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-+ at am__fastdepCC_FALSE@ $(COMPILE) -c `$(CYGPATH_W) '$<'`
-+
-+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ mkid -fID $$unique
- tags: TAGS
-
--ID: $(HEADERS) $(SOURCES) $(LISP)
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- here=`pwd` && cd $(srcdir) \
-- && mkid -f$$here/ID $$unique $(LISP)
--
--TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) $(LISP)
-- tags=; \
-+TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ set x; \
- here=`pwd`; \
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- test -z "$(ETAGS_ARGS)$$unique$(LISP)$$tags" \
-- || (cd $(srcdir) && etags -o $$here/TAGS $(ETAGS_ARGS) $$tags $$unique $(LISP))
--
--mostlyclean-tags:
--
--clean-tags:
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ shift; \
-+ if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
-+ test -n "$$unique" || unique=$$empty_fix; \
-+ if test $$# -gt 0; then \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ "$$@" $$unique; \
-+ else \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ $$unique; \
-+ fi; \
-+ fi
-+ctags: CTAGS
-+CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ test -z "$(CTAGS_ARGS)$$unique" \
-+ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-+ $$unique
-+
-+GTAGS:
-+ here=`$(am__cd) $(top_builddir) && pwd` \
-+ && $(am__cd) $(top_srcdir) \
-+ && gtags -i $(GTAGS_ARGS) "$$here"
-
- distclean-tags:
-- -rm -f TAGS ID
--
--maintainer-clean-tags:
--
--distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
--
--subdir = src/model
-+ -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-
--distdir: $(DISTFILES)
-- @for file in $(DISTFILES); do \
-- d=$(srcdir); \
-- if test -d $$d/$$file; then \
-- cp -pr $$d/$$file $(distdir)/$$file; \
-- else \
-- test -f $(distdir)/$$file \
-- || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
-- || cp -p $$d/$$file $(distdir)/$$file || :; \
-- fi; \
-- done
- check-TESTS: $(TESTS)
-- @failed=0; all=0; \
-+ @failed=0; all=0; xfail=0; xpass=0; skip=0; \
- srcdir=$(srcdir); export srcdir; \
-- for tst in $(TESTS); do \
-- if test -f $$tst; then dir=.; \
-- else dir="$(srcdir)"; fi; \
-- if $(TESTS_ENVIRONMENT) $$dir/$$tst; then \
-+ list=' $(TESTS) '; \
-+ $(am__tty_colors); \
-+ if test -n "$$list"; then \
-+ for tst in $$list; do \
-+ if test -f ./$$tst; then dir=./; \
-+ elif test -f $$tst; then dir=; \
-+ else dir="$(srcdir)/"; fi; \
-+ if $(TESTS_ENVIRONMENT) $${dir}$$tst; then \
- all=`expr $$all + 1`; \
-- echo "PASS: $$tst"; \
-+ case " $(XFAIL_TESTS) " in \
-+ *[\ \ ]$$tst[\ \ ]*) \
-+ xpass=`expr $$xpass + 1`; \
-+ failed=`expr $$failed + 1`; \
-+ col=$$red; res=XPASS; \
-+ ;; \
-+ *) \
-+ col=$$grn; res=PASS; \
-+ ;; \
-+ esac; \
- elif test $$? -ne 77; then \
- all=`expr $$all + 1`; \
-+ case " $(XFAIL_TESTS) " in \
-+ *[\ \ ]$$tst[\ \ ]*) \
-+ xfail=`expr $$xfail + 1`; \
-+ col=$$lgn; res=XFAIL; \
-+ ;; \
-+ *) \
- failed=`expr $$failed + 1`; \
-- echo "FAIL: $$tst"; \
-+ col=$$red; res=FAIL; \
-+ ;; \
-+ esac; \
-+ else \
-+ skip=`expr $$skip + 1`; \
-+ col=$$blu; res=SKIP; \
- fi; \
-+ echo "$${col}$$res$${std}: $$tst"; \
- done; \
-+ if test "$$all" -eq 1; then \
-+ tests="test"; \
-+ All=""; \
-+ else \
-+ tests="tests"; \
-+ All="All "; \
-+ fi; \
-+ if test "$$failed" -eq 0; then \
-+ if test "$$xfail" -eq 0; then \
-+ banner="$$All$$all $$tests passed"; \
-+ else \
-+ if test "$$xfail" -eq 1; then failures=failure; else failures=failures; fi; \
-+ banner="$$All$$all $$tests behaved as expected ($$xfail expected $$failures)"; \
-+ fi; \
-+ else \
-+ if test "$$xpass" -eq 0; then \
-+ banner="$$failed of $$all $$tests failed"; \
-+ else \
-+ if test "$$xpass" -eq 1; then passes=pass; else passes=passes; fi; \
-+ banner="$$failed of $$all $$tests did not behave as expected ($$xpass unexpected $$passes)"; \
-+ fi; \
-+ fi; \
-+ dashes="$$banner"; \
-+ skipped=""; \
-+ if test "$$skip" -ne 0; then \
-+ if test "$$skip" -eq 1; then \
-+ skipped="($$skip test was not run)"; \
-+ else \
-+ skipped="($$skip tests were not run)"; \
-+ fi; \
-+ test `echo "$$skipped" | wc -c` -le `echo "$$banner" | wc -c` || \
-+ dashes="$$skipped"; \
-+ fi; \
-+ report=""; \
-+ if test "$$failed" -ne 0 && test -n "$(PACKAGE_BUGREPORT)"; then \
-+ report="Please report to $(PACKAGE_BUGREPORT)"; \
-+ test `echo "$$report" | wc -c` -le `echo "$$banner" | wc -c` || \
-+ dashes="$$report"; \
-+ fi; \
-+ dashes=`echo "$$dashes" | sed s/./=/g`; \
- if test "$$failed" -eq 0; then \
-- banner="All $$all tests passed"; \
-+ echo "$$grn$$dashes"; \
- else \
-- banner="$$failed of $$all tests failed"; \
-+ echo "$$red$$dashes"; \
- fi; \
-- dashes=`echo "$$banner" | sed s/./=/g`; \
-- echo "$$dashes"; \
- echo "$$banner"; \
-- echo "$$dashes"; \
-- test "$$failed" -eq 0
--info-am:
--info: info-am
--dvi-am:
--dvi: dvi-am
-+ test -z "$$skipped" || echo "$$skipped"; \
-+ test -z "$$report" || echo "$$report"; \
-+ echo "$$dashes$$std"; \
-+ test "$$failed" -eq 0; \
-+ else :; fi
-+
-+distdir: $(DISTFILES)
-+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ list='$(DISTFILES)'; \
-+ dist_files=`for file in $$list; do echo $$file; done | \
-+ sed -e "s|^$$srcdirstrip/||;t" \
-+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-+ case $$dist_files in \
-+ */*) $(MKDIR_P) `echo "$$dist_files" | \
-+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-+ sort -u` ;; \
-+ esac; \
-+ for file in $$dist_files; do \
-+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
-+ if test -d $$d/$$file; then \
-+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-+ if test -d "$(distdir)/$$file"; then \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
-+ else \
-+ test -f "$(distdir)/$$file" \
-+ || cp -p $$d/$$file "$(distdir)/$$file" \
-+ || exit 1; \
-+ fi; \
-+ done
- check-am: all-am
- $(MAKE) $(AM_MAKEFLAGS) check-TESTS
- check: check-am
--installcheck-am:
--installcheck: installcheck-am
--install-exec-am:
-+all-am: Makefile $(PROGRAMS) $(HEADERS)
-+installdirs:
-+install: install-am
- install-exec: install-exec-am
--
--install-data-am:
- install-data: install-data-am
-+uninstall: uninstall-am
-
- install-am: all-am
- @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
--install: install-am
--uninstall-am:
--uninstall: uninstall-am
--all-am: Makefile $(PROGRAMS) $(HEADERS)
--all-redirect: all-am
--install-strip:
-- $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
--installdirs:
--
-
-+installcheck: installcheck-am
-+install-strip:
-+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-+ `test -z '$(STRIP)' || \
-+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
- mostlyclean-generic:
-
- clean-generic:
-
- distclean-generic:
-- -rm -f Makefile $(CONFIG_CLEAN_FILES)
-- -rm -f config.cache config.log stamp-h stamp-h[0-9]*
-+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
- maintainer-clean-generic:
-+ @echo "This command is intended for maintainers to use"
-+ @echo "it deletes files that may require special tools to rebuild."
- -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
--mostlyclean-am: mostlyclean-noinstPROGRAMS mostlyclean-compile \
-- mostlyclean-tags mostlyclean-generic
-+clean: clean-am
-
--mostlyclean: mostlyclean-am
-+clean-am: clean-generic clean-noinstPROGRAMS mostlyclean-am
-
--clean-am: clean-noinstPROGRAMS clean-compile clean-tags clean-generic \
-- mostlyclean-am
-+distclean: distclean-am
-+ -rm -rf ./$(DEPDIR)
-+ -rm -f Makefile
-+distclean-am: clean-am distclean-compile distclean-generic \
-+ distclean-tags
-
--clean: clean-am
-+dvi: dvi-am
-
--distclean-am: distclean-noinstPROGRAMS distclean-compile distclean-tags \
-- distclean-generic clean-am
-+dvi-am:
-
--distclean: distclean-am
-+html: html-am
-
--maintainer-clean-am: maintainer-clean-noinstPROGRAMS \
-- maintainer-clean-compile maintainer-clean-tags \
-- maintainer-clean-generic distclean-am
-- @echo "This command is intended for maintainers to use;"
-- @echo "it deletes files that may require special tools to rebuild."
-+html-am:
-+
-+info: info-am
-+
-+info-am:
-+
-+install-data-am:
-+
-+install-dvi: install-dvi-am
-+
-+install-dvi-am:
-+
-+install-exec-am:
-+
-+install-html: install-html-am
-+
-+install-html-am:
-+
-+install-info: install-info-am
-+
-+install-info-am:
-+
-+install-man:
-+
-+install-pdf: install-pdf-am
-+
-+install-pdf-am:
-+
-+install-ps: install-ps-am
-+
-+install-ps-am:
-+
-+installcheck-am:
-
- maintainer-clean: maintainer-clean-am
-+ -rm -rf ./$(DEPDIR)
-+ -rm -f Makefile
-+maintainer-clean-am: distclean-am maintainer-clean-generic
-+
-+mostlyclean: mostlyclean-am
-+
-+mostlyclean-am: mostlyclean-compile mostlyclean-generic
-+
-+pdf: pdf-am
-+
-+pdf-am:
-+
-+ps: ps-am
-+
-+ps-am:
-+
-+uninstall-am:
-+
-+.MAKE: check-am install-am install-strip
-
--.PHONY: mostlyclean-noinstPROGRAMS distclean-noinstPROGRAMS \
--clean-noinstPROGRAMS maintainer-clean-noinstPROGRAMS \
--mostlyclean-compile distclean-compile clean-compile \
--maintainer-clean-compile tags mostlyclean-tags distclean-tags \
--clean-tags maintainer-clean-tags distdir check-TESTS info-am info \
--dvi-am dvi check check-am installcheck-am installcheck install-exec-am \
--install-exec install-data-am install-data install-am install \
--uninstall-am uninstall all-redirect all-am all installdirs \
--mostlyclean-generic distclean-generic clean-generic \
--maintainer-clean-generic clean mostlyclean distclean maintainer-clean
-+.PHONY: CTAGS GTAGS all all-am check check-TESTS check-am clean \
-+ clean-generic clean-noinstPROGRAMS ctags distclean \
-+ distclean-compile distclean-generic distclean-tags distdir dvi \
-+ dvi-am html html-am info info-am install install-am \
-+ install-data install-data-am install-dvi install-dvi-am \
-+ install-exec install-exec-am install-html install-html-am \
-+ install-info install-info-am install-man install-pdf \
-+ install-pdf-am install-ps install-ps-am install-strip \
-+ installcheck installcheck-am installdirs maintainer-clean \
-+ maintainer-clean-generic mostlyclean mostlyclean-compile \
-+ mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
-+ uninstall-am
-
-
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -ubrN exonerate-2.2.0.orig/src/program/Makefile.in exonerate-2.2.0/src/program/Makefile.in
---- exonerate-2.2.0.orig/src/program/Makefile.in 2008-10-17 12:04:45.000000000 +0200
-+++ exonerate-2.2.0/src/program/Makefile.in 2011-12-12 13:33:17.000000000 +0100
-@@ -1,6 +1,9 @@
--# Makefile.in generated automatically by automake 1.4-p6 from Makefile.am
-+# Makefile.in generated by automake 1.11.1 from Makefile.am.
-+# @configure_input@
-
--# Copyright (C) 1994, 1995-8, 1999, 2001 Free Software Foundation, Inc.
-+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
-+# Inc.
- # This Makefile.in is free software; the Free Software Foundation
- # gives unlimited permission to copy and/or distribute it,
- # with or without modifications, as long as this notice is preserved.
-@@ -10,355 +13,669 @@
- # even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- # PARTICULAR PURPOSE.
-
-+ at SET_MAKE@
-
--SHELL = @SHELL@
--
--srcdir = @srcdir@
--top_srcdir = @top_srcdir@
- VPATH = @srcdir@
--prefix = @prefix@
--exec_prefix = @exec_prefix@
--
--bindir = @bindir@
--sbindir = @sbindir@
--libexecdir = @libexecdir@
--datadir = @datadir@
--sysconfdir = @sysconfdir@
--sharedstatedir = @sharedstatedir@
--localstatedir = @localstatedir@
--libdir = @libdir@
--infodir = @infodir@
--mandir = @mandir@
--includedir = @includedir@
--oldincludedir = /usr/include
--
--DESTDIR =
--
- pkgdatadir = $(datadir)/@PACKAGE@
--pkglibdir = $(libdir)/@PACKAGE@
- pkgincludedir = $(includedir)/@PACKAGE@
--
--top_builddir = ../..
--
--ACLOCAL = @ACLOCAL@
--AUTOCONF = @AUTOCONF@
--AUTOMAKE = @AUTOMAKE@
--AUTOHEADER = @AUTOHEADER@
--
--INSTALL = @INSTALL@
--INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
--INSTALL_DATA = @INSTALL_DATA@
--INSTALL_SCRIPT = @INSTALL_SCRIPT@
--transform = @program_transform_name@
--
-+pkglibdir = $(libdir)/@PACKAGE@
-+pkglibexecdir = $(libexecdir)/@PACKAGE@
-+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-+install_sh_DATA = $(install_sh) -c -m 644
-+install_sh_PROGRAM = $(install_sh) -c
-+install_sh_SCRIPT = $(install_sh) -c
-+INSTALL_HEADER = $(INSTALL_DATA)
-+transform = $(program_transform_name)
- NORMAL_INSTALL = :
- PRE_INSTALL = :
- POST_INSTALL = :
- NORMAL_UNINSTALL = :
- PRE_UNINSTALL = :
- POST_UNINSTALL = :
--host_alias = @host_alias@
-+build_triplet = @build@
- host_triplet = @host@
-+bin_PROGRAMS = exonerate$(EXEEXT) ipcress$(EXEEXT) \
-+ exonerate-server$(EXEEXT)
-+subdir = src/program
-+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
-+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-+am__aclocal_m4_deps = $(top_srcdir)/configure.in
-+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-+ $(ACLOCAL_M4)
-+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
-+CONFIG_CLEAN_FILES =
-+CONFIG_CLEAN_VPATH_FILES =
-+am__installdirs = "$(DESTDIR)$(bindir)"
-+PROGRAMS = $(bin_PROGRAMS)
-+am_exonerate_OBJECTS = exonerate.$(OBJEXT)
-+exonerate_OBJECTS = $(am_exonerate_OBJECTS)
-+am__DEPENDENCIES_1 = $(top_srcdir)/src/comparison/wordhood.o \
-+ $(top_srcdir)/src/comparison/hspset.o \
-+ $(top_srcdir)/src/comparison/seeder.o \
-+ $(top_srcdir)/src/comparison/comparison.o \
-+ $(top_srcdir)/src/database/fastapipe.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/struct/dejavu.o \
-+ $(top_srcdir)/src/struct/fsm.o $(top_srcdir)/src/struct/vfsm.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/hub/gam.o $(top_srcdir)/src/hub/bsam.o \
-+ $(top_srcdir)/src/hub/analysis.o \
-+ $(top_srcdir)/src/general/compoundfile.o $(C4_OBJECTS)
-+am_exonerate_server_OBJECTS = exonerate-server.$(OBJEXT)
-+exonerate_server_OBJECTS = $(am_exonerate_server_OBJECTS)
-+exonerate_server_DEPENDENCIES = $(top_srcdir)/src/general/socket.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/comparison/hspset.o \
-+ $(top_srcdir)/src/comparison/match.o \
-+ $(top_srcdir)/src/comparison/wordhood.o \
-+ $(top_srcdir)/src/database/dataset.o \
-+ $(top_srcdir)/src/database/index.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/struct/bitarray.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o \
-+ $(top_srcdir)/src/struct/splaytree.o \
-+ $(top_srcdir)/src/struct/noitree.o \
-+ $(top_srcdir)/src/struct/vfsm.o \
-+ $(top_srcdir)/src/struct/pqueue.o \
-+ $(top_srcdir)/src/struct/rangetree.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/sequence/sequence.o \
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/submat.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/general/lineparse.o
-+am_ipcress_OBJECTS = ipcress.$(OBJEXT)
-+ipcress_OBJECTS = $(am_ipcress_OBJECTS)
-+ipcress_DEPENDENCIES = $(top_srcdir)/src/comparison/pcr.o \
-+ $(top_srcdir)/src/comparison/wordhood.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/sequence.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/sequence/submat.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o \
-+ $(top_srcdir)/src/struct/fsm.o \
-+ $(top_srcdir)/src/struct/slist.o \
-+ $(top_srcdir)/src/struct/matrix.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/compoundfile.o
-+DEFAULT_INCLUDES = -I. at am__isrc@
-+depcomp = $(SHELL) $(top_srcdir)/depcomp
-+am__depfiles_maybe = depfiles
-+am__mv = mv -f
-+COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
-+ $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
-+CCLD = $(CC)
-+LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
-+SOURCES = $(exonerate_SOURCES) $(EXTRA_exonerate_SOURCES) \
-+ $(exonerate_server_SOURCES) $(ipcress_SOURCES)
-+DIST_SOURCES = $(exonerate_SOURCES) $(EXTRA_exonerate_SOURCES) \
-+ $(exonerate_server_SOURCES) $(ipcress_SOURCES)
-+ETAGS = etags
-+CTAGS = ctags
-+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-+ACLOCAL = @ACLOCAL@
-+AMTAR = @AMTAR@
-+AUTOCONF = @AUTOCONF@
-+AUTOHEADER = @AUTOHEADER@
-+AUTOMAKE = @AUTOMAKE@
-+AWK = @AWK@
- CC = @CC@
-+CCDEPMODE = @CCDEPMODE@
-+CFLAGS = @CFLAGS@
-+CPP = @CPP@
-+CPPFLAGS = @CPPFLAGS@
-+CYGPATH_W = @CYGPATH_W@
-+DEFS = @DEFS@
-+DEPDIR = @DEPDIR@
-+ECHO_C = @ECHO_C@
-+ECHO_N = @ECHO_N@
-+ECHO_T = @ECHO_T@
-+EGREP = @EGREP@
-+EXEEXT = @EXEEXT@
- GLIB_CONFIG = @GLIB_CONFIG@
--HAVE_LIB = @HAVE_LIB@
--LIB = @LIB@
--LTLIB = @LTLIB@
-+GREP = @GREP@
-+INSTALL = @INSTALL@
-+INSTALL_DATA = @INSTALL_DATA@
-+INSTALL_PROGRAM = @INSTALL_PROGRAM@
-+INSTALL_SCRIPT = @INSTALL_SCRIPT@
-+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-+LDFLAGS = @LDFLAGS@
-+LIBOBJS = @LIBOBJS@
-+LIBS = @LIBS@
-+LTLIBOBJS = @LTLIBOBJS@
- MAKEINFO = @MAKEINFO@
-+MKDIR_P = @MKDIR_P@
-+OBJEXT = @OBJEXT@
- PACKAGE = @PACKAGE@
-+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-+PACKAGE_NAME = @PACKAGE_NAME@
-+PACKAGE_STRING = @PACKAGE_STRING@
-+PACKAGE_TARNAME = @PACKAGE_TARNAME@
-+PACKAGE_URL = @PACKAGE_URL@
-+PACKAGE_VERSION = @PACKAGE_VERSION@
-+PATH_SEPARATOR = @PATH_SEPARATOR@
- PKG_CONFIG = @PKG_CONFIG@
-+SET_MAKE = @SET_MAKE@
-+SHELL = @SHELL@
-+STRIP = @STRIP@
- VERSION = @VERSION@
-+abs_builddir = @abs_builddir@
-+abs_srcdir = @abs_srcdir@
-+abs_top_builddir = @abs_top_builddir@
-+abs_top_srcdir = @abs_top_srcdir@
-+ac_ct_CC = @ac_ct_CC@
-+am__include = @am__include@
-+am__leading_dot = @am__leading_dot@
-+am__quote = @am__quote@
-+am__tar = @am__tar@
-+am__untar = @am__untar@
-+bindir = @bindir@
-+build = @build@
-+build_alias = @build_alias@
-+build_cpu = @build_cpu@
-+build_os = @build_os@
-+build_vendor = @build_vendor@
-+builddir = @builddir@
- codegen_extra_ldadd = @codegen_extra_ldadd@
- codegen_extra_sources = @codegen_extra_sources@
-+datadir = @datadir@
- datarootdir = @datarootdir@
-+docdir = @docdir@
-+dvidir = @dvidir@
-+exec_prefix = @exec_prefix@
- glib_cflags = @glib_cflags@
- glib_libs = @glib_libs@
- host = @host@
-+host_alias = @host_alias@
-+host_cpu = @host_cpu@
-+host_os = @host_os@
-+host_vendor = @host_vendor@
-+htmldir = @htmldir@
-+includedir = @includedir@
-+infodir = @infodir@
-+install_sh = @install_sh@
- installed_util_list = @installed_util_list@
-+libdir = @libdir@
-+libexecdir = @libexecdir@
-+localedir = @localedir@
-+localstatedir = @localstatedir@
-+mandir = @mandir@
-+mkdir_p = @mkdir_p@
-+oldincludedir = @oldincludedir@
-+pdfdir = @pdfdir@
-+prefix = @prefix@
-+program_transform_name = @program_transform_name@
-+psdir = @psdir@
-+sbindir = @sbindir@
-+sharedstatedir = @sharedstatedir@
- source_root_dir = @source_root_dir@
-+srcdir = @srcdir@
-+sysconfdir = @sysconfdir@
-+target_alias = @target_alias@
-+top_build_prefix = @top_build_prefix@
-+top_builddir = @top_builddir@
-+top_srcdir = @top_srcdir@
- use_pthreads = @use_pthreads@
--
--bin_PROGRAMS = exonerate ipcress exonerate-server
--
--INCLUDES = -I$(top_srcdir)/src/sequence -I$(top_srcdir)/src/database -I$(top_srcdir)/src/comparison -I$(top_srcdir)/src/struct -I$(top_srcdir)/src/c4 -I$(top_srcdir)/src/bsdp -I$(top_srcdir)/src/sdp -I$(top_srcdir)/src/model -I$(top_srcdir)/src/hub -I$(top_srcdir)/src/general -DHOSTTYPE="\"@host@\"" -DSOURCE_ROOT_DIR="\"@source_root_dir@\""
-+INCLUDES = -I$(top_srcdir)/src/sequence \
-+ -I$(top_srcdir)/src/database \
-+ -I$(top_srcdir)/src/comparison \
-+ -I$(top_srcdir)/src/struct \
-+ -I$(top_srcdir)/src/c4 \
-+ -I$(top_srcdir)/src/bsdp \
-+ -I$(top_srcdir)/src/sdp \
-+ -I$(top_srcdir)/src/model \
-+ -I$(top_srcdir)/src/hub \
-+ -I$(top_srcdir)/src/general \
-+ -DHOSTTYPE="\"@host@\"" \
-+ -DSOURCE_ROOT_DIR="\"@source_root_dir@\""
-
-
- # Missing viterb.o and scheduler.o so codegen versions may be substituted
--C4_OBJECTS = $(top_srcdir)/src/c4/c4.o $(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/cgutil.o $(top_srcdir)/src/c4/opair.o $(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/optimal.o $(top_srcdir)/src/c4/layout.o $(top_srcdir)/src/c4/region.o $(top_srcdir)/src/c4/subopt.o $(top_srcdir)/src/bsdp/bsdp.o $(top_srcdir)/src/bsdp/sar.o $(top_srcdir)/src/bsdp/heuristic.o $(top_srcdir)/src/bsdp/hpair.o $(top_srcdir)/src/sdp/boundary.o $(top_srcdir)/src/sdp/sdp.o $(top_srcdir)/src/sdp/lookahead.o $(top_srcdir)/src/sdp/straceback.o $(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/struct/slist.o $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/rangetree.o $(top_srcdir)/src/sequence/sequence.o $(top_srcdir)/src/sequence/alphabet.o $(top_srcdir)/src/sequence/translate.o $(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/model/affine.o $(top_srcdir)/src/model/est2genome.o $(top_srcdir)/src/model/ner.o $(top_srcdir)/src/model/protein2dna.o $(top_srcdir)/src/model/protein2genome.o $(top_srcdir)/src/model/coding2coding.o $(top_srcdir)/src/model/coding2genome.o $(top_srcdir)/src/model/cdna2genome.o $(top_srcdir)/src/model/genome2genome.o $(top_srcdir)/src/model/ungapped.o $(top_srcdir)/src/model/intron.o $(top_srcdir)/src/model/frameshift.o $(top_srcdir)/src/model/phase.o $(top_srcdir)/src/model/modeltype.o $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/general/lineparse.o $(top_srcdir)/src/general/socket.o $(top_srcdir)/src/comparison/match.o $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o
--
-+C4_OBJECTS = $(top_srcdir)/src/c4/c4.o \
-+ $(top_srcdir)/src/c4/codegen.o \
-+ $(top_srcdir)/src/c4/cgutil.o \
-+ $(top_srcdir)/src/c4/opair.o \
-+ $(top_srcdir)/src/c4/alignment.o \
-+ $(top_srcdir)/src/c4/optimal.o \
-+ $(top_srcdir)/src/c4/layout.o \
-+ $(top_srcdir)/src/c4/region.o \
-+ $(top_srcdir)/src/c4/subopt.o \
-+ $(top_srcdir)/src/bsdp/bsdp.o \
-+ $(top_srcdir)/src/bsdp/sar.o \
-+ $(top_srcdir)/src/bsdp/heuristic.o \
-+ $(top_srcdir)/src/bsdp/hpair.o \
-+ $(top_srcdir)/src/sdp/boundary.o \
-+ $(top_srcdir)/src/sdp/sdp.o \
-+ $(top_srcdir)/src/sdp/lookahead.o \
-+ $(top_srcdir)/src/sdp/straceback.o \
-+ $(top_srcdir)/src/struct/matrix.o \
-+ $(top_srcdir)/src/struct/slist.o \
-+ $(top_srcdir)/src/struct/pqueue.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/rangetree.o \
-+ $(top_srcdir)/src/sequence/sequence.o \
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/model/affine.o \
-+ $(top_srcdir)/src/model/est2genome.o \
-+ $(top_srcdir)/src/model/ner.o \
-+ $(top_srcdir)/src/model/protein2dna.o \
-+ $(top_srcdir)/src/model/protein2genome.o \
-+ $(top_srcdir)/src/model/coding2coding.o \
-+ $(top_srcdir)/src/model/coding2genome.o \
-+ $(top_srcdir)/src/model/cdna2genome.o \
-+ $(top_srcdir)/src/model/genome2genome.o \
-+ $(top_srcdir)/src/model/ungapped.o \
-+ $(top_srcdir)/src/model/intron.o \
-+ $(top_srcdir)/src/model/frameshift.o \
-+ $(top_srcdir)/src/model/phase.o \
-+ $(top_srcdir)/src/model/modeltype.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/general/socket.o \
-+ $(top_srcdir)/src/comparison/match.o \
-+ $(top_srcdir)/src/sequence/submat.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o
-
- EXTRA_exonerate_SOURCES = c4_model_archive.a c4_model_archive.h
--
- BUILT_SOURCES = c4_model_archive.a
- BOOTSTRAPPER = $(top_srcdir)/src/model/bootstrapper
--
--exonerate_COMPONENTS = @codegen_extra_ldadd@ $(top_srcdir)/src/comparison/wordhood.o $(top_srcdir)/src/comparison/hspset.o $(top_srcdir)/src/comparison/seeder.o $(top_srcdir)/src/comparison/comparison.o $(top_srcdir)/src/database/fastapipe.o $(top_srcdir)/src/database/fastadb.o $(top_srcdir)/src/struct/dejavu.o $(top_srcdir)/src/struct/fsm.o $(top_srcdir)/src/struct/vfsm.o $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/hub/gam.o $(top_srcdir)/src/hub/bsam.o $(top_srcdir)/src/hub/analysis.o $(top_srcdir)/src/general/compoundfile.o $(C4_OBJECTS)
--
-+exonerate_COMPONENTS = @codegen_extra_ldadd@ \
-+ $(top_srcdir)/src/comparison/wordhood.o \
-+ $(top_srcdir)/src/comparison/hspset.o \
-+ $(top_srcdir)/src/comparison/seeder.o \
-+ $(top_srcdir)/src/comparison/comparison.o \
-+ $(top_srcdir)/src/database/fastapipe.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/struct/dejavu.o \
-+ $(top_srcdir)/src/struct/fsm.o \
-+ $(top_srcdir)/src/struct/vfsm.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/hub/gam.o \
-+ $(top_srcdir)/src/hub/bsam.o \
-+ $(top_srcdir)/src/hub/analysis.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(C4_OBJECTS)
-
- exonerate_SOURCES = exonerate.c
--exonerate_DEPENDENCIES = @codegen_extra_sources@ Makefile $(exonerate_COMPONENTS)
-+exonerate_DEPENDENCIES = @codegen_extra_sources@ Makefile \
-+ $(exonerate_COMPONENTS)
-
- exonerate_LDADD = $(exonerate_COMPONENTS) -lm
--
- ipcress_SOURCES = ipcress.c
--ipcress_LDADD = $(top_srcdir)/src/comparison/pcr.o $(top_srcdir)/src/comparison/wordhood.o $(top_srcdir)/src/database/fastadb.o $(top_srcdir)/src/sequence/alphabet.o $(top_srcdir)/src/sequence/sequence.o $(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/sequence/translate.o $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/struct/fsm.o $(top_srcdir)/src/struct/slist.o $(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/general/lineparse.o $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/general/compoundfile.o -lm
-+ipcress_LDADD = $(top_srcdir)/src/comparison/pcr.o \
-+ $(top_srcdir)/src/comparison/wordhood.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/sequence.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/sequence/submat.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o \
-+ $(top_srcdir)/src/struct/fsm.o \
-+ $(top_srcdir)/src/struct/slist.o \
-+ $(top_srcdir)/src/struct/matrix.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ -lm
-
- # Files to clear away
--
- exonerate_server_SOURCES = exonerate-server.c
--exonerate_server_LDADD = $(top_srcdir)/src/general/socket.o $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/comparison/hspset.o $(top_srcdir)/src/comparison/match.o $(top_srcdir)/src/comparison/wordhood.o $(top_srcdir)/src/database/dataset.o $(top_srcdir)/src/database/index.o $(top_srcdir)/src/database/fastadb.o $(top_srcdir)/src/struct/bitarray.o $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/struct/splaytree.o $(top_srcdir)/src/struct/noitree.o $(top_srcdir)/src/struct/vfsm.o $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/rangetree.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/sequence/sequence.o $(top_srcdir)/src/sequence/alphabet.o $(top_srcdir)/src/sequence/translate.o $(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/general/compoundfile.o $(top_srcdir)/src/general/lineparse.o -lm
--
-+exonerate_server_LDADD = $(top_srcdir)/src/general/socket.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/comparison/hspset.o \
-+ $(top_srcdir)/src/comparison/match.o \
-+ $(top_srcdir)/src/comparison/wordhood.o \
-+ $(top_srcdir)/src/database/dataset.o \
-+ $(top_srcdir)/src/database/index.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/struct/bitarray.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o \
-+ $(top_srcdir)/src/struct/splaytree.o \
-+ $(top_srcdir)/src/struct/noitree.o \
-+ $(top_srcdir)/src/struct/vfsm.o \
-+ $(top_srcdir)/src/struct/pqueue.o \
-+ $(top_srcdir)/src/struct/rangetree.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/sequence/sequence.o \
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/submat.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ -lm
-
--CLEANFILES = $(EXTRA_exonerate_SOURCES) @codegen_extra_sources@ @codegen_extra_ld_add@
-+CLEANFILES = $(EXTRA_exonerate_SOURCES) @codegen_extra_sources@ \
-+ @codegen_extra_ld_add@
-
- MAINTAINERCLEANFILES = Makefile.in
--mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
--CONFIG_CLEAN_FILES =
--PROGRAMS = $(bin_PROGRAMS)
--
--
--DEFS = @DEFS@ -I. -I$(srcdir)
--CPPFLAGS = @CPPFLAGS@
--LDFLAGS = @LDFLAGS@
--LIBS = @LIBS@
--exonerate_OBJECTS = exonerate.o
--exonerate_LDFLAGS =
--ipcress_OBJECTS = ipcress.o
--ipcress_DEPENDENCIES = $(top_srcdir)/src/comparison/pcr.o \
--$(top_srcdir)/src/comparison/wordhood.o \
--$(top_srcdir)/src/database/fastadb.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/struct/fsm.o \
--$(top_srcdir)/src/struct/slist.o $(top_srcdir)/src/struct/matrix.o \
--$(top_srcdir)/src/struct/recyclebin.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/general/lineparse.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/compoundfile.o
--ipcress_LDFLAGS =
--exonerate_server_OBJECTS = exonerate-server.o
--exonerate_server_DEPENDENCIES = $(top_srcdir)/src/general/socket.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/comparison/hspset.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/comparison/wordhood.o \
--$(top_srcdir)/src/database/dataset.o $(top_srcdir)/src/database/index.o \
--$(top_srcdir)/src/database/fastadb.o \
--$(top_srcdir)/src/struct/bitarray.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/struct/splaytree.o \
--$(top_srcdir)/src/struct/noitree.o $(top_srcdir)/src/struct/vfsm.o \
--$(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/struct/recyclebin.o \
--$(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/general/lineparse.o
--exonerate_server_LDFLAGS =
--CFLAGS = @CFLAGS@
--COMPILE = $(CC) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
--CCLD = $(CC)
--LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(LDFLAGS) -o $@
--DIST_COMMON = Makefile.am Makefile.in
--
--
--DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
-+all: $(BUILT_SOURCES)
-+ $(MAKE) $(AM_MAKEFLAGS) all-am
-
--TAR = tar
--GZIP_ENV = --best
--SOURCES = $(exonerate_SOURCES) $(EXTRA_exonerate_SOURCES) $(ipcress_SOURCES) $(exonerate_server_SOURCES)
--OBJECTS = $(exonerate_OBJECTS) $(ipcress_OBJECTS) $(exonerate_server_OBJECTS)
--
--all: all-redirect
- .SUFFIXES:
--.SUFFIXES: .S .c .o .s
--$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4)
-- cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps src/program/Makefile
--
-+.SUFFIXES: .c .o .obj
-+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
-+ @for dep in $?; do \
-+ case '$(am__configure_deps)' in \
-+ *$$dep*) \
-+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-+ && { if test -f $@; then exit 0; else break; fi; }; \
-+ exit 1;; \
-+ esac; \
-+ done; \
-+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/program/Makefile'; \
-+ $(am__cd) $(top_srcdir) && \
-+ $(AUTOMAKE) --gnu src/program/Makefile
-+.PRECIOUS: Makefile
- Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-- cd $(top_builddir) \
-- && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
--
--
--mostlyclean-binPROGRAMS:
--
--clean-binPROGRAMS:
-- -test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
--
--distclean-binPROGRAMS:
--
--maintainer-clean-binPROGRAMS:
--
-+ @case '$?' in \
-+ *config.status*) \
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-+ *) \
-+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-+ esac;
-+
-+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+
-+$(top_srcdir)/configure: $(am__configure_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(am__aclocal_m4_deps):
- install-binPROGRAMS: $(bin_PROGRAMS)
- @$(NORMAL_INSTALL)
-- $(mkinstalldirs) $(DESTDIR)$(bindir)
-- @list='$(bin_PROGRAMS)'; for p in $$list; do \
-- if test -f $$p; then \
-- echo " $(INSTALL_PROGRAM) $$p $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`"; \
-- $(INSTALL_PROGRAM) $$p $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \
-- else :; fi; \
-- done
-+ test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)"
-+ @list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
-+ for p in $$list; do echo "$$p $$p"; done | \
-+ sed 's/$(EXEEXT)$$//' | \
-+ while read p p1; do if test -f $$p; \
-+ then echo "$$p"; echo "$$p"; else :; fi; \
-+ done | \
-+ sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
-+ -e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
-+ sed 'N;N;N;s,\n, ,g' | \
-+ $(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
-+ { d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \
-+ if ($$2 == $$4) files[d] = files[d] " " $$1; \
-+ else { print "f", $$3 "/" $$4, $$1; } } \
-+ END { for (d in files) print "f", d, files[d] }' | \
-+ while read type dir files; do \
-+ if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
-+ test -z "$$files" || { \
-+ echo " $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \
-+ $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \
-+ } \
-+ ; done
-
- uninstall-binPROGRAMS:
- @$(NORMAL_UNINSTALL)
-- list='$(bin_PROGRAMS)'; for p in $$list; do \
-- rm -f $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \
-- done
-+ @list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
-+ files=`for p in $$list; do echo "$$p"; done | \
-+ sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
-+ -e 's/$$/$(EXEEXT)/' `; \
-+ test -n "$$list" || exit 0; \
-+ echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
-+ cd "$(DESTDIR)$(bindir)" && rm -f $$files
-
--.c.o:
-- $(COMPILE) -c $<
--
--.s.o:
-- $(COMPILE) -c $<
--
--.S.o:
-- $(COMPILE) -c $<
-+clean-binPROGRAMS:
-+ -test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
-+exonerate$(EXEEXT): $(exonerate_OBJECTS) $(exonerate_DEPENDENCIES)
-+ @rm -f exonerate$(EXEEXT)
-+ $(LINK) $(exonerate_OBJECTS) $(exonerate_LDADD) $(LIBS)
-+exonerate-server$(EXEEXT): $(exonerate_server_OBJECTS) $(exonerate_server_DEPENDENCIES)
-+ @rm -f exonerate-server$(EXEEXT)
-+ $(LINK) $(exonerate_server_OBJECTS) $(exonerate_server_LDADD) $(LIBS)
-+ipcress$(EXEEXT): $(ipcress_OBJECTS) $(ipcress_DEPENDENCIES)
-+ @rm -f ipcress$(EXEEXT)
-+ $(LINK) $(ipcress_OBJECTS) $(ipcress_LDADD) $(LIBS)
-
- mostlyclean-compile:
-- -rm -f *.o core *.core
--
--clean-compile:
-+ -rm -f *.$(OBJEXT)
-
- distclean-compile:
- -rm -f *.tab.c
-
--maintainer-clean-compile:
--
--exonerate: $(exonerate_OBJECTS) $(exonerate_DEPENDENCIES)
-- @rm -f exonerate
-- $(LINK) $(exonerate_LDFLAGS) $(exonerate_OBJECTS) $(exonerate_LDADD) $(LIBS)
--
--ipcress: $(ipcress_OBJECTS) $(ipcress_DEPENDENCIES)
-- @rm -f ipcress
-- $(LINK) $(ipcress_LDFLAGS) $(ipcress_OBJECTS) $(ipcress_LDADD) $(LIBS)
--
--exonerate-server: $(exonerate_server_OBJECTS) $(exonerate_server_DEPENDENCIES)
-- @rm -f exonerate-server
-- $(LINK) $(exonerate_server_LDFLAGS) $(exonerate_server_OBJECTS) $(exonerate_server_LDADD) $(LIBS)
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/exonerate-server.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/exonerate.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/ipcress.Po at am__quote@
-
-+.c.o:
-+ at am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
-+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-+ at am__fastdepCC_FALSE@ $(COMPILE) -c $<
-+
-+.c.obj:
-+ at am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
-+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-+ at am__fastdepCC_FALSE@ $(COMPILE) -c `$(CYGPATH_W) '$<'`
-+
-+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ mkid -fID $$unique
- tags: TAGS
-
--ID: $(HEADERS) $(SOURCES) $(LISP)
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- here=`pwd` && cd $(srcdir) \
-- && mkid -f$$here/ID $$unique $(LISP)
--
--TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) $(LISP)
-- tags=; \
-+TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ set x; \
- here=`pwd`; \
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- test -z "$(ETAGS_ARGS)$$unique$(LISP)$$tags" \
-- || (cd $(srcdir) && etags -o $$here/TAGS $(ETAGS_ARGS) $$tags $$unique $(LISP))
--
--mostlyclean-tags:
--
--clean-tags:
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ shift; \
-+ if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
-+ test -n "$$unique" || unique=$$empty_fix; \
-+ if test $$# -gt 0; then \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ "$$@" $$unique; \
-+ else \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ $$unique; \
-+ fi; \
-+ fi
-+ctags: CTAGS
-+CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ test -z "$(CTAGS_ARGS)$$unique" \
-+ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-+ $$unique
-+
-+GTAGS:
-+ here=`$(am__cd) $(top_builddir) && pwd` \
-+ && $(am__cd) $(top_srcdir) \
-+ && gtags -i $(GTAGS_ARGS) "$$here"
-
- distclean-tags:
-- -rm -f TAGS ID
--
--maintainer-clean-tags:
--
--distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
--
--subdir = src/program
-+ -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-
- distdir: $(DISTFILES)
-- @for file in $(DISTFILES); do \
-- d=$(srcdir); \
-+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ list='$(DISTFILES)'; \
-+ dist_files=`for file in $$list; do echo $$file; done | \
-+ sed -e "s|^$$srcdirstrip/||;t" \
-+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-+ case $$dist_files in \
-+ */*) $(MKDIR_P) `echo "$$dist_files" | \
-+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-+ sort -u` ;; \
-+ esac; \
-+ for file in $$dist_files; do \
-+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
- if test -d $$d/$$file; then \
-- cp -pr $$d/$$file $(distdir)/$$file; \
-+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-+ if test -d "$(distdir)/$$file"; then \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
- else \
-- test -f $(distdir)/$$file \
-- || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
-- || cp -p $$d/$$file $(distdir)/$$file || :; \
-+ test -f "$(distdir)/$$file" \
-+ || cp -p $$d/$$file "$(distdir)/$$file" \
-+ || exit 1; \
- fi; \
- done
-- $(MAKE) $(AM_MAKEFLAGS) top_distdir="$(top_distdir)" distdir="$(distdir)" dist-hook
--info-am:
--info: info-am
--dvi-am:
--dvi: dvi-am
-+ $(MAKE) $(AM_MAKEFLAGS) \
-+ top_distdir="$(top_distdir)" distdir="$(distdir)" \
-+ dist-hook
- check-am: all-am
--check: check-am
--installcheck-am:
--installcheck: installcheck-am
--install-exec-am: install-binPROGRAMS
-+check: $(BUILT_SOURCES)
-+ $(MAKE) $(AM_MAKEFLAGS) check-am
-+all-am: Makefile $(PROGRAMS)
-+installdirs:
-+ for dir in "$(DESTDIR)$(bindir)"; do \
-+ test -z "$$dir" || $(MKDIR_P) "$$dir"; \
-+ done
-+install: $(BUILT_SOURCES)
-+ $(MAKE) $(AM_MAKEFLAGS) install-am
- install-exec: install-exec-am
--
--install-data-am:
- install-data: install-data-am
-+uninstall: uninstall-am
-
- install-am: all-am
- @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
--install: install-am
--uninstall-am: uninstall-binPROGRAMS
--uninstall: uninstall-am
--all-am: Makefile $(PROGRAMS)
--all-redirect: all-am
--install-strip:
-- $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
--installdirs:
-- $(mkinstalldirs) $(DESTDIR)$(bindir)
--
-
-+installcheck: installcheck-am
-+install-strip:
-+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-+ `test -z '$(STRIP)' || \
-+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
- mostlyclean-generic:
-
- clean-generic:
- -test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
-
- distclean-generic:
-- -rm -f Makefile $(CONFIG_CLEAN_FILES)
-- -rm -f config.cache config.log stamp-h stamp-h[0-9]*
-+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
- maintainer-clean-generic:
-- -test -z "$(BUILT_SOURCES)$(MAINTAINERCLEANFILES)" || rm -f $(BUILT_SOURCES) $(MAINTAINERCLEANFILES)
--mostlyclean-am: mostlyclean-binPROGRAMS mostlyclean-compile \
-- mostlyclean-tags mostlyclean-generic
-+ @echo "This command is intended for maintainers to use"
-+ @echo "it deletes files that may require special tools to rebuild."
-+ -test -z "$(BUILT_SOURCES)" || rm -f $(BUILT_SOURCES)
-+ -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
-+clean: clean-am
-
--mostlyclean: mostlyclean-am
-+clean-am: clean-binPROGRAMS clean-generic mostlyclean-am
-
--clean-am: clean-binPROGRAMS clean-compile clean-tags clean-generic \
-- mostlyclean-am
-+distclean: distclean-am
-+ -rm -rf ./$(DEPDIR)
-+ -rm -f Makefile
-+distclean-am: clean-am distclean-compile distclean-generic \
-+ distclean-tags
-
--clean: clean-am
-+dvi: dvi-am
-
--distclean-am: distclean-binPROGRAMS distclean-compile distclean-tags \
-- distclean-generic clean-am
-+dvi-am:
-
--distclean: distclean-am
-+html: html-am
-
--maintainer-clean-am: maintainer-clean-binPROGRAMS \
-- maintainer-clean-compile maintainer-clean-tags \
-- maintainer-clean-generic distclean-am
-- @echo "This command is intended for maintainers to use;"
-- @echo "it deletes files that may require special tools to rebuild."
-+html-am:
-+
-+info: info-am
-+
-+info-am:
-+
-+install-data-am:
-+
-+install-dvi: install-dvi-am
-+
-+install-dvi-am:
-+
-+install-exec-am: install-binPROGRAMS
-+
-+install-html: install-html-am
-+
-+install-html-am:
-+
-+install-info: install-info-am
-+
-+install-info-am:
-+
-+install-man:
-+
-+install-pdf: install-pdf-am
-+
-+install-pdf-am:
-+
-+install-ps: install-ps-am
-+
-+install-ps-am:
-+
-+installcheck-am:
-
- maintainer-clean: maintainer-clean-am
-+ -rm -rf ./$(DEPDIR)
-+ -rm -f Makefile
-+maintainer-clean-am: distclean-am maintainer-clean-generic
-+
-+mostlyclean: mostlyclean-am
-+
-+mostlyclean-am: mostlyclean-compile mostlyclean-generic
-+
-+pdf: pdf-am
-+
-+pdf-am:
-+
-+ps: ps-am
-+
-+ps-am:
-+
-+uninstall-am: uninstall-binPROGRAMS
-+
-+.MAKE: all check install install-am install-strip
-
--.PHONY: mostlyclean-binPROGRAMS distclean-binPROGRAMS clean-binPROGRAMS \
--maintainer-clean-binPROGRAMS uninstall-binPROGRAMS install-binPROGRAMS \
--mostlyclean-compile distclean-compile clean-compile \
--maintainer-clean-compile tags mostlyclean-tags distclean-tags \
--clean-tags maintainer-clean-tags distdir info-am info dvi-am dvi check \
--check-am installcheck-am installcheck install-exec-am install-exec \
--install-data-am install-data install-am install uninstall-am uninstall \
--all-redirect all-am all installdirs mostlyclean-generic \
--distclean-generic clean-generic maintainer-clean-generic clean \
--mostlyclean distclean maintainer-clean
-+.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
-+ clean-generic ctags dist-hook distclean distclean-compile \
-+ distclean-generic distclean-tags distdir dvi dvi-am html \
-+ html-am info info-am install install-am install-binPROGRAMS \
-+ install-data install-data-am install-dvi install-dvi-am \
-+ install-exec install-exec-am install-html install-html-am \
-+ install-info install-info-am install-man install-pdf \
-+ install-pdf-am install-ps install-ps-am install-strip \
-+ installcheck installcheck-am installdirs maintainer-clean \
-+ maintainer-clean-generic mostlyclean mostlyclean-compile \
-+ mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
-+ uninstall-am uninstall-binPROGRAMS
-
- c4_model_archive.h: $(BOOTSTRAPPER)
- $(BOOTSTRAPPER) --compiled no
-diff -ubrN exonerate-2.2.0.orig/src/sdp/Makefile.in exonerate-2.2.0/src/sdp/Makefile.in
---- exonerate-2.2.0.orig/src/sdp/Makefile.in 2008-10-17 12:04:37.000000000 +0200
-+++ exonerate-2.2.0/src/sdp/Makefile.in 2011-12-12 13:33:17.000000000 +0100
-@@ -1,6 +1,9 @@
--# Makefile.in generated automatically by automake 1.4-p6 from Makefile.am
-+# Makefile.in generated by automake 1.11.1 from Makefile.am.
-+# @configure_input@
-
--# Copyright (C) 1994, 1995-8, 1999, 2001 Free Software Foundation, Inc.
-+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
-+# Inc.
- # This Makefile.in is free software; the Free Software Foundation
- # gives unlimited permission to copy and/or distribute it,
- # with or without modifications, as long as this notice is preserved.
-@@ -10,404 +13,655 @@
- # even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- # PARTICULAR PURPOSE.
-
-+ at SET_MAKE@
-
--SHELL = @SHELL@
-
--srcdir = @srcdir@
--top_srcdir = @top_srcdir@
- VPATH = @srcdir@
--prefix = @prefix@
--exec_prefix = @exec_prefix@
--
--bindir = @bindir@
--sbindir = @sbindir@
--libexecdir = @libexecdir@
--datadir = @datadir@
--sysconfdir = @sysconfdir@
--sharedstatedir = @sharedstatedir@
--localstatedir = @localstatedir@
--libdir = @libdir@
--infodir = @infodir@
--mandir = @mandir@
--includedir = @includedir@
--oldincludedir = /usr/include
--
--DESTDIR =
--
- pkgdatadir = $(datadir)/@PACKAGE@
--pkglibdir = $(libdir)/@PACKAGE@
- pkgincludedir = $(includedir)/@PACKAGE@
--
--top_builddir = ../..
--
--ACLOCAL = @ACLOCAL@
--AUTOCONF = @AUTOCONF@
--AUTOMAKE = @AUTOMAKE@
--AUTOHEADER = @AUTOHEADER@
--
--INSTALL = @INSTALL@
--INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
--INSTALL_DATA = @INSTALL_DATA@
--INSTALL_SCRIPT = @INSTALL_SCRIPT@
--transform = @program_transform_name@
--
-+pkglibdir = $(libdir)/@PACKAGE@
-+pkglibexecdir = $(libexecdir)/@PACKAGE@
-+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-+install_sh_DATA = $(install_sh) -c -m 644
-+install_sh_PROGRAM = $(install_sh) -c
-+install_sh_SCRIPT = $(install_sh) -c
-+INSTALL_HEADER = $(INSTALL_DATA)
-+transform = $(program_transform_name)
- NORMAL_INSTALL = :
- PRE_INSTALL = :
- POST_INSTALL = :
- NORMAL_UNINSTALL = :
- PRE_UNINSTALL = :
- POST_UNINSTALL = :
--host_alias = @host_alias@
-+build_triplet = @build@
- host_triplet = @host@
-+TESTS = sdp.test$(EXEEXT) lookahead.test$(EXEEXT) \
-+ boundary.test$(EXEEXT) scheduler.test$(EXEEXT) \
-+ straceback.test$(EXEEXT)
-+noinst_PROGRAMS = $(am__EXEEXT_1)
-+subdir = src/sdp
-+DIST_COMMON = $(noinst_HEADERS) $(srcdir)/Makefile.am \
-+ $(srcdir)/Makefile.in
-+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-+am__aclocal_m4_deps = $(top_srcdir)/configure.in
-+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-+ $(ACLOCAL_M4)
-+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
-+CONFIG_CLEAN_FILES =
-+CONFIG_CLEAN_VPATH_FILES =
-+am__EXEEXT_1 = sdp.test$(EXEEXT) lookahead.test$(EXEEXT) \
-+ boundary.test$(EXEEXT) scheduler.test$(EXEEXT) \
-+ straceback.test$(EXEEXT)
-+PROGRAMS = $(noinst_PROGRAMS)
-+am_boundary_test_OBJECTS = boundary.test.$(OBJEXT) boundary.$(OBJEXT)
-+boundary_test_OBJECTS = $(am_boundary_test_OBJECTS)
-+boundary_test_DEPENDENCIES = $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/c4/region.o
-+am_lookahead_test_OBJECTS = lookahead.test.$(OBJEXT) \
-+ lookahead.$(OBJEXT)
-+lookahead_test_OBJECTS = $(am_lookahead_test_OBJECTS)
-+lookahead_test_LDADD = $(LDADD)
-+am_scheduler_test_OBJECTS = scheduler.test.$(OBJEXT) \
-+ scheduler.$(OBJEXT) lookahead.$(OBJEXT) boundary.$(OBJEXT) \
-+ straceback.$(OBJEXT)
-+scheduler_test_OBJECTS = $(am_scheduler_test_OBJECTS)
-+am__DEPENDENCIES_1 = $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o \
-+ $(top_srcdir)/src/sequence/sequence.o \
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/lineparse.o
-+am__DEPENDENCIES_2 = $(top_srcdir)/src/comparison/match.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o \
-+ $(top_srcdir)/src/sequence/submat.o $(C4_OBJ) \
-+ $(am__DEPENDENCIES_1)
-+scheduler_test_DEPENDENCIES = $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/slist.o \
-+ $(top_srcdir)/src/struct/rangetree.o $(am__DEPENDENCIES_2)
-+am_sdp_test_OBJECTS = sdp.test.$(OBJEXT) sdp.$(OBJEXT) \
-+ boundary.$(OBJEXT) scheduler.$(OBJEXT) lookahead.$(OBJEXT) \
-+ straceback.$(OBJEXT)
-+sdp_test_OBJECTS = $(am_sdp_test_OBJECTS)
-+sdp_test_DEPENDENCIES = $(top_srcdir)/src/struct/pqueue.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/slist.o \
-+ $(top_srcdir)/src/struct/rangetree.o \
-+ $(top_srcdir)/src/comparison/hspset.o \
-+ $(top_srcdir)/src/comparison/comparison.o \
-+ $(top_srcdir)/src/comparison/wordhood.o $(am__DEPENDENCIES_2)
-+am_straceback_test_OBJECTS = straceback.test.$(OBJEXT) \
-+ straceback.$(OBJEXT)
-+straceback_test_OBJECTS = $(am_straceback_test_OBJECTS)
-+straceback_test_DEPENDENCIES = $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/slist.o \
-+ $(top_srcdir)/src/struct/rangetree.o $(C4_OBJ) \
-+ $(am__DEPENDENCIES_1)
-+DEFAULT_INCLUDES = -I. at am__isrc@
-+depcomp = $(SHELL) $(top_srcdir)/depcomp
-+am__depfiles_maybe = depfiles
-+am__mv = mv -f
-+COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
-+ $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
-+CCLD = $(CC)
-+LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
-+SOURCES = $(boundary_test_SOURCES) $(lookahead_test_SOURCES) \
-+ $(scheduler_test_SOURCES) $(sdp_test_SOURCES) \
-+ $(straceback_test_SOURCES)
-+DIST_SOURCES = $(boundary_test_SOURCES) $(lookahead_test_SOURCES) \
-+ $(scheduler_test_SOURCES) $(sdp_test_SOURCES) \
-+ $(straceback_test_SOURCES)
-+HEADERS = $(noinst_HEADERS)
-+ETAGS = etags
-+CTAGS = ctags
-+am__tty_colors = \
-+red=; grn=; lgn=; blu=; std=
-+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-+ACLOCAL = @ACLOCAL@
-+AMTAR = @AMTAR@
-+AUTOCONF = @AUTOCONF@
-+AUTOHEADER = @AUTOHEADER@
-+AUTOMAKE = @AUTOMAKE@
-+AWK = @AWK@
- CC = @CC@
-+CCDEPMODE = @CCDEPMODE@
-+CFLAGS = @CFLAGS@
-+CPP = @CPP@
-+CPPFLAGS = @CPPFLAGS@
-+CYGPATH_W = @CYGPATH_W@
-+DEFS = @DEFS@
-+DEPDIR = @DEPDIR@
-+ECHO_C = @ECHO_C@
-+ECHO_N = @ECHO_N@
-+ECHO_T = @ECHO_T@
-+EGREP = @EGREP@
-+EXEEXT = @EXEEXT@
- GLIB_CONFIG = @GLIB_CONFIG@
--HAVE_LIB = @HAVE_LIB@
--LIB = @LIB@
--LTLIB = @LTLIB@
-+GREP = @GREP@
-+INSTALL = @INSTALL@
-+INSTALL_DATA = @INSTALL_DATA@
-+INSTALL_PROGRAM = @INSTALL_PROGRAM@
-+INSTALL_SCRIPT = @INSTALL_SCRIPT@
-+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-+LDFLAGS = @LDFLAGS@
-+LIBOBJS = @LIBOBJS@
-+LIBS = @LIBS@
-+LTLIBOBJS = @LTLIBOBJS@
- MAKEINFO = @MAKEINFO@
-+MKDIR_P = @MKDIR_P@
-+OBJEXT = @OBJEXT@
- PACKAGE = @PACKAGE@
-+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-+PACKAGE_NAME = @PACKAGE_NAME@
-+PACKAGE_STRING = @PACKAGE_STRING@
-+PACKAGE_TARNAME = @PACKAGE_TARNAME@
-+PACKAGE_URL = @PACKAGE_URL@
-+PACKAGE_VERSION = @PACKAGE_VERSION@
-+PATH_SEPARATOR = @PATH_SEPARATOR@
- PKG_CONFIG = @PKG_CONFIG@
-+SET_MAKE = @SET_MAKE@
-+SHELL = @SHELL@
-+STRIP = @STRIP@
- VERSION = @VERSION@
-+abs_builddir = @abs_builddir@
-+abs_srcdir = @abs_srcdir@
-+abs_top_builddir = @abs_top_builddir@
-+abs_top_srcdir = @abs_top_srcdir@
-+ac_ct_CC = @ac_ct_CC@
-+am__include = @am__include@
-+am__leading_dot = @am__leading_dot@
-+am__quote = @am__quote@
-+am__tar = @am__tar@
-+am__untar = @am__untar@
-+bindir = @bindir@
-+build = @build@
-+build_alias = @build_alias@
-+build_cpu = @build_cpu@
-+build_os = @build_os@
-+build_vendor = @build_vendor@
-+builddir = @builddir@
- codegen_extra_ldadd = @codegen_extra_ldadd@
- codegen_extra_sources = @codegen_extra_sources@
-+datadir = @datadir@
- datarootdir = @datarootdir@
-+docdir = @docdir@
-+dvidir = @dvidir@
-+exec_prefix = @exec_prefix@
- glib_cflags = @glib_cflags@
- glib_libs = @glib_libs@
- host = @host@
-+host_alias = @host_alias@
-+host_cpu = @host_cpu@
-+host_os = @host_os@
-+host_vendor = @host_vendor@
-+htmldir = @htmldir@
-+includedir = @includedir@
-+infodir = @infodir@
-+install_sh = @install_sh@
- installed_util_list = @installed_util_list@
-+libdir = @libdir@
-+libexecdir = @libexecdir@
-+localedir = @localedir@
-+localstatedir = @localstatedir@
-+mandir = @mandir@
-+mkdir_p = @mkdir_p@
-+oldincludedir = @oldincludedir@
-+pdfdir = @pdfdir@
-+prefix = @prefix@
-+program_transform_name = @program_transform_name@
-+psdir = @psdir@
-+sbindir = @sbindir@
-+sharedstatedir = @sharedstatedir@
- source_root_dir = @source_root_dir@
-+srcdir = @srcdir@
-+sysconfdir = @sysconfdir@
-+target_alias = @target_alias@
-+top_build_prefix = @top_build_prefix@
-+top_builddir = @top_builddir@
-+top_srcdir = @top_srcdir@
- use_pthreads = @use_pthreads@
--
--TESTS = sdp.test lookahead.test boundary.test scheduler.test straceback.test
--
--
--noinst_PROGRAMS = $(TESTS)
--
--INCLUDES = -I$(top_srcdir)/src/struct -I$(top_srcdir)/src/comparison -I$(top_srcdir)/src/sequence -I$(top_srcdir)/src/general -I$(top_srcdir)/src/c4 -DSOURCE_ROOT_DIR="\"@source_root_dir@\"" -DGLIB_CFLAGS="\"@glib_cflags@\"" -DHOSTTYPE="\"@host@\""
--
-+INCLUDES = -I$(top_srcdir)/src/struct \
-+ -I$(top_srcdir)/src/comparison \
-+ -I$(top_srcdir)/src/sequence \
-+ -I$(top_srcdir)/src/general \
-+ -I$(top_srcdir)/src/c4 \
-+ -DSOURCE_ROOT_DIR="\"@source_root_dir@\"" \
-+ -DGLIB_CFLAGS="\"@glib_cflags@\"" \
-+ -DHOSTTYPE="\"@host@\""
-
- noinst_HEADERS = scheduler.h sdp.h lookahead.h boundary.h straceback.h
--
--SEQUENCE_OBJ = $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o $(top_srcdir)/src/sequence/alphabet.o $(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/sequence/translate.o $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/general/lineparse.o -lm
--
--
--C4_OBJ = $(top_srcdir)/src/c4/c4.o $(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/optimal.o $(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/region.o $(top_srcdir)/src/c4/layout.o $(top_srcdir)/src/c4/viterbi.o $(top_srcdir)/src/c4/subopt.o $(top_srcdir)/src/c4/cgutil.o
--
--
--ALIGNMENT_OBJ = $(top_srcdir)/src/comparison/match.o $(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/sequence/submat.o $(C4_OBJ) $(SEQUENCE_OBJ)
--
--
--sdp_test_SOURCES = sdp.test.c sdp.c boundary.c scheduler.c lookahead.c straceback.c
--
--sdp_test_LDADD = $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/slist.o $(top_srcdir)/src/struct/rangetree.o $(top_srcdir)/src/comparison/hspset.o $(top_srcdir)/src/comparison/comparison.o $(top_srcdir)/src/comparison/wordhood.o $(ALIGNMENT_OBJ)
--
--
--scheduler_test_SOURCES = scheduler.test.c scheduler.c lookahead.c boundary.c straceback.c
--
--scheduler_test_LDADD = $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/slist.o $(top_srcdir)/src/struct/rangetree.o $(ALIGNMENT_OBJ)
--
-+SEQUENCE_OBJ = $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o \
-+ $(top_srcdir)/src/sequence/sequence.o \
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ -lm
-+
-+C4_OBJ = $(top_srcdir)/src/c4/c4.o \
-+ $(top_srcdir)/src/c4/alignment.o \
-+ $(top_srcdir)/src/c4/optimal.o \
-+ $(top_srcdir)/src/c4/codegen.o \
-+ $(top_srcdir)/src/c4/region.o \
-+ $(top_srcdir)/src/c4/layout.o \
-+ $(top_srcdir)/src/c4/viterbi.o \
-+ $(top_srcdir)/src/c4/subopt.o \
-+ $(top_srcdir)/src/c4/cgutil.o
-+
-+ALIGNMENT_OBJ = $(top_srcdir)/src/comparison/match.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o \
-+ $(top_srcdir)/src/sequence/submat.o \
-+ $(C4_OBJ) $(SEQUENCE_OBJ)
-+
-+sdp_test_SOURCES = sdp.test.c sdp.c boundary.c scheduler.c lookahead.c \
-+ straceback.c
-+
-+sdp_test_LDADD = $(top_srcdir)/src/struct/pqueue.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/slist.o \
-+ $(top_srcdir)/src/struct/rangetree.o \
-+ $(top_srcdir)/src/comparison/hspset.o \
-+ $(top_srcdir)/src/comparison/comparison.o \
-+ $(top_srcdir)/src/comparison/wordhood.o \
-+ $(ALIGNMENT_OBJ)
-+
-+scheduler_test_SOURCES = scheduler.test.c scheduler.c lookahead.c \
-+ boundary.c straceback.c
-+
-+scheduler_test_LDADD = $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/slist.o \
-+ $(top_srcdir)/src/struct/rangetree.o \
-+ $(ALIGNMENT_OBJ)
-
- lookahead_test_SOURCES = lookahead.test.c lookahead.c
--
- boundary_test_SOURCES = boundary.test.c boundary.c
--boundary_test_LDADD = $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/c4/region.o
--
-+boundary_test_LDADD = $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/c4/region.o
-
- straceback_test_SOURCES = straceback.test.c straceback.c
--straceback_test_LDADD = $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/slist.o $(top_srcdir)/src/struct/rangetree.o $(C4_OBJ) $(SEQUENCE_OBJ)
-+straceback_test_LDADD = $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/slist.o \
-+ $(top_srcdir)/src/struct/rangetree.o \
-+ $(C4_OBJ) $(SEQUENCE_OBJ)
-
-
- # Files to clear away
--
- MAINTAINERCLEANFILES = Makefile.in
--mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
--CONFIG_CLEAN_FILES =
--PROGRAMS = $(noinst_PROGRAMS)
--
--
--DEFS = @DEFS@ -I. -I$(srcdir)
--CPPFLAGS = @CPPFLAGS@
--LDFLAGS = @LDFLAGS@
--LIBS = @LIBS@
--sdp_test_OBJECTS = sdp.test.o sdp.o boundary.o scheduler.o lookahead.o \
--straceback.o
--sdp_test_DEPENDENCIES = $(top_srcdir)/src/struct/pqueue.o \
--$(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/slist.o \
--$(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/comparison/hspset.o \
--$(top_srcdir)/src/comparison/comparison.o \
--$(top_srcdir)/src/comparison/wordhood.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/c4/c4.o \
--$(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/optimal.o \
--$(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/region.o \
--$(top_srcdir)/src/c4/layout.o $(top_srcdir)/src/c4/viterbi.o \
--$(top_srcdir)/src/c4/subopt.o $(top_srcdir)/src/c4/cgutil.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--sdp_test_LDFLAGS =
--lookahead_test_OBJECTS = lookahead.test.o lookahead.o
--lookahead_test_LDADD = $(LDADD)
--lookahead_test_DEPENDENCIES =
--lookahead_test_LDFLAGS =
--boundary_test_OBJECTS = boundary.test.o boundary.o
--boundary_test_DEPENDENCIES = $(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/c4/region.o
--boundary_test_LDFLAGS =
--scheduler_test_OBJECTS = scheduler.test.o scheduler.o lookahead.o \
--boundary.o straceback.o
--scheduler_test_DEPENDENCIES = $(top_srcdir)/src/struct/recyclebin.o \
--$(top_srcdir)/src/struct/slist.o $(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/c4/c4.o \
--$(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/optimal.o \
--$(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/region.o \
--$(top_srcdir)/src/c4/layout.o $(top_srcdir)/src/c4/viterbi.o \
--$(top_srcdir)/src/c4/subopt.o $(top_srcdir)/src/c4/cgutil.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--scheduler_test_LDFLAGS =
--straceback_test_OBJECTS = straceback.test.o straceback.o
--straceback_test_DEPENDENCIES = $(top_srcdir)/src/struct/recyclebin.o \
--$(top_srcdir)/src/struct/slist.o $(top_srcdir)/src/struct/rangetree.o \
--$(top_srcdir)/src/c4/c4.o $(top_srcdir)/src/c4/alignment.o \
--$(top_srcdir)/src/c4/optimal.o $(top_srcdir)/src/c4/codegen.o \
--$(top_srcdir)/src/c4/region.o $(top_srcdir)/src/c4/layout.o \
--$(top_srcdir)/src/c4/viterbi.o $(top_srcdir)/src/c4/subopt.o \
--$(top_srcdir)/src/c4/cgutil.o $(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--straceback_test_LDFLAGS =
--CFLAGS = @CFLAGS@
--COMPILE = $(CC) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
--CCLD = $(CC)
--LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(LDFLAGS) -o $@
--HEADERS = $(noinst_HEADERS)
--
--DIST_COMMON = Makefile.am Makefile.in
--
--
--DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
--
--TAR = tar
--GZIP_ENV = --best
--SOURCES = $(sdp_test_SOURCES) $(lookahead_test_SOURCES) $(boundary_test_SOURCES) $(scheduler_test_SOURCES) $(straceback_test_SOURCES)
--OBJECTS = $(sdp_test_OBJECTS) $(lookahead_test_OBJECTS) $(boundary_test_OBJECTS) $(scheduler_test_OBJECTS) $(straceback_test_OBJECTS)
-+all: all-am
-
--all: all-redirect
- .SUFFIXES:
--.SUFFIXES: .S .c .o .s
--$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4)
-- cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps src/sdp/Makefile
--
-+.SUFFIXES: .c .o .obj
-+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
-+ @for dep in $?; do \
-+ case '$(am__configure_deps)' in \
-+ *$$dep*) \
-+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-+ && { if test -f $@; then exit 0; else break; fi; }; \
-+ exit 1;; \
-+ esac; \
-+ done; \
-+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/sdp/Makefile'; \
-+ $(am__cd) $(top_srcdir) && \
-+ $(AUTOMAKE) --gnu src/sdp/Makefile
-+.PRECIOUS: Makefile
- Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-- cd $(top_builddir) \
-- && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
--
--
--mostlyclean-noinstPROGRAMS:
-+ @case '$?' in \
-+ *config.status*) \
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-+ *) \
-+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-+ esac;
-+
-+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+
-+$(top_srcdir)/configure: $(am__configure_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(am__aclocal_m4_deps):
-
- clean-noinstPROGRAMS:
- -test -z "$(noinst_PROGRAMS)" || rm -f $(noinst_PROGRAMS)
--
--distclean-noinstPROGRAMS:
--
--maintainer-clean-noinstPROGRAMS:
--
--.c.o:
-- $(COMPILE) -c $<
--
--.s.o:
-- $(COMPILE) -c $<
--
--.S.o:
-- $(COMPILE) -c $<
-+boundary.test$(EXEEXT): $(boundary_test_OBJECTS) $(boundary_test_DEPENDENCIES)
-+ @rm -f boundary.test$(EXEEXT)
-+ $(LINK) $(boundary_test_OBJECTS) $(boundary_test_LDADD) $(LIBS)
-+lookahead.test$(EXEEXT): $(lookahead_test_OBJECTS) $(lookahead_test_DEPENDENCIES)
-+ @rm -f lookahead.test$(EXEEXT)
-+ $(LINK) $(lookahead_test_OBJECTS) $(lookahead_test_LDADD) $(LIBS)
-+scheduler.test$(EXEEXT): $(scheduler_test_OBJECTS) $(scheduler_test_DEPENDENCIES)
-+ @rm -f scheduler.test$(EXEEXT)
-+ $(LINK) $(scheduler_test_OBJECTS) $(scheduler_test_LDADD) $(LIBS)
-+sdp.test$(EXEEXT): $(sdp_test_OBJECTS) $(sdp_test_DEPENDENCIES)
-+ @rm -f sdp.test$(EXEEXT)
-+ $(LINK) $(sdp_test_OBJECTS) $(sdp_test_LDADD) $(LIBS)
-+straceback.test$(EXEEXT): $(straceback_test_OBJECTS) $(straceback_test_DEPENDENCIES)
-+ @rm -f straceback.test$(EXEEXT)
-+ $(LINK) $(straceback_test_OBJECTS) $(straceback_test_LDADD) $(LIBS)
-
- mostlyclean-compile:
-- -rm -f *.o core *.core
--
--clean-compile:
-+ -rm -f *.$(OBJEXT)
-
- distclean-compile:
- -rm -f *.tab.c
-
--maintainer-clean-compile:
--
--sdp.test: $(sdp_test_OBJECTS) $(sdp_test_DEPENDENCIES)
-- @rm -f sdp.test
-- $(LINK) $(sdp_test_LDFLAGS) $(sdp_test_OBJECTS) $(sdp_test_LDADD) $(LIBS)
--
--lookahead.test: $(lookahead_test_OBJECTS) $(lookahead_test_DEPENDENCIES)
-- @rm -f lookahead.test
-- $(LINK) $(lookahead_test_LDFLAGS) $(lookahead_test_OBJECTS) $(lookahead_test_LDADD) $(LIBS)
--
--boundary.test: $(boundary_test_OBJECTS) $(boundary_test_DEPENDENCIES)
-- @rm -f boundary.test
-- $(LINK) $(boundary_test_LDFLAGS) $(boundary_test_OBJECTS) $(boundary_test_LDADD) $(LIBS)
--
--scheduler.test: $(scheduler_test_OBJECTS) $(scheduler_test_DEPENDENCIES)
-- @rm -f scheduler.test
-- $(LINK) $(scheduler_test_LDFLAGS) $(scheduler_test_OBJECTS) $(scheduler_test_LDADD) $(LIBS)
--
--straceback.test: $(straceback_test_OBJECTS) $(straceback_test_DEPENDENCIES)
-- @rm -f straceback.test
-- $(LINK) $(straceback_test_LDFLAGS) $(straceback_test_OBJECTS) $(straceback_test_LDADD) $(LIBS)
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/boundary.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/boundary.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/lookahead.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/lookahead.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/scheduler.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/scheduler.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sdp.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sdp.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/straceback.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/straceback.test.Po at am__quote@
-
-+.c.o:
-+ at am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
-+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-+ at am__fastdepCC_FALSE@ $(COMPILE) -c $<
-+
-+.c.obj:
-+ at am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
-+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-+ at am__fastdepCC_FALSE@ $(COMPILE) -c `$(CYGPATH_W) '$<'`
-+
-+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ mkid -fID $$unique
- tags: TAGS
-
--ID: $(HEADERS) $(SOURCES) $(LISP)
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- here=`pwd` && cd $(srcdir) \
-- && mkid -f$$here/ID $$unique $(LISP)
--
--TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) $(LISP)
-- tags=; \
-+TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ set x; \
- here=`pwd`; \
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- test -z "$(ETAGS_ARGS)$$unique$(LISP)$$tags" \
-- || (cd $(srcdir) && etags -o $$here/TAGS $(ETAGS_ARGS) $$tags $$unique $(LISP))
--
--mostlyclean-tags:
--
--clean-tags:
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ shift; \
-+ if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
-+ test -n "$$unique" || unique=$$empty_fix; \
-+ if test $$# -gt 0; then \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ "$$@" $$unique; \
-+ else \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ $$unique; \
-+ fi; \
-+ fi
-+ctags: CTAGS
-+CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ test -z "$(CTAGS_ARGS)$$unique" \
-+ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-+ $$unique
-+
-+GTAGS:
-+ here=`$(am__cd) $(top_builddir) && pwd` \
-+ && $(am__cd) $(top_srcdir) \
-+ && gtags -i $(GTAGS_ARGS) "$$here"
-
- distclean-tags:
-- -rm -f TAGS ID
--
--maintainer-clean-tags:
--
--distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
--
--subdir = src/sdp
-+ -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-
--distdir: $(DISTFILES)
-- @for file in $(DISTFILES); do \
-- d=$(srcdir); \
-- if test -d $$d/$$file; then \
-- cp -pr $$d/$$file $(distdir)/$$file; \
-- else \
-- test -f $(distdir)/$$file \
-- || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
-- || cp -p $$d/$$file $(distdir)/$$file || :; \
-- fi; \
-- done
- check-TESTS: $(TESTS)
-- @failed=0; all=0; \
-+ @failed=0; all=0; xfail=0; xpass=0; skip=0; \
- srcdir=$(srcdir); export srcdir; \
-- for tst in $(TESTS); do \
-- if test -f $$tst; then dir=.; \
-- else dir="$(srcdir)"; fi; \
-- if $(TESTS_ENVIRONMENT) $$dir/$$tst; then \
-+ list=' $(TESTS) '; \
-+ $(am__tty_colors); \
-+ if test -n "$$list"; then \
-+ for tst in $$list; do \
-+ if test -f ./$$tst; then dir=./; \
-+ elif test -f $$tst; then dir=; \
-+ else dir="$(srcdir)/"; fi; \
-+ if $(TESTS_ENVIRONMENT) $${dir}$$tst; then \
- all=`expr $$all + 1`; \
-- echo "PASS: $$tst"; \
-+ case " $(XFAIL_TESTS) " in \
-+ *[\ \ ]$$tst[\ \ ]*) \
-+ xpass=`expr $$xpass + 1`; \
-+ failed=`expr $$failed + 1`; \
-+ col=$$red; res=XPASS; \
-+ ;; \
-+ *) \
-+ col=$$grn; res=PASS; \
-+ ;; \
-+ esac; \
- elif test $$? -ne 77; then \
- all=`expr $$all + 1`; \
-+ case " $(XFAIL_TESTS) " in \
-+ *[\ \ ]$$tst[\ \ ]*) \
-+ xfail=`expr $$xfail + 1`; \
-+ col=$$lgn; res=XFAIL; \
-+ ;; \
-+ *) \
- failed=`expr $$failed + 1`; \
-- echo "FAIL: $$tst"; \
-+ col=$$red; res=FAIL; \
-+ ;; \
-+ esac; \
-+ else \
-+ skip=`expr $$skip + 1`; \
-+ col=$$blu; res=SKIP; \
- fi; \
-+ echo "$${col}$$res$${std}: $$tst"; \
- done; \
-+ if test "$$all" -eq 1; then \
-+ tests="test"; \
-+ All=""; \
-+ else \
-+ tests="tests"; \
-+ All="All "; \
-+ fi; \
-+ if test "$$failed" -eq 0; then \
-+ if test "$$xfail" -eq 0; then \
-+ banner="$$All$$all $$tests passed"; \
-+ else \
-+ if test "$$xfail" -eq 1; then failures=failure; else failures=failures; fi; \
-+ banner="$$All$$all $$tests behaved as expected ($$xfail expected $$failures)"; \
-+ fi; \
-+ else \
-+ if test "$$xpass" -eq 0; then \
-+ banner="$$failed of $$all $$tests failed"; \
-+ else \
-+ if test "$$xpass" -eq 1; then passes=pass; else passes=passes; fi; \
-+ banner="$$failed of $$all $$tests did not behave as expected ($$xpass unexpected $$passes)"; \
-+ fi; \
-+ fi; \
-+ dashes="$$banner"; \
-+ skipped=""; \
-+ if test "$$skip" -ne 0; then \
-+ if test "$$skip" -eq 1; then \
-+ skipped="($$skip test was not run)"; \
-+ else \
-+ skipped="($$skip tests were not run)"; \
-+ fi; \
-+ test `echo "$$skipped" | wc -c` -le `echo "$$banner" | wc -c` || \
-+ dashes="$$skipped"; \
-+ fi; \
-+ report=""; \
-+ if test "$$failed" -ne 0 && test -n "$(PACKAGE_BUGREPORT)"; then \
-+ report="Please report to $(PACKAGE_BUGREPORT)"; \
-+ test `echo "$$report" | wc -c` -le `echo "$$banner" | wc -c` || \
-+ dashes="$$report"; \
-+ fi; \
-+ dashes=`echo "$$dashes" | sed s/./=/g`; \
- if test "$$failed" -eq 0; then \
-- banner="All $$all tests passed"; \
-+ echo "$$grn$$dashes"; \
- else \
-- banner="$$failed of $$all tests failed"; \
-+ echo "$$red$$dashes"; \
- fi; \
-- dashes=`echo "$$banner" | sed s/./=/g`; \
-- echo "$$dashes"; \
- echo "$$banner"; \
-- echo "$$dashes"; \
-- test "$$failed" -eq 0
--info-am:
--info: info-am
--dvi-am:
--dvi: dvi-am
-+ test -z "$$skipped" || echo "$$skipped"; \
-+ test -z "$$report" || echo "$$report"; \
-+ echo "$$dashes$$std"; \
-+ test "$$failed" -eq 0; \
-+ else :; fi
-+
-+distdir: $(DISTFILES)
-+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ list='$(DISTFILES)'; \
-+ dist_files=`for file in $$list; do echo $$file; done | \
-+ sed -e "s|^$$srcdirstrip/||;t" \
-+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-+ case $$dist_files in \
-+ */*) $(MKDIR_P) `echo "$$dist_files" | \
-+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-+ sort -u` ;; \
-+ esac; \
-+ for file in $$dist_files; do \
-+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
-+ if test -d $$d/$$file; then \
-+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-+ if test -d "$(distdir)/$$file"; then \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
-+ else \
-+ test -f "$(distdir)/$$file" \
-+ || cp -p $$d/$$file "$(distdir)/$$file" \
-+ || exit 1; \
-+ fi; \
-+ done
- check-am: all-am
- $(MAKE) $(AM_MAKEFLAGS) check-TESTS
- check: check-am
--installcheck-am:
--installcheck: installcheck-am
--install-exec-am:
-+all-am: Makefile $(PROGRAMS) $(HEADERS)
-+installdirs:
-+install: install-am
- install-exec: install-exec-am
--
--install-data-am:
- install-data: install-data-am
-+uninstall: uninstall-am
-
- install-am: all-am
- @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
--install: install-am
--uninstall-am:
--uninstall: uninstall-am
--all-am: Makefile $(PROGRAMS) $(HEADERS)
--all-redirect: all-am
--install-strip:
-- $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
--installdirs:
--
-
-+installcheck: installcheck-am
-+install-strip:
-+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-+ `test -z '$(STRIP)' || \
-+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
- mostlyclean-generic:
-
- clean-generic:
-
- distclean-generic:
-- -rm -f Makefile $(CONFIG_CLEAN_FILES)
-- -rm -f config.cache config.log stamp-h stamp-h[0-9]*
-+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
- maintainer-clean-generic:
-+ @echo "This command is intended for maintainers to use"
-+ @echo "it deletes files that may require special tools to rebuild."
- -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
--mostlyclean-am: mostlyclean-noinstPROGRAMS mostlyclean-compile \
-- mostlyclean-tags mostlyclean-generic
-+clean: clean-am
-
--mostlyclean: mostlyclean-am
-+clean-am: clean-generic clean-noinstPROGRAMS mostlyclean-am
-
--clean-am: clean-noinstPROGRAMS clean-compile clean-tags clean-generic \
-- mostlyclean-am
-+distclean: distclean-am
-+ -rm -rf ./$(DEPDIR)
-+ -rm -f Makefile
-+distclean-am: clean-am distclean-compile distclean-generic \
-+ distclean-tags
-
--clean: clean-am
-+dvi: dvi-am
-
--distclean-am: distclean-noinstPROGRAMS distclean-compile distclean-tags \
-- distclean-generic clean-am
-+dvi-am:
-
--distclean: distclean-am
-+html: html-am
-
--maintainer-clean-am: maintainer-clean-noinstPROGRAMS \
-- maintainer-clean-compile maintainer-clean-tags \
-- maintainer-clean-generic distclean-am
-- @echo "This command is intended for maintainers to use;"
-- @echo "it deletes files that may require special tools to rebuild."
-+html-am:
-+
-+info: info-am
-+
-+info-am:
-+
-+install-data-am:
-+
-+install-dvi: install-dvi-am
-+
-+install-dvi-am:
-+
-+install-exec-am:
-+
-+install-html: install-html-am
-+
-+install-html-am:
-+
-+install-info: install-info-am
-+
-+install-info-am:
-+
-+install-man:
-+
-+install-pdf: install-pdf-am
-+
-+install-pdf-am:
-+
-+install-ps: install-ps-am
-+
-+install-ps-am:
-+
-+installcheck-am:
-
- maintainer-clean: maintainer-clean-am
-+ -rm -rf ./$(DEPDIR)
-+ -rm -f Makefile
-+maintainer-clean-am: distclean-am maintainer-clean-generic
-+
-+mostlyclean: mostlyclean-am
-+
-+mostlyclean-am: mostlyclean-compile mostlyclean-generic
-+
-+pdf: pdf-am
-+
-+pdf-am:
-+
-+ps: ps-am
-+
-+ps-am:
-+
-+uninstall-am:
-+
-+.MAKE: check-am install-am install-strip
-
--.PHONY: mostlyclean-noinstPROGRAMS distclean-noinstPROGRAMS \
--clean-noinstPROGRAMS maintainer-clean-noinstPROGRAMS \
--mostlyclean-compile distclean-compile clean-compile \
--maintainer-clean-compile tags mostlyclean-tags distclean-tags \
--clean-tags maintainer-clean-tags distdir check-TESTS info-am info \
--dvi-am dvi check check-am installcheck-am installcheck install-exec-am \
--install-exec install-data-am install-data install-am install \
--uninstall-am uninstall all-redirect all-am all installdirs \
--mostlyclean-generic distclean-generic clean-generic \
--maintainer-clean-generic clean mostlyclean distclean maintainer-clean
-+.PHONY: CTAGS GTAGS all all-am check check-TESTS check-am clean \
-+ clean-generic clean-noinstPROGRAMS ctags distclean \
-+ distclean-compile distclean-generic distclean-tags distdir dvi \
-+ dvi-am html html-am info info-am install install-am \
-+ install-data install-data-am install-dvi install-dvi-am \
-+ install-exec install-exec-am install-html install-html-am \
-+ install-info install-info-am install-man install-pdf \
-+ install-pdf-am install-ps install-ps-am install-strip \
-+ installcheck installcheck-am installdirs maintainer-clean \
-+ maintainer-clean-generic mostlyclean mostlyclean-compile \
-+ mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
-+ uninstall-am
-
-
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -ubrN exonerate-2.2.0.orig/src/sequence/Makefile.in exonerate-2.2.0/src/sequence/Makefile.in
---- exonerate-2.2.0.orig/src/sequence/Makefile.in 2008-10-17 12:05:02.000000000 +0200
-+++ exonerate-2.2.0/src/sequence/Makefile.in 2011-12-12 13:33:17.000000000 +0100
-@@ -1,6 +1,9 @@
--# Makefile.in generated automatically by automake 1.4-p6 from Makefile.am
-+# Makefile.in generated by automake 1.11.1 from Makefile.am.
-+# @configure_input@
-
--# Copyright (C) 1994, 1995-8, 1999, 2001 Free Software Foundation, Inc.
-+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
-+# Inc.
- # This Makefile.in is free software; the Free Software Foundation
- # gives unlimited permission to copy and/or distribute it,
- # with or without modifications, as long as this notice is preserved.
-@@ -10,359 +13,599 @@
- # even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- # PARTICULAR PURPOSE.
-
-+ at SET_MAKE@
-
--SHELL = @SHELL@
-
--srcdir = @srcdir@
--top_srcdir = @top_srcdir@
- VPATH = @srcdir@
--prefix = @prefix@
--exec_prefix = @exec_prefix@
--
--bindir = @bindir@
--sbindir = @sbindir@
--libexecdir = @libexecdir@
--datadir = @datadir@
--sysconfdir = @sysconfdir@
--sharedstatedir = @sharedstatedir@
--localstatedir = @localstatedir@
--libdir = @libdir@
--infodir = @infodir@
--mandir = @mandir@
--includedir = @includedir@
--oldincludedir = /usr/include
--
--DESTDIR =
--
- pkgdatadir = $(datadir)/@PACKAGE@
--pkglibdir = $(libdir)/@PACKAGE@
- pkgincludedir = $(includedir)/@PACKAGE@
--
--top_builddir = ../..
--
--ACLOCAL = @ACLOCAL@
--AUTOCONF = @AUTOCONF@
--AUTOMAKE = @AUTOMAKE@
--AUTOHEADER = @AUTOHEADER@
--
--INSTALL = @INSTALL@
--INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
--INSTALL_DATA = @INSTALL_DATA@
--INSTALL_SCRIPT = @INSTALL_SCRIPT@
--transform = @program_transform_name@
--
-+pkglibdir = $(libdir)/@PACKAGE@
-+pkglibexecdir = $(libexecdir)/@PACKAGE@
-+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-+install_sh_DATA = $(install_sh) -c -m 644
-+install_sh_PROGRAM = $(install_sh) -c
-+install_sh_SCRIPT = $(install_sh) -c
-+INSTALL_HEADER = $(INSTALL_DATA)
-+transform = $(program_transform_name)
- NORMAL_INSTALL = :
- PRE_INSTALL = :
- POST_INSTALL = :
- NORMAL_UNINSTALL = :
- PRE_UNINSTALL = :
- POST_UNINSTALL = :
--host_alias = @host_alias@
-+build_triplet = @build@
- host_triplet = @host@
-+TESTS = sequence.test$(EXEEXT) submat.test$(EXEEXT) \
-+ translate.test$(EXEEXT) splice.test$(EXEEXT) \
-+ alphabet.test$(EXEEXT) codonsubmat.test$(EXEEXT)
-+noinst_PROGRAMS = $(am__EXEEXT_1)
-+subdir = src/sequence
-+DIST_COMMON = $(noinst_HEADERS) $(srcdir)/Makefile.am \
-+ $(srcdir)/Makefile.in
-+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-+am__aclocal_m4_deps = $(top_srcdir)/configure.in
-+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-+ $(ACLOCAL_M4)
-+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
-+CONFIG_CLEAN_FILES =
-+CONFIG_CLEAN_VPATH_FILES =
-+am__EXEEXT_1 = sequence.test$(EXEEXT) submat.test$(EXEEXT) \
-+ translate.test$(EXEEXT) splice.test$(EXEEXT) \
-+ alphabet.test$(EXEEXT) codonsubmat.test$(EXEEXT)
-+PROGRAMS = $(noinst_PROGRAMS)
-+am_alphabet_test_OBJECTS = alphabet.test.$(OBJEXT) alphabet.$(OBJEXT)
-+alphabet_test_OBJECTS = $(am_alphabet_test_OBJECTS)
-+alphabet_test_DEPENDENCIES = $(top_srcdir)/src/general/argument.o
-+am_codonsubmat_test_OBJECTS = codonsubmat.test.$(OBJEXT) \
-+ codonsubmat.$(OBJEXT)
-+codonsubmat_test_OBJECTS = $(am_codonsubmat_test_OBJECTS)
-+codonsubmat_test_DEPENDENCIES = $(top_srcdir)/src/general/argument.o
-+am_sequence_test_OBJECTS = sequence.test.$(OBJEXT) sequence.$(OBJEXT) \
-+ alphabet.$(OBJEXT) translate.$(OBJEXT) splice.$(OBJEXT)
-+sequence_test_OBJECTS = $(am_sequence_test_OBJECTS)
-+am__DEPENDENCIES_1 = $(top_srcdir)/src/struct/matrix.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/lineparse.o
-+sequence_test_DEPENDENCIES = $(am__DEPENDENCIES_1)
-+am_splice_test_OBJECTS = splice.test.$(OBJEXT) splice.$(OBJEXT)
-+splice_test_OBJECTS = $(am_splice_test_OBJECTS)
-+splice_test_DEPENDENCIES = $(am__DEPENDENCIES_1)
-+am_submat_test_OBJECTS = submat.test.$(OBJEXT) submat.$(OBJEXT)
-+submat_test_OBJECTS = $(am_submat_test_OBJECTS)
-+submat_test_LDADD = $(LDADD)
-+am_translate_test_OBJECTS = translate.test.$(OBJEXT) \
-+ translate.$(OBJEXT)
-+translate_test_OBJECTS = $(am_translate_test_OBJECTS)
-+translate_test_DEPENDENCIES = $(top_srcdir)/src/general/argument.o
-+DEFAULT_INCLUDES = -I. at am__isrc@
-+depcomp = $(SHELL) $(top_srcdir)/depcomp
-+am__depfiles_maybe = depfiles
-+am__mv = mv -f
-+COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
-+ $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
-+CCLD = $(CC)
-+LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
-+SOURCES = $(alphabet_test_SOURCES) $(codonsubmat_test_SOURCES) \
-+ $(sequence_test_SOURCES) $(splice_test_SOURCES) \
-+ $(submat_test_SOURCES) $(translate_test_SOURCES)
-+DIST_SOURCES = $(alphabet_test_SOURCES) $(codonsubmat_test_SOURCES) \
-+ $(sequence_test_SOURCES) $(splice_test_SOURCES) \
-+ $(submat_test_SOURCES) $(translate_test_SOURCES)
-+HEADERS = $(noinst_HEADERS)
-+ETAGS = etags
-+CTAGS = ctags
-+am__tty_colors = \
-+red=; grn=; lgn=; blu=; std=
-+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-+ACLOCAL = @ACLOCAL@
-+AMTAR = @AMTAR@
-+AUTOCONF = @AUTOCONF@
-+AUTOHEADER = @AUTOHEADER@
-+AUTOMAKE = @AUTOMAKE@
-+AWK = @AWK@
- CC = @CC@
-+CCDEPMODE = @CCDEPMODE@
-+CFLAGS = @CFLAGS@
-+CPP = @CPP@
-+CPPFLAGS = @CPPFLAGS@
-+CYGPATH_W = @CYGPATH_W@
-+DEFS = @DEFS@
-+DEPDIR = @DEPDIR@
-+ECHO_C = @ECHO_C@
-+ECHO_N = @ECHO_N@
-+ECHO_T = @ECHO_T@
-+EGREP = @EGREP@
-+EXEEXT = @EXEEXT@
- GLIB_CONFIG = @GLIB_CONFIG@
--HAVE_LIB = @HAVE_LIB@
--LIB = @LIB@
--LTLIB = @LTLIB@
-+GREP = @GREP@
-+INSTALL = @INSTALL@
-+INSTALL_DATA = @INSTALL_DATA@
-+INSTALL_PROGRAM = @INSTALL_PROGRAM@
-+INSTALL_SCRIPT = @INSTALL_SCRIPT@
-+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-+LDFLAGS = @LDFLAGS@
-+LIBOBJS = @LIBOBJS@
-+LIBS = @LIBS@
-+LTLIBOBJS = @LTLIBOBJS@
- MAKEINFO = @MAKEINFO@
-+MKDIR_P = @MKDIR_P@
-+OBJEXT = @OBJEXT@
- PACKAGE = @PACKAGE@
-+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-+PACKAGE_NAME = @PACKAGE_NAME@
-+PACKAGE_STRING = @PACKAGE_STRING@
-+PACKAGE_TARNAME = @PACKAGE_TARNAME@
-+PACKAGE_URL = @PACKAGE_URL@
-+PACKAGE_VERSION = @PACKAGE_VERSION@
-+PATH_SEPARATOR = @PATH_SEPARATOR@
- PKG_CONFIG = @PKG_CONFIG@
-+SET_MAKE = @SET_MAKE@
-+SHELL = @SHELL@
-+STRIP = @STRIP@
- VERSION = @VERSION@
-+abs_builddir = @abs_builddir@
-+abs_srcdir = @abs_srcdir@
-+abs_top_builddir = @abs_top_builddir@
-+abs_top_srcdir = @abs_top_srcdir@
-+ac_ct_CC = @ac_ct_CC@
-+am__include = @am__include@
-+am__leading_dot = @am__leading_dot@
-+am__quote = @am__quote@
-+am__tar = @am__tar@
-+am__untar = @am__untar@
-+bindir = @bindir@
-+build = @build@
-+build_alias = @build_alias@
-+build_cpu = @build_cpu@
-+build_os = @build_os@
-+build_vendor = @build_vendor@
-+builddir = @builddir@
- codegen_extra_ldadd = @codegen_extra_ldadd@
- codegen_extra_sources = @codegen_extra_sources@
-+datadir = @datadir@
- datarootdir = @datarootdir@
-+docdir = @docdir@
-+dvidir = @dvidir@
-+exec_prefix = @exec_prefix@
- glib_cflags = @glib_cflags@
- glib_libs = @glib_libs@
- host = @host@
-+host_alias = @host_alias@
-+host_cpu = @host_cpu@
-+host_os = @host_os@
-+host_vendor = @host_vendor@
-+htmldir = @htmldir@
-+includedir = @includedir@
-+infodir = @infodir@
-+install_sh = @install_sh@
- installed_util_list = @installed_util_list@
-+libdir = @libdir@
-+libexecdir = @libexecdir@
-+localedir = @localedir@
-+localstatedir = @localstatedir@
-+mandir = @mandir@
-+mkdir_p = @mkdir_p@
-+oldincludedir = @oldincludedir@
-+pdfdir = @pdfdir@
-+prefix = @prefix@
-+program_transform_name = @program_transform_name@
-+psdir = @psdir@
-+sbindir = @sbindir@
-+sharedstatedir = @sharedstatedir@
- source_root_dir = @source_root_dir@
-+srcdir = @srcdir@
-+sysconfdir = @sysconfdir@
-+target_alias = @target_alias@
-+top_build_prefix = @top_build_prefix@
-+top_builddir = @top_builddir@
-+top_srcdir = @top_srcdir@
- use_pthreads = @use_pthreads@
-+INCLUDES = -I$(top_srcdir)/src/struct \
-+ -I$(top_srcdir)/src/general
-
--TESTS = sequence.test submat.test translate.test splice.test alphabet.test codonsubmat.test
--
--noinst_PROGRAMS = $(TESTS)
--
--INCLUDES = -I$(top_srcdir)/src/struct -I$(top_srcdir)/src/general
--
--
--noinst_HEADERS = sequence.h submat.h translate.h splice.h alphabet.h codonsubmat.h
--
-+noinst_HEADERS = sequence.h submat.h translate.h splice.h alphabet.h \
-+ codonsubmat.h
-
- splice_test_SOURCES = splice.test.c splice.c
--SPLICE_OBJ = $(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/general/lineparse.o -lm
-+SPLICE_OBJ = $(top_srcdir)/src/struct/matrix.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ -lm
-
- splice_test_LDADD = $(SPLICE_OBJ)
--
--sequence_test_SOURCES = sequence.test.c sequence.c alphabet.c translate.c splice.c
-+sequence_test_SOURCES = sequence.test.c sequence.c alphabet.c translate.c \
-+ splice.c
-
- sequence_test_LDADD = $(SPLICE_OBJ)
- submat_test_SOURCES = submat.test.c submat.c
--
- translate_test_SOURCES = translate.test.c translate.c
- translate_test_LDADD = $(top_srcdir)/src/general/argument.o
--
- alphabet_test_SOURCES = alphabet.test.c alphabet.c
- alphabet_test_LDADD = $(top_srcdir)/src/general/argument.o
--
- codonsubmat_test_SOURCES = codonsubmat.test.c codonsubmat.c
- codonsubmat_test_LDADD = $(top_srcdir)/src/general/argument.o -lm
-
- # Files to clear away
--
- MAINTAINERCLEANFILES = Makefile.in
--mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
--CONFIG_CLEAN_FILES =
--PROGRAMS = $(noinst_PROGRAMS)
--
--
--DEFS = @DEFS@ -I. -I$(srcdir)
--CPPFLAGS = @CPPFLAGS@
--LDFLAGS = @LDFLAGS@
--LIBS = @LIBS@
--sequence_test_OBJECTS = sequence.test.o sequence.o alphabet.o \
--translate.o splice.o
--sequence_test_DEPENDENCIES = $(top_srcdir)/src/struct/matrix.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--sequence_test_LDFLAGS =
--submat_test_OBJECTS = submat.test.o submat.o
--submat_test_LDADD = $(LDADD)
--submat_test_DEPENDENCIES =
--submat_test_LDFLAGS =
--translate_test_OBJECTS = translate.test.o translate.o
--translate_test_DEPENDENCIES = $(top_srcdir)/src/general/argument.o
--translate_test_LDFLAGS =
--splice_test_OBJECTS = splice.test.o splice.o
--splice_test_DEPENDENCIES = $(top_srcdir)/src/struct/matrix.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/lineparse.o
--splice_test_LDFLAGS =
--alphabet_test_OBJECTS = alphabet.test.o alphabet.o
--alphabet_test_DEPENDENCIES = $(top_srcdir)/src/general/argument.o
--alphabet_test_LDFLAGS =
--codonsubmat_test_OBJECTS = codonsubmat.test.o codonsubmat.o
--codonsubmat_test_DEPENDENCIES = $(top_srcdir)/src/general/argument.o
--codonsubmat_test_LDFLAGS =
--CFLAGS = @CFLAGS@
--COMPILE = $(CC) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
--CCLD = $(CC)
--LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(LDFLAGS) -o $@
--HEADERS = $(noinst_HEADERS)
--
--DIST_COMMON = Makefile.am Makefile.in
--
--
--DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
--
--TAR = tar
--GZIP_ENV = --best
--SOURCES = $(sequence_test_SOURCES) $(submat_test_SOURCES) $(translate_test_SOURCES) $(splice_test_SOURCES) $(alphabet_test_SOURCES) $(codonsubmat_test_SOURCES)
--OBJECTS = $(sequence_test_OBJECTS) $(submat_test_OBJECTS) $(translate_test_OBJECTS) $(splice_test_OBJECTS) $(alphabet_test_OBJECTS) $(codonsubmat_test_OBJECTS)
-+all: all-am
-
--all: all-redirect
- .SUFFIXES:
--.SUFFIXES: .S .c .o .s
--$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4)
-- cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps src/sequence/Makefile
--
-+.SUFFIXES: .c .o .obj
-+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
-+ @for dep in $?; do \
-+ case '$(am__configure_deps)' in \
-+ *$$dep*) \
-+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-+ && { if test -f $@; then exit 0; else break; fi; }; \
-+ exit 1;; \
-+ esac; \
-+ done; \
-+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/sequence/Makefile'; \
-+ $(am__cd) $(top_srcdir) && \
-+ $(AUTOMAKE) --gnu src/sequence/Makefile
-+.PRECIOUS: Makefile
- Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-- cd $(top_builddir) \
-- && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
--
--
--mostlyclean-noinstPROGRAMS:
-+ @case '$?' in \
-+ *config.status*) \
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-+ *) \
-+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-+ esac;
-+
-+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+
-+$(top_srcdir)/configure: $(am__configure_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(am__aclocal_m4_deps):
-
- clean-noinstPROGRAMS:
- -test -z "$(noinst_PROGRAMS)" || rm -f $(noinst_PROGRAMS)
--
--distclean-noinstPROGRAMS:
--
--maintainer-clean-noinstPROGRAMS:
--
--.c.o:
-- $(COMPILE) -c $<
--
--.s.o:
-- $(COMPILE) -c $<
--
--.S.o:
-- $(COMPILE) -c $<
-+alphabet.test$(EXEEXT): $(alphabet_test_OBJECTS) $(alphabet_test_DEPENDENCIES)
-+ @rm -f alphabet.test$(EXEEXT)
-+ $(LINK) $(alphabet_test_OBJECTS) $(alphabet_test_LDADD) $(LIBS)
-+codonsubmat.test$(EXEEXT): $(codonsubmat_test_OBJECTS) $(codonsubmat_test_DEPENDENCIES)
-+ @rm -f codonsubmat.test$(EXEEXT)
-+ $(LINK) $(codonsubmat_test_OBJECTS) $(codonsubmat_test_LDADD) $(LIBS)
-+sequence.test$(EXEEXT): $(sequence_test_OBJECTS) $(sequence_test_DEPENDENCIES)
-+ @rm -f sequence.test$(EXEEXT)
-+ $(LINK) $(sequence_test_OBJECTS) $(sequence_test_LDADD) $(LIBS)
-+splice.test$(EXEEXT): $(splice_test_OBJECTS) $(splice_test_DEPENDENCIES)
-+ @rm -f splice.test$(EXEEXT)
-+ $(LINK) $(splice_test_OBJECTS) $(splice_test_LDADD) $(LIBS)
-+submat.test$(EXEEXT): $(submat_test_OBJECTS) $(submat_test_DEPENDENCIES)
-+ @rm -f submat.test$(EXEEXT)
-+ $(LINK) $(submat_test_OBJECTS) $(submat_test_LDADD) $(LIBS)
-+translate.test$(EXEEXT): $(translate_test_OBJECTS) $(translate_test_DEPENDENCIES)
-+ @rm -f translate.test$(EXEEXT)
-+ $(LINK) $(translate_test_OBJECTS) $(translate_test_LDADD) $(LIBS)
-
- mostlyclean-compile:
-- -rm -f *.o core *.core
--
--clean-compile:
-+ -rm -f *.$(OBJEXT)
-
- distclean-compile:
- -rm -f *.tab.c
-
--maintainer-clean-compile:
--
--sequence.test: $(sequence_test_OBJECTS) $(sequence_test_DEPENDENCIES)
-- @rm -f sequence.test
-- $(LINK) $(sequence_test_LDFLAGS) $(sequence_test_OBJECTS) $(sequence_test_LDADD) $(LIBS)
--
--submat.test: $(submat_test_OBJECTS) $(submat_test_DEPENDENCIES)
-- @rm -f submat.test
-- $(LINK) $(submat_test_LDFLAGS) $(submat_test_OBJECTS) $(submat_test_LDADD) $(LIBS)
--
--translate.test: $(translate_test_OBJECTS) $(translate_test_DEPENDENCIES)
-- @rm -f translate.test
-- $(LINK) $(translate_test_LDFLAGS) $(translate_test_OBJECTS) $(translate_test_LDADD) $(LIBS)
--
--splice.test: $(splice_test_OBJECTS) $(splice_test_DEPENDENCIES)
-- @rm -f splice.test
-- $(LINK) $(splice_test_LDFLAGS) $(splice_test_OBJECTS) $(splice_test_LDADD) $(LIBS)
--
--alphabet.test: $(alphabet_test_OBJECTS) $(alphabet_test_DEPENDENCIES)
-- @rm -f alphabet.test
-- $(LINK) $(alphabet_test_LDFLAGS) $(alphabet_test_OBJECTS) $(alphabet_test_LDADD) $(LIBS)
--
--codonsubmat.test: $(codonsubmat_test_OBJECTS) $(codonsubmat_test_DEPENDENCIES)
-- @rm -f codonsubmat.test
-- $(LINK) $(codonsubmat_test_LDFLAGS) $(codonsubmat_test_OBJECTS) $(codonsubmat_test_LDADD) $(LIBS)
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/alphabet.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/alphabet.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/codonsubmat.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/codonsubmat.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sequence.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sequence.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/splice.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/splice.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/submat.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/submat.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/translate.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/translate.test.Po at am__quote@
-
-+.c.o:
-+ at am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
-+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-+ at am__fastdepCC_FALSE@ $(COMPILE) -c $<
-+
-+.c.obj:
-+ at am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
-+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-+ at am__fastdepCC_FALSE@ $(COMPILE) -c `$(CYGPATH_W) '$<'`
-+
-+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ mkid -fID $$unique
- tags: TAGS
-
--ID: $(HEADERS) $(SOURCES) $(LISP)
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- here=`pwd` && cd $(srcdir) \
-- && mkid -f$$here/ID $$unique $(LISP)
--
--TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) $(LISP)
-- tags=; \
-+TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ set x; \
- here=`pwd`; \
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- test -z "$(ETAGS_ARGS)$$unique$(LISP)$$tags" \
-- || (cd $(srcdir) && etags -o $$here/TAGS $(ETAGS_ARGS) $$tags $$unique $(LISP))
--
--mostlyclean-tags:
--
--clean-tags:
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ shift; \
-+ if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
-+ test -n "$$unique" || unique=$$empty_fix; \
-+ if test $$# -gt 0; then \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ "$$@" $$unique; \
-+ else \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ $$unique; \
-+ fi; \
-+ fi
-+ctags: CTAGS
-+CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ test -z "$(CTAGS_ARGS)$$unique" \
-+ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-+ $$unique
-+
-+GTAGS:
-+ here=`$(am__cd) $(top_builddir) && pwd` \
-+ && $(am__cd) $(top_srcdir) \
-+ && gtags -i $(GTAGS_ARGS) "$$here"
-
- distclean-tags:
-- -rm -f TAGS ID
--
--maintainer-clean-tags:
--
--distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
-+ -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-
--subdir = src/sequence
--
--distdir: $(DISTFILES)
-- @for file in $(DISTFILES); do \
-- d=$(srcdir); \
-- if test -d $$d/$$file; then \
-- cp -pr $$d/$$file $(distdir)/$$file; \
-- else \
-- test -f $(distdir)/$$file \
-- || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
-- || cp -p $$d/$$file $(distdir)/$$file || :; \
-- fi; \
-- done
- check-TESTS: $(TESTS)
-- @failed=0; all=0; \
-+ @failed=0; all=0; xfail=0; xpass=0; skip=0; \
- srcdir=$(srcdir); export srcdir; \
-- for tst in $(TESTS); do \
-- if test -f $$tst; then dir=.; \
-- else dir="$(srcdir)"; fi; \
-- if $(TESTS_ENVIRONMENT) $$dir/$$tst; then \
-+ list=' $(TESTS) '; \
-+ $(am__tty_colors); \
-+ if test -n "$$list"; then \
-+ for tst in $$list; do \
-+ if test -f ./$$tst; then dir=./; \
-+ elif test -f $$tst; then dir=; \
-+ else dir="$(srcdir)/"; fi; \
-+ if $(TESTS_ENVIRONMENT) $${dir}$$tst; then \
- all=`expr $$all + 1`; \
-- echo "PASS: $$tst"; \
-+ case " $(XFAIL_TESTS) " in \
-+ *[\ \ ]$$tst[\ \ ]*) \
-+ xpass=`expr $$xpass + 1`; \
-+ failed=`expr $$failed + 1`; \
-+ col=$$red; res=XPASS; \
-+ ;; \
-+ *) \
-+ col=$$grn; res=PASS; \
-+ ;; \
-+ esac; \
- elif test $$? -ne 77; then \
- all=`expr $$all + 1`; \
-+ case " $(XFAIL_TESTS) " in \
-+ *[\ \ ]$$tst[\ \ ]*) \
-+ xfail=`expr $$xfail + 1`; \
-+ col=$$lgn; res=XFAIL; \
-+ ;; \
-+ *) \
- failed=`expr $$failed + 1`; \
-- echo "FAIL: $$tst"; \
-+ col=$$red; res=FAIL; \
-+ ;; \
-+ esac; \
-+ else \
-+ skip=`expr $$skip + 1`; \
-+ col=$$blu; res=SKIP; \
- fi; \
-+ echo "$${col}$$res$${std}: $$tst"; \
- done; \
-+ if test "$$all" -eq 1; then \
-+ tests="test"; \
-+ All=""; \
-+ else \
-+ tests="tests"; \
-+ All="All "; \
-+ fi; \
- if test "$$failed" -eq 0; then \
-- banner="All $$all tests passed"; \
-+ if test "$$xfail" -eq 0; then \
-+ banner="$$All$$all $$tests passed"; \
- else \
-- banner="$$failed of $$all tests failed"; \
-+ if test "$$xfail" -eq 1; then failures=failure; else failures=failures; fi; \
-+ banner="$$All$$all $$tests behaved as expected ($$xfail expected $$failures)"; \
-+ fi; \
-+ else \
-+ if test "$$xpass" -eq 0; then \
-+ banner="$$failed of $$all $$tests failed"; \
-+ else \
-+ if test "$$xpass" -eq 1; then passes=pass; else passes=passes; fi; \
-+ banner="$$failed of $$all $$tests did not behave as expected ($$xpass unexpected $$passes)"; \
-+ fi; \
-+ fi; \
-+ dashes="$$banner"; \
-+ skipped=""; \
-+ if test "$$skip" -ne 0; then \
-+ if test "$$skip" -eq 1; then \
-+ skipped="($$skip test was not run)"; \
-+ else \
-+ skipped="($$skip tests were not run)"; \
-+ fi; \
-+ test `echo "$$skipped" | wc -c` -le `echo "$$banner" | wc -c` || \
-+ dashes="$$skipped"; \
-+ fi; \
-+ report=""; \
-+ if test "$$failed" -ne 0 && test -n "$(PACKAGE_BUGREPORT)"; then \
-+ report="Please report to $(PACKAGE_BUGREPORT)"; \
-+ test `echo "$$report" | wc -c` -le `echo "$$banner" | wc -c` || \
-+ dashes="$$report"; \
-+ fi; \
-+ dashes=`echo "$$dashes" | sed s/./=/g`; \
-+ if test "$$failed" -eq 0; then \
-+ echo "$$grn$$dashes"; \
-+ else \
-+ echo "$$red$$dashes"; \
- fi; \
-- dashes=`echo "$$banner" | sed s/./=/g`; \
-- echo "$$dashes"; \
- echo "$$banner"; \
-- echo "$$dashes"; \
-- test "$$failed" -eq 0
--info-am:
--info: info-am
--dvi-am:
--dvi: dvi-am
-+ test -z "$$skipped" || echo "$$skipped"; \
-+ test -z "$$report" || echo "$$report"; \
-+ echo "$$dashes$$std"; \
-+ test "$$failed" -eq 0; \
-+ else :; fi
-+
-+distdir: $(DISTFILES)
-+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ list='$(DISTFILES)'; \
-+ dist_files=`for file in $$list; do echo $$file; done | \
-+ sed -e "s|^$$srcdirstrip/||;t" \
-+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-+ case $$dist_files in \
-+ */*) $(MKDIR_P) `echo "$$dist_files" | \
-+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-+ sort -u` ;; \
-+ esac; \
-+ for file in $$dist_files; do \
-+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
-+ if test -d $$d/$$file; then \
-+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-+ if test -d "$(distdir)/$$file"; then \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
-+ else \
-+ test -f "$(distdir)/$$file" \
-+ || cp -p $$d/$$file "$(distdir)/$$file" \
-+ || exit 1; \
-+ fi; \
-+ done
- check-am: all-am
- $(MAKE) $(AM_MAKEFLAGS) check-TESTS
- check: check-am
--installcheck-am:
--installcheck: installcheck-am
--install-exec-am:
-+all-am: Makefile $(PROGRAMS) $(HEADERS)
-+installdirs:
-+install: install-am
- install-exec: install-exec-am
--
--install-data-am:
- install-data: install-data-am
-+uninstall: uninstall-am
-
- install-am: all-am
- @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
--install: install-am
--uninstall-am:
--uninstall: uninstall-am
--all-am: Makefile $(PROGRAMS) $(HEADERS)
--all-redirect: all-am
--install-strip:
-- $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
--installdirs:
--
-
-+installcheck: installcheck-am
-+install-strip:
-+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-+ `test -z '$(STRIP)' || \
-+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
- mostlyclean-generic:
-
- clean-generic:
-
- distclean-generic:
-- -rm -f Makefile $(CONFIG_CLEAN_FILES)
-- -rm -f config.cache config.log stamp-h stamp-h[0-9]*
-+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
- maintainer-clean-generic:
-+ @echo "This command is intended for maintainers to use"
-+ @echo "it deletes files that may require special tools to rebuild."
- -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
--mostlyclean-am: mostlyclean-noinstPROGRAMS mostlyclean-compile \
-- mostlyclean-tags mostlyclean-generic
-+clean: clean-am
-
--mostlyclean: mostlyclean-am
-+clean-am: clean-generic clean-noinstPROGRAMS mostlyclean-am
-
--clean-am: clean-noinstPROGRAMS clean-compile clean-tags clean-generic \
-- mostlyclean-am
-+distclean: distclean-am
-+ -rm -rf ./$(DEPDIR)
-+ -rm -f Makefile
-+distclean-am: clean-am distclean-compile distclean-generic \
-+ distclean-tags
-
--clean: clean-am
-+dvi: dvi-am
-
--distclean-am: distclean-noinstPROGRAMS distclean-compile distclean-tags \
-- distclean-generic clean-am
-+dvi-am:
-
--distclean: distclean-am
-+html: html-am
-
--maintainer-clean-am: maintainer-clean-noinstPROGRAMS \
-- maintainer-clean-compile maintainer-clean-tags \
-- maintainer-clean-generic distclean-am
-- @echo "This command is intended for maintainers to use;"
-- @echo "it deletes files that may require special tools to rebuild."
-+html-am:
-+
-+info: info-am
-+
-+info-am:
-+
-+install-data-am:
-+
-+install-dvi: install-dvi-am
-+
-+install-dvi-am:
-+
-+install-exec-am:
-+
-+install-html: install-html-am
-+
-+install-html-am:
-+
-+install-info: install-info-am
-+
-+install-info-am:
-+
-+install-man:
-+
-+install-pdf: install-pdf-am
-+
-+install-pdf-am:
-+
-+install-ps: install-ps-am
-+
-+install-ps-am:
-+
-+installcheck-am:
-
- maintainer-clean: maintainer-clean-am
-+ -rm -rf ./$(DEPDIR)
-+ -rm -f Makefile
-+maintainer-clean-am: distclean-am maintainer-clean-generic
-+
-+mostlyclean: mostlyclean-am
-+
-+mostlyclean-am: mostlyclean-compile mostlyclean-generic
-+
-+pdf: pdf-am
-+
-+pdf-am:
-+
-+ps: ps-am
-+
-+ps-am:
-+
-+uninstall-am:
-+
-+.MAKE: check-am install-am install-strip
-
--.PHONY: mostlyclean-noinstPROGRAMS distclean-noinstPROGRAMS \
--clean-noinstPROGRAMS maintainer-clean-noinstPROGRAMS \
--mostlyclean-compile distclean-compile clean-compile \
--maintainer-clean-compile tags mostlyclean-tags distclean-tags \
--clean-tags maintainer-clean-tags distdir check-TESTS info-am info \
--dvi-am dvi check check-am installcheck-am installcheck install-exec-am \
--install-exec install-data-am install-data install-am install \
--uninstall-am uninstall all-redirect all-am all installdirs \
--mostlyclean-generic distclean-generic clean-generic \
--maintainer-clean-generic clean mostlyclean distclean maintainer-clean
-+.PHONY: CTAGS GTAGS all all-am check check-TESTS check-am clean \
-+ clean-generic clean-noinstPROGRAMS ctags distclean \
-+ distclean-compile distclean-generic distclean-tags distdir dvi \
-+ dvi-am html html-am info info-am install install-am \
-+ install-data install-data-am install-dvi install-dvi-am \
-+ install-exec install-exec-am install-html install-html-am \
-+ install-info install-info-am install-man install-pdf \
-+ install-pdf-am install-ps install-ps-am install-strip \
-+ installcheck installcheck-am installdirs maintainer-clean \
-+ maintainer-clean-generic mostlyclean mostlyclean-compile \
-+ mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
-+ uninstall-am
-
-
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -ubrN exonerate-2.2.0.orig/src/struct/Makefile.in exonerate-2.2.0/src/struct/Makefile.in
---- exonerate-2.2.0.orig/src/struct/Makefile.in 2008-10-17 12:05:01.000000000 +0200
-+++ exonerate-2.2.0/src/struct/Makefile.in 2011-12-12 13:33:17.000000000 +0100
-@@ -1,6 +1,9 @@
--# Makefile.in generated automatically by automake 1.4-p6 from Makefile.am
-+# Makefile.in generated by automake 1.11.1 from Makefile.am.
-+# @configure_input@
-
--# Copyright (C) 1994, 1995-8, 1999, 2001 Free Software Foundation, Inc.
-+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
-+# Inc.
- # This Makefile.in is free software; the Free Software Foundation
- # gives unlimited permission to copy and/or distribute it,
- # with or without modifications, as long as this notice is preserved.
-@@ -10,401 +13,653 @@
- # even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- # PARTICULAR PURPOSE.
-
-+ at SET_MAKE@
-
--SHELL = @SHELL@
-
--srcdir = @srcdir@
--top_srcdir = @top_srcdir@
- VPATH = @srcdir@
--prefix = @prefix@
--exec_prefix = @exec_prefix@
--
--bindir = @bindir@
--sbindir = @sbindir@
--libexecdir = @libexecdir@
--datadir = @datadir@
--sysconfdir = @sysconfdir@
--sharedstatedir = @sharedstatedir@
--localstatedir = @localstatedir@
--libdir = @libdir@
--infodir = @infodir@
--mandir = @mandir@
--includedir = @includedir@
--oldincludedir = /usr/include
--
--DESTDIR =
--
- pkgdatadir = $(datadir)/@PACKAGE@
--pkglibdir = $(libdir)/@PACKAGE@
- pkgincludedir = $(includedir)/@PACKAGE@
--
--top_builddir = ../..
--
--ACLOCAL = @ACLOCAL@
--AUTOCONF = @AUTOCONF@
--AUTOMAKE = @AUTOMAKE@
--AUTOHEADER = @AUTOHEADER@
--
--INSTALL = @INSTALL@
--INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
--INSTALL_DATA = @INSTALL_DATA@
--INSTALL_SCRIPT = @INSTALL_SCRIPT@
--transform = @program_transform_name@
--
-+pkglibdir = $(libdir)/@PACKAGE@
-+pkglibexecdir = $(libexecdir)/@PACKAGE@
-+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-+install_sh_DATA = $(install_sh) -c -m 644
-+install_sh_PROGRAM = $(install_sh) -c
-+install_sh_SCRIPT = $(install_sh) -c
-+INSTALL_HEADER = $(INSTALL_DATA)
-+transform = $(program_transform_name)
- NORMAL_INSTALL = :
- PRE_INSTALL = :
- POST_INSTALL = :
- NORMAL_UNINSTALL = :
- PRE_UNINSTALL = :
- POST_UNINSTALL = :
--host_alias = @host_alias@
-+build_triplet = @build@
- host_triplet = @host@
-+TESTS = fsm.test$(EXEEXT) matrix.test$(EXEEXT) pqueue.test$(EXEEXT) \
-+ slist.test$(EXEEXT) rangetree.test$(EXEEXT) vfsm.test$(EXEEXT) \
-+ recyclebin.test$(EXEEXT) sparsecache.test$(EXEEXT) \
-+ dejavu.test$(EXEEXT) bitarray.test$(EXEEXT) \
-+ splaytree.test$(EXEEXT) noitree.test$(EXEEXT)
-+noinst_PROGRAMS = $(am__EXEEXT_1)
-+subdir = src/struct
-+DIST_COMMON = $(noinst_HEADERS) $(srcdir)/Makefile.am \
-+ $(srcdir)/Makefile.in
-+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-+am__aclocal_m4_deps = $(top_srcdir)/configure.in
-+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-+ $(ACLOCAL_M4)
-+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
-+CONFIG_CLEAN_FILES =
-+CONFIG_CLEAN_VPATH_FILES =
-+am__EXEEXT_1 = fsm.test$(EXEEXT) matrix.test$(EXEEXT) \
-+ pqueue.test$(EXEEXT) slist.test$(EXEEXT) \
-+ rangetree.test$(EXEEXT) vfsm.test$(EXEEXT) \
-+ recyclebin.test$(EXEEXT) sparsecache.test$(EXEEXT) \
-+ dejavu.test$(EXEEXT) bitarray.test$(EXEEXT) \
-+ splaytree.test$(EXEEXT) noitree.test$(EXEEXT)
-+PROGRAMS = $(noinst_PROGRAMS)
-+am_bitarray_test_OBJECTS = bitarray.test.$(OBJEXT) bitarray.$(OBJEXT)
-+bitarray_test_OBJECTS = $(am_bitarray_test_OBJECTS)
-+bitarray_test_LDADD = $(LDADD)
-+am_dejavu_test_OBJECTS = dejavu.test.$(OBJEXT) dejavu.$(OBJEXT)
-+dejavu_test_OBJECTS = $(am_dejavu_test_OBJECTS)
-+dejavu_test_LDADD = $(LDADD)
-+am_fsm_test_OBJECTS = fsm.test.$(OBJEXT) fsm.$(OBJEXT)
-+fsm_test_OBJECTS = $(am_fsm_test_OBJECTS)
-+fsm_test_DEPENDENCIES = recyclebin.o
-+am_matrix_test_OBJECTS = matrix.test.$(OBJEXT) matrix.$(OBJEXT)
-+matrix_test_OBJECTS = $(am_matrix_test_OBJECTS)
-+matrix_test_LDADD = $(LDADD)
-+am_noitree_test_OBJECTS = noitree.test.$(OBJEXT) noitree.$(OBJEXT)
-+noitree_test_OBJECTS = $(am_noitree_test_OBJECTS)
-+noitree_test_DEPENDENCIES = recyclebin.o splaytree.o
-+am_pqueue_test_OBJECTS = pqueue.test.$(OBJEXT) pqueue.$(OBJEXT) \
-+ recyclebin.$(OBJEXT)
-+pqueue_test_OBJECTS = $(am_pqueue_test_OBJECTS)
-+pqueue_test_LDADD = $(LDADD)
-+am_rangetree_test_OBJECTS = rangetree.test.$(OBJEXT) \
-+ rangetree.$(OBJEXT)
-+rangetree_test_OBJECTS = $(am_rangetree_test_OBJECTS)
-+rangetree_test_DEPENDENCIES = recyclebin.o
-+am_recyclebin_test_OBJECTS = recyclebin.test.$(OBJEXT) \
-+ recyclebin.$(OBJEXT)
-+recyclebin_test_OBJECTS = $(am_recyclebin_test_OBJECTS)
-+recyclebin_test_LDADD = $(LDADD)
-+am_slist_test_OBJECTS = slist.test.$(OBJEXT) slist.$(OBJEXT) \
-+ recyclebin.$(OBJEXT)
-+slist_test_OBJECTS = $(am_slist_test_OBJECTS)
-+slist_test_LDADD = $(LDADD)
-+am_sparsecache_test_OBJECTS = sparsecache.test.$(OBJEXT) \
-+ sparsecache.$(OBJEXT)
-+sparsecache_test_OBJECTS = $(am_sparsecache_test_OBJECTS)
-+sparsecache_test_LDADD = $(LDADD)
-+am_splaytree_test_OBJECTS = splaytree.test.$(OBJEXT) \
-+ splaytree.$(OBJEXT)
-+splaytree_test_OBJECTS = $(am_splaytree_test_OBJECTS)
-+splaytree_test_DEPENDENCIES = recyclebin.o
-+am_vfsm_test_OBJECTS = vfsm.test.$(OBJEXT) vfsm.$(OBJEXT)
-+vfsm_test_OBJECTS = $(am_vfsm_test_OBJECTS)
-+vfsm_test_DEPENDENCIES =
-+DEFAULT_INCLUDES = -I. at am__isrc@
-+depcomp = $(SHELL) $(top_srcdir)/depcomp
-+am__depfiles_maybe = depfiles
-+am__mv = mv -f
-+COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
-+ $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
-+CCLD = $(CC)
-+LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
-+SOURCES = $(bitarray_test_SOURCES) $(dejavu_test_SOURCES) \
-+ $(fsm_test_SOURCES) $(matrix_test_SOURCES) \
-+ $(noitree_test_SOURCES) $(pqueue_test_SOURCES) \
-+ $(rangetree_test_SOURCES) $(recyclebin_test_SOURCES) \
-+ $(slist_test_SOURCES) $(sparsecache_test_SOURCES) \
-+ $(splaytree_test_SOURCES) $(vfsm_test_SOURCES)
-+DIST_SOURCES = $(bitarray_test_SOURCES) $(dejavu_test_SOURCES) \
-+ $(fsm_test_SOURCES) $(matrix_test_SOURCES) \
-+ $(noitree_test_SOURCES) $(pqueue_test_SOURCES) \
-+ $(rangetree_test_SOURCES) $(recyclebin_test_SOURCES) \
-+ $(slist_test_SOURCES) $(sparsecache_test_SOURCES) \
-+ $(splaytree_test_SOURCES) $(vfsm_test_SOURCES)
-+HEADERS = $(noinst_HEADERS)
-+ETAGS = etags
-+CTAGS = ctags
-+am__tty_colors = \
-+red=; grn=; lgn=; blu=; std=
-+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-+ACLOCAL = @ACLOCAL@
-+AMTAR = @AMTAR@
-+AUTOCONF = @AUTOCONF@
-+AUTOHEADER = @AUTOHEADER@
-+AUTOMAKE = @AUTOMAKE@
-+AWK = @AWK@
- CC = @CC@
-+CCDEPMODE = @CCDEPMODE@
-+CFLAGS = @CFLAGS@
-+CPP = @CPP@
-+CPPFLAGS = @CPPFLAGS@
-+CYGPATH_W = @CYGPATH_W@
-+DEFS = @DEFS@
-+DEPDIR = @DEPDIR@
-+ECHO_C = @ECHO_C@
-+ECHO_N = @ECHO_N@
-+ECHO_T = @ECHO_T@
-+EGREP = @EGREP@
-+EXEEXT = @EXEEXT@
- GLIB_CONFIG = @GLIB_CONFIG@
--HAVE_LIB = @HAVE_LIB@
--LIB = @LIB@
--LTLIB = @LTLIB@
-+GREP = @GREP@
-+INSTALL = @INSTALL@
-+INSTALL_DATA = @INSTALL_DATA@
-+INSTALL_PROGRAM = @INSTALL_PROGRAM@
-+INSTALL_SCRIPT = @INSTALL_SCRIPT@
-+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-+LDFLAGS = @LDFLAGS@
-+LIBOBJS = @LIBOBJS@
-+LIBS = @LIBS@
-+LTLIBOBJS = @LTLIBOBJS@
- MAKEINFO = @MAKEINFO@
-+MKDIR_P = @MKDIR_P@
-+OBJEXT = @OBJEXT@
- PACKAGE = @PACKAGE@
-+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-+PACKAGE_NAME = @PACKAGE_NAME@
-+PACKAGE_STRING = @PACKAGE_STRING@
-+PACKAGE_TARNAME = @PACKAGE_TARNAME@
-+PACKAGE_URL = @PACKAGE_URL@
-+PACKAGE_VERSION = @PACKAGE_VERSION@
-+PATH_SEPARATOR = @PATH_SEPARATOR@
- PKG_CONFIG = @PKG_CONFIG@
-+SET_MAKE = @SET_MAKE@
-+SHELL = @SHELL@
-+STRIP = @STRIP@
- VERSION = @VERSION@
-+abs_builddir = @abs_builddir@
-+abs_srcdir = @abs_srcdir@
-+abs_top_builddir = @abs_top_builddir@
-+abs_top_srcdir = @abs_top_srcdir@
-+ac_ct_CC = @ac_ct_CC@
-+am__include = @am__include@
-+am__leading_dot = @am__leading_dot@
-+am__quote = @am__quote@
-+am__tar = @am__tar@
-+am__untar = @am__untar@
-+bindir = @bindir@
-+build = @build@
-+build_alias = @build_alias@
-+build_cpu = @build_cpu@
-+build_os = @build_os@
-+build_vendor = @build_vendor@
-+builddir = @builddir@
- codegen_extra_ldadd = @codegen_extra_ldadd@
- codegen_extra_sources = @codegen_extra_sources@
-+datadir = @datadir@
- datarootdir = @datarootdir@
-+docdir = @docdir@
-+dvidir = @dvidir@
-+exec_prefix = @exec_prefix@
- glib_cflags = @glib_cflags@
- glib_libs = @glib_libs@
- host = @host@
-+host_alias = @host_alias@
-+host_cpu = @host_cpu@
-+host_os = @host_os@
-+host_vendor = @host_vendor@
-+htmldir = @htmldir@
-+includedir = @includedir@
-+infodir = @infodir@
-+install_sh = @install_sh@
- installed_util_list = @installed_util_list@
-+libdir = @libdir@
-+libexecdir = @libexecdir@
-+localedir = @localedir@
-+localstatedir = @localstatedir@
-+mandir = @mandir@
-+mkdir_p = @mkdir_p@
-+oldincludedir = @oldincludedir@
-+pdfdir = @pdfdir@
-+prefix = @prefix@
-+program_transform_name = @program_transform_name@
-+psdir = @psdir@
-+sbindir = @sbindir@
-+sharedstatedir = @sharedstatedir@
- source_root_dir = @source_root_dir@
-+srcdir = @srcdir@
-+sysconfdir = @sysconfdir@
-+target_alias = @target_alias@
-+top_build_prefix = @top_build_prefix@
-+top_builddir = @top_builddir@
-+top_srcdir = @top_srcdir@
- use_pthreads = @use_pthreads@
--
--TESTS = fsm.test matrix.test pqueue.test slist.test rangetree.test vfsm.test recyclebin.test sparsecache.test dejavu.test bitarray.test splaytree.test noitree.test
--
--noinst_PROGRAMS = $(TESTS)
--
--noinst_HEADERS = fsm.h matrix.h pqueue.h slist.h rangetree.h vfsm.h recyclebin.h sparsecache.h dejavu.h bitarray.h splaytree.h noitree.h
--
-+noinst_HEADERS = fsm.h matrix.h pqueue.h slist.h rangetree.h vfsm.h \
-+ recyclebin.h sparsecache.h dejavu.h bitarray.h \
-+ splaytree.h noitree.h
-
- fsm_test_SOURCES = fsm.test.c fsm.c
- fsm_test_LDADD = recyclebin.o
--
- matrix_test_SOURCES = matrix.test.c matrix.c
- pqueue_test_SOURCES = pqueue.test.c pqueue.c recyclebin.c
- slist_test_SOURCES = slist.test.c slist.c recyclebin.c
- rangetree_test_SOURCES = rangetree.test.c rangetree.c
- rangetree_test_LDADD = recyclebin.o
--
- vfsm_test_SOURCES = vfsm.test.c vfsm.c
- vfsm_test_LDADD = -lm
--
- recyclebin_test_SOURCES = recyclebin.test.c recyclebin.c
- sparsecache_test_SOURCES = sparsecache.test.c sparsecache.c
- dejavu_test_SOURCES = dejavu.test.c dejavu.c
- bitarray_test_SOURCES = bitarray.test.c bitarray.c
--
- splaytree_test_SOURCES = splaytree.test.c splaytree.c
- splaytree_test_LDADD = recyclebin.o
--
- noitree_test_SOURCES = noitree.test.c noitree.c
- noitree_test_LDADD = recyclebin.o splaytree.o
-
- # Files to clear away
--
- MAINTAINERCLEANFILES = Makefile.in
--mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
--CONFIG_CLEAN_FILES =
--PROGRAMS = $(noinst_PROGRAMS)
--
--
--DEFS = @DEFS@ -I. -I$(srcdir)
--CPPFLAGS = @CPPFLAGS@
--LDFLAGS = @LDFLAGS@
--LIBS = @LIBS@
--fsm_test_OBJECTS = fsm.test.o fsm.o
--fsm_test_DEPENDENCIES = recyclebin.o
--fsm_test_LDFLAGS =
--matrix_test_OBJECTS = matrix.test.o matrix.o
--matrix_test_LDADD = $(LDADD)
--matrix_test_DEPENDENCIES =
--matrix_test_LDFLAGS =
--pqueue_test_OBJECTS = pqueue.test.o pqueue.o recyclebin.o
--pqueue_test_LDADD = $(LDADD)
--pqueue_test_DEPENDENCIES =
--pqueue_test_LDFLAGS =
--slist_test_OBJECTS = slist.test.o slist.o recyclebin.o
--slist_test_LDADD = $(LDADD)
--slist_test_DEPENDENCIES =
--slist_test_LDFLAGS =
--rangetree_test_OBJECTS = rangetree.test.o rangetree.o
--rangetree_test_DEPENDENCIES = recyclebin.o
--rangetree_test_LDFLAGS =
--vfsm_test_OBJECTS = vfsm.test.o vfsm.o
--vfsm_test_DEPENDENCIES =
--vfsm_test_LDFLAGS =
--recyclebin_test_OBJECTS = recyclebin.test.o recyclebin.o
--recyclebin_test_LDADD = $(LDADD)
--recyclebin_test_DEPENDENCIES =
--recyclebin_test_LDFLAGS =
--sparsecache_test_OBJECTS = sparsecache.test.o sparsecache.o
--sparsecache_test_LDADD = $(LDADD)
--sparsecache_test_DEPENDENCIES =
--sparsecache_test_LDFLAGS =
--dejavu_test_OBJECTS = dejavu.test.o dejavu.o
--dejavu_test_LDADD = $(LDADD)
--dejavu_test_DEPENDENCIES =
--dejavu_test_LDFLAGS =
--bitarray_test_OBJECTS = bitarray.test.o bitarray.o
--bitarray_test_LDADD = $(LDADD)
--bitarray_test_DEPENDENCIES =
--bitarray_test_LDFLAGS =
--splaytree_test_OBJECTS = splaytree.test.o splaytree.o
--splaytree_test_DEPENDENCIES = recyclebin.o
--splaytree_test_LDFLAGS =
--noitree_test_OBJECTS = noitree.test.o noitree.o
--noitree_test_DEPENDENCIES = recyclebin.o splaytree.o
--noitree_test_LDFLAGS =
--CFLAGS = @CFLAGS@
--COMPILE = $(CC) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
--CCLD = $(CC)
--LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(LDFLAGS) -o $@
--HEADERS = $(noinst_HEADERS)
--
--DIST_COMMON = Makefile.am Makefile.in
--
-+all: all-am
-
--DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
--
--TAR = tar
--GZIP_ENV = --best
--SOURCES = $(fsm_test_SOURCES) $(matrix_test_SOURCES) $(pqueue_test_SOURCES) $(slist_test_SOURCES) $(rangetree_test_SOURCES) $(vfsm_test_SOURCES) $(recyclebin_test_SOURCES) $(sparsecache_test_SOURCES) $(dejavu_test_SOURCES) $(bitarray_test_SOURCES) $(splaytree_test_SOURCES) $(noitree_test_SOURCES)
--OBJECTS = $(fsm_test_OBJECTS) $(matrix_test_OBJECTS) $(pqueue_test_OBJECTS) $(slist_test_OBJECTS) $(rangetree_test_OBJECTS) $(vfsm_test_OBJECTS) $(recyclebin_test_OBJECTS) $(sparsecache_test_OBJECTS) $(dejavu_test_OBJECTS) $(bitarray_test_OBJECTS) $(splaytree_test_OBJECTS) $(noitree_test_OBJECTS)
--
--all: all-redirect
- .SUFFIXES:
--.SUFFIXES: .S .c .o .s
--$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4)
-- cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps src/struct/Makefile
--
-+.SUFFIXES: .c .o .obj
-+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
-+ @for dep in $?; do \
-+ case '$(am__configure_deps)' in \
-+ *$$dep*) \
-+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-+ && { if test -f $@; then exit 0; else break; fi; }; \
-+ exit 1;; \
-+ esac; \
-+ done; \
-+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/struct/Makefile'; \
-+ $(am__cd) $(top_srcdir) && \
-+ $(AUTOMAKE) --gnu src/struct/Makefile
-+.PRECIOUS: Makefile
- Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-- cd $(top_builddir) \
-- && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
--
--
--mostlyclean-noinstPROGRAMS:
-+ @case '$?' in \
-+ *config.status*) \
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-+ *) \
-+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-+ esac;
-+
-+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+
-+$(top_srcdir)/configure: $(am__configure_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(am__aclocal_m4_deps):
-
- clean-noinstPROGRAMS:
- -test -z "$(noinst_PROGRAMS)" || rm -f $(noinst_PROGRAMS)
--
--distclean-noinstPROGRAMS:
--
--maintainer-clean-noinstPROGRAMS:
--
--.c.o:
-- $(COMPILE) -c $<
--
--.s.o:
-- $(COMPILE) -c $<
--
--.S.o:
-- $(COMPILE) -c $<
-+bitarray.test$(EXEEXT): $(bitarray_test_OBJECTS) $(bitarray_test_DEPENDENCIES)
-+ @rm -f bitarray.test$(EXEEXT)
-+ $(LINK) $(bitarray_test_OBJECTS) $(bitarray_test_LDADD) $(LIBS)
-+dejavu.test$(EXEEXT): $(dejavu_test_OBJECTS) $(dejavu_test_DEPENDENCIES)
-+ @rm -f dejavu.test$(EXEEXT)
-+ $(LINK) $(dejavu_test_OBJECTS) $(dejavu_test_LDADD) $(LIBS)
-+fsm.test$(EXEEXT): $(fsm_test_OBJECTS) $(fsm_test_DEPENDENCIES)
-+ @rm -f fsm.test$(EXEEXT)
-+ $(LINK) $(fsm_test_OBJECTS) $(fsm_test_LDADD) $(LIBS)
-+matrix.test$(EXEEXT): $(matrix_test_OBJECTS) $(matrix_test_DEPENDENCIES)
-+ @rm -f matrix.test$(EXEEXT)
-+ $(LINK) $(matrix_test_OBJECTS) $(matrix_test_LDADD) $(LIBS)
-+noitree.test$(EXEEXT): $(noitree_test_OBJECTS) $(noitree_test_DEPENDENCIES)
-+ @rm -f noitree.test$(EXEEXT)
-+ $(LINK) $(noitree_test_OBJECTS) $(noitree_test_LDADD) $(LIBS)
-+pqueue.test$(EXEEXT): $(pqueue_test_OBJECTS) $(pqueue_test_DEPENDENCIES)
-+ @rm -f pqueue.test$(EXEEXT)
-+ $(LINK) $(pqueue_test_OBJECTS) $(pqueue_test_LDADD) $(LIBS)
-+rangetree.test$(EXEEXT): $(rangetree_test_OBJECTS) $(rangetree_test_DEPENDENCIES)
-+ @rm -f rangetree.test$(EXEEXT)
-+ $(LINK) $(rangetree_test_OBJECTS) $(rangetree_test_LDADD) $(LIBS)
-+recyclebin.test$(EXEEXT): $(recyclebin_test_OBJECTS) $(recyclebin_test_DEPENDENCIES)
-+ @rm -f recyclebin.test$(EXEEXT)
-+ $(LINK) $(recyclebin_test_OBJECTS) $(recyclebin_test_LDADD) $(LIBS)
-+slist.test$(EXEEXT): $(slist_test_OBJECTS) $(slist_test_DEPENDENCIES)
-+ @rm -f slist.test$(EXEEXT)
-+ $(LINK) $(slist_test_OBJECTS) $(slist_test_LDADD) $(LIBS)
-+sparsecache.test$(EXEEXT): $(sparsecache_test_OBJECTS) $(sparsecache_test_DEPENDENCIES)
-+ @rm -f sparsecache.test$(EXEEXT)
-+ $(LINK) $(sparsecache_test_OBJECTS) $(sparsecache_test_LDADD) $(LIBS)
-+splaytree.test$(EXEEXT): $(splaytree_test_OBJECTS) $(splaytree_test_DEPENDENCIES)
-+ @rm -f splaytree.test$(EXEEXT)
-+ $(LINK) $(splaytree_test_OBJECTS) $(splaytree_test_LDADD) $(LIBS)
-+vfsm.test$(EXEEXT): $(vfsm_test_OBJECTS) $(vfsm_test_DEPENDENCIES)
-+ @rm -f vfsm.test$(EXEEXT)
-+ $(LINK) $(vfsm_test_OBJECTS) $(vfsm_test_LDADD) $(LIBS)
-
- mostlyclean-compile:
-- -rm -f *.o core *.core
--
--clean-compile:
-+ -rm -f *.$(OBJEXT)
-
- distclean-compile:
- -rm -f *.tab.c
-
--maintainer-clean-compile:
--
--fsm.test: $(fsm_test_OBJECTS) $(fsm_test_DEPENDENCIES)
-- @rm -f fsm.test
-- $(LINK) $(fsm_test_LDFLAGS) $(fsm_test_OBJECTS) $(fsm_test_LDADD) $(LIBS)
--
--matrix.test: $(matrix_test_OBJECTS) $(matrix_test_DEPENDENCIES)
-- @rm -f matrix.test
-- $(LINK) $(matrix_test_LDFLAGS) $(matrix_test_OBJECTS) $(matrix_test_LDADD) $(LIBS)
--
--pqueue.test: $(pqueue_test_OBJECTS) $(pqueue_test_DEPENDENCIES)
-- @rm -f pqueue.test
-- $(LINK) $(pqueue_test_LDFLAGS) $(pqueue_test_OBJECTS) $(pqueue_test_LDADD) $(LIBS)
--
--slist.test: $(slist_test_OBJECTS) $(slist_test_DEPENDENCIES)
-- @rm -f slist.test
-- $(LINK) $(slist_test_LDFLAGS) $(slist_test_OBJECTS) $(slist_test_LDADD) $(LIBS)
--
--rangetree.test: $(rangetree_test_OBJECTS) $(rangetree_test_DEPENDENCIES)
-- @rm -f rangetree.test
-- $(LINK) $(rangetree_test_LDFLAGS) $(rangetree_test_OBJECTS) $(rangetree_test_LDADD) $(LIBS)
--
--vfsm.test: $(vfsm_test_OBJECTS) $(vfsm_test_DEPENDENCIES)
-- @rm -f vfsm.test
-- $(LINK) $(vfsm_test_LDFLAGS) $(vfsm_test_OBJECTS) $(vfsm_test_LDADD) $(LIBS)
--
--recyclebin.test: $(recyclebin_test_OBJECTS) $(recyclebin_test_DEPENDENCIES)
-- @rm -f recyclebin.test
-- $(LINK) $(recyclebin_test_LDFLAGS) $(recyclebin_test_OBJECTS) $(recyclebin_test_LDADD) $(LIBS)
--
--sparsecache.test: $(sparsecache_test_OBJECTS) $(sparsecache_test_DEPENDENCIES)
-- @rm -f sparsecache.test
-- $(LINK) $(sparsecache_test_LDFLAGS) $(sparsecache_test_OBJECTS) $(sparsecache_test_LDADD) $(LIBS)
--
--dejavu.test: $(dejavu_test_OBJECTS) $(dejavu_test_DEPENDENCIES)
-- @rm -f dejavu.test
-- $(LINK) $(dejavu_test_LDFLAGS) $(dejavu_test_OBJECTS) $(dejavu_test_LDADD) $(LIBS)
--
--bitarray.test: $(bitarray_test_OBJECTS) $(bitarray_test_DEPENDENCIES)
-- @rm -f bitarray.test
-- $(LINK) $(bitarray_test_LDFLAGS) $(bitarray_test_OBJECTS) $(bitarray_test_LDADD) $(LIBS)
--
--splaytree.test: $(splaytree_test_OBJECTS) $(splaytree_test_DEPENDENCIES)
-- @rm -f splaytree.test
-- $(LINK) $(splaytree_test_LDFLAGS) $(splaytree_test_OBJECTS) $(splaytree_test_LDADD) $(LIBS)
--
--noitree.test: $(noitree_test_OBJECTS) $(noitree_test_DEPENDENCIES)
-- @rm -f noitree.test
-- $(LINK) $(noitree_test_LDFLAGS) $(noitree_test_OBJECTS) $(noitree_test_LDADD) $(LIBS)
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/bitarray.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/bitarray.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/dejavu.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/dejavu.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fsm.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fsm.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/matrix.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/matrix.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/noitree.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/noitree.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pqueue.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pqueue.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/rangetree.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/rangetree.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/recyclebin.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/recyclebin.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/slist.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/slist.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sparsecache.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sparsecache.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/splaytree.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/splaytree.test.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/vfsm.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/vfsm.test.Po at am__quote@
-
-+.c.o:
-+ at am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
-+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-+ at am__fastdepCC_FALSE@ $(COMPILE) -c $<
-+
-+.c.obj:
-+ at am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
-+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-+ at am__fastdepCC_FALSE@ $(COMPILE) -c `$(CYGPATH_W) '$<'`
-+
-+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ mkid -fID $$unique
- tags: TAGS
-
--ID: $(HEADERS) $(SOURCES) $(LISP)
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- here=`pwd` && cd $(srcdir) \
-- && mkid -f$$here/ID $$unique $(LISP)
--
--TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) $(LISP)
-- tags=; \
-+TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ set x; \
- here=`pwd`; \
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- test -z "$(ETAGS_ARGS)$$unique$(LISP)$$tags" \
-- || (cd $(srcdir) && etags -o $$here/TAGS $(ETAGS_ARGS) $$tags $$unique $(LISP))
--
--mostlyclean-tags:
--
--clean-tags:
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ shift; \
-+ if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
-+ test -n "$$unique" || unique=$$empty_fix; \
-+ if test $$# -gt 0; then \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ "$$@" $$unique; \
-+ else \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ $$unique; \
-+ fi; \
-+ fi
-+ctags: CTAGS
-+CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ test -z "$(CTAGS_ARGS)$$unique" \
-+ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-+ $$unique
-+
-+GTAGS:
-+ here=`$(am__cd) $(top_builddir) && pwd` \
-+ && $(am__cd) $(top_srcdir) \
-+ && gtags -i $(GTAGS_ARGS) "$$here"
-
- distclean-tags:
-- -rm -f TAGS ID
--
--maintainer-clean-tags:
--
--distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
-+ -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-
--subdir = src/struct
--
--distdir: $(DISTFILES)
-- @for file in $(DISTFILES); do \
-- d=$(srcdir); \
-- if test -d $$d/$$file; then \
-- cp -pr $$d/$$file $(distdir)/$$file; \
-- else \
-- test -f $(distdir)/$$file \
-- || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
-- || cp -p $$d/$$file $(distdir)/$$file || :; \
-- fi; \
-- done
- check-TESTS: $(TESTS)
-- @failed=0; all=0; \
-+ @failed=0; all=0; xfail=0; xpass=0; skip=0; \
- srcdir=$(srcdir); export srcdir; \
-- for tst in $(TESTS); do \
-- if test -f $$tst; then dir=.; \
-- else dir="$(srcdir)"; fi; \
-- if $(TESTS_ENVIRONMENT) $$dir/$$tst; then \
-+ list=' $(TESTS) '; \
-+ $(am__tty_colors); \
-+ if test -n "$$list"; then \
-+ for tst in $$list; do \
-+ if test -f ./$$tst; then dir=./; \
-+ elif test -f $$tst; then dir=; \
-+ else dir="$(srcdir)/"; fi; \
-+ if $(TESTS_ENVIRONMENT) $${dir}$$tst; then \
- all=`expr $$all + 1`; \
-- echo "PASS: $$tst"; \
-+ case " $(XFAIL_TESTS) " in \
-+ *[\ \ ]$$tst[\ \ ]*) \
-+ xpass=`expr $$xpass + 1`; \
-+ failed=`expr $$failed + 1`; \
-+ col=$$red; res=XPASS; \
-+ ;; \
-+ *) \
-+ col=$$grn; res=PASS; \
-+ ;; \
-+ esac; \
- elif test $$? -ne 77; then \
- all=`expr $$all + 1`; \
-+ case " $(XFAIL_TESTS) " in \
-+ *[\ \ ]$$tst[\ \ ]*) \
-+ xfail=`expr $$xfail + 1`; \
-+ col=$$lgn; res=XFAIL; \
-+ ;; \
-+ *) \
- failed=`expr $$failed + 1`; \
-- echo "FAIL: $$tst"; \
-+ col=$$red; res=FAIL; \
-+ ;; \
-+ esac; \
-+ else \
-+ skip=`expr $$skip + 1`; \
-+ col=$$blu; res=SKIP; \
- fi; \
-+ echo "$${col}$$res$${std}: $$tst"; \
- done; \
-+ if test "$$all" -eq 1; then \
-+ tests="test"; \
-+ All=""; \
-+ else \
-+ tests="tests"; \
-+ All="All "; \
-+ fi; \
-+ if test "$$failed" -eq 0; then \
-+ if test "$$xfail" -eq 0; then \
-+ banner="$$All$$all $$tests passed"; \
-+ else \
-+ if test "$$xfail" -eq 1; then failures=failure; else failures=failures; fi; \
-+ banner="$$All$$all $$tests behaved as expected ($$xfail expected $$failures)"; \
-+ fi; \
-+ else \
-+ if test "$$xpass" -eq 0; then \
-+ banner="$$failed of $$all $$tests failed"; \
-+ else \
-+ if test "$$xpass" -eq 1; then passes=pass; else passes=passes; fi; \
-+ banner="$$failed of $$all $$tests did not behave as expected ($$xpass unexpected $$passes)"; \
-+ fi; \
-+ fi; \
-+ dashes="$$banner"; \
-+ skipped=""; \
-+ if test "$$skip" -ne 0; then \
-+ if test "$$skip" -eq 1; then \
-+ skipped="($$skip test was not run)"; \
-+ else \
-+ skipped="($$skip tests were not run)"; \
-+ fi; \
-+ test `echo "$$skipped" | wc -c` -le `echo "$$banner" | wc -c` || \
-+ dashes="$$skipped"; \
-+ fi; \
-+ report=""; \
-+ if test "$$failed" -ne 0 && test -n "$(PACKAGE_BUGREPORT)"; then \
-+ report="Please report to $(PACKAGE_BUGREPORT)"; \
-+ test `echo "$$report" | wc -c` -le `echo "$$banner" | wc -c` || \
-+ dashes="$$report"; \
-+ fi; \
-+ dashes=`echo "$$dashes" | sed s/./=/g`; \
- if test "$$failed" -eq 0; then \
-- banner="All $$all tests passed"; \
-+ echo "$$grn$$dashes"; \
- else \
-- banner="$$failed of $$all tests failed"; \
-+ echo "$$red$$dashes"; \
- fi; \
-- dashes=`echo "$$banner" | sed s/./=/g`; \
-- echo "$$dashes"; \
- echo "$$banner"; \
-- echo "$$dashes"; \
-- test "$$failed" -eq 0
--info-am:
--info: info-am
--dvi-am:
--dvi: dvi-am
-+ test -z "$$skipped" || echo "$$skipped"; \
-+ test -z "$$report" || echo "$$report"; \
-+ echo "$$dashes$$std"; \
-+ test "$$failed" -eq 0; \
-+ else :; fi
-+
-+distdir: $(DISTFILES)
-+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ list='$(DISTFILES)'; \
-+ dist_files=`for file in $$list; do echo $$file; done | \
-+ sed -e "s|^$$srcdirstrip/||;t" \
-+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-+ case $$dist_files in \
-+ */*) $(MKDIR_P) `echo "$$dist_files" | \
-+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-+ sort -u` ;; \
-+ esac; \
-+ for file in $$dist_files; do \
-+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
-+ if test -d $$d/$$file; then \
-+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-+ if test -d "$(distdir)/$$file"; then \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
-+ else \
-+ test -f "$(distdir)/$$file" \
-+ || cp -p $$d/$$file "$(distdir)/$$file" \
-+ || exit 1; \
-+ fi; \
-+ done
- check-am: all-am
- $(MAKE) $(AM_MAKEFLAGS) check-TESTS
- check: check-am
--installcheck-am:
--installcheck: installcheck-am
--install-exec-am:
-+all-am: Makefile $(PROGRAMS) $(HEADERS)
-+installdirs:
-+install: install-am
- install-exec: install-exec-am
--
--install-data-am:
- install-data: install-data-am
-+uninstall: uninstall-am
-
- install-am: all-am
- @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
--install: install-am
--uninstall-am:
--uninstall: uninstall-am
--all-am: Makefile $(PROGRAMS) $(HEADERS)
--all-redirect: all-am
--install-strip:
-- $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
--installdirs:
--
-
-+installcheck: installcheck-am
-+install-strip:
-+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-+ `test -z '$(STRIP)' || \
-+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
- mostlyclean-generic:
-
- clean-generic:
-
- distclean-generic:
-- -rm -f Makefile $(CONFIG_CLEAN_FILES)
-- -rm -f config.cache config.log stamp-h stamp-h[0-9]*
-+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
- maintainer-clean-generic:
-+ @echo "This command is intended for maintainers to use"
-+ @echo "it deletes files that may require special tools to rebuild."
- -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
--mostlyclean-am: mostlyclean-noinstPROGRAMS mostlyclean-compile \
-- mostlyclean-tags mostlyclean-generic
-+clean: clean-am
-
--mostlyclean: mostlyclean-am
-+clean-am: clean-generic clean-noinstPROGRAMS mostlyclean-am
-
--clean-am: clean-noinstPROGRAMS clean-compile clean-tags clean-generic \
-- mostlyclean-am
-+distclean: distclean-am
-+ -rm -rf ./$(DEPDIR)
-+ -rm -f Makefile
-+distclean-am: clean-am distclean-compile distclean-generic \
-+ distclean-tags
-
--clean: clean-am
-+dvi: dvi-am
-
--distclean-am: distclean-noinstPROGRAMS distclean-compile distclean-tags \
-- distclean-generic clean-am
-+dvi-am:
-
--distclean: distclean-am
-+html: html-am
-
--maintainer-clean-am: maintainer-clean-noinstPROGRAMS \
-- maintainer-clean-compile maintainer-clean-tags \
-- maintainer-clean-generic distclean-am
-- @echo "This command is intended for maintainers to use;"
-- @echo "it deletes files that may require special tools to rebuild."
-+html-am:
-+
-+info: info-am
-+
-+info-am:
-+
-+install-data-am:
-+
-+install-dvi: install-dvi-am
-+
-+install-dvi-am:
-+
-+install-exec-am:
-+
-+install-html: install-html-am
-+
-+install-html-am:
-+
-+install-info: install-info-am
-+
-+install-info-am:
-+
-+install-man:
-+
-+install-pdf: install-pdf-am
-+
-+install-pdf-am:
-+
-+install-ps: install-ps-am
-+
-+install-ps-am:
-+
-+installcheck-am:
-
- maintainer-clean: maintainer-clean-am
-+ -rm -rf ./$(DEPDIR)
-+ -rm -f Makefile
-+maintainer-clean-am: distclean-am maintainer-clean-generic
-+
-+mostlyclean: mostlyclean-am
-+
-+mostlyclean-am: mostlyclean-compile mostlyclean-generic
-+
-+pdf: pdf-am
-+
-+pdf-am:
-+
-+ps: ps-am
-+
-+ps-am:
-+
-+uninstall-am:
-+
-+.MAKE: check-am install-am install-strip
-
--.PHONY: mostlyclean-noinstPROGRAMS distclean-noinstPROGRAMS \
--clean-noinstPROGRAMS maintainer-clean-noinstPROGRAMS \
--mostlyclean-compile distclean-compile clean-compile \
--maintainer-clean-compile tags mostlyclean-tags distclean-tags \
--clean-tags maintainer-clean-tags distdir check-TESTS info-am info \
--dvi-am dvi check check-am installcheck-am installcheck install-exec-am \
--install-exec install-data-am install-data install-am install \
--uninstall-am uninstall all-redirect all-am all installdirs \
--mostlyclean-generic distclean-generic clean-generic \
--maintainer-clean-generic clean mostlyclean distclean maintainer-clean
-+.PHONY: CTAGS GTAGS all all-am check check-TESTS check-am clean \
-+ clean-generic clean-noinstPROGRAMS ctags distclean \
-+ distclean-compile distclean-generic distclean-tags distdir dvi \
-+ dvi-am html html-am info info-am install install-am \
-+ install-data install-data-am install-dvi install-dvi-am \
-+ install-exec install-exec-am install-html install-html-am \
-+ install-info install-info-am install-man install-pdf \
-+ install-pdf-am install-ps install-ps-am install-strip \
-+ installcheck installcheck-am installdirs maintainer-clean \
-+ maintainer-clean-generic mostlyclean mostlyclean-compile \
-+ mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
-+ uninstall-am
-
-
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -ubrN exonerate-2.2.0.orig/src/util/Makefile.in exonerate-2.2.0/src/util/Makefile.in
---- exonerate-2.2.0.orig/src/util/Makefile.in 2008-10-17 12:04:46.000000000 +0200
-+++ exonerate-2.2.0/src/util/Makefile.in 2011-12-12 13:33:17.000000000 +0100
-@@ -1,6 +1,9 @@
--# Makefile.in generated automatically by automake 1.4-p6 from Makefile.am
-+# Makefile.in generated by automake 1.11.1 from Makefile.am.
-+# @configure_input@
-
--# Copyright (C) 1994, 1995-8, 1999, 2001 Free Software Foundation, Inc.
-+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
-+# Inc.
- # This Makefile.in is free software; the Free Software Foundation
- # gives unlimited permission to copy and/or distribute it,
- # with or without modifications, as long as this notice is preserved.
-@@ -10,732 +13,958 @@
- # even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- # PARTICULAR PURPOSE.
-
-+ at SET_MAKE@
-
--SHELL = @SHELL@
--
--srcdir = @srcdir@
--top_srcdir = @top_srcdir@
- VPATH = @srcdir@
--prefix = @prefix@
--exec_prefix = @exec_prefix@
--
--bindir = @bindir@
--sbindir = @sbindir@
--libexecdir = @libexecdir@
--datadir = @datadir@
--sysconfdir = @sysconfdir@
--sharedstatedir = @sharedstatedir@
--localstatedir = @localstatedir@
--libdir = @libdir@
--infodir = @infodir@
--mandir = @mandir@
--includedir = @includedir@
--oldincludedir = /usr/include
--
--DESTDIR =
--
- pkgdatadir = $(datadir)/@PACKAGE@
--pkglibdir = $(libdir)/@PACKAGE@
- pkgincludedir = $(includedir)/@PACKAGE@
--
--top_builddir = ../..
--
--ACLOCAL = @ACLOCAL@
--AUTOCONF = @AUTOCONF@
--AUTOMAKE = @AUTOMAKE@
--AUTOHEADER = @AUTOHEADER@
--
--INSTALL = @INSTALL@
--INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
--INSTALL_DATA = @INSTALL_DATA@
--INSTALL_SCRIPT = @INSTALL_SCRIPT@
--transform = @program_transform_name@
--
-+pkglibdir = $(libdir)/@PACKAGE@
-+pkglibexecdir = $(libexecdir)/@PACKAGE@
-+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-+install_sh_DATA = $(install_sh) -c -m 644
-+install_sh_PROGRAM = $(install_sh) -c
-+install_sh_SCRIPT = $(install_sh) -c
-+INSTALL_HEADER = $(INSTALL_DATA)
-+transform = $(program_transform_name)
- NORMAL_INSTALL = :
- PRE_INSTALL = :
- POST_INSTALL = :
- NORMAL_UNINSTALL = :
- PRE_UNINSTALL = :
- POST_UNINSTALL = :
--host_alias = @host_alias@
-+build_triplet = @build@
- host_triplet = @host@
--CC = @CC@
--GLIB_CONFIG = @GLIB_CONFIG@
--HAVE_LIB = @HAVE_LIB@
--LIB = @LIB@
--LTLIB = @LTLIB@
--MAKEINFO = @MAKEINFO@
--PACKAGE = @PACKAGE@
--PKG_CONFIG = @PKG_CONFIG@
--VERSION = @VERSION@
--codegen_extra_ldadd = @codegen_extra_ldadd@
--codegen_extra_sources = @codegen_extra_sources@
--datarootdir = @datarootdir@
--glib_cflags = @glib_cflags@
--glib_libs = @glib_libs@
--host = @host@
--installed_util_list = @installed_util_list@
--source_root_dir = @source_root_dir@
--use_pthreads = @use_pthreads@
--
--bin_PROGRAMS = @installed_util_list@
--
--EXTRA_PROGRAMS = fastaclean fastaclip fastachecksum fastacomposition fastadiff fastaexplode fastafetch fastahardmask fastaindex fastalength fastanrdb fastaoverlap fastareformat fastaremove fastarevcomp fastasoftmask fastasort fastasplit fastasubseq fastatranslate fastavalidcds fasta2esd fastaannotatecdna esd2esi
--
--
--INCLUDES = -I$(top_srcdir)/src/sequence -I$(top_srcdir)/src/database -I$(top_srcdir)/src/struct -I$(top_srcdir)/src/comparison -I$(top_srcdir)/src/general
--
--
--LDADD = $(top_srcdir)/src/sequence/sequence.o $(top_srcdir)/src/sequence/alphabet.o $(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/sequence/translate.o $(top_srcdir)/src/database/fastadb.o $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/general/compoundfile.o $(top_srcdir)/src/general/lineparse.o $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/struct/matrix.o -lm
--
--
--fastaclean_SOURCES = fastaclean.c
--fastaclip_SOURCES = fastaclip.c
--fastachecksum_SOURCES = fastachecksum.c
--fastacomposition_SOURCES = fastacomposition.c
--fastadiff_SOURCES = fastadiff.c
--fastaexplode_SOURCES = fastaexplode.c
--fastafetch_SOURCES = fastafetch.c
--fastahardmask_SOURCES = fastahardmask.c
--fastaindex_SOURCES = fastaindex.c
--fastalength_SOURCES = fastalength.c
--fastanrdb_SOURCES = fastanrdb.c
--fastaoverlap_SOURCES = fastaoverlap.c
--fastareformat_SOURCES = fastareformat.c
--fastaremove_SOURCES = fastaremove.c
--fastarevcomp_SOURCES = fastarevcomp.c
--fastasoftmask_SOURCES = fastasoftmask.c
--fastasort_SOURCES = fastasort.c
--fastasplit_SOURCES = fastasplit.c
--fastasubseq_SOURCES = fastasubseq.c
--fastatranslate_SOURCES = fastatranslate.c
--fasta2esd_SOURCES = fasta2esd.c
--fastaannotatecdna_SOURCES = fastaannotatecdna.c
--esd2esi_SOURCES = esd2esi.c
--
--fasta2esd_LDADD = $(top_srcdir)/src/database/dataset.o $(top_srcdir)/src/struct/bitarray.o $(LDADD)
--
--
--esd2esi_LDADD = $(top_srcdir)/src/database/dataset.o $(top_srcdir)/src/database/index.o $(top_srcdir)/src/struct/bitarray.o $(top_srcdir)/src/struct/vfsm.o $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/rangetree.o $(top_srcdir)/src/struct/noitree.o $(top_srcdir)/src/struct/splaytree.o $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/comparison/wordhood.o $(top_srcdir)/src/comparison/hspset.o $(top_srcdir)/src/comparison/match.o $(LDADD)
--
--
--EXTRA_fastavalidcds_SOURCES = fastavalidcds.c
--
--# Files to clear away
--
--MAINTAINERCLEANFILES = Makefile.in
-+EXTRA_PROGRAMS = fastaclean$(EXEEXT) fastaclip$(EXEEXT) \
-+ fastachecksum$(EXEEXT) fastacomposition$(EXEEXT) \
-+ fastadiff$(EXEEXT) fastaexplode$(EXEEXT) fastafetch$(EXEEXT) \
-+ fastahardmask$(EXEEXT) fastaindex$(EXEEXT) \
-+ fastalength$(EXEEXT) fastanrdb$(EXEEXT) fastaoverlap$(EXEEXT) \
-+ fastareformat$(EXEEXT) fastaremove$(EXEEXT) \
-+ fastarevcomp$(EXEEXT) fastasoftmask$(EXEEXT) \
-+ fastasort$(EXEEXT) fastasplit$(EXEEXT) fastasubseq$(EXEEXT) \
-+ fastatranslate$(EXEEXT) fastavalidcds$(EXEEXT) \
-+ fasta2esd$(EXEEXT) fastaannotatecdna$(EXEEXT) esd2esi$(EXEEXT)
-+subdir = src/util
-+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
-+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-+am__aclocal_m4_deps = $(top_srcdir)/configure.in
-+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-+ $(ACLOCAL_M4)
- mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
- CONFIG_CLEAN_FILES =
-+CONFIG_CLEAN_VPATH_FILES =
-+am__installdirs = "$(DESTDIR)$(bindir)"
- PROGRAMS = $(bin_PROGRAMS)
--
--
--DEFS = @DEFS@ -I. -I$(srcdir)
--CPPFLAGS = @CPPFLAGS@
--LDFLAGS = @LDFLAGS@
--LIBS = @LIBS@
--fastaclean_OBJECTS = fastaclean.o
-+am_esd2esi_OBJECTS = esd2esi.$(OBJEXT)
-+esd2esi_OBJECTS = $(am_esd2esi_OBJECTS)
-+am__DEPENDENCIES_1 = $(top_srcdir)/src/sequence/sequence.o \
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o
-+esd2esi_DEPENDENCIES = $(top_srcdir)/src/database/dataset.o \
-+ $(top_srcdir)/src/database/index.o \
-+ $(top_srcdir)/src/struct/bitarray.o \
-+ $(top_srcdir)/src/struct/vfsm.o \
-+ $(top_srcdir)/src/struct/pqueue.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/rangetree.o \
-+ $(top_srcdir)/src/struct/noitree.o \
-+ $(top_srcdir)/src/struct/splaytree.o \
-+ $(top_srcdir)/src/sequence/submat.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o \
-+ $(top_srcdir)/src/comparison/wordhood.o \
-+ $(top_srcdir)/src/comparison/hspset.o \
-+ $(top_srcdir)/src/comparison/match.o $(am__DEPENDENCIES_1)
-+am_fasta2esd_OBJECTS = fasta2esd.$(OBJEXT)
-+fasta2esd_OBJECTS = $(am_fasta2esd_OBJECTS)
-+fasta2esd_DEPENDENCIES = $(top_srcdir)/src/database/dataset.o \
-+ $(top_srcdir)/src/struct/bitarray.o $(am__DEPENDENCIES_1)
-+am_fastaannotatecdna_OBJECTS = fastaannotatecdna.$(OBJEXT)
-+fastaannotatecdna_OBJECTS = $(am_fastaannotatecdna_OBJECTS)
-+fastaannotatecdna_LDADD = $(LDADD)
-+fastaannotatecdna_DEPENDENCIES = \
-+ $(top_srcdir)/src/sequence/sequence.o \
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o
-+am_fastachecksum_OBJECTS = fastachecksum.$(OBJEXT)
-+fastachecksum_OBJECTS = $(am_fastachecksum_OBJECTS)
-+fastachecksum_LDADD = $(LDADD)
-+fastachecksum_DEPENDENCIES = $(top_srcdir)/src/sequence/sequence.o \
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o
-+am_fastaclean_OBJECTS = fastaclean.$(OBJEXT)
-+fastaclean_OBJECTS = $(am_fastaclean_OBJECTS)
- fastaclean_LDADD = $(LDADD)
- fastaclean_DEPENDENCIES = $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/database/fastadb.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/general/lineparse.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o
--fastaclean_LDFLAGS =
--fastaclip_OBJECTS = fastaclip.o
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o
-+am_fastaclip_OBJECTS = fastaclip.$(OBJEXT)
-+fastaclip_OBJECTS = $(am_fastaclip_OBJECTS)
- fastaclip_LDADD = $(LDADD)
- fastaclip_DEPENDENCIES = $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/database/fastadb.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/general/lineparse.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o
--fastaclip_LDFLAGS =
--fastachecksum_OBJECTS = fastachecksum.o
--fastachecksum_LDADD = $(LDADD)
--fastachecksum_DEPENDENCIES = $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/database/fastadb.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/general/lineparse.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o
--fastachecksum_LDFLAGS =
--fastacomposition_OBJECTS = fastacomposition.o
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o
-+am_fastacomposition_OBJECTS = fastacomposition.$(OBJEXT)
-+fastacomposition_OBJECTS = $(am_fastacomposition_OBJECTS)
- fastacomposition_LDADD = $(LDADD)
- fastacomposition_DEPENDENCIES = $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/database/fastadb.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/general/lineparse.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o
--fastacomposition_LDFLAGS =
--fastadiff_OBJECTS = fastadiff.o
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o
-+am_fastadiff_OBJECTS = fastadiff.$(OBJEXT)
-+fastadiff_OBJECTS = $(am_fastadiff_OBJECTS)
- fastadiff_LDADD = $(LDADD)
- fastadiff_DEPENDENCIES = $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/database/fastadb.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/general/lineparse.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o
--fastadiff_LDFLAGS =
--fastaexplode_OBJECTS = fastaexplode.o
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o
-+am_fastaexplode_OBJECTS = fastaexplode.$(OBJEXT)
-+fastaexplode_OBJECTS = $(am_fastaexplode_OBJECTS)
- fastaexplode_LDADD = $(LDADD)
- fastaexplode_DEPENDENCIES = $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/database/fastadb.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/general/lineparse.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o
--fastaexplode_LDFLAGS =
--fastafetch_OBJECTS = fastafetch.o
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o
-+am_fastafetch_OBJECTS = fastafetch.$(OBJEXT)
-+fastafetch_OBJECTS = $(am_fastafetch_OBJECTS)
- fastafetch_LDADD = $(LDADD)
- fastafetch_DEPENDENCIES = $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/database/fastadb.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/general/lineparse.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o
--fastafetch_LDFLAGS =
--fastahardmask_OBJECTS = fastahardmask.o
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o
-+am_fastahardmask_OBJECTS = fastahardmask.$(OBJEXT)
-+fastahardmask_OBJECTS = $(am_fastahardmask_OBJECTS)
- fastahardmask_LDADD = $(LDADD)
- fastahardmask_DEPENDENCIES = $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/database/fastadb.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/general/lineparse.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o
--fastahardmask_LDFLAGS =
--fastaindex_OBJECTS = fastaindex.o
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o
-+am_fastaindex_OBJECTS = fastaindex.$(OBJEXT)
-+fastaindex_OBJECTS = $(am_fastaindex_OBJECTS)
- fastaindex_LDADD = $(LDADD)
- fastaindex_DEPENDENCIES = $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/database/fastadb.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/general/lineparse.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o
--fastaindex_LDFLAGS =
--fastalength_OBJECTS = fastalength.o
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o
-+am_fastalength_OBJECTS = fastalength.$(OBJEXT)
-+fastalength_OBJECTS = $(am_fastalength_OBJECTS)
- fastalength_LDADD = $(LDADD)
- fastalength_DEPENDENCIES = $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/database/fastadb.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/general/lineparse.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o
--fastalength_LDFLAGS =
--fastanrdb_OBJECTS = fastanrdb.o
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o
-+am_fastanrdb_OBJECTS = fastanrdb.$(OBJEXT)
-+fastanrdb_OBJECTS = $(am_fastanrdb_OBJECTS)
- fastanrdb_LDADD = $(LDADD)
- fastanrdb_DEPENDENCIES = $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/database/fastadb.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/general/lineparse.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o
--fastanrdb_LDFLAGS =
--fastaoverlap_OBJECTS = fastaoverlap.o
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o
-+am_fastaoverlap_OBJECTS = fastaoverlap.$(OBJEXT)
-+fastaoverlap_OBJECTS = $(am_fastaoverlap_OBJECTS)
- fastaoverlap_LDADD = $(LDADD)
- fastaoverlap_DEPENDENCIES = $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/database/fastadb.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/general/lineparse.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o
--fastaoverlap_LDFLAGS =
--fastareformat_OBJECTS = fastareformat.o
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o
-+am_fastareformat_OBJECTS = fastareformat.$(OBJEXT)
-+fastareformat_OBJECTS = $(am_fastareformat_OBJECTS)
- fastareformat_LDADD = $(LDADD)
- fastareformat_DEPENDENCIES = $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/database/fastadb.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/general/lineparse.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o
--fastareformat_LDFLAGS =
--fastaremove_OBJECTS = fastaremove.o
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o
-+am_fastaremove_OBJECTS = fastaremove.$(OBJEXT)
-+fastaremove_OBJECTS = $(am_fastaremove_OBJECTS)
- fastaremove_LDADD = $(LDADD)
- fastaremove_DEPENDENCIES = $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/database/fastadb.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/general/lineparse.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o
--fastaremove_LDFLAGS =
--fastarevcomp_OBJECTS = fastarevcomp.o
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o
-+am_fastarevcomp_OBJECTS = fastarevcomp.$(OBJEXT)
-+fastarevcomp_OBJECTS = $(am_fastarevcomp_OBJECTS)
- fastarevcomp_LDADD = $(LDADD)
- fastarevcomp_DEPENDENCIES = $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/database/fastadb.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/general/lineparse.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o
--fastarevcomp_LDFLAGS =
--fastasoftmask_OBJECTS = fastasoftmask.o
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o
-+am_fastasoftmask_OBJECTS = fastasoftmask.$(OBJEXT)
-+fastasoftmask_OBJECTS = $(am_fastasoftmask_OBJECTS)
- fastasoftmask_LDADD = $(LDADD)
- fastasoftmask_DEPENDENCIES = $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/database/fastadb.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/general/lineparse.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o
--fastasoftmask_LDFLAGS =
--fastasort_OBJECTS = fastasort.o
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o
-+am_fastasort_OBJECTS = fastasort.$(OBJEXT)
-+fastasort_OBJECTS = $(am_fastasort_OBJECTS)
- fastasort_LDADD = $(LDADD)
- fastasort_DEPENDENCIES = $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/database/fastadb.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/general/lineparse.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o
--fastasort_LDFLAGS =
--fastasplit_OBJECTS = fastasplit.o
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o
-+am_fastasplit_OBJECTS = fastasplit.$(OBJEXT)
-+fastasplit_OBJECTS = $(am_fastasplit_OBJECTS)
- fastasplit_LDADD = $(LDADD)
- fastasplit_DEPENDENCIES = $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/database/fastadb.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/general/lineparse.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o
--fastasplit_LDFLAGS =
--fastasubseq_OBJECTS = fastasubseq.o
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o
-+am_fastasubseq_OBJECTS = fastasubseq.$(OBJEXT)
-+fastasubseq_OBJECTS = $(am_fastasubseq_OBJECTS)
- fastasubseq_LDADD = $(LDADD)
- fastasubseq_DEPENDENCIES = $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/database/fastadb.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/general/lineparse.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o
--fastasubseq_LDFLAGS =
--fastatranslate_OBJECTS = fastatranslate.o
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o
-+am_fastatranslate_OBJECTS = fastatranslate.$(OBJEXT)
-+fastatranslate_OBJECTS = $(am_fastatranslate_OBJECTS)
- fastatranslate_LDADD = $(LDADD)
- fastatranslate_DEPENDENCIES = $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/database/fastadb.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/general/lineparse.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o
--fastatranslate_LDFLAGS =
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o
- fastavalidcds_SOURCES = fastavalidcds.c
--fastavalidcds_OBJECTS = fastavalidcds.o
-+fastavalidcds_OBJECTS = fastavalidcds.$(OBJEXT)
- fastavalidcds_LDADD = $(LDADD)
- fastavalidcds_DEPENDENCIES = $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/database/fastadb.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/general/lineparse.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o
--fastavalidcds_LDFLAGS =
--fasta2esd_OBJECTS = fasta2esd.o
--fasta2esd_DEPENDENCIES = $(top_srcdir)/src/database/dataset.o \
--$(top_srcdir)/src/struct/bitarray.o \
--$(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/database/fastadb.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/general/lineparse.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o
--fasta2esd_LDFLAGS =
--fastaannotatecdna_OBJECTS = fastaannotatecdna.o
--fastaannotatecdna_LDADD = $(LDADD)
--fastaannotatecdna_DEPENDENCIES = $(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/database/fastadb.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/general/lineparse.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o
--fastaannotatecdna_LDFLAGS =
--esd2esi_OBJECTS = esd2esi.o
--esd2esi_DEPENDENCIES = $(top_srcdir)/src/database/dataset.o \
--$(top_srcdir)/src/database/index.o $(top_srcdir)/src/struct/bitarray.o \
--$(top_srcdir)/src/struct/vfsm.o $(top_srcdir)/src/struct/pqueue.o \
--$(top_srcdir)/src/struct/recyclebin.o \
--$(top_srcdir)/src/struct/rangetree.o $(top_srcdir)/src/struct/noitree.o \
--$(top_srcdir)/src/struct/splaytree.o \
--$(top_srcdir)/src/sequence/submat.o \
--$(top_srcdir)/src/sequence/codonsubmat.o \
--$(top_srcdir)/src/comparison/wordhood.o \
--$(top_srcdir)/src/comparison/hspset.o \
--$(top_srcdir)/src/comparison/match.o \
--$(top_srcdir)/src/sequence/sequence.o \
--$(top_srcdir)/src/sequence/alphabet.o \
--$(top_srcdir)/src/sequence/splice.o \
--$(top_srcdir)/src/sequence/translate.o \
--$(top_srcdir)/src/database/fastadb.o \
--$(top_srcdir)/src/general/argument.o \
--$(top_srcdir)/src/general/compoundfile.o \
--$(top_srcdir)/src/general/lineparse.o \
--$(top_srcdir)/src/struct/sparsecache.o \
--$(top_srcdir)/src/struct/matrix.o
--esd2esi_LDFLAGS =
--CFLAGS = @CFLAGS@
--COMPILE = $(CC) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o
-+DEFAULT_INCLUDES = -I. at am__isrc@
-+depcomp = $(SHELL) $(top_srcdir)/depcomp
-+am__depfiles_maybe = depfiles
-+am__mv = mv -f
-+COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
-+ $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
- CCLD = $(CC)
--LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(LDFLAGS) -o $@
--DIST_COMMON = Makefile.am Makefile.in
-+LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
-+SOURCES = $(esd2esi_SOURCES) $(fasta2esd_SOURCES) \
-+ $(fastaannotatecdna_SOURCES) $(fastachecksum_SOURCES) \
-+ $(fastaclean_SOURCES) $(fastaclip_SOURCES) \
-+ $(fastacomposition_SOURCES) $(fastadiff_SOURCES) \
-+ $(fastaexplode_SOURCES) $(fastafetch_SOURCES) \
-+ $(fastahardmask_SOURCES) $(fastaindex_SOURCES) \
-+ $(fastalength_SOURCES) $(fastanrdb_SOURCES) \
-+ $(fastaoverlap_SOURCES) $(fastareformat_SOURCES) \
-+ $(fastaremove_SOURCES) $(fastarevcomp_SOURCES) \
-+ $(fastasoftmask_SOURCES) $(fastasort_SOURCES) \
-+ $(fastasplit_SOURCES) $(fastasubseq_SOURCES) \
-+ $(fastatranslate_SOURCES) $(EXTRA_fastavalidcds_SOURCES) \
-+ fastavalidcds.c
-+DIST_SOURCES = $(esd2esi_SOURCES) $(fasta2esd_SOURCES) \
-+ $(fastaannotatecdna_SOURCES) $(fastachecksum_SOURCES) \
-+ $(fastaclean_SOURCES) $(fastaclip_SOURCES) \
-+ $(fastacomposition_SOURCES) $(fastadiff_SOURCES) \
-+ $(fastaexplode_SOURCES) $(fastafetch_SOURCES) \
-+ $(fastahardmask_SOURCES) $(fastaindex_SOURCES) \
-+ $(fastalength_SOURCES) $(fastanrdb_SOURCES) \
-+ $(fastaoverlap_SOURCES) $(fastareformat_SOURCES) \
-+ $(fastaremove_SOURCES) $(fastarevcomp_SOURCES) \
-+ $(fastasoftmask_SOURCES) $(fastasort_SOURCES) \
-+ $(fastasplit_SOURCES) $(fastasubseq_SOURCES) \
-+ $(fastatranslate_SOURCES) $(EXTRA_fastavalidcds_SOURCES) \
-+ fastavalidcds.c
-+ETAGS = etags
-+CTAGS = ctags
-+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-+ACLOCAL = @ACLOCAL@
-+AMTAR = @AMTAR@
-+AUTOCONF = @AUTOCONF@
-+AUTOHEADER = @AUTOHEADER@
-+AUTOMAKE = @AUTOMAKE@
-+AWK = @AWK@
-+CC = @CC@
-+CCDEPMODE = @CCDEPMODE@
-+CFLAGS = @CFLAGS@
-+CPP = @CPP@
-+CPPFLAGS = @CPPFLAGS@
-+CYGPATH_W = @CYGPATH_W@
-+DEFS = @DEFS@
-+DEPDIR = @DEPDIR@
-+ECHO_C = @ECHO_C@
-+ECHO_N = @ECHO_N@
-+ECHO_T = @ECHO_T@
-+EGREP = @EGREP@
-+EXEEXT = @EXEEXT@
-+GLIB_CONFIG = @GLIB_CONFIG@
-+GREP = @GREP@
-+INSTALL = @INSTALL@
-+INSTALL_DATA = @INSTALL_DATA@
-+INSTALL_PROGRAM = @INSTALL_PROGRAM@
-+INSTALL_SCRIPT = @INSTALL_SCRIPT@
-+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-+LDFLAGS = @LDFLAGS@
-+LIBOBJS = @LIBOBJS@
-+LIBS = @LIBS@
-+LTLIBOBJS = @LTLIBOBJS@
-+MAKEINFO = @MAKEINFO@
-+MKDIR_P = @MKDIR_P@
-+OBJEXT = @OBJEXT@
-+PACKAGE = @PACKAGE@
-+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-+PACKAGE_NAME = @PACKAGE_NAME@
-+PACKAGE_STRING = @PACKAGE_STRING@
-+PACKAGE_TARNAME = @PACKAGE_TARNAME@
-+PACKAGE_URL = @PACKAGE_URL@
-+PACKAGE_VERSION = @PACKAGE_VERSION@
-+PATH_SEPARATOR = @PATH_SEPARATOR@
-+PKG_CONFIG = @PKG_CONFIG@
-+SET_MAKE = @SET_MAKE@
-+SHELL = @SHELL@
-+STRIP = @STRIP@
-+VERSION = @VERSION@
-+abs_builddir = @abs_builddir@
-+abs_srcdir = @abs_srcdir@
-+abs_top_builddir = @abs_top_builddir@
-+abs_top_srcdir = @abs_top_srcdir@
-+ac_ct_CC = @ac_ct_CC@
-+am__include = @am__include@
-+am__leading_dot = @am__leading_dot@
-+am__quote = @am__quote@
-+am__tar = @am__tar@
-+am__untar = @am__untar@
-+bindir = @bindir@
-+build = @build@
-+build_alias = @build_alias@
-+build_cpu = @build_cpu@
-+build_os = @build_os@
-+build_vendor = @build_vendor@
-+builddir = @builddir@
-+codegen_extra_ldadd = @codegen_extra_ldadd@
-+codegen_extra_sources = @codegen_extra_sources@
-+datadir = @datadir@
-+datarootdir = @datarootdir@
-+docdir = @docdir@
-+dvidir = @dvidir@
-+exec_prefix = @exec_prefix@
-+glib_cflags = @glib_cflags@
-+glib_libs = @glib_libs@
-+host = @host@
-+host_alias = @host_alias@
-+host_cpu = @host_cpu@
-+host_os = @host_os@
-+host_vendor = @host_vendor@
-+htmldir = @htmldir@
-+includedir = @includedir@
-+infodir = @infodir@
-+install_sh = @install_sh@
-+installed_util_list = @installed_util_list@
-+libdir = @libdir@
-+libexecdir = @libexecdir@
-+localedir = @localedir@
-+localstatedir = @localstatedir@
-+mandir = @mandir@
-+mkdir_p = @mkdir_p@
-+oldincludedir = @oldincludedir@
-+pdfdir = @pdfdir@
-+prefix = @prefix@
-+program_transform_name = @program_transform_name@
-+psdir = @psdir@
-+sbindir = @sbindir@
-+sharedstatedir = @sharedstatedir@
-+source_root_dir = @source_root_dir@
-+srcdir = @srcdir@
-+sysconfdir = @sysconfdir@
-+target_alias = @target_alias@
-+top_build_prefix = @top_build_prefix@
-+top_builddir = @top_builddir@
-+top_srcdir = @top_srcdir@
-+use_pthreads = @use_pthreads@
-+bin_PROGRAMS = @installed_util_list@
-+INCLUDES = -I$(top_srcdir)/src/sequence \
-+ -I$(top_srcdir)/src/database \
-+ -I$(top_srcdir)/src/struct \
-+ -I$(top_srcdir)/src/comparison \
-+ -I$(top_srcdir)/src/general
-+
-+LDADD = $(top_srcdir)/src/sequence/sequence.o \
-+ $(top_srcdir)/src/sequence/alphabet.o \
-+ $(top_srcdir)/src/sequence/splice.o \
-+ $(top_srcdir)/src/sequence/translate.o \
-+ $(top_srcdir)/src/database/fastadb.o \
-+ $(top_srcdir)/src/general/argument.o \
-+ $(top_srcdir)/src/general/compoundfile.o \
-+ $(top_srcdir)/src/general/lineparse.o \
-+ $(top_srcdir)/src/struct/sparsecache.o \
-+ $(top_srcdir)/src/struct/matrix.o \
-+ -lm
-
-+fastaclean_SOURCES = fastaclean.c
-+fastaclip_SOURCES = fastaclip.c
-+fastachecksum_SOURCES = fastachecksum.c
-+fastacomposition_SOURCES = fastacomposition.c
-+fastadiff_SOURCES = fastadiff.c
-+fastaexplode_SOURCES = fastaexplode.c
-+fastafetch_SOURCES = fastafetch.c
-+fastahardmask_SOURCES = fastahardmask.c
-+fastaindex_SOURCES = fastaindex.c
-+fastalength_SOURCES = fastalength.c
-+fastanrdb_SOURCES = fastanrdb.c
-+fastaoverlap_SOURCES = fastaoverlap.c
-+fastareformat_SOURCES = fastareformat.c
-+fastaremove_SOURCES = fastaremove.c
-+fastarevcomp_SOURCES = fastarevcomp.c
-+fastasoftmask_SOURCES = fastasoftmask.c
-+fastasort_SOURCES = fastasort.c
-+fastasplit_SOURCES = fastasplit.c
-+fastasubseq_SOURCES = fastasubseq.c
-+fastatranslate_SOURCES = fastatranslate.c
-+fasta2esd_SOURCES = fasta2esd.c
-+fastaannotatecdna_SOURCES = fastaannotatecdna.c
-+esd2esi_SOURCES = esd2esi.c
-+fasta2esd_LDADD = $(top_srcdir)/src/database/dataset.o \
-+ $(top_srcdir)/src/struct/bitarray.o \
-+ $(LDADD)
-+
-+esd2esi_LDADD = $(top_srcdir)/src/database/dataset.o \
-+ $(top_srcdir)/src/database/index.o \
-+ $(top_srcdir)/src/struct/bitarray.o \
-+ $(top_srcdir)/src/struct/vfsm.o \
-+ $(top_srcdir)/src/struct/pqueue.o \
-+ $(top_srcdir)/src/struct/recyclebin.o \
-+ $(top_srcdir)/src/struct/rangetree.o \
-+ $(top_srcdir)/src/struct/noitree.o \
-+ $(top_srcdir)/src/struct/splaytree.o \
-+ $(top_srcdir)/src/sequence/submat.o \
-+ $(top_srcdir)/src/sequence/codonsubmat.o \
-+ $(top_srcdir)/src/comparison/wordhood.o \
-+ $(top_srcdir)/src/comparison/hspset.o \
-+ $(top_srcdir)/src/comparison/match.o \
-+ $(LDADD)
-
--DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
-+EXTRA_fastavalidcds_SOURCES = fastavalidcds.c
-
--TAR = tar
--GZIP_ENV = --best
--SOURCES = $(fastaclean_SOURCES) $(fastaclip_SOURCES) $(fastachecksum_SOURCES) $(fastacomposition_SOURCES) $(fastadiff_SOURCES) $(fastaexplode_SOURCES) $(fastafetch_SOURCES) $(fastahardmask_SOURCES) $(fastaindex_SOURCES) $(fastalength_SOURCES) $(fastanrdb_SOURCES) $(fastaoverlap_SOURCES) $(fastareformat_SOURCES) $(fastaremove_SOURCES) $(fastarevcomp_SOURCES) $(fastasoftmask_SOURCES) $(fastasort_SOURCES) $(fastasplit_SOURCES) $(fastasubseq_SOURCES) $(fastatranslate_SOURCES) fastavalidcds.c $(EXTRA_fastavalidcds_SOURCES) $(fasta2esd_SOURCES) $(fastaannotatecdna_SOURCES) $(esd2esi_SOURCES)
--OBJECTS = $(fastaclean_OBJECTS) $(fastaclip_OBJECTS) $(fastachecksum_OBJECTS) $(fastacomposition_OBJECTS) $(fastadiff_OBJECTS) $(fastaexplode_OBJECTS) $(fastafetch_OBJECTS) $(fastahardmask_OBJECTS) $(fastaindex_OBJECTS) $(fastalength_OBJECTS) $(fastanrdb_OBJECTS) $(fastaoverlap_OBJECTS) $(fastareformat_OBJECTS) $(fastaremove_OBJECTS) $(fastarevcomp_OBJECTS) $(fastasoftmask_OBJECTS) $(fastasort_OBJECTS) $(fastasplit_OBJECTS) $(fastasubseq_OBJECTS) $(fastatranslate_OBJECTS) fastavalidcds.o $(fasta2esd_OBJECTS) $(fastaannotatecdna_OBJECTS) $(esd2esi_OBJECTS)
-+# Files to clear away
-+MAINTAINERCLEANFILES = Makefile.in
-+all: all-am
-
--all: all-redirect
- .SUFFIXES:
--.SUFFIXES: .S .c .o .s
--$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4)
-- cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps src/util/Makefile
--
-+.SUFFIXES: .c .o .obj
-+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
-+ @for dep in $?; do \
-+ case '$(am__configure_deps)' in \
-+ *$$dep*) \
-+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-+ && { if test -f $@; then exit 0; else break; fi; }; \
-+ exit 1;; \
-+ esac; \
-+ done; \
-+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/util/Makefile'; \
-+ $(am__cd) $(top_srcdir) && \
-+ $(AUTOMAKE) --gnu src/util/Makefile
-+.PRECIOUS: Makefile
- Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-- cd $(top_builddir) \
-- && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
--
--
--mostlyclean-binPROGRAMS:
--
--clean-binPROGRAMS:
-- -test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
--
--distclean-binPROGRAMS:
--
--maintainer-clean-binPROGRAMS:
--
-+ @case '$?' in \
-+ *config.status*) \
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-+ *) \
-+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-+ esac;
-+
-+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+
-+$(top_srcdir)/configure: $(am__configure_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(am__aclocal_m4_deps):
- install-binPROGRAMS: $(bin_PROGRAMS)
- @$(NORMAL_INSTALL)
-- $(mkinstalldirs) $(DESTDIR)$(bindir)
-- @list='$(bin_PROGRAMS)'; for p in $$list; do \
-- if test -f $$p; then \
-- echo " $(INSTALL_PROGRAM) $$p $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`"; \
-- $(INSTALL_PROGRAM) $$p $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \
-- else :; fi; \
-- done
-+ test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)"
-+ @list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
-+ for p in $$list; do echo "$$p $$p"; done | \
-+ sed 's/$(EXEEXT)$$//' | \
-+ while read p p1; do if test -f $$p; \
-+ then echo "$$p"; echo "$$p"; else :; fi; \
-+ done | \
-+ sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
-+ -e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
-+ sed 'N;N;N;s,\n, ,g' | \
-+ $(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
-+ { d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \
-+ if ($$2 == $$4) files[d] = files[d] " " $$1; \
-+ else { print "f", $$3 "/" $$4, $$1; } } \
-+ END { for (d in files) print "f", d, files[d] }' | \
-+ while read type dir files; do \
-+ if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
-+ test -z "$$files" || { \
-+ echo " $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \
-+ $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \
-+ } \
-+ ; done
-
- uninstall-binPROGRAMS:
- @$(NORMAL_UNINSTALL)
-- list='$(bin_PROGRAMS)'; for p in $$list; do \
-- rm -f $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \
-- done
--
--.c.o:
-- $(COMPILE) -c $<
--
--.s.o:
-- $(COMPILE) -c $<
-+ @list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
-+ files=`for p in $$list; do echo "$$p"; done | \
-+ sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
-+ -e 's/$$/$(EXEEXT)/' `; \
-+ test -n "$$list" || exit 0; \
-+ echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
-+ cd "$(DESTDIR)$(bindir)" && rm -f $$files
-
--.S.o:
-- $(COMPILE) -c $<
-+clean-binPROGRAMS:
-+ -test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
-+esd2esi$(EXEEXT): $(esd2esi_OBJECTS) $(esd2esi_DEPENDENCIES)
-+ @rm -f esd2esi$(EXEEXT)
-+ $(LINK) $(esd2esi_OBJECTS) $(esd2esi_LDADD) $(LIBS)
-+fasta2esd$(EXEEXT): $(fasta2esd_OBJECTS) $(fasta2esd_DEPENDENCIES)
-+ @rm -f fasta2esd$(EXEEXT)
-+ $(LINK) $(fasta2esd_OBJECTS) $(fasta2esd_LDADD) $(LIBS)
-+fastaannotatecdna$(EXEEXT): $(fastaannotatecdna_OBJECTS) $(fastaannotatecdna_DEPENDENCIES)
-+ @rm -f fastaannotatecdna$(EXEEXT)
-+ $(LINK) $(fastaannotatecdna_OBJECTS) $(fastaannotatecdna_LDADD) $(LIBS)
-+fastachecksum$(EXEEXT): $(fastachecksum_OBJECTS) $(fastachecksum_DEPENDENCIES)
-+ @rm -f fastachecksum$(EXEEXT)
-+ $(LINK) $(fastachecksum_OBJECTS) $(fastachecksum_LDADD) $(LIBS)
-+fastaclean$(EXEEXT): $(fastaclean_OBJECTS) $(fastaclean_DEPENDENCIES)
-+ @rm -f fastaclean$(EXEEXT)
-+ $(LINK) $(fastaclean_OBJECTS) $(fastaclean_LDADD) $(LIBS)
-+fastaclip$(EXEEXT): $(fastaclip_OBJECTS) $(fastaclip_DEPENDENCIES)
-+ @rm -f fastaclip$(EXEEXT)
-+ $(LINK) $(fastaclip_OBJECTS) $(fastaclip_LDADD) $(LIBS)
-+fastacomposition$(EXEEXT): $(fastacomposition_OBJECTS) $(fastacomposition_DEPENDENCIES)
-+ @rm -f fastacomposition$(EXEEXT)
-+ $(LINK) $(fastacomposition_OBJECTS) $(fastacomposition_LDADD) $(LIBS)
-+fastadiff$(EXEEXT): $(fastadiff_OBJECTS) $(fastadiff_DEPENDENCIES)
-+ @rm -f fastadiff$(EXEEXT)
-+ $(LINK) $(fastadiff_OBJECTS) $(fastadiff_LDADD) $(LIBS)
-+fastaexplode$(EXEEXT): $(fastaexplode_OBJECTS) $(fastaexplode_DEPENDENCIES)
-+ @rm -f fastaexplode$(EXEEXT)
-+ $(LINK) $(fastaexplode_OBJECTS) $(fastaexplode_LDADD) $(LIBS)
-+fastafetch$(EXEEXT): $(fastafetch_OBJECTS) $(fastafetch_DEPENDENCIES)
-+ @rm -f fastafetch$(EXEEXT)
-+ $(LINK) $(fastafetch_OBJECTS) $(fastafetch_LDADD) $(LIBS)
-+fastahardmask$(EXEEXT): $(fastahardmask_OBJECTS) $(fastahardmask_DEPENDENCIES)
-+ @rm -f fastahardmask$(EXEEXT)
-+ $(LINK) $(fastahardmask_OBJECTS) $(fastahardmask_LDADD) $(LIBS)
-+fastaindex$(EXEEXT): $(fastaindex_OBJECTS) $(fastaindex_DEPENDENCIES)
-+ @rm -f fastaindex$(EXEEXT)
-+ $(LINK) $(fastaindex_OBJECTS) $(fastaindex_LDADD) $(LIBS)
-+fastalength$(EXEEXT): $(fastalength_OBJECTS) $(fastalength_DEPENDENCIES)
-+ @rm -f fastalength$(EXEEXT)
-+ $(LINK) $(fastalength_OBJECTS) $(fastalength_LDADD) $(LIBS)
-+fastanrdb$(EXEEXT): $(fastanrdb_OBJECTS) $(fastanrdb_DEPENDENCIES)
-+ @rm -f fastanrdb$(EXEEXT)
-+ $(LINK) $(fastanrdb_OBJECTS) $(fastanrdb_LDADD) $(LIBS)
-+fastaoverlap$(EXEEXT): $(fastaoverlap_OBJECTS) $(fastaoverlap_DEPENDENCIES)
-+ @rm -f fastaoverlap$(EXEEXT)
-+ $(LINK) $(fastaoverlap_OBJECTS) $(fastaoverlap_LDADD) $(LIBS)
-+fastareformat$(EXEEXT): $(fastareformat_OBJECTS) $(fastareformat_DEPENDENCIES)
-+ @rm -f fastareformat$(EXEEXT)
-+ $(LINK) $(fastareformat_OBJECTS) $(fastareformat_LDADD) $(LIBS)
-+fastaremove$(EXEEXT): $(fastaremove_OBJECTS) $(fastaremove_DEPENDENCIES)
-+ @rm -f fastaremove$(EXEEXT)
-+ $(LINK) $(fastaremove_OBJECTS) $(fastaremove_LDADD) $(LIBS)
-+fastarevcomp$(EXEEXT): $(fastarevcomp_OBJECTS) $(fastarevcomp_DEPENDENCIES)
-+ @rm -f fastarevcomp$(EXEEXT)
-+ $(LINK) $(fastarevcomp_OBJECTS) $(fastarevcomp_LDADD) $(LIBS)
-+fastasoftmask$(EXEEXT): $(fastasoftmask_OBJECTS) $(fastasoftmask_DEPENDENCIES)
-+ @rm -f fastasoftmask$(EXEEXT)
-+ $(LINK) $(fastasoftmask_OBJECTS) $(fastasoftmask_LDADD) $(LIBS)
-+fastasort$(EXEEXT): $(fastasort_OBJECTS) $(fastasort_DEPENDENCIES)
-+ @rm -f fastasort$(EXEEXT)
-+ $(LINK) $(fastasort_OBJECTS) $(fastasort_LDADD) $(LIBS)
-+fastasplit$(EXEEXT): $(fastasplit_OBJECTS) $(fastasplit_DEPENDENCIES)
-+ @rm -f fastasplit$(EXEEXT)
-+ $(LINK) $(fastasplit_OBJECTS) $(fastasplit_LDADD) $(LIBS)
-+fastasubseq$(EXEEXT): $(fastasubseq_OBJECTS) $(fastasubseq_DEPENDENCIES)
-+ @rm -f fastasubseq$(EXEEXT)
-+ $(LINK) $(fastasubseq_OBJECTS) $(fastasubseq_LDADD) $(LIBS)
-+fastatranslate$(EXEEXT): $(fastatranslate_OBJECTS) $(fastatranslate_DEPENDENCIES)
-+ @rm -f fastatranslate$(EXEEXT)
-+ $(LINK) $(fastatranslate_OBJECTS) $(fastatranslate_LDADD) $(LIBS)
-+fastavalidcds$(EXEEXT): $(fastavalidcds_OBJECTS) $(fastavalidcds_DEPENDENCIES)
-+ @rm -f fastavalidcds$(EXEEXT)
-+ $(LINK) $(fastavalidcds_OBJECTS) $(fastavalidcds_LDADD) $(LIBS)
-
- mostlyclean-compile:
-- -rm -f *.o core *.core
--
--clean-compile:
-+ -rm -f *.$(OBJEXT)
-
- distclean-compile:
- -rm -f *.tab.c
-
--maintainer-clean-compile:
--
--fastaclean: $(fastaclean_OBJECTS) $(fastaclean_DEPENDENCIES)
-- @rm -f fastaclean
-- $(LINK) $(fastaclean_LDFLAGS) $(fastaclean_OBJECTS) $(fastaclean_LDADD) $(LIBS)
--
--fastaclip: $(fastaclip_OBJECTS) $(fastaclip_DEPENDENCIES)
-- @rm -f fastaclip
-- $(LINK) $(fastaclip_LDFLAGS) $(fastaclip_OBJECTS) $(fastaclip_LDADD) $(LIBS)
--
--fastachecksum: $(fastachecksum_OBJECTS) $(fastachecksum_DEPENDENCIES)
-- @rm -f fastachecksum
-- $(LINK) $(fastachecksum_LDFLAGS) $(fastachecksum_OBJECTS) $(fastachecksum_LDADD) $(LIBS)
--
--fastacomposition: $(fastacomposition_OBJECTS) $(fastacomposition_DEPENDENCIES)
-- @rm -f fastacomposition
-- $(LINK) $(fastacomposition_LDFLAGS) $(fastacomposition_OBJECTS) $(fastacomposition_LDADD) $(LIBS)
--
--fastadiff: $(fastadiff_OBJECTS) $(fastadiff_DEPENDENCIES)
-- @rm -f fastadiff
-- $(LINK) $(fastadiff_LDFLAGS) $(fastadiff_OBJECTS) $(fastadiff_LDADD) $(LIBS)
--
--fastaexplode: $(fastaexplode_OBJECTS) $(fastaexplode_DEPENDENCIES)
-- @rm -f fastaexplode
-- $(LINK) $(fastaexplode_LDFLAGS) $(fastaexplode_OBJECTS) $(fastaexplode_LDADD) $(LIBS)
--
--fastafetch: $(fastafetch_OBJECTS) $(fastafetch_DEPENDENCIES)
-- @rm -f fastafetch
-- $(LINK) $(fastafetch_LDFLAGS) $(fastafetch_OBJECTS) $(fastafetch_LDADD) $(LIBS)
--
--fastahardmask: $(fastahardmask_OBJECTS) $(fastahardmask_DEPENDENCIES)
-- @rm -f fastahardmask
-- $(LINK) $(fastahardmask_LDFLAGS) $(fastahardmask_OBJECTS) $(fastahardmask_LDADD) $(LIBS)
--
--fastaindex: $(fastaindex_OBJECTS) $(fastaindex_DEPENDENCIES)
-- @rm -f fastaindex
-- $(LINK) $(fastaindex_LDFLAGS) $(fastaindex_OBJECTS) $(fastaindex_LDADD) $(LIBS)
--
--fastalength: $(fastalength_OBJECTS) $(fastalength_DEPENDENCIES)
-- @rm -f fastalength
-- $(LINK) $(fastalength_LDFLAGS) $(fastalength_OBJECTS) $(fastalength_LDADD) $(LIBS)
--
--fastanrdb: $(fastanrdb_OBJECTS) $(fastanrdb_DEPENDENCIES)
-- @rm -f fastanrdb
-- $(LINK) $(fastanrdb_LDFLAGS) $(fastanrdb_OBJECTS) $(fastanrdb_LDADD) $(LIBS)
--
--fastaoverlap: $(fastaoverlap_OBJECTS) $(fastaoverlap_DEPENDENCIES)
-- @rm -f fastaoverlap
-- $(LINK) $(fastaoverlap_LDFLAGS) $(fastaoverlap_OBJECTS) $(fastaoverlap_LDADD) $(LIBS)
--
--fastareformat: $(fastareformat_OBJECTS) $(fastareformat_DEPENDENCIES)
-- @rm -f fastareformat
-- $(LINK) $(fastareformat_LDFLAGS) $(fastareformat_OBJECTS) $(fastareformat_LDADD) $(LIBS)
--
--fastaremove: $(fastaremove_OBJECTS) $(fastaremove_DEPENDENCIES)
-- @rm -f fastaremove
-- $(LINK) $(fastaremove_LDFLAGS) $(fastaremove_OBJECTS) $(fastaremove_LDADD) $(LIBS)
--
--fastarevcomp: $(fastarevcomp_OBJECTS) $(fastarevcomp_DEPENDENCIES)
-- @rm -f fastarevcomp
-- $(LINK) $(fastarevcomp_LDFLAGS) $(fastarevcomp_OBJECTS) $(fastarevcomp_LDADD) $(LIBS)
--
--fastasoftmask: $(fastasoftmask_OBJECTS) $(fastasoftmask_DEPENDENCIES)
-- @rm -f fastasoftmask
-- $(LINK) $(fastasoftmask_LDFLAGS) $(fastasoftmask_OBJECTS) $(fastasoftmask_LDADD) $(LIBS)
--
--fastasort: $(fastasort_OBJECTS) $(fastasort_DEPENDENCIES)
-- @rm -f fastasort
-- $(LINK) $(fastasort_LDFLAGS) $(fastasort_OBJECTS) $(fastasort_LDADD) $(LIBS)
--
--fastasplit: $(fastasplit_OBJECTS) $(fastasplit_DEPENDENCIES)
-- @rm -f fastasplit
-- $(LINK) $(fastasplit_LDFLAGS) $(fastasplit_OBJECTS) $(fastasplit_LDADD) $(LIBS)
--
--fastasubseq: $(fastasubseq_OBJECTS) $(fastasubseq_DEPENDENCIES)
-- @rm -f fastasubseq
-- $(LINK) $(fastasubseq_LDFLAGS) $(fastasubseq_OBJECTS) $(fastasubseq_LDADD) $(LIBS)
--
--fastatranslate: $(fastatranslate_OBJECTS) $(fastatranslate_DEPENDENCIES)
-- @rm -f fastatranslate
-- $(LINK) $(fastatranslate_LDFLAGS) $(fastatranslate_OBJECTS) $(fastatranslate_LDADD) $(LIBS)
--
--fastavalidcds: $(fastavalidcds_OBJECTS) $(fastavalidcds_DEPENDENCIES)
-- @rm -f fastavalidcds
-- $(LINK) $(fastavalidcds_LDFLAGS) $(fastavalidcds_OBJECTS) $(fastavalidcds_LDADD) $(LIBS)
--
--fasta2esd: $(fasta2esd_OBJECTS) $(fasta2esd_DEPENDENCIES)
-- @rm -f fasta2esd
-- $(LINK) $(fasta2esd_LDFLAGS) $(fasta2esd_OBJECTS) $(fasta2esd_LDADD) $(LIBS)
--
--fastaannotatecdna: $(fastaannotatecdna_OBJECTS) $(fastaannotatecdna_DEPENDENCIES)
-- @rm -f fastaannotatecdna
-- $(LINK) $(fastaannotatecdna_LDFLAGS) $(fastaannotatecdna_OBJECTS) $(fastaannotatecdna_LDADD) $(LIBS)
--
--esd2esi: $(esd2esi_OBJECTS) $(esd2esi_DEPENDENCIES)
-- @rm -f esd2esi
-- $(LINK) $(esd2esi_LDFLAGS) $(esd2esi_OBJECTS) $(esd2esi_LDADD) $(LIBS)
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/esd2esi.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fasta2esd.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fastaannotatecdna.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fastachecksum.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fastaclean.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fastaclip.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fastacomposition.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fastadiff.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fastaexplode.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fastafetch.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fastahardmask.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fastaindex.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fastalength.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fastanrdb.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fastaoverlap.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fastareformat.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fastaremove.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fastarevcomp.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fastasoftmask.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fastasort.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fastasplit.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fastasubseq.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fastatranslate.Po at am__quote@
-+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fastavalidcds.Po at am__quote@
-
-+.c.o:
-+ at am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
-+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-+ at am__fastdepCC_FALSE@ $(COMPILE) -c $<
-+
-+.c.obj:
-+ at am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
-+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
-+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-+ at am__fastdepCC_FALSE@ $(COMPILE) -c `$(CYGPATH_W) '$<'`
-+
-+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ mkid -fID $$unique
- tags: TAGS
-
--ID: $(HEADERS) $(SOURCES) $(LISP)
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- here=`pwd` && cd $(srcdir) \
-- && mkid -f$$here/ID $$unique $(LISP)
--
--TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) $(LISP)
-- tags=; \
-+TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ set x; \
- here=`pwd`; \
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- test -z "$(ETAGS_ARGS)$$unique$(LISP)$$tags" \
-- || (cd $(srcdir) && etags -o $$here/TAGS $(ETAGS_ARGS) $$tags $$unique $(LISP))
--
--mostlyclean-tags:
--
--clean-tags:
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ shift; \
-+ if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
-+ test -n "$$unique" || unique=$$empty_fix; \
-+ if test $$# -gt 0; then \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ "$$@" $$unique; \
-+ else \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ $$unique; \
-+ fi; \
-+ fi
-+ctags: CTAGS
-+CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ test -z "$(CTAGS_ARGS)$$unique" \
-+ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-+ $$unique
-+
-+GTAGS:
-+ here=`$(am__cd) $(top_builddir) && pwd` \
-+ && $(am__cd) $(top_srcdir) \
-+ && gtags -i $(GTAGS_ARGS) "$$here"
-
- distclean-tags:
-- -rm -f TAGS ID
--
--maintainer-clean-tags:
--
--distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
--
--subdir = src/util
-+ -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-
- distdir: $(DISTFILES)
-- @for file in $(DISTFILES); do \
-- d=$(srcdir); \
-+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ list='$(DISTFILES)'; \
-+ dist_files=`for file in $$list; do echo $$file; done | \
-+ sed -e "s|^$$srcdirstrip/||;t" \
-+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-+ case $$dist_files in \
-+ */*) $(MKDIR_P) `echo "$$dist_files" | \
-+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-+ sort -u` ;; \
-+ esac; \
-+ for file in $$dist_files; do \
-+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
- if test -d $$d/$$file; then \
-- cp -pr $$d/$$file $(distdir)/$$file; \
-+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-+ if test -d "$(distdir)/$$file"; then \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
- else \
-- test -f $(distdir)/$$file \
-- || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
-- || cp -p $$d/$$file $(distdir)/$$file || :; \
-+ test -f "$(distdir)/$$file" \
-+ || cp -p $$d/$$file "$(distdir)/$$file" \
-+ || exit 1; \
- fi; \
- done
--info-am:
--info: info-am
--dvi-am:
--dvi: dvi-am
- check-am: all-am
- check: check-am
--installcheck-am:
--installcheck: installcheck-am
--install-exec-am: install-binPROGRAMS
-+all-am: Makefile $(PROGRAMS)
-+installdirs:
-+ for dir in "$(DESTDIR)$(bindir)"; do \
-+ test -z "$$dir" || $(MKDIR_P) "$$dir"; \
-+ done
-+install: install-am
- install-exec: install-exec-am
--
--install-data-am:
- install-data: install-data-am
-+uninstall: uninstall-am
-
- install-am: all-am
- @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
--install: install-am
--uninstall-am: uninstall-binPROGRAMS
--uninstall: uninstall-am
--all-am: Makefile $(PROGRAMS)
--all-redirect: all-am
--install-strip:
-- $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
--installdirs:
-- $(mkinstalldirs) $(DESTDIR)$(bindir)
--
-
-+installcheck: installcheck-am
-+install-strip:
-+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-+ `test -z '$(STRIP)' || \
-+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
- mostlyclean-generic:
-
- clean-generic:
-
- distclean-generic:
-- -rm -f Makefile $(CONFIG_CLEAN_FILES)
-- -rm -f config.cache config.log stamp-h stamp-h[0-9]*
-+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
- maintainer-clean-generic:
-+ @echo "This command is intended for maintainers to use"
-+ @echo "it deletes files that may require special tools to rebuild."
- -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
--mostlyclean-am: mostlyclean-binPROGRAMS mostlyclean-compile \
-- mostlyclean-tags mostlyclean-generic
-+clean: clean-am
-
--mostlyclean: mostlyclean-am
-+clean-am: clean-binPROGRAMS clean-generic mostlyclean-am
-
--clean-am: clean-binPROGRAMS clean-compile clean-tags clean-generic \
-- mostlyclean-am
-+distclean: distclean-am
-+ -rm -rf ./$(DEPDIR)
-+ -rm -f Makefile
-+distclean-am: clean-am distclean-compile distclean-generic \
-+ distclean-tags
-
--clean: clean-am
-+dvi: dvi-am
-
--distclean-am: distclean-binPROGRAMS distclean-compile distclean-tags \
-- distclean-generic clean-am
-+dvi-am:
-
--distclean: distclean-am
-+html: html-am
-
--maintainer-clean-am: maintainer-clean-binPROGRAMS \
-- maintainer-clean-compile maintainer-clean-tags \
-- maintainer-clean-generic distclean-am
-- @echo "This command is intended for maintainers to use;"
-- @echo "it deletes files that may require special tools to rebuild."
-+html-am:
-+
-+info: info-am
-+
-+info-am:
-+
-+install-data-am:
-+
-+install-dvi: install-dvi-am
-+
-+install-dvi-am:
-+
-+install-exec-am: install-binPROGRAMS
-+
-+install-html: install-html-am
-+
-+install-html-am:
-+
-+install-info: install-info-am
-+
-+install-info-am:
-+
-+install-man:
-+
-+install-pdf: install-pdf-am
-+
-+install-pdf-am:
-+
-+install-ps: install-ps-am
-+
-+install-ps-am:
-+
-+installcheck-am:
-
- maintainer-clean: maintainer-clean-am
-+ -rm -rf ./$(DEPDIR)
-+ -rm -f Makefile
-+maintainer-clean-am: distclean-am maintainer-clean-generic
-+
-+mostlyclean: mostlyclean-am
-+
-+mostlyclean-am: mostlyclean-compile mostlyclean-generic
-+
-+pdf: pdf-am
-+
-+pdf-am:
-+
-+ps: ps-am
-+
-+ps-am:
-+
-+uninstall-am: uninstall-binPROGRAMS
-+
-+.MAKE: install-am install-strip
-
--.PHONY: mostlyclean-binPROGRAMS distclean-binPROGRAMS clean-binPROGRAMS \
--maintainer-clean-binPROGRAMS uninstall-binPROGRAMS install-binPROGRAMS \
--mostlyclean-compile distclean-compile clean-compile \
--maintainer-clean-compile tags mostlyclean-tags distclean-tags \
--clean-tags maintainer-clean-tags distdir info-am info dvi-am dvi check \
--check-am installcheck-am installcheck install-exec-am install-exec \
--install-data-am install-data install-am install uninstall-am uninstall \
--all-redirect all-am all installdirs mostlyclean-generic \
--distclean-generic clean-generic maintainer-clean-generic clean \
--mostlyclean distclean maintainer-clean
-+.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
-+ clean-generic ctags distclean distclean-compile \
-+ distclean-generic distclean-tags distdir dvi dvi-am html \
-+ html-am info info-am install install-am install-binPROGRAMS \
-+ install-data install-data-am install-dvi install-dvi-am \
-+ install-exec install-exec-am install-html install-html-am \
-+ install-info install-info-am install-man install-pdf \
-+ install-pdf-am install-ps install-ps-am install-strip \
-+ installcheck installcheck-am installdirs maintainer-clean \
-+ maintainer-clean-generic mostlyclean mostlyclean-compile \
-+ mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
-+ uninstall-am uninstall-binPROGRAMS
-
-
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -ubrN exonerate-2.2.0.orig/test/data/cdna/Makefile.in exonerate-2.2.0/test/data/cdna/Makefile.in
---- exonerate-2.2.0.orig/test/data/cdna/Makefile.in 2008-10-17 12:04:47.000000000 +0200
-+++ exonerate-2.2.0/test/data/cdna/Makefile.in 2011-12-12 13:33:17.000000000 +0100
-@@ -1,6 +1,9 @@
--# Makefile.in generated automatically by automake 1.4-p6 from Makefile.am
-+# Makefile.in generated by automake 1.11.1 from Makefile.am.
-+# @configure_input@
-
--# Copyright (C) 1994, 1995-8, 1999, 2001 Free Software Foundation, Inc.
-+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
-+# Inc.
- # This Makefile.in is free software; the Free Software Foundation
- # gives unlimited permission to copy and/or distribute it,
- # with or without modifications, as long as this notice is preserved.
-@@ -10,175 +13,322 @@
- # even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- # PARTICULAR PURPOSE.
-
--
--SHELL = @SHELL@
--
--srcdir = @srcdir@
--top_srcdir = @top_srcdir@
-+ at SET_MAKE@
- VPATH = @srcdir@
--prefix = @prefix@
--exec_prefix = @exec_prefix@
--
--bindir = @bindir@
--sbindir = @sbindir@
--libexecdir = @libexecdir@
--datadir = @datadir@
--sysconfdir = @sysconfdir@
--sharedstatedir = @sharedstatedir@
--localstatedir = @localstatedir@
--libdir = @libdir@
--infodir = @infodir@
--mandir = @mandir@
--includedir = @includedir@
--oldincludedir = /usr/include
--
--DESTDIR =
--
- pkgdatadir = $(datadir)/@PACKAGE@
--pkglibdir = $(libdir)/@PACKAGE@
- pkgincludedir = $(includedir)/@PACKAGE@
--
--top_builddir = ../../..
--
--ACLOCAL = @ACLOCAL@
--AUTOCONF = @AUTOCONF@
--AUTOMAKE = @AUTOMAKE@
--AUTOHEADER = @AUTOHEADER@
--
--INSTALL = @INSTALL@
--INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
--INSTALL_DATA = @INSTALL_DATA@
--INSTALL_SCRIPT = @INSTALL_SCRIPT@
--transform = @program_transform_name@
--
-+pkglibdir = $(libdir)/@PACKAGE@
-+pkglibexecdir = $(libexecdir)/@PACKAGE@
-+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-+install_sh_DATA = $(install_sh) -c -m 644
-+install_sh_PROGRAM = $(install_sh) -c
-+install_sh_SCRIPT = $(install_sh) -c
-+INSTALL_HEADER = $(INSTALL_DATA)
-+transform = $(program_transform_name)
- NORMAL_INSTALL = :
- PRE_INSTALL = :
- POST_INSTALL = :
- NORMAL_UNINSTALL = :
- PRE_UNINSTALL = :
- POST_UNINSTALL = :
--host_alias = @host_alias@
-+build_triplet = @build@
- host_triplet = @host@
-+subdir = test/data/cdna
-+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
-+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-+am__aclocal_m4_deps = $(top_srcdir)/configure.in
-+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-+ $(ACLOCAL_M4)
-+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
-+CONFIG_CLEAN_FILES =
-+CONFIG_CLEAN_VPATH_FILES =
-+SOURCES =
-+DIST_SOURCES =
-+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-+ACLOCAL = @ACLOCAL@
-+AMTAR = @AMTAR@
-+AUTOCONF = @AUTOCONF@
-+AUTOHEADER = @AUTOHEADER@
-+AUTOMAKE = @AUTOMAKE@
-+AWK = @AWK@
- CC = @CC@
-+CCDEPMODE = @CCDEPMODE@
-+CFLAGS = @CFLAGS@
-+CPP = @CPP@
-+CPPFLAGS = @CPPFLAGS@
-+CYGPATH_W = @CYGPATH_W@
-+DEFS = @DEFS@
-+DEPDIR = @DEPDIR@
-+ECHO_C = @ECHO_C@
-+ECHO_N = @ECHO_N@
-+ECHO_T = @ECHO_T@
-+EGREP = @EGREP@
-+EXEEXT = @EXEEXT@
- GLIB_CONFIG = @GLIB_CONFIG@
--HAVE_LIB = @HAVE_LIB@
--LIB = @LIB@
--LTLIB = @LTLIB@
-+GREP = @GREP@
-+INSTALL = @INSTALL@
-+INSTALL_DATA = @INSTALL_DATA@
-+INSTALL_PROGRAM = @INSTALL_PROGRAM@
-+INSTALL_SCRIPT = @INSTALL_SCRIPT@
-+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-+LDFLAGS = @LDFLAGS@
-+LIBOBJS = @LIBOBJS@
-+LIBS = @LIBS@
-+LTLIBOBJS = @LTLIBOBJS@
- MAKEINFO = @MAKEINFO@
-+MKDIR_P = @MKDIR_P@
-+OBJEXT = @OBJEXT@
- PACKAGE = @PACKAGE@
-+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-+PACKAGE_NAME = @PACKAGE_NAME@
-+PACKAGE_STRING = @PACKAGE_STRING@
-+PACKAGE_TARNAME = @PACKAGE_TARNAME@
-+PACKAGE_URL = @PACKAGE_URL@
-+PACKAGE_VERSION = @PACKAGE_VERSION@
-+PATH_SEPARATOR = @PATH_SEPARATOR@
- PKG_CONFIG = @PKG_CONFIG@
-+SET_MAKE = @SET_MAKE@
-+SHELL = @SHELL@
-+STRIP = @STRIP@
- VERSION = @VERSION@
-+abs_builddir = @abs_builddir@
-+abs_srcdir = @abs_srcdir@
-+abs_top_builddir = @abs_top_builddir@
-+abs_top_srcdir = @abs_top_srcdir@
-+ac_ct_CC = @ac_ct_CC@
-+am__include = @am__include@
-+am__leading_dot = @am__leading_dot@
-+am__quote = @am__quote@
-+am__tar = @am__tar@
-+am__untar = @am__untar@
-+bindir = @bindir@
-+build = @build@
-+build_alias = @build_alias@
-+build_cpu = @build_cpu@
-+build_os = @build_os@
-+build_vendor = @build_vendor@
-+builddir = @builddir@
- codegen_extra_ldadd = @codegen_extra_ldadd@
- codegen_extra_sources = @codegen_extra_sources@
-+datadir = @datadir@
- datarootdir = @datarootdir@
-+docdir = @docdir@
-+dvidir = @dvidir@
-+exec_prefix = @exec_prefix@
- glib_cflags = @glib_cflags@
- glib_libs = @glib_libs@
- host = @host@
-+host_alias = @host_alias@
-+host_cpu = @host_cpu@
-+host_os = @host_os@
-+host_vendor = @host_vendor@
-+htmldir = @htmldir@
-+includedir = @includedir@
-+infodir = @infodir@
-+install_sh = @install_sh@
- installed_util_list = @installed_util_list@
-+libdir = @libdir@
-+libexecdir = @libexecdir@
-+localedir = @localedir@
-+localstatedir = @localstatedir@
-+mandir = @mandir@
-+mkdir_p = @mkdir_p@
-+oldincludedir = @oldincludedir@
-+pdfdir = @pdfdir@
-+prefix = @prefix@
-+program_transform_name = @program_transform_name@
-+psdir = @psdir@
-+sbindir = @sbindir@
-+sharedstatedir = @sharedstatedir@
- source_root_dir = @source_root_dir@
-+srcdir = @srcdir@
-+sysconfdir = @sysconfdir@
-+target_alias = @target_alias@
-+top_build_prefix = @top_build_prefix@
-+top_builddir = @top_builddir@
-+top_srcdir = @top_srcdir@
- use_pthreads = @use_pthreads@
--
--EXTRA_DIST = calm.human.dna.fasta htrt.human.dna.fasta p53.human.dna.fasta tube.drome.dna.fasta
--
-+EXTRA_DIST = calm.human.dna.fasta htrt.human.dna.fasta \
-+ p53.human.dna.fasta tube.drome.dna.fasta
-
- MAINTAINERCLEANFILES = Makefile.in
--mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
--CONFIG_CLEAN_FILES =
--DIST_COMMON = Makefile.am Makefile.in
-+all: all-am
-
--
--DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
--
--TAR = tar
--GZIP_ENV = --best
--all: all-redirect
- .SUFFIXES:
--$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4)
-- cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps test/data/cdna/Makefile
--
-+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
-+ @for dep in $?; do \
-+ case '$(am__configure_deps)' in \
-+ *$$dep*) \
-+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-+ && { if test -f $@; then exit 0; else break; fi; }; \
-+ exit 1;; \
-+ esac; \
-+ done; \
-+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu test/data/cdna/Makefile'; \
-+ $(am__cd) $(top_srcdir) && \
-+ $(AUTOMAKE) --gnu test/data/cdna/Makefile
-+.PRECIOUS: Makefile
- Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-- cd $(top_builddir) \
-- && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
--
-+ @case '$?' in \
-+ *config.status*) \
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-+ *) \
-+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-+ esac;
-+
-+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+
-+$(top_srcdir)/configure: $(am__configure_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(am__aclocal_m4_deps):
- tags: TAGS
- TAGS:
-
-+ctags: CTAGS
-+CTAGS:
-
--distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
--
--subdir = test/data/cdna
-
- distdir: $(DISTFILES)
-- @for file in $(DISTFILES); do \
-- d=$(srcdir); \
-+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ list='$(DISTFILES)'; \
-+ dist_files=`for file in $$list; do echo $$file; done | \
-+ sed -e "s|^$$srcdirstrip/||;t" \
-+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-+ case $$dist_files in \
-+ */*) $(MKDIR_P) `echo "$$dist_files" | \
-+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-+ sort -u` ;; \
-+ esac; \
-+ for file in $$dist_files; do \
-+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
- if test -d $$d/$$file; then \
-- cp -pr $$d/$$file $(distdir)/$$file; \
-+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-+ if test -d "$(distdir)/$$file"; then \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
- else \
-- test -f $(distdir)/$$file \
-- || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
-- || cp -p $$d/$$file $(distdir)/$$file || :; \
-+ test -f "$(distdir)/$$file" \
-+ || cp -p $$d/$$file "$(distdir)/$$file" \
-+ || exit 1; \
- fi; \
- done
--info-am:
--info: info-am
--dvi-am:
--dvi: dvi-am
- check-am: all-am
- check: check-am
--installcheck-am:
--installcheck: installcheck-am
--install-exec-am:
-+all-am: Makefile
-+installdirs:
-+install: install-am
- install-exec: install-exec-am
--
--install-data-am:
- install-data: install-data-am
-+uninstall: uninstall-am
-
- install-am: all-am
- @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
--install: install-am
--uninstall-am:
--uninstall: uninstall-am
--all-am: Makefile
--all-redirect: all-am
--install-strip:
-- $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
--installdirs:
--
-
-+installcheck: installcheck-am
-+install-strip:
-+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-+ `test -z '$(STRIP)' || \
-+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
- mostlyclean-generic:
-
- clean-generic:
-
- distclean-generic:
-- -rm -f Makefile $(CONFIG_CLEAN_FILES)
-- -rm -f config.cache config.log stamp-h stamp-h[0-9]*
-+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
- maintainer-clean-generic:
-+ @echo "This command is intended for maintainers to use"
-+ @echo "it deletes files that may require special tools to rebuild."
- -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
--mostlyclean-am: mostlyclean-generic
--
--mostlyclean: mostlyclean-am
-+clean: clean-am
-
- clean-am: clean-generic mostlyclean-am
-
--clean: clean-am
-+distclean: distclean-am
-+ -rm -f Makefile
-+distclean-am: clean-am distclean-generic
-
--distclean-am: distclean-generic clean-am
-+dvi: dvi-am
-
--distclean: distclean-am
-+dvi-am:
-
--maintainer-clean-am: maintainer-clean-generic distclean-am
-- @echo "This command is intended for maintainers to use;"
-- @echo "it deletes files that may require special tools to rebuild."
-+html: html-am
-+
-+html-am:
-+
-+info: info-am
-+
-+info-am:
-+
-+install-data-am:
-+
-+install-dvi: install-dvi-am
-+
-+install-dvi-am:
-+
-+install-exec-am:
-+
-+install-html: install-html-am
-+
-+install-html-am:
-+
-+install-info: install-info-am
-+
-+install-info-am:
-+
-+install-man:
-+
-+install-pdf: install-pdf-am
-+
-+install-pdf-am:
-+
-+install-ps: install-ps-am
-+
-+install-ps-am:
-+
-+installcheck-am:
-
- maintainer-clean: maintainer-clean-am
-+ -rm -f Makefile
-+maintainer-clean-am: distclean-am maintainer-clean-generic
-+
-+mostlyclean: mostlyclean-am
-+
-+mostlyclean-am: mostlyclean-generic
-+
-+pdf: pdf-am
-+
-+pdf-am:
-+
-+ps: ps-am
-+
-+ps-am:
-+
-+uninstall-am:
-+
-+.MAKE: install-am install-strip
-
--.PHONY: tags distdir info-am info dvi-am dvi check check-am \
--installcheck-am installcheck install-exec-am install-exec \
--install-data-am install-data install-am install uninstall-am uninstall \
--all-redirect all-am all installdirs mostlyclean-generic \
--distclean-generic clean-generic maintainer-clean-generic clean \
--mostlyclean distclean maintainer-clean
-+.PHONY: all all-am check check-am clean clean-generic distclean \
-+ distclean-generic distdir dvi dvi-am html html-am info info-am \
-+ install install-am install-data install-data-am install-dvi \
-+ install-dvi-am install-exec install-exec-am install-html \
-+ install-html-am install-info install-info-am install-man \
-+ install-pdf install-pdf-am install-ps install-ps-am \
-+ install-strip installcheck installcheck-am installdirs \
-+ maintainer-clean maintainer-clean-generic mostlyclean \
-+ mostlyclean-generic pdf pdf-am ps ps-am uninstall uninstall-am
-
-
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -ubrN exonerate-2.2.0.orig/test/data/Makefile.in exonerate-2.2.0/test/data/Makefile.in
---- exonerate-2.2.0.orig/test/data/Makefile.in 2008-10-17 12:04:47.000000000 +0200
-+++ exonerate-2.2.0/test/data/Makefile.in 2011-12-12 13:33:17.000000000 +0100
-@@ -1,6 +1,9 @@
--# Makefile.in generated automatically by automake 1.4-p6 from Makefile.am
-+# Makefile.in generated by automake 1.11.1 from Makefile.am.
-+# @configure_input@
-
--# Copyright (C) 1994, 1995-8, 1999, 2001 Free Software Foundation, Inc.
-+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
-+# Inc.
- # This Makefile.in is free software; the Free Software Foundation
- # gives unlimited permission to copy and/or distribute it,
- # with or without modifications, as long as this notice is preserved.
-@@ -10,95 +13,216 @@
- # even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- # PARTICULAR PURPOSE.
-
--
--SHELL = @SHELL@
--
--srcdir = @srcdir@
--top_srcdir = @top_srcdir@
-+ at SET_MAKE@
- VPATH = @srcdir@
--prefix = @prefix@
--exec_prefix = @exec_prefix@
--
--bindir = @bindir@
--sbindir = @sbindir@
--libexecdir = @libexecdir@
--datadir = @datadir@
--sysconfdir = @sysconfdir@
--sharedstatedir = @sharedstatedir@
--localstatedir = @localstatedir@
--libdir = @libdir@
--infodir = @infodir@
--mandir = @mandir@
--includedir = @includedir@
--oldincludedir = /usr/include
--
--DESTDIR =
--
- pkgdatadir = $(datadir)/@PACKAGE@
--pkglibdir = $(libdir)/@PACKAGE@
- pkgincludedir = $(includedir)/@PACKAGE@
--
--top_builddir = ../..
--
--ACLOCAL = @ACLOCAL@
--AUTOCONF = @AUTOCONF@
--AUTOMAKE = @AUTOMAKE@
--AUTOHEADER = @AUTOHEADER@
--
--INSTALL = @INSTALL@
--INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
--INSTALL_DATA = @INSTALL_DATA@
--INSTALL_SCRIPT = @INSTALL_SCRIPT@
--transform = @program_transform_name@
--
-+pkglibdir = $(libdir)/@PACKAGE@
-+pkglibexecdir = $(libexecdir)/@PACKAGE@
-+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-+install_sh_DATA = $(install_sh) -c -m 644
-+install_sh_PROGRAM = $(install_sh) -c
-+install_sh_SCRIPT = $(install_sh) -c
-+INSTALL_HEADER = $(INSTALL_DATA)
-+transform = $(program_transform_name)
- NORMAL_INSTALL = :
- PRE_INSTALL = :
- POST_INSTALL = :
- NORMAL_UNINSTALL = :
- PRE_UNINSTALL = :
- POST_UNINSTALL = :
--host_alias = @host_alias@
-+build_triplet = @build@
- host_triplet = @host@
-+subdir = test/data
-+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
-+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-+am__aclocal_m4_deps = $(top_srcdir)/configure.in
-+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-+ $(ACLOCAL_M4)
-+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
-+CONFIG_CLEAN_FILES =
-+CONFIG_CLEAN_VPATH_FILES =
-+SOURCES =
-+DIST_SOURCES =
-+RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
-+ html-recursive info-recursive install-data-recursive \
-+ install-dvi-recursive install-exec-recursive \
-+ install-html-recursive install-info-recursive \
-+ install-pdf-recursive install-ps-recursive install-recursive \
-+ installcheck-recursive installdirs-recursive pdf-recursive \
-+ ps-recursive uninstall-recursive
-+RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive \
-+ distclean-recursive maintainer-clean-recursive
-+AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
-+ $(RECURSIVE_CLEAN_TARGETS:-recursive=) tags TAGS ctags CTAGS \
-+ distdir
-+ETAGS = etags
-+CTAGS = ctags
-+DIST_SUBDIRS = $(SUBDIRS)
-+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-+am__relativize = \
-+ dir0=`pwd`; \
-+ sed_first='s,^\([^/]*\)/.*$$,\1,'; \
-+ sed_rest='s,^[^/]*/*,,'; \
-+ sed_last='s,^.*/\([^/]*\)$$,\1,'; \
-+ sed_butlast='s,/*[^/]*$$,,'; \
-+ while test -n "$$dir1"; do \
-+ first=`echo "$$dir1" | sed -e "$$sed_first"`; \
-+ if test "$$first" != "."; then \
-+ if test "$$first" = ".."; then \
-+ dir2=`echo "$$dir0" | sed -e "$$sed_last"`/"$$dir2"; \
-+ dir0=`echo "$$dir0" | sed -e "$$sed_butlast"`; \
-+ else \
-+ first2=`echo "$$dir2" | sed -e "$$sed_first"`; \
-+ if test "$$first2" = "$$first"; then \
-+ dir2=`echo "$$dir2" | sed -e "$$sed_rest"`; \
-+ else \
-+ dir2="../$$dir2"; \
-+ fi; \
-+ dir0="$$dir0"/"$$first"; \
-+ fi; \
-+ fi; \
-+ dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \
-+ done; \
-+ reldir="$$dir2"
-+ACLOCAL = @ACLOCAL@
-+AMTAR = @AMTAR@
-+AUTOCONF = @AUTOCONF@
-+AUTOHEADER = @AUTOHEADER@
-+AUTOMAKE = @AUTOMAKE@
-+AWK = @AWK@
- CC = @CC@
-+CCDEPMODE = @CCDEPMODE@
-+CFLAGS = @CFLAGS@
-+CPP = @CPP@
-+CPPFLAGS = @CPPFLAGS@
-+CYGPATH_W = @CYGPATH_W@
-+DEFS = @DEFS@
-+DEPDIR = @DEPDIR@
-+ECHO_C = @ECHO_C@
-+ECHO_N = @ECHO_N@
-+ECHO_T = @ECHO_T@
-+EGREP = @EGREP@
-+EXEEXT = @EXEEXT@
- GLIB_CONFIG = @GLIB_CONFIG@
--HAVE_LIB = @HAVE_LIB@
--LIB = @LIB@
--LTLIB = @LTLIB@
-+GREP = @GREP@
-+INSTALL = @INSTALL@
-+INSTALL_DATA = @INSTALL_DATA@
-+INSTALL_PROGRAM = @INSTALL_PROGRAM@
-+INSTALL_SCRIPT = @INSTALL_SCRIPT@
-+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-+LDFLAGS = @LDFLAGS@
-+LIBOBJS = @LIBOBJS@
-+LIBS = @LIBS@
-+LTLIBOBJS = @LTLIBOBJS@
- MAKEINFO = @MAKEINFO@
-+MKDIR_P = @MKDIR_P@
-+OBJEXT = @OBJEXT@
- PACKAGE = @PACKAGE@
-+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-+PACKAGE_NAME = @PACKAGE_NAME@
-+PACKAGE_STRING = @PACKAGE_STRING@
-+PACKAGE_TARNAME = @PACKAGE_TARNAME@
-+PACKAGE_URL = @PACKAGE_URL@
-+PACKAGE_VERSION = @PACKAGE_VERSION@
-+PATH_SEPARATOR = @PATH_SEPARATOR@
- PKG_CONFIG = @PKG_CONFIG@
-+SET_MAKE = @SET_MAKE@
-+SHELL = @SHELL@
-+STRIP = @STRIP@
- VERSION = @VERSION@
-+abs_builddir = @abs_builddir@
-+abs_srcdir = @abs_srcdir@
-+abs_top_builddir = @abs_top_builddir@
-+abs_top_srcdir = @abs_top_srcdir@
-+ac_ct_CC = @ac_ct_CC@
-+am__include = @am__include@
-+am__leading_dot = @am__leading_dot@
-+am__quote = @am__quote@
-+am__tar = @am__tar@
-+am__untar = @am__untar@
-+bindir = @bindir@
-+build = @build@
-+build_alias = @build_alias@
-+build_cpu = @build_cpu@
-+build_os = @build_os@
-+build_vendor = @build_vendor@
-+builddir = @builddir@
- codegen_extra_ldadd = @codegen_extra_ldadd@
- codegen_extra_sources = @codegen_extra_sources@
-+datadir = @datadir@
- datarootdir = @datarootdir@
-+docdir = @docdir@
-+dvidir = @dvidir@
-+exec_prefix = @exec_prefix@
- glib_cflags = @glib_cflags@
- glib_libs = @glib_libs@
- host = @host@
-+host_alias = @host_alias@
-+host_cpu = @host_cpu@
-+host_os = @host_os@
-+host_vendor = @host_vendor@
-+htmldir = @htmldir@
-+includedir = @includedir@
-+infodir = @infodir@
-+install_sh = @install_sh@
- installed_util_list = @installed_util_list@
-+libdir = @libdir@
-+libexecdir = @libexecdir@
-+localedir = @localedir@
-+localstatedir = @localstatedir@
-+mandir = @mandir@
-+mkdir_p = @mkdir_p@
-+oldincludedir = @oldincludedir@
-+pdfdir = @pdfdir@
-+prefix = @prefix@
-+program_transform_name = @program_transform_name@
-+psdir = @psdir@
-+sbindir = @sbindir@
-+sharedstatedir = @sharedstatedir@
- source_root_dir = @source_root_dir@
-+srcdir = @srcdir@
-+sysconfdir = @sysconfdir@
-+target_alias = @target_alias@
-+top_build_prefix = @top_build_prefix@
-+top_builddir = @top_builddir@
-+top_srcdir = @top_srcdir@
- use_pthreads = @use_pthreads@
--
- SUBDIRS = cdna protein
--
- MAINTAINERCLEANFILES = Makefile.in
--mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
--CONFIG_CLEAN_FILES =
--DIST_COMMON = Makefile.am Makefile.in
--
-+all: all-recursive
-
--DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
--
--TAR = tar
--GZIP_ENV = --best
--all: all-redirect
- .SUFFIXES:
--$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4)
-- cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps test/data/Makefile
--
-+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
-+ @for dep in $?; do \
-+ case '$(am__configure_deps)' in \
-+ *$$dep*) \
-+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-+ && { if test -f $@; then exit 0; else break; fi; }; \
-+ exit 1;; \
-+ esac; \
-+ done; \
-+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu test/data/Makefile'; \
-+ $(am__cd) $(top_srcdir) && \
-+ $(AUTOMAKE) --gnu test/data/Makefile
-+.PRECIOUS: Makefile
- Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-- cd $(top_builddir) \
-- && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
--
-+ @case '$?' in \
-+ *config.status*) \
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-+ *) \
-+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-+ esac;
-+
-+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+
-+$(top_srcdir)/configure: $(am__configure_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(am__aclocal_m4_deps):
-
- # This directory's subdirectories are mostly independent; you can cd
- # into them and run `make' without going through this Makefile.
-@@ -106,13 +230,14 @@
- # (1) if the variable is set in `config.status', edit `config.status'
- # (which will cause the Makefiles to be regenerated when you run `make');
- # (2) otherwise, pass the desired values on the `make' command line.
--
-- at SET_MAKE@
--
--all-recursive install-data-recursive install-exec-recursive \
--installdirs-recursive install-recursive uninstall-recursive \
--check-recursive installcheck-recursive info-recursive dvi-recursive:
-- @set fnord $(MAKEFLAGS); amf=$$2; \
-+$(RECURSIVE_TARGETS):
-+ @fail= failcom='exit 1'; \
-+ for f in x $$MAKEFLAGS; do \
-+ case $$f in \
-+ *=* | --[!k]*);; \
-+ *k*) failcom='fail=yes';; \
-+ esac; \
-+ done; \
- dot_seen=no; \
- target=`echo $@ | sed s/-recursive//`; \
- list='$(SUBDIRS)'; for subdir in $$list; do \
-@@ -123,22 +248,32 @@
- else \
- local_target="$$target"; \
- fi; \
-- (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-- || case "$$amf" in *=*) exit 1;; *k*) fail=yes;; *) exit 1;; esac; \
-+ ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-+ || eval $$failcom; \
- done; \
- if test "$$dot_seen" = "no"; then \
- $(MAKE) $(AM_MAKEFLAGS) "$$target-am" || exit 1; \
- fi; test -z "$$fail"
-
--mostlyclean-recursive clean-recursive distclean-recursive \
--maintainer-clean-recursive:
-- @set fnord $(MAKEFLAGS); amf=$$2; \
-+$(RECURSIVE_CLEAN_TARGETS):
-+ @fail= failcom='exit 1'; \
-+ for f in x $$MAKEFLAGS; do \
-+ case $$f in \
-+ *=* | --[!k]*);; \
-+ *k*) failcom='fail=yes';; \
-+ esac; \
-+ done; \
- dot_seen=no; \
-- rev=''; list='$(SUBDIRS)'; for subdir in $$list; do \
-+ case "$@" in \
-+ distclean-* | maintainer-clean-*) list='$(DIST_SUBDIRS)' ;; \
-+ *) list='$(SUBDIRS)' ;; \
-+ esac; \
-+ rev=''; for subdir in $$list; do \
-+ if test "$$subdir" = "."; then :; else \
- rev="$$subdir $$rev"; \
-- test "$$subdir" != "." || dot_seen=yes; \
-+ fi; \
- done; \
-- test "$$dot_seen" = "no" && rev=". $$rev"; \
-+ rev="$$rev ."; \
- target=`echo $@ | sed s/-recursive//`; \
- for subdir in $$rev; do \
- echo "Making $$target in $$subdir"; \
-@@ -147,141 +282,253 @@
- else \
- local_target="$$target"; \
- fi; \
-- (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-- || case "$$amf" in *=*) exit 1;; *k*) fail=yes;; *) exit 1;; esac; \
-+ ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-+ || eval $$failcom; \
- done && test -z "$$fail"
- tags-recursive:
- list='$(SUBDIRS)'; for subdir in $$list; do \
-- test "$$subdir" = . || (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
-+ test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
-+ done
-+ctags-recursive:
-+ list='$(SUBDIRS)'; for subdir in $$list; do \
-+ test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \
- done
-
-+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ mkid -fID $$unique
- tags: TAGS
-
--ID: $(HEADERS) $(SOURCES) $(LISP)
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- here=`pwd` && cd $(srcdir) \
-- && mkid -f$$here/ID $$unique $(LISP)
--
--TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) $(LISP)
-- tags=; \
-+TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ set x; \
- here=`pwd`; \
-+ if ($(ETAGS) --etags-include --version) >/dev/null 2>&1; then \
-+ include_option=--etags-include; \
-+ empty_fix=.; \
-+ else \
-+ include_option=--include; \
-+ empty_fix=; \
-+ fi; \
- list='$(SUBDIRS)'; for subdir in $$list; do \
- if test "$$subdir" = .; then :; else \
-- test -f $$subdir/TAGS && tags="$$tags -i $$here/$$subdir/TAGS"; \
-+ test ! -f $$subdir/TAGS || \
-+ set "$$@" "$$include_option=$$here/$$subdir/TAGS"; \
- fi; \
- done; \
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- test -z "$(ETAGS_ARGS)$$unique$(LISP)$$tags" \
-- || (cd $(srcdir) && etags -o $$here/TAGS $(ETAGS_ARGS) $$tags $$unique $(LISP))
--
--mostlyclean-tags:
--
--clean-tags:
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ shift; \
-+ if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
-+ test -n "$$unique" || unique=$$empty_fix; \
-+ if test $$# -gt 0; then \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ "$$@" $$unique; \
-+ else \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ $$unique; \
-+ fi; \
-+ fi
-+ctags: CTAGS
-+CTAGS: ctags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ test -z "$(CTAGS_ARGS)$$unique" \
-+ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-+ $$unique
-+
-+GTAGS:
-+ here=`$(am__cd) $(top_builddir) && pwd` \
-+ && $(am__cd) $(top_srcdir) \
-+ && gtags -i $(GTAGS_ARGS) "$$here"
-
- distclean-tags:
-- -rm -f TAGS ID
--
--maintainer-clean-tags:
--
--distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
--
--subdir = test/data
-+ -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-
- distdir: $(DISTFILES)
-- @for file in $(DISTFILES); do \
-- d=$(srcdir); \
-+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ list='$(DISTFILES)'; \
-+ dist_files=`for file in $$list; do echo $$file; done | \
-+ sed -e "s|^$$srcdirstrip/||;t" \
-+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-+ case $$dist_files in \
-+ */*) $(MKDIR_P) `echo "$$dist_files" | \
-+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-+ sort -u` ;; \
-+ esac; \
-+ for file in $$dist_files; do \
-+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
- if test -d $$d/$$file; then \
-- cp -pr $$d/$$file $(distdir)/$$file; \
-+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-+ if test -d "$(distdir)/$$file"; then \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
- else \
-- test -f $(distdir)/$$file \
-- || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
-- || cp -p $$d/$$file $(distdir)/$$file || :; \
-+ test -f "$(distdir)/$$file" \
-+ || cp -p $$d/$$file "$(distdir)/$$file" \
-+ || exit 1; \
- fi; \
- done
-- for subdir in $(SUBDIRS); do \
-+ @list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
- if test "$$subdir" = .; then :; else \
-- test -d $(distdir)/$$subdir \
-- || mkdir $(distdir)/$$subdir \
-+ test -d "$(distdir)/$$subdir" \
-+ || $(MKDIR_P) "$(distdir)/$$subdir" \
- || exit 1; \
-- chmod 777 $(distdir)/$$subdir; \
-- (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir=../$(top_distdir) distdir=../$(distdir)/$$subdir distdir) \
-+ fi; \
-+ done
-+ @list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
-+ if test "$$subdir" = .; then :; else \
-+ dir1=$$subdir; dir2="$(distdir)/$$subdir"; \
-+ $(am__relativize); \
-+ new_distdir=$$reldir; \
-+ dir1=$$subdir; dir2="$(top_distdir)"; \
-+ $(am__relativize); \
-+ new_top_distdir=$$reldir; \
-+ echo " (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir="$$new_top_distdir" distdir="$$new_distdir" \\"; \
-+ echo " am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)"; \
-+ ($(am__cd) $$subdir && \
-+ $(MAKE) $(AM_MAKEFLAGS) \
-+ top_distdir="$$new_top_distdir" \
-+ distdir="$$new_distdir" \
-+ am__remove_distdir=: \
-+ am__skip_length_check=: \
-+ am__skip_mode_fix=: \
-+ distdir) \
- || exit 1; \
- fi; \
- done
--info-am:
--info: info-recursive
--dvi-am:
--dvi: dvi-recursive
- check-am: all-am
- check: check-recursive
--installcheck-am:
--installcheck: installcheck-recursive
--install-exec-am:
-+all-am: Makefile
-+installdirs: installdirs-recursive
-+installdirs-am:
-+install: install-recursive
- install-exec: install-exec-recursive
--
--install-data-am:
- install-data: install-data-recursive
-+uninstall: uninstall-recursive
-
- install-am: all-am
- @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
--install: install-recursive
--uninstall-am:
--uninstall: uninstall-recursive
--all-am: Makefile
--all-redirect: all-recursive
--install-strip:
-- $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
--installdirs: installdirs-recursive
--installdirs-am:
--
-
-+installcheck: installcheck-recursive
-+install-strip:
-+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-+ `test -z '$(STRIP)' || \
-+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
- mostlyclean-generic:
-
- clean-generic:
-
- distclean-generic:
-- -rm -f Makefile $(CONFIG_CLEAN_FILES)
-- -rm -f config.cache config.log stamp-h stamp-h[0-9]*
-+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
- maintainer-clean-generic:
-+ @echo "This command is intended for maintainers to use"
-+ @echo "it deletes files that may require special tools to rebuild."
- -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
--mostlyclean-am: mostlyclean-tags mostlyclean-generic
-+clean: clean-recursive
-
--mostlyclean: mostlyclean-recursive
-+clean-am: clean-generic mostlyclean-am
-
--clean-am: clean-tags clean-generic mostlyclean-am
-+distclean: distclean-recursive
-+ -rm -f Makefile
-+distclean-am: clean-am distclean-generic distclean-tags
-
--clean: clean-recursive
-+dvi: dvi-recursive
-
--distclean-am: distclean-tags distclean-generic clean-am
-+dvi-am:
-
--distclean: distclean-recursive
-+html: html-recursive
-
--maintainer-clean-am: maintainer-clean-tags maintainer-clean-generic \
-- distclean-am
-- @echo "This command is intended for maintainers to use;"
-- @echo "it deletes files that may require special tools to rebuild."
-+html-am:
-+
-+info: info-recursive
-+
-+info-am:
-+
-+install-data-am:
-+
-+install-dvi: install-dvi-recursive
-+
-+install-dvi-am:
-+
-+install-exec-am:
-+
-+install-html: install-html-recursive
-+
-+install-html-am:
-+
-+install-info: install-info-recursive
-+
-+install-info-am:
-+
-+install-man:
-+
-+install-pdf: install-pdf-recursive
-+
-+install-pdf-am:
-+
-+install-ps: install-ps-recursive
-+
-+install-ps-am:
-+
-+installcheck-am:
-
- maintainer-clean: maintainer-clean-recursive
-+ -rm -f Makefile
-+maintainer-clean-am: distclean-am maintainer-clean-generic
-+
-+mostlyclean: mostlyclean-recursive
-+
-+mostlyclean-am: mostlyclean-generic
-+
-+pdf: pdf-recursive
-+
-+pdf-am:
-+
-+ps: ps-recursive
-+
-+ps-am:
-+
-+uninstall-am:
-+
-+.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) ctags-recursive \
-+ install-am install-strip tags-recursive
-
--.PHONY: install-data-recursive uninstall-data-recursive \
--install-exec-recursive uninstall-exec-recursive installdirs-recursive \
--uninstalldirs-recursive all-recursive check-recursive \
--installcheck-recursive info-recursive dvi-recursive \
--mostlyclean-recursive distclean-recursive clean-recursive \
--maintainer-clean-recursive tags tags-recursive mostlyclean-tags \
--distclean-tags clean-tags maintainer-clean-tags distdir info-am info \
--dvi-am dvi check check-am installcheck-am installcheck install-exec-am \
--install-exec install-data-am install-data install-am install \
--uninstall-am uninstall all-redirect all-am all installdirs-am \
--installdirs mostlyclean-generic distclean-generic clean-generic \
--maintainer-clean-generic clean mostlyclean distclean maintainer-clean
-+.PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
-+ all all-am check check-am clean clean-generic ctags \
-+ ctags-recursive distclean distclean-generic distclean-tags \
-+ distdir dvi dvi-am html html-am info info-am install \
-+ install-am install-data install-data-am install-dvi \
-+ install-dvi-am install-exec install-exec-am install-html \
-+ install-html-am install-info install-info-am install-man \
-+ install-pdf install-pdf-am install-ps install-ps-am \
-+ install-strip installcheck installcheck-am installdirs \
-+ installdirs-am maintainer-clean maintainer-clean-generic \
-+ mostlyclean mostlyclean-generic pdf pdf-am ps ps-am tags \
-+ tags-recursive uninstall uninstall-am
-
-
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -ubrN exonerate-2.2.0.orig/test/data/protein/Makefile.in exonerate-2.2.0/test/data/protein/Makefile.in
---- exonerate-2.2.0.orig/test/data/protein/Makefile.in 2008-10-17 12:04:48.000000000 +0200
-+++ exonerate-2.2.0/test/data/protein/Makefile.in 2011-12-12 13:33:17.000000000 +0100
-@@ -1,6 +1,9 @@
--# Makefile.in generated automatically by automake 1.4-p6 from Makefile.am
-+# Makefile.in generated by automake 1.11.1 from Makefile.am.
-+# @configure_input@
-
--# Copyright (C) 1994, 1995-8, 1999, 2001 Free Software Foundation, Inc.
-+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
-+# Inc.
- # This Makefile.in is free software; the Free Software Foundation
- # gives unlimited permission to copy and/or distribute it,
- # with or without modifications, as long as this notice is preserved.
-@@ -10,175 +13,322 @@
- # even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- # PARTICULAR PURPOSE.
-
--
--SHELL = @SHELL@
--
--srcdir = @srcdir@
--top_srcdir = @top_srcdir@
-+ at SET_MAKE@
- VPATH = @srcdir@
--prefix = @prefix@
--exec_prefix = @exec_prefix@
--
--bindir = @bindir@
--sbindir = @sbindir@
--libexecdir = @libexecdir@
--datadir = @datadir@
--sysconfdir = @sysconfdir@
--sharedstatedir = @sharedstatedir@
--localstatedir = @localstatedir@
--libdir = @libdir@
--infodir = @infodir@
--mandir = @mandir@
--includedir = @includedir@
--oldincludedir = /usr/include
--
--DESTDIR =
--
- pkgdatadir = $(datadir)/@PACKAGE@
--pkglibdir = $(libdir)/@PACKAGE@
- pkgincludedir = $(includedir)/@PACKAGE@
--
--top_builddir = ../../..
--
--ACLOCAL = @ACLOCAL@
--AUTOCONF = @AUTOCONF@
--AUTOMAKE = @AUTOMAKE@
--AUTOHEADER = @AUTOHEADER@
--
--INSTALL = @INSTALL@
--INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
--INSTALL_DATA = @INSTALL_DATA@
--INSTALL_SCRIPT = @INSTALL_SCRIPT@
--transform = @program_transform_name@
--
-+pkglibdir = $(libdir)/@PACKAGE@
-+pkglibexecdir = $(libexecdir)/@PACKAGE@
-+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-+install_sh_DATA = $(install_sh) -c -m 644
-+install_sh_PROGRAM = $(install_sh) -c
-+install_sh_SCRIPT = $(install_sh) -c
-+INSTALL_HEADER = $(INSTALL_DATA)
-+transform = $(program_transform_name)
- NORMAL_INSTALL = :
- PRE_INSTALL = :
- POST_INSTALL = :
- NORMAL_UNINSTALL = :
- PRE_UNINSTALL = :
- POST_UNINSTALL = :
--host_alias = @host_alias@
-+build_triplet = @build@
- host_triplet = @host@
-+subdir = test/data/protein
-+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
-+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-+am__aclocal_m4_deps = $(top_srcdir)/configure.in
-+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-+ $(ACLOCAL_M4)
-+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
-+CONFIG_CLEAN_FILES =
-+CONFIG_CLEAN_VPATH_FILES =
-+SOURCES =
-+DIST_SOURCES =
-+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-+ACLOCAL = @ACLOCAL@
-+AMTAR = @AMTAR@
-+AUTOCONF = @AUTOCONF@
-+AUTOHEADER = @AUTOHEADER@
-+AUTOMAKE = @AUTOMAKE@
-+AWK = @AWK@
- CC = @CC@
-+CCDEPMODE = @CCDEPMODE@
-+CFLAGS = @CFLAGS@
-+CPP = @CPP@
-+CPPFLAGS = @CPPFLAGS@
-+CYGPATH_W = @CYGPATH_W@
-+DEFS = @DEFS@
-+DEPDIR = @DEPDIR@
-+ECHO_C = @ECHO_C@
-+ECHO_N = @ECHO_N@
-+ECHO_T = @ECHO_T@
-+EGREP = @EGREP@
-+EXEEXT = @EXEEXT@
- GLIB_CONFIG = @GLIB_CONFIG@
--HAVE_LIB = @HAVE_LIB@
--LIB = @LIB@
--LTLIB = @LTLIB@
-+GREP = @GREP@
-+INSTALL = @INSTALL@
-+INSTALL_DATA = @INSTALL_DATA@
-+INSTALL_PROGRAM = @INSTALL_PROGRAM@
-+INSTALL_SCRIPT = @INSTALL_SCRIPT@
-+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-+LDFLAGS = @LDFLAGS@
-+LIBOBJS = @LIBOBJS@
-+LIBS = @LIBS@
-+LTLIBOBJS = @LTLIBOBJS@
- MAKEINFO = @MAKEINFO@
-+MKDIR_P = @MKDIR_P@
-+OBJEXT = @OBJEXT@
- PACKAGE = @PACKAGE@
-+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-+PACKAGE_NAME = @PACKAGE_NAME@
-+PACKAGE_STRING = @PACKAGE_STRING@
-+PACKAGE_TARNAME = @PACKAGE_TARNAME@
-+PACKAGE_URL = @PACKAGE_URL@
-+PACKAGE_VERSION = @PACKAGE_VERSION@
-+PATH_SEPARATOR = @PATH_SEPARATOR@
- PKG_CONFIG = @PKG_CONFIG@
-+SET_MAKE = @SET_MAKE@
-+SHELL = @SHELL@
-+STRIP = @STRIP@
- VERSION = @VERSION@
-+abs_builddir = @abs_builddir@
-+abs_srcdir = @abs_srcdir@
-+abs_top_builddir = @abs_top_builddir@
-+abs_top_srcdir = @abs_top_srcdir@
-+ac_ct_CC = @ac_ct_CC@
-+am__include = @am__include@
-+am__leading_dot = @am__leading_dot@
-+am__quote = @am__quote@
-+am__tar = @am__tar@
-+am__untar = @am__untar@
-+bindir = @bindir@
-+build = @build@
-+build_alias = @build_alias@
-+build_cpu = @build_cpu@
-+build_os = @build_os@
-+build_vendor = @build_vendor@
-+builddir = @builddir@
- codegen_extra_ldadd = @codegen_extra_ldadd@
- codegen_extra_sources = @codegen_extra_sources@
-+datadir = @datadir@
- datarootdir = @datarootdir@
-+docdir = @docdir@
-+dvidir = @dvidir@
-+exec_prefix = @exec_prefix@
- glib_cflags = @glib_cflags@
- glib_libs = @glib_libs@
- host = @host@
-+host_alias = @host_alias@
-+host_cpu = @host_cpu@
-+host_os = @host_os@
-+host_vendor = @host_vendor@
-+htmldir = @htmldir@
-+includedir = @includedir@
-+infodir = @infodir@
-+install_sh = @install_sh@
- installed_util_list = @installed_util_list@
-+libdir = @libdir@
-+libexecdir = @libexecdir@
-+localedir = @localedir@
-+localstatedir = @localstatedir@
-+mandir = @mandir@
-+mkdir_p = @mkdir_p@
-+oldincludedir = @oldincludedir@
-+pdfdir = @pdfdir@
-+prefix = @prefix@
-+program_transform_name = @program_transform_name@
-+psdir = @psdir@
-+sbindir = @sbindir@
-+sharedstatedir = @sharedstatedir@
- source_root_dir = @source_root_dir@
-+srcdir = @srcdir@
-+sysconfdir = @sysconfdir@
-+target_alias = @target_alias@
-+top_build_prefix = @top_build_prefix@
-+top_builddir = @top_builddir@
-+top_srcdir = @top_srcdir@
- use_pthreads = @use_pthreads@
--
--EXTRA_DIST = calm.human.protein.fasta htrt.human.protein.fasta p53.human.protein.fasta tube.drome.protein.fasta
--
-+EXTRA_DIST = calm.human.protein.fasta htrt.human.protein.fasta \
-+ p53.human.protein.fasta tube.drome.protein.fasta
-
- MAINTAINERCLEANFILES = Makefile.in
--mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
--CONFIG_CLEAN_FILES =
--DIST_COMMON = Makefile.am Makefile.in
-+all: all-am
-
--
--DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
--
--TAR = tar
--GZIP_ENV = --best
--all: all-redirect
- .SUFFIXES:
--$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4)
-- cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps test/data/protein/Makefile
--
-+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
-+ @for dep in $?; do \
-+ case '$(am__configure_deps)' in \
-+ *$$dep*) \
-+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-+ && { if test -f $@; then exit 0; else break; fi; }; \
-+ exit 1;; \
-+ esac; \
-+ done; \
-+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu test/data/protein/Makefile'; \
-+ $(am__cd) $(top_srcdir) && \
-+ $(AUTOMAKE) --gnu test/data/protein/Makefile
-+.PRECIOUS: Makefile
- Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-- cd $(top_builddir) \
-- && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
--
-+ @case '$?' in \
-+ *config.status*) \
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-+ *) \
-+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-+ esac;
-+
-+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+
-+$(top_srcdir)/configure: $(am__configure_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(am__aclocal_m4_deps):
- tags: TAGS
- TAGS:
-
-+ctags: CTAGS
-+CTAGS:
-
--distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
--
--subdir = test/data/protein
-
- distdir: $(DISTFILES)
-- @for file in $(DISTFILES); do \
-- d=$(srcdir); \
-+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ list='$(DISTFILES)'; \
-+ dist_files=`for file in $$list; do echo $$file; done | \
-+ sed -e "s|^$$srcdirstrip/||;t" \
-+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-+ case $$dist_files in \
-+ */*) $(MKDIR_P) `echo "$$dist_files" | \
-+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-+ sort -u` ;; \
-+ esac; \
-+ for file in $$dist_files; do \
-+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
- if test -d $$d/$$file; then \
-- cp -pr $$d/$$file $(distdir)/$$file; \
-+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-+ if test -d "$(distdir)/$$file"; then \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
- else \
-- test -f $(distdir)/$$file \
-- || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
-- || cp -p $$d/$$file $(distdir)/$$file || :; \
-+ test -f "$(distdir)/$$file" \
-+ || cp -p $$d/$$file "$(distdir)/$$file" \
-+ || exit 1; \
- fi; \
- done
--info-am:
--info: info-am
--dvi-am:
--dvi: dvi-am
- check-am: all-am
- check: check-am
--installcheck-am:
--installcheck: installcheck-am
--install-exec-am:
-+all-am: Makefile
-+installdirs:
-+install: install-am
- install-exec: install-exec-am
--
--install-data-am:
- install-data: install-data-am
-+uninstall: uninstall-am
-
- install-am: all-am
- @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
--install: install-am
--uninstall-am:
--uninstall: uninstall-am
--all-am: Makefile
--all-redirect: all-am
--install-strip:
-- $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
--installdirs:
--
-
-+installcheck: installcheck-am
-+install-strip:
-+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-+ `test -z '$(STRIP)' || \
-+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
- mostlyclean-generic:
-
- clean-generic:
-
- distclean-generic:
-- -rm -f Makefile $(CONFIG_CLEAN_FILES)
-- -rm -f config.cache config.log stamp-h stamp-h[0-9]*
-+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
- maintainer-clean-generic:
-+ @echo "This command is intended for maintainers to use"
-+ @echo "it deletes files that may require special tools to rebuild."
- -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
--mostlyclean-am: mostlyclean-generic
--
--mostlyclean: mostlyclean-am
-+clean: clean-am
-
- clean-am: clean-generic mostlyclean-am
-
--clean: clean-am
-+distclean: distclean-am
-+ -rm -f Makefile
-+distclean-am: clean-am distclean-generic
-
--distclean-am: distclean-generic clean-am
-+dvi: dvi-am
-
--distclean: distclean-am
-+dvi-am:
-
--maintainer-clean-am: maintainer-clean-generic distclean-am
-- @echo "This command is intended for maintainers to use;"
-- @echo "it deletes files that may require special tools to rebuild."
-+html: html-am
-+
-+html-am:
-+
-+info: info-am
-+
-+info-am:
-+
-+install-data-am:
-+
-+install-dvi: install-dvi-am
-+
-+install-dvi-am:
-+
-+install-exec-am:
-+
-+install-html: install-html-am
-+
-+install-html-am:
-+
-+install-info: install-info-am
-+
-+install-info-am:
-+
-+install-man:
-+
-+install-pdf: install-pdf-am
-+
-+install-pdf-am:
-+
-+install-ps: install-ps-am
-+
-+install-ps-am:
-+
-+installcheck-am:
-
- maintainer-clean: maintainer-clean-am
-+ -rm -f Makefile
-+maintainer-clean-am: distclean-am maintainer-clean-generic
-+
-+mostlyclean: mostlyclean-am
-+
-+mostlyclean-am: mostlyclean-generic
-+
-+pdf: pdf-am
-+
-+pdf-am:
-+
-+ps: ps-am
-+
-+ps-am:
-+
-+uninstall-am:
-+
-+.MAKE: install-am install-strip
-
--.PHONY: tags distdir info-am info dvi-am dvi check check-am \
--installcheck-am installcheck install-exec-am install-exec \
--install-data-am install-data install-am install uninstall-am uninstall \
--all-redirect all-am all installdirs mostlyclean-generic \
--distclean-generic clean-generic maintainer-clean-generic clean \
--mostlyclean distclean maintainer-clean
-+.PHONY: all all-am check check-am clean clean-generic distclean \
-+ distclean-generic distdir dvi dvi-am html html-am info info-am \
-+ install install-am install-data install-data-am install-dvi \
-+ install-dvi-am install-exec install-exec-am install-html \
-+ install-html-am install-info install-info-am install-man \
-+ install-pdf install-pdf-am install-ps install-ps-am \
-+ install-strip installcheck installcheck-am installdirs \
-+ maintainer-clean maintainer-clean-generic mostlyclean \
-+ mostlyclean-generic pdf pdf-am ps ps-am uninstall uninstall-am
-
-
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -ubrN exonerate-2.2.0.orig/test/exonerate/Makefile.in exonerate-2.2.0/test/exonerate/Makefile.in
---- exonerate-2.2.0.orig/test/exonerate/Makefile.in 2008-10-17 12:04:48.000000000 +0200
-+++ exonerate-2.2.0/test/exonerate/Makefile.in 2011-12-12 13:33:17.000000000 +0100
-@@ -1,6 +1,9 @@
--# Makefile.in generated automatically by automake 1.4-p6 from Makefile.am
-+# Makefile.in generated by automake 1.11.1 from Makefile.am.
-+# @configure_input@
-
--# Copyright (C) 1994, 1995-8, 1999, 2001 Free Software Foundation, Inc.
-+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
-+# Inc.
- # This Makefile.in is free software; the Free Software Foundation
- # gives unlimited permission to copy and/or distribute it,
- # with or without modifications, as long as this notice is preserved.
-@@ -10,204 +13,419 @@
- # even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- # PARTICULAR PURPOSE.
-
--
--SHELL = @SHELL@
--
--srcdir = @srcdir@
--top_srcdir = @top_srcdir@
-+ at SET_MAKE@
- VPATH = @srcdir@
--prefix = @prefix@
--exec_prefix = @exec_prefix@
--
--bindir = @bindir@
--sbindir = @sbindir@
--libexecdir = @libexecdir@
--datadir = @datadir@
--sysconfdir = @sysconfdir@
--sharedstatedir = @sharedstatedir@
--localstatedir = @localstatedir@
--libdir = @libdir@
--infodir = @infodir@
--mandir = @mandir@
--includedir = @includedir@
--oldincludedir = /usr/include
--
--DESTDIR =
--
- pkgdatadir = $(datadir)/@PACKAGE@
--pkglibdir = $(libdir)/@PACKAGE@
- pkgincludedir = $(includedir)/@PACKAGE@
--
--top_builddir = ../..
--
--ACLOCAL = @ACLOCAL@
--AUTOCONF = @AUTOCONF@
--AUTOMAKE = @AUTOMAKE@
--AUTOHEADER = @AUTOHEADER@
--
--INSTALL = @INSTALL@
--INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
--INSTALL_DATA = @INSTALL_DATA@
--INSTALL_SCRIPT = @INSTALL_SCRIPT@
--transform = @program_transform_name@
--
-+pkglibdir = $(libdir)/@PACKAGE@
-+pkglibexecdir = $(libexecdir)/@PACKAGE@
-+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-+install_sh_DATA = $(install_sh) -c -m 644
-+install_sh_PROGRAM = $(install_sh) -c
-+install_sh_SCRIPT = $(install_sh) -c
-+INSTALL_HEADER = $(INSTALL_DATA)
-+transform = $(program_transform_name)
- NORMAL_INSTALL = :
- PRE_INSTALL = :
- POST_INSTALL = :
- NORMAL_UNINSTALL = :
- PRE_UNINSTALL = :
- POST_UNINSTALL = :
--host_alias = @host_alias@
-+build_triplet = @build@
- host_triplet = @host@
-+subdir = test/exonerate
-+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
-+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-+am__aclocal_m4_deps = $(top_srcdir)/configure.in
-+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-+ $(ACLOCAL_M4)
-+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
-+CONFIG_CLEAN_FILES =
-+CONFIG_CLEAN_VPATH_FILES =
-+SOURCES =
-+DIST_SOURCES =
-+am__tty_colors = \
-+red=; grn=; lgn=; blu=; std=
-+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-+ACLOCAL = @ACLOCAL@
-+AMTAR = @AMTAR@
-+AUTOCONF = @AUTOCONF@
-+AUTOHEADER = @AUTOHEADER@
-+AUTOMAKE = @AUTOMAKE@
-+AWK = @AWK@
- CC = @CC@
-+CCDEPMODE = @CCDEPMODE@
-+CFLAGS = @CFLAGS@
-+CPP = @CPP@
-+CPPFLAGS = @CPPFLAGS@
-+CYGPATH_W = @CYGPATH_W@
-+DEFS = @DEFS@
-+DEPDIR = @DEPDIR@
-+ECHO_C = @ECHO_C@
-+ECHO_N = @ECHO_N@
-+ECHO_T = @ECHO_T@
-+EGREP = @EGREP@
-+EXEEXT = @EXEEXT@
- GLIB_CONFIG = @GLIB_CONFIG@
--HAVE_LIB = @HAVE_LIB@
--LIB = @LIB@
--LTLIB = @LTLIB@
-+GREP = @GREP@
-+INSTALL = @INSTALL@
-+INSTALL_DATA = @INSTALL_DATA@
-+INSTALL_PROGRAM = @INSTALL_PROGRAM@
-+INSTALL_SCRIPT = @INSTALL_SCRIPT@
-+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-+LDFLAGS = @LDFLAGS@
-+LIBOBJS = @LIBOBJS@
-+LIBS = @LIBS@
-+LTLIBOBJS = @LTLIBOBJS@
- MAKEINFO = @MAKEINFO@
-+MKDIR_P = @MKDIR_P@
-+OBJEXT = @OBJEXT@
- PACKAGE = @PACKAGE@
-+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-+PACKAGE_NAME = @PACKAGE_NAME@
-+PACKAGE_STRING = @PACKAGE_STRING@
-+PACKAGE_TARNAME = @PACKAGE_TARNAME@
-+PACKAGE_URL = @PACKAGE_URL@
-+PACKAGE_VERSION = @PACKAGE_VERSION@
-+PATH_SEPARATOR = @PATH_SEPARATOR@
- PKG_CONFIG = @PKG_CONFIG@
-+SET_MAKE = @SET_MAKE@
-+SHELL = @SHELL@
-+STRIP = @STRIP@
- VERSION = @VERSION@
-+abs_builddir = @abs_builddir@
-+abs_srcdir = @abs_srcdir@
-+abs_top_builddir = @abs_top_builddir@
-+abs_top_srcdir = @abs_top_srcdir@
-+ac_ct_CC = @ac_ct_CC@
-+am__include = @am__include@
-+am__leading_dot = @am__leading_dot@
-+am__quote = @am__quote@
-+am__tar = @am__tar@
-+am__untar = @am__untar@
-+bindir = @bindir@
-+build = @build@
-+build_alias = @build_alias@
-+build_cpu = @build_cpu@
-+build_os = @build_os@
-+build_vendor = @build_vendor@
-+builddir = @builddir@
- codegen_extra_ldadd = @codegen_extra_ldadd@
- codegen_extra_sources = @codegen_extra_sources@
-+datadir = @datadir@
- datarootdir = @datarootdir@
-+docdir = @docdir@
-+dvidir = @dvidir@
-+exec_prefix = @exec_prefix@
- glib_cflags = @glib_cflags@
- glib_libs = @glib_libs@
- host = @host@
-+host_alias = @host_alias@
-+host_cpu = @host_cpu@
-+host_os = @host_os@
-+host_vendor = @host_vendor@
-+htmldir = @htmldir@
-+includedir = @includedir@
-+infodir = @infodir@
-+install_sh = @install_sh@
- installed_util_list = @installed_util_list@
-+libdir = @libdir@
-+libexecdir = @libexecdir@
-+localedir = @localedir@
-+localstatedir = @localstatedir@
-+mandir = @mandir@
-+mkdir_p = @mkdir_p@
-+oldincludedir = @oldincludedir@
-+pdfdir = @pdfdir@
-+prefix = @prefix@
-+program_transform_name = @program_transform_name@
-+psdir = @psdir@
-+sbindir = @sbindir@
-+sharedstatedir = @sharedstatedir@
- source_root_dir = @source_root_dir@
-+srcdir = @srcdir@
-+sysconfdir = @sysconfdir@
-+target_alias = @target_alias@
-+top_build_prefix = @top_build_prefix@
-+top_builddir = @top_builddir@
-+top_srcdir = @top_srcdir@
- use_pthreads = @use_pthreads@
--
- TESTS = exonerate.simple.test.sh
--
- EXTRA_DIST = $(TESTS)
-
- # Files to clear away
--
- MAINTAINERCLEANFILES = Makefile.in
--mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
--CONFIG_CLEAN_FILES =
--DIST_COMMON = Makefile.am Makefile.in
--
--
--DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
-+all: all-am
-
--TAR = tar
--GZIP_ENV = --best
--all: all-redirect
- .SUFFIXES:
--$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4)
-- cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps test/exonerate/Makefile
--
-+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
-+ @for dep in $?; do \
-+ case '$(am__configure_deps)' in \
-+ *$$dep*) \
-+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-+ && { if test -f $@; then exit 0; else break; fi; }; \
-+ exit 1;; \
-+ esac; \
-+ done; \
-+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu test/exonerate/Makefile'; \
-+ $(am__cd) $(top_srcdir) && \
-+ $(AUTOMAKE) --gnu test/exonerate/Makefile
-+.PRECIOUS: Makefile
- Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-- cd $(top_builddir) \
-- && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
--
-+ @case '$?' in \
-+ *config.status*) \
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-+ *) \
-+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-+ esac;
-+
-+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+
-+$(top_srcdir)/configure: $(am__configure_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(am__aclocal_m4_deps):
- tags: TAGS
- TAGS:
-
-+ctags: CTAGS
-+CTAGS:
-
--distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
--
--subdir = test/exonerate
-
--distdir: $(DISTFILES)
-- @for file in $(DISTFILES); do \
-- d=$(srcdir); \
-- if test -d $$d/$$file; then \
-- cp -pr $$d/$$file $(distdir)/$$file; \
-- else \
-- test -f $(distdir)/$$file \
-- || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
-- || cp -p $$d/$$file $(distdir)/$$file || :; \
-- fi; \
-- done
- check-TESTS: $(TESTS)
-- @failed=0; all=0; \
-+ @failed=0; all=0; xfail=0; xpass=0; skip=0; \
- srcdir=$(srcdir); export srcdir; \
-- for tst in $(TESTS); do \
-- if test -f $$tst; then dir=.; \
-- else dir="$(srcdir)"; fi; \
-- if $(TESTS_ENVIRONMENT) $$dir/$$tst; then \
-+ list=' $(TESTS) '; \
-+ $(am__tty_colors); \
-+ if test -n "$$list"; then \
-+ for tst in $$list; do \
-+ if test -f ./$$tst; then dir=./; \
-+ elif test -f $$tst; then dir=; \
-+ else dir="$(srcdir)/"; fi; \
-+ if $(TESTS_ENVIRONMENT) $${dir}$$tst; then \
- all=`expr $$all + 1`; \
-- echo "PASS: $$tst"; \
-+ case " $(XFAIL_TESTS) " in \
-+ *[\ \ ]$$tst[\ \ ]*) \
-+ xpass=`expr $$xpass + 1`; \
-+ failed=`expr $$failed + 1`; \
-+ col=$$red; res=XPASS; \
-+ ;; \
-+ *) \
-+ col=$$grn; res=PASS; \
-+ ;; \
-+ esac; \
- elif test $$? -ne 77; then \
- all=`expr $$all + 1`; \
-+ case " $(XFAIL_TESTS) " in \
-+ *[\ \ ]$$tst[\ \ ]*) \
-+ xfail=`expr $$xfail + 1`; \
-+ col=$$lgn; res=XFAIL; \
-+ ;; \
-+ *) \
- failed=`expr $$failed + 1`; \
-- echo "FAIL: $$tst"; \
-+ col=$$red; res=FAIL; \
-+ ;; \
-+ esac; \
-+ else \
-+ skip=`expr $$skip + 1`; \
-+ col=$$blu; res=SKIP; \
- fi; \
-+ echo "$${col}$$res$${std}: $$tst"; \
- done; \
-+ if test "$$all" -eq 1; then \
-+ tests="test"; \
-+ All=""; \
-+ else \
-+ tests="tests"; \
-+ All="All "; \
-+ fi; \
-+ if test "$$failed" -eq 0; then \
-+ if test "$$xfail" -eq 0; then \
-+ banner="$$All$$all $$tests passed"; \
-+ else \
-+ if test "$$xfail" -eq 1; then failures=failure; else failures=failures; fi; \
-+ banner="$$All$$all $$tests behaved as expected ($$xfail expected $$failures)"; \
-+ fi; \
-+ else \
-+ if test "$$xpass" -eq 0; then \
-+ banner="$$failed of $$all $$tests failed"; \
-+ else \
-+ if test "$$xpass" -eq 1; then passes=pass; else passes=passes; fi; \
-+ banner="$$failed of $$all $$tests did not behave as expected ($$xpass unexpected $$passes)"; \
-+ fi; \
-+ fi; \
-+ dashes="$$banner"; \
-+ skipped=""; \
-+ if test "$$skip" -ne 0; then \
-+ if test "$$skip" -eq 1; then \
-+ skipped="($$skip test was not run)"; \
-+ else \
-+ skipped="($$skip tests were not run)"; \
-+ fi; \
-+ test `echo "$$skipped" | wc -c` -le `echo "$$banner" | wc -c` || \
-+ dashes="$$skipped"; \
-+ fi; \
-+ report=""; \
-+ if test "$$failed" -ne 0 && test -n "$(PACKAGE_BUGREPORT)"; then \
-+ report="Please report to $(PACKAGE_BUGREPORT)"; \
-+ test `echo "$$report" | wc -c` -le `echo "$$banner" | wc -c` || \
-+ dashes="$$report"; \
-+ fi; \
-+ dashes=`echo "$$dashes" | sed s/./=/g`; \
- if test "$$failed" -eq 0; then \
-- banner="All $$all tests passed"; \
-+ echo "$$grn$$dashes"; \
- else \
-- banner="$$failed of $$all tests failed"; \
-+ echo "$$red$$dashes"; \
- fi; \
-- dashes=`echo "$$banner" | sed s/./=/g`; \
-- echo "$$dashes"; \
- echo "$$banner"; \
-- echo "$$dashes"; \
-- test "$$failed" -eq 0
--info-am:
--info: info-am
--dvi-am:
--dvi: dvi-am
-+ test -z "$$skipped" || echo "$$skipped"; \
-+ test -z "$$report" || echo "$$report"; \
-+ echo "$$dashes$$std"; \
-+ test "$$failed" -eq 0; \
-+ else :; fi
-+
-+distdir: $(DISTFILES)
-+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ list='$(DISTFILES)'; \
-+ dist_files=`for file in $$list; do echo $$file; done | \
-+ sed -e "s|^$$srcdirstrip/||;t" \
-+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-+ case $$dist_files in \
-+ */*) $(MKDIR_P) `echo "$$dist_files" | \
-+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-+ sort -u` ;; \
-+ esac; \
-+ for file in $$dist_files; do \
-+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
-+ if test -d $$d/$$file; then \
-+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-+ if test -d "$(distdir)/$$file"; then \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
-+ else \
-+ test -f "$(distdir)/$$file" \
-+ || cp -p $$d/$$file "$(distdir)/$$file" \
-+ || exit 1; \
-+ fi; \
-+ done
- check-am: all-am
- $(MAKE) $(AM_MAKEFLAGS) check-TESTS
- check: check-am
--installcheck-am:
--installcheck: installcheck-am
--install-exec-am:
-+all-am: Makefile
-+installdirs:
-+install: install-am
- install-exec: install-exec-am
--
--install-data-am:
- install-data: install-data-am
-+uninstall: uninstall-am
-
- install-am: all-am
- @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
--install: install-am
--uninstall-am:
--uninstall: uninstall-am
--all-am: Makefile
--all-redirect: all-am
--install-strip:
-- $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
--installdirs:
--
-
-+installcheck: installcheck-am
-+install-strip:
-+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-+ `test -z '$(STRIP)' || \
-+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
- mostlyclean-generic:
-
- clean-generic:
-
- distclean-generic:
-- -rm -f Makefile $(CONFIG_CLEAN_FILES)
-- -rm -f config.cache config.log stamp-h stamp-h[0-9]*
-+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
- maintainer-clean-generic:
-+ @echo "This command is intended for maintainers to use"
-+ @echo "it deletes files that may require special tools to rebuild."
- -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
--mostlyclean-am: mostlyclean-generic
--
--mostlyclean: mostlyclean-am
-+clean: clean-am
-
- clean-am: clean-generic mostlyclean-am
-
--clean: clean-am
-+distclean: distclean-am
-+ -rm -f Makefile
-+distclean-am: clean-am distclean-generic
-
--distclean-am: distclean-generic clean-am
-+dvi: dvi-am
-
--distclean: distclean-am
-+dvi-am:
-
--maintainer-clean-am: maintainer-clean-generic distclean-am
-- @echo "This command is intended for maintainers to use;"
-- @echo "it deletes files that may require special tools to rebuild."
-+html: html-am
-+
-+html-am:
-+
-+info: info-am
-+
-+info-am:
-+
-+install-data-am:
-+
-+install-dvi: install-dvi-am
-+
-+install-dvi-am:
-+
-+install-exec-am:
-+
-+install-html: install-html-am
-+
-+install-html-am:
-+
-+install-info: install-info-am
-+
-+install-info-am:
-+
-+install-man:
-+
-+install-pdf: install-pdf-am
-+
-+install-pdf-am:
-+
-+install-ps: install-ps-am
-+
-+install-ps-am:
-+
-+installcheck-am:
-
- maintainer-clean: maintainer-clean-am
-+ -rm -f Makefile
-+maintainer-clean-am: distclean-am maintainer-clean-generic
-+
-+mostlyclean: mostlyclean-am
-+
-+mostlyclean-am: mostlyclean-generic
-+
-+pdf: pdf-am
-+
-+pdf-am:
-+
-+ps: ps-am
-+
-+ps-am:
-+
-+uninstall-am:
-+
-+.MAKE: check-am install-am install-strip
-
--.PHONY: tags distdir check-TESTS info-am info dvi-am dvi check check-am \
--installcheck-am installcheck install-exec-am install-exec \
--install-data-am install-data install-am install uninstall-am uninstall \
--all-redirect all-am all installdirs mostlyclean-generic \
--distclean-generic clean-generic maintainer-clean-generic clean \
--mostlyclean distclean maintainer-clean
-+.PHONY: all all-am check check-TESTS check-am clean clean-generic \
-+ distclean distclean-generic distdir dvi dvi-am html html-am \
-+ info info-am install install-am install-data install-data-am \
-+ install-dvi install-dvi-am install-exec install-exec-am \
-+ install-html install-html-am install-info install-info-am \
-+ install-man install-pdf install-pdf-am install-ps \
-+ install-ps-am install-strip installcheck installcheck-am \
-+ installdirs maintainer-clean maintainer-clean-generic \
-+ mostlyclean mostlyclean-generic pdf pdf-am ps ps-am uninstall \
-+ uninstall-am
-
-
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -ubrN exonerate-2.2.0.orig/test/ipcress/Makefile.in exonerate-2.2.0/test/ipcress/Makefile.in
---- exonerate-2.2.0.orig/test/ipcress/Makefile.in 2008-10-17 12:04:48.000000000 +0200
-+++ exonerate-2.2.0/test/ipcress/Makefile.in 2011-12-12 13:33:17.000000000 +0100
-@@ -1,6 +1,9 @@
--# Makefile.in generated automatically by automake 1.4-p6 from Makefile.am
-+# Makefile.in generated by automake 1.11.1 from Makefile.am.
-+# @configure_input@
-
--# Copyright (C) 1994, 1995-8, 1999, 2001 Free Software Foundation, Inc.
-+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
-+# Inc.
- # This Makefile.in is free software; the Free Software Foundation
- # gives unlimited permission to copy and/or distribute it,
- # with or without modifications, as long as this notice is preserved.
-@@ -10,204 +13,419 @@
- # even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- # PARTICULAR PURPOSE.
-
--
--SHELL = @SHELL@
--
--srcdir = @srcdir@
--top_srcdir = @top_srcdir@
-+ at SET_MAKE@
- VPATH = @srcdir@
--prefix = @prefix@
--exec_prefix = @exec_prefix@
--
--bindir = @bindir@
--sbindir = @sbindir@
--libexecdir = @libexecdir@
--datadir = @datadir@
--sysconfdir = @sysconfdir@
--sharedstatedir = @sharedstatedir@
--localstatedir = @localstatedir@
--libdir = @libdir@
--infodir = @infodir@
--mandir = @mandir@
--includedir = @includedir@
--oldincludedir = /usr/include
--
--DESTDIR =
--
- pkgdatadir = $(datadir)/@PACKAGE@
--pkglibdir = $(libdir)/@PACKAGE@
- pkgincludedir = $(includedir)/@PACKAGE@
--
--top_builddir = ../..
--
--ACLOCAL = @ACLOCAL@
--AUTOCONF = @AUTOCONF@
--AUTOMAKE = @AUTOMAKE@
--AUTOHEADER = @AUTOHEADER@
--
--INSTALL = @INSTALL@
--INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
--INSTALL_DATA = @INSTALL_DATA@
--INSTALL_SCRIPT = @INSTALL_SCRIPT@
--transform = @program_transform_name@
--
-+pkglibdir = $(libdir)/@PACKAGE@
-+pkglibexecdir = $(libexecdir)/@PACKAGE@
-+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-+install_sh_DATA = $(install_sh) -c -m 644
-+install_sh_PROGRAM = $(install_sh) -c
-+install_sh_SCRIPT = $(install_sh) -c
-+INSTALL_HEADER = $(INSTALL_DATA)
-+transform = $(program_transform_name)
- NORMAL_INSTALL = :
- PRE_INSTALL = :
- POST_INSTALL = :
- NORMAL_UNINSTALL = :
- PRE_UNINSTALL = :
- POST_UNINSTALL = :
--host_alias = @host_alias@
-+build_triplet = @build@
- host_triplet = @host@
-+subdir = test/ipcress
-+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
-+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-+am__aclocal_m4_deps = $(top_srcdir)/configure.in
-+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-+ $(ACLOCAL_M4)
-+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
-+CONFIG_CLEAN_FILES =
-+CONFIG_CLEAN_VPATH_FILES =
-+SOURCES =
-+DIST_SOURCES =
-+am__tty_colors = \
-+red=; grn=; lgn=; blu=; std=
-+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-+ACLOCAL = @ACLOCAL@
-+AMTAR = @AMTAR@
-+AUTOCONF = @AUTOCONF@
-+AUTOHEADER = @AUTOHEADER@
-+AUTOMAKE = @AUTOMAKE@
-+AWK = @AWK@
- CC = @CC@
-+CCDEPMODE = @CCDEPMODE@
-+CFLAGS = @CFLAGS@
-+CPP = @CPP@
-+CPPFLAGS = @CPPFLAGS@
-+CYGPATH_W = @CYGPATH_W@
-+DEFS = @DEFS@
-+DEPDIR = @DEPDIR@
-+ECHO_C = @ECHO_C@
-+ECHO_N = @ECHO_N@
-+ECHO_T = @ECHO_T@
-+EGREP = @EGREP@
-+EXEEXT = @EXEEXT@
- GLIB_CONFIG = @GLIB_CONFIG@
--HAVE_LIB = @HAVE_LIB@
--LIB = @LIB@
--LTLIB = @LTLIB@
-+GREP = @GREP@
-+INSTALL = @INSTALL@
-+INSTALL_DATA = @INSTALL_DATA@
-+INSTALL_PROGRAM = @INSTALL_PROGRAM@
-+INSTALL_SCRIPT = @INSTALL_SCRIPT@
-+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-+LDFLAGS = @LDFLAGS@
-+LIBOBJS = @LIBOBJS@
-+LIBS = @LIBS@
-+LTLIBOBJS = @LTLIBOBJS@
- MAKEINFO = @MAKEINFO@
-+MKDIR_P = @MKDIR_P@
-+OBJEXT = @OBJEXT@
- PACKAGE = @PACKAGE@
-+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-+PACKAGE_NAME = @PACKAGE_NAME@
-+PACKAGE_STRING = @PACKAGE_STRING@
-+PACKAGE_TARNAME = @PACKAGE_TARNAME@
-+PACKAGE_URL = @PACKAGE_URL@
-+PACKAGE_VERSION = @PACKAGE_VERSION@
-+PATH_SEPARATOR = @PATH_SEPARATOR@
- PKG_CONFIG = @PKG_CONFIG@
-+SET_MAKE = @SET_MAKE@
-+SHELL = @SHELL@
-+STRIP = @STRIP@
- VERSION = @VERSION@
-+abs_builddir = @abs_builddir@
-+abs_srcdir = @abs_srcdir@
-+abs_top_builddir = @abs_top_builddir@
-+abs_top_srcdir = @abs_top_srcdir@
-+ac_ct_CC = @ac_ct_CC@
-+am__include = @am__include@
-+am__leading_dot = @am__leading_dot@
-+am__quote = @am__quote@
-+am__tar = @am__tar@
-+am__untar = @am__untar@
-+bindir = @bindir@
-+build = @build@
-+build_alias = @build_alias@
-+build_cpu = @build_cpu@
-+build_os = @build_os@
-+build_vendor = @build_vendor@
-+builddir = @builddir@
- codegen_extra_ldadd = @codegen_extra_ldadd@
- codegen_extra_sources = @codegen_extra_sources@
-+datadir = @datadir@
- datarootdir = @datarootdir@
-+docdir = @docdir@
-+dvidir = @dvidir@
-+exec_prefix = @exec_prefix@
- glib_cflags = @glib_cflags@
- glib_libs = @glib_libs@
- host = @host@
-+host_alias = @host_alias@
-+host_cpu = @host_cpu@
-+host_os = @host_os@
-+host_vendor = @host_vendor@
-+htmldir = @htmldir@
-+includedir = @includedir@
-+infodir = @infodir@
-+install_sh = @install_sh@
- installed_util_list = @installed_util_list@
-+libdir = @libdir@
-+libexecdir = @libexecdir@
-+localedir = @localedir@
-+localstatedir = @localstatedir@
-+mandir = @mandir@
-+mkdir_p = @mkdir_p@
-+oldincludedir = @oldincludedir@
-+pdfdir = @pdfdir@
-+prefix = @prefix@
-+program_transform_name = @program_transform_name@
-+psdir = @psdir@
-+sbindir = @sbindir@
-+sharedstatedir = @sharedstatedir@
- source_root_dir = @source_root_dir@
-+srcdir = @srcdir@
-+sysconfdir = @sysconfdir@
-+target_alias = @target_alias@
-+top_build_prefix = @top_build_prefix@
-+top_builddir = @top_builddir@
-+top_srcdir = @top_srcdir@
- use_pthreads = @use_pthreads@
--
- TESTS = ipcress.simple.test.sh
--
- EXTRA_DIST = $(TESTS)
-
- # Files to clear away
--
- MAINTAINERCLEANFILES = Makefile.in
--mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
--CONFIG_CLEAN_FILES =
--DIST_COMMON = Makefile.am Makefile.in
--
--
--DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
-+all: all-am
-
--TAR = tar
--GZIP_ENV = --best
--all: all-redirect
- .SUFFIXES:
--$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4)
-- cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps test/ipcress/Makefile
--
-+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
-+ @for dep in $?; do \
-+ case '$(am__configure_deps)' in \
-+ *$$dep*) \
-+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-+ && { if test -f $@; then exit 0; else break; fi; }; \
-+ exit 1;; \
-+ esac; \
-+ done; \
-+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu test/ipcress/Makefile'; \
-+ $(am__cd) $(top_srcdir) && \
-+ $(AUTOMAKE) --gnu test/ipcress/Makefile
-+.PRECIOUS: Makefile
- Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-- cd $(top_builddir) \
-- && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
--
-+ @case '$?' in \
-+ *config.status*) \
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-+ *) \
-+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-+ esac;
-+
-+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+
-+$(top_srcdir)/configure: $(am__configure_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(am__aclocal_m4_deps):
- tags: TAGS
- TAGS:
-
-+ctags: CTAGS
-+CTAGS:
-
--distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
--
--subdir = test/ipcress
-
--distdir: $(DISTFILES)
-- @for file in $(DISTFILES); do \
-- d=$(srcdir); \
-- if test -d $$d/$$file; then \
-- cp -pr $$d/$$file $(distdir)/$$file; \
-- else \
-- test -f $(distdir)/$$file \
-- || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
-- || cp -p $$d/$$file $(distdir)/$$file || :; \
-- fi; \
-- done
- check-TESTS: $(TESTS)
-- @failed=0; all=0; \
-+ @failed=0; all=0; xfail=0; xpass=0; skip=0; \
- srcdir=$(srcdir); export srcdir; \
-- for tst in $(TESTS); do \
-- if test -f $$tst; then dir=.; \
-- else dir="$(srcdir)"; fi; \
-- if $(TESTS_ENVIRONMENT) $$dir/$$tst; then \
-+ list=' $(TESTS) '; \
-+ $(am__tty_colors); \
-+ if test -n "$$list"; then \
-+ for tst in $$list; do \
-+ if test -f ./$$tst; then dir=./; \
-+ elif test -f $$tst; then dir=; \
-+ else dir="$(srcdir)/"; fi; \
-+ if $(TESTS_ENVIRONMENT) $${dir}$$tst; then \
- all=`expr $$all + 1`; \
-- echo "PASS: $$tst"; \
-+ case " $(XFAIL_TESTS) " in \
-+ *[\ \ ]$$tst[\ \ ]*) \
-+ xpass=`expr $$xpass + 1`; \
-+ failed=`expr $$failed + 1`; \
-+ col=$$red; res=XPASS; \
-+ ;; \
-+ *) \
-+ col=$$grn; res=PASS; \
-+ ;; \
-+ esac; \
- elif test $$? -ne 77; then \
- all=`expr $$all + 1`; \
-+ case " $(XFAIL_TESTS) " in \
-+ *[\ \ ]$$tst[\ \ ]*) \
-+ xfail=`expr $$xfail + 1`; \
-+ col=$$lgn; res=XFAIL; \
-+ ;; \
-+ *) \
- failed=`expr $$failed + 1`; \
-- echo "FAIL: $$tst"; \
-+ col=$$red; res=FAIL; \
-+ ;; \
-+ esac; \
-+ else \
-+ skip=`expr $$skip + 1`; \
-+ col=$$blu; res=SKIP; \
- fi; \
-+ echo "$${col}$$res$${std}: $$tst"; \
- done; \
-+ if test "$$all" -eq 1; then \
-+ tests="test"; \
-+ All=""; \
-+ else \
-+ tests="tests"; \
-+ All="All "; \
-+ fi; \
-+ if test "$$failed" -eq 0; then \
-+ if test "$$xfail" -eq 0; then \
-+ banner="$$All$$all $$tests passed"; \
-+ else \
-+ if test "$$xfail" -eq 1; then failures=failure; else failures=failures; fi; \
-+ banner="$$All$$all $$tests behaved as expected ($$xfail expected $$failures)"; \
-+ fi; \
-+ else \
-+ if test "$$xpass" -eq 0; then \
-+ banner="$$failed of $$all $$tests failed"; \
-+ else \
-+ if test "$$xpass" -eq 1; then passes=pass; else passes=passes; fi; \
-+ banner="$$failed of $$all $$tests did not behave as expected ($$xpass unexpected $$passes)"; \
-+ fi; \
-+ fi; \
-+ dashes="$$banner"; \
-+ skipped=""; \
-+ if test "$$skip" -ne 0; then \
-+ if test "$$skip" -eq 1; then \
-+ skipped="($$skip test was not run)"; \
-+ else \
-+ skipped="($$skip tests were not run)"; \
-+ fi; \
-+ test `echo "$$skipped" | wc -c` -le `echo "$$banner" | wc -c` || \
-+ dashes="$$skipped"; \
-+ fi; \
-+ report=""; \
-+ if test "$$failed" -ne 0 && test -n "$(PACKAGE_BUGREPORT)"; then \
-+ report="Please report to $(PACKAGE_BUGREPORT)"; \
-+ test `echo "$$report" | wc -c` -le `echo "$$banner" | wc -c` || \
-+ dashes="$$report"; \
-+ fi; \
-+ dashes=`echo "$$dashes" | sed s/./=/g`; \
- if test "$$failed" -eq 0; then \
-- banner="All $$all tests passed"; \
-+ echo "$$grn$$dashes"; \
- else \
-- banner="$$failed of $$all tests failed"; \
-+ echo "$$red$$dashes"; \
- fi; \
-- dashes=`echo "$$banner" | sed s/./=/g`; \
-- echo "$$dashes"; \
- echo "$$banner"; \
-- echo "$$dashes"; \
-- test "$$failed" -eq 0
--info-am:
--info: info-am
--dvi-am:
--dvi: dvi-am
-+ test -z "$$skipped" || echo "$$skipped"; \
-+ test -z "$$report" || echo "$$report"; \
-+ echo "$$dashes$$std"; \
-+ test "$$failed" -eq 0; \
-+ else :; fi
-+
-+distdir: $(DISTFILES)
-+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ list='$(DISTFILES)'; \
-+ dist_files=`for file in $$list; do echo $$file; done | \
-+ sed -e "s|^$$srcdirstrip/||;t" \
-+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-+ case $$dist_files in \
-+ */*) $(MKDIR_P) `echo "$$dist_files" | \
-+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-+ sort -u` ;; \
-+ esac; \
-+ for file in $$dist_files; do \
-+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
-+ if test -d $$d/$$file; then \
-+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-+ if test -d "$(distdir)/$$file"; then \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
-+ else \
-+ test -f "$(distdir)/$$file" \
-+ || cp -p $$d/$$file "$(distdir)/$$file" \
-+ || exit 1; \
-+ fi; \
-+ done
- check-am: all-am
- $(MAKE) $(AM_MAKEFLAGS) check-TESTS
- check: check-am
--installcheck-am:
--installcheck: installcheck-am
--install-exec-am:
-+all-am: Makefile
-+installdirs:
-+install: install-am
- install-exec: install-exec-am
--
--install-data-am:
- install-data: install-data-am
-+uninstall: uninstall-am
-
- install-am: all-am
- @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
--install: install-am
--uninstall-am:
--uninstall: uninstall-am
--all-am: Makefile
--all-redirect: all-am
--install-strip:
-- $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
--installdirs:
--
-
-+installcheck: installcheck-am
-+install-strip:
-+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-+ `test -z '$(STRIP)' || \
-+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
- mostlyclean-generic:
-
- clean-generic:
-
- distclean-generic:
-- -rm -f Makefile $(CONFIG_CLEAN_FILES)
-- -rm -f config.cache config.log stamp-h stamp-h[0-9]*
-+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
- maintainer-clean-generic:
-+ @echo "This command is intended for maintainers to use"
-+ @echo "it deletes files that may require special tools to rebuild."
- -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
--mostlyclean-am: mostlyclean-generic
--
--mostlyclean: mostlyclean-am
-+clean: clean-am
-
- clean-am: clean-generic mostlyclean-am
-
--clean: clean-am
-+distclean: distclean-am
-+ -rm -f Makefile
-+distclean-am: clean-am distclean-generic
-
--distclean-am: distclean-generic clean-am
-+dvi: dvi-am
-
--distclean: distclean-am
-+dvi-am:
-
--maintainer-clean-am: maintainer-clean-generic distclean-am
-- @echo "This command is intended for maintainers to use;"
-- @echo "it deletes files that may require special tools to rebuild."
-+html: html-am
-+
-+html-am:
-+
-+info: info-am
-+
-+info-am:
-+
-+install-data-am:
-+
-+install-dvi: install-dvi-am
-+
-+install-dvi-am:
-+
-+install-exec-am:
-+
-+install-html: install-html-am
-+
-+install-html-am:
-+
-+install-info: install-info-am
-+
-+install-info-am:
-+
-+install-man:
-+
-+install-pdf: install-pdf-am
-+
-+install-pdf-am:
-+
-+install-ps: install-ps-am
-+
-+install-ps-am:
-+
-+installcheck-am:
-
- maintainer-clean: maintainer-clean-am
-+ -rm -f Makefile
-+maintainer-clean-am: distclean-am maintainer-clean-generic
-+
-+mostlyclean: mostlyclean-am
-+
-+mostlyclean-am: mostlyclean-generic
-+
-+pdf: pdf-am
-+
-+pdf-am:
-+
-+ps: ps-am
-+
-+ps-am:
-+
-+uninstall-am:
-+
-+.MAKE: check-am install-am install-strip
-
--.PHONY: tags distdir check-TESTS info-am info dvi-am dvi check check-am \
--installcheck-am installcheck install-exec-am install-exec \
--install-data-am install-data install-am install uninstall-am uninstall \
--all-redirect all-am all installdirs mostlyclean-generic \
--distclean-generic clean-generic maintainer-clean-generic clean \
--mostlyclean distclean maintainer-clean
-+.PHONY: all all-am check check-TESTS check-am clean clean-generic \
-+ distclean distclean-generic distdir dvi dvi-am html html-am \
-+ info info-am install install-am install-data install-data-am \
-+ install-dvi install-dvi-am install-exec install-exec-am \
-+ install-html install-html-am install-info install-info-am \
-+ install-man install-pdf install-pdf-am install-ps \
-+ install-ps-am install-strip installcheck installcheck-am \
-+ installdirs maintainer-clean maintainer-clean-generic \
-+ mostlyclean mostlyclean-generic pdf pdf-am ps ps-am uninstall \
-+ uninstall-am
-
-
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -ubrN exonerate-2.2.0.orig/test/Makefile.in exonerate-2.2.0/test/Makefile.in
---- exonerate-2.2.0.orig/test/Makefile.in 2008-10-17 12:04:47.000000000 +0200
-+++ exonerate-2.2.0/test/Makefile.in 2011-12-12 13:33:17.000000000 +0100
-@@ -1,6 +1,9 @@
--# Makefile.in generated automatically by automake 1.4-p6 from Makefile.am
-+# Makefile.in generated by automake 1.11.1 from Makefile.am.
-+# @configure_input@
-
--# Copyright (C) 1994, 1995-8, 1999, 2001 Free Software Foundation, Inc.
-+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
-+# Inc.
- # This Makefile.in is free software; the Free Software Foundation
- # gives unlimited permission to copy and/or distribute it,
- # with or without modifications, as long as this notice is preserved.
-@@ -10,95 +13,216 @@
- # even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- # PARTICULAR PURPOSE.
-
--
--SHELL = @SHELL@
--
--srcdir = @srcdir@
--top_srcdir = @top_srcdir@
-+ at SET_MAKE@
- VPATH = @srcdir@
--prefix = @prefix@
--exec_prefix = @exec_prefix@
--
--bindir = @bindir@
--sbindir = @sbindir@
--libexecdir = @libexecdir@
--datadir = @datadir@
--sysconfdir = @sysconfdir@
--sharedstatedir = @sharedstatedir@
--localstatedir = @localstatedir@
--libdir = @libdir@
--infodir = @infodir@
--mandir = @mandir@
--includedir = @includedir@
--oldincludedir = /usr/include
--
--DESTDIR =
--
- pkgdatadir = $(datadir)/@PACKAGE@
--pkglibdir = $(libdir)/@PACKAGE@
- pkgincludedir = $(includedir)/@PACKAGE@
--
--top_builddir = ..
--
--ACLOCAL = @ACLOCAL@
--AUTOCONF = @AUTOCONF@
--AUTOMAKE = @AUTOMAKE@
--AUTOHEADER = @AUTOHEADER@
--
--INSTALL = @INSTALL@
--INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
--INSTALL_DATA = @INSTALL_DATA@
--INSTALL_SCRIPT = @INSTALL_SCRIPT@
--transform = @program_transform_name@
--
-+pkglibdir = $(libdir)/@PACKAGE@
-+pkglibexecdir = $(libexecdir)/@PACKAGE@
-+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-+install_sh_DATA = $(install_sh) -c -m 644
-+install_sh_PROGRAM = $(install_sh) -c
-+install_sh_SCRIPT = $(install_sh) -c
-+INSTALL_HEADER = $(INSTALL_DATA)
-+transform = $(program_transform_name)
- NORMAL_INSTALL = :
- PRE_INSTALL = :
- POST_INSTALL = :
- NORMAL_UNINSTALL = :
- PRE_UNINSTALL = :
- POST_UNINSTALL = :
--host_alias = @host_alias@
-+build_triplet = @build@
- host_triplet = @host@
-+subdir = test
-+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
-+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-+am__aclocal_m4_deps = $(top_srcdir)/configure.in
-+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-+ $(ACLOCAL_M4)
-+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
-+CONFIG_CLEAN_FILES =
-+CONFIG_CLEAN_VPATH_FILES =
-+SOURCES =
-+DIST_SOURCES =
-+RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
-+ html-recursive info-recursive install-data-recursive \
-+ install-dvi-recursive install-exec-recursive \
-+ install-html-recursive install-info-recursive \
-+ install-pdf-recursive install-ps-recursive install-recursive \
-+ installcheck-recursive installdirs-recursive pdf-recursive \
-+ ps-recursive uninstall-recursive
-+RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive \
-+ distclean-recursive maintainer-clean-recursive
-+AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
-+ $(RECURSIVE_CLEAN_TARGETS:-recursive=) tags TAGS ctags CTAGS \
-+ distdir
-+ETAGS = etags
-+CTAGS = ctags
-+DIST_SUBDIRS = $(SUBDIRS)
-+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-+am__relativize = \
-+ dir0=`pwd`; \
-+ sed_first='s,^\([^/]*\)/.*$$,\1,'; \
-+ sed_rest='s,^[^/]*/*,,'; \
-+ sed_last='s,^.*/\([^/]*\)$$,\1,'; \
-+ sed_butlast='s,/*[^/]*$$,,'; \
-+ while test -n "$$dir1"; do \
-+ first=`echo "$$dir1" | sed -e "$$sed_first"`; \
-+ if test "$$first" != "."; then \
-+ if test "$$first" = ".."; then \
-+ dir2=`echo "$$dir0" | sed -e "$$sed_last"`/"$$dir2"; \
-+ dir0=`echo "$$dir0" | sed -e "$$sed_butlast"`; \
-+ else \
-+ first2=`echo "$$dir2" | sed -e "$$sed_first"`; \
-+ if test "$$first2" = "$$first"; then \
-+ dir2=`echo "$$dir2" | sed -e "$$sed_rest"`; \
-+ else \
-+ dir2="../$$dir2"; \
-+ fi; \
-+ dir0="$$dir0"/"$$first"; \
-+ fi; \
-+ fi; \
-+ dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \
-+ done; \
-+ reldir="$$dir2"
-+ACLOCAL = @ACLOCAL@
-+AMTAR = @AMTAR@
-+AUTOCONF = @AUTOCONF@
-+AUTOHEADER = @AUTOHEADER@
-+AUTOMAKE = @AUTOMAKE@
-+AWK = @AWK@
- CC = @CC@
-+CCDEPMODE = @CCDEPMODE@
-+CFLAGS = @CFLAGS@
-+CPP = @CPP@
-+CPPFLAGS = @CPPFLAGS@
-+CYGPATH_W = @CYGPATH_W@
-+DEFS = @DEFS@
-+DEPDIR = @DEPDIR@
-+ECHO_C = @ECHO_C@
-+ECHO_N = @ECHO_N@
-+ECHO_T = @ECHO_T@
-+EGREP = @EGREP@
-+EXEEXT = @EXEEXT@
- GLIB_CONFIG = @GLIB_CONFIG@
--HAVE_LIB = @HAVE_LIB@
--LIB = @LIB@
--LTLIB = @LTLIB@
-+GREP = @GREP@
-+INSTALL = @INSTALL@
-+INSTALL_DATA = @INSTALL_DATA@
-+INSTALL_PROGRAM = @INSTALL_PROGRAM@
-+INSTALL_SCRIPT = @INSTALL_SCRIPT@
-+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-+LDFLAGS = @LDFLAGS@
-+LIBOBJS = @LIBOBJS@
-+LIBS = @LIBS@
-+LTLIBOBJS = @LTLIBOBJS@
- MAKEINFO = @MAKEINFO@
-+MKDIR_P = @MKDIR_P@
-+OBJEXT = @OBJEXT@
- PACKAGE = @PACKAGE@
-+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-+PACKAGE_NAME = @PACKAGE_NAME@
-+PACKAGE_STRING = @PACKAGE_STRING@
-+PACKAGE_TARNAME = @PACKAGE_TARNAME@
-+PACKAGE_URL = @PACKAGE_URL@
-+PACKAGE_VERSION = @PACKAGE_VERSION@
-+PATH_SEPARATOR = @PATH_SEPARATOR@
- PKG_CONFIG = @PKG_CONFIG@
-+SET_MAKE = @SET_MAKE@
-+SHELL = @SHELL@
-+STRIP = @STRIP@
- VERSION = @VERSION@
-+abs_builddir = @abs_builddir@
-+abs_srcdir = @abs_srcdir@
-+abs_top_builddir = @abs_top_builddir@
-+abs_top_srcdir = @abs_top_srcdir@
-+ac_ct_CC = @ac_ct_CC@
-+am__include = @am__include@
-+am__leading_dot = @am__leading_dot@
-+am__quote = @am__quote@
-+am__tar = @am__tar@
-+am__untar = @am__untar@
-+bindir = @bindir@
-+build = @build@
-+build_alias = @build_alias@
-+build_cpu = @build_cpu@
-+build_os = @build_os@
-+build_vendor = @build_vendor@
-+builddir = @builddir@
- codegen_extra_ldadd = @codegen_extra_ldadd@
- codegen_extra_sources = @codegen_extra_sources@
-+datadir = @datadir@
- datarootdir = @datarootdir@
-+docdir = @docdir@
-+dvidir = @dvidir@
-+exec_prefix = @exec_prefix@
- glib_cflags = @glib_cflags@
- glib_libs = @glib_libs@
- host = @host@
-+host_alias = @host_alias@
-+host_cpu = @host_cpu@
-+host_os = @host_os@
-+host_vendor = @host_vendor@
-+htmldir = @htmldir@
-+includedir = @includedir@
-+infodir = @infodir@
-+install_sh = @install_sh@
- installed_util_list = @installed_util_list@
-+libdir = @libdir@
-+libexecdir = @libexecdir@
-+localedir = @localedir@
-+localstatedir = @localstatedir@
-+mandir = @mandir@
-+mkdir_p = @mkdir_p@
-+oldincludedir = @oldincludedir@
-+pdfdir = @pdfdir@
-+prefix = @prefix@
-+program_transform_name = @program_transform_name@
-+psdir = @psdir@
-+sbindir = @sbindir@
-+sharedstatedir = @sharedstatedir@
- source_root_dir = @source_root_dir@
-+srcdir = @srcdir@
-+sysconfdir = @sysconfdir@
-+target_alias = @target_alias@
-+top_build_prefix = @top_build_prefix@
-+top_builddir = @top_builddir@
-+top_srcdir = @top_srcdir@
- use_pthreads = @use_pthreads@
--
- SUBDIRS = data exonerate ipcress util
--
- MAINTAINERCLEANFILES = Makefile.in
--mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
--CONFIG_CLEAN_FILES =
--DIST_COMMON = Makefile.am Makefile.in
--
-+all: all-recursive
-
--DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
--
--TAR = tar
--GZIP_ENV = --best
--all: all-redirect
- .SUFFIXES:
--$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4)
-- cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps test/Makefile
--
-+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
-+ @for dep in $?; do \
-+ case '$(am__configure_deps)' in \
-+ *$$dep*) \
-+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-+ && { if test -f $@; then exit 0; else break; fi; }; \
-+ exit 1;; \
-+ esac; \
-+ done; \
-+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu test/Makefile'; \
-+ $(am__cd) $(top_srcdir) && \
-+ $(AUTOMAKE) --gnu test/Makefile
-+.PRECIOUS: Makefile
- Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-- cd $(top_builddir) \
-- && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
--
-+ @case '$?' in \
-+ *config.status*) \
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-+ *) \
-+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-+ esac;
-+
-+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+
-+$(top_srcdir)/configure: $(am__configure_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(am__aclocal_m4_deps):
-
- # This directory's subdirectories are mostly independent; you can cd
- # into them and run `make' without going through this Makefile.
-@@ -106,13 +230,14 @@
- # (1) if the variable is set in `config.status', edit `config.status'
- # (which will cause the Makefiles to be regenerated when you run `make');
- # (2) otherwise, pass the desired values on the `make' command line.
--
-- at SET_MAKE@
--
--all-recursive install-data-recursive install-exec-recursive \
--installdirs-recursive install-recursive uninstall-recursive \
--check-recursive installcheck-recursive info-recursive dvi-recursive:
-- @set fnord $(MAKEFLAGS); amf=$$2; \
-+$(RECURSIVE_TARGETS):
-+ @fail= failcom='exit 1'; \
-+ for f in x $$MAKEFLAGS; do \
-+ case $$f in \
-+ *=* | --[!k]*);; \
-+ *k*) failcom='fail=yes';; \
-+ esac; \
-+ done; \
- dot_seen=no; \
- target=`echo $@ | sed s/-recursive//`; \
- list='$(SUBDIRS)'; for subdir in $$list; do \
-@@ -123,22 +248,32 @@
- else \
- local_target="$$target"; \
- fi; \
-- (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-- || case "$$amf" in *=*) exit 1;; *k*) fail=yes;; *) exit 1;; esac; \
-+ ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-+ || eval $$failcom; \
- done; \
- if test "$$dot_seen" = "no"; then \
- $(MAKE) $(AM_MAKEFLAGS) "$$target-am" || exit 1; \
- fi; test -z "$$fail"
-
--mostlyclean-recursive clean-recursive distclean-recursive \
--maintainer-clean-recursive:
-- @set fnord $(MAKEFLAGS); amf=$$2; \
-+$(RECURSIVE_CLEAN_TARGETS):
-+ @fail= failcom='exit 1'; \
-+ for f in x $$MAKEFLAGS; do \
-+ case $$f in \
-+ *=* | --[!k]*);; \
-+ *k*) failcom='fail=yes';; \
-+ esac; \
-+ done; \
- dot_seen=no; \
-- rev=''; list='$(SUBDIRS)'; for subdir in $$list; do \
-+ case "$@" in \
-+ distclean-* | maintainer-clean-*) list='$(DIST_SUBDIRS)' ;; \
-+ *) list='$(SUBDIRS)' ;; \
-+ esac; \
-+ rev=''; for subdir in $$list; do \
-+ if test "$$subdir" = "."; then :; else \
- rev="$$subdir $$rev"; \
-- test "$$subdir" != "." || dot_seen=yes; \
-+ fi; \
- done; \
-- test "$$dot_seen" = "no" && rev=". $$rev"; \
-+ rev="$$rev ."; \
- target=`echo $@ | sed s/-recursive//`; \
- for subdir in $$rev; do \
- echo "Making $$target in $$subdir"; \
-@@ -147,141 +282,253 @@
- else \
- local_target="$$target"; \
- fi; \
-- (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-- || case "$$amf" in *=*) exit 1;; *k*) fail=yes;; *) exit 1;; esac; \
-+ ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-+ || eval $$failcom; \
- done && test -z "$$fail"
- tags-recursive:
- list='$(SUBDIRS)'; for subdir in $$list; do \
-- test "$$subdir" = . || (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
-+ test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
-+ done
-+ctags-recursive:
-+ list='$(SUBDIRS)'; for subdir in $$list; do \
-+ test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \
- done
-
-+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ mkid -fID $$unique
- tags: TAGS
-
--ID: $(HEADERS) $(SOURCES) $(LISP)
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- here=`pwd` && cd $(srcdir) \
-- && mkid -f$$here/ID $$unique $(LISP)
--
--TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) $(LISP)
-- tags=; \
-+TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ set x; \
- here=`pwd`; \
-+ if ($(ETAGS) --etags-include --version) >/dev/null 2>&1; then \
-+ include_option=--etags-include; \
-+ empty_fix=.; \
-+ else \
-+ include_option=--include; \
-+ empty_fix=; \
-+ fi; \
- list='$(SUBDIRS)'; for subdir in $$list; do \
- if test "$$subdir" = .; then :; else \
-- test -f $$subdir/TAGS && tags="$$tags -i $$here/$$subdir/TAGS"; \
-+ test ! -f $$subdir/TAGS || \
-+ set "$$@" "$$include_option=$$here/$$subdir/TAGS"; \
- fi; \
- done; \
-- list='$(SOURCES) $(HEADERS)'; \
-- unique=`for i in $$list; do echo $$i; done | \
-- awk ' { files[$$0] = 1; } \
-- END { for (i in files) print i; }'`; \
-- test -z "$(ETAGS_ARGS)$$unique$(LISP)$$tags" \
-- || (cd $(srcdir) && etags -o $$here/TAGS $(ETAGS_ARGS) $$tags $$unique $(LISP))
--
--mostlyclean-tags:
--
--clean-tags:
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ shift; \
-+ if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
-+ test -n "$$unique" || unique=$$empty_fix; \
-+ if test $$# -gt 0; then \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ "$$@" $$unique; \
-+ else \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ $$unique; \
-+ fi; \
-+ fi
-+ctags: CTAGS
-+CTAGS: ctags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ test -z "$(CTAGS_ARGS)$$unique" \
-+ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-+ $$unique
-+
-+GTAGS:
-+ here=`$(am__cd) $(top_builddir) && pwd` \
-+ && $(am__cd) $(top_srcdir) \
-+ && gtags -i $(GTAGS_ARGS) "$$here"
-
- distclean-tags:
-- -rm -f TAGS ID
--
--maintainer-clean-tags:
--
--distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
--
--subdir = test
-+ -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-
- distdir: $(DISTFILES)
-- @for file in $(DISTFILES); do \
-- d=$(srcdir); \
-+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ list='$(DISTFILES)'; \
-+ dist_files=`for file in $$list; do echo $$file; done | \
-+ sed -e "s|^$$srcdirstrip/||;t" \
-+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-+ case $$dist_files in \
-+ */*) $(MKDIR_P) `echo "$$dist_files" | \
-+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-+ sort -u` ;; \
-+ esac; \
-+ for file in $$dist_files; do \
-+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
- if test -d $$d/$$file; then \
-- cp -pr $$d/$$file $(distdir)/$$file; \
-+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-+ if test -d "$(distdir)/$$file"; then \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
- else \
-- test -f $(distdir)/$$file \
-- || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
-- || cp -p $$d/$$file $(distdir)/$$file || :; \
-+ test -f "$(distdir)/$$file" \
-+ || cp -p $$d/$$file "$(distdir)/$$file" \
-+ || exit 1; \
- fi; \
- done
-- for subdir in $(SUBDIRS); do \
-+ @list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
- if test "$$subdir" = .; then :; else \
-- test -d $(distdir)/$$subdir \
-- || mkdir $(distdir)/$$subdir \
-+ test -d "$(distdir)/$$subdir" \
-+ || $(MKDIR_P) "$(distdir)/$$subdir" \
- || exit 1; \
-- chmod 777 $(distdir)/$$subdir; \
-- (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir=../$(top_distdir) distdir=../$(distdir)/$$subdir distdir) \
-+ fi; \
-+ done
-+ @list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
-+ if test "$$subdir" = .; then :; else \
-+ dir1=$$subdir; dir2="$(distdir)/$$subdir"; \
-+ $(am__relativize); \
-+ new_distdir=$$reldir; \
-+ dir1=$$subdir; dir2="$(top_distdir)"; \
-+ $(am__relativize); \
-+ new_top_distdir=$$reldir; \
-+ echo " (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir="$$new_top_distdir" distdir="$$new_distdir" \\"; \
-+ echo " am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)"; \
-+ ($(am__cd) $$subdir && \
-+ $(MAKE) $(AM_MAKEFLAGS) \
-+ top_distdir="$$new_top_distdir" \
-+ distdir="$$new_distdir" \
-+ am__remove_distdir=: \
-+ am__skip_length_check=: \
-+ am__skip_mode_fix=: \
-+ distdir) \
- || exit 1; \
- fi; \
- done
--info-am:
--info: info-recursive
--dvi-am:
--dvi: dvi-recursive
- check-am: all-am
- check: check-recursive
--installcheck-am:
--installcheck: installcheck-recursive
--install-exec-am:
-+all-am: Makefile
-+installdirs: installdirs-recursive
-+installdirs-am:
-+install: install-recursive
- install-exec: install-exec-recursive
--
--install-data-am:
- install-data: install-data-recursive
-+uninstall: uninstall-recursive
-
- install-am: all-am
- @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
--install: install-recursive
--uninstall-am:
--uninstall: uninstall-recursive
--all-am: Makefile
--all-redirect: all-recursive
--install-strip:
-- $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
--installdirs: installdirs-recursive
--installdirs-am:
--
-
-+installcheck: installcheck-recursive
-+install-strip:
-+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-+ `test -z '$(STRIP)' || \
-+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
- mostlyclean-generic:
-
- clean-generic:
-
- distclean-generic:
-- -rm -f Makefile $(CONFIG_CLEAN_FILES)
-- -rm -f config.cache config.log stamp-h stamp-h[0-9]*
-+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
- maintainer-clean-generic:
-+ @echo "This command is intended for maintainers to use"
-+ @echo "it deletes files that may require special tools to rebuild."
- -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
--mostlyclean-am: mostlyclean-tags mostlyclean-generic
-+clean: clean-recursive
-
--mostlyclean: mostlyclean-recursive
-+clean-am: clean-generic mostlyclean-am
-
--clean-am: clean-tags clean-generic mostlyclean-am
-+distclean: distclean-recursive
-+ -rm -f Makefile
-+distclean-am: clean-am distclean-generic distclean-tags
-
--clean: clean-recursive
-+dvi: dvi-recursive
-
--distclean-am: distclean-tags distclean-generic clean-am
-+dvi-am:
-
--distclean: distclean-recursive
-+html: html-recursive
-
--maintainer-clean-am: maintainer-clean-tags maintainer-clean-generic \
-- distclean-am
-- @echo "This command is intended for maintainers to use;"
-- @echo "it deletes files that may require special tools to rebuild."
-+html-am:
-+
-+info: info-recursive
-+
-+info-am:
-+
-+install-data-am:
-+
-+install-dvi: install-dvi-recursive
-+
-+install-dvi-am:
-+
-+install-exec-am:
-+
-+install-html: install-html-recursive
-+
-+install-html-am:
-+
-+install-info: install-info-recursive
-+
-+install-info-am:
-+
-+install-man:
-+
-+install-pdf: install-pdf-recursive
-+
-+install-pdf-am:
-+
-+install-ps: install-ps-recursive
-+
-+install-ps-am:
-+
-+installcheck-am:
-
- maintainer-clean: maintainer-clean-recursive
-+ -rm -f Makefile
-+maintainer-clean-am: distclean-am maintainer-clean-generic
-+
-+mostlyclean: mostlyclean-recursive
-+
-+mostlyclean-am: mostlyclean-generic
-+
-+pdf: pdf-recursive
-+
-+pdf-am:
-+
-+ps: ps-recursive
-+
-+ps-am:
-+
-+uninstall-am:
-+
-+.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) ctags-recursive \
-+ install-am install-strip tags-recursive
-
--.PHONY: install-data-recursive uninstall-data-recursive \
--install-exec-recursive uninstall-exec-recursive installdirs-recursive \
--uninstalldirs-recursive all-recursive check-recursive \
--installcheck-recursive info-recursive dvi-recursive \
--mostlyclean-recursive distclean-recursive clean-recursive \
--maintainer-clean-recursive tags tags-recursive mostlyclean-tags \
--distclean-tags clean-tags maintainer-clean-tags distdir info-am info \
--dvi-am dvi check check-am installcheck-am installcheck install-exec-am \
--install-exec install-data-am install-data install-am install \
--uninstall-am uninstall all-redirect all-am all installdirs-am \
--installdirs mostlyclean-generic distclean-generic clean-generic \
--maintainer-clean-generic clean mostlyclean distclean maintainer-clean
-+.PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
-+ all all-am check check-am clean clean-generic ctags \
-+ ctags-recursive distclean distclean-generic distclean-tags \
-+ distdir dvi dvi-am html html-am info info-am install \
-+ install-am install-data install-data-am install-dvi \
-+ install-dvi-am install-exec install-exec-am install-html \
-+ install-html-am install-info install-info-am install-man \
-+ install-pdf install-pdf-am install-ps install-ps-am \
-+ install-strip installcheck installcheck-am installdirs \
-+ installdirs-am maintainer-clean maintainer-clean-generic \
-+ mostlyclean mostlyclean-generic pdf pdf-am ps ps-am tags \
-+ tags-recursive uninstall uninstall-am
-
-
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -ubrN exonerate-2.2.0.orig/test/util/Makefile.in exonerate-2.2.0/test/util/Makefile.in
---- exonerate-2.2.0.orig/test/util/Makefile.in 2008-10-17 12:04:49.000000000 +0200
-+++ exonerate-2.2.0/test/util/Makefile.in 2011-12-12 13:33:17.000000000 +0100
-@@ -1,6 +1,9 @@
--# Makefile.in generated automatically by automake 1.4-p6 from Makefile.am
-+# Makefile.in generated by automake 1.11.1 from Makefile.am.
-+# @configure_input@
-
--# Copyright (C) 1994, 1995-8, 1999, 2001 Free Software Foundation, Inc.
-+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
-+# Inc.
- # This Makefile.in is free software; the Free Software Foundation
- # gives unlimited permission to copy and/or distribute it,
- # with or without modifications, as long as this notice is preserved.
-@@ -10,205 +13,427 @@
- # even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- # PARTICULAR PURPOSE.
-
--
--SHELL = @SHELL@
--
--srcdir = @srcdir@
--top_srcdir = @top_srcdir@
-+ at SET_MAKE@
- VPATH = @srcdir@
--prefix = @prefix@
--exec_prefix = @exec_prefix@
--
--bindir = @bindir@
--sbindir = @sbindir@
--libexecdir = @libexecdir@
--datadir = @datadir@
--sysconfdir = @sysconfdir@
--sharedstatedir = @sharedstatedir@
--localstatedir = @localstatedir@
--libdir = @libdir@
--infodir = @infodir@
--mandir = @mandir@
--includedir = @includedir@
--oldincludedir = /usr/include
--
--DESTDIR =
--
- pkgdatadir = $(datadir)/@PACKAGE@
--pkglibdir = $(libdir)/@PACKAGE@
- pkgincludedir = $(includedir)/@PACKAGE@
--
--top_builddir = ../..
--
--ACLOCAL = @ACLOCAL@
--AUTOCONF = @AUTOCONF@
--AUTOMAKE = @AUTOMAKE@
--AUTOHEADER = @AUTOHEADER@
--
--INSTALL = @INSTALL@
--INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
--INSTALL_DATA = @INSTALL_DATA@
--INSTALL_SCRIPT = @INSTALL_SCRIPT@
--transform = @program_transform_name@
--
-+pkglibdir = $(libdir)/@PACKAGE@
-+pkglibexecdir = $(libexecdir)/@PACKAGE@
-+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-+install_sh_DATA = $(install_sh) -c -m 644
-+install_sh_PROGRAM = $(install_sh) -c
-+install_sh_SCRIPT = $(install_sh) -c
-+INSTALL_HEADER = $(INSTALL_DATA)
-+transform = $(program_transform_name)
- NORMAL_INSTALL = :
- PRE_INSTALL = :
- POST_INSTALL = :
- NORMAL_UNINSTALL = :
- PRE_UNINSTALL = :
- POST_UNINSTALL = :
--host_alias = @host_alias@
-+build_triplet = @build@
- host_triplet = @host@
-+subdir = test/util
-+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
-+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-+am__aclocal_m4_deps = $(top_srcdir)/configure.in
-+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-+ $(ACLOCAL_M4)
-+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
-+CONFIG_CLEAN_FILES =
-+CONFIG_CLEAN_VPATH_FILES =
-+SOURCES =
-+DIST_SOURCES =
-+am__tty_colors = \
-+red=; grn=; lgn=; blu=; std=
-+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-+ACLOCAL = @ACLOCAL@
-+AMTAR = @AMTAR@
-+AUTOCONF = @AUTOCONF@
-+AUTOHEADER = @AUTOHEADER@
-+AUTOMAKE = @AUTOMAKE@
-+AWK = @AWK@
- CC = @CC@
-+CCDEPMODE = @CCDEPMODE@
-+CFLAGS = @CFLAGS@
-+CPP = @CPP@
-+CPPFLAGS = @CPPFLAGS@
-+CYGPATH_W = @CYGPATH_W@
-+DEFS = @DEFS@
-+DEPDIR = @DEPDIR@
-+ECHO_C = @ECHO_C@
-+ECHO_N = @ECHO_N@
-+ECHO_T = @ECHO_T@
-+EGREP = @EGREP@
-+EXEEXT = @EXEEXT@
- GLIB_CONFIG = @GLIB_CONFIG@
--HAVE_LIB = @HAVE_LIB@
--LIB = @LIB@
--LTLIB = @LTLIB@
-+GREP = @GREP@
-+INSTALL = @INSTALL@
-+INSTALL_DATA = @INSTALL_DATA@
-+INSTALL_PROGRAM = @INSTALL_PROGRAM@
-+INSTALL_SCRIPT = @INSTALL_SCRIPT@
-+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-+LDFLAGS = @LDFLAGS@
-+LIBOBJS = @LIBOBJS@
-+LIBS = @LIBS@
-+LTLIBOBJS = @LTLIBOBJS@
- MAKEINFO = @MAKEINFO@
-+MKDIR_P = @MKDIR_P@
-+OBJEXT = @OBJEXT@
- PACKAGE = @PACKAGE@
-+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-+PACKAGE_NAME = @PACKAGE_NAME@
-+PACKAGE_STRING = @PACKAGE_STRING@
-+PACKAGE_TARNAME = @PACKAGE_TARNAME@
-+PACKAGE_URL = @PACKAGE_URL@
-+PACKAGE_VERSION = @PACKAGE_VERSION@
-+PATH_SEPARATOR = @PATH_SEPARATOR@
- PKG_CONFIG = @PKG_CONFIG@
-+SET_MAKE = @SET_MAKE@
-+SHELL = @SHELL@
-+STRIP = @STRIP@
- VERSION = @VERSION@
-+abs_builddir = @abs_builddir@
-+abs_srcdir = @abs_srcdir@
-+abs_top_builddir = @abs_top_builddir@
-+abs_top_srcdir = @abs_top_srcdir@
-+ac_ct_CC = @ac_ct_CC@
-+am__include = @am__include@
-+am__leading_dot = @am__leading_dot@
-+am__quote = @am__quote@
-+am__tar = @am__tar@
-+am__untar = @am__untar@
-+bindir = @bindir@
-+build = @build@
-+build_alias = @build_alias@
-+build_cpu = @build_cpu@
-+build_os = @build_os@
-+build_vendor = @build_vendor@
-+builddir = @builddir@
- codegen_extra_ldadd = @codegen_extra_ldadd@
- codegen_extra_sources = @codegen_extra_sources@
-+datadir = @datadir@
- datarootdir = @datarootdir@
-+docdir = @docdir@
-+dvidir = @dvidir@
-+exec_prefix = @exec_prefix@
- glib_cflags = @glib_cflags@
- glib_libs = @glib_libs@
- host = @host@
-+host_alias = @host_alias@
-+host_cpu = @host_cpu@
-+host_os = @host_os@
-+host_vendor = @host_vendor@
-+htmldir = @htmldir@
-+includedir = @includedir@
-+infodir = @infodir@
-+install_sh = @install_sh@
- installed_util_list = @installed_util_list@
-+libdir = @libdir@
-+libexecdir = @libexecdir@
-+localedir = @localedir@
-+localstatedir = @localstatedir@
-+mandir = @mandir@
-+mkdir_p = @mkdir_p@
-+oldincludedir = @oldincludedir@
-+pdfdir = @pdfdir@
-+prefix = @prefix@
-+program_transform_name = @program_transform_name@
-+psdir = @psdir@
-+sbindir = @sbindir@
-+sharedstatedir = @sharedstatedir@
- source_root_dir = @source_root_dir@
-+srcdir = @srcdir@
-+sysconfdir = @sysconfdir@
-+target_alias = @target_alias@
-+top_build_prefix = @top_build_prefix@
-+top_builddir = @top_builddir@
-+top_srcdir = @top_srcdir@
- use_pthreads = @use_pthreads@
--
--TESTS = fastaclean.test.sh fastaclip.test.sh fastacomposition.test.sh fastadiff.test.sh fastaexpode.test.sh fastaindex.fastafetch.test.sh fastalength.test.sh fastanrdb.test.sh fastaoverlap.test.sh fastarefomat.test.sh fastaremove.test.sh fastarevcomp.test.sh fastasoftmask.fastahardmask.test.sh fastasort.test.sh fastasplit.test.sh fastasubseq.test.sh fastatranslate.test.sh fastavalidcds.test.sh
--
-+TESTS = fastaclean.test.sh fastaclip.test.sh fastacomposition.test.sh \
-+ fastadiff.test.sh fastaexpode.test.sh \
-+ fastaindex.fastafetch.test.sh fastalength.test.sh \
-+ fastanrdb.test.sh fastaoverlap.test.sh fastarefomat.test.sh \
-+ fastaremove.test.sh fastarevcomp.test.sh \
-+ fastasoftmask.fastahardmask.test.sh fastasort.test.sh \
-+ fastasplit.test.sh fastasubseq.test.sh fastatranslate.test.sh \
-+ fastavalidcds.test.sh
-
- EXTRA_DIST = $(TESTS)
-
- # Files to clear away
--
- MAINTAINERCLEANFILES = Makefile.in
--mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
--CONFIG_CLEAN_FILES =
--DIST_COMMON = Makefile.am Makefile.in
--
--
--DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
-+all: all-am
-
--TAR = tar
--GZIP_ENV = --best
--all: all-redirect
- .SUFFIXES:
--$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4)
-- cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps test/util/Makefile
--
-+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
-+ @for dep in $?; do \
-+ case '$(am__configure_deps)' in \
-+ *$$dep*) \
-+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-+ && { if test -f $@; then exit 0; else break; fi; }; \
-+ exit 1;; \
-+ esac; \
-+ done; \
-+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu test/util/Makefile'; \
-+ $(am__cd) $(top_srcdir) && \
-+ $(AUTOMAKE) --gnu test/util/Makefile
-+.PRECIOUS: Makefile
- Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-- cd $(top_builddir) \
-- && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
--
-+ @case '$?' in \
-+ *config.status*) \
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-+ *) \
-+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-+ esac;
-+
-+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+
-+$(top_srcdir)/configure: $(am__configure_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
-+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-+$(am__aclocal_m4_deps):
- tags: TAGS
- TAGS:
-
-+ctags: CTAGS
-+CTAGS:
-
--distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
--
--subdir = test/util
-
--distdir: $(DISTFILES)
-- @for file in $(DISTFILES); do \
-- d=$(srcdir); \
-- if test -d $$d/$$file; then \
-- cp -pr $$d/$$file $(distdir)/$$file; \
-- else \
-- test -f $(distdir)/$$file \
-- || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
-- || cp -p $$d/$$file $(distdir)/$$file || :; \
-- fi; \
-- done
- check-TESTS: $(TESTS)
-- @failed=0; all=0; \
-+ @failed=0; all=0; xfail=0; xpass=0; skip=0; \
- srcdir=$(srcdir); export srcdir; \
-- for tst in $(TESTS); do \
-- if test -f $$tst; then dir=.; \
-- else dir="$(srcdir)"; fi; \
-- if $(TESTS_ENVIRONMENT) $$dir/$$tst; then \
-+ list=' $(TESTS) '; \
-+ $(am__tty_colors); \
-+ if test -n "$$list"; then \
-+ for tst in $$list; do \
-+ if test -f ./$$tst; then dir=./; \
-+ elif test -f $$tst; then dir=; \
-+ else dir="$(srcdir)/"; fi; \
-+ if $(TESTS_ENVIRONMENT) $${dir}$$tst; then \
- all=`expr $$all + 1`; \
-- echo "PASS: $$tst"; \
-+ case " $(XFAIL_TESTS) " in \
-+ *[\ \ ]$$tst[\ \ ]*) \
-+ xpass=`expr $$xpass + 1`; \
-+ failed=`expr $$failed + 1`; \
-+ col=$$red; res=XPASS; \
-+ ;; \
-+ *) \
-+ col=$$grn; res=PASS; \
-+ ;; \
-+ esac; \
- elif test $$? -ne 77; then \
- all=`expr $$all + 1`; \
-+ case " $(XFAIL_TESTS) " in \
-+ *[\ \ ]$$tst[\ \ ]*) \
-+ xfail=`expr $$xfail + 1`; \
-+ col=$$lgn; res=XFAIL; \
-+ ;; \
-+ *) \
- failed=`expr $$failed + 1`; \
-- echo "FAIL: $$tst"; \
-+ col=$$red; res=FAIL; \
-+ ;; \
-+ esac; \
-+ else \
-+ skip=`expr $$skip + 1`; \
-+ col=$$blu; res=SKIP; \
- fi; \
-+ echo "$${col}$$res$${std}: $$tst"; \
- done; \
-+ if test "$$all" -eq 1; then \
-+ tests="test"; \
-+ All=""; \
-+ else \
-+ tests="tests"; \
-+ All="All "; \
-+ fi; \
-+ if test "$$failed" -eq 0; then \
-+ if test "$$xfail" -eq 0; then \
-+ banner="$$All$$all $$tests passed"; \
-+ else \
-+ if test "$$xfail" -eq 1; then failures=failure; else failures=failures; fi; \
-+ banner="$$All$$all $$tests behaved as expected ($$xfail expected $$failures)"; \
-+ fi; \
-+ else \
-+ if test "$$xpass" -eq 0; then \
-+ banner="$$failed of $$all $$tests failed"; \
-+ else \
-+ if test "$$xpass" -eq 1; then passes=pass; else passes=passes; fi; \
-+ banner="$$failed of $$all $$tests did not behave as expected ($$xpass unexpected $$passes)"; \
-+ fi; \
-+ fi; \
-+ dashes="$$banner"; \
-+ skipped=""; \
-+ if test "$$skip" -ne 0; then \
-+ if test "$$skip" -eq 1; then \
-+ skipped="($$skip test was not run)"; \
-+ else \
-+ skipped="($$skip tests were not run)"; \
-+ fi; \
-+ test `echo "$$skipped" | wc -c` -le `echo "$$banner" | wc -c` || \
-+ dashes="$$skipped"; \
-+ fi; \
-+ report=""; \
-+ if test "$$failed" -ne 0 && test -n "$(PACKAGE_BUGREPORT)"; then \
-+ report="Please report to $(PACKAGE_BUGREPORT)"; \
-+ test `echo "$$report" | wc -c` -le `echo "$$banner" | wc -c` || \
-+ dashes="$$report"; \
-+ fi; \
-+ dashes=`echo "$$dashes" | sed s/./=/g`; \
- if test "$$failed" -eq 0; then \
-- banner="All $$all tests passed"; \
-+ echo "$$grn$$dashes"; \
- else \
-- banner="$$failed of $$all tests failed"; \
-+ echo "$$red$$dashes"; \
- fi; \
-- dashes=`echo "$$banner" | sed s/./=/g`; \
-- echo "$$dashes"; \
- echo "$$banner"; \
-- echo "$$dashes"; \
-- test "$$failed" -eq 0
--info-am:
--info: info-am
--dvi-am:
--dvi: dvi-am
-+ test -z "$$skipped" || echo "$$skipped"; \
-+ test -z "$$report" || echo "$$report"; \
-+ echo "$$dashes$$std"; \
-+ test "$$failed" -eq 0; \
-+ else :; fi
-+
-+distdir: $(DISTFILES)
-+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ list='$(DISTFILES)'; \
-+ dist_files=`for file in $$list; do echo $$file; done | \
-+ sed -e "s|^$$srcdirstrip/||;t" \
-+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-+ case $$dist_files in \
-+ */*) $(MKDIR_P) `echo "$$dist_files" | \
-+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-+ sort -u` ;; \
-+ esac; \
-+ for file in $$dist_files; do \
-+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
-+ if test -d $$d/$$file; then \
-+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-+ if test -d "$(distdir)/$$file"; then \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
-+ else \
-+ test -f "$(distdir)/$$file" \
-+ || cp -p $$d/$$file "$(distdir)/$$file" \
-+ || exit 1; \
-+ fi; \
-+ done
- check-am: all-am
- $(MAKE) $(AM_MAKEFLAGS) check-TESTS
- check: check-am
--installcheck-am:
--installcheck: installcheck-am
--install-exec-am:
-+all-am: Makefile
-+installdirs:
-+install: install-am
- install-exec: install-exec-am
--
--install-data-am:
- install-data: install-data-am
-+uninstall: uninstall-am
-
- install-am: all-am
- @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
--install: install-am
--uninstall-am:
--uninstall: uninstall-am
--all-am: Makefile
--all-redirect: all-am
--install-strip:
-- $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
--installdirs:
--
-
-+installcheck: installcheck-am
-+install-strip:
-+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-+ `test -z '$(STRIP)' || \
-+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
- mostlyclean-generic:
-
- clean-generic:
-
- distclean-generic:
-- -rm -f Makefile $(CONFIG_CLEAN_FILES)
-- -rm -f config.cache config.log stamp-h stamp-h[0-9]*
-+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
- maintainer-clean-generic:
-+ @echo "This command is intended for maintainers to use"
-+ @echo "it deletes files that may require special tools to rebuild."
- -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
--mostlyclean-am: mostlyclean-generic
--
--mostlyclean: mostlyclean-am
-+clean: clean-am
-
- clean-am: clean-generic mostlyclean-am
-
--clean: clean-am
-+distclean: distclean-am
-+ -rm -f Makefile
-+distclean-am: clean-am distclean-generic
-
--distclean-am: distclean-generic clean-am
-+dvi: dvi-am
-
--distclean: distclean-am
-+dvi-am:
-
--maintainer-clean-am: maintainer-clean-generic distclean-am
-- @echo "This command is intended for maintainers to use;"
-- @echo "it deletes files that may require special tools to rebuild."
-+html: html-am
-+
-+html-am:
-+
-+info: info-am
-+
-+info-am:
-+
-+install-data-am:
-+
-+install-dvi: install-dvi-am
-+
-+install-dvi-am:
-+
-+install-exec-am:
-+
-+install-html: install-html-am
-+
-+install-html-am:
-+
-+install-info: install-info-am
-+
-+install-info-am:
-+
-+install-man:
-+
-+install-pdf: install-pdf-am
-+
-+install-pdf-am:
-+
-+install-ps: install-ps-am
-+
-+install-ps-am:
-+
-+installcheck-am:
-
- maintainer-clean: maintainer-clean-am
-+ -rm -f Makefile
-+maintainer-clean-am: distclean-am maintainer-clean-generic
-+
-+mostlyclean: mostlyclean-am
-+
-+mostlyclean-am: mostlyclean-generic
-+
-+pdf: pdf-am
-+
-+pdf-am:
-+
-+ps: ps-am
-+
-+ps-am:
-+
-+uninstall-am:
-+
-+.MAKE: check-am install-am install-strip
-
--.PHONY: tags distdir check-TESTS info-am info dvi-am dvi check check-am \
--installcheck-am installcheck install-exec-am install-exec \
--install-data-am install-data install-am install uninstall-am uninstall \
--all-redirect all-am all installdirs mostlyclean-generic \
--distclean-generic clean-generic maintainer-clean-generic clean \
--mostlyclean distclean maintainer-clean
-+.PHONY: all all-am check check-TESTS check-am clean clean-generic \
-+ distclean distclean-generic distdir dvi dvi-am html html-am \
-+ info info-am install install-am install-data install-data-am \
-+ install-dvi install-dvi-am install-exec install-exec-am \
-+ install-html install-html-am install-info install-info-am \
-+ install-man install-pdf install-pdf-am install-ps \
-+ install-ps-am install-strip installcheck installcheck-am \
-+ installdirs maintainer-clean maintainer-clean-generic \
-+ mostlyclean mostlyclean-generic pdf pdf-am ps ps-am uninstall \
-+ uninstall-am
-
-
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
More information about the debian-med-commit
mailing list