[med-svn] r8915 - in trunk/packages/exonerate/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Mon Dec 12 13:13:36 UTC 2011
Author: tille
Date: 2011-12-12 13:13:36 +0000 (Mon, 12 Dec 2011)
New Revision: 8915
Added:
trunk/packages/exonerate/trunk/debian/patches/autoreconf.patch
Modified:
trunk/packages/exonerate/trunk/debian/changelog
trunk/packages/exonerate/trunk/debian/control
trunk/packages/exonerate/trunk/debian/patches/series
trunk/packages/exonerate/trunk/debian/rules
Log:
Fix build issue via autoreconf and apply this as patch; switch to short dh
Modified: trunk/packages/exonerate/trunk/debian/changelog
===================================================================
--- trunk/packages/exonerate/trunk/debian/changelog 2011-12-12 13:04:23 UTC (rev 8914)
+++ trunk/packages/exonerate/trunk/debian/changelog 2011-12-12 13:13:36 UTC (rev 8915)
@@ -14,8 +14,8 @@
(Thanks to Micah Gersten <micahg at ubuntu.com>)
Closes: #651802
* debian/rules:
- - Adding quilt to apply the patch
- - Fix clean target
+ - Convert to short dh notation
+ - Remove codegen in clean target
-- Andreas Tille <tille at debian.org> Mon, 12 Dec 2011 13:13:02 +0100
Modified: trunk/packages/exonerate/trunk/debian/control
===================================================================
--- trunk/packages/exonerate/trunk/debian/control 2011-12-12 13:04:23 UTC (rev 8914)
+++ trunk/packages/exonerate/trunk/debian/control 2011-12-12 13:13:36 UTC (rev 8915)
@@ -6,7 +6,7 @@
Uploaders: Steffen Moeller <moeller at debian.org>,
Charles Plessy <plessy at debian.org>,
Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 8), autotools-dev, libglib2.0-dev, libreadline-dev, cdbs, quilt
+Build-Depends: debhelper (>= 8), autotools-dev, libglib2.0-dev, libreadline-dev
Standards-Version: 3.9.2
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/exonerate/trunk/
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/exonerate/trunk/
Added: trunk/packages/exonerate/trunk/debian/patches/autoreconf.patch
===================================================================
--- trunk/packages/exonerate/trunk/debian/patches/autoreconf.patch (rev 0)
+++ trunk/packages/exonerate/trunk/debian/patches/autoreconf.patch 2011-12-12 13:13:36 UTC (rev 8915)
@@ -0,0 +1,29367 @@
+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 @@
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+- 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,
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++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 "$$dist_files" | \
++ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
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++installdirs: installdirs-recursive
++installdirs-am:
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+ install-exec: install-exec-recursive
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++ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+ mostlyclean-generic:
+
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+
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+- -rm -f config.cache config.log stamp-h stamp-h[0-9]*
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+
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++distclean: distclean-recursive
++ -rm -f Makefile
++distclean-am: clean-am distclean-generic distclean-tags
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++dvi: dvi-recursive
+
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++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:
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++info: info-recursive
++
++info-am:
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++install-data-am:
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++install-dvi: install-dvi-recursive
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++install-dvi-am:
++
++install-exec-am:
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++install-html: install-html-recursive
++
++install-html-am:
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++install-info: install-info-recursive
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++install-man:
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++install-pdf: install-pdf-recursive
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++install-pdf-am:
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++install-ps: install-ps-recursive
++
++install-ps-am:
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++installcheck-am:
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+ maintainer-clean: maintainer-clean-recursive
++ -rm -f Makefile
++maintainer-clean-am: distclean-am maintainer-clean-generic
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++mostlyclean: mostlyclean-recursive
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++mostlyclean-am: mostlyclean-generic
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++pdf: pdf-recursive
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++ps-am:
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++.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@
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+-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@
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++am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
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++INSTALL_HEADER = $(INSTALL_DATA)
++transform = $(program_transform_name)
+ NORMAL_INSTALL = :
+ PRE_INSTALL = :
+ POST_INSTALL = :
+ NORMAL_UNINSTALL = :
+ PRE_UNINSTALL = :
+ POST_UNINSTALL = :
+-host_alias = @host_alias@
++build_triplet = @build@
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++RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
++ html-recursive info-recursive install-data-recursive \
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++ while test -n "$$dir1"; do \
++ first=`echo "$$dir1" | sed -e "$$sed_first"`; \
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++ dir2=`echo "$$dir2" | sed -e "$$sed_rest"`; \
++ else \
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++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) $(top_srcdir)/mkinstalldirs
+-CONFIG_CLEAN_FILES =
+-DIST_COMMON = Makefile.am Makefile.in
+-
++all: all-recursive
+
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+-
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+-GZIP_ENV = --best
+-all: all-redirect
+ .SUFFIXES:
+-$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4)
+- cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps doc/man/Makefile
+-
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++ @for dep in $?; do \
++ case '$(am__configure_deps)' in \
++ *$$dep*) \
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++ exit 1;; \
++ esac; \
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++ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu doc/man/Makefile'; \
++ $(am__cd) $(top_srcdir) && \
++ $(AUTOMAKE) --gnu doc/man/Makefile
++.PRECIOUS: Makefile
+ Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+- cd $(top_builddir) \
+- && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
+-
++ @case '$?' in \
++ *config.status*) \
++ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
++ *) \
++ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
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++ esac;
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++ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
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++ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
++$(ACLOCAL_M4): $(am__aclocal_m4_deps)
++ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
++$(am__aclocal_m4_deps):
+
+ # This directory's subdirectories are mostly independent; you can cd
+ # into them and run `make' without going through this Makefile.
+@@ -106,13 +230,14 @@
+ # (1) if the variable is set in `config.status', edit `config.status'
+ # (which will cause the Makefiles to be regenerated when you run `make');
+ # (2) otherwise, pass the desired values on the `make' command line.
+-
+- at SET_MAKE@
+-
+-all-recursive install-data-recursive install-exec-recursive \
+-installdirs-recursive install-recursive uninstall-recursive \
+-check-recursive installcheck-recursive info-recursive dvi-recursive:
+- @set fnord $(MAKEFLAGS); amf=$$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 "$$fail"
+
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+-maintainer-clean-recursive:
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++$(RECURSIVE_CLEAN_TARGETS):
++ @fail= failcom='exit 1'; \
++ for f in x $$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 "$$fail"
+ tags-recursive:
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+- test "$$subdir" = . || (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
++ test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
++ done
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++ test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \
+ done
+
++ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
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++ if test -f "$$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
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+ # 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 @@
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++++ exonerate-2.2.0/Makefile.in 2011-12-12 13:33:17.000000000 +0100
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++ *) \
++ 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@
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+-
++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)
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++CONFIG_CLEAN_VPATH_FILES =
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++ hpair.test$(EXEEXT) sar.test$(EXEEXT)
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++ $(top_srcdir)/src/struct/pqueue.o \
++ $(top_srcdir)/src/struct/recyclebin.o
++am_heuristic_test_OBJECTS = heuristic.test.$(OBJEXT) \
++ heuristic.$(OBJEXT)
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++ $(top_srcdir)/src/struct/matrix.o \
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++ $(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)
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++ $(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)
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++ $(top_srcdir)/src/struct/recyclebin.o \
++ $(top_srcdir)/src/struct/rangetree.o $(am__DEPENDENCIES_2)
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++SOURCES = $(bsdp_test_SOURCES) $(heuristic_test_SOURCES) \
++ $(hpair_test_SOURCES) $(sar_test_SOURCES)
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++AUTOHEADER = @AUTOHEADER@
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+ CC = @CC@
++CCDEPMODE = @CCDEPMODE@
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++CPPFLAGS = @CPPFLAGS@
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++ECHO_N = @ECHO_N@
++ECHO_T = @ECHO_T@
++EGREP = @EGREP@
++EXEEXT = @EXEEXT@
+ GLIB_CONFIG = @GLIB_CONFIG@
+-HAVE_LIB = @HAVE_LIB@
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+ PKG_CONFIG = @PKG_CONFIG@
++SET_MAKE = @SET_MAKE@
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+ VERSION = @VERSION@
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++build_vendor = @build_vendor@
++builddir = @builddir@
+ codegen_extra_ldadd = @codegen_extra_ldadd@
+ codegen_extra_sources = @codegen_extra_sources@
++datadir = @datadir@
+ datarootdir = @datarootdir@
++docdir = @docdir@
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+ glib_cflags = @glib_cflags@
+ glib_libs = @glib_libs@
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+ installed_util_list = @installed_util_list@
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++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;; \
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+ distclean-tags:
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+ # 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 @@
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++# 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@
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++ $(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) \
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+
+
+ # 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@
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+-
++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
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++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 = $(am__EXEEXT_1)
++subdir = src/comparison
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++CONFIG_CLEAN_VPATH_FILES =
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++ pcr.test$(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)
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++ $(top_srcdir)/src/struct/matrix.o \
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++ $(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) \
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++ $(top_srcdir)/src/struct/recyclebin.o $(am__DEPENDENCIES_1)
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++ $(top_srcdir)/src/sequence/codonsubmat.o $(am__DEPENDENCIES_1)
++am_pcr_test_OBJECTS = pcr.test.$(OBJEXT) pcr.$(OBJEXT) \
++ wordhood.$(OBJEXT)
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++ $(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) \
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++seeder_test_OBJECTS = $(am_seeder_test_OBJECTS)
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++ $(top_srcdir)/src/sequence/codonsubmat.o \
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++ $(top_srcdir)/src/struct/fsm.o $(top_srcdir)/src/struct/vfsm.o \
++ $(top_srcdir)/src/struct/pqueue.o $(am__DEPENDENCIES_1)
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++ $(top_srcdir)/src/sequence/codonsubmat.o $(am__DEPENDENCIES_1)
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++ $(match_test_SOURCES) $(pcr_test_SOURCES) \
++ $(seeder_test_SOURCES) $(wordhood_test_SOURCES)
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++ $(match_test_SOURCES) $(pcr_test_SOURCES) \
++ $(seeder_test_SOURCES) $(wordhood_test_SOURCES)
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++AUTOHEADER = @AUTOHEADER@
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++AWK = @AWK@
+ CC = @CC@
++CCDEPMODE = @CCDEPMODE@
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++CPPFLAGS = @CPPFLAGS@
++CYGPATH_W = @CYGPATH_W@
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++ECHO_N = @ECHO_N@
++ECHO_T = @ECHO_T@
++EGREP = @EGREP@
++EXEEXT = @EXEEXT@
+ GLIB_CONFIG = @GLIB_CONFIG@
+-HAVE_LIB = @HAVE_LIB@
+-LIB = @LIB@
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++INSTALL = @INSTALL@
++INSTALL_DATA = @INSTALL_DATA@
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++LIBS = @LIBS@
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+ MAKEINFO = @MAKEINFO@
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++PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
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++PACKAGE_TARNAME = @PACKAGE_TARNAME@
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++PATH_SEPARATOR = @PATH_SEPARATOR@
+ PKG_CONFIG = @PKG_CONFIG@
++SET_MAKE = @SET_MAKE@
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++STRIP = @STRIP@
+ VERSION = @VERSION@
++abs_builddir = @abs_builddir@
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+ codegen_extra_ldadd = @codegen_extra_ldadd@
+ codegen_extra_sources = @codegen_extra_sources@
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+ glib_cflags = @glib_cflags@
+ glib_libs = @glib_libs@
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++htmldir = @htmldir@
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+ installed_util_list = @installed_util_list@
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++libexecdir = @libexecdir@
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++prefix = @prefix@
++program_transform_name = @program_transform_name@
++psdir = @psdir@
++sbindir = @sbindir@
++sharedstatedir = @sharedstatedir@
+ source_root_dir = @source_root_dir@
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++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)
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+ # 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@
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+-
+-DESTDIR =
+-
+ pkgdatadir = $(datadir)/@PACKAGE@
+-pkglibdir = $(libdir)/@PACKAGE@
+ pkgincludedir = $(includedir)/@PACKAGE@
+-
+-top_builddir = ../..
+-
+-ACLOCAL = @ACLOCAL@
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+-
+-INSTALL = @INSTALL@
+-INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
+-INSTALL_DATA = @INSTALL_DATA@
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+-
++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)
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++fastadb_test_DEPENDENCIES = $(top_srcdir)/src/general/compoundfile.o \
++ $(am__DEPENDENCIES_1)
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++ fastapipe.$(OBJEXT)
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++ $(top_srcdir)/src/general/compoundfile.o $(am__DEPENDENCIES_1)
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++ $(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 \
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++ $(top_srcdir)/src/sequence/codonsubmat.o $(am__DEPENDENCIES_1)
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++ $(fastapipe_test_SOURCES) $(index_test_SOURCES)
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++ $(fastapipe_test_SOURCES) $(index_test_SOURCES)
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++red=; grn=; lgn=; blu=; std=
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+ CC = @CC@
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++EGREP = @EGREP@
++EXEEXT = @EXEEXT@
+ GLIB_CONFIG = @GLIB_CONFIG@
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+ MAKEINFO = @MAKEINFO@
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++PACKAGE_VERSION = @PACKAGE_VERSION@
++PATH_SEPARATOR = @PATH_SEPARATOR@
+ PKG_CONFIG = @PKG_CONFIG@
++SET_MAKE = @SET_MAKE@
++SHELL = @SHELL@
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+ VERSION = @VERSION@
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++builddir = @builddir@
+ codegen_extra_ldadd = @codegen_extra_ldadd@
+ codegen_extra_sources = @codegen_extra_sources@
++datadir = @datadir@
+ datarootdir = @datarootdir@
++docdir = @docdir@
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++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@
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++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@
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++ 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
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+ # 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@
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++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@
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++ 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 $(LISP))
+-
+-mostlyclean-tags:
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++ list='$(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; \
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++ $(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; } \
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++ 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 ./$$tst; then dir=./; \
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++ else dir="$(srcdir)/"; fi; \
++ if $(TESTS_ENVIRONMENT) $${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; \
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++ 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 "$$xfail" -eq 0; then \
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++ if test "$$skip" -eq 1; then \
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++ dashes="$$skipped"; \
++ fi; \
++ report=""; \
++ if test "$$failed" -ne 0 && test -n "$(PACKAGE_BUGREPORT)"; then \
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++ dashes="$$report"; \
++ fi; \
++ dashes=`echo "$$dashes" | sed s/./=/g`; \
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++ for file in $$dist_files; do \
++ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
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++ 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 \
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+
+
+ # 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 @@
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++# Makefile.in generated by automake 1.11.1 from Makefile.am.
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+
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++# 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 @@
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+-
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+-
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++ -I$(top_srcdir)/src/database \
++ -I$(top_srcdir)/src/comparison \
++ -I$(top_srcdir)/src/struct \
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++ -I$(top_srcdir)/src/general \
++ -DHOSTTYPE="\"@host@\"" \
++ -DSOURCE_ROOT_DIR="\"@source_root_dir@\""
+
+ noinst_HEADERS = gam.h analysis.h bsam.h
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+-
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++ $(top_srcdir)/src/c4/codegen.o \
++ $(top_srcdir)/src/c4/cgutil.o \
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++ $(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 \
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++ $(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 \
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++ $(top_srcdir)/src/sequence/codonsubmat.o \
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++ $(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 $(subdir)/$@ $(am__depfiles_maybe);; \
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++
++$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
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++
++$(top_srcdir)/configure: $(am__configure_deps)
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++ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
++$(am__aclocal_m4_deps):
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+ clean-noinstPROGRAMS:
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+-
+-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) $(bsam_test_DEPENDENCIES)
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++ @rm -f gam.test$(EXEEXT)
++ $(LINK) $(gam_test_OBJECTS) $(gam_test_LDADD) $(LIBS)
+
+ mostlyclean-compile:
+- -rm -f *.o core *.core
+-
+-clean-compile:
++ -rm -f *.$(OBJEXT)
+
+ distclean-compile:
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+
+-maintainer-clean-compile:
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+-gam.test: $(gam_test_OBJECTS) $(gam_test_DEPENDENCIES)
+- @rm -f gam.test
+- $(LINK) $(gam_test_LDFLAGS) $(gam_test_OBJECTS) $(gam_test_LDADD) $(LIBS)
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+-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@
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++ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gam.test.Po at am__quote@
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++.c.o:
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++ 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
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+-installcheck: installcheck-am
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++all-am: Makefile $(PROGRAMS) $(HEADERS)
++installdirs:
++install: install-am
+ install-exec: install-exec-am
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+
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++ $(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
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+
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+- 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:
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++install-dvi: install-dvi-am
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++install-dvi-am:
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++install-exec-am:
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++install-html: install-html-am
++
++install-html-am:
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++install-info: install-info-am
++
++install-info-am:
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++install-man:
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++install-pdf: install-pdf-am
++
++install-pdf-am:
++
++install-ps: install-ps-am
++
++install-ps-am:
++
++installcheck-am:
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+ 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
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++pdf: pdf-am
++
++pdf-am:
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++ps: ps-am
++
++ps-am:
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++uninstall-am:
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++.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
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++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 \
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++am__relativize = \
++ dir0=`pwd`; \
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++ 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"`; \
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++AMTAR = @AMTAR@
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+ GLIB_CONFIG = @GLIB_CONFIG@
+-HAVE_LIB = @HAVE_LIB@
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++LDFLAGS = @LDFLAGS@
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+ MAKEINFO = @MAKEINFO@
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++OBJEXT = @OBJEXT@
+ PACKAGE = @PACKAGE@
++PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
++PACKAGE_NAME = @PACKAGE_NAME@
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++PACKAGE_TARNAME = @PACKAGE_TARNAME@
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++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@
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++builddir = @builddir@
+ codegen_extra_ldadd = @codegen_extra_ldadd@
+ codegen_extra_sources = @codegen_extra_sources@
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++docdir = @docdir@
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+ glib_cflags = @glib_cflags@
+ glib_libs = @glib_libs@
+ host = @host@
++host_alias = @host_alias@
++host_cpu = @host_cpu@
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++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@
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++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) $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
++ done
++ctags-recursive:
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++ test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \
+ done
+
++ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
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++ unique=`for i in $$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 $$# -gt 0; then \
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++ "$$@" $$unique; \
++ else \
++ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
++ $$unique; \
++ fi; \
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++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 \
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+
+
+ # 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@
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+-transform = @program_transform_name@
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++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 \
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+-$(top_srcdir)/src/struct/recyclebin.o \
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+-$(top_srcdir)/src/sequence/alphabet.o \
+-$(top_srcdir)/src/sequence/translate.o \
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+-$(top_srcdir)/src/sequence/codonsubmat.o \
+-$(top_srcdir)/src/general/compoundfile.o \
+-$(top_srcdir)/src/general/lineparse.o
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++ $(MAKE) $(AM_MAKEFLAGS) all-am
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+-OBJECTS = $(exonerate_OBJECTS) $(ipcress_OBJECTS) $(exonerate_server_OBJECTS)
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+-all: all-redirect
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++ @for dep in $?; do \
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++ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
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++ $(AUTOMAKE) --gnu src/program/Makefile
++.PRECIOUS: Makefile
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+-
+-mostlyclean-binPROGRAMS:
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+-clean-binPROGRAMS:
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++ *) \
++ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
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++ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
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++ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
++$(am__aclocal_m4_deps):
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+ @$(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/$$/$(EXEEXT)/'`; \
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+- done
++ test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)"
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++ for p in $$list; do echo "$$p $$p"; done | \
++ sed 's/$(EXEEXT)$$//' | \
++ while read p p1; do if test -f $$p; \
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++ 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; \
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++ 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; \
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++ 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)' \
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++ test -n "$$list" || exit 0; \
++ echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
++ cd "$(DESTDIR)$(bindir)" && rm -f $$files
+
+-.c.o:
+- $(COMPILE) -c $<
+-
+-.s.o:
+- $(COMPILE) -c $<
+-
+-.S.o:
+- $(COMPILE) -c $<
++clean-binPROGRAMS:
++ -test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
++exonerate$(EXEEXT): $(exonerate_OBJECTS) $(exonerate_DEPENDENCIES)
++ @rm -f exonerate$(EXEEXT)
++ $(LINK) $(exonerate_OBJECTS) $(exonerate_LDADD) $(LIBS)
++exonerate-server$(EXEEXT): $(exonerate_server_OBJECTS) $(exonerate_server_DEPENDENCIES)
++ @rm -f exonerate-server$(EXEEXT)
++ $(LINK) $(exonerate_server_OBJECTS) $(exonerate_server_LDADD) $(LIBS)
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++ @rm -f ipcress$(EXEEXT)
++ $(LINK) $(ipcress_OBJECTS) $(ipcress_LDADD) $(LIBS)
+
+ mostlyclean-compile:
+- -rm -f *.o core *.core
+-
+-clean-compile:
++ -rm -f *.$(OBJEXT)
+
+ distclean-compile:
+ -rm -f *.tab.c
+
+-maintainer-clean-compile:
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+-exonerate: $(exonerate_OBJECTS) $(exonerate_DEPENDENCIES)
+- @rm -f exonerate
+- $(LINK) $(exonerate_LDFLAGS) $(exonerate_OBJECTS) $(exonerate_LDADD) $(LIBS)
+-
+-ipcress: $(ipcress_OBJECTS) $(ipcress_DEPENDENCIES)
+- @rm -f ipcress
+- $(LINK) $(ipcress_LDFLAGS) $(ipcress_OBJECTS) $(ipcress_LDADD) $(LIBS)
+-
+-exonerate-server: $(exonerate_server_OBJECTS) $(exonerate_server_DEPENDENCIES)
+- @rm -f exonerate-server
+- $(LINK) $(exonerate_server_LDFLAGS) $(exonerate_server_OBJECTS) $(exonerate_server_LDADD) $(LIBS)
++ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/exonerate-server.Po at am__quote@
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++.c.o:
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++ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
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++ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
++ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
++ unique=`for i in $$list; do \
++ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
++ done | \
++ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
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++ mkid -fID $$unique
+ tags: TAGS
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+-ID: $(HEADERS) $(SOURCES) $(LISP)
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+- awk ' { files[$$0] = 1; } \
+- END { for (i in files) print i; }'`; \
+- here=`pwd` && cd $(srcdir) \
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+-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) $(LISP)
+- tags=; \
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++ set x; \
+ here=`pwd`; \
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+- unique=`for i in $$list; do echo $$i; done | \
+- awk ' { files[$$0] = 1; } \
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+- test -z "$(ETAGS_ARGS)$$unique$(LISP)$$tags" \
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+-mostlyclean-tags:
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++ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
++ unique=`for i in $$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; }; }'`; \
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++ $(TAGS_FILES) $(LISP)
++ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
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++ here=`$(am__cd) $(top_builddir) && pwd` \
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+
+ distclean-tags:
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+-maintainer-clean-tags:
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+-distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
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+-subdir = src/program
++ -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
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+ distdir: $(DISTFILES)
+- @for file in $(DISTFILES); do \
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++ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
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++ */*) $(MKDIR_P) `echo "$$dist_files" | \
++ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
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++ for file in $$dist_files; do \
++ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+ if test -d $$d/$$file; then \
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++ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
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++ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
++ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
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++ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
+ else \
+- test -f $(distdir)/$$file \
+- || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
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++ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+ mostlyclean-generic:
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+ clean-generic:
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+
+ distclean-generic:
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+- -rm -f config.cache config.log stamp-h stamp-h[0-9]*
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+ c4_model_archive.h: $(BOOTSTRAPPER)
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+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@
+
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+-top_srcdir = @top_srcdir@
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+-prefix = @prefix@
+-exec_prefix = @exec_prefix@
+-
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+-sbindir = @sbindir@
+-libexecdir = @libexecdir@
+-datadir = @datadir@
+-sysconfdir = @sysconfdir@
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+-localstatedir = @localstatedir@
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+-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@
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+-INSTALL = @INSTALL@
+-INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
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++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
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++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@
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++am__include = @am__include@
++am__leading_dot = @am__leading_dot@
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++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)
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+ # 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 @@
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++# Makefile.in generated by automake 1.11.1 from Makefile.am.
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++# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
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+ # This Makefile.in is free software; the Free Software Foundation
+ # gives unlimited permission to copy and/or distribute it,
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+@@ -10,359 +13,599 @@
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++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
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++ $(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)
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++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@
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++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; \
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+--- 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 @@
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++# 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,
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+ # This Makefile.in is free software; the Free Software Foundation
+ # gives unlimited permission to copy and/or distribute it,
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+@@ -10,401 +13,653 @@
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+
++ at SET_MAKE@
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+ rangetree_test_SOURCES = rangetree.test.c rangetree.c
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+ sparsecache_test_SOURCES = sparsecache.test.c sparsecache.c
+ dejavu_test_SOURCES = dejavu.test.c dejavu.c
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+--- 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 @@
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++# 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@
+-
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++transform = $(program_transform_name)
+ NORMAL_INSTALL = :
+ PRE_INSTALL = :
+ POST_INSTALL = :
+ NORMAL_UNINSTALL = :
+ PRE_UNINSTALL = :
+ POST_UNINSTALL = :
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++build_triplet = @build@
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+-
+-
+-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
+-
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+-
+-
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+-
+-
+-EXTRA_fastavalidcds_SOURCES = fastavalidcds.c
+-
+-# Files to clear away
+-
+-MAINTAINERCLEANFILES = Makefile.in
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++ fastachecksum$(EXEEXT) fastacomposition$(EXEEXT) \
++ fastadiff$(EXEEXT) fastaexplode$(EXEEXT) fastafetch$(EXEEXT) \
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++ fastarevcomp$(EXEEXT) fastasoftmask$(EXEEXT) \
++ fastasort$(EXEEXT) fastasplit$(EXEEXT) fastasubseq$(EXEEXT) \
++ fastatranslate$(EXEEXT) fastavalidcds$(EXEEXT) \
++ fasta2esd$(EXEEXT) fastaannotatecdna$(EXEEXT) esd2esi$(EXEEXT)
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+-
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++ $(top_srcdir)/src/database/fastadb.o \
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++ $(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 \
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++am_fasta2esd_OBJECTS = fasta2esd.$(OBJEXT)
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++ $(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 \
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+-$(top_srcdir)/src/sequence/translate.o \
+-$(top_srcdir)/src/database/fastadb.o \
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+-$(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 \
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++ $(top_srcdir)/src/general/lineparse.o \
++ $(top_srcdir)/src/struct/sparsecache.o \
++ $(top_srcdir)/src/struct/matrix.o
++am_fastaclip_OBJECTS = fastaclip.$(OBJEXT)
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+ fastaclip_LDADD = $(LDADD)
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+-$(top_srcdir)/src/sequence/alphabet.o \
+-$(top_srcdir)/src/sequence/splice.o \
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+-$(top_srcdir)/src/general/lineparse.o \
+-$(top_srcdir)/src/struct/sparsecache.o \
+-$(top_srcdir)/src/struct/matrix.o
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+-fastachecksum_OBJECTS = fastachecksum.o
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+-$(top_srcdir)/src/sequence/alphabet.o \
+-$(top_srcdir)/src/sequence/splice.o \
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+-$(top_srcdir)/src/database/fastadb.o \
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+-$(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 \
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+-$(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 \
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++ $(top_srcdir)/src/struct/sparsecache.o \
++ $(top_srcdir)/src/struct/matrix.o
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++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 \
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+-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@
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++ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/fastarevcomp.Po at am__quote@
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++ 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
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++.c.obj:
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++ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
++ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
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++ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
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++ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
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++ $(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)'; \
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+- awk ' { files[$$0] = 1; } \
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+- here=`pwd` && cd $(srcdir) \
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+-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) $(LISP)
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++TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
++ $(TAGS_FILES) $(LISP)
++ set x; \
+ here=`pwd`; \
+- list='$(SOURCES) $(HEADERS)'; \
+- unique=`for i in $$list; do echo $$i; done | \
+- awk ' { files[$$0] = 1; } \
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++ fi; \
++ fi
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++ $(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[$$0] = 1; nonempty = 1; } \
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++ $$unique
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++GTAGS:
++ here=`$(am__cd) $(top_builddir) && pwd` \
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++ && gtags -i $(GTAGS_ARGS) "$$here"
+
+ distclean-tags:
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+-maintainer-clean-tags:
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+-distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
+-
+-subdir = src/util
++ -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
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+ distdir: $(DISTFILES)
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++ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
++ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
++ list='$(DISTFILES)'; \
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++ */*) $(MKDIR_P) `echo "$$dist_files" | \
++ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
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++ esac; \
++ for file in $$dist_files; do \
++ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+ if test -d $$d/$$file; then \
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++ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
++ if test -d "$(distdir)/$$file"; then \
++ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
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++ 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; \
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+ check-am: all-am
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+ install-exec: install-exec-am
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++ `test -z '$(STRIP)' || \
++ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+ mostlyclean-generic:
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+ clean-generic:
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+ distclean-generic:
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+ maintainer-clean-generic:
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+
+ # 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@
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+-exec_prefix = @exec_prefix@
+-
+-bindir = @bindir@
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+-
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+-
+ pkgdatadir = $(datadir)/@PACKAGE@
+-pkglibdir = $(libdir)/@PACKAGE@
+ pkgincludedir = $(includedir)/@PACKAGE@
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+-top_builddir = ../../..
+-
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+-AUTOCONF = @AUTOCONF@
+-AUTOMAKE = @AUTOMAKE@
+-AUTOHEADER = @AUTOHEADER@
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++pkglibdir = $(libdir)/@PACKAGE@
++pkglibexecdir = $(libexecdir)/@PACKAGE@
++am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
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++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@
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++AUTOHEADER = @AUTOHEADER@
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++CFLAGS = @CFLAGS@
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++CPPFLAGS = @CPPFLAGS@
++CYGPATH_W = @CYGPATH_W@
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++ECHO_N = @ECHO_N@
++ECHO_T = @ECHO_T@
++EGREP = @EGREP@
++EXEEXT = @EXEEXT@
+ GLIB_CONFIG = @GLIB_CONFIG@
+-HAVE_LIB = @HAVE_LIB@
+-LIB = @LIB@
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++GREP = @GREP@
++INSTALL = @INSTALL@
++INSTALL_DATA = @INSTALL_DATA@
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++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@
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++PACKAGE_TARNAME = @PACKAGE_TARNAME@
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++SET_MAKE = @SET_MAKE@
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+ VERSION = @VERSION@
++abs_builddir = @abs_builddir@
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++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:
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++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; } \
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++ test -z "$(CTAGS_ARGS)$$unique" \
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++ $$unique
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++GTAGS:
++ here=`$(am__cd) $(top_builddir) && pwd` \
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++ && 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/$$file; then \
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++ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
++ if test -d "$(distdir)/$$file"; then \
++ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
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++ if test -d $(srcdir)/$$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)/$$file 2> /dev/null \
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++ test -f "$(distdir)/$$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; \
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++ @list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
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++ dir1=$$subdir; dir2="$(distdir)/$$subdir"; \
++ $(am__relativize); \
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++ echo " (cd $$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)"; \
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++ $(MAKE) $(AM_MAKEFLAGS) \
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++ 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:
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+-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:
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+-all-am: Makefile
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+-installdirs: installdirs-recursive
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+
++installcheck: installcheck-recursive
++install-strip:
++ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
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++ `test -z '$(STRIP)' || \
++ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+ mostlyclean-generic:
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+ clean-generic:
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+ distclean-generic:
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+
+ maintainer-clean-generic:
++ @echo "This command is intended for maintainers to use"
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+ -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
+-mostlyclean-am: mostlyclean-tags mostlyclean-generic
++clean: clean-recursive
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+-mostlyclean: mostlyclean-recursive
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+-clean-am: clean-tags clean-generic mostlyclean-am
++distclean: distclean-recursive
++ -rm -f Makefile
++distclean-am: clean-am distclean-generic distclean-tags
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+-clean: clean-recursive
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+-distclean-am: distclean-tags distclean-generic clean-am
++dvi-am:
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+-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;"
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++html-am:
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++info: info-recursive
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++info-am:
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++install-data-am:
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++install-dvi: install-dvi-recursive
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++install-html: install-html-recursive
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++install-html-am:
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++install-ps: install-ps-recursive
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++install-ps-am:
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++installcheck-am:
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+ maintainer-clean: maintainer-clean-recursive
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++maintainer-clean-am: distclean-am maintainer-clean-generic
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++mostlyclean: mostlyclean-recursive
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++mostlyclean-am: mostlyclean-generic
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++pdf: pdf-recursive
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++.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) ctags-recursive \
++ install-am install-strip tags-recursive
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+-maintainer-clean-generic clean mostlyclean distclean maintainer-clean
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++ all all-am check check-am clean clean-generic ctags \
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++ distdir dvi dvi-am html html-am info info-am install \
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++ 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@
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+-exec_prefix = @exec_prefix@
+-
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+-libexecdir = @libexecdir@
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+-
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+-
+ pkgdatadir = $(datadir)/@PACKAGE@
+-pkglibdir = $(libdir)/@PACKAGE@
+ pkgincludedir = $(includedir)/@PACKAGE@
+-
+-top_builddir = ../../..
+-
+-ACLOCAL = @ACLOCAL@
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+-
+-INSTALL = @INSTALL@
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++am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
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++INSTALL_HEADER = $(INSTALL_DATA)
++transform = $(program_transform_name)
+ NORMAL_INSTALL = :
+ PRE_INSTALL = :
+ POST_INSTALL = :
+ NORMAL_UNINSTALL = :
+ PRE_UNINSTALL = :
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++top_srcdir = @top_srcdir@
+ use_pthreads = @use_pthreads@
+-
+-EXTRA_DIST = calm.human.protein.fasta htrt.human.protein.fasta p53.human.protein.fasta tube.drome.protein.fasta
+-
++EXTRA_DIST = calm.human.protein.fasta htrt.human.protein.fasta \
++ p53.human.protein.fasta tube.drome.protein.fasta
+
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++all: all-am
+
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+-
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+ .SUFFIXES:
+-$(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 \
++ *$$dep*) \
++ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
++ && { if test -f $@; then exit 0; else break; fi; }; \
++ exit 1;; \
++ esac; \
++ done; \
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++ $(am__cd) $(top_srcdir) && \
++ $(AUTOMAKE) --gnu test/data/protein/Makefile
++.PRECIOUS: Makefile
+ Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+- cd $(top_builddir) \
+- && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
+-
++ @case '$?' in \
++ *config.status*) \
++ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
++ *) \
++ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
++ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
++ esac;
++
++$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
++ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
++
++$(top_srcdir)/configure: $(am__configure_deps)
++ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
++$(ACLOCAL_M4): $(am__aclocal_m4_deps)
++ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
++$(am__aclocal_m4_deps):
+ tags: TAGS
+ TAGS:
+
++ctags: CTAGS
++CTAGS:
+
+-distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
+-
+-subdir = test/data/protein
+
+ distdir: $(DISTFILES)
+- @for file in $(DISTFILES); do \
+- d=$(srcdir); \
++ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/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:
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++install-html: install-html-am
++
++install-html-am:
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++install-info: install-info-am
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++install-info-am:
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++install-man:
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++install-pdf: install-pdf-am
++
++install-pdf-am:
++
++install-ps: install-ps-am
++
++install-ps-am:
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++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@
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++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@
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++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@
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++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@
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++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@
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++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
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+ .SUFFIXES:
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+- 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 \
++ *$$dep*) \
++ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
++ && { if test -f $@; then exit 0; else break; fi; }; \
++ exit 1;; \
++ esac; \
++ done; \
++ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu test/exonerate/Makefile'; \
++ $(am__cd) $(top_srcdir) && \
++ $(AUTOMAKE) --gnu test/exonerate/Makefile
++.PRECIOUS: Makefile
+ Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+- cd $(top_builddir) \
+- && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
+-
++ @case '$?' in \
++ *config.status*) \
++ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
++ *) \
++ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
++ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
++ esac;
++
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++ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
++
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++ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
++$(ACLOCAL_M4): $(am__aclocal_m4_deps)
++ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
++$(am__aclocal_m4_deps):
+ tags: TAGS
+ TAGS:
+
++ctags: CTAGS
++CTAGS:
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+-distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
+-
+-subdir = test/exonerate
+
+-distdir: $(DISTFILES)
+- @for file in $(DISTFILES); do \
+- d=$(srcdir); \
+- if test -d $$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 "$$list"; then \
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++ if test -f ./$$tst; then dir=./; \
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++ 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 $$failures)"; \
++ fi; \
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++ if test "$$xpass" -eq 0; then \
++ banner="$$failed of $$all $$tests failed"; \
++ else \
++ if test "$$xpass" -eq 1; then passes=pass; else passes=passes; fi; \
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++ skipped="($$skip test was not run)"; \
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++ dashes="$$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:
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++ test -z "$$skipped" || echo "$$skipped"; \
++ test -z "$$report" || echo "$$report"; \
++ echo "$$dashes$$std"; \
++ test "$$failed" -eq 0; \
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++
++distdir: $(DISTFILES)
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++ list='$(DISTFILES)'; \
++ dist_files=`for file in $$list; do echo $$file; done | \
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++ -e "s|^$$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
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+-uninstall: uninstall-am
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+- $(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
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+ clean-am: clean-generic mostlyclean-am
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+-clean: clean-am
++distclean: distclean-am
++ -rm -f Makefile
++distclean-am: clean-am distclean-generic
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+-distclean-am: distclean-generic clean-am
++dvi: dvi-am
+
+-distclean: distclean-am
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+-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:
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++install-dvi: install-dvi-am
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++install-dvi-am:
++
++install-exec-am:
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++install-html: install-html-am
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++install-pdf-am:
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++install-ps: install-ps-am
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++installcheck-am:
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+ maintainer-clean: maintainer-clean-am
++ -rm -f Makefile
++maintainer-clean-am: distclean-am maintainer-clean-generic
++
++mostlyclean: mostlyclean-am
++
++mostlyclean-am: mostlyclean-generic
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++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 \
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++.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@
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++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
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++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@
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++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@
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++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@
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+ codegen_extra_ldadd = @codegen_extra_ldadd@
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+ glib_cflags = @glib_cflags@
+ glib_libs = @glib_libs@
+ host = @host@
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++host_cpu = @host_cpu@
++host_os = @host_os@
++host_vendor = @host_vendor@
++htmldir = @htmldir@
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+ installed_util_list = @installed_util_list@
++libdir = @libdir@
++libexecdir = @libexecdir@
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++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
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+-
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+
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++ && { 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) \
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+-
++ @case '$?' in \
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++ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
++ *) \
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+
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+- @for file in $(DISTFILES); do \
+- d=$(srcdir); \
+- if test -d $$d/$$file; then \
+- cp -pr $$d/$$file $(distdir)/$$file; \
+- else \
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+- || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
+- || cp -p $$d/$$file $(distdir)/$$file || :; \
+- fi; \
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+ check-TESTS: $(TESTS)
+- @failed=0; all=0; \
++ @failed=0; all=0; xfail=0; xpass=0; skip=0; \
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++ *) \
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++ xfail=`expr $$xfail + 1`; \
++ col=$$lgn; res=XFAIL; \
++ ;; \
++ *) \
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++ col=$$blu; res=SKIP; \
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++ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+ mostlyclean-generic:
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++ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
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++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)"; \
++ $(am__relativize); \
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+ || exit 1; \
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++ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+ mostlyclean-generic:
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+ distclean-generic:
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++html: html-recursive
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+- @echo "This command is intended for maintainers to use;"
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++ 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@
+-
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++ at SET_MAKE@
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+-
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+-
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+-
+ pkgdatadir = $(datadir)/@PACKAGE@
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++transform = $(program_transform_name)
+ NORMAL_INSTALL = :
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++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
+-
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++ 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
+
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+
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+-
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++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.
Modified: trunk/packages/exonerate/trunk/debian/patches/series
===================================================================
--- trunk/packages/exonerate/trunk/debian/patches/series 2011-12-12 13:04:23 UTC (rev 8914)
+++ trunk/packages/exonerate/trunk/debian/patches/series 2011-12-12 13:13:36 UTC (rev 8915)
@@ -1 +1,2 @@
+autoreconf.patch
fix_build-as-needed.patch
Modified: trunk/packages/exonerate/trunk/debian/rules
===================================================================
--- trunk/packages/exonerate/trunk/debian/rules 2011-12-12 13:04:23 UTC (rev 8914)
+++ trunk/packages/exonerate/trunk/debian/rules 2011-12-12 13:13:36 UTC (rev 8915)
@@ -1,10 +1,15 @@
#!/usr/bin/make -f
+# -*- makefile -*-
+# debian/rules file for exonerate
+# Andreas Tille <tille at debian.org>
+# GPL
-include /usr/share/cdbs/1/class/autotools.mk
-include /usr/share/cdbs/1/rules/debhelper.mk
-include /usr/share/cdbs/1/rules/patchsys-quilt.mk
+%:
+ dh $@
-DEB_MAKE_CHECK_TARGET = -C test check
+override_dh_auto_clean:
+ dh_auto_clean
+ rm -rf codegen
-clean::
- rm -rf config.status
+override_dh_auto_test:
+ $(MAKE) -C test check
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