[med-svn] [probabel] 01/03: Imported Upstream version 0.4.4
Lennart Karssen
lckarssen-guest at moszumanska.debian.org
Fri Nov 7 22:58:40 UTC 2014
This is an automated email from the git hooks/post-receive script.
lckarssen-guest pushed a commit to branch master
in repository probabel.
commit 82d925a29f90d54cf40277c6fd1968121f15b202
Author: L.C. Karssen <lennart at karssen.org>
Date: Fri Nov 7 17:41:18 2014 +0100
Imported Upstream version 0.4.4
---
Makefile.in | 11 +-
aclocal.m4 | 154 ++++++++++++-----
checks/Makefile.in | 2 +-
checks/R-tests/Makefile.in | 2 +-
configure | 268 ++++++++++++++----------------
configure.ac | 12 +-
doc/ChangeLog | 11 ++
doc/Makefile.in | 18 +-
doc/ProbABEL_manual.tex | 12 +-
doc/pacoxph.1 | 2 +-
doc/palinear.1 | 2 +-
doc/palogist.1 | 2 +-
doc/probabel.1 | 2 +-
doc/probabel.pl.1 | 2 +-
examples/Makefile.in | 2 +-
src/Makefile.am | 24 ++-
src/Makefile.in | 405 ++++++++++++++++++++++-----------------------
src/config.h.in | 3 -
src/coxph_data.cpp | 46 +++--
src/main.cpp | 2 +-
20 files changed, 524 insertions(+), 458 deletions(-)
diff --git a/Makefile.in b/Makefile.in
index 6a577d3..8b3f5f3 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -1,4 +1,4 @@
-# Makefile.in generated by automake 1.13.3 from Makefile.am.
+# Makefile.in generated by automake 1.14.1 from Makefile.am.
# @configure_input@
# Copyright (C) 1994-2013 Free Software Foundation, Inc.
@@ -511,10 +511,16 @@ dist-xz: distdir
$(am__post_remove_distdir)
dist-tarZ: distdir
+ @echo WARNING: "Support for shar distribution archives is" \
+ "deprecated." >&2
+ @echo WARNING: "It will be removed altogether in Automake 2.0" >&2
tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z
$(am__post_remove_distdir)
dist-shar: distdir
+ @echo WARNING: "Support for distribution archives compressed with" \
+ "legacy program 'compress' is deprecated." >&2
+ @echo WARNING: "It will be removed altogether in Automake 2.0" >&2
shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz
$(am__post_remove_distdir)
@@ -556,9 +562,10 @@ distcheck: dist
&& dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \
&& am__cwd=`pwd` \
&& $(am__cd) $(distdir)/_build \
- && ../configure --srcdir=.. --prefix="$$dc_install_base" \
+ && ../configure \
$(AM_DISTCHECK_CONFIGURE_FLAGS) \
$(DISTCHECK_CONFIGURE_FLAGS) \
+ --srcdir=.. --prefix="$$dc_install_base" \
&& $(MAKE) $(AM_MAKEFLAGS) \
&& $(MAKE) $(AM_MAKEFLAGS) dvi \
&& $(MAKE) $(AM_MAKEFLAGS) check \
diff --git a/aclocal.m4 b/aclocal.m4
index 913076e..0d3fc74 100644
--- a/aclocal.m4
+++ b/aclocal.m4
@@ -1,4 +1,4 @@
-# generated automatically by aclocal 1.13.3 -*- Autoconf -*-
+# generated automatically by aclocal 1.14.1 -*- Autoconf -*-
# Copyright (C) 1996-2013 Free Software Foundation, Inc.
@@ -32,10 +32,10 @@ To do so, use the procedure documented by the package, typically 'autoreconf'.])
# generated from the m4 files accompanying Automake X.Y.
# (This private macro should not be called outside this file.)
AC_DEFUN([AM_AUTOMAKE_VERSION],
-[am__api_version='1.13'
+[am__api_version='1.14'
dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to
dnl require some minimum version. Point them to the right macro.
-m4_if([$1], [1.13.3], [],
+m4_if([$1], [1.14.1], [],
[AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl
])
@@ -51,7 +51,7 @@ m4_define([_AM_AUTOCONF_VERSION], [])
# Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced.
# This function is AC_REQUIREd by AM_INIT_AUTOMAKE.
AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
-[AM_AUTOMAKE_VERSION([1.13.3])dnl
+[AM_AUTOMAKE_VERSION([1.14.1])dnl
m4_ifndef([AC_AUTOCONF_VERSION],
[m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
_AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
@@ -418,6 +418,12 @@ AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
# 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.
+dnl Redefine AC_PROG_CC to automatically invoke _AM_PROG_CC_C_O.
+m4_define([AC_PROG_CC],
+m4_defn([AC_PROG_CC])
+[_AM_PROG_CC_C_O
+])
+
# AM_INIT_AUTOMAKE(PACKAGE, VERSION, [NO-DEFINE])
# AM_INIT_AUTOMAKE([OPTIONS])
# -----------------------------------------------
@@ -526,7 +532,48 @@ dnl macro 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
-])
+
+# POSIX will say in a future version that running "rm -f" with no argument
+# is OK; and we want to be able to make that assumption in our Makefile
+# recipes. So use an aggressive probe to check that the usage we want is
+# actually supported "in the wild" to an acceptable degree.
+# See automake bug#10828.
+# To make any issue more visible, cause the running configure to be aborted
+# by default if the 'rm' program in use doesn't match our expectations; the
+# user can still override this though.
+if rm -f && rm -fr && rm -rf; then : OK; else
+ cat >&2 <<'END'
+Oops!
+
+Your 'rm' program seems unable to run without file operands specified
+on the command line, even when the '-f' option is present. This is contrary
+to the behaviour of most rm programs out there, and not conforming with
+the upcoming POSIX standard: <http://austingroupbugs.net/view.php?id=542>
+
+Please tell bug-automake at gnu.org about your system, including the value
+of your $PATH and any error possibly output before this message. This
+can help us improve future automake versions.
+
+END
+ if test x"$ACCEPT_INFERIOR_RM_PROGRAM" = x"yes"; then
+ echo 'Configuration will proceed anyway, since you have set the' >&2
+ echo 'ACCEPT_INFERIOR_RM_PROGRAM variable to "yes"' >&2
+ echo >&2
+ else
+ cat >&2 <<'END'
+Aborting the configuration process, to ensure you take notice of the issue.
+
+You can download and install GNU coreutils to get an 'rm' implementation
+that behaves properly: <http://www.gnu.org/software/coreutils/>.
+
+If you want to complete the configuration process using your problematic
+'rm' anyway, export the environment variable ACCEPT_INFERIOR_RM_PROGRAM
+to "yes", and re-run configure.
+
+END
+ AC_MSG_ERROR([Your 'rm' program is bad, sorry.])
+ fi
+fi])
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
@@ -534,7 +581,6 @@ 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.
@@ -682,38 +728,6 @@ AC_MSG_RESULT([$_am_result])
rm -f confinc confmf
])
-# Copyright (C) 1999-2013 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_CC_C_O
-# --------------
-# Like AC_PROG_CC_C_O, but changed for automake.
-AC_DEFUN([AM_PROG_CC_C_O],
-[AC_REQUIRE([AC_PROG_CC_C_O])dnl
-AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
-AC_REQUIRE_AUX_FILE([compile])dnl
-# FIXME: we rely on the cache variable name because
-# there is no other way.
-set dummy $CC
-am_cc=`echo $[2] | sed ['s/[^a-zA-Z0-9_]/_/g;s/^[0-9]/_/']`
-eval am_t=\$ac_cv_prog_cc_${am_cc}_c_o
-if test "$am_t" != yes; then
- # Losing compiler, so override with the script.
- # FIXME: It is wrong to rewrite CC.
- # But if we don't then we get into trouble of one sort or another.
- # A longer-term fix would be to have automake use am__CC in this case,
- # and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
- CC="$am_aux_dir/compile $CC"
-fi
-dnl Make sure AC_PROG_CC is never called again, or it will override our
-dnl setting of CC.
-m4_define([AC_PROG_CC],
- [m4_fatal([AC_PROG_CC cannot be called after AM_PROG_CC_C_O])])
-])
-
# Fake the existence of programs that GNU maintainers use. -*- Autoconf -*-
# Copyright (C) 1997-2013 Free Software Foundation, Inc.
@@ -784,6 +798,70 @@ AC_DEFUN([_AM_SET_OPTIONS],
AC_DEFUN([_AM_IF_OPTION],
[m4_ifset(_AM_MANGLE_OPTION([$1]), [$2], [$3])])
+# Copyright (C) 1999-2013 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_CC_C_O
+# ---------------
+# Like AC_PROG_CC_C_O, but changed for automake. We rewrite AC_PROG_CC
+# to automatically call this.
+AC_DEFUN([_AM_PROG_CC_C_O],
+[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
+AC_REQUIRE_AUX_FILE([compile])dnl
+AC_LANG_PUSH([C])dnl
+AC_CACHE_CHECK(
+ [whether $CC understands -c and -o together],
+ [am_cv_prog_cc_c_o],
+ [AC_LANG_CONFTEST([AC_LANG_PROGRAM([])])
+ # Make sure it works both with $CC and with simple cc.
+ # Following AC_PROG_CC_C_O, we do the test twice because some
+ # compilers refuse to overwrite an existing .o file with -o,
+ # though they will create one.
+ am_cv_prog_cc_c_o=yes
+ for am_i in 1 2; do
+ if AM_RUN_LOG([$CC -c conftest.$ac_ext -o conftest2.$ac_objext]) \
+ && test -f conftest2.$ac_objext; then
+ : OK
+ else
+ am_cv_prog_cc_c_o=no
+ break
+ fi
+ done
+ rm -f core conftest*
+ unset am_i])
+if test "$am_cv_prog_cc_c_o" != yes; then
+ # Losing compiler, so override with the script.
+ # FIXME: It is wrong to rewrite CC.
+ # But if we don't then we get into trouble of one sort or another.
+ # A longer-term fix would be to have automake use am__CC in this case,
+ # and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
+ CC="$am_aux_dir/compile $CC"
+fi
+AC_LANG_POP([C])])
+
+# For backward compatibility.
+AC_DEFUN_ONCE([AM_PROG_CC_C_O], [AC_REQUIRE([AC_PROG_CC])])
+
+# Copyright (C) 2001-2013 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_RUN_LOG(COMMAND)
+# -------------------
+# Run COMMAND, save the exit status in ac_status, and log it.
+# (This has been adapted from Autoconf's _AC_RUN_LOG macro.)
+AC_DEFUN([AM_RUN_LOG],
+[{ echo "$as_me:$LINENO: $1" >&AS_MESSAGE_LOG_FD
+ ($1) >&AS_MESSAGE_LOG_FD 2>&AS_MESSAGE_LOG_FD
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&AS_MESSAGE_LOG_FD
+ (exit $ac_status); }])
+
# Check to make sure that the build environment is sane. -*- Autoconf -*-
# Copyright (C) 1996-2013 Free Software Foundation, Inc.
diff --git a/checks/Makefile.in b/checks/Makefile.in
index 452d1dd..d169580 100644
--- a/checks/Makefile.in
+++ b/checks/Makefile.in
@@ -1,4 +1,4 @@
-# Makefile.in generated by automake 1.13.3 from Makefile.am.
+# Makefile.in generated by automake 1.14.1 from Makefile.am.
# @configure_input@
# Copyright (C) 1994-2013 Free Software Foundation, Inc.
diff --git a/checks/R-tests/Makefile.in b/checks/R-tests/Makefile.in
index df0a3ec..78624bc 100644
--- a/checks/R-tests/Makefile.in
+++ b/checks/R-tests/Makefile.in
@@ -1,4 +1,4 @@
-# Makefile.in generated by automake 1.13.3 from Makefile.am.
+# Makefile.in generated by automake 1.14.1 from Makefile.am.
# @configure_input@
# Copyright (C) 1994-2013 Free Software Foundation, Inc.
diff --git a/configure b/configure
index bb7b684..ecec200 100755
--- a/configure
+++ b/configure
@@ -1,6 +1,6 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for ProbABEL 0.4.3.
+# Generated by GNU Autoconf 2.69 for ProbABEL 0.4.4.
#
# Report bugs to <genabel-devel at r-forge.wu-wien.ac.at>.
#
@@ -580,8 +580,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='ProbABEL'
PACKAGE_TARNAME='probabel'
-PACKAGE_VERSION='0.4.3'
-PACKAGE_STRING='ProbABEL 0.4.3'
+PACKAGE_VERSION='0.4.4'
+PACKAGE_STRING='ProbABEL 0.4.4'
PACKAGE_BUGREPORT='genabel-devel at r-forge.wu-wien.ac.at'
PACKAGE_URL=''
@@ -1305,7 +1305,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
-\`configure' configures ProbABEL 0.4.3 to adapt to many kinds of systems.
+\`configure' configures ProbABEL 0.4.4 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1371,7 +1371,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of ProbABEL 0.4.3:";;
+ short | recursive ) echo "Configuration of ProbABEL 0.4.4:";;
esac
cat <<\_ACEOF
@@ -1484,7 +1484,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-ProbABEL configure 0.4.3
+ProbABEL configure 0.4.4
generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1945,7 +1945,7 @@ 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 ProbABEL $as_me 0.4.3, which was
+It was created by ProbABEL $as_me 0.4.4, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
@@ -2293,7 +2293,7 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $
ac_compiler_gnu=$ac_cv_c_compiler_gnu
-am__api_version='1.13'
+am__api_version='1.14'
ac_aux_dir=
for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do
@@ -2808,7 +2808,7 @@ fi
# Define the identity of the package.
PACKAGE='probabel'
- VERSION='0.4.3'
+ VERSION='0.4.4'
cat >>confdefs.h <<_ACEOF
@@ -2859,6 +2859,47 @@ am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'
+# POSIX will say in a future version that running "rm -f" with no argument
+# is OK; and we want to be able to make that assumption in our Makefile
+# recipes. So use an aggressive probe to check that the usage we want is
+# actually supported "in the wild" to an acceptable degree.
+# See automake bug#10828.
+# To make any issue more visible, cause the running configure to be aborted
+# by default if the 'rm' program in use doesn't match our expectations; the
+# user can still override this though.
+if rm -f && rm -fr && rm -rf; then : OK; else
+ cat >&2 <<'END'
+Oops!
+
+Your 'rm' program seems unable to run without file operands specified
+on the command line, even when the '-f' option is present. This is contrary
+to the behaviour of most rm programs out there, and not conforming with
+the upcoming POSIX standard: <http://austingroupbugs.net/view.php?id=542>
+
+Please tell bug-automake at gnu.org about your system, including the value
+of your $PATH and any error possibly output before this message. This
+can help us improve future automake versions.
+
+END
+ if test x"$ACCEPT_INFERIOR_RM_PROGRAM" = x"yes"; then
+ echo 'Configuration will proceed anyway, since you have set the' >&2
+ echo 'ACCEPT_INFERIOR_RM_PROGRAM variable to "yes"' >&2
+ echo >&2
+ else
+ cat >&2 <<'END'
+Aborting the configuration process, to ensure you take notice of the issue.
+
+You can download and install GNU coreutils to get an 'rm' implementation
+that behaves properly: <http://www.gnu.org/software/coreutils/>.
+
+If you want to complete the configuration process using your problematic
+'rm' anyway, export the environment variable ACCEPT_INFERIOR_RM_PROGRAM
+to "yes", and re-run configure.
+
+END
+ as_fn_error $? "Your 'rm' program is bad, sorry." "$LINENO" 5
+ fi
+fi
# Check whether --enable-silent-rules was given.
if test "${enable_silent_rules+set}" = set; then :
enableval=$enable_silent_rules;
@@ -3719,6 +3760,65 @@ 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
+
+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
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC understands -c and -o together" >&5
+$as_echo_n "checking whether $CC understands -c and -o together... " >&6; }
+if ${am_cv_prog_cc_c_o+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+ # Make sure it works both with $CC and with simple cc.
+ # Following AC_PROG_CC_C_O, we do the test twice because some
+ # compilers refuse to overwrite an existing .o file with -o,
+ # though they will create one.
+ am_cv_prog_cc_c_o=yes
+ for am_i in 1 2; do
+ if { echo "$as_me:$LINENO: $CC -c conftest.$ac_ext -o conftest2.$ac_objext" >&5
+ ($CC -c conftest.$ac_ext -o conftest2.$ac_objext) >&5 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } \
+ && test -f conftest2.$ac_objext; then
+ : OK
+ else
+ am_cv_prog_cc_c_o=no
+ break
+ fi
+ done
+ rm -f core conftest*
+ unset am_i
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_prog_cc_c_o" >&5
+$as_echo "$am_cv_prog_cc_c_o" >&6; }
+if test "$am_cv_prog_cc_c_o" != yes; then
+ # Losing compiler, so override with the script.
+ # FIXME: It is wrong to rewrite CC.
+ # But if we don't then we get into trouble of one sort or another.
+ # A longer-term fix would be to have automake use am__CC in this case,
+ # and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
+ CC="$am_aux_dir/compile $CC"
+fi
+ac_ext=c
+ac_cpp='$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="${am__leading_dot}deps"
ac_config_commands="$ac_config_commands depfiles"
@@ -3911,131 +4011,6 @@ else
fi
-if test "x$CC" != xcc; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC and cc understand -c and -o together" >&5
-$as_echo_n "checking whether $CC and cc understand -c and -o together... " >&6; }
-else
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether cc understands -c and -o together" >&5
-$as_echo_n "checking whether cc understands -c and -o together... " >&6; }
-fi
-set dummy $CC; ac_cc=`$as_echo "$2" |
- sed 's/[^a-zA-Z0-9_]/_/g;s/^[0-9]/_/'`
-if eval \${ac_cv_prog_cc_${ac_cc}_c_o+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-
-int
-main ()
-{
-
- ;
- return 0;
-}
-_ACEOF
-# Make sure it works both with $CC and with simple cc.
-# We do the test twice because some compilers refuse to overwrite an
-# existing .o file with -o, though they will create one.
-ac_try='$CC -c conftest.$ac_ext -o conftest2.$ac_objext >&5'
-rm -f conftest2.*
-if { { 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 $ac_status = 0; } &&
- test -f conftest2.$ac_objext && { { 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 $ac_status = 0; };
-then
- eval ac_cv_prog_cc_${ac_cc}_c_o=yes
- if test "x$CC" != xcc; then
- # Test first that cc exists at all.
- if { ac_try='cc -c conftest.$ac_ext >&5'
- { { 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 $ac_status = 0; }; }; then
- ac_try='cc -c conftest.$ac_ext -o conftest2.$ac_objext >&5'
- rm -f conftest2.*
- if { { case "(($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 $ac_status = 0; } &&
- test -f conftest2.$ac_objext && { { 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 $ac_status = 0; };
- then
- # cc works too.
- :
- else
- # cc exists but doesn't like -o.
- eval ac_cv_prog_cc_${ac_cc}_c_o=no
- fi
- fi
- fi
-else
- eval ac_cv_prog_cc_${ac_cc}_c_o=no
-fi
-rm -f core conftest*
-
-fi
-if eval test \$ac_cv_prog_cc_${ac_cc}_c_o = yes; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
-$as_echo "yes" >&6; }
-else
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-$as_echo "no" >&6; }
-
-$as_echo "#define NO_MINUS_C_MINUS_O 1" >>confdefs.h
-
-fi
-
-# FIXME: we rely on the cache variable name because
-# there is no other way.
-set dummy $CC
-am_cc=`echo $2 | sed 's/[^a-zA-Z0-9_]/_/g;s/^[0-9]/_/'`
-eval am_t=\$ac_cv_prog_cc_${am_cc}_c_o
-if test "$am_t" != yes; then
- # Losing compiler, so override with the script.
- # FIXME: It is wrong to rewrite CC.
- # But if we don't then we get into trouble of one sort or another.
- # A longer-term fix would be to have automake use am__CC in this case,
- # and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
- CC="$am_aux_dir/compile $CC"
-fi
-
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ln -s works" >&5
@@ -4055,7 +4030,7 @@ if test -z "$CXXFLAGS"; then
fi
if test -z "$CPPFLAGS"; then
# User did not set CPPFLAGS, so we can put in our own defaults
- CPPFLAGS="-Wall"
+ CPPFLAGS="-Wall -DNDEBUG"
fi
# If CXXFLAGS/CPPFLAGS are already set AC_PROG_CXX will not overwrite them
# with its own defaults
@@ -4447,7 +4422,8 @@ fi
#Tell compiler to build not R version of filevector
-CXXFLAGS+=" -D_NOT_R_FILEVECTOR"
+CPPFLAGS="$CPPFLAGS -D_NOT_R_FILEVECTOR"
+
# Since most of our code is in C++, set that language as the default
@@ -5086,11 +5062,9 @@ $as_echo "$as_me: building using the Eigen headers enabled" >&6;}
# Check whether --with-eigen-include-path was given.
if test "${with_eigen_include_path+set}" = set; then :
- withval=$with_eigen_include_path; CXXFLAGS+=" -I${withval}"
- CPPFLAGS+=" -I${withval}"
+ withval=$with_eigen_include_path; CPPFLAGS+=" -I${withval}"
else
- CXXFLAGS+=' -I/usr/include/eigen3'
- CPPFLAGS+=' -I/usr/include/eigen3'
+ CPPFLAGS+=' -I/usr/include/eigen3'
fi
@@ -5364,7 +5338,7 @@ else
We can't simply define LARGE_OFF_T to be 9223372036854775807,
since some C++ compilers masquerading as C compilers
incorrectly reject 9223372036854775807. */
-#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))
+#define LARGE_OFF_T ((((off_t) 1 << 31) << 31) - 1 + (((off_t) 1 << 31) << 31))
int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721
&& LARGE_OFF_T % 2147483647 == 1)
? 1 : -1];
@@ -5410,7 +5384,7 @@ else
We can't simply define LARGE_OFF_T to be 9223372036854775807,
since some C++ compilers masquerading as C compilers
incorrectly reject 9223372036854775807. */
-#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))
+#define LARGE_OFF_T ((((off_t) 1 << 31) << 31) - 1 + (((off_t) 1 << 31) << 31))
int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721
&& LARGE_OFF_T % 2147483647 == 1)
? 1 : -1];
@@ -5434,7 +5408,7 @@ rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
We can't simply define LARGE_OFF_T to be 9223372036854775807,
since some C++ compilers masquerading as C compilers
incorrectly reject 9223372036854775807. */
-#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))
+#define LARGE_OFF_T ((((off_t) 1 << 31) << 31) - 1 + (((off_t) 1 << 31) << 31))
int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721
&& LARGE_OFF_T % 2147483647 == 1)
? 1 : -1];
@@ -5479,7 +5453,7 @@ else
We can't simply define LARGE_OFF_T to be 9223372036854775807,
since some C++ compilers masquerading as C compilers
incorrectly reject 9223372036854775807. */
-#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))
+#define LARGE_OFF_T ((((off_t) 1 << 31) << 31) - 1 + (((off_t) 1 << 31) << 31))
int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721
&& LARGE_OFF_T % 2147483647 == 1)
? 1 : -1];
@@ -5503,7 +5477,7 @@ rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
We can't simply define LARGE_OFF_T to be 9223372036854775807,
since some C++ compilers masquerading as C compilers
incorrectly reject 9223372036854775807. */
-#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))
+#define LARGE_OFF_T ((((off_t) 1 << 31) << 31) - 1 + (((off_t) 1 << 31) << 31))
int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721
&& LARGE_OFF_T % 2147483647 == 1)
? 1 : -1];
@@ -6491,7 +6465,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
-This file was extended by ProbABEL $as_me 0.4.3, which was
+This file was extended by ProbABEL $as_me 0.4.4, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -6557,7 +6531,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
-ProbABEL config.status 0.4.3
+ProbABEL config.status 0.4.4
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
diff --git a/configure.ac b/configure.ac
index 3a59486..ec2776d 100644
--- a/configure.ac
+++ b/configure.ac
@@ -2,7 +2,7 @@
# Process this file with autoconf to produce a configure script.
AC_PREREQ([2.67])
-AC_INIT(ProbABEL, 0.4.3, genabel-devel at r-forge.wu-wien.ac.at)
+AC_INIT(ProbABEL, 0.4.4, genabel-devel at r-forge.wu-wien.ac.at)
AM_INIT_AUTOMAKE([silent-rules subdir-objects])
AM_SILENT_RULES([yes])
AC_CONFIG_SRCDIR([src/data.h])
@@ -25,7 +25,7 @@ if test -z "$CXXFLAGS"; then
fi
if test -z "$CPPFLAGS"; then
# User did not set CPPFLAGS, so we can put in our own defaults
- CPPFLAGS="-Wall"
+ CPPFLAGS="-Wall -DNDEBUG"
fi
# If CXXFLAGS/CPPFLAGS are already set AC_PROG_CXX will not overwrite them
# with its own defaults
@@ -33,7 +33,7 @@ AC_PROG_CXX
#Tell compiler to build not R version of filevector
-CXXFLAGS+=" -D_NOT_R_FILEVECTOR"
+AC_SUBST(CPPFLAGS, "$CPPFLAGS -D_NOT_R_FILEVECTOR")
# Since most of our code is in C++, set that language as the default
@@ -65,10 +65,8 @@ if test "x$with_eigen" != "xno"; then
AC_ARG_WITH([eigen-include-path],
[AS_HELP_STRING([--with-eigen-include-path],
[location of the Eigen headers, defaults to /usr/include/eigen3])],
- [CXXFLAGS+=" -I${withval}"
- CPPFLAGS+=" -I${withval}"],
- [CXXFLAGS+=' -I/usr/include/eigen3'
- CPPFLAGS+=' -I/usr/include/eigen3'])
+ [CPPFLAGS+=" -I${withval}"],
+ [CPPFLAGS+=' -I/usr/include/eigen3'])
# Check for the EIGEN header files
AC_CHECK_HEADERS([Eigen/Dense Eigen/LU])
diff --git a/doc/ChangeLog b/doc/ChangeLog
index 22ff7ed..d8fbac6 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,3 +1,14 @@
+***** v.0.4.4 (2014.11.07)
+* Fixed bug #5729 in the Cox PH module. Some checks for problems with the
+ regression were incorrectly implemented. Thanks to Matthias Wuttke from
+ the University Medical Centre Freiburg, Anne Grotenhuis from the Radboud
+ Medical Centre Nijmegen, and Luba Pardo and Joris Verkouteren from the
+ Erasmus Medical Centre Rotterdam for their time and effort in reporting
+ the bug, helping to identify the problem and testing the fix.
+* Backported fix of bug #5982: ProbABEL's make install fails on MacOS X
+ and FreeBSD with sed error. Thanks to forum user mmold for reporting the bug.
+
+
***** v.0.4.3 (2014.04.01)
* Speed-up of a factor of ~ 2 for linear, logistic and Cox regression when
using filevector input files.
diff --git a/doc/Makefile.in b/doc/Makefile.in
index b93b8c0..19fd069 100644
--- a/doc/Makefile.in
+++ b/doc/Makefile.in
@@ -1,4 +1,4 @@
-# Makefile.in generated by automake 1.13.3 from Makefile.am.
+# Makefile.in generated by automake 1.14.1 from Makefile.am.
# @configure_input@
# Copyright (C) 1994-2013 Free Software Foundation, Inc.
@@ -102,18 +102,6 @@ AM_V_at = $(am__v_at_ at AM_V@)
am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
am__v_at_0 = @
am__v_at_1 =
-COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
- $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
-AM_V_CC = $(am__v_CC_ at AM_V@)
-am__v_CC_ = $(am__v_CC_ at AM_DEFAULT_V@)
-am__v_CC_0 = @echo " CC " $@;
-am__v_CC_1 =
-CCLD = $(CC)
-LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
-AM_V_CCLD = $(am__v_CCLD_ at AM_V@)
-am__v_CCLD_ = $(am__v_CCLD_ at AM_DEFAULT_V@)
-am__v_CCLD_0 = @echo " CCLD " $@;
-am__v_CCLD_1 =
SOURCES =
DIST_SOURCES =
am__can_run_installinfo = \
@@ -283,9 +271,9 @@ $(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am $(am__confi
exit 1;; \
esac; \
done; \
- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu doc/Makefile'; \
+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign doc/Makefile'; \
$(am__cd) $(top_srcdir) && \
- $(AUTOMAKE) --gnu doc/Makefile
+ $(AUTOMAKE) --foreign doc/Makefile
.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
diff --git a/doc/ProbABEL_manual.tex b/doc/ProbABEL_manual.tex
index aeba9cd..bf8b8d0 100644
--- a/doc/ProbABEL_manual.tex
+++ b/doc/ProbABEL_manual.tex
@@ -1,6 +1,6 @@
\documentclass[12pt,a4paper]{article}
-\title{Manual for ProbABEL v0.4.3}
+\title{Manual for ProbABEL v0.4.4}
\author{\emph{Current Programmers:} Lennart Karssen$^{1,2}$, Maarten
Kooyman$^2$, \\
Yurii Aulchenko$^{1,3}$ \\
@@ -11,7 +11,7 @@
$^{2}${\small Erasmus MC, Rotterdam}\\
$^{3}${\small Institute of Cytology and Genetics SD RAS, Novosibirsk}
}
-\date{April 1, 2014}
+\date{November 7, 2014}
\usepackage[utf8]{inputenc}
@@ -237,8 +237,8 @@ user at server:~$ mv eigen-eigen-6b38706d90a9 EIGEN
Now it's time to extract the \PA{} source code and move into the
directory that is created:
\begin{lstlisting}
-user at server:~$ tar -xzf probabel-0.4.3.tar.gz
-user at server:~$ cd probabel-0.4.3
+user at server:~$ tar -xzf probabel-0.4.4.tar.gz
+user at server:~$ cd probabel-0.4.4
\end{lstlisting}
With the following command we will indicate where the EIGEN files can
be found and where we want to install \PA{}. Let's install in a
@@ -463,7 +463,7 @@ you run either program with the \texttt{--help} option, you will get a
short explanation to the command line options:
\begin{verbatim}
user at server:~$ palogist --help
-probabel v. 0.4.3
+probabel v. 0.4.4
(C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR
Using EIGEN version 3.1.2 for matrix operations
@@ -1028,7 +1028,7 @@ BMC Bioinformatics. 2010, 11:134.
\end{quote}
A proper reference may look like
\begin{quote}
-For the analysis of imputed data, we used \PA{} v.0.4.3
+For the analysis of imputed data, we used \PA{} v.0.4.4
from the \texttt{GenABEL} suite of programs (Aulchenko \emph{et al.}, 2010).
\end{quote}
diff --git a/doc/pacoxph.1 b/doc/pacoxph.1
index 4fe3121..5f01bd0 100644
--- a/doc/pacoxph.1
+++ b/doc/pacoxph.1
@@ -1,4 +1,4 @@
-.TH pacoxph 1 "01 April 2014" "ProbABEL 0.4.3"
+.TH pacoxph 1 "7 November 2014" "ProbABEL 0.4.4"
.SH NAME
pacoxph \- Perform Genome-Wide Association Analysis using a linear model
.SH SYNOPSIS
diff --git a/doc/palinear.1 b/doc/palinear.1
index ecdf295..85bb6ba 100644
--- a/doc/palinear.1
+++ b/doc/palinear.1
@@ -1,4 +1,4 @@
-.TH palinear 1 "01 April 2014" "ProbABEL 0.4.3"
+.TH palinear 1 "7 November 2014" "ProbABEL 0.4.4"
.SH NAME
palinear \- Perform Genome-Wide Association Analysis using a linear model
.SH SYNOPSIS
diff --git a/doc/palogist.1 b/doc/palogist.1
index e950026..6cd95d1 100644
--- a/doc/palogist.1
+++ b/doc/palogist.1
@@ -1,4 +1,4 @@
-.TH palogist 1 "01 April 2014" "ProbABEL 0.4.3"
+.TH palogist 1 "7 November 2014" "ProbABEL 0.4.4"
.SH NAME
palogist \- Perform Genome-Wide Association Analysis using a linear model
.SH SYNOPSIS
diff --git a/doc/probabel.1 b/doc/probabel.1
index bd37640..86f928b 100644
--- a/doc/probabel.1
+++ b/doc/probabel.1
@@ -1,4 +1,4 @@
-.TH ProbABEL 1 "01 April 2014" "ProbABEL 0.4.3"
+.TH ProbABEL 1 "7 November 2014" "ProbABEL 0.4.4"
.SH NAME
probabel \- Wrapper around the three ProbABEL binaries, simplifying their use
.SH SYNOPSIS
diff --git a/doc/probabel.pl.1 b/doc/probabel.pl.1
index bd37640..86f928b 100644
--- a/doc/probabel.pl.1
+++ b/doc/probabel.pl.1
@@ -1,4 +1,4 @@
-.TH ProbABEL 1 "01 April 2014" "ProbABEL 0.4.3"
+.TH ProbABEL 1 "7 November 2014" "ProbABEL 0.4.4"
.SH NAME
probabel \- Wrapper around the three ProbABEL binaries, simplifying their use
.SH SYNOPSIS
diff --git a/examples/Makefile.in b/examples/Makefile.in
index 4d6d1bf..2c12be8 100644
--- a/examples/Makefile.in
+++ b/examples/Makefile.in
@@ -1,4 +1,4 @@
-# Makefile.in generated by automake 1.13.3 from Makefile.am.
+# Makefile.in generated by automake 1.14.1 from Makefile.am.
# @configure_input@
# Copyright (C) 1994-2013 Free Software Foundation, Inc.
diff --git a/src/Makefile.am b/src/Makefile.am
index 2d1ceaf..f239de3 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -52,29 +52,27 @@ endif
palinear_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS)
-palinear_CXXFLAGS = -DLINEAR $(AM_CXXFLAGS)
-palinear_CPPFLAGS = $(AM_CPPFLAGS)
+palinear_CPPFLAGS = -DLINEAR $(AM_CPPFLAGS)
if WITH_EIGEN
palinear_SOURCES += $(EIGENFILES)
-palinear_CXXFLAGS += -DEIGEN
+palinear_CPPFLAGS += -DEIGEN
endif
palogist_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS)
-palogist_CXXFLAGS = -DLOGISTIC $(AM_CXXFLAGS)
-palogist_CPPFLAGS = $(AM_CPPFLAGS)
+palogist_CPPFLAGS = -DLOGISTIC $(AM_CPPFLAGS)
if WITH_EIGEN
palogist_SOURCES += $(EIGENFILES)
-palogist_CXXFLAGS += -DEIGEN
+palogist_CPPFLAGS += -DEIGEN
endif
pacoxph_SOURCES = $(COXSRC) $(REGFILES) $(FVSRC) $(FVHEADERS) \
$(RHEADERS) survS.h survproto.h coxph_data.h coxph_data.cpp
-pacoxph_CXXFLAGS = -DCOXPH -I $(top_srcdir)/src/include $(AM_CXXFLAGS)
-pacoxph_CPPFLAGS = $(AM_CPPFLAGS)
-pacoxph_CFLAGS = -DCOXPH -I $(top_srcdir)/src/include $(AM_CFLAGS)
+pacoxph_CXXFLAGS = -I $(top_srcdir)/src/include $(AM_CXXFLAGS)
+pacoxph_CPPFLAGS = -DCOXPH $(AM_CPPFLAGS)
+pacoxph_CFLAGS = -I $(top_srcdir)/src/include $(AM_CFLAGS)
if WITH_EIGEN
pacoxph_SOURCES += $(EIGENFILES)
-pacoxph_CXXFLAGS += -DEIGEN
+pacoxph_CPPFLAGS += -DEIGEN
endif
extract_snp_SOURCES = extract-snp.cpp $(FVSRC) $(FVHEADERS)
@@ -92,10 +90,10 @@ dist_sysconf_DATA = probabel_config.cfg.example
## Insert the correct values of several variables in the installed
## probabel script
install-exec-hook:
- $(SED) -i "s;probabel_config.cfg;@sysconfdir@/probabel_config.cfg;" \
+ $(SED) -i -e "s;probabel_config.cfg;@sysconfdir@/probabel_config.cfg;" \
$(DESTDIR)$(bindir)/probabel
- $(SED) -i "s;\./;@bindir@/;" $(DESTDIR)$(bindir)/probabel
- $(SED) -i "s;PROBABEL_VERSION;@VERSION@;" $(DESTDIR)$(bindir)/probabel
+ $(SED) -i -e "s;\./;@bindir@/;" $(DESTDIR)$(bindir)/probabel
+ $(SED) -i -e "s;PROBABEL_VERSION;@VERSION@;" $(DESTDIR)$(bindir)/probabel
ln -s $(DESTDIR)$(bindir)/probabel $(DESTDIR)$(bindir)/probabel.pl
## Make the script executable
diff --git a/src/Makefile.in b/src/Makefile.in
index 7093c49..0115de9 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -1,4 +1,4 @@
-# Makefile.in generated by automake 1.13.3 from Makefile.am.
+# Makefile.in generated by automake 1.14.1 from Makefile.am.
# @configure_input@
# Copyright (C) 1994-2013 Free Software Foundation, Inc.
@@ -215,8 +215,6 @@ am_palinear_OBJECTS = $(am__objects_9) $(am__objects_10) \
$(am__objects_2) $(am__objects_12)
palinear_OBJECTS = $(am_palinear_OBJECTS)
palinear_LDADD = $(LDADD)
-palinear_LINK = $(CXXLD) $(palinear_CXXFLAGS) $(CXXFLAGS) \
- $(AM_LDFLAGS) $(LDFLAGS) -o $@
am__palogist_SOURCES_DIST = data.h data.cpp gendata.h gendata.cpp \
mematrix.h mematri1.h command_line_settings.h \
command_line_settings.cpp reg1.h usage.h usage.cpp main.cpp \
@@ -256,8 +254,6 @@ am_palogist_OBJECTS = $(am__objects_13) $(am__objects_14) \
$(am__objects_2) $(am__objects_16)
palogist_OBJECTS = $(am_palogist_OBJECTS)
palogist_LDADD = $(LDADD)
-palogist_LINK = $(CXXLD) $(palogist_CXXFLAGS) $(CXXFLAGS) \
- $(AM_LDFLAGS) $(LDFLAGS) -o $@
am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
am__vpath_adj = case $$p in \
$(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
@@ -487,18 +483,15 @@ RHEADERS = include/R.h include/Rmath.h include/R_ext/Arith.h \
@BUILD_pacoxph_TRUE at COXBASE = coxfit2 chinv2 cholesky2 chsolve2 dmatrix
@BUILD_pacoxph_TRUE at COXSRC = $(COXBASE:=.c)
palinear_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS) $(am__append_5)
-palinear_CXXFLAGS = -DLINEAR $(AM_CXXFLAGS) $(am__append_6)
-palinear_CPPFLAGS = $(AM_CPPFLAGS)
+palinear_CPPFLAGS = -DLINEAR $(AM_CPPFLAGS) $(am__append_6)
palogist_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS) $(am__append_7)
-palogist_CXXFLAGS = -DLOGISTIC $(AM_CXXFLAGS) $(am__append_8)
-palogist_CPPFLAGS = $(AM_CPPFLAGS)
+palogist_CPPFLAGS = -DLOGISTIC $(AM_CPPFLAGS) $(am__append_8)
pacoxph_SOURCES = $(COXSRC) $(REGFILES) $(FVSRC) $(FVHEADERS) \
$(RHEADERS) survS.h survproto.h coxph_data.h coxph_data.cpp \
$(am__append_9)
-pacoxph_CXXFLAGS = -DCOXPH -I $(top_srcdir)/src/include $(AM_CXXFLAGS) \
- $(am__append_10)
-pacoxph_CPPFLAGS = $(AM_CPPFLAGS)
-pacoxph_CFLAGS = -DCOXPH -I $(top_srcdir)/src/include $(AM_CFLAGS)
+pacoxph_CXXFLAGS = -I $(top_srcdir)/src/include $(AM_CXXFLAGS)
+pacoxph_CPPFLAGS = -DCOXPH $(AM_CPPFLAGS) $(am__append_10)
+pacoxph_CFLAGS = -I $(top_srcdir)/src/include $(AM_CFLAGS)
extract_snp_SOURCES = extract-snp.cpp $(FVSRC) $(FVHEADERS)
dist_bin_SCRIPTS = probabel
scriptdir = $(pkgdatadir)/scripts
@@ -518,9 +511,9 @@ $(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am $(am__confi
exit 1;; \
esac; \
done; \
- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/Makefile'; \
+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign src/Makefile'; \
$(am__cd) $(top_srcdir) && \
- $(AUTOMAKE) --gnu src/Makefile
+ $(AUTOMAKE) --foreign src/Makefile
.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
@@ -541,8 +534,8 @@ $(ACLOCAL_M4): @MAINTAINER_MODE_TRUE@ $(am__aclocal_m4_deps)
$(am__aclocal_m4_deps):
config.h: stamp-h1
- @if test ! -f $@; then rm -f stamp-h1; else :; fi
- @if test ! -f $@; then $(MAKE) $(AM_MAKEFLAGS) stamp-h1; else :; fi
+ @test -f $@ || rm -f stamp-h1
+ @test -f $@ || $(MAKE) $(AM_MAKEFLAGS) stamp-h1
stamp-h1: $(srcdir)/config.h.in $(top_builddir)/config.status
@rm -f stamp-h1
@@ -673,7 +666,7 @@ fvlib/palinear-Transposer.$(OBJEXT): fvlib/$(am__dirstamp) \
palinear$(EXEEXT): $(palinear_OBJECTS) $(palinear_DEPENDENCIES) $(EXTRA_palinear_DEPENDENCIES)
@rm -f palinear$(EXEEXT)
- $(AM_V_CXXLD)$(palinear_LINK) $(palinear_OBJECTS) $(palinear_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(palinear_OBJECTS) $(palinear_LDADD) $(LIBS)
fvlib/palogist-AbstractMatrix.$(OBJEXT): fvlib/$(am__dirstamp) \
fvlib/$(DEPDIR)/$(am__dirstamp)
fvlib/palogist-CastUtils.$(OBJEXT): fvlib/$(am__dirstamp) \
@@ -697,7 +690,7 @@ fvlib/palogist-Transposer.$(OBJEXT): fvlib/$(am__dirstamp) \
palogist$(EXEEXT): $(palogist_OBJECTS) $(palogist_DEPENDENCIES) $(EXTRA_palogist_DEPENDENCIES)
@rm -f palogist$(EXEEXT)
- $(AM_V_CXXLD)$(palogist_LINK) $(palogist_OBJECTS) $(palogist_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(palogist_OBJECTS) $(palogist_LDADD) $(LIBS)
install-dist_binSCRIPTS: $(dist_bin_SCRIPTS)
@$(NORMAL_INSTALL)
@list='$(dist_bin_SCRIPTS)'; test -n "$(bindir)" || list=; \
@@ -1267,648 +1260,648 @@ pacoxph-eigen_mematrix.obj: eigen_mematrix.cpp
@am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(pacoxph_CPPFLAGS) $(CPPFLAGS) $(pacoxph_CXXFLAGS) $(CXXFLAGS) -c -o pacoxph-eigen_mematrix.obj `if test -f 'eigen_mematrix.cpp'; then $(CYGPATH_W) 'eigen_mematrix.cpp'; else $(CYGPATH_W) '$(srcdir)/eigen_mematrix.cpp'; fi`
palinear-data.o: data.cpp
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -MT palinear-data.o -MD -MP -MF $(DEPDIR)/palinear-data.Tpo -c -o palinear-data.o `test -f 'data.cpp' || echo '$(srcdir)/'`data.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT palinear-data.o -MD -MP -MF $(DEPDIR)/palinear-data.Tpo -c -o palinear-data.o `test -f 'data.cpp' || echo '$(srcdir)/'`data.cpp
@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/palinear-data.Tpo $(DEPDIR)/palinear-data.Po
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='data.cpp' object='palinear-data.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -c -o palinear-data.o `test -f 'data.cpp' || echo '$(srcdir)/'`data.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o palinear-data.o `test -f 'data.cpp' || echo '$(srcdir)/'`data.cpp
palinear-data.obj: data.cpp
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -MT palinear-data.obj -MD -MP -MF $(DEPDIR)/palinear-data.Tpo -c -o palinear-data.obj `if test -f 'data.cpp'; then $(CYGPATH_W) 'data.cpp'; else $(CYGPATH_W) '$(srcdir)/data.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT palinear-data.obj -MD -MP -MF $(DEPDIR)/palinear-data.Tpo -c -o palinear-data.obj `if test -f 'data.cpp'; then $(CYGPATH_W) 'data.cpp'; else $(CYGPATH_W) '$(srcdir)/data.cpp'; fi`
@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/palinear-data.Tpo $(DEPDIR)/palinear-data.Po
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='data.cpp' object='palinear-data.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -c -o palinear-data.obj `if test -f 'data.cpp'; then $(CYGPATH_W) 'data.cpp'; else $(CYGPATH_W) '$(srcdir)/data.cpp'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o palinear-data.obj `if test -f 'data.cpp'; then $(CYGPATH_W) 'data.cpp'; else $(CYGPATH_W) '$(srcdir)/data.cpp'; fi`
palinear-gendata.o: gendata.cpp
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -MT palinear-gendata.o -MD -MP -MF $(DEPDIR)/palinear-gendata.Tpo -c -o palinear-gendata.o `test -f 'gendata.cpp' || echo '$(srcdir)/'`gendata.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT palinear-gendata.o -MD -MP -MF $(DEPDIR)/palinear-gendata.Tpo -c -o palinear-gendata.o `test -f 'gendata.cpp' || echo '$(srcdir)/'`gendata.cpp
@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/palinear-gendata.Tpo $(DEPDIR)/palinear-gendata.Po
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='gendata.cpp' object='palinear-gendata.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -c -o palinear-gendata.o `test -f 'gendata.cpp' || echo '$(srcdir)/'`gendata.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o palinear-gendata.o `test -f 'gendata.cpp' || echo '$(srcdir)/'`gendata.cpp
palinear-gendata.obj: gendata.cpp
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -MT palinear-gendata.obj -MD -MP -MF $(DEPDIR)/palinear-gendata.Tpo -c -o palinear-gendata.obj `if test -f 'gendata.cpp'; then $(CYGPATH_W) 'gendata.cpp'; else $(CYGPATH_W) '$(srcdir)/gendata.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT palinear-gendata.obj -MD -MP -MF $(DEPDIR)/palinear-gendata.Tpo -c -o palinear-gendata.obj `if test -f 'gendata.cpp'; then $(CYGPATH_W) 'gendata.cpp'; else $(CYGPATH_W) '$(srcdir)/gendata.cpp'; fi`
@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/palinear-gendata.Tpo $(DEPDIR)/palinear-gendata.Po
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='gendata.cpp' object='palinear-gendata.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o palinear-gendata.obj `if test -f 'gendata.cpp'; then $(CYGPATH_W) 'gendata.cpp'; else $(CYGPATH_W) '$(srcdir)/gendata.cpp'; fi`
palinear-command_line_settings.o: command_line_settings.cpp
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -MT palinear-command_line_settings.o -MD -MP -MF $(DEPDIR)/palinear-command_line_settings.Tpo -c -o palinear-command_line_settings.o `test -f 'command_line_settings.cpp' || echo '$(srcdir)/'`command_line_settings.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT palinear-command_line_settings.o -MD -MP -MF $(DEPDIR)/palinear-command_line_settings.Tpo -c -o palinear-command_line_settings.o `test -f 'command_line_settings.cpp' || echo '$(srcdir)/'`command_line_settings.cpp
@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/palinear-command_line_settings.Tpo $(DEPDIR)/palinear-command_line_settings.Po
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='command_line_settings.cpp' object='palinear-command_line_settings.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -c -o palinear-command_line_settings.o `test -f 'command_line_settings.cpp' || echo '$(srcdir)/'`command_line_settings.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o palinear-command_line_settings.o `test -f 'command_line_settings.cpp' || echo '$(srcdir)/'`command_line_settings.cpp
palinear-command_line_settings.obj: command_line_settings.cpp
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -MT palinear-command_line_settings.obj -MD -MP -MF $(DEPDIR)/palinear-command_line_settings.Tpo -c -o palinear-command_line_settings.obj `if test -f 'command_line_settings.cpp'; then $(CYGPATH_W) 'command_line_settings.cpp'; else $(CYGPATH_W) '$(srcdir)/command_line_settings.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT palinear-command_line_settings.obj -MD -MP -MF $(DEPDIR)/palinear-command_line_settings.Tpo -c -o palinear-command_line_settings.obj `if test -f 'command_line_settings.cpp'; then $(CYGPATH_W) 'command_line_settings.cpp'; else $(CYGPATH_W) '$(srcdir)/command_line_settings.cpp'; fi`
@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/palinear-command_line_settings.Tpo $(DEPDIR)/palinear-command_line_settings.Po
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='command_line_settings.cpp' object='palinear-command_line_settings.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o palinear-command_line_settings.obj `if test -f 'command_line_settings.cpp'; then $(CYGPATH_W) 'command_line_settings.cpp'; else $(CYGPATH_W) '$(srcdir)/command_line_settings.cpp'; fi`
palinear-usage.o: usage.cpp
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -MT palinear-usage.o -MD -MP -MF $(DEPDIR)/palinear-usage.Tpo -c -o palinear-usage.o `test -f 'usage.cpp' || echo '$(srcdir)/'`usage.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT palinear-usage.o -MD -MP -MF $(DEPDIR)/palinear-usage.Tpo -c -o palinear-usage.o `test -f 'usage.cpp' || echo '$(srcdir)/'`usage.cpp
@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/palinear-usage.Tpo $(DEPDIR)/palinear-usage.Po
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='usage.cpp' object='palinear-usage.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -c -o palinear-usage.o `test -f 'usage.cpp' || echo '$(srcdir)/'`usage.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o palinear-usage.o `test -f 'usage.cpp' || echo '$(srcdir)/'`usage.cpp
palinear-usage.obj: usage.cpp
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -MT palinear-usage.obj -MD -MP -MF $(DEPDIR)/palinear-usage.Tpo -c -o palinear-usage.obj `if test -f 'usage.cpp'; then $(CYGPATH_W) 'usage.cpp'; else $(CYGPATH_W) '$(srcdir)/usage.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT palinear-usage.obj -MD -MP -MF $(DEPDIR)/palinear-usage.Tpo -c -o palinear-usage.obj `if test -f 'usage.cpp'; then $(CYGPATH_W) 'usage.cpp'; else $(CYGPATH_W) '$(srcdir)/usage.cpp'; fi`
@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/palinear-usage.Tpo $(DEPDIR)/palinear-usage.Po
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='usage.cpp' object='palinear-usage.obj' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o palinear-usage.obj `if test -f 'usage.cpp'; then $(CYGPATH_W) 'usage.cpp'; else $(CYGPATH_W) '$(srcdir)/usage.cpp'; fi`
palinear-main.o: main.cpp
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -MT palinear-main.o -MD -MP -MF $(DEPDIR)/palinear-main.Tpo -c -o palinear-main.o `test -f 'main.cpp' || echo '$(srcdir)/'`main.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT palinear-main.o -MD -MP -MF $(DEPDIR)/palinear-main.Tpo -c -o palinear-main.o `test -f 'main.cpp' || echo '$(srcdir)/'`main.cpp
@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/palinear-main.Tpo $(DEPDIR)/palinear-main.Po
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+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o palinear-main.o `test -f 'main.cpp' || echo '$(srcdir)/'`main.cpp
palinear-main.obj: main.cpp
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -MT palinear-main.obj -MD -MP -MF $(DEPDIR)/palinear-main.Tpo -c -o palinear-main.obj `if test -f 'main.cpp'; then $(CYGPATH_W) 'main.cpp'; else $(CYGPATH_W) '$(srcdir)/main.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT palinear-main.obj -MD -MP -MF $(DEPDIR)/palinear-main.Tpo -c -o palinear-main.obj `if test -f 'main.cpp'; then $(CYGPATH_W) 'main.cpp'; else $(CYGPATH_W) '$(srcdir)/main.cpp'; fi`
@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/palinear-main.Tpo $(DEPDIR)/palinear-main.Po
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palinear-utilities.o: utilities.cpp
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+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT palinear-utilities.o -MD -MP -MF $(DEPDIR)/palinear-utilities.Tpo -c -o palinear-utilities.o `test -f 'utilities.cpp' || echo '$(srcdir)/'`utilities.cpp
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palinear-utilities.obj: utilities.cpp
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fvlib/palinear-Logger.o: fvlib/Logger.cpp
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fvlib/palogist-Transposer.obj: fvlib/Transposer.cpp
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(palogist_CXXFLAGS) $(CXXFLAGS) -MT fvlib/palogist-Transposer.obj -MD -MP -MF fvlib/$(DEPDIR)/palogist-Transposer.Tpo -c -o fvlib/palogist-Transposer.obj `if test -f 'fvlib/Transposer.cpp'; then $(CYGPATH_W) 'fvlib/Transposer.cpp'; else $(CYGPATH_W) '$(srcdir)/fvlib/Transposer.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT fvlib/palogist-Transposer.obj -MD -MP -MF fvlib/$(DEPDIR)/palogist-Transposer.Tpo -c -o fvlib/palogist-Transposer.obj `if test -f 'fvlib/Transposer.cpp'; then $(CYGPATH_W) 'fvlib/Transposer.cpp'; else $(CYGPATH_W) '$(srcdir)/fvlib/Transposer.cpp'; fi`
@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) fvlib/$(DEPDIR)/palogist-Transposer.Tpo fvlib/$(DEPDIR)/palogist-Transposer.Po
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='fvlib/Transposer.cpp' object='fvlib/palogist-Transposer.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(palogist_CXXFLAGS) $(CXXFLAGS) -c -o fvlib/palogist-Transposer.obj `if test -f 'fvlib/Transposer.cpp'; then $(CYGPATH_W) 'fvlib/Transposer.cpp'; else $(CYGPATH_W) '$(srcdir)/fvlib/Transposer.cpp'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o fvlib/palogist-Transposer.obj `if test -f 'fvlib/Transposer.cpp'; then $(CYGPATH_W) 'fvlib/Transposer.cpp'; else $(CYGPATH_W) '$(srcdir)/fvlib/Transposer.cpp'; fi`
palogist-eigen_mematrix.o: eigen_mematrix.cpp
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(palogist_CXXFLAGS) $(CXXFLAGS) -MT palogist-eigen_mematrix.o -MD -MP -MF $(DEPDIR)/palogist-eigen_mematrix.Tpo -c -o palogist-eigen_mematrix.o `test -f 'eigen_mematrix.cpp' || echo '$(srcdir)/'`eigen_mematrix.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT palogist-eigen_mematrix.o -MD -MP -MF $(DEPDIR)/palogist-eigen_mematrix.Tpo -c -o palogist-eigen_mematrix.o `test -f 'eigen_mematrix.cpp' || echo '$(srcdir)/'`eigen_mematrix.cpp
@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/palogist-eigen_mematrix.Tpo $(DEPDIR)/palogist-eigen_mematrix.Po
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='eigen_mematrix.cpp' object='palogist-eigen_mematrix.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(palogist_CXXFLAGS) $(CXXFLAGS) -c -o palogist-eigen_mematrix.o `test -f 'eigen_mematrix.cpp' || echo '$(srcdir)/'`eigen_mematrix.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o palogist-eigen_mematrix.o `test -f 'eigen_mematrix.cpp' || echo '$(srcdir)/'`eigen_mematrix.cpp
palogist-eigen_mematrix.obj: eigen_mematrix.cpp
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(palogist_CXXFLAGS) $(CXXFLAGS) -MT palogist-eigen_mematrix.obj -MD -MP -MF $(DEPDIR)/palogist-eigen_mematrix.Tpo -c -o palogist-eigen_mematrix.obj `if test -f 'eigen_mematrix.cpp'; then $(CYGPATH_W) 'eigen_mematrix.cpp'; else $(CYGPATH_W) '$(srcdir)/eigen_mematrix.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT palogist-eigen_mematrix.obj -MD -MP -MF $(DEPDIR)/palogist-eigen_mematrix.Tpo -c -o palogist-eigen_mematrix.obj `if test -f 'eigen_mematrix.cpp'; then $(CYGPATH_W) 'eigen_mematrix.cpp'; else $(CYGPATH_W) '$(srcdir)/eigen_mematrix.cpp'; fi`
@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/palogist-eigen_mematrix.Tpo $(DEPDIR)/palogist-eigen_mematrix.Po
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='eigen_mematrix.cpp' object='palogist-eigen_mematrix.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(palogist_CXXFLAGS) $(CXXFLAGS) -c -o palogist-eigen_mematrix.obj `if test -f 'eigen_mematrix.cpp'; then $(CYGPATH_W) 'eigen_mematrix.cpp'; else $(CYGPATH_W) '$(srcdir)/eigen_mematrix.cpp'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o palogist-eigen_mematrix.obj `if test -f 'eigen_mematrix.cpp'; then $(CYGPATH_W) 'eigen_mematrix.cpp'; else $(CYGPATH_W) '$(srcdir)/eigen_mematrix.cpp'; fi`
install-dist_scriptDATA: $(dist_script_DATA)
@$(NORMAL_INSTALL)
@list='$(dist_script_DATA)'; test -n "$(scriptdir)" || list=; \
@@ -2167,10 +2160,10 @@ uninstall-am: uninstall-binPROGRAMS uninstall-dist_binSCRIPTS \
install-exec-hook:
- $(SED) -i "s;probabel_config.cfg;@sysconfdir@/probabel_config.cfg;" \
+ $(SED) -i -e "s;probabel_config.cfg;@sysconfdir@/probabel_config.cfg;" \
$(DESTDIR)$(bindir)/probabel
- $(SED) -i "s;\./;@bindir@/;" $(DESTDIR)$(bindir)/probabel
- $(SED) -i "s;PROBABEL_VERSION;@VERSION@;" $(DESTDIR)$(bindir)/probabel
+ $(SED) -i -e "s;\./;@bindir@/;" $(DESTDIR)$(bindir)/probabel
+ $(SED) -i -e "s;PROBABEL_VERSION;@VERSION@;" $(DESTDIR)$(bindir)/probabel
ln -s $(DESTDIR)$(bindir)/probabel $(DESTDIR)$(bindir)/probabel.pl
install-data-hook:
diff --git a/src/config.h.in b/src/config.h.in
index 4fc07a4..bcd1c0d 100644
--- a/src/config.h.in
+++ b/src/config.h.in
@@ -96,9 +96,6 @@
/* Define to 1 if the system has the type `_Bool'. */
#undef HAVE__BOOL
-/* Define to 1 if your C compiler doesn't accept -c and -o together. */
-#undef NO_MINUS_C_MINUS_O
-
/* Name of package */
#undef PACKAGE
diff --git a/src/coxph_data.cpp b/src/coxph_data.cpp
index 0d0495d..1e6e70a 100644
--- a/src/coxph_data.cpp
+++ b/src/coxph_data.cpp
@@ -438,16 +438,23 @@ void coxph_reg::estimate(coxph_data &cdatain, const int verbose,
niter = maxiter;
+
// Check the results of the Cox fit; mirrored from the same checks
- // in coxph_fit.S from the R survival package
+ // in coxph.fit.S and coxph.R from the R survival package.
- bool setToZero = false;
+ bool setToNAN = false;
+ // Based on coxph.fit.S lines with 'which.sing' and coxph.R line
+ // with if(any(is.NA(coefficients))). These lines set coefficients
+ // to NA if flag < nvar (with nvar = ncol(x)) and maxiter >
+ // 0. coxph.R then checks for any NAs in the coefficients and
+ // outputs the warning message if NAs were found.
if (flag < X.nrow && maxiter > 0) {
cerr << "Warning for " << snpinfo.name[cursnp]
<< ": X matrix deemed to be singular,"
- << " setting beta and se to 'nan'\n";
- setToZero = true;
+ << " setting beta and se to 'NaN'\n";
+
+ setToNAN = true;
}
if (niter >= maxiterinput)
@@ -461,23 +468,38 @@ void coxph_reg::estimate(coxph_data &cdatain, const int verbose,
{
cerr << "Warning for " << snpinfo.name[cursnp]
<< ": Cox regression ran out of iterations and did not converge,"
- << " setting beta and se to 'nan'\n";
- setToZero = true;
+ << " setting beta and se to 'NaN'\n";
+ setToNAN = true;
} else {
#if EIGEN
VectorXd ueigen = u.data;
MatrixXd imateigen = imat.data;
VectorXd infs = ueigen.transpose() * imateigen;
+ infs = infs.cwiseAbs();
VectorXd betaeigen = beta.data;
- if ( infs.norm() > eps ||
- infs.norm() > sqrt(eps) * betaeigen.norm() )
- {
+ bool problems = false;
+
+ assert(betaeigen.size() == infs.size());
+
+ // We check the beta's for all coefficients
+ // (incl. covariates), maybe stick to only checking the SNP
+ // coefficient?
+ for (int i = 0; i < infs.size(); i++) {
+ if (infs[i] > eps && infs[i] > sqrt(eps) * abs(betaeigen[i])) {
+ problems = true;
+ }
+ }
+
+ if (problems) {
cerr << "Warning for " << snpinfo.name[cursnp]
<< ": beta may be infinite,"
- << " setting beta and se to 'nan'\n";
+ << " setting beta and se to 'NaN'\n";
- setToZero = true;
+ setToNAN = true;
}
+
+ // cout << "beta values for SNP: " << snpinfo.name[cursnp]
+ // << " are: " << betaeigen << std::endl;
#else
cerr << "Warning for " << snpinfo.name[cursnp]
<< ": can't check for infinite betas."
@@ -488,7 +510,7 @@ void coxph_reg::estimate(coxph_data &cdatain, const int verbose,
for (int i = 0; i < X.nrow; i++)
{
- if (setToZero)
+ if (setToNAN)
{
// Cox regression failed
sebeta[i] = NAN;
diff --git a/src/main.cpp b/src/main.cpp
index 5543c90..71b1729 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -83,7 +83,7 @@
/// Maximum number of iterations we allow the regression to run
#define MAXITER 20
/// Tolerance for convergence
-#define EPS 1.e-8
+#define EPS 1.e-9
/// Precision for the Cholesky decomposition
#define CHOLTOL 1.5e-12
--
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