This is an automated email from the git hooks/post-receive script. lkajan pushed a commit to branch master in repository freecontact.
commit a603e0a71c0cc2a9c6dfb587a2ce8eb866087a99 Author: Laszlo Kajan <[email protected]> Date: Wed Sep 18 15:54:24 2013 +0200 Imported Upstream version 1.0.18 --- ChangeLog | 8 + Makefile.in | 10 +- aclocal.m4 | 122 +++++++++++++- compile | 347 ++++++++++++++++++++++++++++++++++++++ configure | 175 +++++++++++++++++-- configure.ac | 3 +- lib/Makefile.in | 6 +- lib/config.h | 9 +- lib/config.hin | 3 + lib/freecontact.cpp | 30 +++- lib/freecontact.h | 19 +-- missing | 461 +++++++++++++++++---------------------------------- src/Makefile.in | 2 +- src/freecontact.cpp | 8 +- 14 files changed, 840 insertions(+), 363 deletions(-) diff --git a/ChangeLog b/ChangeLog index 1754298..6a96f06 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,11 @@ +freecontact (1.0.18) unstable; urgency=low + + * Fixed compiler SSE2 support detection problem (Debian bug #721380). + * Fixed perlpod =item <number> issue (Debian bug #721381). + * Fixed issue with including x86intrin.h on non-x86 (Debian bug #721379). + + -- Laszlo Kajan <[email protected]> Tue, 17 Sep 2013 17:10:34 +0200 + freecontact (1.0.17) unstable; urgency=low * Edited _print_help() message. diff --git a/Makefile.in b/Makefile.in index bf82a11..b9b3256 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 from Makefile.am. # @configure_input@ # Copyright (C) 1994-2013 Free Software Foundation, Inc. @@ -80,7 +80,7 @@ host_triplet = @host@ subdir = . DIST_COMMON = INSTALL NEWS README AUTHORS ChangeLog \ $(srcdir)/Makefile.in $(srcdir)/Makefile.am \ - $(top_srcdir)/configure $(am__configure_deps) COPYING \ + $(top_srcdir)/configure $(am__configure_deps) COPYING compile \ config.guess config.sub depcomp install-sh missing ltmain.sh ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 am__aclocal_m4_deps = $(top_srcdir)/m4/ax_blas.m4 \ @@ -631,10 +631,16 @@ 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) diff --git a/aclocal.m4 b/aclocal.m4 index 4bcf28e..762f927 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 -*- 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], [], [AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl ]) @@ -51,7 +51,7 @@ m4_define([_AM_AUTOCONF_VERSION], []) # Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced. # This function is AC_REQUIREd by AM_INIT_AUTOMAKE. AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION], -[AM_AUTOMAKE_VERSION([1.13.3])dnl +[AM_AUTOMAKE_VERSION([1.14])dnl m4_ifndef([AC_AUTOCONF_VERSION], [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl _AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))]) @@ -455,6 +455,12 @@ AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS], # This macro actually does too much. Some checks are only needed if # your package does certain things. But this isn't really a big deal. +dnl Redefine AC_PROG_CC to automatically invoke _AM_PROG_CC_C_O. +m4_define([AC_PROG_CC], +m4_defn([AC_PROG_CC]) +[_AM_PROG_CC_C_O +]) + # AM_INIT_AUTOMAKE(PACKAGE, VERSION, [NO-DEFINE]) # AM_INIT_AUTOMAKE([OPTIONS]) # ----------------------------------------------- @@ -563,7 +569,48 @@ dnl macro is hooked onto _AC_COMPILER_EXEEXT early, see below. AC_CONFIG_COMMANDS_PRE(dnl [m4_provide_if([_AM_COMPILER_EXEEXT], [AM_CONDITIONAL([am__EXEEXT], [test -n "$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 [email protected] 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 @@ -571,7 +618,6 @@ 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. @@ -753,6 +799,70 @@ 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. 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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. + +# This file is maintained in Automake, please report +# bugs to <[email protected]> or send patches to +# <[email protected]>. + +nl=' +' + +# We need space, tab and new line, in precisely that order. Quoting is +# there to prevent tools from complaining about whitespace usage. +IFS=" "" $nl" + +file_conv= + +# func_file_conv build_file lazy +# Convert a $build file to $host form and store it in $file +# Currently only supports Windows hosts. If the determined conversion +# type is listed in (the comma separated) LAZY, no conversion will +# take place. +func_file_conv () +{ + file=$1 + case $file in + / | /[!/]*) # absolute file, and not a UNC file + if test -z "$file_conv"; then + # lazily determine how to convert abs files + case `uname -s` in + MINGW*) + file_conv=mingw + ;; + CYGWIN*) + file_conv=cygwin + ;; + *) + file_conv=wine + ;; + esac + fi + case $file_conv/,$2, in + *,$file_conv,*) + ;; + mingw/*) + file=`cmd //C echo "$file " | sed -e 's/"\(.*\) " *$/\1/'` + ;; + cygwin/*) + file=`cygpath -m "$file" || echo "$file"` + ;; + wine/*) + file=`winepath -w "$file" || echo "$file"` + ;; + esac + ;; + esac +} + +# func_cl_dashL linkdir +# Make cl look for libraries in LINKDIR +func_cl_dashL () +{ + func_file_conv "$1" + if test -z "$lib_path"; then + lib_path=$file + else + lib_path="$lib_path;$file" + fi + linker_opts="$linker_opts -LIBPATH:$file" +} + +# func_cl_dashl library +# Do a library search-path lookup for cl +func_cl_dashl () +{ + lib=$1 + found=no + save_IFS=$IFS + IFS=';' + for dir in $lib_path $LIB + do + IFS=$save_IFS + if $shared && test -f "$dir/$lib.dll.lib"; then + found=yes + lib=$dir/$lib.dll.lib + break + fi + if test -f "$dir/$lib.lib"; then + found=yes + lib=$dir/$lib.lib + break + fi + if test -f "$dir/lib$lib.a"; then + found=yes + lib=$dir/lib$lib.a + break + fi + done + IFS=$save_IFS + + if test "$found" != yes; then + lib=$lib.lib + fi +} + +# func_cl_wrapper cl arg... +# Adjust compile command to suit cl +func_cl_wrapper () +{ + # Assume a capable shell + lib_path= + shared=: + linker_opts= + for arg + do + if test -n "$eat"; then + eat= + else + case $1 in + -o) + # configure might choose to run compile as 'compile cc -o foo foo.c'. + eat=1 + case $2 in + *.o | *.[oO][bB][jJ]) + func_file_conv "$2" + set x "$@" -Fo"$file" + shift + ;; + *) + func_file_conv "$2" + set x "$@" -Fe"$file" + shift + ;; + esac + ;; + -I) + eat=1 + func_file_conv "$2" mingw + set x "$@" -I"$file" + shift + ;; + -I*) + func_file_conv "${1#-I}" mingw + set x "$@" -I"$file" + shift + ;; + -l) + eat=1 + func_cl_dashl "$2" + set x "$@" "$lib" + shift + ;; + -l*) + func_cl_dashl "${1#-l}" + set x "$@" "$lib" + shift + ;; + -L) + eat=1 + func_cl_dashL "$2" + ;; + -L*) + func_cl_dashL "${1#-L}" + ;; + -static) + shared=false + ;; + -Wl,*) + arg=${1#-Wl,} + save_ifs="$IFS"; IFS=',' + for flag in $arg; do + IFS="$save_ifs" + linker_opts="$linker_opts $flag" + done + IFS="$save_ifs" + ;; + -Xlinker) + eat=1 + linker_opts="$linker_opts $2" + ;; + -*) + set x "$@" "$1" + shift + ;; + *.cc | *.CC | *.cxx | *.CXX | *.[cC]++) + func_file_conv "$1" + set x "$@" -Tp"$file" + shift + ;; + *.c | *.cpp | *.CPP | *.lib | *.LIB | *.Lib | *.OBJ | *.obj | *.[oO]) + func_file_conv "$1" mingw + set x "$@" "$file" + shift + ;; + *) + set x "$@" "$1" + shift + ;; + esac + fi + shift + done + if test -n "$linker_opts"; then + linker_opts="-link$linker_opts" + fi + exec "$@" $linker_opts + exit 1 +} + +eat= + +case $1 in + '') + echo "$0: No command. Try '$0 --help' for more information." 1>&2 + exit 1; + ;; + -h | --h*) + cat <<\EOF +Usage: compile [--help] [--version] PROGRAM [ARGS] + +Wrapper for compilers which do not understand '-c -o'. +Remove '-o dest.o' from ARGS, run PROGRAM with the remaining +arguments, and rename the output as expected. + +If you are trying to build a whole package this is not the +right script to run: please start by reading the file 'INSTALL'. + +Report bugs to <[email protected]>. +EOF + exit $? + ;; + -v | --v*) + echo "compile $scriptversion" + exit $? + ;; + cl | *[/\\]cl | cl.exe | *[/\\]cl.exe ) + func_cl_wrapper "$@" # Doesn't return... + ;; +esac + +ofile= +cfile= + +for arg +do + if test -n "$eat"; then + eat= + else + case $1 in + -o) + # configure might choose to run compile as 'compile cc -o foo foo.c'. + # So we strip '-o arg' only if arg is an object. + eat=1 + case $2 in + *.o | *.obj) + ofile=$2 + ;; + *) + set x "$@" -o "$2" + shift + ;; + esac + ;; + *.c) + cfile=$1 + set x "$@" "$1" + shift + ;; + *) + set x "$@" "$1" + shift + ;; + esac + fi + shift +done + +if test -z "$ofile" || test -z "$cfile"; then + # If no '-o' option was seen then we might have been invoked from a + # pattern rule where we don't need one. That is ok -- this is a + # normal compilation that the losing compiler can handle. If no + # '.c' file was seen then we are probably linking. That is also + # ok. + exec "$@" +fi + +# Name of file we expect compiler to create. +cofile=`echo "$cfile" | sed 's|^.*[\\/]||; s|^[a-zA-Z]:||; s/\.c$/.o/'` + +# Create the lock directory. +# Note: use '[/\\:.-]' here to ensure that we don't use the same name +# that we are using for the .o file. Also, base the name on the expected +# object file name, since that is what matters with a parallel build. +lockdir=`echo "$cofile" | sed -e 's|[/\\:.-]|_|g'`.d +while true; do + if mkdir "$lockdir" >/dev/null 2>&1; then + break + fi + sleep 1 +done +# FIXME: race condition here if user kills between mkdir and trap. +trap "rmdir '$lockdir'; exit 1" 1 2 15 + +# Run the compile. +"$@" +ret=$? + +if test -f "$cofile"; then + test "$cofile" = "$ofile" || mv "$cofile" "$ofile" +elif test -f "${cofile}bj"; then + test "${cofile}bj" = "$ofile" || mv "${cofile}bj" "$ofile" +fi + +rmdir "$lockdir" +exit $ret + +# Local Variables: +# mode: shell-script +# sh-indentation: 2 +# eval: (add-hook 'write-file-hooks 'time-stamp) +# time-stamp-start: "scriptversion=" +# time-stamp-format: "%:y-%02m-%02d.%02H" +# time-stamp-time-zone: "UTC" +# time-stamp-end: "; # UTC" +# End: diff --git a/configure b/configure index 0694ec3..bcc5c29 100755 --- a/configure +++ b/configure @@ -1,6 +1,6 @@ #! /bin/sh # Guess values for system-dependent variables and create Makefiles. -# Generated by GNU Autoconf 2.69 for freecontact 1.0.17. +# Generated by GNU Autoconf 2.69 for freecontact 1.0.18. # # Report bugs to <[email protected]>. # @@ -590,8 +590,8 @@ MAKEFLAGS= # Identity of this package. PACKAGE_NAME='freecontact' PACKAGE_TARNAME='freecontact' -PACKAGE_VERSION='1.0.17' -PACKAGE_STRING='freecontact 1.0.17' +PACKAGE_VERSION='1.0.18' +PACKAGE_STRING='freecontact 1.0.18' PACKAGE_BUGREPORT='[email protected]' PACKAGE_URL='' @@ -632,6 +632,7 @@ ac_includes_default="\ # include <unistd.h> #endif" +ac_header_list= ac_subst_vars='am__EXEEXT_FALSE am__EXEEXT_TRUE LTLIBOBJS @@ -1424,7 +1425,7 @@ if test "$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 freecontact 1.0.17 to adapt to many kinds of systems. +\`configure' configures freecontact 1.0.18 to adapt to many kinds of systems. Usage: $0 [OPTION]... [VAR=VALUE]... @@ -1494,7 +1495,7 @@ fi if test -n "$ac_init_help"; then case $ac_init_help in - short | recursive ) echo "Configuration of freecontact 1.0.17:";; + short | recursive ) echo "Configuration of freecontact 1.0.18:";; esac cat <<\_ACEOF @@ -1643,7 +1644,7 @@ fi test -n "$ac_init_help" && exit $ac_status if $ac_init_version; then cat <<\_ACEOF -freecontact configure 1.0.17 +freecontact configure 1.0.18 generated by GNU Autoconf 2.69 Copyright (C) 2012 Free Software Foundation, Inc. @@ -2327,11 +2328,42 @@ $as_echo "$ac_res" >&6; } eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno } # ac_fn_cxx_check_func + +# ac_fn_cxx_check_header_compile LINENO HEADER VAR INCLUDES +# --------------------------------------------------------- +# Tests whether HEADER exists and can be compiled using the include files in +# INCLUDES, setting the cache variable VAR accordingly. +ac_fn_cxx_check_header_compile () +{ + as_lineno=${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 <$2> +_ACEOF +if ac_fn_cxx_try_compile "$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_cxx_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 freecontact $as_me 1.0.17, which was +It was created by freecontact $as_me 1.0.18, which was generated by GNU Autoconf 2.69. Invocation command line was $ $0 $@ @@ -2611,6 +2643,7 @@ $as_echo "$as_me: creating cache $cache_file" >&6;} >$cache_file fi +as_fn_append ac_header_list " x86intrin.h" # Check that the precious variables saved in the cache have kept the same # value. ac_cache_corrupted=false @@ -2684,7 +2717,7 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu ac_config_headers="$ac_config_headers lib/config.h:lib/config.hin" -am__api_version='1.13' +am__api_version='1.14' ac_aux_dir= for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do @@ -3199,7 +3232,7 @@ fi # Define the identity of the package. PACKAGE='freecontact' - VERSION='1.0.17' + VERSION='1.0.18' cat >>confdefs.h <<_ACEOF @@ -3250,6 +3283,47 @@ 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 [email protected] 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 ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' @@ -5424,6 +5498,65 @@ ac_compile='$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 + + depcc="$CC" am_compiler_list= { $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5 @@ -26162,6 +26295,26 @@ $as_echo "$as_me: WARNING: Your processor support avx instructions but not your + for ac_header in $ac_header_list +do : + as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` +ac_fn_cxx_check_header_compile "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default +" +if eval test \"x\$"$as_ac_Header"\" = x"yes"; then : + cat >>confdefs.h <<_ACEOF +#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1 +_ACEOF + +fi + +done + + + + + + + @@ -28581,7 +28734,7 @@ cat >>$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 freecontact $as_me 1.0.17, which was +This file was extended by freecontact $as_me 1.0.18, which was generated by GNU Autoconf 2.69. Invocation command line was CONFIG_FILES = $CONFIG_FILES @@ -28647,7 +28800,7 @@ _ACEOF cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`" ac_cs_version="\\ -freecontact config.status 1.0.17 +freecontact config.status 1.0.18 configured by $0, generated by GNU Autoconf 2.69, with options \\"\$ac_cs_config\\" diff --git a/configure.ac b/configure.ac index a3c8d85..672cf72 100644 --- a/configure.ac +++ b/configure.ac @@ -14,7 +14,7 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. # -AC_INIT([freecontact], [1.0.17], [[email protected]]) +AC_INIT([freecontact], [1.0.18], [[email protected]]) AC_CONFIG_MACRO_DIR([m4]) AC_CONFIG_SRCDIR([src/freecontact.cpp]) @@ -69,6 +69,7 @@ AM_COND_IF([HAVE_XSDCXX], ]) AX_EXT +AC_CHECK_HEADERS_ONCE([x86intrin.h]) DX_DOT_FEATURE(OFF) DX_PDF_FEATURE(OFF) diff --git a/lib/Makefile.in b/lib/Makefile.in index 5415728..6b77b87 100644 --- a/lib/Makefile.in +++ b/lib/Makefile.in @@ -1,4 +1,4 @@ -# Makefile.in generated by automake 1.13.3 from Makefile.am. +# Makefile.in generated by automake 1.14 from Makefile.am. # @configure_input@ # Copyright (C) 1994-2013 Free Software Foundation, Inc. @@ -506,8 +506,8 @@ $(ACLOCAL_M4): $(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.hin $(top_builddir)/config.status @rm -f stamp-h1 diff --git a/lib/config.h b/lib/config.h index d336afa..462b4c4 100644 --- a/lib/config.h +++ b/lib/config.h @@ -86,6 +86,9 @@ /* Define to 1 if you have the <unistd.h> header file. */ #define HAVE_UNISTD_H 1 +/* Define to 1 if you have the <x86intrin.h> header file. */ +#define HAVE_X86INTRIN_H 1 + /* Define if XSDCXX is enabled */ #define HAVE_XSDCXX 1 @@ -103,7 +106,7 @@ #define PACKAGE_NAME "freecontact" /* Define to the full name and version of this package. */ -#define PACKAGE_STRING "freecontact 1.0.17" +#define PACKAGE_STRING "freecontact 1.0.18" /* Define to the one symbol short name of this package. */ #define PACKAGE_TARNAME "freecontact" @@ -112,7 +115,7 @@ #define PACKAGE_URL "" /* Define to the version of this package. */ -#define PACKAGE_VERSION "1.0.17" +#define PACKAGE_VERSION "1.0.18" /* Define to necessary symbol if this constant uses a non-standard name on your system. */ @@ -122,4 +125,4 @@ #define STDC_HEADERS 1 /* Version number of package */ -#define VERSION "1.0.17" +#define VERSION "1.0.18" diff --git a/lib/config.hin b/lib/config.hin index 125a234..dc5b745 100644 --- a/lib/config.hin +++ b/lib/config.hin @@ -85,6 +85,9 @@ /* Define to 1 if you have the <unistd.h> header file. */ #undef HAVE_UNISTD_H +/* Define to 1 if you have the <x86intrin.h> header file. */ +#undef HAVE_X86INTRIN_H + /* Define if XSDCXX is enabled */ #undef HAVE_XSDCXX diff --git a/lib/freecontact.cpp b/lib/freecontact.cpp index 077ab6a..4fb2795 100644 --- a/lib/freecontact.cpp +++ b/lib/freecontact.cpp @@ -14,9 +14,8 @@ * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#include "config.h" +#include "freecontact.h" -#include <boost/format.hpp> #ifdef HAVE_OPENMP #include <omp.h> #endif @@ -26,11 +25,9 @@ //#include <memory> // auto_ptr, unique_ptr #include <signal.h> #include <stdio.h> -#include <string.h> #include <sys/time.h> #include <time.h> #include <unistd.h> -#include "freecontact.h" // lkajan: EVfold-mfDCA is calculate_evolutionary_constraints.m @@ -187,6 +184,11 @@ static inline vector<contact_t> static inline uint32_t _cache_holds_nseq(uint16_t __seqsize); +#ifndef __SSE2__ +static inline __m128i _mm_setzero_si128(){ __m128i m; long long *mp = (long long *)&m; mp[1] = mp[0] = 0; return m; } +#endif + + class _glasso_timer { timer_t _timerid; @@ -255,7 +257,7 @@ void predictor::get_seq_weights( // lkajan: allow for other vectorizations as well #define CAN_VECW 0 - #ifdef HAVE_SSE2 + #ifdef __SSE2__ #undef CAN_VECW #define CAN_VECW 1 #endif @@ -299,7 +301,7 @@ void predictor::get_seq_weights( } } } - #ifdef HAVE_SSE2 + #ifdef __SSE2__ else { // lkajan: Dynamically set chunk size according to (L1) cache size (cat /sys/devices/system/cpu/cpu0/cache/index*/{coherency_line_size,level,size,type}). @@ -395,7 +397,7 @@ void predictor::get_seq_weights( } #else // should never happen unless bug else throw std::runtime_error(bo::str(bo::format("ooops, there is a bug in %s around %s:%d") % PACKAGE % __FILE__ % __LINE__ )); - #endif // HAVE_SSE2 + #endif // __SSE2__ __wtot = 0; // total weight of all aligments, EVfold-mfDCA::Meff __aliw = freq_vec_t(__ali.seqcnt); // alignment weight array, EVfold-mfDCA::W @@ -986,6 +988,20 @@ predictor::cont_res_t } +ali_t& ali_t::push(const std::vector<uint8_t>& __al) throw (alilen_error) +{ + if( __al.size() != alilen ) throw alilen_error(bo::str(bo::format("alignment length mismatch, expected %d, got %d") % alilen % __al.size() )); + resize( ++seqcnt*alilen16, _mm_setzero_si128() ); + + uint8_t *alptr = reinterpret_cast<uint8_t*>(data()) + (seqcnt-1) * alilenpad; + memcpy(alptr, __al.data(), __al.size()); + + if( capacity() == size() ) + reserve( size() + 1024*alilen16 ); + return *this; +} + + /// Calculate raw contact scores using given function and collect row/column/overall mean for APC calculation. /** \param [out] __raw_ctscore * \param [out] __apc_bg diff --git a/lib/freecontact.h b/lib/freecontact.h index 38b340c..0608213 100644 --- a/lib/freecontact.h +++ b/lib/freecontact.h @@ -17,6 +17,8 @@ #ifndef LIBFREECONTACT_H #define LIBFREECONTACT_H +#include "config.h" + #include <boost/format.hpp> #include <errno.h> #include <map> @@ -24,7 +26,9 @@ #include <stdint.h> #include <string.h> #include <vector> +#ifdef HAVE_X86INTRIN_H #include <x86intrin.h> +#endif // HAVE_X86INTRIN_H #define LIBFREEC_API __attribute__ ((visibility ("default"))) #define LIBFREEC_LOCAL __attribute__ ((visibility ("hidden"))) @@ -61,10 +65,8 @@ class LIBFREEC_API icme_timeout_error : public std::runtime_error { icme_timeout_error(const std::string& __arg) : std::runtime_error(__arg){} }; -// For ali_t: #ifndef __SSE2__ typedef long long __m128i __attribute__ ((__vector_size__ (16), __may_alias__)); -__m128i _mm_setzero_si128(){ __m128i m; long long *mp = (long long *)&m; mp[1] = mp[0] = 0; return m; } #endif /// Protein sequence alignment. @@ -112,18 +114,7 @@ class LIBFREEC_API ali_t : public std::vector<__m128i> } /// Push a sequence to the alignment. - inline ali_t& push(const std::vector<uint8_t>& __al) throw (alilen_error) - { - if( __al.size() != alilen ) throw alilen_error(bo::str(bo::format("alignment length mismatch, expected %d, got %d") % alilen % __al.size() )); - resize( ++seqcnt*alilen16, _mm_setzero_si128() ); - - uint8_t *alptr = reinterpret_cast<uint8_t*>(data()) + (seqcnt-1) * alilenpad; - memcpy(alptr, __al.data(), __al.size()); - - if( capacity() == size() ) - reserve( size() + 1024*alilen16 ); - return *this; - } + ali_t& push(const std::vector<uint8_t>& __al) throw (alilen_error); /// Push a sequence to the alignment. inline ali_t& push(const std::string& __l) throw (alilen_error) diff --git a/missing b/missing index 28055d2..cdea514 100755 --- a/missing +++ b/missing @@ -1,11 +1,10 @@ #! /bin/sh -# Common stub for a few missing GNU programs while installing. +# Common wrapper for a few potentially missing GNU programs. -scriptversion=2009-04-28.21; # UTC +scriptversion=2012-06-26.16; # UTC -# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006, -# 2008, 2009 Free Software Foundation, Inc. -# Originally by Fran,cois Pinard <[email protected]>, 1996. +# Copyright (C) 1996-2013 Free Software Foundation, Inc. +# Originally written by Fran,cois Pinard <[email protected]>, 1996. # 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 @@ -26,69 +25,40 @@ scriptversion=2009-04-28.21; # UTC # the same distribution terms that you use for the rest of that program. if test $# -eq 0; then - echo 1>&2 "Try \`$0 --help' for more information" + echo 1>&2 "Try '$0 --help' for more information" exit 1 fi -run=: -sed_output='s/.* --output[ =]\([^ ]*\).*/\1/p' -sed_minuso='s/.* -o \([^ ]*\).*/\1/p' - -# In the cases where this matters, `missing' is being run in the -# srcdir already. -if test -f configure.ac; then - configure_ac=configure.ac -else - configure_ac=configure.in -fi +case $1 in -msg="missing on your system" + --is-lightweight) + # Used by our autoconf macros to check whether the available missing + # script is modern enough. + exit 0 + ;; -case $1 in ---run) - # Try to run requested program, and just exit if it succeeds. - run= - shift - "$@" && exit 0 - # Exit code 63 means version mismatch. This often happens - # when the user try to use an ancient version of a tool on - # a file that requires a minimum version. In this case we - # we should proceed has if the program had been absent, or - # if --run hadn't been passed. - if test $? = 63; then - run=: - msg="probably too old" - fi - ;; + --run) + # Back-compat with the calling convention used by older automake. + shift + ;; -h|--h|--he|--hel|--help) echo "\ $0 [OPTION]... PROGRAM [ARGUMENT]... -Handle \`PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an -error status if there is no known handling for PROGRAM. +Run 'PROGRAM [ARGUMENT]...', returning a proper advice when this fails due +to PROGRAM being missing or too old. Options: -h, --help display this help and exit -v, --version output version information and exit - --run try to run the given command, and emulate it if it fails Supported PROGRAM values: - aclocal touch file \`aclocal.m4' - autoconf touch file \`configure' - autoheader touch file \`config.h.in' - autom4te touch the output file, or create a stub one - automake touch all \`Makefile.in' files - bison create \`y.tab.[ch]', if possible, from existing .[ch] - flex create \`lex.yy.c', if possible, from existing .c - help2man touch the output file - lex create \`lex.yy.c', if possible, from existing .c - makeinfo touch the output file - tar try tar, gnutar, gtar, then tar without non-portable flags - yacc create \`y.tab.[ch]', if possible, from existing .[ch] + aclocal autoconf autoheader autom4te automake makeinfo + bison yacc flex lex help2man -Version suffixes to PROGRAM as well as the prefixes \`gnu-', \`gnu', and -\`g' are ignored when checking the name. +Version suffixes to PROGRAM as well as the prefixes 'gnu-', 'gnu', and +'g' are ignored when checking the name. Send bug reports to <[email protected]>." exit $? @@ -100,272 +70,141 @@ Send bug reports to <[email protected]>." ;; -*) - echo 1>&2 "$0: Unknown \`$1' option" - echo 1>&2 "Try \`$0 --help' for more information" + echo 1>&2 "$0: unknown '$1' option" + echo 1>&2 "Try '$0 --help' for more information" exit 1 ;; esac -# normalize program name to check for. -program=`echo "$1" | sed ' - s/^gnu-//; t - s/^gnu//; t - s/^g//; t'` - -# Now exit if we have it, but it failed. Also exit now if we -# don't have it and --version was passed (most likely to detect -# the program). 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Grab either from any GNU archive site." - # The file to touch is that specified with -o ... - file=`echo "$*" | sed -n "$sed_output"` - test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"` - if test -z "$file"; then - # ... or it is the one specified with @setfilename ... - infile=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'` - file=`sed -n ' - /^@setfilename/{ - s/.* \([^ ]*\) *$/\1/ - p - q - }' $infile` - # ... or it is derived from the source name (dir/f.texi becomes f.info) - test -z "$file" && file=`echo "$infile" | sed 's,.*/,,;s,.[^.]*$,,'`.info - fi - # If the file does not exist, the user really needs makeinfo; - # let's fail without touching anything. - test -f $file || exit 1 - touch $file - ;; - - tar*) - shift - - # We have already tried tar in the generic part. - # Look for gnutar/gtar before invocation to avoid ugly error - # messages. - if (gnutar --version > /dev/null 2>&1); then - gnutar "$@" && exit 0 - fi - if (gtar --version > /dev/null 2>&1); then - gtar "$@" && exit 0 - fi - firstarg="$1" - if shift; then - case $firstarg in - *o*) - firstarg=`echo "$firstarg" | sed s/o//` - tar "$firstarg" "$@" && exit 0 - ;; - esac - case $firstarg in - *h*) - firstarg=`echo "$firstarg" | sed s/h//` - tar "$firstarg" "$@" && exit 0 - ;; - esac - fi - - echo 1>&2 "\ -WARNING: I can't seem to be able to run \`tar' with the given arguments. - You may want to install GNU tar or Free paxutils, or check the - command line arguments." - exit 1 - ;; - - *) - echo 1>&2 "\ -WARNING: \`$1' is needed, and is $msg. - You might have modified some files without having the - proper tools for further handling them. Check the \`README' file, - it often tells you about the needed prerequisites for installing - this package. You may also peek at any GNU archive site, in case - some other package would contain this missing \`$1' program." - exit 1 - ;; -esac +# Run the given program, remember its exit status. +"$@"; st=$? + +# If it succeeded, we are done. +test $st -eq 0 && exit 0 + +# Also exit now if we it failed (or wasn't found), and '--version' was +# passed; such an option is passed most likely to detect whether the +# program is present and works. +case $2 in --version|--help) exit $st;; esac + +# Exit code 63 means version mismatch. This often happens when the user +# tries to use an ancient version of a tool on a file that requires a +# minimum version. +if test $st -eq 63; then + msg="probably too old" +elif test $st -eq 127; then + # Program was missing. + msg="missing on your system" +else + # Program was found and executed, but failed. Give up. + exit $st +fi -exit 0 +perl_URL=http://www.perl.org/ +flex_URL=http://flex.sourceforge.net/ +gnu_software_URL=http://www.gnu.org/software + +program_details () +{ + case $1 in + aclocal|automake) + echo "The '$1' program is part of the GNU Automake package:" + echo "<$gnu_software_URL/automake>" + echo "It also requires GNU Autoconf, GNU m4 and Perl in order to run:" + echo "<$gnu_software_URL/autoconf>" + echo "<$gnu_software_URL/m4/>" + echo "<$perl_URL>" + ;; + autoconf|autom4te|autoheader) + echo "The '$1' program is part of the GNU Autoconf package:" + echo "<$gnu_software_URL/autoconf/>" + echo "It also requires GNU m4 and Perl in order to run:" + echo "<$gnu_software_URL/m4/>" + echo "<$perl_URL>" + ;; + esac +} + +give_advice () +{ + # Normalize program name to check for. + normalized_program=`echo "$1" | sed ' + s/^gnu-//; t + s/^gnu//; t + s/^g//; t'` + + printf '%s\n' "'$1' is $msg." + + configure_deps="'configure.ac' or m4 files included by 'configure.ac'" + case $normalized_program in + autoconf*) + echo "You should only need it if you modified 'configure.ac'," + echo "or m4 files included by it." + program_details 'autoconf' + ;; + autoheader*) + echo "You should only need it if you modified 'acconfig.h' or" + echo "$configure_deps." + program_details 'autoheader' + ;; + automake*) + echo "You should only need it if you modified 'Makefile.am' or" + echo "$configure_deps." + program_details 'automake' + ;; + aclocal*) + echo "You should only need it if you modified 'acinclude.m4' or" + echo "$configure_deps." + program_details 'aclocal' + ;; + autom4te*) + echo "You might have modified some maintainer files that require" + echo "the 'automa4te' program to be rebuilt." + program_details 'autom4te' + ;; + bison*|yacc*) + echo "You should only need it if you modified a '.y' file." + echo "You may want to install the GNU Bison package:" + echo "<$gnu_software_URL/bison/>" + ;; + lex*|flex*) + echo "You should only need it if you modified a '.l' file." + echo "You may want to install the Fast Lexical Analyzer package:" + echo "<$flex_URL>" + ;; + help2man*) + echo "You should only need it if you modified a dependency" \ + "of a man page." + echo "You may want to install the GNU Help2man package:" + echo "<$gnu_software_URL/help2man/>" + ;; + makeinfo*) + echo "You should only need it if you modified a '.texi' file, or" + echo "any other file indirectly affecting the aspect of the manual." + echo "You might want to install the Texinfo package:" + echo "<$gnu_software_URL/texinfo/>" + echo "The spurious makeinfo call might also be the consequence of" + echo "using a buggy 'make' (AIX, DU, IRIX), in which case you might" + echo "want to install GNU make:" + echo "<$gnu_software_URL/make/>" + ;; + *) + echo "You might have modified some files without having the proper" + echo "tools for further handling them. Check the 'README' file, it" + echo "often tells you about the needed prerequisites for installing" + echo "this package. You may also peek at any GNU archive site, in" + echo "case some other package contains this missing '$1' program." + ;; + esac +} + +give_advice "$1" | sed -e '1s/^/WARNING: /' \ + -e '2,$s/^/ /' >&2 + +# Propagate the correct exit status (expected to be 127 for a program +# not found, 63 for a program that failed due to version mismatch). +exit $st # Local variables: # eval: (add-hook 'write-file-hooks 'time-stamp) diff --git a/src/Makefile.in b/src/Makefile.in index 4b19bca..0c783b3 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 from Makefile.am. # @configure_input@ # Copyright (C) 1994-2013 Free Software Foundation, Inc. diff --git a/src/freecontact.cpp b/src/freecontact.cpp index 8440e9d..1c5ddd8 100644 --- a/src/freecontact.cpp +++ b/src/freecontact.cpp @@ -339,7 +339,7 @@ PSICOV of D. Jones et al. (2011) [2]. FreeContact is accelerated by a combination of vector instructions, multiple threads, and faster implementation of key parts. -Depending on the alignment, 10-fold or higher speedups are possible. +Depending on the alignment, 8-fold or higher speedups are possible. A sufficiently large alignment is required for meaningful results. As a minimum, an alignment with an effective (after-weighting) sequence count @@ -565,15 +565,15 @@ Print version. =over -=item 0 +=item I<0> No error - success. -=item 1 +=item I<1> Unspecified error. -=item 2 +=item I<2> A timeout (see B<--icme-timeout>) occurred. -- Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/freecontact.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
