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_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4-67- boost_lib_version_req=ifelse([$1], ,1.20.0,$1)
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4:68: boost_lib_version_req_shorten=`expr $boost_lib_version_req : '\([[0-9]]*\.[[0-9]]*\)'`
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4:69: boost_lib_version_req_major=`expr $boost_lib_version_req : '\([[0-9]]*\)'`
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4:70: boost_lib_version_req_minor=`expr $boost_lib_version_req : '[[0-9]]*\.\([[0-9]]*\)'`
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4:71: boost_lib_version_req_sub_minor=`expr $boost_lib_version_req : '[[0-9]]*\.[[0-9]]*\.\([[0-9]]*\)'`
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4-72- if test "x$boost_lib_version_req_sub_minor" = "x" ; then
##############################################
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4-74- fi
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4:75: WANT_BOOST_VERSION=`expr $boost_lib_version_req_major \* 100000 \+ $boost_lib_version_req_minor \* 100 \+ $boost_lib_version_req_sub_minor`
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4-76- AC_MSG_CHECKING(for boostlib >= $boost_lib_version_req)
##############################################
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4-133- if test -d "$ac_boost_path" && test -r "$ac_boost_path"; then
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4:134: for i in `ls -d $ac_boost_path/include/boost-* 2>/dev/null`; do
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4:135: _version_tmp=`echo $i | sed "s#$ac_boost_path##" | sed 's/\/include\/boost-//' | sed 's/_/./'`
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4:136: V_CHECK=`expr $_version_tmp \> $_version`
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4-137- if test "$V_CHECK" = "1" ; then
##############################################
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4-139- fi
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4:140: VERSION_UNDERSCORE=`echo $_version | sed 's/\./_/'`
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4-141- BOOST_CPPFLAGS="-I$ac_boost_path/include/boost-$VERSION_UNDERSCORE"
##############################################
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4-146- if test -d "$ac_boost_path" && test -r "$ac_boost_path"; then
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4:147: for i in `ls -d $ac_boost_path/include/boost-* 2>/dev/null`; do
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4:148: _version_tmp=`echo $i | sed "s#$ac_boost_path##" | sed 's/\/include\/boost-//' | sed 's/_/./'`
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4:149: V_CHECK=`expr $_version_tmp \> $_version`
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4-150- if test "$V_CHECK" = "1" ; then
##############################################
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4-157-
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4:158: VERSION_UNDERSCORE=`echo $_version | sed 's/\./_/'`
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4-159- BOOST_CPPFLAGS="-I$best_path/include/boost-$VERSION_UNDERSCORE"
##############################################
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4-166- if test -d "$BOOST_ROOT" && test -r "$BOOST_ROOT" && test -d "$BOOST_ROOT/stage/lib" && test -r "$BOOST_ROOT/stage/lib"; then
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4:167: version_dir=`expr //$BOOST_ROOT : '.*/\(.*\)'`
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4:168: stage_version=`echo $version_dir | sed 's/boost_//' | sed 's/_/./g'`
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4:169: stage_version_shorten=`expr $stage_version : '\([[0-9]]*\.[[0-9]]*\)'`
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4:170: V_CHECK=`expr $stage_version_shorten \>\= $_version`
cufflinks-2.2.1+dfsg.1/ax_boost_base.m4-171- if test "$V_CHECK" = "1" -a "$ac_boost_lib_path" = "" ; then
##############################################
cufflinks-2.2.1+dfsg.1/ax_boost_serialization.m4-78- AC_DEFINE(HAVE_BOOST_SERIALIZATION,,[define if the Boost::Serialization library is available])
cufflinks-2.2.1+dfsg.1/ax_boost_serialization.m4:79: BOOSTLIBDIR=`echo $BOOST_LDFLAGS | sed -e 's/@<:@^\/@:>@*//'`
cufflinks-2.2.1+dfsg.1/ax_boost_serialization.m4-80-
##############################################
cufflinks-2.2.1+dfsg.1/ax_boost_serialization.m4-83- if test "x$ax_boost_user_serialization_lib" = "x"; then
cufflinks-2.2.1+dfsg.1/ax_boost_serialization.m4:84: for libextension in `ls $BOOSTLIBDIR/libboost_serialization*.so* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_serialization.*\)\.so.*$;\1;'` `ls $BOOSTLIBDIR/libboost_serialization*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_serialization.*\)\.a*$;\1;'`; do
cufflinks-2.2.1+dfsg.1/ax_boost_serialization.m4-85- ax_lib=${libextension}
##############################################
cufflinks-2.2.1+dfsg.1/ax_boost_serialization.m4-90- if test "x$link_serialization" != "xyes"; then
cufflinks-2.2.1+dfsg.1/ax_boost_serialization.m4:91: for libextension in `ls $BOOSTLIBDIR/boost_serialization*.dll* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_serialization.*\)\.dll.*$;\1;'` `ls $BOOSTLIBDIR/libboost_serialization*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_serialization.*\)\.a*$;\1;'` ; do
cufflinks-2.2.1+dfsg.1/ax_boost_serialization.m4-92- ax_lib=${libextension}
##############################################
cufflinks-2.2.1+dfsg.1/ax_boost_serialization.m4-107- if test "x$ax_boost_user_serialization_lib" = "x"; then
cufflinks-2.2.1+dfsg.1/ax_boost_serialization.m4:108: for libextension in `ls $BOOSTLIBDIR/libboost_serialization*.so* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_serialization.*\)\.so.*$;\1;'` `ls $BOOSTLIBDIR/libboost_serialization*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_serialization.*\)\.a*$;\1;'`; do
cufflinks-2.2.1+dfsg.1/ax_boost_serialization.m4-109- ax_lib=${libextension}
##############################################
cufflinks-2.2.1+dfsg.1/ax_boost_serialization.m4-114- if test "x$link_serialization" != "xyes"; then
cufflinks-2.2.1+dfsg.1/ax_boost_serialization.m4:115: for libextension in `ls $BOOSTLIBDIR/boost_serialization*.dll* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_serialization.*\)\.dll.*$;\1;'` `ls $BOOSTLIBDIR/libboost_serialization*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_serialization.*\)\.a*$;\1;'` ; do
cufflinks-2.2.1+dfsg.1/ax_boost_serialization.m4-116- ax_lib=${libextension}
##############################################
cufflinks-2.2.1+dfsg.1/ax_boost_system.m4-78- AC_DEFINE(HAVE_BOOST_SYSTEM,,[define if the Boost::System library is available])
cufflinks-2.2.1+dfsg.1/ax_boost_system.m4:79: BOOSTLIBDIR=`echo $BOOST_LDFLAGS | sed -e 's/@<:@^\/@:>@*//'`
cufflinks-2.2.1+dfsg.1/ax_boost_system.m4-80-
##############################################
cufflinks-2.2.1+dfsg.1/ax_boost_system.m4-83- if test "x$ax_boost_user_system_lib" = "x"; then
cufflinks-2.2.1+dfsg.1/ax_boost_system.m4:84: for libextension in `ls $BOOSTLIBDIR/libboost_system*.so* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_system.*\)\.so.*$;\1;'` `ls $BOOSTLIBDIR/libboost_system*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_system.*\)\.a*$;\1;'`; do
cufflinks-2.2.1+dfsg.1/ax_boost_system.m4-85- ax_lib=${libextension}
##############################################
cufflinks-2.2.1+dfsg.1/ax_boost_system.m4-90- if test "x$link_system" != "xyes"; then
cufflinks-2.2.1+dfsg.1/ax_boost_system.m4:91: for libextension in `ls $BOOSTLIBDIR/boost_system*.dll* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_system.*\)\.dll.*$;\1;'` `ls $BOOSTLIBDIR/libboost_system*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_system.*\)\.a*$;\1;'` ; do
cufflinks-2.2.1+dfsg.1/ax_boost_system.m4-92- ax_lib=${libextension}
##############################################
cufflinks-2.2.1+dfsg.1/ax_boost_system.m4-107- if test "x$ax_boost_user_system_lib" = "x"; then
cufflinks-2.2.1+dfsg.1/ax_boost_system.m4:108: for libextension in `ls $BOOSTLIBDIR/libboost_system*.so* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_system.*\)\.so.*$;\1;'` `ls $BOOSTLIBDIR/libboost_system*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_system.*\)\.a*$;\1;'`; do
cufflinks-2.2.1+dfsg.1/ax_boost_system.m4-109- ax_lib=${libextension}
##############################################
cufflinks-2.2.1+dfsg.1/ax_boost_system.m4-114- if test "x$link_system" != "xyes"; then
cufflinks-2.2.1+dfsg.1/ax_boost_system.m4:115: for libextension in `ls $BOOSTLIBDIR/boost_system*.dll* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_system.*\)\.dll.*$;\1;'` `ls $BOOSTLIBDIR/libboost_system*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_system.*\)\.a*$;\1;'` ; do
cufflinks-2.2.1+dfsg.1/ax_boost_system.m4-116- ax_lib=${libextension}
##############################################
cufflinks-2.2.1+dfsg.1/ax_boost_thread.m4-96- AC_DEFINE(HAVE_BOOST_THREAD,,[define if the Boost::Thread library is available])
cufflinks-2.2.1+dfsg.1/ax_boost_thread.m4:97: BOOSTLIBDIR=`echo $BOOST_LDFLAGS | sed -e 's/@<:@^\/@:>@*//'`
cufflinks-2.2.1+dfsg.1/ax_boost_thread.m4-98-
##############################################
cufflinks-2.2.1+dfsg.1/ax_boost_thread.m4-106- if test "x$ax_boost_user_thread_lib" = "x"; then
cufflinks-2.2.1+dfsg.1/ax_boost_thread.m4:107: for libextension in `ls $BOOSTLIBDIR/libboost_thread*.so* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_thread.*\)\.so.*$;\1;'` `ls $BOOSTLIBDIR/libboost_thread*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_thread.*\)\.a*$;\1;'`; do
cufflinks-2.2.1+dfsg.1/ax_boost_thread.m4-108- ax_lib=${libextension}
##############################################
cufflinks-2.2.1+dfsg.1/ax_boost_thread.m4-113- if test "x$link_thread" != "xyes"; then
cufflinks-2.2.1+dfsg.1/ax_boost_thread.m4:114: for libextension in `ls $BOOSTLIBDIR/boost_thread*.dll* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_thread.*\)\.dll.*$;\1;'` `ls $BOOSTLIBDIR/libboost_thread*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_thread.*\)\.a*$;\1;'` ; do
cufflinks-2.2.1+dfsg.1/ax_boost_thread.m4-115- ax_lib=${libextension}
##############################################
cufflinks-2.2.1+dfsg.1/ax_boost_thread.m4-141- if test "x$ax_boost_user_system_lib" = "x"; then
cufflinks-2.2.1+dfsg.1/ax_boost_thread.m4:142: for libextension in `ls $BOOSTLIBDIR/libboost_system*.so* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_system.*\)\.so.*$;\1;'` `ls $BOOSTLIBDIR/libboost_system*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_system.*\)\.a*$;\1;'`; do
cufflinks-2.2.1+dfsg.1/ax_boost_thread.m4-143- ax_lib=${libextension}
##############################################
cufflinks-2.2.1+dfsg.1/ax_boost_thread.m4-148- if test "x$link_system" != "xyes"; then
cufflinks-2.2.1+dfsg.1/ax_boost_thread.m4:149: for libextension in `ls $BOOSTLIBDIR/boost_system*.dll* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_system.*\)\.dll.*$;\1;'` `ls $BOOSTLIBDIR/libboost_system*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_system.*\)\.a*$;\1;'` ; do
cufflinks-2.2.1+dfsg.1/ax_boost_thread.m4-150- ax_lib=${libextension}
##############################################
cufflinks-2.2.1+dfsg.1/boost.m4-57- if test "$have_boost" = "yes"; then
cufflinks-2.2.1+dfsg.1/boost.m4:58: WANT_BOOST_MAJOR=`expr $boost_min_version : '\([[0-9]]\+\)'`
cufflinks-2.2.1+dfsg.1/boost.m4:59: WANT_BOOST_MINOR=`expr $boost_min_version : '[[0-9]]\+\.\([[0-9]]\+\)'`
cufflinks-2.2.1+dfsg.1/boost.m4:60: WANT_BOOST_SUB_MINOR=`expr $boost_min_version : '[[0-9]]\+\.[[0-9]]\+\.\([[0-9]]\+\)'`
cufflinks-2.2.1+dfsg.1/boost.m4:61: WANT_BOOST_VERSION=`expr $WANT_BOOST_MAJOR \* 100000 \+ $WANT_BOOST_MINOR \* 100 \+ $WANT_BOOST_SUB_MINOR`
cufflinks-2.2.1+dfsg.1/boost.m4-62-
##############################################
cufflinks-2.2.1+dfsg.1/src/cuffmerge-36- -h/--help Prints the help message and exits
cufflinks-2.2.1+dfsg.1/src/cuffmerge:37: -o <output_dir> Directory where merged assembly will be written [ default: ./merged_asm ]
cufflinks-2.2.1+dfsg.1/src/cuffmerge-38- -g/--ref-gtf An optional "reference" annotation GTF.
##############################################
cufflinks-2.2.1+dfsg.1/debian/patches/py2to3.patch-230- if fasta != None:
cufflinks-2.2.1+dfsg.1/debian/patches/py2to3.patch:231:- comp_cmd = '''cuffcompare -o tmp_meta_asm -C -G %s -s %s %s''' % (ref_str, fasta, meta_asm_gtf)
cufflinks-2.2.1+dfsg.1/debian/patches/py2to3.patch-232-+ comp_cmd = '''cuffcompare -o %s -C -G %s -s %s %s''' % (tmp_dir, ref_str, fasta, meta_asm_gtf)
cufflinks-2.2.1+dfsg.1/debian/patches/py2to3.patch-233- else:
cufflinks-2.2.1+dfsg.1/debian/patches/py2to3.patch:234:- comp_cmd = '''cuffcompare -o tmp_meta_asm -C -G %s %s''' % (ref_str, meta_asm_gtf)
cufflinks-2.2.1+dfsg.1/debian/patches/py2to3.patch-235-+ comp_cmd = '''cuffcompare -o %s -C -G %s %s''' % (tmp_dir, ref_str, meta_asm_gtf)
##############################################
cufflinks-2.2.1+dfsg.1/.pc/py2to3.patch/src/cuffmerge-31- -h/--help Prints the help message and exits
cufflinks-2.2.1+dfsg.1/.pc/py2to3.patch/src/cuffmerge:32: -o <output_dir> Directory where merged assembly will be written [ default: ./merged_asm ]
cufflinks-2.2.1+dfsg.1/.pc/py2to3.patch/src/cuffmerge-33- -g/--ref-gtf An optional "reference" annotation GTF.
##############################################
cufflinks-2.2.1+dfsg.1/.pc/py2to3.patch/src/cuffmerge-329- if fasta != None:
cufflinks-2.2.1+dfsg.1/.pc/py2to3.patch/src/cuffmerge:330: comp_cmd = '''cuffcompare -o tmp_meta_asm -C -G %s -s %s %s''' % (ref_str, fasta, meta_asm_gtf)
cufflinks-2.2.1+dfsg.1/.pc/py2to3.patch/src/cuffmerge-331- else:
cufflinks-2.2.1+dfsg.1/.pc/py2to3.patch/src/cuffmerge:332: comp_cmd = '''cuffcompare -o tmp_meta_asm -C -G %s %s''' % (ref_str, meta_asm_gtf)
cufflinks-2.2.1+dfsg.1/.pc/py2to3.patch/src/cuffmerge-333-
##############################################
cufflinks-2.2.1+dfsg.1/.pc/0004-fix-m64-usage-and-lfs.patch/configure.ac-130-if test x"${GCC}" = x"yes" ; then
cufflinks-2.2.1+dfsg.1/.pc/0004-fix-m64-usage-and-lfs.patch/configure.ac:131: gcc_version=`${CC} --version | head -n 1`
cufflinks-2.2.1+dfsg.1/.pc/0004-fix-m64-usage-and-lfs.patch/configure.ac-132- echo " GCC version: ${gcc_version}"
##############################################
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4-63-# bam_lib_version_req=ifelse([$1], ,1.20.0,$1)
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4:64:# bam_lib_version_req_shorten=`expr $bam_lib_version_req : '\([[0-9]]*\.[[0-9]]*\)'`
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4:65:# bam_lib_version_req_major=`expr $bam_lib_version_req : '\([[0-9]]*\)'`
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4:66:# bam_lib_version_req_minor=`expr $bam_lib_version_req : '[[0-9]]*\.\([[0-9]]*\)'`
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4:67:# bam_lib_version_req_sub_minor=`expr $bam_lib_version_req : '[[0-9]]*\.[[0-9]]*\.\([[0-9]]*\)'`
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4-68-# if test "x$bam_lib_version_req_sub_minor" = "x" ; then
##############################################
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4-70-# fi
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4:71:# WANT_BAM_VERSION=`expr $bam_lib_version_req_major \* 100000 \+ $bam_lib_version_req_minor \* 100 \+ $bam_lib_version_req_sub_minor`
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4-72- AC_MSG_CHECKING(for bamlib)
##############################################
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4-120- if test -d "$ac_bam_path" && test -r "$ac_bam_path"; then
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4:121: for i in `ls -d $ac_bam_path/include/bam-* 2>/dev/null`; do
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4:122: _version_tmp=`echo $i | sed "s#$ac_bam_path##" | sed 's/\/include\/bam-//' | sed 's/_/./'`
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4:123: V_CHECK=`expr $_version_tmp \> $_version`
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4-124- if test "$V_CHECK" = "1" ; then
##############################################
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4-126- fi
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4:127: VERSION_UNDERSCORE=`echo $_version | sed 's/\./_/'`
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4-128- BAM_CPPFLAGS="-I$ac_bam_path/include/bam-$VERSION_UNDERSCORE"
##############################################
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4-133- if test -d "$ac_bam_path" && test -r "$ac_bam_path"; then
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4:134: for i in `ls -d $ac_bam_path/include/bam-* 2>/dev/null`; do
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4:135: _version_tmp=`echo $i | sed "s#$ac_bam_path##" | sed 's/\/include\/bam-//' | sed 's/_/./'`
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4:136: V_CHECK=`expr $_version_tmp \> $_version`
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4-137- if test "$V_CHECK" = "1" ; then
##############################################
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4-144-
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4:145: VERSION_UNDERSCORE=`echo $_version | sed 's/\./_/'`
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4-146- BAM_CPPFLAGS="-I$best_path/include/bam-$VERSION_UNDERSCORE"
##############################################
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4-153- if test -d "$BAM_ROOT" && test -r "$BAM_ROOT" && test -d "$BAM_ROOT/stage/lib" && test -r "$BAM_ROOT/stage/lib"; then
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4:154: version_dir=`expr //$BAM_ROOT : '.*/\(.*\)'`
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4:155: stage_version=`echo $version_dir | sed 's/bam_//' | sed 's/_/./g'`
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4:156: stage_version_shorten=`expr $stage_version : '\([[0-9]]*\.[[0-9]]*\)'`
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4:157: V_CHECK=`expr $stage_version_shorten \>\= $_version`
cufflinks-2.2.1+dfsg.1/.pc/0002-bam2samtools.patch/ax_bam.m4-158- if test "$V_CHECK" = "1" -a "$ac_bam_lib_path" = "" ; then
##############################################
cufflinks-2.2.1+dfsg.1/configure.ac-125-if test x"${GCC}" = x"yes" ; then
cufflinks-2.2.1+dfsg.1/configure.ac:126: gcc_version=`${CC} --version | head -n 1`
cufflinks-2.2.1+dfsg.1/configure.ac-127- echo " GCC version: ${gcc_version}"
##############################################
cufflinks-2.2.1+dfsg.1/ax_bam.m4-63-# bam_lib_version_req=ifelse([$1], ,1.20.0,$1)
cufflinks-2.2.1+dfsg.1/ax_bam.m4:64:# bam_lib_version_req_shorten=`expr $bam_lib_version_req : '\([[0-9]]*\.[[0-9]]*\)'`
cufflinks-2.2.1+dfsg.1/ax_bam.m4:65:# bam_lib_version_req_major=`expr $bam_lib_version_req : '\([[0-9]]*\)'`
cufflinks-2.2.1+dfsg.1/ax_bam.m4:66:# bam_lib_version_req_minor=`expr $bam_lib_version_req : '[[0-9]]*\.\([[0-9]]*\)'`
cufflinks-2.2.1+dfsg.1/ax_bam.m4:67:# bam_lib_version_req_sub_minor=`expr $bam_lib_version_req : '[[0-9]]*\.[[0-9]]*\.\([[0-9]]*\)'`
cufflinks-2.2.1+dfsg.1/ax_bam.m4-68-# if test "x$bam_lib_version_req_sub_minor" = "x" ; then
##############################################
cufflinks-2.2.1+dfsg.1/ax_bam.m4-70-# fi
cufflinks-2.2.1+dfsg.1/ax_bam.m4:71:# WANT_BAM_VERSION=`expr $bam_lib_version_req_major \* 100000 \+ $bam_lib_version_req_minor \* 100 \+ $bam_lib_version_req_sub_minor`
cufflinks-2.2.1+dfsg.1/ax_bam.m4-72- AC_MSG_CHECKING(for bamlib)
##############################################
cufflinks-2.2.1+dfsg.1/ax_bam.m4-120- if test -d "$ac_bam_path" && test -r "$ac_bam_path"; then
cufflinks-2.2.1+dfsg.1/ax_bam.m4:121: for i in `ls -d $ac_bam_path/include/bam-* 2>/dev/null`; do
cufflinks-2.2.1+dfsg.1/ax_bam.m4:122: _version_tmp=`echo $i | sed "s#$ac_bam_path##" | sed 's/\/include\/bam-//' | sed 's/_/./'`
cufflinks-2.2.1+dfsg.1/ax_bam.m4:123: V_CHECK=`expr $_version_tmp \> $_version`
cufflinks-2.2.1+dfsg.1/ax_bam.m4-124- if test "$V_CHECK" = "1" ; then
##############################################
cufflinks-2.2.1+dfsg.1/ax_bam.m4-126- fi
cufflinks-2.2.1+dfsg.1/ax_bam.m4:127: VERSION_UNDERSCORE=`echo $_version | sed 's/\./_/'`
cufflinks-2.2.1+dfsg.1/ax_bam.m4-128- BAM_CPPFLAGS="-I$ac_bam_path/include/bam-$VERSION_UNDERSCORE"
##############################################
cufflinks-2.2.1+dfsg.1/ax_bam.m4-133- if test -d "$ac_bam_path" && test -r "$ac_bam_path"; then
cufflinks-2.2.1+dfsg.1/ax_bam.m4:134: for i in `ls -d $ac_bam_path/include/bam-* 2>/dev/null`; do
cufflinks-2.2.1+dfsg.1/ax_bam.m4:135: _version_tmp=`echo $i | sed "s#$ac_bam_path##" | sed 's/\/include\/bam-//' | sed 's/_/./'`
cufflinks-2.2.1+dfsg.1/ax_bam.m4:136: V_CHECK=`expr $_version_tmp \> $_version`
cufflinks-2.2.1+dfsg.1/ax_bam.m4-137- if test "$V_CHECK" = "1" ; then
##############################################
cufflinks-2.2.1+dfsg.1/ax_bam.m4-144-
cufflinks-2.2.1+dfsg.1/ax_bam.m4:145: VERSION_UNDERSCORE=`echo $_version | sed 's/\./_/'`
cufflinks-2.2.1+dfsg.1/ax_bam.m4-146- BAM_CPPFLAGS="-I$best_path/include/bam-$VERSION_UNDERSCORE"
##############################################
cufflinks-2.2.1+dfsg.1/ax_bam.m4-153- if test -d "$BAM_ROOT" && test -r "$BAM_ROOT" && test -d "$BAM_ROOT/stage/lib" && test -r "$BAM_ROOT/stage/lib"; then
cufflinks-2.2.1+dfsg.1/ax_bam.m4:154: version_dir=`expr //$BAM_ROOT : '.*/\(.*\)'`
cufflinks-2.2.1+dfsg.1/ax_bam.m4:155: stage_version=`echo $version_dir | sed 's/bam_//' | sed 's/_/./g'`
cufflinks-2.2.1+dfsg.1/ax_bam.m4:156: stage_version_shorten=`expr $stage_version : '\([[0-9]]*\.[[0-9]]*\)'`
cufflinks-2.2.1+dfsg.1/ax_bam.m4:157: V_CHECK=`expr $stage_version_shorten \>\= $_version`
cufflinks-2.2.1+dfsg.1/ax_bam.m4-158- if test "$V_CHECK" = "1" -a "$ac_bam_lib_path" = "" ; then