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/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
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grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
bowtie2-2.4.2/NEWS-74- * `--interleaved` can now be combined with FASTA inputs (worked only with FASTQ before)
bowtie2-2.4.2/NEWS:75: * Fixed issue whereby large indexes were not successfully found in the `$BOWTIE2_INDEXES` directory
bowtie2-2.4.2/NEWS-76- * Fixed input from FIFOs (e.g. via process substitution) to distinguish gzip-compressed versus uncompressed input
##############################################
bowtie2-2.4.2/fast_mutex.h-153- #if defined(__GNUC__) && (defined(__i386__) || defined(__x86_64__))
bowtie2-2.4.2/fast_mutex.h:154: asm volatile (
bowtie2-2.4.2/fast_mutex.h-155- "movl $1,%%eax\n\t"
##############################################
bowtie2-2.4.2/fast_mutex.h-163- int *ptrLock = &mLock;
bowtie2-2.4.2/fast_mutex.h:164: __asm {
bowtie2-2.4.2/fast_mutex.h-165- mov eax,1
##############################################
bowtie2-2.4.2/fast_mutex.h-171- int newLock = 1;
bowtie2-2.4.2/fast_mutex.h:172: asm volatile (
bowtie2-2.4.2/fast_mutex.h-173- "\n1:\n\t"
##############################################
bowtie2-2.4.2/fast_mutex.h-202- #if defined(__GNUC__) && (defined(__i386__) || defined(__x86_64__))
bowtie2-2.4.2/fast_mutex.h:203: asm volatile (
bowtie2-2.4.2/fast_mutex.h-204- "movl $0,%%eax\n\t"
##############################################
bowtie2-2.4.2/fast_mutex.h-211- int *ptrLock = &mLock;
bowtie2-2.4.2/fast_mutex.h:212: __asm {
bowtie2-2.4.2/fast_mutex.h-213- mov eax,0
##############################################
bowtie2-2.4.2/fast_mutex.h-217- #elif defined(__GNUC__) && (defined(__ppc__))
bowtie2-2.4.2/fast_mutex.h:218: asm volatile (
bowtie2-2.4.2/fast_mutex.h-219- "sync\n\t" // Replace with lwsync where possible?
##############################################
bowtie2-2.4.2/scripts/bowtie2-hbb.sh-46-mkdir /mybin
bowtie2-2.4.2/scripts/bowtie2-hbb.sh:47:echo 'res=`echo $@ | sed "s/-L.*$//"`; /opt/rh/devtoolset-8/root/usr/bin/ar $res;' > /mybin/ar
bowtie2-2.4.2/scripts/bowtie2-hbb.sh-48-chmod +x /mybin/ar && export PATH=/mybin:$PATH
##############################################
bowtie2-2.4.2/scripts/infer_fraglen.pl-81-$index =~ s/^~/$ENV{HOME}/;
bowtie2-2.4.2/scripts/infer_fraglen.pl:82:die "Bad bowtie path: $bowtie2" if system("$bowtie2 --version >/dev/null 2>/dev/null") != 0;
bowtie2-2.4.2/scripts/infer_fraglen.pl-83-die "Bad index: $index" if !checkIndex($index);
##############################################
bowtie2-2.4.2/scripts/infer_fraglen.pl-91-my $tot = 0;
bowtie2-2.4.2/scripts/infer_fraglen.pl:92:system($cmd1) == 0 || die "Error running '$cmd1'";
bowtie2-2.4.2/scripts/infer_fraglen.pl-93-open (M1, ".infer_fraglen.tmp") || die "Could not open '.infer_fraglen.tmp'";
##############################################
bowtie2-2.4.2/scripts/make_a_thaliana_tair.sh-15- fi
bowtie2-2.4.2/scripts/make_a_thaliana_tair.sh:16: curl -o `basename $1` $1
bowtie2-2.4.2/scripts/make_a_thaliana_tair.sh-17- return $?
##############################################
bowtie2-2.4.2/scripts/make_b_taurus_UMD3.sh-50- fi
bowtie2-2.4.2/scripts/make_b_taurus_UMD3.sh:51: curl -o `basename $1` $1
bowtie2-2.4.2/scripts/make_b_taurus_UMD3.sh-52- return $?
##############################################
bowtie2-2.4.2/scripts/make_c_elegans.sh-26- fi
bowtie2-2.4.2/scripts/make_c_elegans.sh:27: curl -o `basename $1` $1
bowtie2-2.4.2/scripts/make_c_elegans.sh-28- return $?
##############################################
bowtie2-2.4.2/scripts/make_canFam2.sh-11- BASE_CHRS="$BASE_CHRS chr$i"
bowtie2-2.4.2/scripts/make_canFam2.sh:12: i=`expr $i + 1`
bowtie2-2.4.2/scripts/make_canFam2.sh-13-done
##############################################
bowtie2-2.4.2/scripts/make_canFam2.sh-25- fi
bowtie2-2.4.2/scripts/make_canFam2.sh:26: curl -o `basename $1` $1
bowtie2-2.4.2/scripts/make_canFam2.sh-27- return $?
##############################################
bowtie2-2.4.2/scripts/make_d_melanogaster.sh-21- fi
bowtie2-2.4.2/scripts/make_d_melanogaster.sh:22: curl -o `basename $1` $1
bowtie2-2.4.2/scripts/make_d_melanogaster.sh-23- return $?
bowtie2-2.4.2/scripts/make_d_melanogaster.sh-24- else
bowtie2-2.4.2/scripts/make_d_melanogaster.sh:25: wget -O `basename $1` $1
bowtie2-2.4.2/scripts/make_d_melanogaster.sh-26- return $?
##############################################
bowtie2-2.4.2/scripts/make_h_sapiens_ncbi36.sh-72-if [ "$?" = "0" ] ; then
bowtie2-2.4.2/scripts/make_h_sapiens_ncbi36.sh:73: echo "h_sapiens_asm index built:"
bowtie2-2.4.2/scripts/make_h_sapiens_ncbi36.sh-74- echo " h_sapiens_asm.1.ebwt h_sapiens_asm.2.ebwt"
##############################################
bowtie2-2.4.2/scripts/make_h_sapiens_ncbi37.sh-65- fi
bowtie2-2.4.2/scripts/make_h_sapiens_ncbi37.sh:66: curl -o `basename $1` $1
bowtie2-2.4.2/scripts/make_h_sapiens_ncbi37.sh-67- return $?
##############################################
bowtie2-2.4.2/scripts/make_h_sapiens_ncbi37.sh-85-for c in $CHRS_TO_INDEX ; do
bowtie2-2.4.2/scripts/make_h_sapiens_ncbi37.sh:86: cbase=`basename ${c}`
bowtie2-2.4.2/scripts/make_h_sapiens_ncbi37.sh-87- if [ ! -f $cbase ] ; then
##############################################
bowtie2-2.4.2/scripts/make_h_sapiens_ncbi37.sh-99-if [ "$?" = "0" ] ; then
bowtie2-2.4.2/scripts/make_h_sapiens_ncbi37.sh:100: echo "h_sapiens_37_asm index built:"
bowtie2-2.4.2/scripts/make_h_sapiens_ncbi37.sh-101- echo " h_sapiens_37_asm.1.ebwt h_sapiens_37_asm.2.ebwt"
##############################################
bowtie2-2.4.2/scripts/make_hg18.sh-84- fi
bowtie2-2.4.2/scripts/make_hg18.sh:85: curl -o `basename $1` $1
bowtie2-2.4.2/scripts/make_hg18.sh-86- return $?
##############################################
bowtie2-2.4.2/scripts/make_hg19.sh-128- fi
bowtie2-2.4.2/scripts/make_hg19.sh:129: curl -o `basename $1` $1
bowtie2-2.4.2/scripts/make_hg19.sh-130- return $?
##############################################
bowtie2-2.4.2/scripts/make_m_musculus_ncbi37.sh-23- fi
bowtie2-2.4.2/scripts/make_m_musculus_ncbi37.sh:24: curl -o `basename $1` $1
bowtie2-2.4.2/scripts/make_m_musculus_ncbi37.sh-25- return $?
##############################################
bowtie2-2.4.2/scripts/make_mm10.sh-98- fi
bowtie2-2.4.2/scripts/make_mm10.sh:99: curl -o `basename $1` $1
bowtie2-2.4.2/scripts/make_mm10.sh-100- return $?
##############################################
bowtie2-2.4.2/scripts/make_mm9.sh-67- fi
bowtie2-2.4.2/scripts/make_mm9.sh:68: curl -o `basename $1` $1
bowtie2-2.4.2/scripts/make_mm9.sh-69- return $?
##############################################
bowtie2-2.4.2/scripts/make_rn4.sh-21- BASE_CHRS="$BASE_CHRS chr$i"
bowtie2-2.4.2/scripts/make_rn4.sh:22: i=`expr $i + 1`
bowtie2-2.4.2/scripts/make_rn4.sh-23-done
##############################################
bowtie2-2.4.2/scripts/make_rn4.sh-60- fi
bowtie2-2.4.2/scripts/make_rn4.sh:61: curl -o `basename $1` $1
bowtie2-2.4.2/scripts/make_rn4.sh-62- return $?
##############################################
bowtie2-2.4.2/scripts/sim/Sim.pm-429- print STDERR "Executing: $cmd\n";
bowtie2-2.4.2/scripts/sim/Sim.pm:430: system($cmd);
bowtie2-2.4.2/scripts/sim/Sim.pm-431- $? == 0 || mydie("Error running '$cmd'; exitlevel=$?");
##############################################
bowtie2-2.4.2/scripts/sim/Sim.pm-436- print STDERR "$cmd\n";
bowtie2-2.4.2/scripts/sim/Sim.pm:437: system($cmd);
bowtie2-2.4.2/scripts/sim/Sim.pm-438- $? == 0 || mydie("Error running '$cmd'; exitlevel=$?");
##############################################
bowtie2-2.4.2/scripts/sim/Sim.pm-912- print "$cmd\n";
bowtie2-2.4.2/scripts/sim/Sim.pm:913: system($cmd);
bowtie2-2.4.2/scripts/sim/Sim.pm-914- $? == 0 ||
##############################################
bowtie2-2.4.2/scripts/sim/Sim.pm-917- print "$cmd\n";
bowtie2-2.4.2/scripts/sim/Sim.pm:918: system($cmd);
bowtie2-2.4.2/scripts/sim/Sim.pm-919- $? == 0 ||
##############################################
bowtie2-2.4.2/scripts/sim/Sim.pm-929- print "$cmd\n";
bowtie2-2.4.2/scripts/sim/Sim.pm:930: system($cmd);
bowtie2-2.4.2/scripts/sim/Sim.pm-931- $? == 0 ||
##############################################
bowtie2-2.4.2/scripts/sim/Sim.pm-936- print "$cmd\n";
bowtie2-2.4.2/scripts/sim/Sim.pm:937: system($cmd);
bowtie2-2.4.2/scripts/sim/Sim.pm-938- $? == 0 ||
##############################################
bowtie2-2.4.2/scripts/sim/Sim.pm-943- print "$cmd\n";
bowtie2-2.4.2/scripts/sim/Sim.pm:944: system($cmd);
bowtie2-2.4.2/scripts/sim/Sim.pm-945- $? == 0 ||
##############################################
bowtie2-2.4.2/scripts/sim/Sim.pm-948- print "$cmd\n";
bowtie2-2.4.2/scripts/sim/Sim.pm:949: system($cmd);
bowtie2-2.4.2/scripts/sim/Sim.pm-950- $? == 0 ||
##############################################
bowtie2-2.4.2/scripts/sim/Sim.pm-961- print "$cmd\n";
bowtie2-2.4.2/scripts/sim/Sim.pm:962: system($cmd);
bowtie2-2.4.2/scripts/sim/Sim.pm-963- $? == 0 || mydie("Command '$cmd' failed with exitlevel $?");
##############################################
bowtie2-2.4.2/scripts/sim/Sim.pm-965- print "$cmd\n";
bowtie2-2.4.2/scripts/sim/Sim.pm:966: system($cmd);
bowtie2-2.4.2/scripts/sim/Sim.pm-967- $? == 0 ||
##############################################
bowtie2-2.4.2/scripts/sim/unit.sh-21-
bowtie2-2.4.2/scripts/sim/unit.sh:22:d=`dirname $0`
bowtie2-2.4.2/scripts/sim/unit.sh:23:for i in `ls $d/*.pm` ; do echo $i ; perl $i --test ; done
##############################################
bowtie2-2.4.2/scripts/test/simple_tests.pl-47-if(! -x $bowtie2 || ! -x $bowtie2_build) {
bowtie2-2.4.2/scripts/test/simple_tests.pl:48: my $bowtie2_dir = `dirname $bowtie2`;
bowtie2-2.4.2/scripts/test/simple_tests.pl:49: my $bowtie2_exe = `basename $bowtie2`;
bowtie2-2.4.2/scripts/test/simple_tests.pl:50: my $bowtie2_build_exe = `basename $bowtie2_build`;
bowtie2-2.4.2/scripts/test/simple_tests.pl-51- chomp($bowtie2_dir);
##############################################
bowtie2-2.4.2/scripts/test/simple_tests.pl-53- chomp($bowtie2_build_exe);
bowtie2-2.4.2/scripts/test/simple_tests.pl:54: system("make -C $bowtie2_dir $bowtie2_exe $bowtie2_build_exe") && die;
bowtie2-2.4.2/scripts/test/simple_tests.pl-55-}
##############################################
bowtie2-2.4.2/scripts/test/simple_tests.pl-59-
bowtie2-2.4.2/scripts/test/simple_tests.pl:60:`$bowtie2 --help` || die "Wrapper terminated with non-zero exit code.";
bowtie2-2.4.2/scripts/test/simple_tests.pl:61:`$bowtie2 --version` || die "Wrapper terminated with non-zero exit code.";
bowtie2-2.4.2/scripts/test/simple_tests.pl-62-
bowtie2-2.4.2/scripts/test/simple_tests.pl:63:my $compiled_with_sra = (`$bowtie2 --version` =~ /USE_SRA/) && defined(which "latf-load");
bowtie2-2.4.2/scripts/test/simple_tests.pl-64-my $should_test_bam = defined(which "samtools");
##############################################
bowtie2-2.4.2/scripts/test/simple_tests.pl-4459- print "$latf_cmd\n";
bowtie2-2.4.2/scripts/test/simple_tests.pl:4460: system($latf_cmd);
bowtie2-2.4.2/scripts/test/simple_tests.pl-4461-}
##############################################
bowtie2-2.4.2/scripts/test/simple_tests.pl-4485- print "$bam_cmd\n";
bowtie2-2.4.2/scripts/test/simple_tests.pl:4486: system($bam_cmd);
bowtie2-2.4.2/scripts/test/simple_tests.pl-4487-}
##############################################
bowtie2-2.4.2/scripts/test/simple_tests.pl-4609- print "$cmd\n";
bowtie2-2.4.2/scripts/test/simple_tests.pl:4610: system($cmd);
bowtie2-2.4.2/scripts/test/simple_tests.pl-4611- ($? == 0) || die "Bad exitlevel from bowtie2-build: $?";
##############################################
bowtie2-2.4.2/third_party/cpuid.h-84-#else
bowtie2-2.4.2/third_party/cpuid.h:85:/* Host GCCs older than 3.0 weren't supporting Intel asm syntax
bowtie2-2.4.2/third_party/cpuid.h-86- nor alternatives in i386 code. */
##############################################
bowtie2-2.4.2/third_party/cpuid.h-140-#else
bowtie2-2.4.2/third_party/cpuid.h:141:/* Host GCCs older than 3.0 weren't supporting Intel asm syntax
bowtie2-2.4.2/third_party/cpuid.h-142- nor alternatives in i386 code. */
##############################################
bowtie2-2.4.2/debian/patches/no_sanity-201- print "$cmd\n";
bowtie2-2.4.2/debian/patches/no_sanity:202: system($cmd);
bowtie2-2.4.2/debian/patches/no_sanity-203- ($? == 0) || die "Bad exitlevel from bowtie2-build: $?";
##############################################
bowtie2-2.4.2/debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch-173-+simple-test: all
bowtie2-2.4.2/debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch:174: eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp` ; \
bowtie2-2.4.2/debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch-175- sh ./scripts/test/simple_tests.sh
##############################################
bowtie2-2.4.2/debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch-179-+random-test: all
bowtie2-2.4.2/debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch:180: eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp` ; \
bowtie2-2.4.2/debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch-181- sh ./scripts/sim/run.sh $(if $(NUM_CORES), $(NUM_CORES), 2)
##############################################
bowtie2-2.4.2/debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch-186- $$DL http://cpanmin.us | perl - -l $(CURDIR)/.tmp App::cpanminus local::lib ; \
bowtie2-2.4.2/debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch:187:- eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp` ; \
bowtie2-2.4.2/debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch-188-- $(CURDIR)/.tmp/bin/cpanm --force File::Which Math::Random Clone Test::Deep Sys::Info ; \
bowtie2-2.4.2/debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch:189:+ eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp`
bowtie2-2.4.2/debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch-190-
##############################################
bowtie2-2.4.2/debian/tests/indexing-ref-genome-9-do
bowtie2-2.4.2/debian/tests/indexing-ref-genome:10: extracted=`echo $file | awk -F/ '{print $NF}'`
bowtie2-2.4.2/debian/tests/indexing-ref-genome-11- zcat $examplesdir/$file >${extracted%.gz}
##############################################
bowtie2-2.4.2/.pc/wrong-interpreter-path.patch/bowtie2-415- push @to_delete, $ofn;
bowtie2-2.4.2/.pc/wrong-interpreter-path.patch/bowtie2:416: system("$build_bin $ofn $ofn") == 0 ||
bowtie2-2.4.2/.pc/wrong-interpreter-path.patch/bowtie2-417- Fail("bowtie2-build returned non-0 exit level.\n");
##############################################
bowtie2-2.4.2/.pc/wrong-interpreter-path.patch/bowtie2-592-} else {
bowtie2-2.4.2/.pc/wrong-interpreter-path.patch/bowtie2:593: $ret = system($cmd);
bowtie2-2.4.2/.pc/wrong-interpreter-path.patch/bowtie2-594-}
##############################################
bowtie2-2.4.2/.pc/hardening.patch/Makefile-327- -DBUILD_TIME="\"`date -u`\"" \
bowtie2-2.4.2/.pc/hardening.patch/Makefile:328: -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
bowtie2-2.4.2/.pc/hardening.patch/Makefile-329- $(FILE_FLAGS) \
##############################################
bowtie2-2.4.2/.pc/hardening.patch/Makefile-552-simple-test: perl-deps both both-debug both-sanitized
bowtie2-2.4.2/.pc/hardening.patch/Makefile:553: eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp` ; \
bowtie2-2.4.2/.pc/hardening.patch/Makefile-554- sh ./scripts/test/simple_tests.sh
##############################################
bowtie2-2.4.2/.pc/hardening.patch/Makefile-557-random-test: all perl-deps
bowtie2-2.4.2/.pc/hardening.patch/Makefile:558: eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp` ; \
bowtie2-2.4.2/.pc/hardening.patch/Makefile-559- sh ./scripts/sim/run.sh $(if $(NUM_CORES), $(NUM_CORES), 2)
##############################################
bowtie2-2.4.2/.pc/hardening.patch/Makefile-567- $$DL http://cpanmin.us | perl - -l $(CURDIR)/.tmp App::cpanminus local::lib ; \
bowtie2-2.4.2/.pc/hardening.patch/Makefile:568: eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp` ; \
bowtie2-2.4.2/.pc/hardening.patch/Makefile-569- $(CURDIR)/.tmp/bin/cpanm --force File::Which Math::Random Clone Test::Deep Sys::Info ; \
##############################################
bowtie2-2.4.2/.pc/reproducible.patch/Makefile-327- -DBUILD_TIME="\"`date -u`\"" \
bowtie2-2.4.2/.pc/reproducible.patch/Makefile:328: -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
bowtie2-2.4.2/.pc/reproducible.patch/Makefile-329- $(FILE_FLAGS) \
##############################################
bowtie2-2.4.2/.pc/reproducible.patch/Makefile-554-simple-test: perl-deps both both-debug both-sanitized
bowtie2-2.4.2/.pc/reproducible.patch/Makefile:555: eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp` ; \
bowtie2-2.4.2/.pc/reproducible.patch/Makefile-556- sh ./scripts/test/simple_tests.sh
##############################################
bowtie2-2.4.2/.pc/reproducible.patch/Makefile-559-random-test: all perl-deps
bowtie2-2.4.2/.pc/reproducible.patch/Makefile:560: eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp` ; \
bowtie2-2.4.2/.pc/reproducible.patch/Makefile-561- sh ./scripts/sim/run.sh $(if $(NUM_CORES), $(NUM_CORES), 2)
##############################################
bowtie2-2.4.2/.pc/reproducible.patch/Makefile-569- $$DL http://cpanmin.us | perl - -l $(CURDIR)/.tmp App::cpanminus local::lib ; \
bowtie2-2.4.2/.pc/reproducible.patch/Makefile:570: eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp` ; \
bowtie2-2.4.2/.pc/reproducible.patch/Makefile-571- $(CURDIR)/.tmp/bin/cpanm --force File::Which Math::Random Clone Test::Deep Sys::Info ; \
##############################################
bowtie2-2.4.2/.pc/skip_test_requiring_non-free_libmath-random-perl.patch/Makefile-327- -DBUILD_TIME="\"`date -u`\"" \
bowtie2-2.4.2/.pc/skip_test_requiring_non-free_libmath-random-perl.patch/Makefile:328: -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
bowtie2-2.4.2/.pc/skip_test_requiring_non-free_libmath-random-perl.patch/Makefile-329- $(FILE_FLAGS) \
##############################################
bowtie2-2.4.2/.pc/skip_test_requiring_non-free_libmath-random-perl.patch/Makefile-554-simple-test: perl-deps both both-debug both-sanitized
bowtie2-2.4.2/.pc/skip_test_requiring_non-free_libmath-random-perl.patch/Makefile:555: eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp` ; \
bowtie2-2.4.2/.pc/skip_test_requiring_non-free_libmath-random-perl.patch/Makefile-556- sh ./scripts/test/simple_tests.sh
##############################################
bowtie2-2.4.2/.pc/skip_test_requiring_non-free_libmath-random-perl.patch/Makefile-559-random-test: all perl-deps
bowtie2-2.4.2/.pc/skip_test_requiring_non-free_libmath-random-perl.patch/Makefile:560: eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp` ; \
bowtie2-2.4.2/.pc/skip_test_requiring_non-free_libmath-random-perl.patch/Makefile-561- sh ./scripts/sim/run.sh $(if $(NUM_CORES), $(NUM_CORES), 2)
##############################################
bowtie2-2.4.2/.pc/skip_test_requiring_non-free_libmath-random-perl.patch/Makefile-569- $$DL http://cpanmin.us | perl - -l $(CURDIR)/.tmp App::cpanminus local::lib ; \
bowtie2-2.4.2/.pc/skip_test_requiring_non-free_libmath-random-perl.patch/Makefile:570: eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp` ; \
bowtie2-2.4.2/.pc/skip_test_requiring_non-free_libmath-random-perl.patch/Makefile-571- $(CURDIR)/.tmp/bin/cpanm --force File::Which Math::Random Clone Test::Deep Sys::Info ; \
##############################################
bowtie2-2.4.2/.pc/correct_64bit_test/Makefile-327- -DBUILD_TIME="\"`date -u`\"" \
bowtie2-2.4.2/.pc/correct_64bit_test/Makefile:328: -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
bowtie2-2.4.2/.pc/correct_64bit_test/Makefile-329- $(FILE_FLAGS) \
##############################################
bowtie2-2.4.2/.pc/correct_64bit_test/Makefile-554-simple-test: all
bowtie2-2.4.2/.pc/correct_64bit_test/Makefile:555: eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp` ; \
bowtie2-2.4.2/.pc/correct_64bit_test/Makefile-556- sh ./scripts/test/simple_tests.sh
##############################################
bowtie2-2.4.2/.pc/correct_64bit_test/Makefile-559-random-test: all
bowtie2-2.4.2/.pc/correct_64bit_test/Makefile:560: eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp` ; \
bowtie2-2.4.2/.pc/correct_64bit_test/Makefile-561- sh ./scripts/sim/run.sh $(if $(NUM_CORES), $(NUM_CORES), 2)
##############################################
bowtie2-2.4.2/.pc/correct_64bit_test/Makefile-569- $$DL http://cpanmin.us | perl - -l $(CURDIR)/.tmp App::cpanminus local::lib ; \
bowtie2-2.4.2/.pc/correct_64bit_test/Makefile:570: eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp`
bowtie2-2.4.2/.pc/correct_64bit_test/Makefile-571-
##############################################
bowtie2-2.4.2/.pc/no_sanity/Makefile-301- -DBUILD_TIME="\"`date -u`\"" \
bowtie2-2.4.2/.pc/no_sanity/Makefile:302: -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
bowtie2-2.4.2/.pc/no_sanity/Makefile-303- $(FILE_FLAGS) \
##############################################
bowtie2-2.4.2/.pc/no_sanity/Makefile-528-simple-test: all
bowtie2-2.4.2/.pc/no_sanity/Makefile:529: eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp` ; \
bowtie2-2.4.2/.pc/no_sanity/Makefile-530- sh ./scripts/test/simple_tests.sh
##############################################
bowtie2-2.4.2/.pc/no_sanity/Makefile-533-random-test: all
bowtie2-2.4.2/.pc/no_sanity/Makefile:534: eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp` ; \
bowtie2-2.4.2/.pc/no_sanity/Makefile-535- sh ./scripts/sim/run.sh $(if $(NUM_CORES), $(NUM_CORES), 2)
##############################################
bowtie2-2.4.2/.pc/no_sanity/Makefile-543- $$DL http://cpanmin.us | perl - -l $(CURDIR)/.tmp App::cpanminus local::lib ; \
bowtie2-2.4.2/.pc/no_sanity/Makefile:544: eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp`
bowtie2-2.4.2/.pc/no_sanity/Makefile-545-
##############################################
bowtie2-2.4.2/.pc/no_sanity/bowtie2-415- push @to_delete, $ofn;
bowtie2-2.4.2/.pc/no_sanity/bowtie2:416: system("$build_bin $ofn $ofn") == 0 ||
bowtie2-2.4.2/.pc/no_sanity/bowtie2-417- Fail("bowtie2-build returned non-0 exit level.\n");
##############################################
bowtie2-2.4.2/.pc/no_sanity/bowtie2-592-} else {
bowtie2-2.4.2/.pc/no_sanity/bowtie2:593: $ret = system($cmd);
bowtie2-2.4.2/.pc/no_sanity/bowtie2-594-}
##############################################
bowtie2-2.4.2/.pc/no_sanity/scripts/test/simple_tests.pl-47-if(! -x $bowtie2 || ! -x $bowtie2_build) {
bowtie2-2.4.2/.pc/no_sanity/scripts/test/simple_tests.pl:48: my $bowtie2_dir = `dirname $bowtie2`;
bowtie2-2.4.2/.pc/no_sanity/scripts/test/simple_tests.pl:49: my $bowtie2_exe = `basename $bowtie2`;
bowtie2-2.4.2/.pc/no_sanity/scripts/test/simple_tests.pl:50: my $bowtie2_build_exe = `basename $bowtie2_build`;
bowtie2-2.4.2/.pc/no_sanity/scripts/test/simple_tests.pl-51- chomp($bowtie2_dir);
##############################################
bowtie2-2.4.2/.pc/no_sanity/scripts/test/simple_tests.pl-53- chomp($bowtie2_build_exe);
bowtie2-2.4.2/.pc/no_sanity/scripts/test/simple_tests.pl:54: system("make -C $bowtie2_dir $bowtie2_exe $bowtie2_build_exe") && die;
bowtie2-2.4.2/.pc/no_sanity/scripts/test/simple_tests.pl-55-}
##############################################
bowtie2-2.4.2/.pc/no_sanity/scripts/test/simple_tests.pl-59-
bowtie2-2.4.2/.pc/no_sanity/scripts/test/simple_tests.pl:60:`$bowtie2 --help` || die "Wrapper terminated with non-zero exit code.";
bowtie2-2.4.2/.pc/no_sanity/scripts/test/simple_tests.pl:61:`$bowtie2 --version` || die "Wrapper terminated with non-zero exit code.";
bowtie2-2.4.2/.pc/no_sanity/scripts/test/simple_tests.pl-62-
bowtie2-2.4.2/.pc/no_sanity/scripts/test/simple_tests.pl:63:my $compiled_with_sra = (`$bowtie2 --version` =~ /USE_SRA/) && defined(which "latf-load");
bowtie2-2.4.2/.pc/no_sanity/scripts/test/simple_tests.pl-64-my $should_test_bam = defined(which "samtools");
##############################################
bowtie2-2.4.2/.pc/no_sanity/scripts/test/simple_tests.pl-4459- print "$latf_cmd\n";
bowtie2-2.4.2/.pc/no_sanity/scripts/test/simple_tests.pl:4460: system($latf_cmd);
bowtie2-2.4.2/.pc/no_sanity/scripts/test/simple_tests.pl-4461-}
##############################################
bowtie2-2.4.2/.pc/no_sanity/scripts/test/simple_tests.pl-4485- print "$bam_cmd\n";
bowtie2-2.4.2/.pc/no_sanity/scripts/test/simple_tests.pl:4486: system($bam_cmd);
bowtie2-2.4.2/.pc/no_sanity/scripts/test/simple_tests.pl-4487-}
##############################################
bowtie2-2.4.2/.pc/no_sanity/scripts/test/simple_tests.pl-4609- print "$cmd\n";
bowtie2-2.4.2/.pc/no_sanity/scripts/test/simple_tests.pl:4610: system($cmd);
bowtie2-2.4.2/.pc/no_sanity/scripts/test/simple_tests.pl-4611- ($? == 0) || die "Bad exitlevel from bowtie2-build: $?";
##############################################
bowtie2-2.4.2/Makefile-282- -DBUILD_TIME="\"`date -u`\"" \
bowtie2-2.4.2/Makefile:283: -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
bowtie2-2.4.2/Makefile-284- $(FILE_FLAGS) \
##############################################
bowtie2-2.4.2/Makefile-502-simple-test: all
bowtie2-2.4.2/Makefile:503: eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp` ; \
bowtie2-2.4.2/Makefile-504- sh ./scripts/test/simple_tests.sh
##############################################
bowtie2-2.4.2/Makefile-507-random-test: all
bowtie2-2.4.2/Makefile:508: eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp` ; \
bowtie2-2.4.2/Makefile-509- sh ./scripts/sim/run.sh $(if $(NUM_CORES), $(NUM_CORES), 2)
##############################################
bowtie2-2.4.2/Makefile-517- $$DL http://cpanmin.us | perl - -l $(CURDIR)/.tmp App::cpanminus local::lib ; \
bowtie2-2.4.2/Makefile:518: eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp`
bowtie2-2.4.2/Makefile-519-
##############################################
bowtie2-2.4.2/bowtie2-413- push @to_delete, $ofn;
bowtie2-2.4.2/bowtie2:414: system("$build_bin $ofn $ofn") == 0 ||
bowtie2-2.4.2/bowtie2-415- Fail("bowtie2-build returned non-0 exit level.\n");
##############################################
bowtie2-2.4.2/bowtie2-587-} else {
bowtie2-2.4.2/bowtie2:588: $ret = system($cmd);
bowtie2-2.4.2/bowtie2-589-}