===========================================================
.___ __ __
_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
bowtie-1.3.0+dfsg1/ebwt.h-1722-static const uint64_t C0F = 0x0F0F0F0F0F0F0F0Fll;
bowtie-1.3.0+dfsg1/ebwt.h:1723:__asm {
bowtie-1.3.0+dfsg1/ebwt.h-1724- MOVD MM0, [ESP+4] ;v_low
##############################################
bowtie-1.3.0+dfsg1/ebwt.h-1798- int64_t count;
bowtie-1.3.0+dfsg1/ebwt.h:1799: asm ("popcntq %[x],%[count]\n": [count] "=&r" (count): [x] "r" (x));
bowtie-1.3.0+dfsg1/ebwt.h-1800- return count;
##############################################
bowtie-1.3.0+dfsg1/fast_mutex.h-153- #if defined(__GNUC__) && (defined(__i386__) || defined(__x86_64__))
bowtie-1.3.0+dfsg1/fast_mutex.h:154: asm volatile (
bowtie-1.3.0+dfsg1/fast_mutex.h-155- "movl $1,%%eax\n\t"
##############################################
bowtie-1.3.0+dfsg1/fast_mutex.h-163- int *ptrLock = &mLock;
bowtie-1.3.0+dfsg1/fast_mutex.h:164: __asm {
bowtie-1.3.0+dfsg1/fast_mutex.h-165- mov eax,1
##############################################
bowtie-1.3.0+dfsg1/fast_mutex.h-171- int newLock = 1;
bowtie-1.3.0+dfsg1/fast_mutex.h:172: asm volatile (
bowtie-1.3.0+dfsg1/fast_mutex.h-173- "\n1:\n\t"
##############################################
bowtie-1.3.0+dfsg1/fast_mutex.h-202- #if defined(__GNUC__) && (defined(__i386__) || defined(__x86_64__))
bowtie-1.3.0+dfsg1/fast_mutex.h:203: asm volatile (
bowtie-1.3.0+dfsg1/fast_mutex.h-204- "movl $0,%%eax\n\t"
##############################################
bowtie-1.3.0+dfsg1/fast_mutex.h-211- int *ptrLock = &mLock;
bowtie-1.3.0+dfsg1/fast_mutex.h:212: __asm {
bowtie-1.3.0+dfsg1/fast_mutex.h-213- mov eax,0
##############################################
bowtie-1.3.0+dfsg1/fast_mutex.h-217- #elif defined(__GNUC__) && (defined(__ppc__))
bowtie-1.3.0+dfsg1/fast_mutex.h:218: asm volatile (
bowtie-1.3.0+dfsg1/fast_mutex.h-219- "sync\n\t" // Replace with lwsync where possible?
##############################################
bowtie-1.3.0+dfsg1/scripts/best_verify.pl-80-my $make = system("gmake -v") == 0 ? "gmake" : "make";
bowtie-1.3.0+dfsg1/scripts/best_verify.pl:81:system($make . " -C $bowtie_dir $bowtie_exe" . $ENV{"MAKE_ARGS"}) == 0 || die;
bowtie-1.3.0+dfsg1/scripts/best_verify.pl-82-
##############################################
bowtie-1.3.0+dfsg1/scripts/infer_fraglen.pl-55-$index =~ s/^~/$ENV{HOME}/;
bowtie-1.3.0+dfsg1/scripts/infer_fraglen.pl:56:die "Bad bowtie path: $bowtie" if system("$bowtie --version >/dev/null 2>/dev/null") != 0;
bowtie-1.3.0+dfsg1/scripts/infer_fraglen.pl-57-die "Bad index: $index" if !checkIndex($index);
##############################################
bowtie-1.3.0+dfsg1/scripts/infer_fraglen.pl-64-my $cmd2 = "$m2cmd | $bowtie $bowtie_args -m 1 -S --sam-nohead $index - |";
bowtie-1.3.0+dfsg1/scripts/infer_fraglen.pl:65:system($cmd1) == 0 || die "Error running '$cmd1'";
bowtie-1.3.0+dfsg1/scripts/infer_fraglen.pl-66-open (M1, ".infer_fraglen.tmp") || die "Could not open '.infer_fraglen.tmp'";
##############################################
bowtie-1.3.0+dfsg1/scripts/make_a_thaliana_tair.sh-15- fi
bowtie-1.3.0+dfsg1/scripts/make_a_thaliana_tair.sh:16: curl -o `basename $1` $1
bowtie-1.3.0+dfsg1/scripts/make_a_thaliana_tair.sh-17- return $?
##############################################
bowtie-1.3.0+dfsg1/scripts/make_b_taurus_UMD3.sh-50- fi
bowtie-1.3.0+dfsg1/scripts/make_b_taurus_UMD3.sh:51: curl -o `basename $1` $1
bowtie-1.3.0+dfsg1/scripts/make_b_taurus_UMD3.sh-52- return $?
##############################################
bowtie-1.3.0+dfsg1/scripts/make_c_elegans.sh-25- fi
bowtie-1.3.0+dfsg1/scripts/make_c_elegans.sh:26: curl -o `basename $1` $1
bowtie-1.3.0+dfsg1/scripts/make_c_elegans.sh-27- return $?
##############################################
bowtie-1.3.0+dfsg1/scripts/make_canFam2.sh-11- BASE_CHRS="$BASE_CHRS chr$i"
bowtie-1.3.0+dfsg1/scripts/make_canFam2.sh:12: i=`expr $i + 1`
bowtie-1.3.0+dfsg1/scripts/make_canFam2.sh-13-done
##############################################
bowtie-1.3.0+dfsg1/scripts/make_canFam2.sh-25- fi
bowtie-1.3.0+dfsg1/scripts/make_canFam2.sh:26: curl -o `basename $1` $1
bowtie-1.3.0+dfsg1/scripts/make_canFam2.sh-27- return $?
##############################################
bowtie-1.3.0+dfsg1/scripts/make_d_melanogaster.sh-18- fi
bowtie-1.3.0+dfsg1/scripts/make_d_melanogaster.sh:19: curl -o `basename $1` $1
bowtie-1.3.0+dfsg1/scripts/make_d_melanogaster.sh-20- return $?
bowtie-1.3.0+dfsg1/scripts/make_d_melanogaster.sh-21- else
bowtie-1.3.0+dfsg1/scripts/make_d_melanogaster.sh:22: wget -O `basename $1` $1
bowtie-1.3.0+dfsg1/scripts/make_d_melanogaster.sh-23- return $?
##############################################
bowtie-1.3.0+dfsg1/scripts/make_galGal3.sh-12- BASE_CHRS="$BASE_CHRS chr$i"
bowtie-1.3.0+dfsg1/scripts/make_galGal3.sh:13: i=`expr $i + 1`
bowtie-1.3.0+dfsg1/scripts/make_galGal3.sh-14-done
##############################################
bowtie-1.3.0+dfsg1/scripts/make_galGal3.sh-38- fi
bowtie-1.3.0+dfsg1/scripts/make_galGal3.sh:39: curl -o `basename $1` $1
bowtie-1.3.0+dfsg1/scripts/make_galGal3.sh-40- return $?
##############################################
bowtie-1.3.0+dfsg1/scripts/make_h_sapiens_ncbi36.sh-72-if [ "$?" = "0" ] ; then
bowtie-1.3.0+dfsg1/scripts/make_h_sapiens_ncbi36.sh:73: echo "h_sapiens_asm index built:"
bowtie-1.3.0+dfsg1/scripts/make_h_sapiens_ncbi36.sh-74- echo " h_sapiens_asm.1.ebwt h_sapiens_asm.2.ebwt"
##############################################
bowtie-1.3.0+dfsg1/scripts/make_h_sapiens_ncbi37.sh-52- fi
bowtie-1.3.0+dfsg1/scripts/make_h_sapiens_ncbi37.sh:53: curl -o `basename $1` $1
bowtie-1.3.0+dfsg1/scripts/make_h_sapiens_ncbi37.sh-54- return $?
##############################################
bowtie-1.3.0+dfsg1/scripts/make_h_sapiens_ncbi37.sh-96-if [ "$?" = "0" ] ; then
bowtie-1.3.0+dfsg1/scripts/make_h_sapiens_ncbi37.sh:97: echo "h_sapiens_37_asm index built:"
bowtie-1.3.0+dfsg1/scripts/make_h_sapiens_ncbi37.sh-98- echo " h_sapiens_37_asm.1.ebwt h_sapiens_37_asm.2.ebwt"
##############################################
bowtie-1.3.0+dfsg1/scripts/make_hg18.sh-85- fi
bowtie-1.3.0+dfsg1/scripts/make_hg18.sh:86: curl -o `basename $1` $1
bowtie-1.3.0+dfsg1/scripts/make_hg18.sh-87- return $?
##############################################
bowtie-1.3.0+dfsg1/scripts/make_hg19.sh-129- fi
bowtie-1.3.0+dfsg1/scripts/make_hg19.sh:130: curl -o `basename $1` $1
bowtie-1.3.0+dfsg1/scripts/make_hg19.sh-131- return $?
##############################################
bowtie-1.3.0+dfsg1/scripts/make_m_musculus_ncbi37.sh-23- fi
bowtie-1.3.0+dfsg1/scripts/make_m_musculus_ncbi37.sh:24: curl -o `basename $1` $1
bowtie-1.3.0+dfsg1/scripts/make_m_musculus_ncbi37.sh-25- return $?
##############################################
bowtie-1.3.0+dfsg1/scripts/make_mm8.sh-67- fi
bowtie-1.3.0+dfsg1/scripts/make_mm8.sh:68: curl -o `basename $1` $1
bowtie-1.3.0+dfsg1/scripts/make_mm8.sh-69- return $?
##############################################
bowtie-1.3.0+dfsg1/scripts/make_mm9.sh-68- fi
bowtie-1.3.0+dfsg1/scripts/make_mm9.sh:69: curl -o `basename $1` $1
bowtie-1.3.0+dfsg1/scripts/make_mm9.sh-70- return $?
##############################################
bowtie-1.3.0+dfsg1/scripts/make_rn4.sh-22- BASE_CHRS="$BASE_CHRS chr$i"
bowtie-1.3.0+dfsg1/scripts/make_rn4.sh:23: i=`expr $i + 1`
bowtie-1.3.0+dfsg1/scripts/make_rn4.sh-24-done
##############################################
bowtie-1.3.0+dfsg1/scripts/make_rn4.sh-61- fi
bowtie-1.3.0+dfsg1/scripts/make_rn4.sh:62: curl -o `basename $1` $1
bowtie-1.3.0+dfsg1/scripts/make_rn4.sh-63- return $?
##############################################
bowtie-1.3.0+dfsg1/scripts/pe_verify.pl-102-my $make = system("gmake -v") == 0 ? "gmake" : "make";
bowtie-1.3.0+dfsg1/scripts/pe_verify.pl:103:system($make . " -C $bowtie_dir $bowtie_exe" . $ENV{"MAKE_ARGS"}) == 0 || die;
bowtie-1.3.0+dfsg1/scripts/pe_verify.pl-104-
##############################################
bowtie-1.3.0+dfsg1/scripts/test/all.sh-5-
bowtie-1.3.0+dfsg1/scripts/test/all.sh:6:d=`dirname $0`
bowtie-1.3.0+dfsg1/scripts/test/all.sh-7-
bowtie-1.3.0+dfsg1/scripts/test/all.sh:8:for i in `ls $d/*.pl` ; do
bowtie-1.3.0+dfsg1/scripts/test/all.sh-9- if ! perl $i ; then
##############################################
bowtie-1.3.0+dfsg1/scripts/test/args.pl-12-my $bowtie_l = $bowtie . " --large-index";
bowtie-1.3.0+dfsg1/scripts/test/args.pl:13:if(system("$bowtie --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/args.pl-14- print STDERR "Could not execute ./bowtie; looking in PATH...\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/args.pl-16- chomp($bowtie);
bowtie-1.3.0+dfsg1/scripts/test/args.pl:17: if(system("$bowtie --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/args.pl-18- die "Could not find bowtie in current directory or in PATH\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/args.pl-23- print STDERR "Making colorspace e_coli index\n";
bowtie-1.3.0+dfsg1/scripts/test/args.pl:24: if(system("$bowtie_build --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/args.pl-25- print STDERR "Could not execute ./bowtie-build; looking in PATH...\n";
bowtie-1.3.0+dfsg1/scripts/test/args.pl:26: $bowtie_build = `which $bowtie_build`;
bowtie-1.3.0+dfsg1/scripts/test/args.pl-27- chomp($bowtie_build);
bowtie-1.3.0+dfsg1/scripts/test/args.pl:28: if(system("$bowtie_build --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/args.pl-29- die "Could not find bowtie-build in current directory or in PATH\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/args.pl-31- }
bowtie-1.3.0+dfsg1/scripts/test/args.pl:32: system("$bowtie_build -C genomes/NC_008253.fna e_coli_c") && die;
bowtie-1.3.0+dfsg1/scripts/test/args.pl-33-} else {
##############################################
bowtie-1.3.0+dfsg1/scripts/test/args.pl-38- my $bowtie_build = "./bowtie-build --large-index";
bowtie-1.3.0+dfsg1/scripts/test/args.pl:39: if(system("$bowtie_build --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/args.pl-40- print STDERR "Could not execute ./bowtie-build; looking in PATH...\n";
bowtie-1.3.0+dfsg1/scripts/test/args.pl:41: $bowtie_build = `which $bowtie_build`;
bowtie-1.3.0+dfsg1/scripts/test/args.pl-42- chomp($bowtie_build);
bowtie-1.3.0+dfsg1/scripts/test/args.pl:43: if(system("$bowtie_build --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/args.pl-44- die "Could not find bowtie-build in current directory or in PATH\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/args.pl-46- }
bowtie-1.3.0+dfsg1/scripts/test/args.pl:47: system("$bowtie_build -C genomes/NC_008253.fna e_coli_c") && die;
bowtie-1.3.0+dfsg1/scripts/test/args.pl-48-} else {
##############################################
bowtie-1.3.0+dfsg1/scripts/test/args.pl-52-if(! -f "e_coli.1.ebwt") {
bowtie-1.3.0+dfsg1/scripts/test/args.pl:53: system("$bowtie_build genomes/NC_008253.fna e_coli") && die;
bowtie-1.3.0+dfsg1/scripts/test/args.pl-54-} else {
##############################################
bowtie-1.3.0+dfsg1/scripts/test/args.pl-57-if(! -f "e_coli.1.ebwtl") {
bowtie-1.3.0+dfsg1/scripts/test/args.pl:58: system("$bowtie_build --large-index genomes/NC_008253.fna e_coli") && die;
bowtie-1.3.0+dfsg1/scripts/test/args.pl-59-} else {
##############################################
bowtie-1.3.0+dfsg1/scripts/test/args.pl-112- print "$cmd\n";
bowtie-1.3.0+dfsg1/scripts/test/args.pl:113: return system($cmd);
bowtie-1.3.0+dfsg1/scripts/test/args.pl-114-}
##############################################
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl-10-my $bowtie = "./bowtie";
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl:11:if(system("$bowtie --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl-12- $bowtie = `which bowtie`;
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl-13- chomp($bowtie);
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl:14: if(system("$bowtie --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl-15- die "Could not find bowtie in current directory or in PATH\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl-21-
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl:22:if(system("$bowtie_d --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl-23- die "Could not find bowtie-debug in current directory or in PATH\n";
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl-24-}
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl:25:if(system("$bowtie_l --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl-26- die "Could not find bowtie large index support build in current directory or in PATH\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl-31- my $bowtie_build = "./bowtie-build";
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl:32: if(system("$bowtie_build --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl-33- print STDERR "Could not execute ./bowtie-build; looking in PATH...\n";
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl:34: $bowtie_build = `which $bowtie_build`;
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl-35- chomp($bowtie_build);
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl:36: if(system("$bowtie_build --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl-37- die "Could not find bowtie-build in current directory or in PATH\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl-39- }
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl:40: system("$bowtie_build -C genomes/NC_008253.fna e_coli_c") && die;
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl-41-} else {
##############################################
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl-46- my $bowtie_build = "./bowtie-build --large-index";
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl:47: if(system("$bowtie_build --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl-48- print STDERR "Could not execute ./bowtie-build; looking in PATH...\n";
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl:49: $bowtie_build = `which $bowtie_build`;
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl-50- chomp($bowtie_build);
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl:51: if(system("$bowtie_build --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl-52- die "Could not find bowtie-build in current directory or in PATH\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl-54- }
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl:55: system("$bowtie_build --large-index -C genomes/NC_008253.fna e_coli_c") && die;
bowtie-1.3.0+dfsg1/scripts/test/cs_dec.pl-56-} else {
##############################################
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-13-my $bowtie = "./bowtie";
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl:14:if(system("$bowtie --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-15- $bowtie = `which bowtie`;
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-16- chomp($bowtie);
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl:17: if(system("$bowtie --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-18- die "Could not find bowtie in current directory or in PATH\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-22-my $bowtie_d = $bowtie . " --debug";
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl:23:if(system("$bowtie_d --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-24- die "Could not find bowtie-debug in current directory or in PATH\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-27-my $bowtie_l = $bowtie . " --large-index --debug";
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl:28:if(system("$bowtie_l --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-29- die "Could not find bowtie large index support build in current directory or in PATH\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-34- my $bowtie_build = "./bowtie-build";
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl:35: if(system("$bowtie_build --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-36- print STDERR "Could not execute ./bowtie-build; looking in PATH...\n";
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl:37: $bowtie_build = `which $bowtie_build`;
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-38- chomp($bowtie_build);
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl:39: if(system("$bowtie_build --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-40- die "Could not find bowtie-build in current directory or in PATH\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-42- }
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl:43: system("$bowtie_build -C genomes/NC_008253.fna e_coli_c") && die;
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-44-} else {
##############################################
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-50- my $bowtie_build = "./bowtie-build --large-index";
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl:51: if(system("$bowtie_build --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-52- print STDERR "Could not execute ./bowtie-build; looking in PATH...\n";
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl:53: $bowtie_build = `which $bowtie_build`;
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-54- chomp($bowtie_build);
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl:55: if(system("$bowtie_build --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-56- die "Could not find bowtie-build in current directory or in PATH\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-58- }
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl:59: system("$bowtie_build --large-index -C genomes/NC_008253.fna e_coli_c") && die;
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-60-} else {
##############################################
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-66- my @r = split(/[:]/, $rstr);
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl:67: system("rm -f $fname");
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-68- open TMPFQ, ">$fname" || die "Could not open $fname for writing\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-75- my @r = split(/[:]/, $rstr);
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl:76: system("rm -f $fname");
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-77- open TMPFQ, ">$fname" || die "Could not open $fname for writing\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-90- my @r = split(/[:]/, $rstr);
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl:91: system("rm -f $fname");
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-92- open TMPFA, ">$fname" || die "Could not open $fname for writing\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-99- my @r = split(/[:]/, $rstr);
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl:100: system("rm -f $fname");
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-101- open TMPR, ">$fname" || die "Could not open $fname for writing\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-108- my @r = split(/[:]/, $rstr);
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl:109: system("rm -f $fname");
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-110- open TMPT, ">$fname" || die "Could not open $fname for writing\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-118- my @r2 = split(/[:]/, $rstr2);
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl:119: system("rm -f $fname");
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-120- open TMPT, ">$fname" || die "Could not open $fname for writing\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-129- $evenodd++;
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl:130: system("rm -f $fname $fname.qv");
bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl-131- open TMPT, ">$fname" || die "Could not open $fname for writing\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/inspect.pl-239- close(D2);
bowtie-1.3.0+dfsg1/scripts/test/inspect.pl:240: system("diff -uw .inspect.pl.$seed.d1 .inspect.pl.$seed.d2");
bowtie-1.3.0+dfsg1/scripts/test/inspect.pl-241- mydie("$_[2]");
##############################################
bowtie-1.3.0+dfsg1/scripts/test/inspect.pl-295- print "$cmd\n";
bowtie-1.3.0+dfsg1/scripts/test/inspect.pl:296: my $bb2out = `$cmd`;
bowtie-1.3.0+dfsg1/scripts/test/inspect.pl-297- print "Old bowtie-build:\n$bb2out\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/inspect.pl-299- print "$cmd\n";
bowtie-1.3.0+dfsg1/scripts/test/inspect.pl:300: my $bbout = `$cmd`;
bowtie-1.3.0+dfsg1/scripts/test/inspect.pl-301- print "New bowtie-build:\n$bbout\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/inspect.pl-305- print "$cmd\n";
bowtie-1.3.0+dfsg1/scripts/test/inspect.pl:306: system($cmd) == 0 || mydie("Exitlevel $? from command '$cmd'");
bowtie-1.3.0+dfsg1/scripts/test/inspect.pl-307- $cmd = "$bi $fn";
bowtie-1.3.0+dfsg1/scripts/test/inspect.pl-308- print "$cmd\n";
bowtie-1.3.0+dfsg1/scripts/test/inspect.pl:309: my $io = trim(`$cmd`);
bowtie-1.3.0+dfsg1/scripts/test/inspect.pl-310- $? == 0 || mydie("Exitlevel $? from command '$cmd'");
##############################################
bowtie-1.3.0+dfsg1/scripts/test/inspect.pl-321- print "$cmd\n";
bowtie-1.3.0+dfsg1/scripts/test/inspect.pl:322: $io = trim(`$cmd`);
bowtie-1.3.0+dfsg1/scripts/test/inspect.pl-323- $? == 0 || mydie("Exitlevel $? from command '$cmd'");
##############################################
bowtie-1.3.0+dfsg1/scripts/test/inspect.pl-340- print "$cmd\n";
bowtie-1.3.0+dfsg1/scripts/test/inspect.pl:341: $io = trim(`$cmd`);
bowtie-1.3.0+dfsg1/scripts/test/inspect.pl-342- $? == 0 || mydie("Exitlevel $? from command '$cmd'");
##############################################
bowtie-1.3.0+dfsg1/scripts/test/inspect.pl-363- print "$cmd\n";
bowtie-1.3.0+dfsg1/scripts/test/inspect.pl:364: my $bao = trim(`$cmd`);
bowtie-1.3.0+dfsg1/scripts/test/inspect.pl-365- reconcileAlsWithRefs($bao, $c, $col);
##############################################
bowtie-1.3.0+dfsg1/scripts/test/inspect.pl-370- print "$cmd\n";
bowtie-1.3.0+dfsg1/scripts/test/inspect.pl:371: my $bao2 = trim(`$cmd`);
bowtie-1.3.0+dfsg1/scripts/test/inspect.pl-372- reconcileAlsWithRefs($bao2, $c, $col);
##############################################
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl-14-my $bowtie_l = $bowtie . " --large-index --debug";
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl:15:if(system("$bowtie --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl-16- $bowtie = `which bowtie`;
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl-17- chomp($bowtie);
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl:18: if(system("$bowtie --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl-19- die "Could not find bowtie in current directory or in PATH\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl-21-}
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl:22:if(system("$bowtie_d --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl-23- die "Could not find bowtie-debug in current directory or in PATH\n";
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl-24-}
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl:25:if(system("$bowtie_l --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl-26- die "Could not find bowtie large index support build in current directory or in PATH\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl-31- my $bowtie_build = "./bowtie-build";
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl:32: if(system("$bowtie_build --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl-33- print STDERR "Could not execute ./bowtie-build; looking in PATH...\n";
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl:34: $bowtie_build = `which $bowtie_build`;
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl-35- chomp($bowtie_build);
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl:36: if(system("$bowtie_build --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl-37- die "Could not find bowtie-build in current directory or in PATH\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl-39- }
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl:40: system("$bowtie_build -C genomes/NC_008253.fna e_coli_c") && die;
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl-41-} else {
##############################################
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl-47- my $bowtie_build = "./bowtie-build --large-index";
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl:48: if(system("$bowtie_build --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl-49- print STDERR "Could not execute ./bowtie-build; looking in PATH...\n";
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl:50: $bowtie_build = `which $bowtie_build`;
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl-51- chomp($bowtie_build);
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl:52: if(system("$bowtie_build --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl-53- die "Could not find bowtie-build in current directory or in PATH\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl-55- }
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl:56: system("$bowtie_build --large-index -C genomes/NC_008253.fna e_coli_c") && die;
bowtie-1.3.0+dfsg1/scripts/test/long_read.pl-57-} else {
##############################################
bowtie-1.3.0+dfsg1/scripts/test/random_bowtie_tests.pl-350- close(CMDTMP);
bowtie-1.3.0+dfsg1/scripts/test/random_bowtie_tests.pl:351: return system($cmd);
bowtie-1.3.0+dfsg1/scripts/test/random_bowtie_tests.pl-352-}
##############################################
bowtie-1.3.0+dfsg1/scripts/test/random_bowtie_tests.pl-358- close(CMDTMP);
bowtie-1.3.0+dfsg1/scripts/test/random_bowtie_tests.pl:359: return `$cmd`;
bowtie-1.3.0+dfsg1/scripts/test/random_bowtie_tests.pl-360-}
##############################################
bowtie-1.3.0+dfsg1/scripts/test/random_bowtie_tests.pl-386- print "$cmd\n";
bowtie-1.3.0+dfsg1/scripts/test/random_bowtie_tests.pl:387: system($cmd) == 0 || die "inspect.pl died with exitlevel $?";
bowtie-1.3.0+dfsg1/scripts/test/random_bowtie_tests.pl-388-
##############################################
bowtie-1.3.0+dfsg1/scripts/test/random_bowtie_tests.pl-788- if($exitOnFail) {
bowtie-1.3.0+dfsg1/scripts/test/random_bowtie_tests.pl:789: my $err = `cat .tmp$seed.stderr 2> /dev/null`;
bowtie-1.3.0+dfsg1/scripts/test/random_bowtie_tests.pl-790- print "Stdout:\n$out\nStderr:\n$err\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/random_bowtie_tests.pl-794- }
bowtie-1.3.0+dfsg1/scripts/test/random_bowtie_tests.pl:795: my $err = `cat .tmp$seed.stderr 2> /dev/null`;
bowtie-1.3.0+dfsg1/scripts/test/random_bowtie_tests.pl-796- # No output?
##############################################
bowtie-1.3.0+dfsg1/scripts/test/random_bowtie_tests.pl-961- if($exitOnFail) {
bowtie-1.3.0+dfsg1/scripts/test/random_bowtie_tests.pl:962: my $err = `cat .tmp$seed.pe_verify.stderr 2> /dev/null`;
bowtie-1.3.0+dfsg1/scripts/test/random_bowtie_tests.pl-963- print "Stdout:\n$out\nStderr:\n$err\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/random_bowtie_tests.pl-978- if($exitOnFail) {
bowtie-1.3.0+dfsg1/scripts/test/random_bowtie_tests.pl:979: my $err = `cat .tmp$seed.best_verify.stderr 2> /dev/null`;
bowtie-1.3.0+dfsg1/scripts/test/random_bowtie_tests.pl-980- print "Stdout:\n$out\nStderr:\n$err\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/random_bowtie_tests_p.sh-22- echo $! >> .randpids
bowtie-1.3.0+dfsg1/scripts/test/random_bowtie_tests_p.sh:23: NUM=`expr $NUM - 1`
bowtie-1.3.0+dfsg1/scripts/test/random_bowtie_tests_p.sh-24-done
##############################################
bowtie-1.3.0+dfsg1/scripts/test/samtools.pl-13-my $bowtie = "./bowtie";
bowtie-1.3.0+dfsg1/scripts/test/samtools.pl:14:if(system("$bowtie --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/samtools.pl-15- $bowtie = `which bowtie`;
bowtie-1.3.0+dfsg1/scripts/test/samtools.pl-16- chomp($bowtie);
bowtie-1.3.0+dfsg1/scripts/test/samtools.pl:17: if(system("$bowtie --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/samtools.pl-18- die "Could not find bowtie in current directory or in PATH\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/samtools.pl-22-my $bowtie_d = $bowtie . " --debug";
bowtie-1.3.0+dfsg1/scripts/test/samtools.pl:23:if(system("$bowtie_d --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/samtools.pl-24- $bowtie_d = `which bowtie-debug`;
bowtie-1.3.0+dfsg1/scripts/test/samtools.pl-25- chomp($bowtie_d);
bowtie-1.3.0+dfsg1/scripts/test/samtools.pl:26: if(system("$bowtie_d --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/samtools.pl-27- die "Could not find bowtie-debug in current directory or in PATH\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/samtools.pl-51- my $bowtie_build = "./bowtie-build";
bowtie-1.3.0+dfsg1/scripts/test/samtools.pl:52: if(system("$bowtie_build --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/samtools.pl-53- print STDERR "Could not execute ./bowtie-build; looking in PATH...\n";
bowtie-1.3.0+dfsg1/scripts/test/samtools.pl:54: $bowtie_build = `which $bowtie_build`;
bowtie-1.3.0+dfsg1/scripts/test/samtools.pl-55- chomp($bowtie_build);
bowtie-1.3.0+dfsg1/scripts/test/samtools.pl:56: if(system("$bowtie_build --version") != 0) {
bowtie-1.3.0+dfsg1/scripts/test/samtools.pl-57- die "Could not find bowtie-build in current directory or in PATH\n";
##############################################
bowtie-1.3.0+dfsg1/scripts/test/samtools.pl-59- }
bowtie-1.3.0+dfsg1/scripts/test/samtools.pl:60: system("$bowtie_build -C genomes/NC_008253.fna e_coli_c") && die;
bowtie-1.3.0+dfsg1/scripts/test/samtools.pl-61-} else {
##############################################
bowtie-1.3.0+dfsg1/scripts/test/samtools.pl-67- print "$cmd\n";
bowtie-1.3.0+dfsg1/scripts/test/samtools.pl:68: return system($cmd);
bowtie-1.3.0+dfsg1/scripts/test/samtools.pl-69-}
##############################################
bowtie-1.3.0+dfsg1/scripts/test/simple_tests.pl-27-if(! -x $bowtie || ! -x $bowtie_build) {
bowtie-1.3.0+dfsg1/scripts/test/simple_tests.pl:28: my $bowtie_dir = `dirname $bowtie`;
bowtie-1.3.0+dfsg1/scripts/test/simple_tests.pl:29: my $bowtie_exe = `basename $bowtie`;
bowtie-1.3.0+dfsg1/scripts/test/simple_tests.pl:30: my $bowtie_build_exe = `basename $bowtie_build`;
bowtie-1.3.0+dfsg1/scripts/test/simple_tests.pl-31- chomp($bowtie_dir);
##############################################
bowtie-1.3.0+dfsg1/scripts/test/simple_tests.pl-33- chomp($bowtie_build_exe);
bowtie-1.3.0+dfsg1/scripts/test/simple_tests.pl:34: system("make -C $bowtie_dir $bowtie_exe $bowtie_build_exe") && die;
bowtie-1.3.0+dfsg1/scripts/test/simple_tests.pl-35-}
##############################################
bowtie-1.3.0+dfsg1/scripts/test/simple_tests.pl-1004- print "$cmd\n";
bowtie-1.3.0+dfsg1/scripts/test/simple_tests.pl:1005: system($cmd);
bowtie-1.3.0+dfsg1/scripts/test/simple_tests.pl-1006- ($? == 0) || die "Bad exitlevel from bowtie-build: $?";
##############################################
bowtie-1.3.0+dfsg1/debian/patches/reproducible.patch-10-- -DBUILD_TIME="\"$(BUILD_DATE)\"" \
bowtie-1.3.0+dfsg1/debian/patches/reproducible.patch:11:- -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
bowtie-1.3.0+dfsg1/debian/patches/reproducible.patch-12-+ -DBUILD_HOST="\"Debian-reproducible\"" \
bowtie-1.3.0+dfsg1/debian/patches/reproducible.patch-13-+ -DBUILD_TIME="\"`dpkg-parsechangelog --show-field Date`\"" \
bowtie-1.3.0+dfsg1/debian/patches/reproducible.patch:14:+ -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1 | sed 's/ *(.*//'`\"" \
bowtie-1.3.0+dfsg1/debian/patches/reproducible.patch-15- $(FILE_FLAGS) \
##############################################
bowtie-1.3.0+dfsg1/debian/patches/simple-test-11- print "$cmd\n";
bowtie-1.3.0+dfsg1/debian/patches/simple-test:12: system($cmd);
bowtie-1.3.0+dfsg1/debian/patches/simple-test-13- ($? == 0) || die "Bad exitlevel from bowtie-build: $?";
##############################################
bowtie-1.3.0+dfsg1/debian/patches/simple-test-29--simple-test: allall perl-deps
bowtie-1.3.0+dfsg1/debian/patches/simple-test:30:- eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \
bowtie-1.3.0+dfsg1/debian/patches/simple-test-31-+simple-test: all
##############################################
bowtie-1.3.0+dfsg1/debian/patches/simple-test-36-+random-test: all
bowtie-1.3.0+dfsg1/debian/patches/simple-test:37: eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \
bowtie-1.3.0+dfsg1/debian/patches/simple-test-38- ./scripts/test/random_bowtie_tests.sh $(*-command-variables-*-)
##############################################
bowtie-1.3.0+dfsg1/debian/tests/run-unit-test-8- if [ "$AUTOPKGTEST_TMP" = "" ] ; then
bowtie-1.3.0+dfsg1/debian/tests/run-unit-test:9: AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
bowtie-1.3.0+dfsg1/debian/tests/run-unit-test-10- fi
##############################################
bowtie-1.3.0+dfsg1/debian/tests/run-unit-test-17-check_result () {
bowtie-1.3.0+dfsg1/debian/tests/run-unit-test:18: EDIFF=`diff -u tests/$1.out $1.out`
bowtie-1.3.0+dfsg1/debian/tests/run-unit-test-19- if ! $EDIFF ; then
##############################################
bowtie-1.3.0+dfsg1/.pc/no_hash_style_both_for_mips.patch/Makefile-236- -DBUILD_TIME="\"$(BUILD_DATE)\"" \
bowtie-1.3.0+dfsg1/.pc/no_hash_style_both_for_mips.patch/Makefile:237: -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
bowtie-1.3.0+dfsg1/.pc/no_hash_style_both_for_mips.patch/Makefile-238- $(FILE_FLAGS) \
##############################################
bowtie-1.3.0+dfsg1/.pc/no_hash_style_both_for_mips.patch/Makefile-430-simple-test: allall perl-deps
bowtie-1.3.0+dfsg1/.pc/no_hash_style_both_for_mips.patch/Makefile:431: eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \
bowtie-1.3.0+dfsg1/.pc/no_hash_style_both_for_mips.patch/Makefile-432- ./scripts/test/simple_tests.pl --bowtie=./bowtie --bowtie-build=./bowtie-build
##############################################
bowtie-1.3.0+dfsg1/.pc/no_hash_style_both_for_mips.patch/Makefile-435-random-test: all perl-deps
bowtie-1.3.0+dfsg1/.pc/no_hash_style_both_for_mips.patch/Makefile:436: eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \
bowtie-1.3.0+dfsg1/.pc/no_hash_style_both_for_mips.patch/Makefile-437- ./scripts/test/random_bowtie_tests.sh $(*-command-variables-*-)
##############################################
bowtie-1.3.0+dfsg1/.pc/no_hash_style_both_for_mips.patch/Makefile-444- $$DL http://cpanmin.us | perl - -l $(CURDIR)/.perllib.tmp App::cpanminus local::lib ; \
bowtie-1.3.0+dfsg1/.pc/no_hash_style_both_for_mips.patch/Makefile:445: eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \
bowtie-1.3.0+dfsg1/.pc/no_hash_style_both_for_mips.patch/Makefile-446- cpanm --force Math::Random Clone Test::Deep Sys::Info -n --quiet; \
##############################################
bowtie-1.3.0+dfsg1/.pc/use-dpkg-buildflags.patch/Makefile-238- -DBUILD_TIME="\"$(BUILD_DATE)\"" \
bowtie-1.3.0+dfsg1/.pc/use-dpkg-buildflags.patch/Makefile:239: -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
bowtie-1.3.0+dfsg1/.pc/use-dpkg-buildflags.patch/Makefile-240- $(FILE_FLAGS) \
##############################################
bowtie-1.3.0+dfsg1/.pc/use-dpkg-buildflags.patch/Makefile-432-simple-test: allall perl-deps
bowtie-1.3.0+dfsg1/.pc/use-dpkg-buildflags.patch/Makefile:433: eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \
bowtie-1.3.0+dfsg1/.pc/use-dpkg-buildflags.patch/Makefile-434- ./scripts/test/simple_tests.pl --bowtie=./bowtie --bowtie-build=./bowtie-build
##############################################
bowtie-1.3.0+dfsg1/.pc/use-dpkg-buildflags.patch/Makefile-437-random-test: all perl-deps
bowtie-1.3.0+dfsg1/.pc/use-dpkg-buildflags.patch/Makefile:438: eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \
bowtie-1.3.0+dfsg1/.pc/use-dpkg-buildflags.patch/Makefile-439- ./scripts/test/random_bowtie_tests.sh $(*-command-variables-*-)
##############################################
bowtie-1.3.0+dfsg1/.pc/use-dpkg-buildflags.patch/Makefile-446- $$DL http://cpanmin.us | perl - -l $(CURDIR)/.perllib.tmp App::cpanminus local::lib ; \
bowtie-1.3.0+dfsg1/.pc/use-dpkg-buildflags.patch/Makefile:447: eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \
bowtie-1.3.0+dfsg1/.pc/use-dpkg-buildflags.patch/Makefile-448- cpanm --force Math::Random Clone Test::Deep Sys::Info -n --quiet; \
##############################################
bowtie-1.3.0+dfsg1/.pc/reproducible.patch/Makefile-238- -DBUILD_TIME="\"$(BUILD_DATE)\"" \
bowtie-1.3.0+dfsg1/.pc/reproducible.patch/Makefile:239: -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
bowtie-1.3.0+dfsg1/.pc/reproducible.patch/Makefile-240- $(FILE_FLAGS) \
##############################################
bowtie-1.3.0+dfsg1/.pc/reproducible.patch/Makefile-432-simple-test: allall perl-deps
bowtie-1.3.0+dfsg1/.pc/reproducible.patch/Makefile:433: eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \
bowtie-1.3.0+dfsg1/.pc/reproducible.patch/Makefile-434- ./scripts/test/simple_tests.pl --bowtie=./bowtie --bowtie-build=./bowtie-build
##############################################
bowtie-1.3.0+dfsg1/.pc/reproducible.patch/Makefile-437-random-test: all perl-deps
bowtie-1.3.0+dfsg1/.pc/reproducible.patch/Makefile:438: eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \
bowtie-1.3.0+dfsg1/.pc/reproducible.patch/Makefile-439- ./scripts/test/random_bowtie_tests.sh $(*-command-variables-*-)
##############################################
bowtie-1.3.0+dfsg1/.pc/reproducible.patch/Makefile-446- $$DL http://cpanmin.us | perl - -l $(CURDIR)/.perllib.tmp App::cpanminus local::lib ; \
bowtie-1.3.0+dfsg1/.pc/reproducible.patch/Makefile:447: eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \
bowtie-1.3.0+dfsg1/.pc/reproducible.patch/Makefile-448- cpanm --force Math::Random Clone Test::Deep Sys::Info -n --quiet; \
##############################################
bowtie-1.3.0+dfsg1/.pc/build-as-Cpp03.patch/Makefile-238- -DBUILD_TIME="\"`dpkg-parsechangelog --show-field Date`\"" \
bowtie-1.3.0+dfsg1/.pc/build-as-Cpp03.patch/Makefile:239: -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1 | sed 's/ *(.*//'`\"" \
bowtie-1.3.0+dfsg1/.pc/build-as-Cpp03.patch/Makefile-240- $(FILE_FLAGS) \
##############################################
bowtie-1.3.0+dfsg1/.pc/build-as-Cpp03.patch/Makefile-432-simple-test: allall perl-deps
bowtie-1.3.0+dfsg1/.pc/build-as-Cpp03.patch/Makefile:433: eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \
bowtie-1.3.0+dfsg1/.pc/build-as-Cpp03.patch/Makefile-434- ./scripts/test/simple_tests.pl --bowtie=./bowtie --bowtie-build=./bowtie-build
##############################################
bowtie-1.3.0+dfsg1/.pc/build-as-Cpp03.patch/Makefile-437-random-test: all perl-deps
bowtie-1.3.0+dfsg1/.pc/build-as-Cpp03.patch/Makefile:438: eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \
bowtie-1.3.0+dfsg1/.pc/build-as-Cpp03.patch/Makefile-439- ./scripts/test/random_bowtie_tests.sh $(*-command-variables-*-)
##############################################
bowtie-1.3.0+dfsg1/.pc/build-as-Cpp03.patch/Makefile-446- $$DL http://cpanmin.us | perl - -l $(CURDIR)/.perllib.tmp App::cpanminus local::lib ; \
bowtie-1.3.0+dfsg1/.pc/build-as-Cpp03.patch/Makefile:447: eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \
bowtie-1.3.0+dfsg1/.pc/build-as-Cpp03.patch/Makefile-448- cpanm --force Math::Random Clone Test::Deep Sys::Info -n --quiet; \
##############################################
bowtie-1.3.0+dfsg1/.pc/simple-test/scripts/test/simple_tests.pl-27-if(! -x $bowtie || ! -x $bowtie_build) {
bowtie-1.3.0+dfsg1/.pc/simple-test/scripts/test/simple_tests.pl:28: my $bowtie_dir = `dirname $bowtie`;
bowtie-1.3.0+dfsg1/.pc/simple-test/scripts/test/simple_tests.pl:29: my $bowtie_exe = `basename $bowtie`;
bowtie-1.3.0+dfsg1/.pc/simple-test/scripts/test/simple_tests.pl:30: my $bowtie_build_exe = `basename $bowtie_build`;
bowtie-1.3.0+dfsg1/.pc/simple-test/scripts/test/simple_tests.pl-31- chomp($bowtie_dir);
##############################################
bowtie-1.3.0+dfsg1/.pc/simple-test/scripts/test/simple_tests.pl-33- chomp($bowtie_build_exe);
bowtie-1.3.0+dfsg1/.pc/simple-test/scripts/test/simple_tests.pl:34: system("make -C $bowtie_dir $bowtie_exe $bowtie_build_exe") && die;
bowtie-1.3.0+dfsg1/.pc/simple-test/scripts/test/simple_tests.pl-35-}
##############################################
bowtie-1.3.0+dfsg1/.pc/simple-test/scripts/test/simple_tests.pl-1004- print "$cmd\n";
bowtie-1.3.0+dfsg1/.pc/simple-test/scripts/test/simple_tests.pl:1005: system($cmd);
bowtie-1.3.0+dfsg1/.pc/simple-test/scripts/test/simple_tests.pl-1006- ($? == 0) || die "Bad exitlevel from bowtie-build: $?";
##############################################
bowtie-1.3.0+dfsg1/.pc/simple-test/Makefile-238- -DBUILD_TIME="\"`dpkg-parsechangelog --show-field Date`\"" \
bowtie-1.3.0+dfsg1/.pc/simple-test/Makefile:239: -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1 | sed 's/ *(.*//'`\"" \
bowtie-1.3.0+dfsg1/.pc/simple-test/Makefile-240- $(FILE_FLAGS) \
##############################################
bowtie-1.3.0+dfsg1/.pc/simple-test/Makefile-432-simple-test: allall perl-deps
bowtie-1.3.0+dfsg1/.pc/simple-test/Makefile:433: eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \
bowtie-1.3.0+dfsg1/.pc/simple-test/Makefile-434- ./scripts/test/simple_tests.pl --bowtie=./bowtie --bowtie-build=./bowtie-build
##############################################
bowtie-1.3.0+dfsg1/.pc/simple-test/Makefile-437-random-test: all perl-deps
bowtie-1.3.0+dfsg1/.pc/simple-test/Makefile:438: eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \
bowtie-1.3.0+dfsg1/.pc/simple-test/Makefile-439- ./scripts/test/random_bowtie_tests.sh $(*-command-variables-*-)
##############################################
bowtie-1.3.0+dfsg1/.pc/simple-test/Makefile-446- $$DL http://cpanmin.us | perl - -l $(CURDIR)/.perllib.tmp App::cpanminus local::lib ; \
bowtie-1.3.0+dfsg1/.pc/simple-test/Makefile:447: eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \
bowtie-1.3.0+dfsg1/.pc/simple-test/Makefile-448- cpanm --force Math::Random Clone Test::Deep Sys::Info -n --quiet; \
##############################################
bowtie-1.3.0+dfsg1/.pc/popcnt_capability.patch/Makefile-238- -DBUILD_TIME="\"`dpkg-parsechangelog --show-field Date`\"" \
bowtie-1.3.0+dfsg1/.pc/popcnt_capability.patch/Makefile:239: -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1 | sed 's/ *(.*//'`\"" \
bowtie-1.3.0+dfsg1/.pc/popcnt_capability.patch/Makefile-240- $(FILE_FLAGS) \
##############################################
bowtie-1.3.0+dfsg1/.pc/popcnt_capability.patch/Makefile-436-random-test: all
bowtie-1.3.0+dfsg1/.pc/popcnt_capability.patch/Makefile:437: eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \
bowtie-1.3.0+dfsg1/.pc/popcnt_capability.patch/Makefile-438- ./scripts/test/random_bowtie_tests.sh $(*-command-variables-*-)
##############################################
bowtie-1.3.0+dfsg1/.pc/popcnt_capability.patch/Makefile-445- $$DL http://cpanmin.us | perl - -l $(CURDIR)/.perllib.tmp App::cpanminus local::lib ; \
bowtie-1.3.0+dfsg1/.pc/popcnt_capability.patch/Makefile:446: eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \
bowtie-1.3.0+dfsg1/.pc/popcnt_capability.patch/Makefile-447- cpanm --force Math::Random Clone Test::Deep Sys::Info -n --quiet; \
##############################################
bowtie-1.3.0+dfsg1/Makefile-238- -DBUILD_TIME="\"`dpkg-parsechangelog --show-field Date`\"" \
bowtie-1.3.0+dfsg1/Makefile:239: -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1 | sed 's/ *(.*//'`\"" \
bowtie-1.3.0+dfsg1/Makefile-240- $(FILE_FLAGS) \
##############################################
bowtie-1.3.0+dfsg1/Makefile-436-random-test: all
bowtie-1.3.0+dfsg1/Makefile:437: eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \
bowtie-1.3.0+dfsg1/Makefile-438- ./scripts/test/random_bowtie_tests.sh $(*-command-variables-*-)
##############################################
bowtie-1.3.0+dfsg1/Makefile-445- $$DL http://cpanmin.us | perl - -l $(CURDIR)/.perllib.tmp App::cpanminus local::lib ; \
bowtie-1.3.0+dfsg1/Makefile:446: eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \
bowtie-1.3.0+dfsg1/Makefile-447- cpanm --force Math::Random Clone Test::Deep Sys::Info -n --quiet; \