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/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Amap.pm-258- return undef unless $exe = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Amap.pm:259: my $string = `$exe 2>&1` ;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Amap.pm-260- #AMAP version 1.09 - align multiple protein sequences and print to standard output
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Amap.pm-339-
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Amap.pm:340: my $status = system($commandstring);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Amap.pm-341- my $outfile = $self->outfile_name();
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Blat.pm-572-
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Blat.pm:573: my $status = system($str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Blat.pm-574- $self->throw( "Blat call ($str) crashed: $? \n") unless $status==0;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/DBA.pm-197- return undef unless defined $exe;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/DBA.pm:198: my $string = `$exe -- ` ;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/DBA.pm-199- $string =~ /\(([\d.]+)\)/;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/DBA.pm-277- $self->debug( "dba command = $commandstring");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/DBA.pm:278: my $status = system($commandstring);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/DBA.pm-279- $self->throw( "DBA call ($commandstring) crashed: $? \n") unless $status==0;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Exonerate.pm-187- return undef unless $exe = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Exonerate.pm:188: my $string = `$exe -v` ;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Exonerate.pm-189- #exonerate from exonerate version 2.0.0\n...
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Exonerate.pm-247- $self->debug( "$str\n");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Exonerate.pm:248: my $status = system($str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Exonerate.pm-249- $self->throw( "Exonerate call ($str) crashed: $? \n") unless $status==0;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Lagan.pm-486- -e $orig || $self->throw("Strange, $orig doesn't seem to exist");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Lagan.pm:487: system("cp $orig $orig.bk") && $self->throw("Backup of $orig failed: $!");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Lagan.pm:488: system("cp $matrix_file $orig") && $self->throw("Copy of $matrix_file -> $orig failed: $!");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Lagan.pm-489- }
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Lagan.pm-510- $self->debug("$command_string\n");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Lagan.pm:511: my $status = system(($version <= 3 ? '_POSIX2_VERSION=1 ' : '').$command_string); # temporary hack whilst lagan script 'rechaos.pl' uses obsolete sort syntax
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Lagan.pm-512-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Lagan.pm-514- my $orig = File::Spec->catfile($PROGRAM_DIR, 'nucmatrix.txt');
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Lagan.pm:515: system("mv $orig.bk $orig") && $self->warn("Restore of $orig from $orig.bk failed: $!");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Lagan.pm-516- }
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/MAFFT.pm-383-
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/MAFFT.pm:384: my $status = system($commandstring);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/MAFFT.pm-385- my $outfile = $self->outfile();
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/MSAProbs.pm-210- return unless $exe = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/MSAProbs.pm:211: my $string = `$exe -version 2>&1` ;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/MSAProbs.pm-212-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/MSAProbs.pm-526-
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/MSAProbs.pm:527: my $status = system($commandstring);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/MSAProbs.pm-528- my $outfile = $self->outfile_name;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Muscle.pm-226- return undef unless $exe = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Muscle.pm:227: my $string = `$exe 2>&1`;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Muscle.pm-228-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Muscle.pm-429-
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Muscle.pm:430: my $status = system($commandstring);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Muscle.pm-431- my $outfile = $self->outfile_name();
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Pal2Nal.pm-267-
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Pal2Nal.pm:268: system($command) && $self->throw("pal2nal call ($command) failed: $! | $?");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Pal2Nal.pm-269- open(my $errfh, '<', $error_file);
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Probalign.pm-247- return undef unless $exe = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Probalign.pm:248: my $string = `$exe 2>&1` ;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Probalign.pm-249- #PROBALIGN version 1.09 - align multiple protein sequences and print to standard output
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Probalign.pm-328-
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Probalign.pm:329: my $status = system($commandstring);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Probalign.pm-330- my $outfile = $self->outfile_name();
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Probcons.pm-276- return undef unless $exe = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Probcons.pm:277: my $string = `$exe 2>&1` ;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Probcons.pm-278- #PROBCONS version 1.09 - align multiple protein sequences and print to standard output
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Probcons.pm-357-
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Probcons.pm:358: my $status = system($commandstring);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Probcons.pm-359- if ($status) {
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Proda.pm-247- return undef unless $exe = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Proda.pm:248: my $string = `$exe 2>&1` ;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Proda.pm-249- #PRODA version 1.09 - align multiple protein sequences and print to standard output
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Proda.pm-328-
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Proda.pm:329: my $status = system($commandstring);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Proda.pm-330- my $outfile = $self->outfile_name();
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Sim4.pm-295- $self->debug( "Sim4 command = $commandstring");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Sim4.pm:296: my $status = system($commandstring);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Sim4.pm-297- $self->throw( "Sim4 call ($commandstring) crashed: $? \n") unless $status==0;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm-322- }
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm:323: my $status = system($para);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm-324- $self->throw("$para crashed: $?\n" )unless ($status==0);
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm-359- }
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm:360: my $status = system($para);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm-361- $self->throw("$para crashed: $?\n" )unless ($status==0);
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Kalign.pm-258- return undef unless $exe = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Kalign.pm:259: my $string = `$exe --show 2>&1` ;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Kalign.pm-260- $string =~ /Kalign\s+\((\d+)\..+\)/m;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Kalign.pm-345-
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Kalign.pm:346: my $status = system($commandstring);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Kalign.pm-347- my $outfile = $self->outfile_name();
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Coil.pm-271- }
bioperl-run-1.7.3/lib/Bio/Tools/Run/Coil.pm:272: my $status = system($str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Coil.pm-273- $self->throw( "Coil call ($str) crashed: $? \n") unless $status==0;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/EMBOSSApplication.pm-230- $self->debug( "Command line: ", $runstring, "\n");
bioperl-run-1.7.3/lib/Bio/Tools/Run/EMBOSSApplication.pm:231: return `$runstring`;
bioperl-run-1.7.3/lib/Bio/Tools/Run/EMBOSSApplication.pm-232-}
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/EMBOSSacd.pm-171- # reading from EMBOSS program acdc stdout (prior to version 2.8.0)
bioperl-run-1.7.3/lib/Bio/Tools/Run/EMBOSSacd.pm:172: $file = `acdc $prog -help -verbose -acdtable 2>&1`;
bioperl-run-1.7.3/lib/Bio/Tools/Run/EMBOSSacd.pm-173- } else {
bioperl-run-1.7.3/lib/Bio/Tools/Run/EMBOSSacd.pm-174- # reading from EMBOSS program acdtable stdout (version 2.8.0 or greater)
bioperl-run-1.7.3/lib/Bio/Tools/Run/EMBOSSacd.pm:175: $file = `acdtable $prog -help -verbose 2>&1`;
bioperl-run-1.7.3/lib/Bio/Tools/Run/EMBOSSacd.pm-176- }
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/ERPIN.pm-304- local $SIG{CHLD} = 'DEFAULT';
bioperl-run-1.7.3/lib/Bio/Tools/Run/ERPIN.pm:305: my $status = system($str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/ERPIN.pm-306- if($status || !-e $outfile || -z $outfile ) {
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Eponine.pm-399- " \n Check your java version, it has to be version 1.2 or later. Eponine crashed ($cmd) crashed: $? \n")
bioperl-run-1.7.3/lib/Bio/Tools/Run/Eponine.pm:400: if (system ($cmd));
bioperl-run-1.7.3/lib/Bio/Tools/Run/Eponine.pm-401-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/FootPrinter.pm-352-
bioperl-run-1.7.3/lib/Bio/Tools/Run/FootPrinter.pm:353: my $status = system($cmd_str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/FootPrinter.pm-354- $self->throw("FootPrinter Call($cmd_str) crashed: $?\n")
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Genewise.pm-210- my $prog = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Genewise.pm:211: my $string = `$prog -version`;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Genewise.pm-212- if( $string =~ /Version:\s+\$\s*Name:\s+(\S+)\s+\$/ ) {
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Genewise.pm-303- $self->debug("genewise command = $commandstring");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Genewise.pm:304: my $status = system("$commandstring > $outfile1");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Genewise.pm-305- $self->throw("Genewise call $commandstring crashed: $? \n") unless $status == 0;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Hmmer.pm-425- if ($progname eq 'hmmbuild') {
bioperl-run-1.7.3/lib/Bio/Tools/Run/Hmmer.pm:426: my $status = system($str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Hmmer.pm-427- return $status ? 0 : 1;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Hmmer.pm-429- else {
bioperl-run-1.7.3/lib/Bio/Tools/Run/Hmmer.pm:430: system($str) && $self->throw("HMMER call ($str) crashed: $?\n");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Hmmer.pm-431- @in = (-file => $outfile);
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Hmmer.pm-459- $str .= " > $null 2> $null" if $self->quiet;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Hmmer.pm:460: my $status = system($str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Hmmer.pm-461- return $status ? 0 : 1;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Infernal.pm-489- my $exe = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Infernal.pm:490: my $string = `$exe -h 2>&1`;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Infernal.pm-491- my $v;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Infernal.pm-988- if ($out) {
bioperl-run-1.7.3/lib/Bio/Tools/Run/Infernal.pm:989: my $status = system($str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Infernal.pm-990- if($status || !-e $out || -z $out ) {
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Infernal.pm-1077- for my $exec (qw(cmalign cmbuild cmcalibrate cmemit cmscore cmsearch cmstat)) {
bioperl-run-1.7.3/lib/Bio/Tools/Run/Infernal.pm:1078: my $output = `$exec --devhelp`;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Infernal.pm-1079- if ($?) {
bioperl-run-1.7.3/lib/Bio/Tools/Run/Infernal.pm:1080: $output = `$exec -h`;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Infernal.pm-1081- }
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/MCS.pm-268- my $cmd = "align2binomial.pl $offset $gtf $aln_file > $binomial_file 2> $error_file";
bioperl-run-1.7.3/lib/Bio/Tools/Run/MCS.pm:269: #system("rm -fr $cwd/mcs_dir; cp -R $temp_dir $cwd/mcs_dir");
bioperl-run-1.7.3/lib/Bio/Tools/Run/MCS.pm:270: my $throw = system($cmd);
bioperl-run-1.7.3/lib/Bio/Tools/Run/MCS.pm-271- open(my $efh, "<", $error_file) || $self->throw("Could not open error file '$error_file'");
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/MCS.pm-282- my $phylo_file = 'align_name.phylo';
bioperl-run-1.7.3/lib/Bio/Tools/Run/MCS.pm:283: system("generate_phyloMAX_score.pl $binomial_file > $phylo_file") && $self->throw("generate_phyloMAX_score.pl call failed: $?, $!");
bioperl-run-1.7.3/lib/Bio/Tools/Run/MCS.pm-284-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/MCS.pm-288- my $bed_file = 'align_name.bed'; # hardcoded in generate_mcs_beta.pl
bioperl-run-1.7.3/lib/Bio/Tools/Run/MCS.pm:289: system("generate_mcs_beta.pl $offset $gtf $phylo_file > $mcs_file") && $self->throw("generate_mcs_beta.pl failed: $?, $!");
bioperl-run-1.7.3/lib/Bio/Tools/Run/MCS.pm-290-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Match.pm-234- $mxprf_file = 'mxprf';
bioperl-run-1.7.3/lib/Bio/Tools/Run/Match.pm:235: system("$exe $mxlib ignored ignored $mxprf_file -p @thresh") && $self->throw("Something went wrong whist creating profile: $! | $?");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Match.pm-236- }
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Match.pm-248-
bioperl-run-1.7.3/lib/Bio/Tools/Run/Match.pm:249: system($cmd_line) && $self->throw("Something went wrong whist running '$cmd_line': $! | $?");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Match.pm-250-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/FastTree.pm-181- return undef unless $exe = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/FastTree.pm:182: my $string = `$exe 2>&1`;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/FastTree.pm-183-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/FastTree.pm-233-
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/FastTree.pm:234: my $status = system($command);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/FastTree.pm-235- my $outfile = $self->outfile_name();
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Gerp.pm-255- # alarm 60;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Gerp.pm:256: # system($command) && $self->throw("gerp call ($command) failed: $! | $?");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Gerp.pm-257- # alarm 0;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Gerp.pm-263- #
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Gerp.pm:264: # system("rm -fr $cwd/gerp_dir; cp -R $temp_dir $cwd/gerp_dir");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Gerp.pm-265-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Gerp.pm-285-
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Gerp.pm:286: #system("rm -fr $cwd/gerp_dir; cp -R $temp_dir $cwd/gerp_dir");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Gerp.pm-287-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Njtree/Best.pm-371- return undef unless $exe = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Njtree/Best.pm:372: my $string = `$exe 2>&1` ;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Njtree/Best.pm-373-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm-387- $self->debug("phastCons training command = $command\n");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm:388: system($command) && $self->throw("phastCons training call ($command) crashed: $?");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm-389-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm-392- $self->debug("phastCons command = $command\n");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm:393: system($command) && $self->throw("phastCons call ($command) crashed: $?");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm-394-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm-296- $self->debug("phyloFit command = $command\n");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm:297: system($command) && $self->throw("phyloFit call ($command) crashed: $?");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm-298-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phyml.pm-335- my $exe = $self->executable || return;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phyml.pm:336: my $string = substr `$exe -h`, 0, 40;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phyml.pm-337- my ($version) = $string =~ /PhyML v([\d+\.]+)/;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phyml.pm-969- $self->debug("Phyml command = $command\n");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phyml.pm:970: `$command`;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phyml.pm-971-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Raxml.pm-189- return undef unless $exe = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Raxml.pm:190: my $string = `$exe -v 2>&1`;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Raxml.pm-191-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Raxml.pm-256-
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Raxml.pm:257: my $status = system($command);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Raxml.pm-258-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Primate.pm-192- return undef unless defined $exe;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Primate.pm:193: my $string = `$exe -v ` ;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Primate.pm-194- $string =~ /\(([\d.]+)\)/;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Primate.pm-264- $self->debug( "primate command = $commandstring");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Primate.pm:265: my $status = system($commandstring);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Primate.pm-266- $self->throw( "primate call ($commandstring) crashed: $? \n") unless $status==0;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Primer3.pm-556- if (!defined $self->{'_progversion'}) {
bioperl-run-1.7.3/lib/Bio/Tools/Run/Primer3.pm:557: my $string = `$exe -about 2>&1`;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Primer3.pm-558- my $v;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Prints.pm-247- my $str =$self->executable." ".$self->DB." ".$self->_input." -fjR >".$outfile;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Prints.pm:248: my $status = system($str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Prints.pm-249- $self->throw( "Prints call ($str) crashed: $? \n") unless $status==0;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Profile.pm-245- my $str =$self->executable.' -fz '.$self->_input." ".$self->DB." > ".$outfile;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Profile.pm:246: my $status = system($str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Profile.pm-247- $self->throw( "Profile call ($str) crashed: $? \n") unless $status==0;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Promoterwise.pm-197- my $prog = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Promoterwise.pm:198: my $string = `$prog -version`;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Promoterwise.pm-199- $string =~ /(Version *)/i;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Pseudowise.pm-270- $self->debug( "pseudowise command = $commandstring\n");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Pseudowise.pm:271:# my $status = system($commandstring);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Pseudowise.pm:272: `$commandstring`;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Pseudowise.pm-273-# $self->throw( "Pseudowise call ($commandstring) crashed: $? \n")
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/RNAMotif.pm-394- local $SIG{CHLD} = 'DEFAULT';
bioperl-run-1.7.3/lib/Bio/Tools/Run/RNAMotif.pm:395: my $status = system($str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/RNAMotif.pm-396- if($status || !-e $outfile ) {
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/RepeatMasker.pm-230- return undef unless $exe;
bioperl-run-1.7.3/lib/Bio/Tools/Run/RepeatMasker.pm:231: my $string = `$exe -- ` ;
bioperl-run-1.7.3/lib/Bio/Tools/Run/RepeatMasker.pm-232- if( $string =~ /\(([\d.]+)\)/ ||
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/RepeatMasker.pm-304- }
bioperl-run-1.7.3/lib/Bio/Tools/Run/RepeatMasker.pm:305: my $status = system($cmd_str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/RepeatMasker.pm-306- $self->throw("Repeat Masker Call($cmd_str) crashed: $?\n")
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Seg.pm-236- my $str =$self->executable." ".$self->_input." -l > ".$outfile;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Seg.pm:237: my $status = system($str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Seg.pm-238- $self->throw( "Seg call ($str) crashed: $? \n") unless $status==0;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Signalp.pm-250- my $str =$self->executable." -t euk -trunc 50 ".$self->{'input'}." > ".$outfile;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Signalp.pm:251: my $status = system($str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Signalp.pm-252- $self->throw( "Signalp call ($str) crashed: $? \n") unless $status==0;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Simprot.pm-440- return undef unless $exe = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Simprot.pm:441: my $string = `$exe 2>&1` ;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Simprot.pm-442-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/StandAloneNCBIBlast.pm-440- $self->debug("$commandstring\n");
bioperl-run-1.7.3/lib/Bio/Tools/Run/StandAloneNCBIBlast.pm:441: system($commandstring) && $self->throw("$executable call crashed: $? | $! | $commandstring\n");
bioperl-run-1.7.3/lib/Bio/Tools/Run/StandAloneNCBIBlast.pm-442-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/StandAloneWUBlast.pm-249- $self->debug("$commandstring\n");
bioperl-run-1.7.3/lib/Bio/Tools/Run/StandAloneWUBlast.pm:250: system($commandstring) && $self->throw("$executable call crashed: $? | $! | $commandstring\n");
bioperl-run-1.7.3/lib/Bio/Tools/Run/StandAloneWUBlast.pm-251-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Tmhmm.pm-294-
bioperl-run-1.7.3/lib/Bio/Tools/Run/Tmhmm.pm:295: my $status = system($str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Tmhmm.pm-296- $self->throw( "Tmhmm call ($str) crashed: $? \n") unless $status==0;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/TribeMCL.pm-667-
bioperl-run-1.7.3/lib/Bio/Tools/Run/TribeMCL.pm:668: my $status = system($cmd);
bioperl-run-1.7.3/lib/Bio/Tools/Run/TribeMCL.pm-669-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/TribeMCL.pm-709- $cmd .= " > $null";
bioperl-run-1.7.3/lib/Bio/Tools/Run/TribeMCL.pm:710: my $status = system($cmd);
bioperl-run-1.7.3/lib/Bio/Tools/Run/TribeMCL.pm-711-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Vista.pm-547- $self->debug($cmd);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Vista.pm:548: my $status = system ($cmd);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Vista.pm-549-
##############################################
bioperl-run-1.7.3/scripts/bp_blast2tree.pl-44-GetOptions(
bioperl-run-1.7.3/scripts/bp_blast2tree.pl:45: 'h|help' => sub { exec('perldoc', $0);
bioperl-run-1.7.3/scripts/bp_blast2tree.pl-46- exit(0); },
##############################################
bioperl-run-1.7.3/scripts/multi_hmmsearch.PLS-66-# Print documentation if help switch was given
bioperl-run-1.7.3/scripts/multi_hmmsearch.PLS:67:exec('perldoc', $0) and exit() if $opt_h;
bioperl-run-1.7.3/scripts/multi_hmmsearch.PLS-68-
##############################################
bioperl-run-1.7.3/scripts/multi_hmmsearch.PLS-112- print "--> Performing hmmsearch in file:\t\t$line\n";
bioperl-run-1.7.3/scripts/multi_hmmsearch.PLS:113: system("$hmmsearch $opt_p $line > multi/$out.hmms");
bioperl-run-1.7.3/scripts/multi_hmmsearch.PLS-114- print "==> hmmsearch results stored in file:\t\tmulti/$out.hmms\n";
##############################################
bioperl-run-1.7.3/scripts/run_neighbor.PLS-38- 'o|out:s' => \$out,
bioperl-run-1.7.3/scripts/run_neighbor.PLS:39: 'h|help' => sub { exec('perldoc',$0); exit(0) }
bioperl-run-1.7.3/scripts/run_neighbor.PLS-40- );
##############################################
bioperl-run-1.7.3/scripts/run_protdist.PLS-47- 'i|in:s' => \$file,
bioperl-run-1.7.3/scripts/run_protdist.PLS:48: 'h|help' => sub { exec('perldoc',$0); exit(0) }
bioperl-run-1.7.3/scripts/run_protdist.PLS-49- );
##############################################
bioperl-run-1.7.3/t/DrawGram.t-27- if( test_debug() ) {
bioperl-run-1.7.3/t/DrawGram.t:28: `gs $file`;
bioperl-run-1.7.3/t/DrawGram.t-29- }
##############################################
bioperl-run-1.7.3/t/DrawGram.t-44- if( test_debug() ) {
bioperl-run-1.7.3/t/DrawGram.t:45: `gs $file`;
bioperl-run-1.7.3/t/DrawGram.t-46- }
##############################################
bioperl-run-1.7.3/t/DrawTree.t-26- if( test_debug() ) {
bioperl-run-1.7.3/t/DrawTree.t:27: `gs $file`;
bioperl-run-1.7.3/t/DrawTree.t-28- } else {
##############################################
bioperl-run-1.7.3/t/DrawTree.t-38- if( test_debug() ) {
bioperl-run-1.7.3/t/DrawTree.t:39: `gs $file`;
bioperl-run-1.7.3/t/DrawTree.t-40- } else {
##############################################
bioperl-run-1.7.3/debian/patches/kalign-version-regex.patch-15- return undef unless $exe = $self->executable;
bioperl-run-1.7.3/debian/patches/kalign-version-regex.patch:16:- my $string = `$exe 2>&1` ;
bioperl-run-1.7.3/debian/patches/kalign-version-regex.patch-17-- $string =~ /Kalign\s+version\s+(\d+\.\d+)/m;
bioperl-run-1.7.3/debian/patches/kalign-version-regex.patch:18:+ my $string = `$exe --show 2>&1` ;
bioperl-run-1.7.3/debian/patches/kalign-version-regex.patch-19-+ $string =~ /Kalign\s+\((\d+)\..+\)/m;
##############################################
bioperl-run-1.7.3/.pc/kalign-input-via-piping.patch/lib/Bio/Tools/Run/Alignment/Kalign.pm-258- return undef unless $exe = $self->executable;
bioperl-run-1.7.3/.pc/kalign-input-via-piping.patch/lib/Bio/Tools/Run/Alignment/Kalign.pm:259: my $string = `$exe 2>&1` ;
bioperl-run-1.7.3/.pc/kalign-input-via-piping.patch/lib/Bio/Tools/Run/Alignment/Kalign.pm-260- $string =~ /Kalign\s+version\s+(\d+\.\d+)/m;
##############################################
bioperl-run-1.7.3/.pc/kalign-input-via-piping.patch/lib/Bio/Tools/Run/Alignment/Kalign.pm-345-
bioperl-run-1.7.3/.pc/kalign-input-via-piping.patch/lib/Bio/Tools/Run/Alignment/Kalign.pm:346: my $status = system($commandstring);
bioperl-run-1.7.3/.pc/kalign-input-via-piping.patch/lib/Bio/Tools/Run/Alignment/Kalign.pm-347- my $outfile = $self->outfile_name();
##############################################
bioperl-run-1.7.3/.pc/kalign-version-regex.patch/lib/Bio/Tools/Run/Alignment/Kalign.pm-258- return undef unless $exe = $self->executable;
bioperl-run-1.7.3/.pc/kalign-version-regex.patch/lib/Bio/Tools/Run/Alignment/Kalign.pm:259: my $string = `$exe 2>&1` ;
bioperl-run-1.7.3/.pc/kalign-version-regex.patch/lib/Bio/Tools/Run/Alignment/Kalign.pm-260- $string =~ /Kalign\s+version\s+(\d+\.\d+)/m;
##############################################
bioperl-run-1.7.3/.pc/kalign-version-regex.patch/lib/Bio/Tools/Run/Alignment/Kalign.pm-345-
bioperl-run-1.7.3/.pc/kalign-version-regex.patch/lib/Bio/Tools/Run/Alignment/Kalign.pm:346: my $status = system($commandstring);
bioperl-run-1.7.3/.pc/kalign-version-regex.patch/lib/Bio/Tools/Run/Alignment/Kalign.pm-347- my $outfile = $self->outfile_name();