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/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
roary-3.13.0+dfsg/lib/Bio/Roary/CombinedProteome.pm-41- {
roary-3.13.0+dfsg/lib/Bio/Roary/CombinedProteome.pm:42: system(join(' ', ("cat", $filename, ">>", $self->output_filename)));
roary-3.13.0+dfsg/lib/Bio/Roary/CombinedProteome.pm-43- }
##############################################
roary-3.13.0+dfsg/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm-58- $self->output_filename($output_filename) if ( defined($output_filename) );
roary-3.13.0+dfsg/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm:59: $self->makeblastdb_exec($makeblastdb_exec) if ( defined($makeblastdb_exec) );
roary-3.13.0+dfsg/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm:60: $self->blastp_exec($blastp_exec) if ( defined($blastp_exec) );
roary-3.13.0+dfsg/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm-61- $self->job_runner($job_runner) if ( defined($job_runner) );
##############################################
roary-3.13.0+dfsg/lib/Bio/Roary/CommandLine/Roary.pm-165- $self->job_runner($job_runner) if ( defined($job_runner) );
roary-3.13.0+dfsg/lib/Bio/Roary/CommandLine/Roary.pm:166: $self->makeblastdb_exec($makeblastdb_exec) if ( defined($makeblastdb_exec) );
roary-3.13.0+dfsg/lib/Bio/Roary/CommandLine/Roary.pm:167: $self->blastp_exec($blastp_exec) if ( defined($blastp_exec) );
roary-3.13.0+dfsg/lib/Bio/Roary/CommandLine/Roary.pm:168: $self->mcxdeblast_exec($mcxdeblast_exec) if ( defined($mcxdeblast_exec) );
roary-3.13.0+dfsg/lib/Bio/Roary/CommandLine/Roary.pm:169: $self->mcl_exec($mcl_exec) if ( defined($mcl_exec) );
roary-3.13.0+dfsg/lib/Bio/Roary/CommandLine/Roary.pm-170- $self->cpus($cpus) if ( defined($cpus) );
##############################################
roary-3.13.0+dfsg/lib/Bio/Roary/External/Blastp.pm-61- $self->logger->info( "Running command: " . $self->_command_to_run() );
roary-3.13.0+dfsg/lib/Bio/Roary/External/Blastp.pm:62: system( $self->_command_to_run );
roary-3.13.0+dfsg/lib/Bio/Roary/External/Blastp.pm-63- 1;
##############################################
roary-3.13.0+dfsg/lib/Bio/Roary/ExtractProteomeFromGFF.pm-119- $self->logger->debug($cmd);
roary-3.13.0+dfsg/lib/Bio/Roary/ExtractProteomeFromGFF.pm:120: system($cmd);
roary-3.13.0+dfsg/lib/Bio/Roary/ExtractProteomeFromGFF.pm-121- unlink( $self->_nucleotide_fasta_file_from_gff_filename );
##############################################
roary-3.13.0+dfsg/lib/Bio/Roary/JobRunner/Local.pm-29- $self->logger->info($command_to_run);
roary-3.13.0+dfsg/lib/Bio/Roary/JobRunner/Local.pm:30: system($command_to_run );
roary-3.13.0+dfsg/lib/Bio/Roary/JobRunner/Local.pm-31- }
##############################################
roary-3.13.0+dfsg/lib/Bio/Roary/JobRunner/Local.pm-44- $self->logger->info($command_to_run);
roary-3.13.0+dfsg/lib/Bio/Roary/JobRunner/Local.pm:45: system($command_to_run );
roary-3.13.0+dfsg/lib/Bio/Roary/JobRunner/Local.pm-46-}
##############################################
roary-3.13.0+dfsg/lib/Bio/Roary/JobRunner/Parallel.pm-42-
roary-3.13.0+dfsg/lib/Bio/Roary/JobRunner/Parallel.pm:43: system($parallel_command);
roary-3.13.0+dfsg/lib/Bio/Roary/JobRunner/Parallel.pm-44- 1;
##############################################
roary-3.13.0+dfsg/lib/Bio/Roary/JobRunner/Parallel.pm-55- $self->logger->info($command_to_run);
roary-3.13.0+dfsg/lib/Bio/Roary/JobRunner/Parallel.pm:56: system($command_to_run );
roary-3.13.0+dfsg/lib/Bio/Roary/JobRunner/Parallel.pm-57-}
##############################################
roary-3.13.0+dfsg/lib/Bio/Roary/JobRunner/Role.pm-54- for my $dir (File::Spec->path) {
roary-3.13.0+dfsg/lib/Bio/Roary/JobRunner/Role.pm:55: for my $exec (@{$executables})
roary-3.13.0+dfsg/lib/Bio/Roary/JobRunner/Role.pm-56- {
##############################################
roary-3.13.0+dfsg/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm-162- . ' -name > /dev/null 2>&1';
roary-3.13.0+dfsg/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm:163: system($cmd);
roary-3.13.0+dfsg/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm-164- unlink( $self->_nucleotide_fasta_file_from_gff_filename );
##############################################
roary-3.13.0+dfsg/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm-92- {
roary-3.13.0+dfsg/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm:93: system( "rm " . $self->blast_results_file_name );
roary-3.13.0+dfsg/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm-94- }
roary-3.13.0+dfsg/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm:95: system( "touch " . $self->blast_results_file_name );
roary-3.13.0+dfsg/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm-96- for my $output_file ( @{$output_files} ) {
roary-3.13.0+dfsg/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm:97: system( "cat $output_file >> " . $self->blast_results_file_name );
roary-3.13.0+dfsg/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm-98- }
##############################################
roary-3.13.0+dfsg/lib/Bio/Roary/SplitGroups.pm-86- my ( $filename, $directories, $suffix ) = fileparse( $fasta_file, qr/\.[^.]*/ );
roary-3.13.0+dfsg/lib/Bio/Roary/SplitGroups.pm:87: system('grep \> '.$fasta_file.'| sed \'s/>//\' >'.$self->_gene_files_temp_dir_obj."/".$filename.$suffix ) ;
roary-3.13.0+dfsg/lib/Bio/Roary/SplitGroups.pm-88-
##############################################
roary-3.13.0+dfsg/lib/Bio/Roary/PostAnalysis.pm-127-
roary-3.13.0+dfsg/lib/Bio/Roary/PostAnalysis.pm:128: system("create_pan_genome_plots") unless ( $self->dont_create_rplots == 1 );
roary-3.13.0+dfsg/lib/Bio/Roary/PostAnalysis.pm-129-
##############################################
roary-3.13.0+dfsg/t/bin/dummy_makeblastdb-12-
roary-3.13.0+dfsg/t/bin/dummy_makeblastdb:13:system("touch $output_filename.phr");
roary-3.13.0+dfsg/t/bin/dummy_makeblastdb:14:system("touch $output_filename.pin");
roary-3.13.0+dfsg/t/bin/dummy_makeblastdb:15:system("touch $output_filename.psq");
roary-3.13.0+dfsg/t/bin/dummy_makeblastdb-16-
##############################################
roary-3.13.0+dfsg/t/bin/dummy_mcl-10-
roary-3.13.0+dfsg/t/bin/dummy_mcl:11:system("touch $output_filename");
roary-3.13.0+dfsg/t/bin/dummy_mcl-12-1;
##############################################
roary-3.13.0+dfsg/t/bin/dummy_segmasker-12-
roary-3.13.0+dfsg/t/bin/dummy_segmasker:13:system("touch $output_filename");
roary-3.13.0+dfsg/t/bin/dummy_segmasker-14-1;
##############################################
roary-3.13.0+dfsg/t/lib/TestHelper.pm-46- open OLDERR, '>&STDERR';
roary-3.13.0+dfsg/t/lib/TestHelper.pm:47: eval("use $script_name ;");
roary-3.13.0+dfsg/t/lib/TestHelper.pm-48- my $returned_values = 0;
##############################################
roary-3.13.0+dfsg/t/lib/TestHelper.pm-51- open STDERR, '>/dev/null' or warn "Can't open /dev/null: $!";
roary-3.13.0+dfsg/t/lib/TestHelper.pm:52: stdout_like { eval("$script_name->new(args => \\\@input_args, script_name => '$script_name')->run;"); } qr/$expected/, "got expected text $expected for $parameters";
roary-3.13.0+dfsg/t/lib/TestHelper.pm-53- close STDERR;
##############################################
roary-3.13.0+dfsg/t/lib/TestHelper.pm-64- open OLDERR, '>&STDERR';
roary-3.13.0+dfsg/t/lib/TestHelper.pm:65: eval("use $script_name ;");
roary-3.13.0+dfsg/t/lib/TestHelper.pm-66- my $returned_values = 0;
##############################################
roary-3.13.0+dfsg/t/lib/TestHelper.pm-69- open STDERR, '>/dev/null' or warn "Can't open /dev/null: $!";
roary-3.13.0+dfsg/t/lib/TestHelper.pm:70: stdout_unlike { eval("$script_name->new(args => \\\@input_args, script_name => '$script_name')->run;"); } qr/$expected/, "got expected text $expected for $parameters";
roary-3.13.0+dfsg/t/lib/TestHelper.pm-71- close STDERR;
##############################################
roary-3.13.0+dfsg/t/lib/TestHelper.pm-83- open OLDOUT, '>&STDOUT';
roary-3.13.0+dfsg/t/lib/TestHelper.pm:84: eval("use $script_name ;");
roary-3.13.0+dfsg/t/lib/TestHelper.pm-85- my $returned_values = 0;
##############################################
roary-3.13.0+dfsg/t/lib/TestHelper.pm-88- open STDOUT, '>/dev/null' or warn "Can't open /dev/null: $!";
roary-3.13.0+dfsg/t/lib/TestHelper.pm:89: stderr_unlike { eval("$script_name->new(args => \\\@input_args, script_name => '$script_name')->run;"); } qr/$expected/, "got expected text $expected for $parameters";
roary-3.13.0+dfsg/t/lib/TestHelper.pm-90- close STDOUT;
##############################################
roary-3.13.0+dfsg/t/lib/TestHelper.pm-100- open OLDOUT, '>&STDOUT';
roary-3.13.0+dfsg/t/lib/TestHelper.pm:101: eval("use $script_name ;");
roary-3.13.0+dfsg/t/lib/TestHelper.pm-102- my $returned_values = 0;
##############################################
roary-3.13.0+dfsg/t/lib/TestHelper.pm-105- open STDOUT, '>/dev/null' or warn "Can't open /dev/null: $!";
roary-3.13.0+dfsg/t/lib/TestHelper.pm:106: stderr_like { eval("$script_name->new(args => \\\@input_args, script_name => '$script_name')->run;"); } qr/$expected/, "got expected text $expected for $parameters";
roary-3.13.0+dfsg/t/lib/TestHelper.pm-107- close STDOUT;
##############################################
roary-3.13.0+dfsg/t/lib/TestHelper.pm-120- open OLDERR, '>&STDERR';
roary-3.13.0+dfsg/t/lib/TestHelper.pm:121: eval("use $script_name ;");
roary-3.13.0+dfsg/t/lib/TestHelper.pm-122- my $returned_values = 0;
##############################################
roary-3.13.0+dfsg/t/lib/TestHelper.pm-133- my $cmd = "$script_name->new(args => \\\@input_args, script_name => '$script_name')->run;";
roary-3.13.0+dfsg/t/lib/TestHelper.pm:134: eval($cmd);
roary-3.13.0+dfsg/t/lib/TestHelper.pm-135- warn $@ if $@;
##############################################
roary-3.13.0+dfsg/t/lib/TestHelper.pm-174- open OLDERR, '>&STDERR';
roary-3.13.0+dfsg/t/lib/TestHelper.pm:175: eval("use $script_name ;");
roary-3.13.0+dfsg/t/lib/TestHelper.pm-176- my $returned_values = 0;
##############################################
roary-3.13.0+dfsg/t/lib/TestHelper.pm-187- my $cmd = "$script_name->new(args => \\\@input_args, script_name => '$script_name')->run;";
roary-3.13.0+dfsg/t/lib/TestHelper.pm:188: eval($cmd);
roary-3.13.0+dfsg/t/lib/TestHelper.pm-189- warn $@ if $@;
##############################################
roary-3.13.0+dfsg/t/lib/TestHelper.pm-229- open OLDERR, '>&STDERR';
roary-3.13.0+dfsg/t/lib/TestHelper.pm:230: eval("use $script_name ;");
roary-3.13.0+dfsg/t/lib/TestHelper.pm-231- my $returned_values = 0;
##############################################
roary-3.13.0+dfsg/t/lib/TestHelper.pm-242- my $cmd = "$script_name->new(args => \\\@input_args, script_name => '$script_name')->run;";
roary-3.13.0+dfsg/t/lib/TestHelper.pm:243: eval($cmd);
roary-3.13.0+dfsg/t/lib/TestHelper.pm-244- warn $@ if $@;
##############################################
roary-3.13.0+dfsg/debian/patches/rename_R_script.patch-10-
roary-3.13.0+dfsg/debian/patches/rename_R_script.patch:11:- system("create_pan_genome_plots.R") unless ( $self->dont_create_rplots == 1 );
roary-3.13.0+dfsg/debian/patches/rename_R_script.patch:12:+ system("create_pan_genome_plots") unless ( $self->dont_create_rplots == 1 );
roary-3.13.0+dfsg/debian/patches/rename_R_script.patch-13-
##############################################
roary-3.13.0+dfsg/.pc/rename_R_script.patch/lib/Bio/Roary/PostAnalysis.pm-127-
roary-3.13.0+dfsg/.pc/rename_R_script.patch/lib/Bio/Roary/PostAnalysis.pm:128: system("create_pan_genome_plots.R") unless ( $self->dont_create_rplots == 1 );
roary-3.13.0+dfsg/.pc/rename_R_script.patch/lib/Bio/Roary/PostAnalysis.pm-129-
##############################################
roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/bin/dummy_makeblastdb-12-
roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/bin/dummy_makeblastdb:13:system("touch $output_filename.phr");
roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/bin/dummy_makeblastdb:14:system("touch $output_filename.pin");
roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/bin/dummy_makeblastdb:15:system("touch $output_filename.psq");
roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/bin/dummy_makeblastdb-16-
##############################################
roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/bin/dummy_mcl-10-
roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/bin/dummy_mcl:11:system("touch $output_filename");
roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/bin/dummy_mcl-12-1;
##############################################
roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/bin/dummy_segmasker-12-
roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/bin/dummy_segmasker:13:system("touch $output_filename");
roary-3.13.0+dfsg/.pc/use-debian-perl-path.patch/t/bin/dummy_segmasker-14-1;