This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch master in repository roary.
commit 39d7e909252471cb3cc102e78c30afb082babd88 Author: Sascha Steinbiss <sa...@debian.org> Date: Mon Jan 22 00:44:37 2018 +0100 change shebang line to raise Standards version --- debian/changelog | 3 + debian/control | 2 +- debian/patches/series | 1 + debian/patches/use-debian-perl-path.patch | 612 ++++++++++++++++++++++++++++++ 4 files changed, 617 insertions(+), 1 deletion(-) diff --git a/debian/changelog b/debian/changelog index f74776b..ac76c80 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,6 +1,9 @@ roary (3.11.4+dfsg-1) unstable; urgency=medium * New upstream release. + * Bump Standards-Version. + * Add patch to use a shebang line of #!/usr/bin/perl, as + mandated by policy 10.4 (>= Standards version 4.1.2) -- Sascha Steinbiss <sa...@debian.org> Mon, 15 Jan 2018 13:40:31 +0100 diff --git a/debian/control b/debian/control index 9b3c31e..6844d8b 100644 --- a/debian/control +++ b/debian/control @@ -35,7 +35,7 @@ Build-Depends: debhelper (>= 10), mafft, fasttree Build-Depends-Indep: perl -Standards-Version: 4.1.1 +Standards-Version: 4.1.3 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/roary.git Vcs-Git: https://anonscm.debian.org/git/debian-med/roary.git Homepage: http://sanger-pathogens.github.io/Roary/ diff --git a/debian/patches/series b/debian/patches/series index 5f6df31..acc8a76 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,2 +1,3 @@ rename_R_script.patch use-dz-starter.patch +use-debian-perl-path.patch diff --git a/debian/patches/use-debian-perl-path.patch b/debian/patches/use-debian-perl-path.patch new file mode 100644 index 0000000..849700a --- /dev/null +++ b/debian/patches/use-debian-perl-path.patch @@ -0,0 +1,612 @@ +Description: use Debian Perl path + According to Policy 10.4 (introduced in Standards version 4.1.2) + the shebang at the top of Perl command scripts must be "#!/usr/bin/perl". + This patches changes the included scripts to conform to this. +Author: Sascha Steinbiss <sa...@debian.org> +--- a/bin/create_pan_genome ++++ b/bin/create_pan_genome +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::CreatePanGenome; + +--- a/bin/extract_proteome_from_gff ++++ b/bin/extract_proteome_from_gff +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::ExtractProteomeFromGFF; + +--- a/bin/iterative_cdhit ++++ b/bin/iterative_cdhit +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::IterativeCdhit; + +--- a/bin/pan_genome_assembly_statistics ++++ b/bin/pan_genome_assembly_statistics +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::AssemblyStatistics; + +--- a/bin/pan_genome_core_alignment ++++ b/bin/pan_genome_core_alignment +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::RoaryCoreAlignment; + +--- a/bin/pan_genome_post_analysis ++++ b/bin/pan_genome_post_analysis +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::RoaryPostAnalysis; + +--- a/bin/pan_genome_reorder_spreadsheet ++++ b/bin/pan_genome_reorder_spreadsheet +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::RoaryReorderSpreadsheet; + +--- a/bin/parallel_all_against_all_blastp ++++ b/bin/parallel_all_against_all_blastp +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::ParallelAllAgainstAllBlastp; + +--- a/bin/protein_alignment_from_nucleotides ++++ b/bin/protein_alignment_from_nucleotides +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::GeneAlignmentFromNucleotides; + +--- a/bin/query_pan_genome ++++ b/bin/query_pan_genome +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::QueryRoary; + +--- a/bin/roary ++++ b/bin/roary +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::Roary; + +--- a/bin/roary-pan_genome_reorder_spreadsheet ++++ b/bin/roary-pan_genome_reorder_spreadsheet +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::RoaryReorderSpreadsheet; + +--- a/bin/roary-query_pan_genome ++++ b/bin/roary-query_pan_genome +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::QueryRoary; + +--- a/bin/roary-unique_genes_per_sample ++++ b/bin/roary-unique_genes_per_sample +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::UniqueGenesPerSample; + +--- a/bin/transfer_annotation_to_groups ++++ b/bin/transfer_annotation_to_groups +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::TransferAnnotationToGroups; + +--- a/t/00_requires_external.t ++++ b/t/00_requires_external.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + use Test::Most; + use FindBin; +--- a/t/Bio/Roary/AccessoryBinaryFasta.t ++++ b/t/Bio/Roary/AccessoryBinaryFasta.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/AccessoryClustering.t ++++ b/t/Bio/Roary/AccessoryClustering.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/AnalyseGroups.t ++++ b/t/Bio/Roary/AnalyseGroups.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/AnnotateGroups.t ++++ b/t/Bio/Roary/AnnotateGroups.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/AssemblyStatistics.t ++++ b/t/Bio/Roary/AssemblyStatistics.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/ChunkFastaFile.t ++++ b/t/Bio/Roary/ChunkFastaFile.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/CombinedProteome.t ++++ b/t/Bio/Roary/CombinedProteome.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/CommandLine/ExtractProteomeFromGff.t ++++ b/t/Bio/Roary/CommandLine/ExtractProteomeFromGff.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use Moose; + use Data::Dumper; + use Cwd; +--- a/t/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.t ++++ b/t/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use Moose; + use Data::Dumper; + use Cwd; +--- a/t/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.t ++++ b/t/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use Moose; + use Data::Dumper; + use Cwd; +--- a/t/Bio/Roary/CommandLine/QueryRoary.t ++++ b/t/Bio/Roary/CommandLine/QueryRoary.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use Moose; + use Data::Dumper; + use Cwd; +--- a/t/Bio/Roary/CommandLine/Roary.t ++++ b/t/Bio/Roary/CommandLine/Roary.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use Moose; + use Data::Dumper; + use File::Path qw( remove_tree); +--- a/t/Bio/Roary/CommandLine/RoaryCoreAlignment.t ++++ b/t/Bio/Roary/CommandLine/RoaryCoreAlignment.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use Moose; + use Data::Dumper; + use Cwd; +--- a/t/Bio/Roary/CommandLine/RoaryPostAnalysis.t ++++ b/t/Bio/Roary/CommandLine/RoaryPostAnalysis.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use Moose; + use Data::Dumper; + use File::Path qw( remove_tree); +--- a/t/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.t ++++ b/t/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use Moose; + use Data::Dumper; + use Cwd; +--- a/t/Bio/Roary/CommandLine/TransferAnnotationToGroups.t ++++ b/t/Bio/Roary/CommandLine/TransferAnnotationToGroups.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use Moose; + use Data::Dumper; + use Cwd; +--- a/t/Bio/Roary/ContigsToGeneIDsFromGFF.t ++++ b/t/Bio/Roary/ContigsToGeneIDsFromGFF.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/EmblGroups.t ++++ b/t/Bio/Roary/EmblGroups.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/External/Blastp.t ++++ b/t/Bio/Roary/External/Blastp.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/External/Cdhit.t ++++ b/t/Bio/Roary/External/Cdhit.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/External/CheckTools.t ++++ b/t/Bio/Roary/External/CheckTools.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/External/Mafft.t ++++ b/t/Bio/Roary/External/Mafft.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/External/Makeblastdb.t ++++ b/t/Bio/Roary/External/Makeblastdb.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/External/Mcl.t ++++ b/t/Bio/Roary/External/Mcl.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/External/Prank.t ++++ b/t/Bio/Roary/External/Prank.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/ExtractCoreGenesFromSpreadsheet.t ++++ b/t/Bio/Roary/ExtractCoreGenesFromSpreadsheet.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/ExtractProteomeFromGFFs.t ++++ b/t/Bio/Roary/ExtractProteomeFromGFFs.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/FilterFullClusters.t ++++ b/t/Bio/Roary/FilterFullClusters.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/GeneNamesFromGFF.t ++++ b/t/Bio/Roary/GeneNamesFromGFF.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/GroupLabels.t ++++ b/t/Bio/Roary/GroupLabels.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/GroupStatistics.t ++++ b/t/Bio/Roary/GroupStatistics.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/InflateClusters.t ++++ b/t/Bio/Roary/InflateClusters.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/OrderGenes.t ++++ b/t/Bio/Roary/OrderGenes.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/Output/CoreGeneAlignmentCoorindatesEMBL.t ++++ b/t/Bio/Roary/Output/CoreGeneAlignmentCoorindatesEMBL.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/Output/DifferenceBetweenSets.t ++++ b/t/Bio/Roary/Output/DifferenceBetweenSets.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/Output/GroupsMultifastaProtein.t ++++ b/t/Bio/Roary/Output/GroupsMultifastaProtein.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/Output/GroupsMultifastas.t ++++ b/t/Bio/Roary/Output/GroupsMultifastas.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/Output/GroupsMultifastasNucleotide.t ++++ b/t/Bio/Roary/Output/GroupsMultifastasNucleotide.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use File::Path qw( remove_tree); +--- a/t/Bio/Roary/Output/NumberOfGroups.t ++++ b/t/Bio/Roary/Output/NumberOfGroups.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/Output/QueryGroups.t ++++ b/t/Bio/Roary/Output/QueryGroups.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/ParallelAllAgainstAllBlast.t ++++ b/t/Bio/Roary/ParallelAllAgainstAllBlast.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/PrepareInputFiles.t ++++ b/t/Bio/Roary/PrepareInputFiles.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/PresenceAbsenceMatrix.t ++++ b/t/Bio/Roary/PresenceAbsenceMatrix.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/QC/Report.t ++++ b/t/Bio/Roary/QC/Report.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/ReformatInputGFFs.t ++++ b/t/Bio/Roary/ReformatInputGFFs.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/ReorderSpreadsheet.t ++++ b/t/Bio/Roary/ReorderSpreadsheet.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/SampleOrder.t ++++ b/t/Bio/Roary/SampleOrder.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/SequenceLengths.t ++++ b/t/Bio/Roary/SequenceLengths.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/SortFasta.t ++++ b/t/Bio/Roary/SortFasta.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/SplitGroups.t ++++ b/t/Bio/Roary/SplitGroups.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/UniqueGenesPerSample.t ++++ b/t/Bio/Roary/UniqueGenesPerSample.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Test::Files; +--- a/t/bin/dummy_blastp ++++ b/t/bin/dummy_blastp +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use Moose; + use Getopt::Long; + my ($output_filename,$query,$db,$evalue,$num_threads,$outfmt,$max_target_seqs) ; +--- a/t/bin/dummy_cd-hit ++++ b/t/bin/dummy_cd-hit +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + system("touch output"); + system("touch output.clstr"); + system("touch output.bak.clstr"); +--- a/t/bin/dummy_makeblastdb ++++ b/t/bin/dummy_makeblastdb +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use Moose; + use Getopt::Long; + my($output_filename,$dbtype,$in,$logfile,$parse_seqids,$mask_data); +--- a/t/bin/dummy_mcl ++++ b/t/bin/dummy_mcl +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use Moose; + use Getopt::Long; + my ($output_filename,$abc_format,$inflation); +--- a/t/bin/dummy_mcxdeblast ++++ b/t/bin/dummy_mcxdeblast +@@ -1,2 +1,2 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + 1; +\ No newline at end of file +--- a/t/bin/dummy_segmasker ++++ b/t/bin/dummy_segmasker +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use Moose; + use Getopt::Long; + my($output_filename,$dbtype,$in,$logfile,$parse_seqids,$mask_data,$infmt,$outfmt); +--- a/t/dummy_blastp ++++ b/t/dummy_blastp +@@ -1,3 +1,3 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + system("touch results.out"); + 1; +\ No newline at end of file +--- a/t/dummy_cd-hit ++++ b/t/dummy_cd-hit +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + system("touch output"); + system("touch output.clstr"); + system("touch output.bak.clstr"); +--- a/t/dummy_makeblastdb ++++ b/t/dummy_makeblastdb +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + system("touch output_contigs.phr"); + system("touch output_contigs.pin"); + system("touch output_contigs.psq"); -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/roary.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit