Andreas Tille pushed to branch master at Debian Med / bioperl-run
Commits: bcf5bc59 by Andreas Tille at 2023-01-20T21:23:00+01:00 Fix test data in BEDtools test - - - - - 0a217147 by Andreas Tille at 2023-01-20T21:25:25+01:00 Fix upstream source download name in watch file - - - - - 329db950 by Andreas Tille at 2023-01-20T21:25:51+01:00 routine-update: Standards-Version: 4.6.2 - - - - - 5c97ae7f by Andreas Tille at 2023-01-20T21:26:01+01:00 Update lintian override info format in d/bioperl-run.lintian-overrides on line 2-6. Changes-By: lintian-brush Fixes: lintian: mismatched-override See-also: https://lintian.debian.org/tags/mismatched-override.html - - - - - 124e1128 by Andreas Tille at 2023-01-20T21:47:08+01:00 Adapt another expected value after data were changed - - - - - 5 changed files: - debian/bioperl-run.lintian-overrides - debian/changelog - debian/control - debian/patches/alternate-data.patch - debian/watch Changes: ===================================== debian/bioperl-run.lintian-overrides ===================================== @@ -1,6 +1,6 @@ # see https://lists.debian.org/debian-med/2018/06/msg00043.html -bioperl-run: script-with-language-extension usr/bin/bp_multi_hmmsearch.pl -bioperl-run: script-with-language-extension usr/bin/bp_panalysis.pl -bioperl-run: script-with-language-extension usr/bin/bp_papplmaker.pl -bioperl-run: script-with-language-extension usr/bin/bp_run_neighbor.pl -bioperl-run: script-with-language-extension usr/bin/bp_run_protdist.pl +bioperl-run: script-with-language-extension [usr/bin/bp_multi_hmmsearch.pl] +bioperl-run: script-with-language-extension [usr/bin/bp_panalysis.pl] +bioperl-run: script-with-language-extension [usr/bin/bp_papplmaker.pl] +bioperl-run: script-with-language-extension [usr/bin/bp_run_neighbor.pl] +bioperl-run: script-with-language-extension [usr/bin/bp_run_protdist.pl] ===================================== debian/changelog ===================================== @@ -1,3 +1,13 @@ +bioperl-run (1.7.3-9) UNRELEASED; urgency=medium + + * Fix test data in BEDtools test + * Fix upstream source download name in watch file + * Standards-Version: 4.6.2 (routine-update) + * Update lintian override info format in d/bioperl-run.lintian-overrides on + line 2-6. + + -- Andreas Tille <[email protected]> Fri, 20 Jan 2023 21:22:00 +0100 + bioperl-run (1.7.3-8) unstable; urgency=medium * Replace skip_tests_for_muscle.patch by adjust-muscle-test.patch. ===================================== debian/control ===================================== @@ -57,7 +57,7 @@ Build-Depends-Indep: perl, pftools [any-amd64], # Needed for the network tests: libwww-perl -Standards-Version: 4.6.0 +Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/bioperl-run Vcs-Git: https://salsa.debian.org/med-team/bioperl-run.git Homepage: https://metacpan.org/release/BioPerl-Run ===================================== debian/patches/alternate-data.patch ===================================== @@ -19,9 +19,23 @@ Forwarded: no Last-Update: 2020-12-04 --- This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ ---- bioperl-run.orig/t/BEDTools.t -+++ bioperl-run/t/BEDTools.t -@@ -182,7 +182,7 @@ +--- a/t/BEDTools.t ++++ b/t/BEDTools.t +@@ -137,11 +137,11 @@ my %result_lookup = ( + 'mask_fasta_from_bed' => 1, # OK + 'shuffle' => 828, # OK + 'window' => 74998, # OK +- 'closest' => 845, # OK ++ 'closest' => 2121, # OK + 'genome_coverage' => 38, # OK + 'merge' => 242, # OK + 'slop' => 828, # OK +- 'complement' => 291, # OK - change in data provided by BEDTools or behaviour of complementBed? was 243 ++ 'complement' => 292, # OK - change in data provided by BEDTools or behaviour of complementBed? was 243 + 'intersect' => 72534, # OK + 'pair_to_bed' => 2, # OK + 'sort' => 828, # OK +@@ -182,7 +182,7 @@ SKIP : { chdir $dir; # Go back to $dir; } else { @@ -30,7 +44,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ ($gene_bed) = `find /usr -name 'knownGene.hg18.chr21.bed' 2>/dev/null`; ($mm8_genome) = `find /usr -name 'mouse.mm8.genome' 2>/dev/null`; ($mm9_genome) = `find /usr -name 'mouse.mm9.genome' 2>/dev/null`; -@@ -326,7 +326,10 @@ +@@ -326,7 +326,10 @@ SKIP : { open (FILE, $file); my $lines =()= <FILE>; close FILE; @@ -41,7 +55,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ } else { $v && diag(" check can get internal result format matches result file"); my $guesser = Bio::Tools::GuessSeqFormat->new( -file => $file ); -@@ -356,8 +359,11 @@ +@@ -356,8 +359,11 @@ SKIP : { isa_ok( $objres, 'Bio::SeqFeature::Collection', "returned object is correct for command '$command'" ); $v && diag(" - correct number of features"); ===================================== debian/watch ===================================== @@ -1,6 +1,5 @@ version=4 -opts="uversionmangle=s/^release-\(.*\)$/\1/;s/[-_]/./g" \ - https://github.com/bioperl/bioperl-run/tags \ - (?:.*?/)?release-v?(\d[\d-]*)\.tar\.gz debian uupdate +opts="uversionmangle=s/^release-\(.*\)$/\1/;s/[-_]/./g,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE@-$1.tar.gz%" \ + https://github.com/bioperl/bioperl-run/tags (?:.*?/)?release-v?(\d[\d-]*)\.tar\.gz # http://search.cpan.org/dist/BioPerl-Run/ .*/BioPerl-Run-v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$ View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/compare/ee00d3360a3607a279338e9b0c92f352eb47cec9...124e11287e5802b78a3d748cd120763652b22006 -- View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/compare/ee00d3360a3607a279338e9b0c92f352eb47cec9...124e11287e5802b78a3d748cd120763652b22006 You're receiving this email because of your account on salsa.debian.org.
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