[med-svn] [Git][med-team/bioperl-run][master] 5 commits: Fix test data in BEDtools test
Andreas Tille (@tille)
gitlab at salsa.debian.org
Fri Jan 20 20:55:54 GMT 2023
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 <tille at debian.org> 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 at -$1.tar.gz%" \
+ https://github.com/bioperl/bioperl-run/tags (?:.*?/)?release-v?(\d[\d-]*)\.tar\.gz
# http://search.cpan.org/dist/BioPerl-Run/ .*/BioPerl-Run-v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$
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
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