Étienne Mollier pushed to branch master at Debian Med / bioperl-run
Commits: 0c1e07eb by Étienne Mollier at 2022-02-10T20:03:27+01:00 initialize changelog - - - - - d09a2a1f by Étienne Mollier at 2022-02-10T20:40:09+01:00 Replace skip_tests_for_muscle.patch by adjust-muscle-test.patch Integration of newer muscle version in debian changed the code path in the way the test may be skipped, breaking autopkgtest of bioperl-run. - - - - - ff03d92a by Étienne Mollier at 2022-02-10T20:44:07+01:00 update changelog - - - - - c15b6b71 by Étienne Mollier at 2022-02-10T20:44:23+01:00 Move libmodule-build-perl from Build-Depends-Indep to Build-Depends. Changes-By: lintian-brush Fixes: lintian: libmodule-build-perl-needs-to-be-in-build-depends See-also: https://lintian.debian.org/tags/libmodule-build-perl-needs-to-be-in-build-depends.html - - - - - ee00d336 by Étienne Mollier at 2022-02-10T20:55:25+01:00 routine-update: Ready to upload to unstable - - - - - 5 changed files: - debian/changelog - debian/control - + debian/patches/adjust-muscle-test.patch - debian/patches/series - − debian/patches/skip_tests_for_muscle.patch Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,12 @@ +bioperl-run (1.7.3-8) unstable; urgency=medium + + * Replace skip_tests_for_muscle.patch by adjust-muscle-test.patch. + Integration of newer muscle version in debian changed the code path in + the way the test may be skipped, breaking autopkgtest of bioperl-run.. + * Move libmodule-build-perl from Build-Depends-Indep to Build-Depends. + + -- Étienne Mollier <[email protected]> Thu, 10 Feb 2022 20:44:28 +0100 + bioperl-run (1.7.3-7) unstable; urgency=medium * d/watch: fix broken link to github and adjust version mangling to fit ===================================== debian/control ===================================== @@ -6,9 +6,8 @@ Uploaders: Charles Plessy <[email protected]>, Section: science Testsuite: autopkgtest-pkg-perl Priority: optional -Build-Depends: debhelper-compat (= 13) +Build-Depends: debhelper-compat (= 13), libmodule-build-perl Build-Depends-Indep: perl, - libmodule-build-perl, bioperl (>= 1.7.4), # Recommended in Build.PL: libalgorithm-diff-perl, ===================================== debian/patches/adjust-muscle-test.patch ===================================== @@ -0,0 +1,25 @@ +Description: adjust skip count for Muscle test + The initial count looks like upstream might have forgotten to update it.. +Author: Étienne Mollier <[email protected]> +Forwarded: no +Last-Update: 2022-02-10 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- bioperl-run.orig/t/Muscle.t ++++ bioperl-run/t/Muscle.t +@@ -33,7 +33,7 @@ + unless ( $version >= 3.6 ) { + skip( + "Only muscle version 3.6 or higher is supported by these tests. Skipping tests", +- 7 ++ 10 + ); + exit(0); + } +@@ -88,4 +88,4 @@ + + is( $s1_perid == 41 || $s1_perid == 42, + 1, 'diff versions of MUSCLE have different vals' ); +-} +\ No newline at end of file ++} ===================================== debian/patches/series ===================================== @@ -7,7 +7,6 @@ skip_tests_for_wise.patch skip_tests_for_phylip.patch skip_tests_for_phyml.patch skip_tests_for_infernal.patch -skip_tests_for_muscle.patch skip_tests_for_ncbi-blast+.patch hyphy.patch remove_tests_for_ensembl.patch @@ -18,3 +17,4 @@ skip-test-for-kalign.patch fix-whatis-entries.patch unscramble-erpin.patch fix-pod-conversion.patch +adjust-muscle-test.patch ===================================== debian/patches/skip_tests_for_muscle.patch deleted ===================================== @@ -1,75 +0,0 @@ -Author: Andreas Tille <[email protected]> -Last-Update: Fri, 16 Dec 2016 09:17:37 +0100 -Description: Exclude some failed test when using muscle. Seems Debian's muscle is newer - ---- a/t/Muscle.t -+++ b/t/Muscle.t -@@ -5,7 +5,7 @@ use strict; - - BEGIN { - use Bio::Root::Test; -- test_begin( -tests => 16 ); -+ test_begin( -tests => 8 ); - use_ok('Bio::Tools::Run::Alignment::Muscle'); - use_ok('Bio::AlignIO'); - use_ok('Bio::SeqIO'); -@@ -39,10 +39,6 @@ SKIP: { - } - cmp_ok( $version, '>=', 3.6, "Code tested only on muscle versions > 3.6" ); - -- $aln = $factory->align($inputfilename); -- ok($aln); -- is( $aln->num_sequences, 7 ); -- - my $str = Bio::SeqIO->new( - -file => test_input_file("cysprot.fa"), - -format => 'Fasta' -@@ -53,11 +49,11 @@ SKIP: { - } - my $seq_array_ref = \@seq_array; - -- $aln = $factory->align($seq_array_ref); -- is $aln->num_sequences, 7; -- my $s1_perid = POSIX::ceil( $aln->average_percentage_identity ); -- is( $s1_perid == 43 || $s1_perid == 44, -- 1, 'diff versions of MUSCLE have different vals' ); -+ #$aln = $factory->align($seq_array_ref); -+ #is $aln->num_sequences, 7; -+ #my $s1_perid = POSIX::ceil( $aln->average_percentage_identity ); -+ #is( $s1_perid == 43 || $s1_perid == 44, -+ # 1, 'diff versions of MUSCLE have different vals' ); - - my $logfile = test_output_file(); - my $outfile = test_output_file(); -@@ -75,17 +71,18 @@ SKIP: { - ); - $factory = Bio::Tools::Run::Alignment::Muscle->new(@params); - is( $factory->log, $logfile, 'log file' ); -- $aln = $factory->align($seq_array_ref); -- is $aln->num_sequences, 7; -- $s1_perid = POSIX::ceil( $aln->average_percentage_identity ); -- is( $s1_perid == 43 || $s1_perid == 44, -- 1, 'diff versions of MUSCLE have different vals' ); -+ #$aln = $factory->align($seq_array_ref); -+ #is $aln->num_sequences, 7; -+ #$s1_perid = POSIX::ceil( $aln->average_percentage_identity ); -+ #is( $s1_perid == 43 || $s1_perid == 44, -+ # 1, 'diff versions of MUSCLE have different vals' ); -+ my $s1_perid; - - $inputfilename = test_input_file("cysprot1a.fa"); -- $aln = $factory->align($inputfilename); -- is $aln->num_sequences, 3; -- $s1_perid = POSIX::ceil( $aln->average_percentage_identity ); -- -- is( $s1_perid == 41 || $s1_perid == 42, -- 1, 'diff versions of MUSCLE have different vals' ); --} -\ No newline at end of file -+ #$aln = $factory->align($inputfilename); -+ #is $aln->num_sequences, 3; -+ #$s1_perid = POSIX::ceil( $aln->average_percentage_identity ); -+ -+ #is( $s1_perid == 41 || $s1_perid == 42, -+ # 1, 'diff versions of MUSCLE have different vals' ); -+} View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/compare/7432ae75eecb558a717e3eebbe8de1c0bbf28b7d...ee00d3360a3607a279338e9b0c92f352eb47cec9 -- View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/compare/7432ae75eecb558a717e3eebbe8de1c0bbf28b7d...ee00d3360a3607a279338e9b0c92f352eb47cec9 You're receiving this email because of your account on salsa.debian.org.
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