[med-svn] [Git][med-team/bioperl][master] 4 commits: fix-missing-Test-modules.patch: new: fix multiple test failures.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sun Jun 21 21:50:22 BST 2026
Étienne Mollier pushed to branch master at Debian Med / bioperl
Commits:
9c3992d5 by Étienne Mollier at 2026-06-21T22:45:14+02:00
fix-missing-Test-modules.patch: new: fix multiple test failures.
Closes: #1136915
- - - - -
da1435e0 by Étienne Mollier at 2026-06-21T22:45:48+02:00
fix-missing-test-differences-import.patch: remove.
The patch is now unneeded, thanks to reexports carried by
fix-missing-Test-modules.patch.
- - - - -
f7f4be4d by Étienne Mollier at 2026-06-21T22:46:43+02:00
d/control: add myself to uploaders.
- - - - -
8ca6a482 by Étienne Mollier at 2026-06-21T22:49:48+02:00
d/changelog: ready for upload to unstable.
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/fix-missing-Test-modules.patch
- − debian/patches/fix-missing-test-differences-import.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-bioperl (1.7.8-4) UNRELEASED; urgency=medium
+bioperl (1.7.8-4) unstable; urgency=medium
[ Michael R. Crusoe ]
* d/control: include libbio-alignio-stockholm-perl which was split
@@ -8,7 +8,12 @@ bioperl (1.7.8-4) UNRELEASED; urgency=medium
* d/watch: version=5
* cme fix dpkg-control
- -- Michael R. Crusoe <crusoe at debian.org> Fri, 20 Mar 2026 14:53:49 +0100
+ [ Étienne Mollier ]
+ * fix-missing-Test-modules.patch: new: fix multiple test failures.
+ (Closes: #1136915)
+ * d/control: add myself to uploaders.
+
+ -- Étienne Mollier <emollier at debian.org> Sun, 21 Jun 2026 22:49:02 +0200
bioperl (1.7.8-3) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -6,6 +6,7 @@ Uploaders:
Steffen Moeller <moeller at debian.org>,
Andreas Tille <tille at debian.org>,
Olivier Sallou <osallou at debian.org>,
+ Étienne Mollier <emollier at debian.org>,
Section: science
Testsuite: autopkgtest-pkg-perl
Build-Depends:
=====================================
debian/patches/fix-missing-Test-modules.patch
=====================================
@@ -0,0 +1,26 @@
+Description: l/B/R/Test.pm: manually export Test::Most submodules.
+ Since recent versions of Test::Most around April or May 2026, the
+ Bio::Root::Test module is not reexporting properly submodules of
+ Test::Most anymore. This patch fixes, or works around, the issue by
+ exporting the missing modules manually.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/1136915
+Forwarded: no
+Last-Update: 2026-06-21
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- bioperl.orig/lib/Bio/Root/Test.pm
++++ bioperl/lib/Bio/Root/Test.pm
+@@ -150,6 +150,12 @@
+
+ our @EXPORT = (
+ @Test::Most::EXPORT,
++ @Test::More::EXPORT,
++ @Test::Exception::EXPORT,
++ @Test::Warn::EXPORT,
++ @Test::Deep::EXPORT,
++ @Test::Diff::EXPORT,
++ @Test::Differences::EXPORT,
+
+ #@Bio::Root::Test::Warn::EXPORT,
+ # Test::Warn method wrappers
=====================================
debian/patches/fix-missing-test-differences-import.patch deleted
=====================================
@@ -1,49 +0,0 @@
-Description: Fix missing Test::Differences import in SimpleAlign test
- - unified_diff and eq_or_diff from Test::Differences
- - lives_ok from Test::Exception
- - Replace two instances of throws_ok which are failing
-Author: Andreas Tille <tille at debian.org>
-Bug-Debian: https://bugs.debian.org/#1136915
-Last-Update: 2026-05-26
-
---- a/t/Align/SimpleAlign.t
-+++ b/t/Align/SimpleAlign.t
-@@ -2,11 +2,13 @@
- # $Id$
-
- use strict;
-+use Test::Differences qw(eq_or_diff unified_diff);
-
- BEGIN {
- use Bio::Root::Test;
-
- test_begin( -tests => 206 );
-+ use Test::Exception qw(lives_ok);
-
- use_ok('Bio::SimpleAlign');
- use_ok('Bio::AlignIO');
-@@ -358,7 +360,8 @@ SKIP: {
- is( $a->get_seq_by_pos(1)->seq, 'AAA', "bug 2793" );
- ok( $a->add_seq( $s21, 2 ), "bug 2793" );
- is( $a->get_seq_by_pos(2)->seq, 'CCC', "bug 2793" );
-- throws_ok { $a->add_seq( $s21, 0 ) } qr/must be >= 1/, 'Bad sequence, bad!';
-+ eval { $a->add_seq( $s21, 0 ) };
-+ like( $@, qr/must be >= 1/, 'Bad sequence, bad!' );
- }
-
- # test for Bio::SimpleAlign annotation method and
---- a/t/Align/AlignStats.t
-+++ b/t/Align/AlignStats.t
-@@ -139,9 +139,9 @@ $in = Bio::AlignIO->new(-file => test_in
- $stats = Bio::Align::DNAStatistics->new(-verbose => 2);
- $aln = $in->next_aln();
- my $matrix;
--throws_ok {
--$matrix = $stats->distance(-align=>$aln,-method=>'Uncorrected');
--} qr/No distance calculated between seq3 and seq4/, "Warn if seqs don't overlap";
-+eval { $matrix = $stats->distance(-align=>$aln,-method=>'Uncorrected') };
-+like( $@, qr/No distance calculated between seq3 and seq4/,
-+ "Warn if seqs don't overlap" );
- $stats->verbose(-1);
- $matrix = $stats->distance(-align=>$aln,-method=>'Uncorrected');
- like($matrix->print_matrix, qr/-1/);
=====================================
debian/patches/series
=====================================
@@ -1,4 +1,4 @@
0001-fix-error-popping-up-with-latest-perl-releases-a80e8a655a953301f71538f9088a613eb63d5a73.patch
0001-fix-error-popping-up-with-latest-perl-releases-01ba1a675c80e7f8b77e05be9055d1208f246083.patch
perl-5.42-precedence.patch
-fix-missing-test-differences-import.patch
+fix-missing-Test-modules.patch
View it on GitLab: https://salsa.debian.org/med-team/bioperl/-/compare/1df5eba98651bf376d37dc4d88432ce1a09db84c...8ca6a4824ddce62402c34b90999b070826e962de
--
View it on GitLab: https://salsa.debian.org/med-team/bioperl/-/compare/1df5eba98651bf376d37dc4d88432ce1a09db84c...8ca6a4824ddce62402c34b90999b070826e962de
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