[med-svn] [Git][med-team/bioperl][master] 3 commits: d/watch: version=5
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue May 26 21:10:11 BST 2026
Andreas Tille pushed to branch master at Debian Med / bioperl
Commits:
f9ffa9f1 by Andreas Tille at 2026-05-26T16:24:26+02:00
d/watch: version=5
- - - - -
9af47621 by Andreas Tille at 2026-05-26T16:26:35+02:00
cme fix dpkg-control
- - - - -
0f140080 by Andreas Tille at 2026-05-26T22:09:50+02:00
First test fixed
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/fix-missing-test-differences-import.patch
- debian/patches/series
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,8 +1,13 @@
bioperl (1.7.8-4) UNRELEASED; urgency=medium
+ [ Michael R. Crusoe ]
* d/control: include libbio-alignio-stockholm-perl which was split
off.
+ [ Andreas Tille ]
+ * d/watch: version=5
+ * cme fix dpkg-control
+
-- Michael R. Crusoe <crusoe at debian.org> Fri, 20 Mar 2026 14:53:49 +0100
bioperl (1.7.8-3) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -1,98 +1,104 @@
Source: bioperl
+Standards-Version: 4.7.4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Charles Plessy <plessy at debian.org>,
- Steffen Moeller <moeller at debian.org>,
- Andreas Tille <tille at debian.org>,
- Olivier Sallou <osallou at debian.org>
+Uploaders:
+ Charles Plessy <plessy at debian.org>,
+ Steffen Moeller <moeller at debian.org>,
+ Andreas Tille <tille at debian.org>,
+ Olivier Sallou <osallou at debian.org>,
Section: science
Testsuite: autopkgtest-pkg-perl
-Build-Depends: debhelper-compat (= 13),
+Build-Depends:
+ debhelper-compat (= 13),
# Unnecessary according to lintian, but building with sbuild shows the contrary.
- libmodule-build-perl
-Build-Depends-Indep: perl,
- rename,
- libio-string-perl,
- libdata-stag-perl,
- libtest-most-perl,
- libbio-alignio-stockholm-perl,
+ libmodule-build-perl,
+Build-Depends-Indep:
+ perl,
+ rename,
+ libio-string-perl,
+ libdata-stag-perl,
+ libtest-most-perl,
+ libbio-alignio-stockholm-perl,
# Recommended in Build.PL (we want them to run the tests)
- libace-perl,
- libalgorithm-munkres-perl,
- libarray-compare-perl,
- libbio-asn1-entrezgene-perl,
- libbio-samtools-perl,
- libclass-unload-perl,
- libcgi-pm-perl,
- libclone-perl,
- libconvert-binary-c-perl,
- libdbd-sqlite3-perl,
- libdbd-mysql-perl,
- libdbd-pg-perl,
- libgraph-perl,
- libgraphviz-perl,
- libhtml-parser-perl,
- libhtml-tableextract-perl,
- liblist-moreutils-perl,
- libpath-class-perl,
- libperlio-eol-perl,
- libpostscript-perl,
- libset-scalar-perl,
- libsoap-lite-perl,
- libsort-naturally-perl,
- libspreadsheet-parseexcel-perl,
- libspreadsheet-writeexcel-perl,
- libstorable-perl,
- libsvg-perl,
- libsvg-graph-perl,
- libtest-memory-cycle-perl,
- libtest-pod-perl,
- libtest-weaken-perl,
- liburi-perl,
- libxml-dom-xpath-perl,
- libxml-parser-perl,
- libxml-sax-perl,
- libxml-sax-writer-perl,
- libxml-twig-perl,
- libxml-simple-perl,
- libxml-writer-perl,
- libxml-libxml-perl,
- libwww-perl,
- libyaml-perl,
- libtest-requiresinternet-perl,
+ libace-perl,
+ libalgorithm-munkres-perl,
+ libarray-compare-perl,
+ libbio-asn1-entrezgene-perl,
+ libbio-samtools-perl,
+ libclass-unload-perl,
+ libcgi-pm-perl,
+ libclone-perl,
+ libconvert-binary-c-perl,
+ libdbd-sqlite3-perl,
+ libdbd-mysql-perl,
+ libdbd-pg-perl,
+ libgraph-perl,
+ libgraphviz-perl,
+ libhtml-parser-perl,
+ libhtml-tableextract-perl,
+ liblist-moreutils-perl,
+ libpath-class-perl,
+ libperlio-eol-perl,
+ libpostscript-perl,
+ libset-scalar-perl,
+ libsoap-lite-perl,
+ libsort-naturally-perl,
+ libspreadsheet-parseexcel-perl,
+ libspreadsheet-writeexcel-perl,
+ libstorable-perl,
+ libsvg-perl,
+ libsvg-graph-perl,
+ libtest-differences-perl,
+ libtest-memory-cycle-perl,
+ libtest-pod-perl,
+ libtest-weaken-perl,
+ liburi-perl,
+ libxml-dom-xpath-perl,
+ libxml-parser-perl,
+ libxml-sax-perl,
+ libxml-sax-writer-perl,
+ libxml-twig-perl,
+ libxml-simple-perl,
+ libxml-writer-perl,
+ libxml-libxml-perl,
+ libwww-perl,
+ libyaml-perl,
+ libtest-requiresinternet-perl,
# Needed to avoid downloading DTDs during the tests and therefore fail when network is not available:
- libxml-sax-expatxs-perl
-Standards-Version: 4.7.2
+ libxml-sax-expatxs-perl,
Vcs-Browser: https://salsa.debian.org/med-team/bioperl
Vcs-Git: https://salsa.debian.org/med-team/bioperl.git
Homepage: http://www.bioperl.org/
Package: bioperl
Architecture: all
-Depends: libbio-perl-perl (= ${source:Version}),
- ${misc:Depends},
- ${perl:Depends},
- libtest-most-perl
-Recommends: bioperl-run,
+Depends:
+ libbio-perl-perl (= ${source:Version}),
+ ${misc:Depends},
+ ${perl:Depends},
+ libtest-most-perl,
+Recommends:
+ bioperl-run,
# for the following see #650412
# most of `binary -help` outputs
- perl-doc,
+ perl-doc,
# some libraries already in libbio-perl-perl's Recommends:
# bp_biofetch_genbank_proxy
- libhttp-message-perl,
- libwww-perl,
- libcache-cache-perl,
+ libhttp-message-perl,
+ libwww-perl,
+ libcache-cache-perl,
# bp_blast2tree
- libbio-perl-run-perl,
+ libbio-perl-run-perl,
# bp_bulk_load_gff
- libdbi-perl,
+ libdbi-perl,
# bp_das_server
- libapache-dbi-perl,
+ libapache-dbi-perl,
# bp_download_query_genbank
- liburi-perl,
+ liburi-perl,
# bp_einfo
# liburi-perl
# libhttp-message-perl
- libxml-simple-perl,
+ libxml-simple-perl,
# bp_fast_load_gff
# libdbi-perl
# bp_fetch [not for local indexing]
@@ -102,7 +108,7 @@ Recommends: bioperl-run,
# libhttp-message-perl
# libdbi-perl
# bp_genbank2gff3
- libyaml-perl,
+ libyaml-perl,
# bp_hivq
# libhttp-message-perl
# libxml-simple-perl
@@ -112,16 +118,17 @@ Recommends: bioperl-run,
# bp_pairwise_kaks
# libbio-perl-run-perl
# bp_process_wormbase
- libace-perl,
+ libace-perl,
# bp_query_entrez_taxa
# bp_remote_blast
# bp_revtrans-motif
- liblist-moreutils-perl,
+ liblist-moreutils-perl,
# bp_taxid4species
- libxml-twig-perl,
+ libxml-twig-perl,
# bp_taxonomy2tree
- libset-scalar-perl,
-Suggests: groff-base
+ libset-scalar-perl,
+Suggests:
+ groff-base,
Description: Perl tools for computational molecular biology
The Bioperl project is a coordinated effort to collect computational methods
routinely used in bioinformatics into a set of standard CPAN-style,
@@ -138,52 +145,53 @@ Description: Perl tools for computational molecular biology
Package: libbio-perl-perl
Architecture: all
Section: perl
-Depends: libio-string-perl,
- libdata-stag-perl,
- ${misc:Depends},
- ${perl:Depends}
-# Temporary workaround as bioperl-run has not been split
-Breaks: libbio-perl-run-perl (<< 1.7.3), roary (<<3.13)
-Replaces: libbio-perl-run-perl (<< 1.7.3)
-Recommends: bioperl-run | libbio-perl-run-perl,
+Depends:
+ libio-string-perl,
+ libdata-stag-perl,
+ ${misc:Depends},
+ ${perl:Depends},
+Recommends:
+ bioperl-run | libbio-perl-run-perl,
# Recommended in Build.PL
- libace-perl,
- libalgorithm-munkres-perl,
- libarray-compare-perl,
- libbio-asn1-entrezgene-perl,
- libclone-perl,
- libconvert-binary-c-perl,
- libdbd-sqlite3-perl,
- libdbd-mysql-perl,
- libdbd-pg-perl,
- libgraph-perl,
- libgraphviz-perl,
- libhtml-parser-perl,
- libhtml-tableextract-perl,
- liblist-moreutils-perl,
- libpostscript-perl,
- libset-scalar-perl,
- libsoap-lite-perl,
- libsort-naturally-perl,
- libspreadsheet-parseexcel-perl,
- libspreadsheet-writeexcel-perl,
- libstorable-perl,
- libsvg-perl,
- libsvg-graph-perl,
- liburi-perl,
- libxml-dom-xpath-perl,
- libxml-parser-perl,
- libxml-sax-perl,
- libxml-sax-writer-perl,
- libxml-simple-perl,
- libxml-twig-perl,
- libxml-writer-perl,
- libxml-libxml-perl,
- libwww-perl
-Suggests: bioperl,
- libxml-sax-expatxs-perl,
+ libace-perl,
+ libalgorithm-munkres-perl,
+ libarray-compare-perl,
+ libbio-asn1-entrezgene-perl,
+ libclone-perl,
+ libconvert-binary-c-perl,
+ libdbd-sqlite3-perl,
+ libdbd-mysql-perl,
+ libdbd-pg-perl,
+ libgraph-perl,
+ libgraphviz-perl,
+ libhtml-parser-perl,
+ libhtml-tableextract-perl,
+ liblist-moreutils-perl,
+ libpostscript-perl,
+ libset-scalar-perl,
+ libsoap-lite-perl,
+ libsort-naturally-perl,
+ libspreadsheet-parseexcel-perl,
+ libspreadsheet-writeexcel-perl,
+ libstorable-perl,
+ libsvg-perl,
+ libsvg-graph-perl,
+ liburi-perl,
+ libxml-dom-xpath-perl,
+ libxml-parser-perl,
+ libxml-sax-perl,
+ libxml-sax-writer-perl,
+ libxml-simple-perl,
+ libxml-twig-perl,
+ libxml-writer-perl,
+ libxml-libxml-perl,
+ libwww-perl,
+Suggests:
+ bioperl,
+ libxml-sax-expatxs-perl,
# Needed to avoid downloading DTDs.
- libbio-alignio-stockholm-perl,
+ libbio-alignio-stockholm-perl,
+# Temporary workaround as bioperl-run has not been split
Description: BioPerl core perl modules
BioPerl is a toolkit of perl modules useful in building bioinformatics
solutions in Perl. It is built in an object-oriented manner so that many
=====================================
debian/patches/fix-missing-test-differences-import.patch
=====================================
@@ -0,0 +1,18 @@
+Description: Fix missing Test::Differences import in SimpleAlign test
+ unified_diff and eq_or_diff are called in t/Align/SimpleAlign.t but
+ Test::Differences is never explicitly imported. These were previously
+ available via transitive imports but this is no longer the case.
+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
+@@ -2,6 +2,7 @@
+ # $Id$
+
+ use strict;
++use Test::Differences qw(eq_or_diff unified_diff);
+
+ BEGIN {
+ use Bio::Root::Test;
=====================================
debian/patches/series
=====================================
@@ -1,3 +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
=====================================
debian/watch
=====================================
@@ -1,3 +1,4 @@
-version=4
+Version: 5
-https://metacpan.org/release/BioPerl .*/BioPerl-v?@ANY_VERSION@@ARCHIVE_EXT@$
+Source: https://metacpan.org/release/BioPerl
+Matching-Pattern: .*/BioPerl-v?@ANY_VERSION@@ARCHIVE_EXT@$
View it on GitLab: https://salsa.debian.org/med-team/bioperl/-/compare/a2376eb9414f1dfab390a2f6dbd324fb456b7989...0f140080167a4fe893fac3fec8024307c52fec7a
--
View it on GitLab: https://salsa.debian.org/med-team/bioperl/-/compare/a2376eb9414f1dfab390a2f6dbd324fb456b7989...0f140080167a4fe893fac3fec8024307c52fec7a
You're receiving this email because of your account on salsa.debian.org. Manage all notifications: https://salsa.debian.org/-/profile/notifications | Help: https://salsa.debian.org/help
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20260526/c24061f8/attachment-0001.htm>
More information about the debian-med-commit
mailing list