[med-svn] [Git][med-team/bioperl][master] 8 commits: Fix warnings with Perl 5.42.
gregor herrmann (@gregoa)
gitlab at salsa.debian.org
Wed Sep 3 16:57:44 BST 2025
gregor herrmann pushed to branch master at Debian Med / bioperl
Commits:
293ce478 by gregor herrmann at 2025-09-03T17:36:46+02:00
Fix warnings with Perl 5.42.
Add two patches from upstream Git, and a new one for precedence issues.
Closes: #1113735
- - - - -
2f147a29 by gregor herrmann at 2025-09-03T17:46:07+02:00
Replace override_dh_clean in d/rules with d/clean.
- - - - -
8c532936 by gregor herrmann at 2025-09-03T17:51:59+02:00
debian/rules: remove unneeded override_dh_installchangelogs.
- - - - -
4b1b802e by gregor herrmann at 2025-09-03T17:53:44+02:00
debian/watch: use uscan macros.
- - - - -
296ce39a by gregor herrmann at 2025-09-03T17:54:26+02:00
Declare compliance with Debian Policy 4.7.2.
- - - - -
3f43e143 by gregor herrmann at 2025-09-03T17:54:58+02:00
Remove «Rules-Requires-Root: no», which is the current default.
- - - - -
289741f7 by gregor herrmann at 2025-09-03T17:55:23+02:00
Remove «Priority: optional», which is the current default.
- - - - -
e994baf9 by gregor herrmann at 2025-09-03T17:57:06+02:00
update changelog
Gbp-Dch: Ignore
- - - - -
9 changed files:
- debian/changelog
- + debian/clean
- debian/control
- + debian/patches/0001-fix-error-popping-up-with-latest-perl-releases-01ba1a675c80e7f8b77e05be9055d1208f246083.patch
- + debian/patches/0001-fix-error-popping-up-with-latest-perl-releases-a80e8a655a953301f71538f9088a613eb63d5a73.patch
- + debian/patches/perl-5.42-precedence.patch
- + debian/patches/series
- debian/rules
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,18 @@
+bioperl (1.7.8-2) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * Fix warnings with Perl 5.42.
+ Add two patches from upstream Git, and a new one for precedence issues.
+ (Closes: #1113735)
+ * Replace override_dh_clean in d/rules with d/clean.
+ * debian/rules: remove unneeded override_dh_installchangelogs.
+ * debian/watch: use uscan macros.
+ * Declare compliance with Debian Policy 4.7.2.
+ * Remove «Rules-Requires-Root: no», which is the current default.
+ * Remove «Priority: optional», which is the current default.
+
+ -- gregor herrmann <gregoa at debian.org> Wed, 03 Sep 2025 17:56:27 +0200
+
bioperl (1.7.8-1) unstable; urgency=medium
* Team Upload.
=====================================
debian/clean
=====================================
@@ -0,0 +1,5 @@
+bioperl.conf
+biodatabases.pod
+biodesign.pod
+bioperl.pod
+bioscripts.pod
=====================================
debian/control
=====================================
@@ -6,7 +6,6 @@ Uploaders: Charles Plessy <plessy at debian.org>,
Olivier Sallou <osallou at debian.org>
Section: science
Testsuite: autopkgtest-pkg-perl
-Priority: optional
Build-Depends: debhelper-compat (= 13),
# Unnecessary according to lintian, but building with sbuild shows the contrary.
libmodule-build-perl
@@ -62,11 +61,10 @@ Build-Depends-Indep: 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: 4.5.1
+Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/bioperl
Vcs-Git: https://salsa.debian.org/med-team/bioperl.git
Homepage: http://www.bioperl.org/
-Rules-Requires-Root: no
Package: bioperl
Architecture: all
=====================================
debian/patches/0001-fix-error-popping-up-with-latest-perl-releases-01ba1a675c80e7f8b77e05be9055d1208f246083.patch
=====================================
@@ -0,0 +1,32 @@
+From 01ba1a675c80e7f8b77e05be9055d1208f246083 Mon Sep 17 00:00:00 2001
+From: Chris Fields <cjfields at illinois.edu>
+Date: Mon, 31 Mar 2025 22:43:57 -0500
+Subject: [PATCH] fix error popping up with latest perl releases
+
+Origin: https://github.com/bioperl/bioperl-live/commit/01ba1a675c80e7f8b77e05be9055d1208f246083
+Bug: https://github.com/bioperl/bioperl-live/issues/394
+
+---
+ bin/bp_find-blast-matches | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/bin/bp_find-blast-matches b/bin/bp_find-blast-matches
+index 25855adea..eddecf6c5 100644
+--- a/bin/bp_find-blast-matches
++++ b/bin/bp_find-blast-matches
+@@ -117,9 +117,9 @@ File::Basename
+
+
+ # Modules
+-use Bio::SearchIO qw(new);
+-use Bio::Seq qw(new);
+-use Bio::SeqIO qw(new);
++use Bio::SearchIO;
++use Bio::Seq;
++use Bio::SeqIO;
+ use File::Basename qw(basename);
+ use Getopt::Long qw(GetOptions);
+ use Pod::Usage;
+--
+2.51.0
+
=====================================
debian/patches/0001-fix-error-popping-up-with-latest-perl-releases-a80e8a655a953301f71538f9088a613eb63d5a73.patch
=====================================
@@ -0,0 +1,28 @@
+From a80e8a655a953301f71538f9088a613eb63d5a73 Mon Sep 17 00:00:00 2001
+From: Chris Fields <cjfields at illinois.edu>
+Date: Mon, 31 Mar 2025 22:41:51 -0500
+Subject: [PATCH] fix error popping up with latest perl releases
+
+Origin: https://github.com/bioperl/bioperl-live/commit/a80e8a655a953301f71538f9088a613eb63d5a73
+Bug: https://github.com/bioperl/bioperl-live/issues/394
+
+---
+ lib/Bio/Tools/Alignment/Consed.pm | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/lib/Bio/Tools/Alignment/Consed.pm b/lib/Bio/Tools/Alignment/Consed.pm
+index 7aa46a871..b36906180 100644
+--- a/lib/Bio/Tools/Alignment/Consed.pm
++++ b/lib/Bio/Tools/Alignment/Consed.pm
+@@ -111,7 +111,7 @@ package Bio::Tools::Alignment::Consed;
+ use strict;
+
+ use FileHandle;
+-use Dumpvalue qw(dumpValue);
++use Dumpvalue;
+ use Bio::Tools::Alignment::Trim;
+ use File::Spec;
+
+--
+2.51.0
+
=====================================
debian/patches/perl-5.42-precedence.patch
=====================================
@@ -0,0 +1,32 @@
+Description: Fix warnings with Perl 5.42
+ Possible precedence problem between ! and numeric eq (==) at /build/bioperl-1.7.8/blib/lib/Bio/AlignIO/Handler/GenericAlignHandler.pm line 98.
+ Possible precedence problem between ! and numeric eq (==) at /build/bioperl-1.7.8/blib/lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 379.
+Origin: vendor
+Bug-Debian: https://bugs.debian.org/1113735
+Author: gregor herrmann <gregoa at debian.org>
+Last-Update: 2025-09-03
+Forwarded: https://github.com/bioperl/bioperl-live/pull/404
+Bug: https://github.com/bioperl/bioperl-live/pull/404
+
+--- a/lib/Bio/AlignIO/Handler/GenericAlignHandler.pm
++++ b/lib/Bio/AlignIO/Handler/GenericAlignHandler.pm
+@@ -95,7 +95,7 @@
+ my $data;
+ if (scalar(@ids)) {
+ for my $id (@ids) {
+- if (!index($id, '-')==0) {
++ if (index($id, '-')!=0) {
+ $id = '-'.$id ;
+ }
+ $data->{$id} = $self->{'_params'}->{$id} if (exists $self->{'_params'}->{$id});
+--- a/lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm
++++ b/lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm
+@@ -376,7 +376,7 @@
+ my ($self, @ids) = @_;
+ my %data;
+ for my $id (@ids) {
+- if (!index($id, '-')==0) {
++ if (index($id, '-')!=0) {
+ $id = '-'.$id ;
+ }
+ $data{$id} = $self->{'_params'}->{$id} if (exists $self->{'_params'}->{$id});
=====================================
debian/patches/series
=====================================
@@ -0,0 +1,3 @@
+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
=====================================
debian/rules
=====================================
@@ -10,13 +10,6 @@ endif
override_dh_auto_configure:
dh_auto_configure -- $(NETWORK)
-override_dh_clean:
- dh_clean build-stamp install-stamp bioperl.conf biodatabases.pod \
- biodesign.pod bioperl.pod bioscripts.pod
-
-override_dh_installchangelogs:
- dh_installchangelogs Changes
-
override_dh_installexamples:
dh_installexamples examples/*
for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
=====================================
debian/watch
=====================================
@@ -1,3 +1,3 @@
version=4
-https://metacpan.org/release/BioPerl/ .*/BioPerl-v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$
+https://metacpan.org/release/BioPerl .*/BioPerl-v?@ANY_VERSION@@ARCHIVE_EXT@$
View it on GitLab: https://salsa.debian.org/med-team/bioperl/-/compare/91524eebe4625a094f9cc0c54ba4c8fa587e993b...e994baf9d6b70c7ed7e0a0ba7bacac911c8dfb4e
--
View it on GitLab: https://salsa.debian.org/med-team/bioperl/-/compare/91524eebe4625a094f9cc0c54ba4c8fa587e993b...e994baf9d6b70c7ed7e0a0ba7bacac911c8dfb4e
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