Package: libbio-perl-perl
Version: 1.7.8-1
Severity: important
Tags: forky sid
User: debian-perl@lists.debian.org
Usertags: perl-5.42-transition

One of the modules in this package warns when used with Perl 5.42
(currently in experimental.)

  $ perl -we 'use Bio::AlignIO::Handler::GenericAlignHandler'
  Possible precedence problem between ! and numeric eq (==) at /usr/share/perl5/Bio/AlignIO/Handler/GenericAlignHandler.pm line 98.

This propagates to other modules using it, regressing the autopkgtest
checks of libbio-alignio-stockholm-perl:

https://ci.debian.net/packages/libb/libbio-alignio-stockholm-perl/unstable/amd64/64017011/

If you want to test changes against Perl 5.42 in experimental and run
into uninstallability problems, there is a test repository of rebuilt
Debian sid packages for amd64 available at <https://perl.debian.net/>.

Hello,

Bug #1113735 in bioperl reported by you has been fixed in the
Git repository and is awaiting an upload. You can see the commit
message below and you can check the diff of the fix at:

https://salsa.debian.org/med-team/bioperl/-/commit/293ce47835f0925d7be708fea3ae140847ae4d77
------------------------------------------------------------------------
Fix warnings with Perl 5.42.

Add two patches from upstream Git, and a new one for precedence issues.

Closes: #1113735
------------------------------------------------------------------------

(this message was generated automatically)
-- 
Greetings

https://bugs.debian.org/1113735

We believe that the bug you reported is fixed in the latest version of
bioperl, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1113735@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
gregor herrmann <gregoa@debian.org> (supplier of updated bioperl package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)
Format: 1.8
Date: Wed, 03 Sep 2025 18:13:25 +0200
Source: bioperl
Architecture: source
Version: 1.7.8-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: gregor herrmann <gregoa@debian.org>
Closes: 1113735
Changes:
 bioperl (1.7.8-2) unstable; 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.
Checksums-Sha1:
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 72367960082a289847de3e276a6a3d393d99fd6c 13112 bioperl_1.7.8-2.debian.tar.xz
Checksums-Sha256:
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Files:
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 e534f0eeb2228d25d20dcc1215324af8 13112 science optional bioperl_1.7.8-2.debian.tar.xz
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