Your message dated Wed, 03 Sep 2025 16:33:55 +0000
with message-id <[email protected]>
and subject line Bug#1113735: fixed in bioperl 1.7.8-2
has caused the Debian Bug report #1113735,
regarding libbio-perl-perl: warns with Perl 5.42: Possible precedence problem
between ! and numeric eq (==)
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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--
1113735: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1113735
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: libbio-perl-perl
Version: 1.7.8-1
Severity: important
Tags: forky sid
User: [email protected]
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/>.
--
Niko Tyni [email protected]
--- End Message ---
--- Begin Message ---
Source: bioperl
Source-Version: 1.7.8-2
Done: gregor herrmann <[email protected]>
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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
gregor herrmann <[email protected]> (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 [email protected])
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Hash: SHA512
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
<[email protected]>
Changed-By: gregor herrmann <[email protected]>
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.
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