bioperl - Debian Package Tracker

general

source: bioperl (main)
version: 1.7.8-3
maintainer: Debian Med Packaging Team (archive) (DMD) (LowNMU)
uploaders: Andreas Tille [DMD] – Charles Plessy [DMD] – Steffen Moeller [DMD] – Olivier Sallou [DMD]
arch: all
std-ver: 4.7.2
VCS: Git (Browse, QA)

versions [more versions can be listed by madison] [old versions available from snapshot.debian.org]

[pool directory]

o-o-stable: 1.7.7-2
oldstable: 1.7.8-1
stable: 1.7.8-1
testing: 1.7.8-3
unstable: 1.7.8-3

versioned links

1.7.7-2: [.dsc, use dget on this link to retrieve source package] [changelog] [copyright] [rules] [control]
1.7.8-1: [.dsc, use dget on this link to retrieve source package] [changelog] [copyright] [rules] [control]
1.7.8-3: [.dsc, use dget on this link to retrieve source package] [changelog] [copyright] [rules] [control]

binaries

bioperl
libbio-perl-perl

action needed

Debci reports failed tests high

unstable: fail (log)
The tests ran in 0:03:04
Last run: 2026-05-28T16:10:23.000Z
Previous status: unknown

testing: fail (log)
The tests ran in 0:01:49
Last run: 2026-05-26T22:29:36.000Z
Previous status: unknown

stable: pass (log)
The tests ran in 0:02:18
Last run: 2025-11-10T03:04:33.000Z
Previous status: unknown

Created: 2026-05-11 Last update: 2026-06-02 07:02

Marked for autoremoval on 30 June: #1136915 high

Version 1.7.8-3 of bioperl is marked for autoremoval from testing on Tue 30 Jun 2026. It is affected by #1136915. The removal of bioperl will also cause the removal of (transitive) reverse dependencies: bio-tradis, cct, grinder, iva, libbio-alignio-stockholm-perl, libbio-asn1-entrezgene-perl, libbio-biblio-perl, libbio-chado-schema-perl, libbio-cluster-perl, libbio-coordinate-perl, libbio-db-ace-perl, libbio-db-biofetch-perl, libbio-db-embl-perl, libbio-db-gff-perl, libbio-db-hts-perl, libbio-db-ncbihelper-perl, libbio-db-refseq-perl, libbio-db-seqfeature-perl, libbio-db-swissprot-perl, libbio-eutilities-perl, libbio-featureio-perl, libbio-graphics-perl, libbio-procedural-perl, libbio-samtools-perl, libbio-searchio-hmmer-perl, libbio-tools-run-remoteblast-perl, libbio-variation-perl, libchado-perl, libgo-perl, libtfbs-perl, metastudent, plasmidid, prokka, roary, velvetoptimiser. You should try to prevent the removal by fixing these RC bugs.

Created: 2026-05-24 Last update: 2026-06-02 07:02

Fails to build during reproducibility testing normal

A package building reproducibly enables third parties to verify that the source matches the distributed binaries. It has been identified that this source package produced different results, failed to build or had other issues in a test environment. Please read about how to improve the situation!

Created: 2026-05-30 Last update: 2026-06-02 06:30

version in VCS is newer than in repository, is it time to upload? normal

vcswatch reports that this package seems to have a new changelog entry (version 1.7.8-4, distribution UNRELEASED) and new commits in its VCS. You should consider whether it's time to make an upload.

Here are the relevant commit messages:

commit 1df5eba98651bf376d37dc4d88432ce1a09db84c
Author: Andreas Tille <tille@debian.org>
Date:   Wed May 27 10:58:29 2026 +0200

    Giving up here and ask for help in Perl group

commit 6de932d8d4b9679436e00091c7d9211d66746f19
Author: Andreas Tille <tille@debian.org>
Date:   Wed May 27 10:08:50 2026 +0200

    Make slow progress in testing.

commit 0f140080167a4fe893fac3fec8024307c52fec7a
Author: Andreas Tille <tille@debian.org>
Date:   Tue May 26 22:09:50 2026 +0200

    First test fixed

commit 9af47621b2c2631e198389fd5da6f660b51c3ef6
Author: Andreas Tille <tille@debian.org>
Date:   Tue May 26 16:26:35 2026 +0200

    cme fix dpkg-control

commit f9ffa9f17736a7dfd050e76eab9da364f0a75ff7
Author: Andreas Tille <tille@debian.org>
Date:   Tue May 26 16:24:26 2026 +0200

    d/watch: version=5

commit a2376eb9414f1dfab390a2f6dbd324fb456b7989
Author: Michael R. Crusoe <crusoe@debian.org>
Date:   Fri Mar 20 14:53:57 2026 +0100

    d/control: include libbio-alignio-stockholm-perl which was split off

commit 3c9c79e069e121f45b3fe910a3508623d9e6c9cf
Author: Michael R. Crusoe <2153-crusoe@users.noreply.salsa.debian.org>
Date:   Fri Mar 20 13:54:52 2026 +0000

    Update debian/gbp.conf

commit ec3e746eac9488f835395e781b2b8872f191fda8
Author: Charles Plessy <plessy@debian.org>
Date:   Sun Jan 25 16:24:04 2026 +0900

    Remove dependencies on GD as bp_chaos_plot was removed earlier.
    
    Closes: #1126366

Created: 2026-01-16 Last update: 2026-05-27 10:32

Standards version of the package is outdated. wishlist

The package should be updated to follow the last version of Debian Policy (Standards-Version 4.7.4 instead of 4.7.2).

Created: 2025-12-23 Last update: 2026-03-31 15:01

news

[rss feed]

[2026-01-27] bioperl 1.7.8-3 MIGRATED to testing (Debian testing watch)
[2026-01-25] Accepted bioperl 1.7.8-3 (source) into unstable (Charles Plessy)
[2025-09-06] bioperl 1.7.8-2 MIGRATED to testing (Debian testing watch)
[2025-09-03] Accepted bioperl 1.7.8-2 (source) into unstable (gregor herrmann)
[2021-08-18] bioperl 1.7.8-1 MIGRATED to testing (Debian testing watch)
[2021-08-15] Accepted bioperl 1.7.8-1 (source) into unstable (Nilesh Patra)
[2020-10-31] bioperl 1.7.7-2 MIGRATED to testing (Debian testing watch)
[2020-10-31] bioperl 1.7.7-2 MIGRATED to testing (Debian testing watch)
[2020-10-28] Accepted bioperl 1.7.7-2 (source) into unstable (Steffen Moeller)
[2019-12-17] bioperl 1.7.7-1 MIGRATED to testing (Debian testing watch)
[2019-12-14] Accepted bioperl 1.7.7-1 (source) into unstable (Michael R. Crusoe) (signed by: Michael Robin Crusoe)
[2019-11-30] bioperl 1.7.6-3 MIGRATED to testing (Debian testing watch)
[2019-11-28] Accepted bioperl 1.7.6-3 (source) into unstable (Michael R. Crusoe) (signed by: Michael Robin Crusoe)
[2019-11-27] Accepted bioperl 1.7.6-2 (source) into unstable (Michael R. Crusoe) (signed by: Michael Robin Crusoe)
[2019-11-26] Accepted bioperl 1.7.6-1 (source) into unstable (Michael R. Crusoe) (signed by: Michael Robin Crusoe)
[2019-07-27] Accepted bioperl 1.7.5-1 (source all) into unstable (Steffen Moeller)
[2019-02-05] Accepted bioperl 1.7.4-1 (source) into unstable (Andreas Tille)
[2018-10-30] bioperl 1.7.2-3 MIGRATED to testing (Debian testing watch)
[2018-10-27] Accepted bioperl 1.7.2-3 (source) into unstable (Andreas Tille)
[2017-12-19] bioperl 1.7.2-2 MIGRATED to testing (Debian testing watch)
[2017-12-13] Accepted bioperl 1.7.2-2 (source) into unstable (gregor herrmann) (signed by: Andreas Tille)
[2017-12-09] bioperl 1.7.2-1 MIGRATED to testing (Debian testing watch)
[2017-12-03] Accepted bioperl 1.7.2-1 (source) into unstable (Andreas Tille)
[2017-09-08] bioperl 1.7.1-3 MIGRATED to testing (Debian testing watch)
[2017-09-02] Accepted bioperl 1.7.1-3 (source) into unstable (Carnë Draug) (signed by: Andreas Tille)
[2017-01-26] bioperl 1.7.1-2 MIGRATED to testing (Debian testing watch)
[2017-01-15] Accepted bioperl 1.7.1-2 (source all) into unstable (Andreas Tille)
[2016-12-16] bioperl 1.7.1-1 MIGRATED to testing (Debian testing watch)
[2016-12-05] Accepted bioperl 1.7.1-1 (source all) into unstable (Andreas Tille)
[2016-07-05] bioperl 1.6.924-5 MIGRATED to testing (Debian testing watch)

bugs [bug history graph]

all: 1
RC: 1
I&N: 0
M&W: 0
F&P: 0
patch: 0

links

homepage
lintian
buildd: logs, reproducibility
popcon
browse source code
other distros
debian patches
debci

ubuntu

[Information about Ubuntu for Debian Developers]

version: 1.7.8-3