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bioperl

Perl tools for computational molecular biology

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general

source: bioperl (main)
version: 1.7.8-4
maintainer: Debian Med Packaging Team (archive) (DMD) (LowNMU)
uploaders: Andreas Tille [DMD] – Charles Plessy [DMD] – Steffen Moeller [DMD] – Olivier Sallou [DMD] – Étienne Mollier [DMD]
arch: all
std-ver: 4.7.4
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: 1.7.8-4

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]
1.7.8-4: [.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 0:02:51
Last run: 2026-06-12T18:34:54.000Z
Previous status: unknown

testing: fail (log)
The tests ran in 0:02:30
Last run: 2026-06-11T20:23:05.000Z
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: 2026-06-23 07:00

Marked for autoremoval on 21 July: #1136915 high

Version 1.7.8-3 of bioperl is marked for autoremoval from testing on Tue 21 Jul 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: 2026-06-23 06:50

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: 2026-06-23 03:00

debian/patches: 1 patch to forward upstream low

Among the 4 debian patches available in version 1.7.8-4 of the package, we noticed the following issues:

1 patch where the metadata indicates that the patch has not yet been forwarded upstream. You should either forward the patch upstream or update the metadata to document its real status.

Created: 2026-06-22 Last update: 2026-06-22 09:32

testing migrations

excuses:
- Migration status for bioperl (1.7.8-3 to 1.7.8-4): Waiting for test results or another package, or too young (no action required now - check later)
- Issues preventing migration:
- ∙ ∙ Autopkgtest for bioperl/1.7.8-4: amd64: Pass, arm64: Pass, i386: Failed (not a regression) ♻ (reference ♻), loong64: Pass, ppc64el: Pass, riscv64: Pass, s390x: Test triggered
- ∙ ∙ Autopkgtest for cct/1:1.0.3-1: amd64: Pass, arm64: Pass, i386: Pass, loong64: Pass, ppc64el: Pass, riscv64: Pass, s390x: Test triggered
- ∙ ∙ Autopkgtest for grinder/0.5.4-6: amd64: Pass, arm64: Pass, i386: Pass, loong64: Pass, ppc64el: Pass, riscv64: Pass, s390x: Test triggered
- ∙ ∙ Autopkgtest for libbio-alignio-stockholm-perl/1.7.3-2: amd64: Pass, arm64: Pass, i386: Pass, loong64: Pass, ppc64el: Pass, riscv64: Pass, s390x: Test triggered
- ∙ ∙ Autopkgtest for libbio-asn1-entrezgene-perl/1.730-3: amd64: Pass, arm64: Pass, i386: Pass, loong64: Pass, ppc64el: Pass, riscv64: Pass, s390x: Test triggered
- ∙ ∙ Autopkgtest for libbio-biblio-perl/1.70-2: amd64: Pass, arm64: Pass, i386: Pass, loong64: Pass, ppc64el: Pass, riscv64: Pass, s390x: Test triggered
- ∙ ∙ Autopkgtest for libbio-chado-schema-perl/0.20000-3: amd64: Pass, arm64: Pass, i386: Pass, loong64: Pass, ppc64el: Pass, riscv64: Pass, s390x: Test triggered
- ∙ ∙ Autopkgtest for libbio-cluster-perl/1.7.3-6: amd64: Pass, arm64: Pass, i386: Pass, loong64: Pass, ppc64el: Pass, riscv64: Pass, s390x: Test triggered
- ∙ ∙ Autopkgtest for libbio-coordinate-perl/1.7.1-4: amd64: Pass, arm64: Pass, i386: Pass, loong64: Pass, ppc64el: Pass, riscv64: Pass, s390x: Test triggered
- ∙ ∙ Autopkgtest for libbio-db-ace-perl/1.7.3-2: amd64: Pass, arm64: Pass, i386: Pass, loong64: Pass, ppc64el: Pass, riscv64: Pass, s390x: Test triggered
- ∙ ∙ Autopkgtest for libbio-db-biofetch-perl/1.7.3-4: amd64: No tests, superficial or marked flaky ♻, arm64: No tests, superficial or marked flaky ♻ (reference ♻), i386: No tests, superficial or marked flaky ♻ (reference ♻), loong64: No tests, superficial or marked flaky ♻ (reference ♻), ppc64el: No tests, superficial or marked flaky ♻ (reference ♻), riscv64: No tests, superficial or marked flaky ♻, s390x: Test triggered
- ∙ ∙ Autopkgtest for libbio-db-embl-perl/1.7.4-4: amd64: No tests, superficial or marked flaky ♻, arm64: No tests, superficial or marked flaky ♻ (reference ♻), i386: No tests, superficial or marked flaky ♻ (reference ♻), loong64: No tests, superficial or marked flaky ♻ (reference ♻), ppc64el: No tests, superficial or marked flaky ♻ (reference ♻), riscv64: No tests, superficial or marked flaky ♻, s390x: Test triggered
- ∙ ∙ Autopkgtest for libbio-db-gff-perl/1.7.4-1: amd64: Pass, arm64: Pass, i386: Pass, loong64: Pass, ppc64el: Pass, riscv64: Pass, s390x: Test triggered
- ∙ ∙ Autopkgtest for libbio-db-hts-perl/3.01-6: amd64: Pass, arm64: Pass, i386: Pass, loong64: Pass, ppc64el: Pass, riscv64: Pass, s390x: Test triggered
- ∙ ∙ Autopkgtest for libbio-db-ncbihelper-perl/1.7.8-1: amd64: No tests, superficial or marked flaky ♻, arm64: No tests, superficial or marked flaky ♻ (reference ♻), i386: No tests, superficial or marked flaky ♻ (reference ♻), loong64: No tests, superficial or marked flaky ♻ (reference ♻), ppc64el: No tests, superficial or marked flaky ♻ (reference ♻), riscv64: No tests, superficial or marked flaky ♻, s390x: Test triggered
- ∙ ∙ Autopkgtest for libbio-db-refseq-perl/1.7.4-2: amd64: Pass, arm64: Pass, i386: Pass, loong64: Pass, ppc64el: Pass, riscv64: Pass, s390x: Test triggered
- ∙ ∙ Autopkgtest for libbio-db-seqfeature-perl/1.7.5-1: amd64: Pass, arm64: Pass, i386: Pass, loong64: Pass, ppc64el: Pass, riscv64: Pass, s390x: Test triggered
- ∙ ∙ Autopkgtest for libbio-db-swissprot-perl/1.7.4-2: amd64: Pass, arm64: Pass, i386: Pass, loong64: Pass, ppc64el: Pass, riscv64: Pass, s390x: Test triggered
- ∙ ∙ Autopkgtest for libbio-eutilities-perl/1.77-3: amd64: Pass, arm64: Pass, i386: Pass, loong64: Pass, ppc64el: Pass, riscv64: Pass, s390x: Test triggered
- ∙ ∙ Autopkgtest for libbio-featureio-perl/1.6.905-2: amd64: Pass, arm64: Pass, i386: Pass, loong64: Pass, ppc64el: Pass, riscv64: Pass, s390x: Test triggered
- ∙ ∙ Autopkgtest for libbio-graphics-perl/2.40-7: amd64: Pass, arm64: Pass, i386: Pass, loong64: Pass, ppc64el: Pass, riscv64: Pass, s390x: Test triggered
- ∙ ∙ Autopkgtest for libbio-procedural-perl/1.7.4-5: amd64: Pass, arm64: Pass, i386: Pass, loong64: Pass, ppc64el: Pass, riscv64: Pass, s390x: Test triggered
- ∙ ∙ Autopkgtest for libbio-samtools-perl/1.43-5: amd64: Pass, arm64: Pass, i386: Pass, loong64: Pass, ppc64el: Pass, riscv64: Pass, s390x: Test triggered
- ∙ ∙ Autopkgtest for libbio-searchio-hmmer-perl/1.7.3-2: amd64: Pass, arm64: Pass, i386: Pass, loong64: Pass, ppc64el: Pass, riscv64: Pass, s390x: Test triggered
- ∙ ∙ Autopkgtest for libbio-tools-run-remoteblast-perl/1.7.3-3: amd64: Pass, arm64: Pass, i386: Pass, loong64: Pass, ppc64el: Pass, riscv64: Pass, s390x: Test triggered
- ∙ ∙ Autopkgtest for libbio-variation-perl/1.7.5-3: amd64: Pass, arm64: Pass, i386: Pass, loong64: Pass, ppc64el: Pass, riscv64: Pass, s390x: Test triggered
- ∙ ∙ Autopkgtest for libgo-perl/0.15-10: amd64: Pass, arm64: Pass, i386: Pass, loong64: Pass, ppc64el: Pass, riscv64: Pass, s390x: Test triggered
- ∙ ∙ Autopkgtest for libtfbs-perl/0.7.1+ds-5: amd64: Pass, arm64: Pass, i386: Pass, loong64: Pass, ppc64el: Pass, riscv64: Pass, s390x: Test triggered
- ∙ ∙ Autopkgtest for prokka/1.14.6+dfsg-6: amd64: Pass, arm64: Pass, i386: Failed (not a regression) ♻ (reference ♻), loong64: No tests, superficial or marked flaky ♻ (reference ♻), ppc64el: No tests, superficial or marked flaky ♻ (reference ♻), riscv64: No tests, superficial or marked flaky ♻, s390x: Test triggered
- ∙ ∙ Autopkgtest for roary/3.13.0+dfsg-2: amd64: Pass, arm64: Pass, i386: Failed (not a regression) ♻ (reference ♻), loong64: Pass, ppc64el: Pass, riscv64: Pass, s390x: Test triggered
- ∙ ∙ Autopkgtest for velvetoptimiser/2.2.6-5: amd64: Pass, arm64: Pass, i386: Pass, loong64: Pass, ppc64el: Pass, riscv64: Pass, s390x: Test triggered
- ∙ ∙ Too young, only 1 of 5 days old
- Additional info (not blocking):
- ∙ ∙ Updating bioperl will fix bugs in testing: #1136915
- ∙ ∙ Piuparts tested OK - https://piuparts.debian.org/sid/source/b/bioperl.html
- ∙ ∙ Reproduced on amd64 - info
- ∙ ∙ Reproduced on arm64 - info
- ∙ ∙ Reproduced on armhf - info
- ∙ ∙ Reproduced on i386 - info
- Not considered

news

[2026-06-21] Accepted bioperl 1.7.8-4 (source) into unstable (Étienne Mollier)
[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)

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bugs [bug history graph]

all: 0

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