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general
  • source: python-biopython (main)
  • version: 1.87+dfsg-1
  • maintainer: Debian Med Packaging Team (archive) (DMD) (LowNMU)
  • uploaders: Andreas Tille [DMD] – Charles Plessy [DMD] – Étienne Mollier [DMD]
  • arch: all any
  • 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: 1.78+dfsg-4
  • oldstable: 1.80+dfsg-4
  • stable: 1.85+dfsg-4
  • testing: 1.86+dfsg-1
  • unstable: 1.87+dfsg-1
versioned links
  • 1.78+dfsg-4: [.dsc, use dget on this link to retrieve source package] [changelog] [copyright] [rules] [control]
  • 1.80+dfsg-4: [.dsc, use dget on this link to retrieve source package] [changelog] [copyright] [rules] [control]
  • 1.85+dfsg-4: [.dsc, use dget on this link to retrieve source package] [changelog] [copyright] [rules] [control]
  • 1.86+dfsg-1: [.dsc, use dget on this link to retrieve source package] [changelog] [copyright] [rules] [control]
  • 1.87+dfsg-1: [.dsc, use dget on this link to retrieve source package] [changelog] [copyright] [rules] [control]
binaries
  • python-biopython-doc
  • python3-biopython
  • python3-biopython-sql
action needed
Marked for autoremoval on 08 June due to starlette: #1131072, #1135451, #1134850 high
Version 1.86+dfsg-1 of python-biopython is marked for autoremoval from testing on Mon 08 Jun 2026. It is affected by #1131072, #1135451. The removal of python-biopython will also cause the removal of (transitive) reverse dependencies: ariba, augur, busco, changeo, cutesv, elpa-snakemake, gasic, graphlan, gubbins, idseq-bench, insilicoseq, kaptive, kleborate, mcaller, mdanalysis, metaphlan, mirtop, nanofilt, nanolyse, nanostat, ncbi-acc-download, optimir, pairtools, parsnp, peptidebuilder, presto, pychopper, pyensembl, pyfastx, python-bcbio-gff, python-bioframe, python-cai, python-cgecore, python-cooler, python-datacache, python-dynasor, python-gffutils, python-nanoget, python-pauvre, python-prodigy, python-pyani, python-pyfaidx, python-seqcluster, python-treetime, qcat, readucks, recan, resfinder, seqmagick, seqsero, snakemake, srst2, virulencefinder, xpore, yanagiba. It depends (transitively) on starlette, affected by #1134850. You should try to prevent the removal by fixing these RC bugs.
Created: 2026-04-21 Last update: 2026-05-21 01:19
1 security issue in forky high

There is 1 open security issue in forky.

1 important issue:
  • CVE-2025-68463: Bio.Entrez in Biopython through 186 allows doctype XXE.
Created: 2025-12-18 Last update: 2026-05-13 23:18
The package has not entered testing even though the delay is over normal
The package has not entered testing even though the 5-day delay is over. Check why.
Created: 2026-05-19 Last update: 2026-05-21 01:18
Depends on packages which need a new maintainer normal
The packages that python-biopython depends on which need a new maintainer are:
  • w3c-sgml-lib (#739087)
    • Depends: w3c-sgml-lib
Created: 2022-03-06 Last update: 2026-05-20 23:00
Does not build reproducibly during 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: 2025-11-01 Last update: 2026-05-20 19:32
debian/patches: 1 patch to forward upstream low

Among the 4 debian patches available in version 1.87+dfsg-1 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: 2024-09-14 Last update: 2026-05-14 09:03
1 low-priority security issue in trixie low

There is 1 open security issue in trixie.

1 issue left for the package maintainer to handle:
  • CVE-2025-68463: (needs triaging) Bio.Entrez in Biopython through 186 allows doctype XXE.

You can find information about how to handle this issue in the security team's documentation.

Created: 2025-12-18 Last update: 2026-05-13 23:18
1 low-priority security issue in bookworm low

There is 1 open security issue in bookworm.

1 issue left for the package maintainer to handle:
  • CVE-2025-68463: (needs triaging) Bio.Entrez in Biopython through 186 allows doctype XXE.

You can find information about how to handle this issue in the security team's documentation.

Created: 2025-12-18 Last update: 2026-05-13 23:18
testing migrations
  • excuses:
    • Migration status for python-biopython (1.86+dfsg-1 to 1.87+dfsg-1): Waiting for test results or another package, or too young (no action required now - check later)
    • Issues preventing migration:
    • ∙ ∙ Autopkgtest for mdanalysis: amd64: Test triggered (failure will be ignored), arm64: Test triggered (failure will be ignored), i386: Test triggered (failure will be ignored), ppc64el: Test triggered (failure will be ignored), riscv64: Test triggered (failure will be ignored), s390x: Test triggered (failure will be ignored)
    • ∙ ∙ Autopkgtest for metaphlan/4.0.4+ds-1: amd64: Pass, arm64: Pass, i386: Failed (not a regression) ♻ (reference ♻), ppc64el: Pass, riscv64: Test triggered, s390x: Failed (not a regression) ♻ (reference ♻)
    • ∙ ∙ Autopkgtest for ncbi-acc-download/0.2.8-3: amd64: Pass, arm64: Pass, i386: Pass, ppc64el: Pass, riscv64: Test triggered, s390x: Pass
    • ∙ ∙ Autopkgtest for python-biopython/1.87+dfsg-1: amd64: Pass, arm64: Pass, i386: Pass, ppc64el: Pass, riscv64: Pass, s390x: Pass
    • Additional info (not blocking):
    • ∙ ∙ Updating python-biopython will fix bugs in testing: #1131072, #1135451
    • ∙ ∙ Piuparts tested OK - https://piuparts.debian.org/sid/source/p/python-biopython.html
    • ∙ ∙ Reproduced on amd64 - info
    • ∙ ∙ Reproduced on arm64 - info
    • ∙ ∙ Reproduced on armhf - info
    • ∙ ∙ Reproduced on i386 - info
    • ∙ ∙ 7 days old (needed 5 days)
    • Not considered
news
[rss feed]
  • [2026-05-13] Accepted python-biopython 1.87+dfsg-1 (source) into unstable (Karsten Schöke)
  • [2025-11-01] python-biopython 1.86+dfsg-1 MIGRATED to testing (Debian testing watch)
  • [2025-10-29] Accepted python-biopython 1.86+dfsg-1 (source) into unstable (Étienne Mollier)
  • [2025-09-16] python-biopython 1.85+dfsg-5 MIGRATED to testing (Debian testing watch)
  • [2025-09-14] Accepted python-biopython 1.85+dfsg-5 (source) into unstable (Étienne Mollier)
  • [2025-04-15] python-biopython 1.85+dfsg-4 MIGRATED to testing (Debian testing watch)
  • [2025-04-11] Accepted python-biopython 1.85+dfsg-4 (source) into unstable (Santiago Vila)
  • [2025-04-11] Accepted python-biopython 1.85+dfsg-3 (source) into unstable (Santiago Vila)
  • [2025-02-13] python-biopython 1.85+dfsg-2 MIGRATED to testing (Debian testing watch)
  • [2025-02-06] Accepted python-biopython 1.85+dfsg-2 (source) into unstable (Michael R. Crusoe)
  • [2025-01-29] Accepted python-biopython 1.85+dfsg-1 (source) into unstable (Michael R. Crusoe)
  • [2024-11-02] python-biopython 1.84+dfsg-4 MIGRATED to testing (Debian testing watch)
  • [2024-10-31] Accepted python-biopython 1.84+dfsg-4 (source) into unstable (Étienne Mollier)
  • [2024-10-20] python-biopython 1.84+dfsg-3 MIGRATED to testing (Debian testing watch)
  • [2024-10-18] Accepted python-biopython 1.84+dfsg-3 (source) into unstable (Étienne Mollier)
  • [2024-09-25] Accepted python-biopython 1.84+dfsg-2 (source) into unstable (Étienne Mollier)
  • [2024-09-23] Accepted python-biopython 1.84+dfsg-1 (source) into unstable (Étienne Mollier)
  • [2024-09-20] python-biopython 1.83+dfsg1-5 MIGRATED to testing (Debian testing watch)
  • [2024-09-16] Accepted python-biopython 1.84+dfsg-1~0exp1 (source) into experimental (Étienne Mollier)
  • [2024-09-14] Accepted python-biopython 1.83+dfsg1-5 (source) into unstable (Michael R. Crusoe)
  • [2024-09-08] python-biopython 1.83+dfsg1-4 MIGRATED to testing (Debian testing watch)
  • [2024-09-06] Accepted python-biopython 1.83+dfsg1-4 (source) into unstable (Étienne Mollier)
  • [2024-05-25] python-biopython 1.83+dfsg1-3 MIGRATED to testing (Debian testing watch)
  • [2024-05-22] Accepted python-biopython 1.83+dfsg1-3 (source) into unstable (Étienne Mollier)
  • [2024-05-03] python-biopython 1.83+dfsg1-2 MIGRATED to testing (Debian testing watch)
  • [2024-04-17] Accepted python-biopython 1.83+dfsg1-2 (source) into unstable (Andrius Merkys)
  • [2024-03-21] Accepted python-biopython 1.83+dfsg1-1 (source) into unstable (Étienne Mollier)
  • [2024-03-10] Accepted python-biopython 1.83+dfsg-1 (source) into unstable (Étienne Mollier)
  • [2023-12-24] python-biopython 1.81+dfsg-3 MIGRATED to testing (Debian testing watch)
  • [2023-12-19] Accepted python-biopython 1.81+dfsg-3 (source) into unstable (Étienne Mollier)
  • 1
  • 2
bugs [bug history graph]
  • all: 0
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ubuntu Ubuntu logo [Information about Ubuntu for Debian Developers]
  • version: 1.86+dfsg-1ubuntu1
  • patches for 1.86+dfsg-1ubuntu1

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