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bwa-mem2

Sequence alignment using Burrows-Wheeler Transform

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general
  • source: bwa-mem2 (main)
  • version: 2.2.1-1
  • maintainer: Debian Med Packaging Team (archive) (DMD) (LowNMU)
  • uploaders: Dylan Aïssi [DMD] – Michael R. Crusoe [DMD]
  • arch: any
  • std-ver: 4.6.0
  • VCS: Git (Browse, QA)
versions [more versions can be listed by madison] [old versions available from snapshot.debian.org]
[pool directory]
  • unstable: 2.2.1-1
versioned links
  • 2.2.1-1: [.dsc, use dget on this link to retrieve source package] [changelog] [copyright] [rules] [control]
binaries
  • bwa-mem2
action needed
Problems while searching for a new upstream version high
uscan had problems while searching for a new upstream version:
In debian/watch no matching files for watch line
  https://github.com/bwa-mem2/bwa-mem2/releases .*/download/v(?:[-_]?[Vv]?(\d[\-+\.:\~\da-zA-Z]*))/Source_code_including_submodules(?i)(?:\.(?:tar\.xz|tar\.bz2|tar\.gz|tar\.zstd?|zip|tgz|tbz|txz))
Created: 2025-04-18 Last update: 2025-05-20 08:31
The package has not entered testing even though the delay is over normal
The package has not entered testing even though the 20-day delay is over. Check why.
Created: 2025-04-27 Last update: 2025-05-20 09:32
50 new commits since last upload, is it time to release? normal
vcswatch reports that this package seems to have new commits in its VCS but has not yet updated debian/changelog. You should consider updating the Debian changelog and uploading this new version into the archive.

Here are the relevant commit logs:
commit 7151fe2fea4918da6ae48327ba3895f65b684857
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Wed Apr 16 14:42:34 2025 +0200

    d/copyright: add Cisco; clarify patch licensing

commit e7d5d1f6e809cce8221c68a5f9f43624f8a17ca4
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Feb 27 12:18:45 2025 +0100

    clean up changelog and upload to the NEW queue

commit 173864cead8ce7efeb2ac9220f9f9f1a6e9bab87
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Feb 27 12:30:46 2025 +0100

    improve the hardening patch

commit cabf1480df85263495f8a3e7d5279ccb453ad89c
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Feb 27 11:15:07 2025 +0100

    Update SIMDe patch

commit 0e4faf01399559270233f9a9ad7036ae8b0c4b35
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Feb 27 11:01:09 2025 +0100

    Add patch to support newer GCC

commit 238a2ec0118e6a69bdcc4030109dc7ef66732988
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Feb 27 10:22:27 2025 +0100

    cherry-pick all patches since 2.2.1 from upstream

commit 53f902e6fa27171793e7f98fc1a553c5cc0fa27d
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Nov 18 18:55:34 2021 +0100

    routine-update: Ready to upload to unstable

commit 0dd1f6f2e976c4bc4c05128870d6fdfb04c94e47
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Nov 18 18:55:29 2021 +0100

    routine-update: Standards-Version: 4.6.0

commit f66536d2c5689eb7ef5d3ad30c3126a8f8cd45a4
Merge: dde9762 d40c35b
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Nov 18 18:55:28 2021 +0100

    Update upstream source from tag 'upstream/2.2.1'
    
    Update to upstream version '2.2.1'
    with Debian dir ea51a5e5c08b1396f08d49919b9fb87cf60c5379

commit dde9762da7e3e93168b44e20f90f591f0a1323aa
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Nov 18 18:55:27 2021 +0100

    routine-update: New upstream version

commit a7f38675c6c0d9ec41cd660b2eb38165cc9af080
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Mon Mar 8 15:57:47 2021 +0100

    clean up changelog

commit dacaf997ca18d4050411a8b8259631d941aabb49
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Mon Mar 8 15:56:07 2021 +0100

    freshen patches

commit 97e792924249221e3ca80ec1ddeee76eaa15dfb7
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Mon Mar 8 15:51:38 2021 +0100

    routine-update: Standards-Version: 4.5.1

commit af1a6ff7325bcff8ddff03be128695ec171db262
Merge: 8cc2416 944b4a3
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Mon Mar 8 15:51:38 2021 +0100

    Update upstream source from tag 'upstream/2.2'
    
    Update to upstream version '2.2'
    with Debian dir 641b535d170a3c4220914da80bf42481634eb5ca

commit 8cc24166ae2d2f120cfd5ca78bea7f29adf0bd67
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Mon Mar 8 15:51:37 2021 +0100

    routine-update: New upstream version

commit 1fafa249549e580b0b786a4b25f19c703e90791c
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Mon Mar 8 15:42:51 2021 +0100

    debian/watch: fix target URL pattern

commit 73e6f44a7ea277d2fb1c8afbe482f121f19e875e
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Mon Mar 8 15:41:12 2021 +0100

    tidy changelog

commit 7f44836367952bad93cebe969a6f27f9b706c426
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Jul 23 09:49:07 2020 +0200

    forward patches upstream

commit 2beaa4ed674c5da7f27491f06782596dd3845391
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Jul 23 09:44:59 2020 +0200

    Add autopkgtests.

commit 18d063f78d51b58c00b69aa2cc5ca8d94abc3abc
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Jul 9 18:00:50 2020 +0200

    add docs & manpages

commit ca3d33966ae1448d0553d739605c323101022c82
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Jul 9 17:35:17 2020 +0200

    build a sse2 version

commit cd73bceb9024bc8d90ef69e2a214529d505bce0e
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Jul 9 17:20:44 2020 +0200

    simde patch tweak

commit 38b60641f668efa5f50dd544792853310d86ce2f
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Jul 9 17:19:53 2020 +0200

    license fixup

commit 466c9ca17158e513a8419062706b83ef9bf768fe
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Jul 9 16:18:14 2020 +0200

    simde fixup

commit fe69a7ee423676e3eb7873669598bc4d5f986b25
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Jul 9 16:11:08 2020 +0200

    GPL code is gone

commit cde6c0c6e2bc12751da4bc8229b0e068bf8e74ce
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Jul 9 16:05:44 2020 +0200

    enable building on non-x86

commit 136e1c2535604898ddb16de565c561b343f862eb
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Jul 9 15:26:21 2020 +0200

    fix a typo

commit 6c023326f30a7fa1a139718a9432fb8eac0e267c
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Jul 9 15:06:07 2020 +0200

    improve package hardening

commit 6fc71bf93b0e8ed2660262b1a66c5e0e0da09523
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Jul 9 15:46:37 2020 +0200

    update watch file to get complete source tarball

commit 7d7ceefbc2e38ab01a92c408892471a342619200
Merge: 1efdfd9 943ea89
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Jul 9 14:48:24 2020 +0200

    Update upstream source from tag 'upstream/2.0'
    
    Update to upstream version '2.0'
    with Debian dir 54c277f71ab2d3fede4d157464c241fbb56723f5

commit 1efdfd99be6fcc0e1daded50b2e767d19da0625a
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Jul 9 14:36:28 2020 +0200

    add myself as an uploader

commit 449cfa68ad75c473966317c496f6af8787e2c9fb
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Jul 9 14:35:33 2020 +0200

    force enable clean

commit 4a24a794d3c25ca8561fdbb68cb4a911a6882ac4
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Jul 9 14:34:37 2020 +0200

    changelog cleanup

commit a9cb6a6bb94146b861106becd67a82d29fe81799
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Jul 9 14:31:24 2020 +0200

    Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
    
    Changes-By: lintian-brush
    Fixes: lintian: upstream-metadata-missing-bug-tracking
    See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
    Fixes: lintian: upstream-metadata-missing-repository
    See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html

commit b564f02f68cdd82d926bc4a1bdf5aee7c7783f99
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Jul 9 14:31:19 2020 +0200

    routine-update: Rules-Requires-Root: no

commit 70bd59d47d05788689125df5d54ac5091d2e9193
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Jul 9 14:31:17 2020 +0200

    routine-update: Add salsa-ci file

commit 281c94c5aa752a014b6151744538d2623d07affe
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Jul 9 14:31:10 2020 +0200

    routine-update: debhelper-compat 13

commit 2bb69a6678f0a78953c86d3123293fb6678c0dba
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Jul 9 14:31:08 2020 +0200

    routine-update: Standards-Version: 4.5.0

commit 5c21c9c23b0a07057733b4fc3d7974aa1ab8d222
Merge: 142ea31 7d804db
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Jul 9 14:31:07 2020 +0200

    Update upstream source from tag 'upstream/2.0'
    
    Update to upstream version '2.0'
    with Debian dir b36079e07bdf3cee927b23be8aedb278267eafb8

commit 142ea312f583856f5f71dc1208b0f9774fbdc355
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Thu Jul 9 14:31:01 2020 +0200

    routine-update: New upstream version

commit 09c222411d613152d38fa0a9936c9065e9f7a40b
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Tue Feb 4 09:37:57 2020 +0100

    Remove obsolete fields Name, Contact from debian/upstream/metadata.

commit c9faa474173e67c774c027b4ca9b6e4a5a5bc3ad
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Tue Feb 4 09:37:56 2020 +0100

    R-U: Trailing whitespace in debian/rules

commit e3639bb677a19fcdf42db251765a55593c4ab028
Merge: 5eca9f2 5b47604
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Tue Feb 4 09:37:53 2020 +0100

    Update upstream source from tag 'upstream/2.0_pre2'
    
    Update to upstream version '2.0~pre2'
    with Debian dir 88a6d0300c70e95c18bbe4eb7b35f57d60b3af4a

commit 5eca9f2aba465c7a20ca38b63987d09bdb005106
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Tue Feb 4 09:37:52 2020 +0100

    routine-update: New upstream version

commit 1a7719176cd841c928a5d6e8b0a25d2edc1ec7a9
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Tue Feb 4 09:37:41 2020 +0100

    find the prereleases

commit 202049a0466a4371ff57f3c4a36ab9fc7053d658
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Tue Feb 4 09:37:10 2020 +0100

    build multi-dispatch version

commit 2b45c70cc01a6b905db1fa9713863bf67fb41e3b
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Tue Feb 4 08:31:23 2020 +0000

    uh-oh, no one filed an ITP! :-)

commit c4496f5e706329ed06e85230f551b30e110709b8
Author: Steffen Moeller <moeller@debian.org>
Date:   Thu Oct 3 23:12:23 2019 +0200

    d/u/metadata: yamllint

commit a3c529a6e731ed165f52bc04cc2d30f9af3412ac
Author: Dylan Aïssi <daissi@debian.org>
Date:   Tue Jul 30 17:08:25 2019 +0200

    Add debian/install

commit 3b3ad2331ef002bce2238061fe9ebe3a9c491467
Author: Dylan Aïssi <daissi@debian.org>
Date:   Tue Jul 30 17:05:24 2019 +0200

    Initial debian/
Created: 2025-04-17 Last update: 2025-05-18 19:04
lintian reports 16 warnings normal
Lintian reports 16 warnings about this package. You should make the package lintian clean getting rid of them.
Created: 2025-04-17 Last update: 2025-04-17 21:00
debian/patches: 1 patch to forward upstream low

Among the 10 debian patches available in version 2.2.1-1 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: 2025-04-17 Last update: 2025-04-17 22:03
Standards version of the package is outdated. wishlist
The package should be updated to follow the last version of Debian Policy (Standards-Version 4.7.2 instead of 4.6.0).
Created: 2025-04-17 Last update: 2025-04-17 19:03
testing migrations
  • excuses:
    • Migration status for bwa-mem2 (- to 2.2.1-1): BLOCKED: Needs an approval (either due to a freeze, the source suite or a manual hint)
    • Issues preventing migration:
    • ∙ ∙ blocked by freeze: is not in testing
    • Additional info:
    • ∙ ∙ Piuparts tested OK - https://piuparts.debian.org/sid/source/b/bwa-mem2.html
    • ∙ ∙ autopkgtest for bwa-mem2/2.2.1-1: amd64: Pass, i386: Pass
    • ∙ ∙ Reproducible on amd64 - info ♻
    • ∙ ∙ Waiting for reproducibility test results on armhf - info ♻
    • ∙ ∙ Reproducible on i386 - info ♻
    • ∙ ∙ 33 days old (needed 20 days)
    • Not considered
news
[rss feed]
  • [2025-04-17] Accepted bwa-mem2 2.2.1-1 (source amd64) into unstable (Debian FTP Masters) (signed by: Michael R. Crusoe)
bugs [bug history graph]
  • all: 0
links
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  • lintian (0, 16)
  • buildd: logs, cross
  • popcon
  • browse source code
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  • debci
ubuntu Ubuntu logo [Information about Ubuntu for Debian Developers]
  • version: 2.2.1-1

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