Source: diamond-aligner
Version: 2.1.14-1
Severity: serious
Control: close -1 2.2.6-1
Tags: sid forky
User: release.debian.org@packages.debian.org
Usertags: out-of-sync
X-Debbugs-CC: debian-s390@lists.debian.org
User: debian-s390@lists.debian.org
Usertags: s390x

tl;dr: the package failed to build on s390x. Its tests failed.

Dear maintainer(s),

The Release Team considers packages that are out-of-sync between testing
and unstable for more than 30 days as having a Release Critical bug in
testing [1]. Your package src:diamond-aligner has been trying to migrate
for 34 days [2], hence this bug report. The current output of the
migration software for this package is copied to the bottom of this
report and should list the reason why the package is blocked. Regularly,
reporting issues against reverse (build/test/regular) dependencies is
what needs to happen. If this has already been done, than this bug is
just for tracking purposes.

If a package is out of sync between unstable and testing for a longer
period, this usually means that bugs in the package in testing cannot be
fixed via unstable. Blocked packages can have impact on other packages,
which makes preparing for the release more difficult. The situation that
caused this bug report might even be the result of such an issue. We
expect maintainers to fix issues that hamper the migration of their
package in a timely manner. If your package in this situation due to
another package, consider helping out.

This bug will trigger auto-removal when appropriate. As with all new
bugs, there will be at least 30 days before the package is auto-removed.

This bug submission immediately closes the bug with the version in
unstable, so if that version or a later version migrates, this bug will
no longer affect testing. This bug is also tagged to only affect sid and
forky, so it doesn't affect (old-)stable.

If you believe your package is unable to migrate to testing due to
issues beyond your control, don't hesitate to contact the Release Team.

This bug report has been automatically generated. If you have any
comments with regards to the content or the process, please reach out to me.

Paul

[1] https://lists.debian.org/debian-devel-announce/2023/06/msg00001.html
[2] https://qa.debian.org/excuses.php?package=diamond-aligner

Current text from [2]:
Migration status for diamond-aligner (2.1.14-1 to 2.2.6-1): BLOCKED:
Maybe temporary, maybe blocked but Britney is missing information (check
below)
Issues preventing migration:
∙ ∙ Missing build on s390x
∙ ∙ Lintian check waiting for test results on s390x - info
Additional info (not blocking):
∙ ∙ Piuparts tested OK -
https://piuparts.debian.org/sid/source/d/diamond-aligner.html
∙ ∙ Autopkgtest for diamond-aligner/2.2.6-1: amd64: Pass, arm64: Pass,
ppc64el: Pass, riscv64: Pass
∙ ∙ Reproduced on amd64 - info
∙ ∙ Reproduced on arm64 - info
∙ ∙ Reproduced on armhf - info
∙ ∙ Reproduced on i386 - info
∙ ∙ Required age reduced by 3 days because of autopkgtest
∙ ∙ 13 days old (needed 2 days)

Hi,

The s390x FTBFS in 2.2.6-1 is a big-endian bug, and upstream has
already fixed it:


https://github.com/bbuchfink/diamond/commit/093dafab9f9ecf2a0666ddd0dda48e9eff29b7c6
  (https://github.com/bbuchfink/diamond/pull/986, merged 2026-09-26, not
  in any release yet)

DatabaseFile::is_diamond_db() reads the .dmnd magic number as raw bytes
and does not convert it from the on-disk little-endian format. On s390x
the comparison fails, so diamond treats the database as FASTA, and the
build-time test fails with:

  Opening the database... Error: Error opening file test/C.faa.diamond. No
such file or directory

The commit adds the missing byteswap there and in read_seqinfo().

We have applied it in Ubuntu on top of 2.2.5-2, together with a backport
of the 2.2.6 generic FingerPrint code. The s390x build now passes, and
all 20 diamond blastp runs in debian/tests/diamond-calls complete.

The commit applies to 2.2.6 unchanged; it is the same code that Ubuntu
tested on 2.2.5. Adding it as a patch to 2.2.6-1 should fix s390x and
unblock the migration.

The patch with a DEP-3 header is attached.

Cheers,
Sebastien

Hi,

Maybe it helps the maintainers if I reopen/clone the bug to expose the
patch?

Paul

We believe that the bug you reported is fixed in the latest version of
diamond-aligner, 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 1152701@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated diamond-aligner 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 ftpmaster@ftp-master.debian.org)
Format: 1.8
Date: Sun, 01 Nov 2026 06:58:44 +0100
Source: diamond-aligner
Architecture: source
Version: 2.2.8-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Closes: 1152701
Changes:
 diamond-aligner (2.2.8-2) unstable; urgency=medium
 .
   * Add patch for s390x which is missing in upstream release
     Closes: #1152701
Checksums-Sha1:
 e7558cb9f2bd58f9957be701f83b350dac20753f 2247 diamond-aligner_2.2.8-2.dsc
 41d1351bce6e355c2592eb9e0fa4ae2dd599069c 137328 diamond-aligner_2.2.8-2.debian.tar.xz
 04c973a3278d85ad16d07d6d7db6afbe398c7cfe 7091 diamond-aligner_2.2.8-2_amd64.buildinfo
Checksums-Sha256:
 ebe4e223702f08ce749a2a681e01abff1ad6664a1dc982e22be676a81a70454e 2247 diamond-aligner_2.2.8-2.dsc
 be3bfbb17ea2ff094ca451856ece4f92f0a3abea6b3eb6e3e948aef088cdf626 137328 diamond-aligner_2.2.8-2.debian.tar.xz
 9c1028b92e957ef92f34b905689a34b8f2809dc086811891cb952679ae796022 7091 diamond-aligner_2.2.8-2_amd64.buildinfo
Files:
 0003464b46ee87581b1023d5361a28bd 2247 science optional diamond-aligner_2.2.8-2.dsc
 f6ee3ac3b732f9772ef377334c5f31a2 137328 science optional diamond-aligner_2.2.8-2.debian.tar.xz
 cceb492aaba73f56da2ab391a207ac1b 7091 science optional diamond-aligner_2.2.8-2_amd64.buildinfo
-----BEGIN PGP SIGNATURE-----
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=fkp1
-----END PGP SIGNATURE-----