Your message dated Mon, 29 Sep 2025 13:19:16 +0000
with message-id <[email protected]>
and subject line Bug#1103312: fixed in hmmer 3.4+dfsg-3
has caused the Debian Bug report #1103312,
regarding hmmer: FTBFS with the nocheck build profile
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1103312: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1103312
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:hmmer
Version: 3.4+dfsg-2
Severity: important
Tags: trixie sid ftbfs
User: [email protected]
Usertags: ftbfs-nocheck-profile
Dear maintainer:
During a rebuild of all packages in unstable using the nocheck build profile,
your package failed to build:
--------------------------------------------------------------------------------
[...]
make[4]: Leaving directory '/<<PKGBUILDDIR>>/documentation/man'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/documentation'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
mkdir -p /<<PKGBUILDDIR>>/debian/hmmer/usr/lib/x86_64-linux-gnu/hmmer/
cp src/hmmc2 /<<PKGBUILDDIR>>/debian/hmmer/usr/lib/x86_64-linux-gnu/hmmer/
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_install
dh_installdocs
dh_installchangelogs
debian/rules override_dh_installexamples
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installexamples
mkdir -p
/<<PKGBUILDDIR>>/debian/hmmer-examples/usr/share/doc/hmmer/examples/src/impl
find src/ -maxdepth 1 -name "*_utest" -exec cp \{\}
/<<PKGBUILDDIR>>/debian/hmmer-examples/usr/share/doc/hmmer/examples/src/ \;
find src/impl_sse -name "*_utest" -exec cp \{\}
/<<PKGBUILDDIR>>/debian/hmmer-examples/usr/share/doc/hmmer/examples/src/impl \;
cp src/itest_brute
/<<PKGBUILDDIR>>/debian/hmmer-examples/usr/share/doc/hmmer/examples/src
cp: cannot stat 'src/itest_brute': No such file or directory
make[1]: *** [debian/rules:70: override_dh_installexamples] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:18: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202504/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:hmmer, so that this is still
visible in the BTS web page for this package.
Notes:
* When a package is built with the nocheck profile, it means:
- DEB_BUILD_OPTIONS=nocheck
(the tests should be skipped during the build)
- DEB_BUILD_PROFILES=nocheck
(Build-Depends marked <!nocheck> are not installed)
- The contents of the package is allowed to be different than normal
* This category of bugs was going to be RC for trixie, but
according to the Release Managers it's a little bit late in the
release cycle to introduce a bunch of RC bugs of this type.
* In addition to the above, this package also fails when
using DEB_BUILD_OPTIONS=nocheck alone. In this mode:
- DEB_BUILD_OPTIONS=nocheck
(the tests should be skipped during the build)
- Build-Depends marked <!nocheck> are installed as normal
- The contents of the package should not change compared
to a regular build
Thanks.
--- End Message ---
--- Begin Message ---
Source: hmmer
Source-Version: 3.4+dfsg-3
Done: Santiago Vila <[email protected]>
We believe that the bug you reported is fixed in the latest version of
hmmer, 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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Santiago Vila <[email protected]> (supplier of updated hmmer 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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Mon, 29 Sep 2025 14:45:00 +0200
Source: hmmer
Architecture: source
Version: 3.4+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Santiago Vila <[email protected]>
Closes: 1103312
Changes:
hmmer (3.4+dfsg-3) unstable; urgency=medium
.
* Team upload.
.
[ Michael R. Crusoe ]
* d/rules: use DEB_BUILD_OPTION_PARALLEL instead of nproc to respect Debian
Policy 4.9.1.
.
[ Santiago Vila ]
* d/rules: Put V=VERBOSE at the beginning to be used in all targets.
* d/rules: Do not filter nocheck in override_dh_auto_test, dh already does
that.
* d/rules: make tests after dh_auto_build, required by dh_installexamples.
Fixes FTBFS when built with nocheck build profile. Closes: #1103312.
* d/rules: Use execute_after_* where possible.
* d/salsa-ci.yml: Use the simplified form.
* d/salsa-ci.yml: Disable reprotest job, it does not work.
* d/salsa-ci.yml: Enable nocheck build profile job.
* d/control: Drop "Rules-Required-Root: no", no longer needed.
* d/control: Update standards-version.
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