[Debian-med-packaging] Bug#1103312: hmmer: FTBFS with the nocheck build profile

[Santiago Vila]

Package: src:hmmer
Version: 3.4+dfsg-2
Severity: important
Tags: trixie sid ftbfs
User: debian-qa at lists.debian.org
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.