Package: src:sift
Version: 6.2.1-1
Severity: important
Tags: trixie sid ftbfs
User: debian-qa@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:

--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
if [ -e src/Makefile -a -e src/deps.mk ]; then make -j2 nocheck -C src prefix=/usr distclean; fi
rm -f info_on_seqs.1 SIFT_for_submitting_fasta_seq.csh.1
# remove pre-compiled binaries from bin - thanks to Michael Bienia <geser@ubuntu.com>
rm -f bin/choose_seqs_via_psiblastseedmedian
rm -f bin/clump_output_alignedseq
rm -f bin/consensus_to_seq
rm -f bin/fastaseqs
rm -f bin/info_on_seqs
rm -f bin/process_alignment
rm -f bin/psiblast_res_to_fasta_dbpairwise
rm -f bin/seqs_from_psiblast_res
rm -f src/choose_seqs_via_psiblastseedmedian
rm -f src/clump_output_alignedseq
rm -f src/consensus_to_seq
rm -f src/deps.mk
rm -f src/info_on_seqs
rm -f src/psiblast_res_to_fasta_dbpairwise
rm -f src/seqs_from_psiblast_res
find . -name "*.o" -delete
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/sift.substvars debian/files
rm -fr -- debian/sift/ debian/tmp/
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
-o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
\) -exec rm -f {} + \) -o \
\( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \)
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
pod2man -c 'User Commands' --release="6.2.1" info_on_seqs.pod > info_on_seqs.1 pod2man -c 'User Commands' --release="6.2.1" SIFT_for_submitting_fasta_seq.csh.pod > SIFT_for_submitting_fasta_seq.csh.1
make -j2 nocheck -C src prefix=/usr VERSION=6.2.1 deps.mk && \
make -j2 nocheck -C src prefix=/usr VERSION=6.2.1
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -MM -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -Wno-unused-result -I/usr/include/blimps -O2 -D__
MAKE_PREFIX__=\"/usr\" choose_seqs_via_psiblastseedmedian.c clump_output_alignedseq.c consensus_to_seq.c info_on_seqs.c psiblast_res_to_fasta_dbpairwise.c seqs_from_psiblast_res.c > deps.mk
make[2]: *** No rule to make target 'nocheck'. Stop.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: *** [debian/rules:54: override_dh_auto_build] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:22: 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:sift, 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.

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