[Debian-med-packaging] Bug#1045535: jellyfish1: Fails to build source after successful build

[Lucas Nussbaum]

Source: jellyfish1
Version: 1.1.11-8
Severity: minor
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-sab-20230813 ftbfs-source-after-build
User: debian-qa at lists.debian.org
Usertags: qa-doublebuild

Hi,

This package fails to build a source package after a successful build
(dpkg-buildpackage ; dpkg-buildpackage -S).

This is probably a clear violation of Debian Policy section 4.9 (clean target),
but this is filed as severity:minor for now, because a discussion on
debian-devel showed that we might want to revisit the requirement of a working
'clean' target.

More information about this class of issues, included common problems and
solutions, is available at
https://wiki.debian.org/qa.debian.org/FTBFS/SourceAfterBuild

Relevant part of the build log:
> cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -S
> ----------------------------------------------------------------------------------------------------------------------------
> 
> dpkg-buildpackage: info: source package jellyfish1
> dpkg-buildpackage: info: source version 1.1.11-8
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
>  dpkg-source --before-build .
>  debian/rules clean
> dh clean
>    dh_auto_clean
> 	make -j8 distclean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> test -z "libgtest.a libgtest_main.a" || rm -f libgtest.a libgtest_main.a
> test -z "libjellyfish-1.1.la" || rm -f libjellyfish-1.1.la
> rm -rf .libs _libs
>  rm -f bin/jellyfish
> cd tests; rm -f seq10m* seq1m* *_0 *_1 *_2 *_S *.md5sum *.histo *.stats *.timing *.query *.dump *.fa
> rm -f *.o
> test -z "tests/generate_sequence.log tests/serial_hashing.log tests/parallel_hashing.log tests/serial_direct_indexing.log tests/parallel_direct_indexing.log tests/raw_hash.log tests/generate_fastq_sequence.log tests/parallel_fastq_hashing.log tests/multi_file.log tests/multi_file_fastq.log tests/from_stream.log tests/parallel_fastq_sequence_hashing.log tests/from_stream_fastq.log tests/merge.log tests/min_qual.log tests/big.log tests/parsers.log tests/small.log tests/parallel_fastq_direct_indexing.log unit_tests/unit_tests.log" || rm -f tests/generate_sequence.log tests/serial_hashing.log tests/parallel_hashing.log tests/serial_direct_indexing.log tests/parallel_direct_indexing.log tests/raw_hash.log tests/generate_fastq_sequence.log tests/parallel_fastq_hashing.log tests/multi_file.log tests/multi_file_fastq.log 
> tests/from_stream.log tests/parallel_fastq_sequence_hashing.log tests/from_stream_fastq.log tests/merge.log tests/min_qual.log tests/big.log tests/parsers.log tests/small.log tests/parallel_fastq_direct_indexing.log unit_tests/unit_tests.log
>  rm -f bin/generate_sequence bin/test_double_fifo_input bin/test_read_parser bin/test_all
> rm -f *.lo
> rm -rf bin/.libs bin/_libs
> rm -f jellyfish/*.o
> rm -f *.tab.c
> test -z "tests/generate_sequence.trs tests/serial_hashing.trs tests/parallel_hashing.trs tests/serial_direct_indexing.trs tests/parallel_direct_indexing.trs tests/raw_hash.trs tests/generate_fastq_sequence.trs tests/parallel_fastq_hashing.trs tests/multi_file.trs tests/multi_file_fastq.trs tests/from_stream.trs tests/parallel_fastq_sequence_hashing.trs tests/from_stream_fastq.trs tests/merge.trs tests/min_qual.trs tests/big.trs tests/parsers.trs tests/small.trs tests/parallel_fastq_direct_indexing.trs unit_tests/unit_tests.trs" || rm -f tests/generate_sequence.trs tests/serial_hashing.trs tests/parallel_hashing.trs tests/serial_direct_indexing.trs tests/parallel_direct_indexing.trs tests/raw_hash.trs tests/generate_fastq_sequence.trs tests/parallel_fastq_hashing.trs tests/multi_file.trs tests/multi_file_fastq.trs 
> tests/from_stream.trs tests/parallel_fastq_sequence_hashing.trs tests/from_stream_fastq.trs tests/merge.trs tests/min_qual.trs tests/big.trs tests/parsers.trs tests/small.trs tests/parallel_fastq_direct_indexing.trs unit_tests/unit_tests.trs
> rm -f ./so_locations
> test -z "tests/compat.sh jellyfish-1.1.pc" || rm -f tests/compat.sh jellyfish-1.1.pc
> rm -f config.h stamp-h1
> rm -f libtool config.lt
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> rm -rf jellyfish/.libs jellyfish/_libs
> rm -f jellyfish/*.lo
> test . = "." || test -z "" || rm -f 
> rm -f cscope.out cscope.in.out cscope.po.out cscope.files
> test -z "test-suite.log" || rm -f test-suite.log
> rm -f bin/.dirstamp
> rm -f unit_tests/*.o
> rm -f unit_tests/gtest/src/*.o
> rm -f jellyfish/.deps/.dirstamp
> rm -f jellyfish/.dirstamp
> rm -f unit_tests/.deps/.dirstamp
> rm -f unit_tests/.dirstamp
> rm -f unit_tests/gtest/src/.deps/.dirstamp
> rm -f unit_tests/gtest/src/.dirstamp
> rm -f config.status config.cache config.log configure.lineno config.status.lineno
> rm -f jellyfish/.deps/allocators_mmap.Plo
> rm -f jellyfish/.deps/backtrace.Plo
> rm -f jellyfish/.deps/cite.Po
> rm -f jellyfish/.deps/dbg.Plo
> rm -f jellyfish/.deps/dna_codes.Plo
> rm -f jellyfish/.deps/dump_fastq_main.Po
> rm -f jellyfish/.deps/dump_main.Po
> rm -f jellyfish/.deps/err.Plo
> rm -f jellyfish/.deps/file_parser.Plo
> rm -f jellyfish/.deps/floats.Plo
> rm -f jellyfish/.deps/generate_sequence.Po
> rm -f jellyfish/.deps/half.Plo
> rm -f jellyfish/.deps/hash_fastq_merge.Po
> rm -f jellyfish/.deps/hash_merge.Po
> rm -f jellyfish/.deps/histo_fastq_main.Po
> rm -f jellyfish/.deps/histo_main.Po
> rm -f jellyfish/.deps/jellyfish.Po
> rm -f jellyfish/.deps/mapped_file.Plo
> rm -f jellyfish/.deps/mer_counter.Po
> rm -f jellyfish/.deps/mersenne.Po
> rm -f jellyfish/.deps/misc.Plo
> rm -f jellyfish/.deps/parse_dna.Plo
> rm -f jellyfish/.deps/parse_quake.Plo
> rm -f jellyfish/.deps/parse_qual_dna.Plo
> rm -f jellyfish/.deps/parse_read.Plo
> rm -f jellyfish/.deps/query_main.Po
> rm -f jellyfish/.deps/read_parser.Plo
> rm -f jellyfish/.deps/seq_qual_parser.Plo
> rm -f jellyfish/.deps/sequence_parser.Plo
> rm -f jellyfish/.deps/square_binary_matrix.Plo
> rm -f jellyfish/.deps/stats_main.Po
> rm -f jellyfish/.deps/storage.Plo
> rm -f jellyfish/.deps/test_double_fifo_input.Po
> rm -f jellyfish/.deps/test_read_parser.Po
> rm -f jellyfish/.deps/thread_exec.Plo
> rm -f jellyfish/.deps/time.Plo
> rm -f jellyfish/.deps/yaggo.Po
> rm -f unit_tests/.deps/bin_test_all-test_offsets_key_value.Po
> rm -f unit_tests/.deps/bin_test_all-test_simple_circular_buffer.Po
> rm -f unit_tests/.deps/bin_test_all-test_square_binary_matrix.Po
> rm -f unit_tests/gtest/src/.deps/libgtest_a-gtest-all.Po
> rm -f unit_tests/gtest/src/.deps/libgtest_main_a-gtest_main.Po
> rm -f Makefile
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_autoreconf_clean
>    debian/rules override_dh_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_clean
> if [ -d debian/tmp_save_tests ] ; then \
>     mv debian/tmp_save_tests/* tests ; \
>     rmdir debian/tmp_save_tests ; \
> fi
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building jellyfish1 using existing ./jellyfish1_1.1.11.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: ignoring deletion of file install-sh, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file aclocal.m4, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file Makefile.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file ltmain.sh, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file configure, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file config.h.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file depcomp, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file missing, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file m4/ltsugar.m4, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file m4/lt~obsolete.m4, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file m4/ltversion.m4, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file m4/libtool.m4, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file m4/ltoptions.m4, use --include-removal to override
> dpkg-source: info: local changes detected, the modified files are:
>  jellyfish1-1.1.11/tests/compat.sh
> dpkg-source: error: aborting due to unexpected upstream changes, see /tmp/jellyfish1_1.1.11-8.diff._PXNPE
> dpkg-source: info: Hint: make sure the version in debian/changelog matches the unpacked source tree
> dpkg-source: info: you can integrate the local changes with dpkg-source --commit
> dpkg-buildpackage: error: dpkg-source -b . subprocess returned exit status 2
> 
> E: Command 'cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -S' failed to run.


The full build log is available from:
http://qa-logs.debian.net/2023/08/13/jellyfish1_1.1.11-8_unstable.log

If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects

If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.