[Debian-med-packaging] Bug#1046793: jellyfish: Fails to build source after successful build

Sun Aug 13 20:20:49 BST 2023

Source: jellyfish
Version: 2.3.0-16
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 jellyfish
> dpkg-buildpackage: info: source version 2.3.0-16
> 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 --with python3
>    dh_auto_clean
> 	make -j8 distclean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> test -z "libgtest.la libgtest_main.la" || rm -f libgtest.la libgtest_main.la
>  rm -f bin/jellyfish
> test -z "swig/python/swig_wrap.cpp swig/python/dna_jellyfish.py swig/python/__init__.pyc  swig/perl5/swig_wrap.cpp swig/perl5/jellyfish.pm" || rm -f swig/python/swig_wrap.cpp swig/python/dna_jellyfish.py swig/python/__init__.pyc  swig/perl5/swig_wrap.cpp swig/perl5/jellyfish.pm
> test -z "libjellyfish-2.0.la" || rm -f libjellyfish-2.0.la
> rm -rf .libs _libs
> cd tests; rm -f *
>  rm -f bin/generate_sequence bin/fastq2sam bin/test_all
> test -z "swig/perl5/jellyfish.la" || rm -f swig/perl5/jellyfish.la
> test -z "swig/python/_dna_jellyfish.la" || rm -f swig/python/_dna_jellyfish.la
> test -z "" || rm -f 
> rm -f ./so_locations
> rm -f *.o
> rm -rf bin/.libs bin/_libs
> test -z "tests/generate_sequence.log tests/parallel_hashing.log tests/merge.log tests/bloom_filter.log tests/big.log tests/subset_hashing.log tests/multi_file.log tests/bloom_counter.log tests/large_key.log tests/sam.log tests/small_mers.log tests/swig_python.log tests/swig_ruby.log tests/swig_perl.log unit_tests/unit_tests.log" || rm -f tests/generate_sequence.log tests/parallel_hashing.log tests/merge.log tests/bloom_filter.log tests/big.log tests/subset_hashing.log tests/multi_file.log tests/bloom_counter.log tests/large_key.log tests/sam.log tests/small_mers.log tests/swig_python.log tests/swig_ruby.log tests/swig_perl.log unit_tests/unit_tests.log
> rm -f *.lo
> rm -f jellyfish/*.o
> rm -f swig/perl5/so_locations
> rm -f swig/python/so_locations
> test -z "tests/generate_sequence.trs tests/parallel_hashing.trs tests/merge.trs tests/bloom_filter.trs tests/big.trs tests/subset_hashing.trs tests/multi_file.trs tests/bloom_counter.trs tests/large_key.trs tests/sam.trs tests/small_mers.trs tests/swig_python.trs tests/swig_ruby.trs tests/swig_perl.trs unit_tests/unit_tests.trs" || rm -f tests/generate_sequence.trs tests/parallel_hashing.trs tests/merge.trs tests/bloom_filter.trs tests/big.trs tests/subset_hashing.trs tests/multi_file.trs tests/bloom_counter.trs tests/large_key.trs tests/sam.trs tests/small_mers.trs tests/swig_python.trs tests/swig_ruby.trs tests/swig_perl.trs unit_tests/unit_tests.trs
> rm -f ./so_locations
> rm -f *.tab.c
> test -z "compat.sh jellyfish-2.0.pc" || rm -f compat.sh jellyfish-2.0.pc
> rm -f lib/*.o
> rm -f config.h stamp-h1
> test -z "test-suite.log" || rm -f test-suite.log
> rm -f libtool config.lt
> test . = "." || test -z "" || rm -f 
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> rm -f lib/*.lo
> rm -f bin/.dirstamp
> rm -rf lib/.libs lib/_libs
> rm -f cscope.out cscope.in.out cscope.po.out cscope.files
> rm -f jellyfish/.deps/.dirstamp
> rm -f sub_commands/*.o
> rm -rf swig/perl5/.libs swig/perl5/_libs
> rm -f jellyfish/.dirstamp
> rm -f swig/perl5/*.o
> rm -rf swig/python/.libs swig/python/_libs
> rm -f lib/.deps/.dirstamp
> rm -f swig/perl5/*.lo
> rm -f lib/.dirstamp
> rm -rf swig/ruby/.libs swig/ruby/_libs
> rm -f swig/python/*.o
> rm -f sub_commands/.deps/.dirstamp
> rm -rf unit_tests/gtest/src/.libs unit_tests/gtest/src/_libs
> rm -f swig/python/*.lo
> rm -f sub_commands/.dirstamp
> rm -f swig/ruby/*.o
> rm -f swig/perl5/.deps/.dirstamp
> rm -f swig/ruby/*.lo
> rm -f swig/perl5/.dirstamp
> rm -f unit_tests/*.o
> rm -f swig/python/.deps/.dirstamp
> rm -f swig/python/.dirstamp
> rm -f swig/ruby/.deps/.dirstamp
> rm -f swig/ruby/.dirstamp
> rm -f unit_tests/.deps/.dirstamp
> rm -f unit_tests/gtest/src/*.o
> rm -f unit_tests/.dirstamp
> rm -f unit_tests/gtest/src/.deps/.dirstamp
> rm -f unit_tests/gtest/src/*.lo
> rm -f unit_tests/gtest/src/.dirstamp
> test -z "sub_commands/count_main_cmdline.hpp sub_commands/info_main_cmdline.hpp sub_commands/dump_main_cmdline.hpp sub_commands/histo_main_cmdline.hpp sub_commands/stats_main_cmdline.hpp sub_commands/merge_main_cmdline.hpp sub_commands/bc_main_cmdline.hpp sub_commands/query_main_cmdline.hpp sub_commands/cite_main_cmdline.hpp sub_commands/mem_main_cmdline.hpp jellyfish/generate_sequence_cmdline.hpp jellyfish/fastq2sam_cmdline.hpp unit_tests/test_main_cmdline.hpp swig/python/swig_wrap.cpp swig/python/dna_jellyfish.py  swig/perl5/swig_wrap.cpp swig/perl5/jellyfish.pm" || rm -f sub_commands/count_main_cmdline.hpp sub_commands/info_main_cmdline.hpp sub_commands/dump_main_cmdline.hpp sub_commands/histo_main_cmdline.hpp sub_commands/stats_main_cmdline.hpp sub_commands/merge_main_cmdline.hpp sub_commands/bc_main_cmdline.hpp 
> sub_commands/query_main_cmdline.hpp sub_commands/cite_main_cmdline.hpp sub_commands/mem_main_cmdline.hpp jellyfish/generate_sequence_cmdline.hpp jellyfish/fastq2sam_cmdline.hpp unit_tests/test_main_cmdline.hpp swig/python/swig_wrap.cpp swig/python/dna_jellyfish.py  swig/perl5/swig_wrap.cpp swig/perl5/jellyfish.pm
> rm -f config.status config.cache config.log configure.lineno config.status.lineno
> rm -f jellyfish/.deps/backtrace.Po
> rm -f jellyfish/.deps/bin_test_all-backtrace.Po
> rm -f jellyfish/.deps/dbg.Po
> rm -f jellyfish/.deps/fastq2sam.Po
> rm -f jellyfish/.deps/generate_sequence.Po
> rm -f jellyfish/.deps/merge_files.Po
> rm -f jellyfish/.deps/mersenne.Po
> rm -f lib/.deps/allocators_mmap.Plo
> rm -f lib/.deps/generator_manager.Plo
> rm -f lib/.deps/int128.Plo
> rm -f lib/.deps/jsoncpp.Plo
> rm -f lib/.deps/mer_dna.Plo
> rm -f lib/.deps/misc.Plo
> rm -f lib/.deps/rectangular_binary_matrix.Plo
> rm -f lib/.deps/storage.Plo
> rm -f lib/.deps/thread_exec.Plo
> rm -f lib/.deps/time.Plo
> rm -f sub_commands/.deps/bc_main.Po
> rm -f sub_commands/.deps/cite_main.Po
> rm -f sub_commands/.deps/count_main.Po
> rm -f sub_commands/.deps/dump_main.Po
> rm -f sub_commands/.deps/histo_main.Po
> rm -f sub_commands/.deps/info_main.Po
> rm -f sub_commands/.deps/jellyfish.Po
> rm -f sub_commands/.deps/mem_main.Po
> rm -f sub_commands/.deps/merge_main.Po
> rm -f sub_commands/.deps/query_main.Po
> rm -f sub_commands/.deps/stats_main.Po
> rm -f swig/perl5/.deps/swig_perl5_jellyfish_la-swig_wrap.Plo
> rm -f swig/python/.deps/swig_python__dna_jellyfish_la-swig_wrap.Plo
> rm -f swig/ruby/.deps/swig_ruby_jellyfish_la-swig_wrap.Plo
> rm -f unit_tests/.deps/bin_test_all-test_allocators_mmap.Po
> rm -f unit_tests/.deps/bin_test_all-test_atomic_bits_array.Po
> rm -f unit_tests/.deps/bin_test_all-test_cooperative_pool2.Po
> rm -f unit_tests/.deps/bin_test_all-test_dumpers.Po
> rm -f unit_tests/.deps/bin_test_all-test_file_header.Po
> rm -f unit_tests/.deps/bin_test_all-test_generator_manager.Po
> rm -f unit_tests/.deps/bin_test_all-test_hash_counter.Po
> rm -f unit_tests/.deps/bin_test_all-test_int128.Po
> rm -f unit_tests/.deps/bin_test_all-test_large_hash_array.Po
> rm -f unit_tests/.deps/bin_test_all-test_main.Po
> rm -f unit_tests/.deps/bin_test_all-test_mapped_file.Po
> rm -f unit_tests/.deps/bin_test_all-test_mer_dna.Po
> rm -f unit_tests/.deps/bin_test_all-test_mer_dna_bloom_counter.Po
> rm -f unit_tests/.deps/bin_test_all-test_mer_heap.Po
> rm -f unit_tests/.deps/bin_test_all-test_mer_iterator.Po
> rm -f unit_tests/.deps/bin_test_all-test_mer_overlap_sequence_parser.Po
> rm -f unit_tests/.deps/bin_test_all-test_misc.Po
> rm -f unit_tests/.deps/bin_test_all-test_offsets_key_value.Po
> rm -f unit_tests/.deps/bin_test_all-test_rectangular_binary_matrix.Po
> rm -f unit_tests/.deps/bin_test_all-test_simple_circular_buffer.Po
> rm -f unit_tests/.deps/bin_test_all-test_stdio_filebuf.Po
> rm -f unit_tests/.deps/bin_test_all-test_stream_iterator.Po
> rm -f unit_tests/.deps/bin_test_all-test_text_dumper.Po
> rm -f unit_tests/.deps/bin_test_all-test_token_ring.Po
> rm -f unit_tests/.deps/bin_test_all-test_whole_sequence_parser.Po
> rm -f unit_tests/gtest/src/.deps/libgtest_la-gtest-all.Plo
> rm -f unit_tests/gtest/src/.deps/libgtest_main_la-gtest_main.Plo
> 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
> rm -f tests/compat.sh
> rm -f swig/python/jellyfish* # swig/python/dna_jellyfish.py
> rm -f swig/perl5/blib/arch/auto/jellyfish/jellyfish.so
> rm -f swig/perl5/blib/bin/.exists
> rm -f swig/perl5/blib/lib/.exists
> rm -f swig/perl5/blib/lib/auto/jellyfish/.exists
> rm -f swig/perl5/blib/man1/.exists
> rm -f swig/perl5/blib/man3/.exists
> rm -f swig/perl5/blib/script/.exists
> rm -f swig/perl5/jellyfish.bs
> rm -f swig/perl5/pm_to_blib
> rm -rf swig/perl5/MYMETA.json swig/perl5/MYMETA.yml swig/perl5/Makefile swig/perl5/blib/
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building jellyfish using existing ./jellyfish_2.3.0.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: ignoring deletion of file swig/python/jellyfish.py, use --include-removal to override
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_dna_jellyfish/build/_dna_jellyfish.cpython-311-x86_64-linux-gnu.so: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_dna_jellyfish/build/_dna_jellyfish.cpython-311-x86_64-linux-gnu.so in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of '.pybuild/cpython3_3.11_dna_jellyfish/build/_dna_jellyfish.cpython-311-x86_64-linux-gnu.so' will not be represented in diff
> dpkg-source: error: cannot represent change to swig/python/__pycache__/dna_jellyfish.cpython-311.pyc: binary file contents changed
> dpkg-source: error: add swig/python/__pycache__/dna_jellyfish.cpython-311.pyc in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to swig/python/build/temp.linux-x86_64-3.11/swig_wrap.o: binary file contents changed
> dpkg-source: error: add swig/python/build/temp.linux-x86_64-3.11/swig_wrap.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: unrepresentable changes to source
> dpkg-buildpackage: error: dpkg-source -b . subprocess returned exit status 1
> 
> 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/jellyfish_2.3.0-16_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.