Source: jellyfish Version: 2.3.0-16 Severity: minor Tags: trixie sid ftbfs User: [email protected] Usertags: ftbfs-sab-20230813 ftbfs-source-after-build User: [email protected] 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 <[email protected]> > 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.
