Your message dated Tue, 05 Dec 2023 18:51:17 +0000
with message-id <[email protected]>
and subject line Bug#1046793: fixed in jellyfish 2.3.0-17
has caused the Debian Bug report #1046793,
regarding jellyfish: Fails to build source after successful build
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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--
1046793: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1046793
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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.
--- End Message ---
--- Begin Message ---
Source: jellyfish
Source-Version: 2.3.0-17
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
jellyfish, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <[email protected]> (supplier of updated jellyfish package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Tue, 05 Dec 2023 19:11:55 +0100
Source: jellyfish
Architecture: source
Version: 2.3.0-17
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1046793
Changes:
jellyfish (2.3.0-17) unstable; urgency=medium
.
* d/clean: new: cleanup build artifacts. (Closes: #1046793)
* d/rules: cleanup dh_auto_clean override.
This is made possible by the introduction of the d/clean file.
* d/rules: remove config.h from header package.
This fixes PACKAGE_NAME macro definition collision with potential
autotools consumers in reverse dependencies, per lintian warning.
* d/libjellyfish-2.0-2.lintian-overrides: fix broken override.
* d/libjellyfish-2.0-2.lintian-overrides: remove unused override.
* d/jellyfish-examples.lintian-overrides: renamed.
The file is renamed to d/jellyfish.lintian-overrides. The content is also
adjusted to reflect that the overriden spelling error moved package.
Checksums-Sha1:
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Checksums-Sha256:
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Files:
aedc1413c8dd94f38bb5475e72e50db5 3228 science optional jellyfish_2.3.0-17.dsc
61938abe1804b98ab11fe36e9e9ba2d8 15980 science optional
jellyfish_2.3.0-17.debian.tar.xz
b12efe890b81ac946f7f46403077283e 11739 science optional
jellyfish_2.3.0-17_amd64.buildinfo
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