Your message dated Thu, 26 Mar 2020 12:34:43 +0000
with message-id <[email protected]>
and subject line Bug#954589: fixed in seqan3 3.0.1+ds-9
has caused the Debian Bug report #954589,
regarding seqan3: FTBFS: two_dimensional_matrix_test.cpp:43:15: error: invalid
type ‘__vector(1) int’ as initializer for a vector of type ‘const __vector(1)
int’
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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--
954589: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=954589
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: seqan3
Version: 3.0.1+ds-8
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20200321 ftbfs-bullseye
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1
> -Ivendor/googletest/googletest/include -I/<<PKGBUILDDIR>>/test/include
> -I/<<PKGBUILDDIR>>/include -isystem
> /<<PKGBUILDDIR>>/submodules/sdsl-lite/include -g -O2
> -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -fuse-ld=gold -DNDEBUG -O3 -std=c++2a -Wdate-time
> -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Werror -fconcepts -pthread -MD
> -MT
> alignment/matrix/detail/CMakeFiles/two_dimensional_matrix_test.dir/two_dimensional_matrix_test.cpp.o
> -MF
> alignment/matrix/detail/CMakeFiles/two_dimensional_matrix_test.dir/two_dimensional_matrix_test.cpp.o.d
> -o
> alignment/matrix/detail/CMakeFiles/two_dimensional_matrix_test.dir/two_dimensional_matrix_test.cpp.o
> -c
> /<<PKGBUILDDIR>>/test/unit/alignment/matrix/detail/two_dimensional_matrix_test.cpp
> /<<PKGBUILDDIR>>/test/unit/alignment/matrix/detail/two_dimensional_matrix_test.cpp:
> In instantiation of ‘std::vector<T> create_matrix_storage() [with score_type
> = __vector(1) int; seqan3::detail::matrix_major_order order =
> seqan3::detail::matrix_major_order::row]’:
> /usr/include/gtest/internal/gtest-internal.h:460:40: recursively required
> from
> ‘gtest_suite_iterator_fixture_::compare_geq<seqan3::detail::two_dimensional_matrix<__vector(1)
> int, std::allocator<__vector(1) int>,
> seqan3::detail::matrix_major_order::column> >::compare_geq()’
> /usr/include/gtest/internal/gtest-internal.h:460:40: required from
> ‘testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest()
> [with TestClass =
> gtest_suite_iterator_fixture_::compare_geq<seqan3::detail::two_dimensional_matrix<__vector(1)
> int, std::allocator<__vector(1) int>,
> seqan3::detail::matrix_major_order::column> >]’
> /usr/include/gtest/internal/gtest-internal.h:460:9: required from here
> /<<PKGBUILDDIR>>/test/unit/alignment/matrix/detail/two_dimensional_matrix_test.cpp:43:15:
> error: invalid type ‘__vector(1) int’ as initializer for a vector of type
> ‘const __vector(1) int’
> 43 | storage_t row_wise
> | ^~~~~~~~
> /<<PKGBUILDDIR>>/test/unit/alignment/matrix/detail/two_dimensional_matrix_test.cpp:50:15:
> error: invalid type ‘__vector(1) int’ as initializer for a vector of type
> ‘const __vector(1) int’
> 50 | storage_t column_wise
> | ^~~~~~~~~~~
> /<<PKGBUILDDIR>>/test/unit/alignment/matrix/detail/two_dimensional_matrix_test.cpp:
> In instantiation of ‘std::vector<T> create_matrix_storage() [with score_type
> = __vector(1) int; seqan3::detail::matrix_major_order order =
> seqan3::detail::matrix_major_order::column]’:
> /usr/include/gtest/internal/gtest-internal.h:460:40: recursively required
> from
> ‘gtest_suite_iterator_fixture_::compare_geq<seqan3::detail::two_dimensional_matrix<__vector(1)
> int, std::allocator<__vector(1) int>,
> seqan3::detail::matrix_major_order::column> >::compare_geq()’
> /usr/include/gtest/internal/gtest-internal.h:460:40: required from
> ‘testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest()
> [with TestClass =
> gtest_suite_iterator_fixture_::compare_geq<seqan3::detail::two_dimensional_matrix<__vector(1)
> int, std::allocator<__vector(1) int>,
> seqan3::detail::matrix_major_order::column> >]’
> /usr/include/gtest/internal/gtest-internal.h:460:9: required from here
> /<<PKGBUILDDIR>>/test/unit/alignment/matrix/detail/two_dimensional_matrix_test.cpp:43:15:
> error: invalid type ‘__vector(1) int’ as initializer for a vector of type
> ‘const __vector(1) int’
> 43 | storage_t row_wise
> | ^~~~~~~~
> /<<PKGBUILDDIR>>/test/unit/alignment/matrix/detail/two_dimensional_matrix_test.cpp:50:15:
> error: invalid type ‘__vector(1) int’ as initializer for a vector of type
> ‘const __vector(1) int’
> 50 | storage_t column_wise
> | ^~~~~~~~~~~
> [67/502] : && /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold
> -DNDEBUG -O3 -std=c++2a -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro
> alignment/matrix/detail/CMakeFiles/alignment_trace_matrix_full_test.dir/alignment_trace_matrix_full_test.cpp.o
> -o alignment/matrix/detail/alignment_trace_matrix_full_test -pthread
> /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libbz2.so -lrt
> lib/libgtest_main.a lib/libgtest.a -lpthread && cd
> /<<PKGBUILDDIR>>/build_unit/alignment/matrix/detail && /usr/bin/cmake -D
> TEST_TARGET=alignment_trace_matrix_full_test -D
> TEST_EXECUTABLE=/<<PKGBUILDDIR>>/build_unit/alignment/matrix/detail/alignment_trace_matrix_full_test
> -D TEST_EXECUTOR= -D
> TEST_WORKING_DIR=/<<PKGBUILDDIR>>/build_unit/alignment/matrix/detail -D
> TEST_EXTRA_ARGS= -D TEST_PROPERTIES= -D
> TEST_PREFIX=alignment/matrix/detail/alignment_trace_matrix_full_test:: -D
> TEST_SUFFIX= -D NO_PRETTY_TYPES=FALSE -D NO_PRETTY_VALUES=FALSE -D
> TEST_LIST=alignment_trace_matrix_full_test_TESTS -D
> CTEST_FILE=/<<PKGBUILDDIR>>/build_unit/alignment/matrix/detail/alignment_trace_matrix_full_test[1]_tests.cmake
> -D TEST_DISCOVERY_TIMEOUT=5 -P
> /usr/share/cmake-3.16/Modules/GoogleTestAddTests.cmake
> [68/502] /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1
> -Ivendor/googletest/googletest/include -I/<<PKGBUILDDIR>>/test/include
> -I/<<PKGBUILDDIR>>/include -isystem
> /<<PKGBUILDDIR>>/submodules/sdsl-lite/include -g -O2
> -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -fuse-ld=gold -DNDEBUG -O3 -std=c++2a -Wdate-time
> -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Werror -fconcepts -pthread -MD
> -MT
> alignment/matrix/detail/CMakeFiles/alignment_trace_matrix_full_banded_test.dir/alignment_trace_matrix_full_banded_test.cpp.o
> -MF
> alignment/matrix/detail/CMakeFiles/alignment_trace_matrix_full_banded_test.dir/alignment_trace_matrix_full_banded_test.cpp.o.d
> -o
> alignment/matrix/detail/CMakeFiles/alignment_trace_matrix_full_banded_test.dir/alignment_trace_matrix_full_banded_test.cpp.o
> -c
> /<<PKGBUILDDIR>>/test/unit/alignment/matrix/detail/alignment_trace_matrix_full_banded_test.cpp
> [69/502] /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1
> -Ivendor/googletest/googletest/include -I/<<PKGBUILDDIR>>/test/include
> -I/<<PKGBUILDDIR>>/include -isystem
> /<<PKGBUILDDIR>>/submodules/sdsl-lite/include -g -O2
> -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -fuse-ld=gold -DNDEBUG -O3 -std=c++2a -Wdate-time
> -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Werror -fconcepts -pthread -MD
> -MT
> alignment/matrix/detail/CMakeFiles/aligned_sequence_builder_test.dir/aligned_sequence_builder_test.cpp.o
> -MF
> alignment/matrix/detail/CMakeFiles/aligned_sequence_builder_test.dir/aligned_sequence_builder_test.cpp.o.d
> -o
> alignment/matrix/detail/CMakeFiles/aligned_sequence_builder_test.dir/aligned_sequence_builder_test.cpp.o
> -c
> /<<PKGBUILDDIR>>/test/unit/alignment/matrix/detail/aligned_sequence_builder_test.cpp
> ninja: build stopped: subcommand failed.
> dh_auto_build: error: cd build_unit && LC_ALL=C.UTF-8 ninja -j4 -v returned
> exit code 1
> make[1]: *** [debian/rules:39: override_dh_auto_build] Error 25
The full build log is available from:
http://qa-logs.debian.net/2020/03/21/seqan3_3.0.1+ds-8_unstable.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.
--- End Message ---
--- Begin Message ---
Source: seqan3
Source-Version: 3.0.1+ds-9
Done: [email protected] (Michael R. Crusoe)
We believe that the bug you reported is fixed in the latest version of
seqan3, 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.
Michael R. Crusoe <[email protected]> (supplier of updated seqan3
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: Wed, 25 Mar 2020 22:01:41 +0100
Source: seqan3
Architecture: source
Version: 3.0.1+ds-9
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Michael R. Crusoe <[email protected]>
Closes: 954589
Changes:
seqan3 (3.0.1+ds-9) unstable; urgency=medium
.
* Fix FTBFS with patch from upstream. Closes: #954589
* Standards-Version: 4.5.0 (routine-update)
* Add salsa-ci file (routine-update)
* Wrap long lines in changelog entries: 3.0.0+ds2-4.
* Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
Repository-Browse.
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