[Debian-med-packaging] Bug#954589: seqan3: FTBFS: two_dimensional_matrix_test.cpp:43:15: error: invalid type ‘__vector?=(1) =?UTF-8?Q?int’ as initializer for a vector of type ‘const __vector(1) int’

[Lucas Nussbaum]

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.