[Debian-med-packaging] Bug#952203: seqan: FTBFS: dh_auto_test: error: cd obj-x86_64-linux-gnu && make -j4 test ARGS\+=-j4 returned exit code 2
Lucas Nussbaum
lucas at debian.org
Sun Feb 23 13:14:14 GMT 2020
Source: seqan
Version: 1.4.2+dfsg-3
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20200222 ftbfs-bullseye
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> Running tests...
> /usr/bin/ctest --force-new-ctest-process -j4
> Test project /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
> Start 1: test_demo_align_align
> Start 2: test_demo_align_compute_alignment_stats
> Start 3: test_demo_align_gaps_example
> Start 4: test_demo_align_global_alignment_banded
> 1/95 Test #1: test_demo_align_align .............................................. Passed 0.03 sec
> Start 5: test_demo_align_global_alignment_unbanded
> 2/95 Test #2: test_demo_align_compute_alignment_stats ............................ Passed 0.03 sec
> Start 6: test_demo_align_integrate_align
> 3/95 Test #4: test_demo_align_global_alignment_banded ............................ Passed 0.03 sec
> Start 7: test_demo_bam_io_bam_stream
> 4/95 Test #3: test_demo_align_gaps_example ....................................... Passed 0.03 sec
> Start 8: test_demo_find_finder_index
> 5/95 Test #5: test_demo_align_global_alignment_unbanded .......................... Passed 0.03 sec
> Start 9: test_demo_find_finder_online
> 6/95 Test #6: test_demo_align_integrate_align .................................... Passed 0.03 sec
> Start 10: test_demo_graph_graph_algo_dijkstra
> 7/95 Test #7: test_demo_bam_io_bam_stream ........................................ Passed 0.03 sec
> Start 11: test_demo_graph_algorithms_all_pairs_shortest_path
> 8/95 Test #8: test_demo_find_finder_index ........................................ Passed 0.03 sec
> Start 12: test_demo_graph_algorithms_bellman_ford_algorithm
> 9/95 Test #9: test_demo_find_finder_online ....................................... Passed 0.03 sec
> Start 13: test_demo_graph_algorithms_breadth_first_search
> 10/95 Test #10: test_demo_graph_graph_algo_dijkstra ................................ Passed 0.03 sec
> Start 14: test_demo_graph_algorithms_dag_shortest_path
> 11/95 Test #11: test_demo_graph_algorithms_all_pairs_shortest_path ................. Passed 0.03 sec
> Start 15: test_demo_graph_algorithms_depth_first_search
> 12/95 Test #12: test_demo_graph_algorithms_bellman_ford_algorithm .................. Passed 0.03 sec
> Start 16: test_demo_graph_algorithms_dijkstra
> 13/95 Test #13: test_demo_graph_algorithms_breadth_first_search .................... Passed 0.03 sec
> Start 17: test_demo_graph_algorithms_floyd_warshall_algorithm
> 14/95 Test #14: test_demo_graph_algorithms_dag_shortest_path ....................... Passed 0.03 sec
> Start 18: test_demo_graph_algorithms_ford_fulkerson_algorithm
> 15/95 Test #15: test_demo_graph_algorithms_depth_first_search ...................... Passed 0.03 sec
> Start 19: test_demo_graph_algorithms_kruskals_algorithm
> 16/95 Test #16: test_demo_graph_algorithms_dijkstra ................................ Passed 0.03 sec
> Start 20: test_demo_graph_algorithms_prims_algorithm
> 17/95 Test #17: test_demo_graph_algorithms_floyd_warshall_algorithm ................ Passed 0.03 sec
> Start 21: test_demo_graph_algorithms_strongly_connected_components
> 18/95 Test #18: test_demo_graph_algorithms_ford_fulkerson_algorithm ................ Passed 0.03 sec
> Start 22: test_demo_graph_algorithms_topological_sort
> 19/95 Test #19: test_demo_graph_algorithms_kruskals_algorithm ...................... Passed 0.03 sec
> Start 23: test_demo_graph_algorithms_transitive_closure
> 20/95 Test #20: test_demo_graph_algorithms_prims_algorithm ......................... Passed 0.03 sec
> Start 24: test_demo_index_index_begin_atEnd_representative
> 21/95 Test #21: test_demo_graph_algorithms_strongly_connected_components ........... Passed 0.03 sec
> Start 25: test_demo_index_index_counting
> 22/95 Test #22: test_demo_graph_algorithms_topological_sort ........................ Passed 0.03 sec
> Start 26: test_demo_index_index_finder
> 23/95 Test #23: test_demo_graph_algorithms_transitive_closure ...................... Passed 0.03 sec
> Start 27: test_demo_index_index_getOccurrences_getFrequency_range_getFibre
> 24/95 Test #24: test_demo_index_index_begin_atEnd_representative ................... Passed 0.03 sec
> Start 28: test_demo_index_index_iterator
> 25/95 Test #26: test_demo_index_index_finder ....................................... Passed 0.03 sec
> Start 29: test_demo_index_index_iterator_short
> 26/95 Test #25: test_demo_index_index_counting ..................................... Passed 0.03 sec
> Start 30: test_demo_index_index_length_countSequences
> 27/95 Test #27: test_demo_index_index_getOccurrences_getFrequency_range_getFibre ... Passed 0.03 sec
> Start 31: test_demo_index_index_mummy
> 28/95 Test #28: test_demo_index_index_iterator ..................................... Passed 0.03 sec
> Start 32: test_demo_index_index_open_save
> 29/95 Test #29: test_demo_index_index_iterator_short ............................... Passed 0.03 sec
> Start 33: test_demo_index_index_textAt_indexText_saAt_indexRequire
> 30/95 Test #30: test_demo_index_index_length_countSequences ........................ Passed 0.03 sec
> Start 34: test_demo_input_output_record_reader
> 31/95 Test #31: test_demo_index_index_mummy ........................................ Passed 0.03 sec
> Start 35: test_demo_misc_enumerate_strings
> 32/95 Test #32: test_demo_index_index_open_save .................................... Passed 0.03 sec
> Start 36: test_demo_modifier_modified_string
> 33/95 Test #33: test_demo_index_index_textAt_indexText_saAt_indexRequire ........... Passed 0.03 sec
> Start 37: test_demo_modifier_modified_string_mod_view
> 34/95 Test #35: test_demo_misc_enumerate_strings ................................... Passed 0.03 sec
> Start 38: test_demo_modifier_modified_string_nested
> 35/95 Test #34: test_demo_input_output_record_reader ............................... Passed 0.03 sec
> Start 39: test_demo_score_score
> 36/95 Test #36: test_demo_modifier_modified_string ................................. Passed 0.03 sec
> Start 40: test_demo_seeds_seeds_extension
> 37/95 Test #37: test_demo_modifier_modified_string_mod_view ........................ Passed 0.03 sec
> Start 41: test_demo_seq_io_fai_index_example
> 38/95 Test #38: test_demo_modifier_modified_string_nested .......................... Passed 0.03 sec
> Start 42: test_demo_seq_io_sequence_stream_read
> 39/95 Test #39: test_demo_score_score .............................................. Passed 0.03 sec
> Start 43: test_demo_sequence_string2
> 40/95 Test #40: test_demo_seeds_seeds_extension .................................... Passed 0.03 sec
> Start 44: test_demo_sequence_stringset
> 41/95 Test #41: test_demo_seq_io_fai_index_example ................................. Passed 0.03 sec
> Start 45: test_test_align
> 42/95 Test #42: test_demo_seq_io_sequence_stream_read .............................. Passed 0.03 sec
> Start 46: test_test_arg_parse
> 43/95 Test #43: test_demo_sequence_string2 ......................................... Passed 0.03 sec
> Start 47: test_test_bam_io
> 44/95 Test #44: test_demo_sequence_stringset ....................................... Passed 0.03 sec
> Start 48: test_test_basic_exception
> 45/95 Test #48: test_test_basic_exception .......................................... Passed 0.00 sec
> Start 49: test_test_basic_metaprogramming
> 46/95 Test #45: test_test_align .................................................... Passed 0.01 sec
> Start 50: test_test_basic_fundamental
> 47/95 Test #46: test_test_arg_parse ................................................ Passed 0.01 sec
> Start 51: test_test_basic_concept
> 48/95 Test #49: test_test_basic_metaprogramming .................................... Passed 0.00 sec
> Start 52: test_test_basic_alphabet
> 49/95 Test #50: test_test_basic_fundamental ........................................ Passed 0.00 sec
> Start 53: test_test_basic_aggregate
> 50/95 Test #47: test_test_bam_io ................................................... Passed 0.01 sec
> Start 54: test_test_basic_allocator
> 51/95 Test #51: test_test_basic_concept ............................................ Passed 0.00 sec
> Start 55: test_test_basic_parallelism
> 52/95 Test #52: test_test_basic_alphabet ........................................... Passed 0.00 sec
> Start 56: test_test_basic_math
> 53/95 Test #53: test_test_basic_aggregate .......................................... Passed 0.00 sec
> Start 57: test_test_basic_smart_pointer
> 54/95 Test #54: test_test_basic_allocator .......................................... Passed 0.00 sec
> Start 58: test_test_basic_container
> 55/95 Test #55: test_test_basic_parallelism ........................................ Passed 0.00 sec
> Start 59: test_test_basic_proxy
> 56/95 Test #56: test_test_basic_math ............................................... Passed 0.00 sec
> Start 60: test_test_basic_iterator
> 57/95 Test #57: test_test_basic_smart_pointer ...................................... Passed 0.00 sec
> Start 61: test_test_consensus
> 58/95 Test #58: test_test_basic_container .......................................... Passed 0.00 sec
> Start 62: test_test_file
> 59/95 Test #59: test_test_basic_proxy .............................................. Passed 0.00 sec
> Start 63: test_test_find
> 60/95 Test #60: test_test_basic_iterator ........................................... Passed 0.00 sec
> Start 64: test_test_gff_io
> 61/95 Test #62: test_test_file ..................................................... Passed 0.00 sec
> Start 65: test_test_graph_algorithms
> 62/95 Test #64: test_test_gff_io ................................................... Passed 0.00 sec
> Start 66: test_test_graph_align
> 63/95 Test #65: test_test_graph_algorithms ......................................... Passed 0.01 sec
> Start 67: test_test_graph_msa
> 64/95 Test #66: test_test_graph_align .............................................. Passed 0.00 sec
> Start 68: test_test_graph_types
> 65/95 Test #61: test_test_consensus ................................................ Passed 0.01 sec
> Start 69: test_test_index_creation
> 66/95 Test #68: test_test_graph_types .............................................. Passed 0.00 sec
> Start 70: test_test_index_crosscompare_char
> 67/95 Test #70: test_test_index_crosscompare_char .................................. Passed 0.08 sec
> Start 71: test_test_index_crosscompare_char_dfi
> 68/95 Test #71: test_test_index_crosscompare_char_dfi .............................. Passed 0.02 sec
> Start 72: test_test_index_crosscompare_dna
> 69/95 Test #72: test_test_index_crosscompare_dna ................................... Passed 0.01 sec
> Start 73: test_test_index_crosscompare_dna_dfi
> 70/95 Test #73: test_test_index_crosscompare_dna_dfi ............................... Passed 0.00 sec
> Start 74: test_test_index_qgram
> 71/95 Test #74: test_test_index_qgram .............................................. Passed 0.00 sec
> Start 75: test_test_index_sa_bwtwalk
> 72/95 Test #67: test_test_graph_msa ................................................ Passed 0.23 sec
> Start 76: test_test_index_shapes
> 73/95 Test #76: test_test_index_shapes ............................................. Passed 0.00 sec
> Start 77: test_test_index_drawing
> 74/95 Test #77: test_test_index_drawing ............................................ Passed 0.00 sec
> Start 78: test_test_index_fm
> 75/95 Test #63: test_test_find ..................................................... Passed 0.39 sec
> Start 79: test_test_index_stree_iterators
> 76/95 Test #75: test_test_index_sa_bwtwalk ......................................... Passed 0.27 sec
> Start 80: test_test_index_repeats
> 77/95 Test #80: test_test_index_repeats ............................................ Passed 0.21 sec
> Start 81: test_test_map
> 78/95 Test #79: test_test_index_stree_iterators ....................................***Exception: SegFault 0.61 sec
> TEST SUITE test_index
> SEQAN_ENABLE_DEBUG == 1
> SEQAN_ENABLE_TESTING == 1
> SEQAN_ENABLE_CHECKPOINTS == 0
> SEQAN_CXX_FLAGS == "SEQAN_CXX_FLAGS_NOT_SET"
> testEmptyIndex OK
> testIssue509 OK
> testIssue509b OK
> parentEdgeLabel:
> a parentEdgeLabel: a
> aa parentEdgeLabel: a
> aaacatatz parentEdgeLabel: acatatz
> aacatatz parentEdgeLabel: catatz
> aca parentEdgeLabel: ca
> acaaacatatz parentEdgeLabel: aacatatz
> acatatz parentEdgeLabel: tatz
> at parentEdgeLabel: t
> atatz parentEdgeLabel: atz
> atz parentEdgeLabel: z
> ca parentEdgeLabel: ca
> caaacatatz parentEdgeLabel: aacatatz
> catatz parentEdgeLabel: tatz
> t parentEdgeLabel: t
> tatz parentEdgeLabel: atz
> tz parentEdgeLabel: z
> z parentEdgeLabel: z
>
> Dir (wotd)
> 0: 0 (LastChild/SENTINELS)
> 1: 2
> 2: 0
> 3: 9
> 4: 6
> 5: 21
> 6: 8
> 7: 23
> 8: 10 (Leaf/Uneval) (LastChild/SENTINELS)
> 9: 1
> 10: 15
> 11: 2
> 12: 17
> 13: 4 (LastChild/SENTINELS)
> 14: 19
> 15: 2 (Leaf/Uneval)
> 16: 1 (Leaf/Uneval) (LastChild/SENTINELS)
> 17: 3 (Leaf/Uneval)
> 18: 3 (Leaf/Uneval) (LastChild/SENTINELS)
> 19: 2 (Leaf/Uneval)
> 20: 5 (Leaf/Uneval) (LastChild/SENTINELS)
> 21: 2 (Leaf/Uneval)
> 22: 7 (Leaf/Uneval) (LastChild/SENTINELS)
> 23: 1 (Leaf/Uneval)
> 24: 9 (Leaf/Uneval) (LastChild/SENTINELS)
>
> SA
> 0: 2 aaacatatz
> 1: 3 aacatatz
> 2: 0 acaaacatatz
> 3: 4 acatatz
> 4: 6 atatz
> 5: 8 atz
> 6: 1 caaacatatz
> 7: 5 catatz
> 8: 7 tatz
> 9: 9 tz
> 10: 10 z
>
> testSTreeIterators_Wotd OK
> parentEdgeLabel:
> a parentEdgeLabel: a
> aca parentEdgeLabel: ca
> acaaacatatz parentEdgeLabel: aacatatz
> acatatz parentEdgeLabel: tatz
> aa parentEdgeLabel: a
> aaacatatz parentEdgeLabel: acatatz
> aacatatz parentEdgeLabel: catatz
> at parentEdgeLabel: t
> atatz parentEdgeLabel: atz
> atz parentEdgeLabel: z
> ca parentEdgeLabel: ca
> caaacatatz parentEdgeLabel: aacatatz
> catatz parentEdgeLabel: tatz
> t parentEdgeLabel: t
> tatz parentEdgeLabel: atz
> tz parentEdgeLabel: z
> z parentEdgeLabel: z
>
> Dir (wotd)
> 0: 0 (LastChild/SENTINELS)
> 1: 2
> 2: 0
> 3: 9
> 4: 1
> 5: 21
> 6: 7
> 7: 23
> 8: 10 (Leaf/Uneval) (LastChild/SENTINELS)
> 9: 1
> 10: 15
> 11: 3
> 12: 17
> 13: 7 (LastChild/SENTINELS)
> 14: 19
> 15: 3 (Leaf/Uneval)
> 16: 7 (Leaf/Uneval) (LastChild/SENTINELS)
> 17: 4 (Leaf/Uneval)
> 18: 5 (Leaf/Uneval) (LastChild/SENTINELS)
> 19: 8 (Leaf/Uneval)
> 20: 10 (Leaf/Uneval) (LastChild/SENTINELS)
> 21: 3 (Leaf/Uneval)
> 22: 7 (Leaf/Uneval) (LastChild/SENTINELS)
> 23: 8 (Leaf/Uneval)
> 24: 10 (Leaf/Uneval) (LastChild/SENTINELS)
>
> SA
> 0: 4 acatatz
> 1: 5 catatz
> 2: 3 aacatatz
> 3: 7 tatz
> 4: 8 atz
> 5: 10 z
> 6: 3 aacatatz
> 7: 7 tatz
> 8: 8 atz
> 9: 10 z
> 10: 10 z
>
> testSTreeIterators_WotdOriginal OK
> parentEdgeLabel:
> a parentEdgeLabel: a
> aa parentEdgeLabel: a
> aaacatatz parentEdgeLabel: acatatz
> aacatatz parentEdgeLabel: catatz
> aca parentEdgeLabel: ca
> acaaacatatz parentEdgeLabel: aacatatz
> acatatz parentEdgeLabel: tatz
> at parentEdgeLabel: t
> atatz parentEdgeLabel: atz
> atz parentEdgeLabel: z
> ca parentEdgeLabel: ca
> caaacatatz parentEdgeLabel: aacatatz
> catatz parentEdgeLabel: tatz
> t parentEdgeLabel: t
> tatz parentEdgeLabel: atz
> tz parentEdgeLabel: z
> z parentEdgeLabel: z
>
> SA
> 0: 2 aaacatatz
> 1: 3 aacatatz
> 2: 0 acaaacatatz
> 3: 4 acatatz
> 4: 6 atatz
> 5: 8 atz
> 6: 1 caaacatatz
> 7: 5 catatz
> 8: 7 tatz
> 9: 9 tz
> 10: 10 z
>
> LCP
> 0: 2
> 1: 1
> 2: 3
> 3: 1
> 4: 2
> 5: 0
> 6: 2
> 7: 0
> 8: 1
> 9: 0
> 10: 0
>
> Childtab
> 0: 6
> 1: 1
> 2: 4
> 3: 3
> 4: 5
> 5: 2
> 6: 8
> 7: 7
> 8: 10
> 9: 9
> 10: 11
>
> testSTreeIterators_Esa OK
> testFind_Esa_Mlr OK
> testCompareIndices_Esa_Wotd OK
> BottomUp without empty edges
> 1 AC
> 2 AC
> 1 C
> 2 C
>
> BottomUp with empty edges
> 1 AC
> 1 AC
> 2 AC
> 1 C
> 1 C
> 2 C
>
> TopDown postorder without empty edges
> 2 AC
> 2 C
> 4
>
> TopDown postorder with empty edges
> 1 AC
> 1 AC
> 2 AC
> 1 C
> 1 C
> 2 C
> 4
>
> TopDown preorder without empty edges
> 2 C
>
> TopDown preorder with empty edges
> 4
> 2 AC
> 1 AC
> 1 AC
> 2 C
> 1 C
> 1 C
>
> TopDown with empty edges
> 4
> 2 AC
>
> TopDown with empty edges
> 4
> 2 AC
> 1 AC
> testMultiIndex OK
>
>
> stack trace:
> 0 [0x55fc80c8cda9] /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/test_index_stree_iterators(+0x48da9)
> 1 [0x7f00d04bafe0] /lib/x86_64-linux-gnu/libc.so.6(+0x39fe0)
> 2 [0x55fc80d27f2e] seqan::_skew7ExtendComp<seqan::Triple<unsigned long, seqan::Tuple<unsigned long, 3u, void>, seqan::Tuple<unsigned long, 5u, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 2u, int>::operator()(seqan::Triple<unsigned long, seqan::Tuple<unsigned long, 3u, void>, seqan::Tuple<unsigned long, 5u, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> > const&, seqan::Triple<unsigned long, seqan::Tuple<unsigned long, 3u, void>, seqan::Tuple<unsigned long, 5u, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> > const&) const + 0x2e
> 3 [0x55fc80d286b7] void std::__insertion_sort<seqan::Triple<unsigned long, seqan::Tuple<unsigned long, 3u, void>, seqan::Tuple<unsigned long, 5u, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >*, __gnu_cxx::__ops::_Iter_comp_iter<seqan::AdaptorCompare2Less<seqan::_skew7ExtendComp<seqan::Triple<unsigned long, seqan::Tuple<unsigned long, 3u, void>, seqan::Tuple<unsigned long, 5u, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 2u, int> > > >(seqan::Triple<unsigned long, seqan::Tuple<unsigned long, 3u, void>, seqan::Tuple<unsigned long, 5u, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >*, seqan::Triple<unsigned long, seqan::Tuple<unsigned long, 3u, void>, seqan::Tuple<unsigned long, 5u, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >*, __gnu_cxx::__ops::_Iter_comp_iter<seqan::AdaptorCompare2Less<seqan::_skew7ExtendComp<seqan::Triple<unsigned long, seqan::Tuple<unsigned long, 3u, void>, seqan::Tuple<unsigned long, 5u, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 2u, int> > >) + 0x67
> 4 [0x55fc80d2d7b5] /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/test_index_stree_iterators(+0xe97b5)
> 5 [0x55fc80d4fd0b] bool seqan::Pipe<seqan::Pipe<seqan::Pool<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, unsigned long>, unsigned long, seqan::File<seqan::Async<void> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, unsigned long> > >, seqan::Skew7>::process<seqan::Pipe<seqan::Pool<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, unsigned long>, unsigned long, seqan::File<seqan::Async<void> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, unsigned long> > > >(seqan::Pipe<seqan::Pool<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, unsigned long>, unsigned long, seqan::File<seqan::Async<void> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, unsigned long> > >&) + 0x72b
> 6 [0x55fc80d52823] seqan::Pipe<seqan::Pipe<seqan::Pool<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, unsigned long>, unsigned long, seqan::File<seqan::Async<void> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, unsigned long> > >, seqan::Skew7>::Pipe(seqan::Pipe<seqan::Pool<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, unsigned long>, unsigned long, seqan::File<seqan::Async<void> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, unsigned long> > >&) + 0x6a3
> 7 [0x55fc80d66bf9] bool seqan::Pipe<seqan::Pipe<seqan::Pipe<seqan::String<char, seqan::Alloc<void> >, seqan::Source<void> >, seqan::Caster<unsigned char, seqan::CasterReinterpret> >, seqan::Multi<seqan::Skew7, seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, seqan::String<unsigned long, seqan::Alloc<void> > > >::process<seqan::Pipe<seqan::Pipe<seqan::String<char, seqan::Alloc<void> >, seqan::Source<void> >, seqan::Caster<unsigned char, seqan::CasterReinterpret> > >(seqan::Pipe<seqan::Pipe<seqan::String<char, seqan::Alloc<void> >, seqan::Source<void> >, seqan::Caster<unsigned char, seqan::CasterReinterpret> >&) + 0xb79
> 8 [0x55fc80d67609] seqan::Pipe<seqan::Pipe<seqan::Pipe<seqan::String<char, seqan::Alloc<void> >, seqan::Source<void> >, seqan::Caster<unsigned char, seqan::CasterReinterpret> >, seqan::Multi<seqan::Skew7, seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, seqan::String<unsigned long, seqan::Alloc<void> > > >::Pipe<seqan::String<unsigned long, seqan::Alloc<void> > >(seqan::Pipe<seqan::Pipe<seqan::String<char, seqan::Alloc<void> >, seqan::Source<void> >, seqan::Caster<unsigned char, seqan::CasterReinterpret> >&, seqan::String<unsigned long, seqan::Alloc<void> > const&, seqan::EnableIf<seqan::IsSameType<seqan::String<unsigned long, seqan::Alloc<void> >, seqan::String<unsigned long, seqan::Alloc<void> > >, void>::Type*) + 0x609
> 9 [0x55fc80c95960] /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/test_index_stree_iterators(+0x51960)
> 10 [0x55fc80d676c0] void seqan::_indexRequireBottomUpIteration<seqan::StringSet<seqan::String<char, seqan::Alloc<void> >, seqan::Owner<seqan::ConcatDirect<void> > >, void>(seqan::Index<seqan::StringSet<seqan::String<char, seqan::Alloc<void> >, seqan::Owner<seqan::ConcatDirect<void> > >, seqan::IndexEsa<void> >&) + 0x70
> 11 [0x55fc80d67a7f] void seqan::SEQAN_TEST_testMUMs<true>() + 0x2ff
> 12 [0x55fc80c89a6a] main + 0x1da
> 13 [0x7f00d04a7bbb] __libc_start_main + 0xeb
> 14 [0x55fc80c89c8a] _start + 0x2a
>
>
> Start 82: test_test_misc
> 79/95 Test #82: test_test_misc ..................................................... Passed 0.01 sec
> Start 83: test_test_misc_cmdparser
> 80/95 Test #83: test_test_misc_cmdparser ........................................... Passed 0.00 sec
> Start 84: test_test_modifier
> 81/95 Test #84: test_test_modifier ................................................. Passed 0.00 sec
> Start 85: test_test_parallel
> 82/95 Test #85: test_test_parallel ................................................. Passed 0.02 sec
> Start 86: test_test_pipe
> 83/95 Test #81: test_test_map ...................................................... Passed 0.51 sec
> Start 87: test_test_random
> 84/95 Test #87: test_test_random ................................................... Passed 0.02 sec
> Start 88: test_test_score
> 85/95 Test #88: test_test_score .................................................... Passed 0.01 sec
> Start 89: test_test_seeds
> 86/95 Test #89: test_test_seeds .................................................... Passed 0.04 sec
> Start 90: test_test_seq_io
> 87/95 Test #90: test_test_seq_io ................................................... Passed 0.02 sec
> Start 91: test_test_sequence
> 88/95 Test #91: test_test_sequence ................................................. Passed 0.01 sec
> Start 92: test_test_sequence_journaled
> 89/95 Test #92: test_test_sequence_journaled ....................................... Passed 0.03 sec
> Start 93: test_test_store
> 90/95 Test #93: test_test_store .................................................... Passed 0.33 sec
> Start 94: test_test_stream
> 91/95 Test #86: test_test_pipe ..................................................... Passed 0.64 sec
> Start 95: test_test_find_swift
> 92/95 Test #95: test_test_find_swift ............................................... Passed 0.00 sec
> 93/95 Test #94: test_test_stream ................................................... Passed 5.13 sec
> 94/95 Test #69: test_test_index_creation ........................................... Passed 8.57 sec
> 95/95 Test #78: test_test_index_fm .................................................***Exception: SegFault 10.70 sec
> TEST SUITE test_fm_index_beta
> SEQAN_ENABLE_DEBUG == 1
> SEQAN_ENABLE_TESTING == 1
> SEQAN_ENABLE_CHECKPOINTS == 0
> SEQAN_CXX_FLAGS == "SEQAN_CXX_FLAGS_NOT_SET"
> test_rsbs_defaultConstructor OK
> test_rsbs_resize OK
> test_rsbs_getBuPos OK
> test_rsbs_getSBuPos OK
> test_rsbs_getPosInBu OK
> test_rsbs_isBitSet OK
> test_rsbs_append_value OK
> test_rsbs_rank OK
> test_rsbs_update_ranks_ OK
> test_rsbs_constructor OK
> test_rsbs_equalOperator OK
> test_rsbs_assignOperator OK
> test_rsbs_open_save OK
> test_rsbs_iterator_get_value OK
> prefix_sum_table_constructor OK
> prefix_sum_table_get_alphabet_size OK
> prefix_sum_table_get_character_position OK
> prefix_sum_table_get_character OK
> prefix_sum_table_determine_sentinel_substitute OK
> prefix_sum_table_get_pivot_position OK
> prefix_sum_table_prefix_sum OK
> prefix_sum_table_get_value OK
> prefix_sum_table_length OK
> prefix_sum_table_insert_sentinel_ OK
> prefix_sum_table_resize OK
> prefix_sum_table_set_prefix_sum OK
> prefix_sum_table_value OK
> prefix_sum_table_open_save OK
> wavelet_tree_structure_constructor OK
> wavelet_tree_structure_clear OK
> wavelet_tree_structure_empty OK
> wavelet_tree_structure_get_fibre OK
> wavelet_tree_structure_length OK
> wavelet_tree_structure_resize OK
> wavelet_tree_structure_open_save OK
> wavelet_tree_structure_iterator_begin OK
> wavelet_tree_structure_iterator_container OK
> wavelet_tree_structure_iterator_end OK
> wavelet_tree_structure_iterator_get_character OK
> wavelet_tree_structure_iterator_get_child_pos OK
> wavelet_tree_structure_iterator_get_num_child_vertices OK
> wavelet_tree_structure_iterator_get_position OK
> wavelet_tree_structure_iterator_go_child OK
> wavelet_tree_structure_iterator_go_down OK
> wavelet_tree_structure_iterator_go_right OK
> wavelet_tree_structure_iterator_go_to_position OK
> wavelet_tree_structure_iterator_go_up OK
> wavelet_tree_structure_iterator_is_leaf OK
> wavelet_tree_structure_iterator_is_root OK
> wavelet_tree_structure_iterator_set_and_go_right OK
> wavelet_tree_structure_iterator_set_character OK
> wavelet_tree_structure_iterator_set_child_vertices_ OK
> wavelet_tree_structure_iterator_set_left_child_pos_ OK
> wavelet_tree_structure_iterator_set_position_ OK
> wavelet_tree_structure_iterator_set_right_child_pos_ OK
> sparse_string_get_value OK
> sparse_string_clear_length_resize OK
> sparse_string_empty OK
> sparse_string_get_fibre OK
> compressed_sa_clear_length_resize OK
> compressed_sa_empty OK
> compressed_sa_create_compressed_sa OK
> compressed_sa_get_fibre OK
> compressed_sa_get_next_pos_ OK
> compressed_sa_set_lf_table OK
> compressed_sa_value_access OK
> compressed_sa_open_save OK
> compressed_sa_iterator_begin OK
> compressed_sa_iterator_end OK
> test_lf_table_lf_mapping OK
> test_fm_index_constructor OK
> test_fm_index_clear OK
> test_fm_index_determine_sentinel_substitute_ OK
> test_fm_index_empty OK
> test_fm_index_find_first_index_ OK
> test_fm_index_get_fibre OK
>
>
> stack trace:
> 0 [0x55eb2e19af09] /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/test_index_fm(+0xc5f09)
> 1 [0x7fadd258dfe0] /lib/x86_64-linux-gnu/libc.so.6(+0x39fe0)
> 2 [0x55eb2e32901e] seqan::_skew7ExtendComp<seqan::Triple<unsigned long, seqan::Tuple<unsigned long, 3u, void>, seqan::Tuple<unsigned long, 5u, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 2u, int>::operator()(seqan::Triple<unsigned long, seqan::Tuple<unsigned long, 3u, void>, seqan::Tuple<unsigned long, 5u, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> > const&, seqan::Triple<unsigned long, seqan::Tuple<unsigned long, 3u, void>, seqan::Tuple<unsigned long, 5u, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> > const&) const + 0x2e
> 3 [0x55eb2e329c95] void std::__introsort_loop<seqan::Triple<unsigned long, seqan::Tuple<unsigned long, 3u, void>, seqan::Tuple<unsigned long, 5u, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >*, long, __gnu_cxx::__ops::_Iter_comp_iter<seqan::AdaptorCompare2Less<seqan::_skew7ExtendComp<seqan::Triple<unsigned long, seqan::Tuple<unsigned long, 3u, void>, seqan::Tuple<unsigned long, 5u, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 2u, int> > > >(seqan::Triple<unsigned long, seqan::Tuple<unsigned long, 3u, void>, seqan::Tuple<unsigned long, 5u, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >*, seqan::Triple<unsigned long, seqan::Tuple<unsigned long, 3u, void>, seqan::Tuple<unsigned long, 5u, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >*, long, __gnu_cxx::__ops::_Iter_comp_iter<seqan::AdaptorCompare2Less<seqan::_skew7ExtendComp<seqan::Triple<unsigned long, seqan::Tuple<unsigned long, 3u, void>, seqan::Tuple<unsigned long, 5u, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 2u, int> > >) + 0x65
> 4 [0x55eb2e32d6fe] /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/test_index_fm(+0x2586fe)
> 5 [0x55eb2e3874a7] bool seqan::Pipe<seqan::Pipe<seqan::Pool<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, unsigned long>, unsigned long, seqan::File<seqan::Async<void> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, unsigned long> > >, seqan::Skew7>::process<seqan::Pipe<seqan::Pool<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, unsigned long>, unsigned long, seqan::File<seqan::Async<void> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, unsigned long> > > >(seqan::Pipe<seqan::Pool<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, unsigned long>, unsigned long, seqan::File<seqan::Async<void> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, unsigned long> > >&) + 0x4f7
> 6 [0x55eb2e388673] seqan::Pipe<seqan::Pipe<seqan::Pool<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, unsigned long>, unsigned long, seqan::File<seqan::Async<void> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, unsigned long> > >, seqan::Skew7>::Pipe(seqan::Pipe<seqan::Pool<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, unsigned long>, unsigned long, seqan::File<seqan::Async<void> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, unsigned long> > >&) + 0x6a3
> 7 [0x55eb2e389259] bool seqan::Pipe<seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> > > >, seqan::Source<void> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::CasterReinterpret> >, seqan::Multi<seqan::Skew7, seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, seqan::String<unsigned long, seqan::Alloc<void> > > >::process<seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> > > >, seqan::Source<void> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::CasterReinterpret> > >(seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> > > >, seqan::Source<void> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::CasterReinterpret> >&) + 0xb99
> 8 [0x55eb2e389e1f] seqan::Pipe<seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> > > >, seqan::Source<void> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::CasterReinterpret> >, seqan::Multi<seqan::Skew7, seqan::Pair<unsigned long, unsigned long, seqan::Tag<seqan::Pack_> >, seqan::String<unsigned long, seqan::Alloc<void> > > >::Pipe<seqan::String<unsigned long, seqan::Alloc<void> > >(seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> > > >, seqan::Source<void> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::CasterReinterpret> >&, seqan::String<unsigned long, seqan::Alloc<void> > const&, seqan::EnableIf<seqan::IsSameType<seqan::String<unsigned long, seqan::Alloc<void> >, seqan::String<unsigned long, seqan::Alloc<void> > >, void>::Type*) + 0x5cf
> 9 [0x55eb2e1a6e44] /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/test_index_fm(+0xd1e44)
> 10 [0x55eb2e393917] void fmIndexSearch<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> > >, seqan::WT<void>, void>(seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> > >, seqan::FMIndex<seqan::WT<void>, void> >) + 0x27b7
> 11 [0x55eb2e3b7c22] void SEQAN_TEST_test_fm_index_search<true>() + 0x482
> 12 [0x55eb2e1915d1] main + 0xfd1
> 13 [0x7fadd257abbb] __libc_start_main + 0xeb
> 14 [0x55eb2e191d6a] _start + 0x2a
>
>
>
> 98% tests passed, 2 tests failed out of 95
>
> Total Test time (real) = 11.33 sec
>
> The following tests FAILED:
> 78 - test_test_index_fm (SEGFAULT)
> 79 - test_test_index_stree_iterators (SEGFAULT)
> Errors while running CTest
> make[2]: *** [Makefile:87: test] Error 8
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> dh_auto_test: error: cd obj-x86_64-linux-gnu && make -j4 test ARGS\+=-j4 returned exit code 2
The full build log is available from:
http://qa-logs.debian.net/2020/02/22/seqan_1.4.2+dfsg-3_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.
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