[Debian-med-packaging] Bug#980685: 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
Wed Jan 20 20:47:31 GMT 2021
Source: seqan
Version: 1.4.2+dfsg-4
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20210120 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
> 1/93 Test #1: test_demo_align_align .............................................. Passed 0.05 sec
> Start 5: test_demo_align_global_alignment_unbanded
> 2/93 Test #2: test_demo_align_compute_alignment_stats ............................ Passed 0.05 sec
> Start 6: test_demo_align_integrate_align
> 3/93 Test #4: test_demo_align_global_alignment_banded ............................ Passed 0.05 sec
> Start 7: test_demo_bam_io_bam_stream
> 4/93 Test #3: test_demo_align_gaps_example ....................................... Passed 0.05 sec
> Start 8: test_demo_find_finder_index
> 5/93 Test #5: test_demo_align_global_alignment_unbanded .......................... Passed 0.05 sec
> Start 9: test_demo_find_finder_online
> 6/93 Test #6: test_demo_align_integrate_align .................................... Passed 0.05 sec
> Start 10: test_demo_graph_graph_algo_dijkstra
> 7/93 Test #7: test_demo_bam_io_bam_stream ........................................***Failed 0.05 sec
> Loading files "/<<PKGBUILDDIR>>/core/demos/bam_io/bam_stream.cpp.stdout", "None".
> Running /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/demo_bam_io_bam_stream.
> ERROR: Return code of /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/demo_bam_io_bam_stream was 1.
>
> Start 11: test_demo_graph_algorithms_all_pairs_shortest_path
> 8/93 Test #8: test_demo_find_finder_index ........................................ Passed 0.05 sec
> Start 12: test_demo_graph_algorithms_bellman_ford_algorithm
> 9/93 Test #9: test_demo_find_finder_online ....................................... Passed 0.05 sec
> Start 13: test_demo_graph_algorithms_breadth_first_search
> 10/93 Test #10: test_demo_graph_graph_algo_dijkstra ................................ Passed 0.05 sec
> Start 14: test_demo_graph_algorithms_dag_shortest_path
> 11/93 Test #11: test_demo_graph_algorithms_all_pairs_shortest_path ................. Passed 0.05 sec
> Start 15: test_demo_graph_algorithms_depth_first_search
> 12/93 Test #12: test_demo_graph_algorithms_bellman_ford_algorithm .................. Passed 0.05 sec
> Start 16: test_demo_graph_algorithms_dijkstra
> 13/93 Test #13: test_demo_graph_algorithms_breadth_first_search .................... Passed 0.05 sec
> Start 17: test_demo_graph_algorithms_floyd_warshall_algorithm
> 14/93 Test #14: test_demo_graph_algorithms_dag_shortest_path ....................... Passed 0.05 sec
> Start 18: test_demo_graph_algorithms_ford_fulkerson_algorithm
> 15/93 Test #15: test_demo_graph_algorithms_depth_first_search ...................... Passed 0.05 sec
> Start 19: test_demo_graph_algorithms_kruskals_algorithm
> 16/93 Test #16: test_demo_graph_algorithms_dijkstra ................................ Passed 0.05 sec
> Start 20: test_demo_graph_algorithms_prims_algorithm
> 17/93 Test #17: test_demo_graph_algorithms_floyd_warshall_algorithm ................ Passed 0.05 sec
> Start 21: test_demo_graph_algorithms_strongly_connected_components
> 18/93 Test #18: test_demo_graph_algorithms_ford_fulkerson_algorithm ................ Passed 0.05 sec
> Start 22: test_demo_graph_algorithms_topological_sort
> 19/93 Test #19: test_demo_graph_algorithms_kruskals_algorithm ...................... Passed 0.05 sec
> Start 23: test_demo_graph_algorithms_transitive_closure
> 20/93 Test #20: test_demo_graph_algorithms_prims_algorithm ......................... Passed 0.05 sec
> Start 24: test_demo_index_index_begin_atEnd_representative
> 21/93 Test #21: test_demo_graph_algorithms_strongly_connected_components ........... Passed 0.05 sec
> Start 25: test_demo_index_index_counting
> 22/93 Test #22: test_demo_graph_algorithms_topological_sort ........................ Passed 0.05 sec
> Start 26: test_demo_index_index_finder
> 23/93 Test #23: test_demo_graph_algorithms_transitive_closure ...................... Passed 0.05 sec
> Start 27: test_demo_index_index_getOccurrences_getFrequency_range_getFibre
> 24/93 Test #24: test_demo_index_index_begin_atEnd_representative ................... Passed 0.05 sec
> Start 28: test_demo_index_index_iterator
> 25/93 Test #25: test_demo_index_index_counting ..................................... Passed 0.05 sec
> Start 29: test_demo_index_index_iterator_short
> 26/93 Test #26: test_demo_index_index_finder ....................................... Passed 0.05 sec
> Start 30: test_demo_index_index_length_countSequences
> 27/93 Test #27: test_demo_index_index_getOccurrences_getFrequency_range_getFibre ... Passed 0.05 sec
> Start 31: test_demo_index_index_mummy
> 28/93 Test #28: test_demo_index_index_iterator ..................................... Passed 0.05 sec
> Start 32: test_demo_index_index_open_save
> 29/93 Test #29: test_demo_index_index_iterator_short ............................... Passed 0.05 sec
> Start 33: test_demo_index_index_textAt_indexText_saAt_indexRequire
> 30/93 Test #30: test_demo_index_index_length_countSequences ........................ Passed 0.05 sec
> Start 34: test_demo_input_output_record_reader
> 31/93 Test #31: test_demo_index_index_mummy ........................................ Passed 0.05 sec
> Start 35: test_demo_misc_enumerate_strings
> 32/93 Test #32: test_demo_index_index_open_save .................................... Passed 0.05 sec
> Start 36: test_demo_modifier_modified_string
> 33/93 Test #33: test_demo_index_index_textAt_indexText_saAt_indexRequire ........... Passed 0.05 sec
> Start 37: test_demo_modifier_modified_string_mod_view
> 34/93 Test #34: test_demo_input_output_record_reader ............................... Passed 0.05 sec
> Start 38: test_demo_modifier_modified_string_nested
> 35/93 Test #35: test_demo_misc_enumerate_strings ................................... Passed 0.05 sec
> Start 39: test_demo_score_score
> 36/93 Test #36: test_demo_modifier_modified_string ................................. Passed 0.05 sec
> Start 40: test_demo_seeds_seeds_extension
> 37/93 Test #37: test_demo_modifier_modified_string_mod_view ........................ Passed 0.05 sec
> Start 41: test_demo_seq_io_fai_index_example
> 38/93 Test #38: test_demo_modifier_modified_string_nested .......................... Passed 0.05 sec
> Start 42: test_demo_seq_io_sequence_stream_read
> 39/93 Test #39: test_demo_score_score .............................................. Passed 0.05 sec
> Start 43: test_demo_sequence_string2
> 40/93 Test #40: test_demo_seeds_seeds_extension .................................... Passed 0.05 sec
> Start 44: test_demo_sequence_stringset
> 41/93 Test #42: test_demo_seq_io_sequence_stream_read ..............................***Failed 0.05 sec
> Loading files "/<<PKGBUILDDIR>>/core/demos/seq_io/sequence_stream_read.cpp.stdout", "None".
> Running /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/demo_seq_io_sequence_stream_read.
> ERROR: Return code of /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/demo_seq_io_sequence_stream_read was 1.
>
> Start 45: test_test_align
> 42/93 Test #41: test_demo_seq_io_fai_index_example .................................***Failed 0.05 sec
> Loading files "/<<PKGBUILDDIR>>/core/demos/seq_io/fai_index_example.cpp.stdout", "None".
> Running /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/demo_seq_io_fai_index_example.
> ERROR: Return code of /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/demo_seq_io_fai_index_example was 1.
>
> Start 46: test_test_arg_parse
> 43/93 Test #43: test_demo_sequence_string2 ......................................... Passed 0.05 sec
> Start 47: test_test_bam_io
> 44/93 Test #44: test_demo_sequence_stringset ....................................... Passed 0.05 sec
> Start 48: test_test_basic_exception
> 45/93 Test #46: test_test_arg_parse ................................................***Failed 0.00 sec
> TEST SUITE test_arg_parse
> SEQAN_ENABLE_DEBUG == 1
> SEQAN_ENABLE_TESTING == 1
> SEQAN_ENABLE_CHECKPOINTS == 0
> SEQAN_CXX_FLAGS == "SEQAN_CXX_FLAGS_NOT_SET"
> test_unset_value OK
> test_unset_values OK
> test_int_short_argument OK
> test_int_long_argument OK
> test_non_int_argument OK
> test_int64_short_argument OK
> test_int64_long_argument OK
> test_non_int64_argument OK
> test_double_short_argument OK
> test_double_long_argument OK
> test_non_double_argument OK
> test_double_scientific_notation OK
> test_string_short_argument OK
> test_string_long_argument OK
> test_string_missing_argument OK
> test_string_list OK
> test_min_max_double_values_in_range OK
> test_min_max_double_values_to_small OK
> test_min_max_double_values_to_big OK
> test_min_max_int_values_in_range OK
> test_min_max_int_values_to_small OK
> test_min_max_int_values_to_big OK
> test_allowed_values_contained OK
> test_allowed_values_not_contained OK
> test_input_file_short OK
> test_input_file_long OK
> test_input_file_missing OK
> test_input_file_invalid_type OK
> test_input_file_valid_type OK
> test_input_file_extension OK
> test_input_file_auto_file_ext_option OK
> test_output_file_short OK
> test_output_file_long OK
> test_output_file_missing OK
> test_output_file_invalid_type OK
> test_output_file_valid_type OK
> test_output_file_extension OK
> test_output_file_extension_targz OK
> test_output_file_explicit_extension_valid OK
> test_output_file_explicit_extension_invalid OK
> test_argument_string OK
> test_argument_not_all_set OK
> test_argument_double OK
> test_argument_not_a_double OK
> test_argument_auto_file_ext_option OK
> test_int_list_option OK
> test_double_list_option OK
> test_double_list_option_not_enough_arguments OK
> test_boolean_flags OK
> test_combined_boolean_flags OK
> test_long_short_flag_name OK
> test_argument_string_label OK
> test_argument_int_label OK
> test_argument_double_label OK
> test_argument_inputfile_label OK
> test_argument_outputfile_label OK
> test_argument_user_defined_label OK
> test_argument_invalid_cast OK
> test_argument_min_max_boundaries OK
> test_argument_valid_values OK
> test_argument_parser OK
> test_default_value OK
> test_isDouble OK
> test_isInt OK
> Couldn't open file "./core/tests/arg_parse/test_app.ctd"
> ./core/tests/arg_parse/test_arg_parse_ctd_support.h:98 Assertion failed : seqan::_compareTextFilesAlt(toCString(outPath), toCString(goldPath)) should be true but was 0
>
> stack trace:
> 0 [0x55b965f78ee5] seqan::ClassTest::fail() + 0x15
> 1 [0x55b965fa9328] void SEQAN_TEST_test_arg_parse_ctd_support<true>() + 0x1408
> 2 [0x55b965f72904] main + 0x5a4
> 3 [0x7fc049257d0a] __libc_start_main + 0xea
> 4 [0x55b965f72c9a] _start + 0x2a
>
> test_arg_parse_ctd_support FAILED
> **************************************
> Total Check Points : 0
> Found Check Points : 0
> Lost Check Points : 0
> --------------------------------------
> Total Tests: 65
> Skipped: 0
> Errors: 1
> **************************************
>
> Start 49: test_test_basic_metaprogramming
> 46/93 Test #47: test_test_bam_io ...................................................***Failed 0.01 sec
> TEST SUITE test_bam_io
> SEQAN_ENABLE_DEBUG == 1
> SEQAN_ENABLE_TESTING == 1
> SEQAN_ENABLE_CHECKPOINTS == 0
> SEQAN_CXX_FLAGS == "SEQAN_CXX_FLAGS_NOT_SET"
> test_bam_io_bam_alignment_record_class OK
> test_bam_io_bam_alignment_record_has_flag_multiple OK
> test_bam_io_bam_alignment_record_has_flag_unmapped OK
> test_bam_io_bam_alignment_record_has_flag_next_unmapped OK
> test_bam_io_bam_alignment_record_has_flag_rc OK
> test_bam_io_bam_alignment_record_has_flag_next_rc OK
> test_bam_io_bam_alignment_record_has_flag_first OK
> test_bam_io_bam_alignment_record_has_flag_last OK
> test_bam_io_bam_alignment_record_has_flag_secondary OK
> test_bam_io_bam_alignment_record_has_flag_qc_no_pass OK
> test_bam_io_bam_alignment_record_has_flag_duplicate OK
> test_bam_io_bam_alignment_record_has_flag_supplementary OK
> test_bam_io_bam_header_class OK
> test_bam_io_bam_header_typedefs OK
> test_bam_io_bam_header_record_class OK
> test_bam_io_bam_header_record_typedefs OK
> test_bam_io_bam_header_record_find_tag_key OK
> test_bam_io_bam_header_record_get_tag_value OK
> test_bam_io_bam_io_context_standalone OK
> test_bam_io_bam_io_context_fragment_store OK
> test_assign_tags_bam_to_sam_two_tags OK
> test_assign_tags_bam_to_sam_type_A OK
> test_assign_tags_bam_to_sam_type_c OK
> test_assign_tags_bam_to_sam_type_C OK
> test_assign_tags_bam_to_sam_type_s OK
> test_assign_tags_bam_to_sam_type_S OK
> test_assign_tags_bam_to_sam_type_i OK
> test_assign_tags_bam_to_sam_type_I OK
> test_assign_tags_bam_to_sam_type_f OK
> test_assign_tags_bam_to_sam_type_Z OK
> test_assign_tags_bam_to_sam_type_H OK
> test_assign_tags_bam_to_sam_type_Bc OK
> test_assign_tags_bam_to_sam_type_BC OK
> test_assign_tags_bam_to_sam_type_Bs OK
> test_assign_tags_bam_to_sam_type_BS OK
> test_assign_tags_bam_to_sam_type_Bi OK
> test_assign_tags_bam_to_sam_type_BI OK
> test_assign_tags_bam_to_sam_type_Bf OK
> test_assign_tags_sam_to_bam_two_tags OK
> test_assign_tags_sam_to_bam_type_A OK
> test_assign_tags_sam_to_bam_type_i OK
> test_assign_tags_sam_to_bam_type_f OK
> test_assign_tags_sam_to_bam_type_Z OK
> test_assign_tags_sam_to_bam_type_H OK
> test_assign_tags_sam_to_bam_type_Bc OK
> test_assign_tags_sam_to_bam_type_BC OK
> test_assign_tags_sam_to_bam_type_Bs OK
> test_assign_tags_sam_to_bam_type_BS OK
> test_assign_tags_sam_to_bam_type_Bi OK
> test_assign_tags_sam_to_bam_type_BI OK
> test_assign_tags_sam_to_bam_type_Bf OK
> test_bam_tags_dict_get_type_size OK
> test_bam_tags_dict_get_type OK
> test_bam_tags_dict_length OK
> test_bam_tags_dict_extract_value_type_A OK
> test_bam_tags_dict_extract_value_type_c OK
> test_bam_tags_dict_extract_value_type_C OK
> test_bam_tags_dict_extract_value_type_s OK
> test_bam_tags_dict_extract_value_type_S OK
> test_bam_tags_dict_extract_value_type_i OK
> test_bam_tags_dict_extract_value_type_I OK
> test_bam_tags_dict_get_value_type_A OK
> test_bam_tags_dict_get_value_type_c OK
> test_bam_tags_dict_get_value_type_C OK
> test_bam_tags_dict_get_value_type_s OK
> test_bam_tags_dict_get_value_type_S OK
> test_bam_tags_dict_get_value_type_i OK
> test_bam_tags_dict_get_value_type_I OK
> test_bam_tags_dict_get_value_type_f OK
> test_bam_tags_dict_get_value_type_Z OK
> test_bam_tags_dict_get_value_type_H OK
> test_bam_tags_dict_get_value_type_Bc OK
> test_bam_tags_dict_get_value_type_BC OK
> test_bam_tags_dict_get_value_type_Bs OK
> test_bam_tags_dict_get_value_type_BS OK
> test_bam_tags_dict_get_value_type_Bi OK
> test_bam_tags_dict_get_value_type_BI OK
> test_bam_tags_dict_get_value_type_Bf OK
> test_bam_tags_dict_erase_tag OK
> test_bam_tags_dict_set_tag_value OK
> test_bam_io_sam_read_header OK
> test_bam_io_sam_read_alignment OK
> test_bam_io_sam_write_header OK
> test_bam_io_sam_write_alignment OK
> Open failed on file ./core/tests/bam_io/small.bam. (No such file or directory)
> lseek returned -1. (Bad file descriptor)
> lseek returned -1. (Bad file descriptor)
> lseek returned -1. (Bad file descriptor)
> seek returned ffffffffffffffff instead of 0
> ./core/tests/bam_io/test_read_bam.h:57 Assertion failed : open(stream, toCString(bamFilename), "r") should be true but was 0
>
> stack trace:
> 0 [0x55ac6ee65a55] seqan::ClassTest::fail() + 0x15
> 1 [0x55ac6ee913a3] void SEQAN_TEST_test_bam_io_bam_read_header<true>() + 0xdd3
> 2 [0x55ac6ee5ac0e] main + 0x80e
> 3 [0x7f83d1140d0a] __libc_start_main + 0xea
> 4 [0x55ac6ee5b2ba] _start + 0x2a
>
> test_bam_io_bam_read_header FAILED
> Open failed on file ./core/tests/bam_io/small.bam. (No such file or directory)
> lseek returned -1. (Bad file descriptor)
> lseek returned -1. (Bad file descriptor)
> lseek returned -1. (Bad file descriptor)
> seek returned ffffffffffffffff instead of 0
> ./core/tests/bam_io/test_read_bam.h:112 Assertion failed : open(stream, toCString(bamFilename), "r") should be true but was 0
>
> stack trace:
> 0 [0x55ac6ee65a55] seqan::ClassTest::fail() + 0x15
> 1 [0x55ac6ee9ff4a] void SEQAN_TEST_test_bam_io_bam_read_alignment<true>() + 0x112a
> 2 [0x55ac6ee5ac24] main + 0x824
> 3 [0x7f83d1140d0a] __libc_start_main + 0xea
> 4 [0x55ac6ee5b2ba] _start + 0x2a
>
> test_bam_io_bam_read_alignment FAILED
> test_bam_io_bam_write_header OK
> test_bam_io_bam_write_alignment OK
> ./core/tests/bam_io/test_bam_index.h:52 Assertion failed : read(baiIndex, toCString(baiFilename)) == 0 was: 1 != 0
>
> stack trace:
> 0 [0x55ac6ee65a55] seqan::ClassTest::fail() + 0x15
> 1 [0x55ac6ee922d5] void SEQAN_TEST_test_bam_io_bam_index_bai<true>() + 0xe65
> 2 [0x55ac6ee5ac66] main + 0x866
> 3 [0x7f83d1140d0a] __libc_start_main + 0xea
> 4 [0x55ac6ee5b2ba] _start + 0x2a
>
> test_bam_io_bam_index_bai FAILED
> ./core/tests/bam_io/test_bam_stream.h:417 Assertion failed : isGood(bamStream) should be true but was 0
>
> stack trace:
> 0 [0x55ac6ee65a55] seqan::ClassTest::fail() + 0x15
> 1 [0x55ac6ee87a66] void SEQAN_TEST_test_bam_io_bam_stream_sam_file_size<true>() + 0x276
> 2 [0x55ac6ee5ac7c] main + 0x87c
> 3 [0x7f83d1140d0a] __libc_start_main + 0xea
> 4 [0x55ac6ee5b2ba] _start + 0x2a
>
> test_bam_io_bam_stream_sam_file_size FAILED
> ./core/tests/bam_io/test_bam_stream.h:55 Assertion failed : isGood(bamIO) should be true but was 0
>
> stack trace:
> 0 [0x55ac6ee65a55] seqan::ClassTest::fail() + 0x15
> 1 [0x55ac6ee5df43] testBamIOBamStreamReadHeader(char const*) + 0x713
> 2 [0x55ac6ee5ac99] main + 0x899
> 3 [0x7f83d1140d0a] __libc_start_main + 0xea
> 4 [0x55ac6ee5b2ba] _start + 0x2a
>
> test_bam_io_bam_stream_sam_read_header FAILED
> ./core/tests/bam_io/test_bam_stream.h:128 Assertion failed : isGood(bamIO) should be true but was 0
>
> stack trace:
> 0 [0x55ac6ee65a55] seqan::ClassTest::fail() + 0x15
> 1 [0x55ac6ee630b8] testBamIOBamStreamReadRecords(char const*) + 0x1b88
> 2 [0x55ac6ee5acb6] main + 0x8b6
> 3 [0x7f83d1140d0a] __libc_start_main + 0xea
> 4 [0x55ac6ee5b2ba] _start + 0x2a
>
> test_bam_io_bam_stream_sam_read_records FAILED
> ./core/tests/bam_io/test_bam_stream.h:280 Assertion failed : seqan::_compareTextFiles(toCString(tmpPath), toCString(filePath)) should be true but was 0
>
> stack trace:
> 0 [0x55ac6ee65a55] seqan::ClassTest::fail() + 0x15
> 1 [0x55ac6ee60323] testBamIOBamStreamWriteHeader(char const*) + 0xaa3
> 2 [0x55ac6ee5acd3] main + 0x8d3
> 3 [0x7f83d1140d0a] __libc_start_main + 0xea
> 4 [0x55ac6ee5b2ba] _start + 0x2a
>
> test_bam_io_bam_stream_sam_write_header FAILED
> ./core/tests/bam_io/test_bam_stream.h:394 Assertion failed : seqan::_compareTextFiles(toCString(tmpPath), toCString(filePath)) should be true but was 0
>
> stack trace:
> 0 [0x55ac6ee65a55] seqan::ClassTest::fail() + 0x15
> 1 [0x55ac6ee5f830] testBamIOBamStreamWriteRecords(char const*) + 0x1470
> 2 [0x55ac6ee5acf0] main + 0x8f0
> 3 [0x7f83d1140d0a] __libc_start_main + 0xea
> 4 [0x55ac6ee5b2ba] _start + 0x2a
>
> test_bam_io_bam_stream_sam_write_records FAILED
> ./core/tests/bam_io/test_bam_stream.h:436 Assertion failed : isGood(bamStream) should be true but was 0
>
> stack trace:
> 0 [0x55ac6ee65a55] seqan::ClassTest::fail() + 0x15
> 1 [0x55ac6ee87d3b] void SEQAN_TEST_test_bam_io_bam_stream_bam_file_size<true>() + 0x29b
> 2 [0x55ac6ee5ad06] main + 0x906
> 3 [0x7f83d1140d0a] __libc_start_main + 0xea
> 4 [0x55ac6ee5b2ba] _start + 0x2a
>
> test_bam_io_bam_stream_bam_file_size FAILED
> ./core/tests/bam_io/test_bam_stream.h:55 Assertion failed : isGood(bamIO) should be true but was 0
>
> stack trace:
> 0 [0x55ac6ee65a55] seqan::ClassTest::fail() + 0x15
> 1 [0x55ac6ee5df43] testBamIOBamStreamReadHeader(char const*) + 0x713
> 2 [0x55ac6ee5ad23] main + 0x923
> 3 [0x7f83d1140d0a] __libc_start_main + 0xea
> 4 [0x55ac6ee5b2ba] _start + 0x2a
>
> test_bam_io_bam_stream_bam_read_header FAILED
> ./core/tests/bam_io/test_bam_stream.h:128 Assertion failed : isGood(bamIO) should be true but was 0
>
> stack trace:
> 0 [0x55ac6ee65a55] seqan::ClassTest::fail() + 0x15
> 1 [0x55ac6ee630b8] testBamIOBamStreamReadRecords(char const*) + 0x1b88
> 2 [0x55ac6ee5ad40] main + 0x940
> 3 [0x7f83d1140d0a] __libc_start_main + 0xea
> 4 [0x55ac6ee5b2ba] _start + 0x2a
>
> test_bam_io_bam_stream_bam_read_records FAILED
> ./core/tests/bam_io/test_bam_stream.h:217 Assertion failed : isGood(bamIO) should be true but was 0
>
> stack trace:
> 0 [0x55ac6ee65a55] seqan::ClassTest::fail() + 0x15
> 1 [0x55ac6ee88507] void SEQAN_TEST_test_bam_io_bam_stream_bam_read_ex1<true>() + 0x787
> 2 [0x55ac6ee5ad56] main + 0x956
> 3 [0x7f83d1140d0a] __libc_start_main + 0xea
> 4 [0x55ac6ee5b2ba] _start + 0x2a
>
> test_bam_io_bam_stream_bam_read_ex1 FAILED
> ./core/tests/bam_io/test_bam_stream.h:278 Assertion failed : seqan::_compareBinaryFiles(toCString(tmpPath), toCString(filePath)) should be true but was 0
>
> stack trace:
> 0 [0x55ac6ee65a55] seqan::ClassTest::fail() + 0x15
> 1 [0x55ac6ee60178] testBamIOBamStreamWriteHeader(char const*) + 0x8f8
> 2 [0x55ac6ee5ad73] main + 0x973
> 3 [0x7f83d1140d0a] __libc_start_main + 0xea
> 4 [0x55ac6ee5b2ba] _start + 0x2a
>
> test_bam_io_bam_stream_bam_write_header FAILED
> ./core/tests/bam_io/test_bam_stream.h:392 Assertion failed : seqan::_compareBinaryFiles(toCString(tmpPath), toCString(filePath)) should be true but was 0
>
> stack trace:
> 0 [0x55ac6ee65a55] seqan::ClassTest::fail() + 0x15
> 1 [0x55ac6ee5f496] testBamIOBamStreamWriteRecords(char const*) + 0x10d6
> 2 [0x55ac6ee5ad90] main + 0x990
> 3 [0x7f83d1140d0a] __libc_start_main + 0xea
> 4 [0x55ac6ee5b2ba] _start + 0x2a
>
> test_bam_io_bam_stream_bam_write_records FAILED
> ./core/tests/bam_io/test_bam_stream.h:94 Assertion failed : isGood(bamStreamIn) should be true but was 0
>
> stack trace:
> 0 [0x55ac6ee65a55] seqan::ClassTest::fail() + 0x15
> 1 [0x55ac6ee8e687] void SEQAN_TEST_test_bam_io_bam_stream_issue_489<true>() + 0x5e7
> 2 [0x55ac6ee5ada6] main + 0x9a6
> 3 [0x7f83d1140d0a] __libc_start_main + 0xea
> 4 [0x55ac6ee5b2ba] _start + 0x2a
>
> test_bam_io_bam_stream_issue_489 FAILED
> **************************************
> Total Check Points : 0
> Found Check Points : 0
> Lost Check Points : 0
> --------------------------------------
> Total Tests: 101
> Skipped: 0
> Errors: 15
> **************************************
>
> Start 50: test_test_basic_fundamental
> 47/93 Test #48: test_test_basic_exception .......................................... Passed 0.01 sec
> Start 51: test_test_basic_concept
> 48/93 Test #49: test_test_basic_metaprogramming .................................... Passed 0.01 sec
> Start 52: test_test_basic_alphabet
> 49/93 Test #45: test_test_align .................................................... Passed 0.01 sec
> Start 53: test_test_basic_aggregate
> 50/93 Test #50: test_test_basic_fundamental ........................................ Passed 0.00 sec
> Start 54: test_test_basic_allocator
> 51/93 Test #51: test_test_basic_concept ............................................ Passed 0.00 sec
> Start 55: test_test_basic_parallelism
> 52/93 Test #52: test_test_basic_alphabet ........................................... Passed 0.00 sec
> Start 56: test_test_basic_math
> 53/93 Test #53: test_test_basic_aggregate .......................................... Passed 0.00 sec
> Start 57: test_test_basic_smart_pointer
> 54/93 Test #54: test_test_basic_allocator .......................................... Passed 0.00 sec
> Start 58: test_test_basic_container
> 55/93 Test #55: test_test_basic_parallelism ........................................ Passed 0.00 sec
> Start 59: test_test_basic_proxy
> 56/93 Test #56: test_test_basic_math ............................................... Passed 0.00 sec
> Start 60: test_test_basic_iterator
> 57/93 Test #57: test_test_basic_smart_pointer ...................................... Passed 0.00 sec
> Start 61: test_test_consensus
> 58/93 Test #58: test_test_basic_container .......................................... Passed 0.00 sec
> Start 62: test_test_file
> 59/93 Test #59: test_test_basic_proxy .............................................. Passed 0.00 sec
> Start 63: test_test_find
> 60/93 Test #60: test_test_basic_iterator ........................................... Passed 0.00 sec
> Start 64: test_test_gff_io
> 61/93 Test #61: test_test_consensus ................................................***Failed 0.00 sec
> TEST SUITE test_consensus
> SEQAN_ENABLE_DEBUG == 1
> SEQAN_ENABLE_TESTING == 1
> SEQAN_ENABLE_CHECKPOINTS == 0
> SEQAN_CXX_FLAGS == "SEQAN_CXX_FLAGS_NOT_SET"
> ./core/tests/consensus/test_consensus_realign.h:54 Assertion failed : samIn.good() should be true but was 0
>
> stack trace:
> 0 [0x55d1a7c2e0b5] seqan::ClassTest::fail() + 0x15
> 1 [0x55d1a7c6b206] void SEQAN_TEST_test_consensus_realign_one_contig_small<true>() + 0x3676
> 2 [0x55d1a7c286c6] main + 0x46
> 3 [0x7f69ff59fd0a] __libc_start_main + 0xea
> 4 [0x55d1a7c2884a] _start + 0x2a
>
> test_consensus_realign_one_contig_small FAILED
> **************************************
> Total Check Points : 0
> Found Check Points : 0
> Lost Check Points : 0
> --------------------------------------
> Total Tests: 1
> Skipped: 0
> Errors: 1
> **************************************
>
> Start 65: test_test_graph_algorithms
> 62/93 Test #62: test_test_file .....................................................***Failed 0.01 sec
> TEST SUITE test_file
> SEQAN_ENABLE_DEBUG == 1
> SEQAN_ENABLE_TESTING == 1
> SEQAN_ENABLE_CHECKPOINTS == 0
> SEQAN_CXX_FLAGS == "SEQAN_CXX_FLAGS_NOT_SET"
> test_file_stream OK
> test_file_cstream OK
> test_file_raw OK
> ./core/tests/file/test_file.h:572 Assertion failed : file_1 should be true but was 0
>
> stack trace:
> 0 [0x56399739d5c5] seqan::ClassTest::fail() + 0x15
> 1 [0x56399739bd57] Test_Fasta_Read(char const*) + 0x957
> 2 [0x5639973a74b9] void SEQAN_TEST_test_file_fasta_crlf<true>() + 0x49
> 3 [0x5639973998e6] main + 0x66
> 4 [0x7f177b7cbd0a] __libc_start_main + 0xea
> 5 [0x563997399b6a] _start + 0x2a
>
> test_file_fasta_crlf FAILED
> ./core/tests/file/test_file.h:572 Assertion failed : file_1 should be true but was 0
>
> stack trace:
> 0 [0x56399739d5c5] seqan::ClassTest::fail() + 0x15
> 1 [0x56399739bd57] Test_Fasta_Read(char const*) + 0x957
> 2 [0x5639973a7519] void SEQAN_TEST_test_file_fasta_lf<true>() + 0x49
> 3 [0x5639973998fc] main + 0x7c
> 4 [0x7f177b7cbd0a] __libc_start_main + 0xea
> 5 [0x563997399b6a] _start + 0x2a
>
> test_file_fasta_lf FAILED
> ./core/tests/file/test_file.h:572 Assertion failed : file_1 should be true but was 0
>
> stack trace:
> 0 [0x56399739d5c5] seqan::ClassTest::fail() + 0x15
> 1 [0x56399739bd57] Test_Fasta_Read(char const*) + 0x957
> 2 [0x5639973a7579] void SEQAN_TEST_test_file_fasta_cr<true>() + 0x49
> 3 [0x563997399912] main + 0x92
> 4 [0x7f177b7cbd0a] __libc_start_main + 0xea
> 5 [0x563997399b6a] _start + 0x2a
>
> test_file_fasta_cr FAILED
> test_file_fasta_write OK
> ./core/tests/file/test_file.h:728 Assertion failed : file_1 should be true but was 0
>
> stack trace:
> 0 [0x56399739d5c5] seqan::ClassTest::fail() + 0x15
> 1 [0x5639973bd8f4] void SEQAN_TEST_test_file_fasta_align<true>() + 0x3974
> 2 [0x56399739993e] main + 0xbe
> 3 [0x7f177b7cbd0a] __libc_start_main + 0xea
> 4 [0x563997399b6a] _start + 0x2a
>
> test_file_fasta_align FAILED
> ./core/tests/file/test_file.h:926 Assertion failed : fl should be true but was 0
>
> stack trace:
> 0 [0x56399739d5c5] seqan::ClassTest::fail() + 0x15
> 1 [0x5639973a7c79] void SEQAN_TEST_test_file_embl<true>() + 0x6e9
> 2 [0x563997399954] main + 0xd4
> 3 [0x7f177b7cbd0a] __libc_start_main + 0xea
> 4 [0x563997399b6a] _start + 0x2a
>
> test_file_embl FAILED
> ./core/tests/file/test_file.h:979 Assertion failed : fl should be true but was 0
>
> stack trace:
> 0 [0x56399739d5c5] seqan::ClassTest::fail() + 0x15
> 1 [0x5639973ab06a] void SEQAN_TEST_test_file_genbank<true>() + 0xc7a
> 2 [0x56399739996a] main + 0xea
> 3 [0x7f177b7cbd0a] __libc_start_main + 0xea
> 4 [0x563997399b6a] _start + 0x2a
>
> test_file_genbank FAILED
> ./core/tests/file/test_file.h:1071 Assertion failed : file_fasta should be true but was 0
>
> stack trace:
> 0 [0x56399739d5c5] seqan::ClassTest::fail() + 0x15
> 1 [0x5639973a64fe] void SEQAN_TEST_test_file_reader_string<true>() + 0xf6e
> 2 [0x563997399980] main + 0x100
> 3 [0x7f177b7cbd0a] __libc_start_main + 0xea
> 4 [0x563997399b6a] _start + 0x2a
>
> test_file_reader_string FAILED
> ./core/tests/file/test_file.h:1260 Assertion failed : file_fasta should be true but was 0
>
> stack trace:
> 0 [0x56399739d5c5] seqan::ClassTest::fail() + 0x15
> 1 [0x5639973af15c] void SEQAN_TEST_test_file_reader_string3<true>() + 0x4ac
> 2 [0x563997399996] main + 0x116
> 3 [0x7f177b7cbd0a] __libc_start_main + 0xea
> 4 [0x563997399b6a] _start + 0x2a
>
> test_file_reader_string3 FAILED
> ./core/tests/file/test_embl.h:67 Assertion failed : count == 3 was: 0 != 3
>
> stack trace:
> 0 [0x56399739d5c5] seqan::ClassTest::fail() + 0x15
> 1 [0x5639973afa78] void SEQAN_TEST_test_file_embl_file<true>() + 0x578
> 2 [0x5639973999ac] main + 0x12c
> 3 [0x7f177b7cbd0a] __libc_start_main + 0xea
> 4 [0x563997399b6a] _start + 0x2a
>
> test_file_embl_file FAILED
> ./core/tests/file/test_embl.h:87 Assertion failed : line == "SCL gene." was: != SCL gene.
>
> stack trace:
> 0 [0x56399739d5c5] seqan::ClassTest::fail() + 0x15
> 1 [0x5639973a87b6] void SEQAN_TEST_test_file_embl_meta<true>() + 0x666
> 2 [0x5639973999c2] main + 0x142
> 3 [0x7f177b7cbd0a] __libc_start_main + 0xea
> 4 [0x563997399b6a] _start + 0x2a
>
> test_file_embl_meta FAILED
> **************************************
> Total Check Points : 0
> Found Check Points : 0
> Lost Check Points : 0
> --------------------------------------
> Total Tests: 14
> Skipped: 0
> Errors: 10
> **************************************
>
> Start 66: test_test_graph_align
> 63/93 Test #64: test_test_gff_io ...................................................***Failed 0.01 sec
> TEST SUITE test_gff_io
> SEQAN_ENABLE_DEBUG == 1
> SEQAN_ENABLE_TESTING == 1
> SEQAN_ENABLE_CHECKPOINTS == 0
> SEQAN_CXX_FLAGS == "SEQAN_CXX_FLAGS_NOT_SET"
> ./core/tests/gff_io/test_gff_io.h:51 Assertion failed : f.good() should be true but was 0
>
> stack trace:
> 0 [0x55c5c42e0f05] seqan::ClassTest::fail() + 0x15
> 1 [0x55c5c42eddd6] void SEQAN_TEST_test_store_io_read_record_gff<true>() + 0xc56
> 2 [0x55c5c42dc7d4] main + 0x24
> 3 [0x7fba5d639d0a] __libc_start_main + 0xea
> 4 [0x55c5c42dca5a] _start + 0x2a
>
> test_store_io_read_record_gff FAILED
> ./core/tests/gff_io/test_gff_io.h:108 Assertion failed : f.good() should be true but was 0
>
> stack trace:
> 0 [0x55c5c42e0f05] seqan::ClassTest::fail() + 0x15
> 1 [0x55c5c42ef341] void SEQAN_TEST_test_store_io_read_record_context_gff<true>() + 0xe81
> 2 [0x55c5c42dc7ea] main + 0x3a
> 3 [0x7fba5d639d0a] __libc_start_main + 0xea
> 4 [0x55c5c42dca5a] _start + 0x2a
>
> test_store_io_read_record_context_gff FAILED
> test_store_io_read_record_context_empty_trailing_attribute_gff OK
> ./core/tests/gff_io/test_gff_io.h:222 Assertion failed : fin.good() should be true but was 0
>
> stack trace:
> 0 [0x55c5c42e0f05] seqan::ClassTest::fail() + 0x15
> 1 [0x55c5c42ee42d] void SEQAN_TEST_test_store_io_write_record_gff<true>() + 0x54d
> 2 [0x55c5c42dc816] main + 0x66
> 3 [0x7fba5d639d0a] __libc_start_main + 0xea
> 4 [0x55c5c42dca5a] _start + 0x2a
>
> test_store_io_write_record_gff FAILED
> ./core/tests/gff_io/test_gff_io.h:249 Assertion failed : fin.good() should be true but was 0
>
> stack trace:
> 0 [0x55c5c42e0f05] seqan::ClassTest::fail() + 0x15
> 1 [0x55c5c42efd26] void SEQAN_TEST_test_store_io_write_record_context_gff<true>() + 0x8a6
> 2 [0x55c5c42dc82c] main + 0x7c
> 3 [0x7fba5d639d0a] __libc_start_main + 0xea
> 4 [0x55c5c42dca5a] _start + 0x2a
>
> test_store_io_write_record_context_gff FAILED
> ./core/tests/gff_io/test_gff_io.h:289 Assertion failed : f.good() should be true but was 0
>
> stack trace:
> 0 [0x55c5c42e0f05] seqan::ClassTest::fail() + 0x15
> 1 [0x55c5c42f2356] void SEQAN_TEST_test_store_io_read_record_gtf<true>() + 0xc56
> 2 [0x55c5c42dc842] main + 0x92
> 3 [0x7fba5d639d0a] __libc_start_main + 0xea
> 4 [0x55c5c42dca5a] _start + 0x2a
>
> test_store_io_read_record_gtf FAILED
> ./core/tests/gff_io/test_gff_io.h:415 Assertion failed : f.good() should be true but was 0
>
> stack trace:
> 0 [0x55c5c42e0f05] seqan::ClassTest::fail() + 0x15
> 1 [0x55c5c42f0c61] void SEQAN_TEST_test_store_io_read_record_context_gtf<true>() + 0xe81
> 2 [0x55c5c42dc858] main + 0xa8
> 3 [0x7fba5d639d0a] __libc_start_main + 0xea
> 4 [0x55c5c42dca5a] _start + 0x2a
>
> test_store_io_read_record_context_gtf FAILED
> ./core/tests/gff_io/test_gff_io.h:348 Assertion failed : f.good() should be true but was 0
>
> stack trace:
> 0 [0x55c5c42e0f05] seqan::ClassTest::fail() + 0x15
> 1 [0x55c5c42f35da] void SEQAN_TEST_test_store_io_read_record_gtf_pseudogenes<true>() + 0x117a
> 2 [0x55c5c42dc86e] main + 0xbe
> 3 [0x7fba5d639d0a] __libc_start_main + 0xea
> 4 [0x55c5c42dca5a] _start + 0x2a
>
> test_store_io_read_record_gtf_pseudogenes FAILED
> ./core/tests/gff_io/test_gff_io.h:479 Assertion failed : fin.good() should be true but was 0
>
> stack trace:
> 0 [0x55c5c42e0f05] seqan::ClassTest::fail() + 0x15
> 1 [0x55c5c42f3c7d] void SEQAN_TEST_test_store_io_write_record_gtf<true>() + 0x54d
> 2 [0x55c5c42dc884] main + 0xd4
> 3 [0x7fba5d639d0a] __libc_start_main + 0xea
> 4 [0x55c5c42dca5a] _start + 0x2a
>
> test_store_io_write_record_gtf FAILED
> ./core/tests/gff_io/test_gff_io.h:506 Assertion failed : fin.good() should be true but was 0
>
> stack trace:
> 0 [0x55c5c42e0f05] seqan::ClassTest::fail() + 0x15
> 1 [0x55c5c42f1646] void SEQAN_TEST_test_store_io_write_record_context_gtf<true>() + 0x8a6
> 2 [0x55c5c42dc89a] main + 0xea
> 3 [0x7fba5d639d0a] __libc_start_main + 0xea
> 4 [0x55c5c42dca5a] _start + 0x2a
>
> test_store_io_write_record_context_gtf FAILED
> ./core/tests/gff_io/test_gff_io.h:547 Assertion failed : isGood(gffStream) should be true but was 0
>
> stack trace:
> 0 [0x55c5c42e0f05] seqan::ClassTest::fail() + 0x15
> 1 [0x55c5c42f4acd] void SEQAN_TEST_test_store_io_gff_stream_read_record_gff<true>() + 0xdbd
> 2 [0x55c5c42dc8b0] main + 0x100
> 3 [0x7fba5d639d0a] __libc_start_main + 0xea
> 4 [0x55c5c42dca5a] _start + 0x2a
>
> test_store_io_gff_stream_read_record_gff FAILED
> ./core/tests/gff_io/test_gff_io.h:602 Assertion failed : isGood(gffStream) should be true but was 0
>
> stack trace:
> 0 [0x55c5c42e0f05] seqan::ClassTest::fail() + 0x15
> 1 [0x55c5c42f58b0] void SEQAN_TEST_test_store_io_gff_stream_read_record_gtf<true>() + 0xd10
> 2 [0x55c5c42dc8c6] main + 0x116
> 3 [0x7fba5d639d0a] __libc_start_main + 0xea
> 4 [0x55c5c42dca5a] _start + 0x2a
>
> test_store_io_gff_stream_read_record_gtf FAILED
> ./core/tests/gff_io/test_gff_io.h:655 Assertion failed : isGood(inStream) should be true but was 0
>
> stack trace:
> 0 [0x55c5c42e0f05] seqan::ClassTest::fail() + 0x15
> 1 [0x55c5c42f648a] void SEQAN_TEST_test_store_io_gff_stream_write_record_gff<true>() + 0xb0a
> 2 [0x55c5c42dc8dc] main + 0x12c
> 3 [0x7fba5d639d0a] __libc_start_main + 0xea
> 4 [0x55c5c42dca5a] _start + 0x2a
>
> test_store_io_gff_stream_write_record_gff FAILED
> ./core/tests/gff_io/test_gff_io.h:687 Assertion failed : isGood(inStream) should be true but was 0
>
> stack trace:
> 0 [0x55c5c42e0f05] seqan::ClassTest::fail() + 0x15
> 1 [0x55c5c42f700a] void SEQAN_TEST_test_store_io_gff_stream_write_record_gtf<true>() + 0xb0a
> 2 [0x55c5c42dc8f2] main + 0x142
> 3 [0x7fba5d639d0a] __libc_start_main + 0xea
> 4 [0x55c5c42dca5a] _start + 0x2a
>
> test_store_io_gff_stream_write_record_gtf FAILED
> **************************************
> Total Check Points : 0
> Found Check Points : 0
> Lost Check Points : 0
> --------------------------------------
> Total Tests: 14
> Skipped: 0
> Errors: 13
> **************************************
>
> Start 67: test_test_graph_msa
> 64/93 Test #65: test_test_graph_algorithms ......................................... Passed 0.01 sec
> Start 68: test_test_graph_types
> 65/93 Test #66: test_test_graph_align .............................................. Passed 0.00 sec
> Start 69: test_test_index_creation
> 66/93 Test #68: test_test_graph_types .............................................. Passed 0.00 sec
> Start 70: test_test_index_crosscompare_char
> 67/93 Test #70: test_test_index_crosscompare_char .................................. Passed 0.05 sec
> Start 71: test_test_index_crosscompare_char_dfi
> 68/93 Test #71: test_test_index_crosscompare_char_dfi .............................. Passed 0.01 sec
> Start 72: test_test_index_crosscompare_dna
> 69/93 Test #72: test_test_index_crosscompare_dna ................................... Passed 0.00 sec
> Start 73: test_test_index_crosscompare_dna_dfi
> 70/93 Test #73: test_test_index_crosscompare_dna_dfi ............................... Passed 0.00 sec
> Start 74: test_test_index_qgram
> 71/93 Test #74: test_test_index_qgram .............................................. Passed 0.00 sec
> Start 75: test_test_index_sa_bwtwalk
> 72/93 Test #75: test_test_index_sa_bwtwalk .........................................***Failed 0.00 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"
> ./core/include/seqan/file/file_format_raw.h:93 Assertion failed : _streamEOF(file) should be false but was 1
>
> stack trace:
> 0 [0x563926d6e585] seqan::ClassTest::fail() + 0x15
> 1 [0x563926d7e619] void seqan::SEQAN_TEST_testBWTWalk<true>() + 0x3779
> 2 [0x563926d6c726] main + 0x46
> 3 [0x7f51b3812d0a] __libc_start_main + 0xea
> 4 [0x563926d6c82a] _start + 0x2a
>
> testBWTWalk FAILED
> **************************************
> Total Check Points : 0
> Found Check Points : 0
> Lost Check Points : 0
> --------------------------------------
> Total Tests: 1
> Skipped: 0
> Errors: 1
> **************************************
>
> Start 76: test_test_index_shapes
> 73/93 Test #76: test_test_index_shapes ............................................. Passed 0.00 sec
> Start 77: test_test_index_drawing
> 74/93 Test #77: test_test_index_drawing ............................................ Passed 0.00 sec
> Start 78: test_test_index_repeats
> 75/93 Test #78: test_test_index_repeats ............................................ Passed 0.09 sec
> Start 79: test_test_map
> 76/93 Test #67: test_test_graph_msa ................................................ Passed 0.20 sec
> Start 80: test_test_misc
> 77/93 Test #80: test_test_misc ..................................................... Passed 0.00 sec
> Start 81: test_test_misc_cmdparser
> 78/93 Test #81: test_test_misc_cmdparser ........................................... Passed 0.00 sec
> Start 82: test_test_modifier
> 79/93 Test #82: test_test_modifier ................................................. Passed 0.00 sec
> Start 83: test_test_parallel
> 80/93 Test #63: test_test_find ..................................................... Passed 0.33 sec
> Start 84: test_test_pipe
> 81/93 Test #79: test_test_map ...................................................... Passed 0.49 sec
> Start 85: test_test_random
> 82/93 Test #85: test_test_random ................................................... Passed 0.04 sec
> Start 86: test_test_score
> 83/93 Test #86: test_test_score ....................................................***Failed 0.02 sec
> TEST SUITE test_score
> SEQAN_ENABLE_DEBUG == 1
> SEQAN_ENABLE_TESTING == 1
> SEQAN_ENABLE_CHECKPOINTS == 0
> SEQAN_CXX_FLAGS == "SEQAN_CXX_FLAGS_NOT_SET"
> test_score_gap_open OK
> test_score_simple OK
> test_score_edit OK
> ./core/tests/score/test_score.cpp:63 Assertion failed : score(mat1, a, b) == score(mat2, a, b) was: 4 != 0 (a = A, b = A)
>
> stack trace:
> 0 [0x557172d92595] seqan::ClassTest::fail() + 0x15
> 1 [0x557172d94ccf] /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/test_score(+0xaccf)
> 2 [0x557172d9ba2e] void SEQAN_TEST_test_score_matrix<true>() + 0x7fe
> 3 [0x557172d8f726] main + 0x66
> 4 [0x7f4dfc2fad0a] __libc_start_main + 0xea
> 5 [0x557172d8f8aa] _start + 0x2a
>
> test_score_matrix FAILED
> ./core/tests/score/test_score.cpp:63 Assertion failed : score(mat1, a, b) == score(mat2, a, b) was: 4 != 0 (a = A, b = A)
>
> stack trace:
> 0 [0x557172d92595] seqan::ClassTest::fail() + 0x15
> 1 [0x557172d94ccf] /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/test_score(+0xaccf)
> 2 [0x557172d9d5a7] void SEQAN_TEST_test_score_matrix_file<true>() + 0x2f7
> 3 [0x557172d8f73c] main + 0x7c
> 4 [0x7f4dfc2fad0a] __libc_start_main + 0xea
> 5 [0x557172d8f8aa] _start + 0x2a
>
> test_score_matrix_file FAILED
> test_score_matrix_sprintf_value OK
> ./core/tests/score/test_score.cpp:63 Assertion failed : score(mat1, a, b) == score(mat2, a, b) was: 0 != 4 (a = A, b = A)
>
> stack trace:
> 0 [0x557172d92595] seqan::ClassTest::fail() + 0x15
> 1 [0x557172d9cfd2] void SEQAN_TEST_test_score_matrix_data<true>() + 0x1122
> 2 [0x557172d8f768] main + 0xa8
> 3 [0x7f4dfc2fad0a] __libc_start_main + 0xea
> 4 [0x557172d8f8aa] _start + 0x2a
>
> test_score_matrix_data FAILED
> test_score_sequence_entry_for_score OK
> **************************************
> Total Check Points : 0
> Found Check Points : 0
> Lost Check Points : 0
> --------------------------------------
> Total Tests: 8
> Skipped: 0
> Errors: 3
> **************************************
>
> Start 87: test_test_seeds
> 84/93 Test #87: test_test_seeds .................................................... Passed 0.09 sec
> Start 88: test_test_seq_io
> 85/93 Test #88: test_test_seq_io ...................................................***Failed 0.04 sec
> TEST SUITE test_seq_io
> SEQAN_ENABLE_DEBUG == 1
> SEQAN_ENABLE_TESTING == 1
> SEQAN_ENABLE_CHECKPOINTS == 0
> SEQAN_CXX_FLAGS == "SEQAN_CXX_FLAGS_NOT_SET"
> ./core/tests/seq_io/test_sequence_stream.h:56 Assertion failed : seqan::readFasta(seq, toCString(filePath)) == 0 was: 1 != 0
>
> stack trace:
> 0 [0x55d98ff75aa5] seqan::ClassTest::fail() + 0x15
> 1 [0x55d98ffb3da7] void SEQAN_TEST_test_seq_io_read_fasta<true>() + 0x167
> 2 [0x55d98ff6957e] main + 0x2e
> 3 [0x7ff5c7f69d0a] __libc_start_main + 0xea
> 4 [0x55d98ff6a20a] _start + 0x2a
>
> test_seq_io_read_fasta FAILED
> ./core/tests/seq_io/test_sequence_stream.h:74 Assertion failed : isGood(seqIO) should be true but was 0
>
> stack trace:
> 0 [0x55d98ff75aa5] seqan::ClassTest::fail() + 0x15
> 1 [0x55d98ffb3f25] void SEQAN_TEST_test_seq_io_sequence_stream_recognize_file_type_text_fasta<true>() + 0x135
> 2 [0x55d98ff69594] main + 0x44
> 3 [0x7ff5c7f69d0a] __libc_start_main + 0xea
> 4 [0x55d98ff6a20a] _start + 0x2a
>
> test_seq_io_sequence_stream_recognize_file_type_text_fasta FAILED
> ./core/tests/seq_io/test_sequence_stream.h:90 Assertion failed : isGood(seqIO) should be true but was 0
>
> stack trace:
> 0 [0x55d98ff75aa5] seqan::ClassTest::fail() + 0x15
> 1 [0x55d98ffb4095] void SEQAN_TEST_test_seq_io_sequence_stream_recognize_file_type_gz_fasta<true>() + 0x135
> 2 [0x55d98ff695aa] main + 0x5a
> 3 [0x7ff5c7f69d0a] __libc_start_main + 0xea
> 4 [0x55d98ff6a20a] _start + 0x2a
>
> test_seq_io_sequence_stream_recognize_file_type_gz_fasta FAILED
> test_seq_io_sequence_stream_recognize_file_type_bz2_fasta OK
> ./core/tests/seq_io/test_sequence_stream.h:127 Assertion failed : isGood(seqIO) should be true but was 0
>
> stack trace:
> 0 [0x55d98ff75aa5] seqan::ClassTest::fail() + 0x15
> 1 [0x55d98ffb4205] void SEQAN_TEST_test_seq_io_sequence_stream_recognize_file_format_text_fasta<true>() + 0x135
> 2 [0x55d98ff695d1] main + 0x81
> 3 [0x7ff5c7f69d0a] __libc_start_main + 0xea
> 4 [0x55d98ff6a20a] _start + 0x2a
>
> test_seq_io_sequence_stream_recognize_file_format_text_fasta FAILED
> ./core/tests/seq_io/test_sequence_stream.h:142 Assertion failed : isGood(seqIO) should be true but was 0
>
> stack trace:
> 0 [0x55d98ff75aa5] seqan::ClassTest::fail() + 0x15
> 1 [0x55d98ffb4375] void SEQAN_TEST_test_seq_io_sequence_stream_recognize_file_format_text_fastq<true>() + 0x135
> 2 [0x55d98ff695e7] main + 0x97
> 3 [0x7ff5c7f69d0a] __libc_start_main + 0xea
> 4 [0x55d98ff6a20a] _start + 0x2a
>
> test_seq_io_sequence_stream_recognize_file_format_text_fastq FAILED
> ./core/tests/seq_io/test_sequence_stream.h:164 Assertion failed : 0 == readRecord(id, seq, seqIO) was: 0 != 1
>
> stack trace:
> 0 [0x55d98ff75aa5] seqan::ClassTest::fail() + 0x15
> 1 [0x55d98ffb474d] void SEQAN_TEST_test_seq_io_sequence_stream_read_record_text_fasta<true>() + 0x39d
> 2 [0x55d98ff695fd] main + 0xad
> 3 [0x7ff5c7f69d0a] __libc_start_main + 0xea
> 4 [0x55d98ff6a20a] _start + 0x2a
>
> test_seq_io_sequence_stream_read_record_text_fasta FAILED
> ./core/tests/seq_io/test_sequence_stream.h:193 Assertion failed : 0 == readBatch(ids, seqs, seqIO, 2) was: 0 != 1
>
> stack trace:
> 0 [0x55d98ff75aa5] seqan::ClassTest::fail() + 0x15
> 1 [0x55d98ffb4cc6] void SEQAN_TEST_test_seq_io_sequence_stream_read_batch_text_fasta<true>() + 0x4f6
> 2 [0x55d98ff69613] main + 0xc3
> 3 [0x7ff5c7f69d0a] __libc_start_main + 0xea
> 4 [0x55d98ff6a20a] _start + 0x2a
>
> test_seq_io_sequence_stream_read_batch_text_fasta FAILED
> ./core/tests/seq_io/test_sequence_stream.h:222 Assertion failed : 0 == readAll(ids, seqs, seqIO) was: 0 != 1
>
> stack trace:
> 0 [0x55d98ff75aa5] seqan::ClassTest::fail() + 0x15
> 1 [0x55d98ffb5e5e] void SEQAN_TEST_test_seq_io_sequence_stream_read_all_text_fasta<true>() + 0x110e
> 2 [0x55d98ff69629] main + 0xd9
> 3 [0x7ff5c7f69d0a] __libc_start_main + 0xea
> 4 [0x55d98ff6a20a] _start + 0x2a
>
> test_seq_io_sequence_stream_read_all_text_fasta FAILED
> ./core/tests/seq_io/test_sequence_stream.h:265 Assertion failed : seqan::_compareTextFiles(toCString(pathToExpected), toCString(filePath)) should be true but was 0 (Output should match example.)
>
> stack trace:
> 0 [0x55d98ff75aa5] seqan::ClassTest::fail() + 0x15
> 1 [0x55d98ffb928f] void SEQAN_TEST_test_seq_io_sequence_stream_write_record_text_fasta<true>() + 0x2ef
> 2 [0x55d98ff6963f] main + 0xef
> 3 [0x7ff5c7f69d0a] __libc_start_main + 0xea
> 4 [0x55d98ff6a20a] _start + 0x2a
>
> test_seq_io_sequence_stream_write_record_text_fasta FAILED
> ./core/tests/seq_io/test_sequence_stream.h:294 Assertion failed : seqan::_compareTextFiles(toCString(pathToExpected), toCString(filePath)) should be true but was 0 (Output should match example.)
>
> stack trace:
> 0 [0x55d98ff75aa5] seqan::ClassTest::fail() + 0x15
> 1 [0x55d98ffb95df] void SEQAN_TEST_test_seq_io_sequence_stream_write_all_text_fasta<true>() + 0x2ef
> 2 [0x55d98ff69655] main + 0x105
> 3 [0x7ff5c7f69d0a] __libc_start_main + 0xea
> 4 [0x55d98ff6a20a] _start + 0x2a
>
> test_seq_io_sequence_stream_write_all_text_fasta FAILED
> ./core/tests/seq_io/test_sequence_stream.h:323 Assertion failed : seqan::_compareTextFiles(toCString(pathToExpected), toCString(filePath)) should be true but was 0 (Output should match example.)
>
> stack trace:
> 0 [0x55d98ff75aa5] seqan::ClassTest::fail() + 0x15
> 1 [0x55d98ffb992f] void SEQAN_TEST_test_seq_io_sequence_stream_write_record_text_fastq_no_qual<true>() + 0x2ef
> 2 [0x55d98ff6966b] main + 0x11b
> 3 [0x7ff5c7f69d0a] __libc_start_main + 0xea
> 4 [0x55d98ff6a20a] _start + 0x2a
>
> test_seq_io_sequence_stream_write_record_text_fastq_no_qual FAILED
> ./core/tests/seq_io/test_sequence_stream.h:356 Assertion failed : seqan::_compareTextFiles(toCString(pathToExpected), toCString(filePath)) should be true but was 0 (Output should match example.)
>
> stack trace:
> 0 [0x55d98ff75aa5] seqan::ClassTest::fail() + 0x15
> 1 [0x55d98ffba6de] void SEQAN_TEST_test_seq_io_sequence_stream_write_record_text_fastq_with_qual<true>() + 0x6be
> 2 [0x55d98ff69681] main + 0x131
> 3 [0x7ff5c7f69d0a] __libc_start_main + 0xea
> 4 [0x55d98ff6a20a] _start + 0x2a
>
> test_seq_io_sequence_stream_write_record_text_fastq_with_qual FAILED
> ./core/tests/seq_io/test_sequence_stream.h:385 Assertion failed : seqan::_compareTextFiles(toCString(pathToExpected), toCString(filePath)) should be true but was 0 (Output should match example.)
>
> stack trace:
> 0 [0x55d98ff75aa5] seqan::ClassTest::fail() + 0x15
> 1 [0x55d98ffb9c7f] void SEQAN_TEST_test_seq_io_sequence_stream_write_all_text_fastq_no_qual<true>() + 0x2ef
> 2 [0x55d98ff69697] main + 0x147
> 3 [0x7ff5c7f69d0a] __libc_start_main + 0xea
> 4 [0x55d98ff6a20a] _start + 0x2a
>
> test_seq_io_sequence_stream_write_all_text_fastq_no_qual FAILED
> ./core/tests/seq_io/test_sequence_stream.h:418 Assertion failed : seqan::_compareTextFiles(toCString(pathToExpected), toCString(filePath)) should be true but was 0 (Output should match example.)
>
> stack trace:
> 0 [0x55d98ff75aa5] seqan::ClassTest::fail() + 0x15
> 1 [0x55d98ffbae1e] void SEQAN_TEST_test_seq_io_sequence_stream_write_all_text_fastq_with_qual<true>() + 0x6be
> 2 [0x55d98ff696ad] main + 0x15d
> 3 [0x7ff5c7f69d0a] __libc_start_main + 0xea
> 4 [0x55d98ff6a20a] _start + 0x2a
>
> test_seq_io_sequence_stream_write_all_text_fastq_with_qual FAILED
> test_seq_io_genomic_region_default_constructed OK
> test_seq_io_genomic_region_from_string OK
> test_seq_io_genomic_region_clear OK
> test_seq_io_genomic_region_parse_chrom OK
> test_seq_io_genomic_region_parse_chrom_begin OK
> test_seq_io_genomic_region_parse_chrom_begin_end OK
> Open failed on file ./core/tests/seq_io/adeno_genome.fa: "No such file or directory"
> ./core/tests/seq_io/test_fai_index.h:46 Assertion failed : build(faiIndex, toCString(filePath)) == 0 was: 1 != 0
>
> stack trace:
> 0 [0x55d98ff75aa5] seqan::ClassTest::fail() + 0x15
> 1 [0x55d98ffb65d5] void SEQAN_TEST_test_seq_io_genomic_fai_index_build<true>() + 0x4d5
> 2 [0x55d98ff69747] main + 0x1f7
> 3 [0x7ff5c7f69d0a] __libc_start_main + 0xea
> 4 [0x55d98ff6a20a] _start + 0x2a
>
> test_seq_io_genomic_fai_index_build FAILED
> Open failed on file ./core/tests/seq_io/adeno_genome.fa: "No such file or directory"
> ./core/tests/seq_io/test_fai_index.h:61 Assertion failed : build(faiIndex, toCString(filePath)) == 0 was: 1 != 0
>
> stack trace:
> 0 [0x55d98ff75aa5] seqan::ClassTest::fail() + 0x15
> 1 [0x55d98ffb68b2] void SEQAN_TEST_test_seq_io_genomic_fai_index_write<true>() + 0x262
> 2 [0x55d98ff6975d] main + 0x20d
> 3 [0x7ff5c7f69d0a] __libc_start_main + 0xea
> 4 [0x55d98ff6a20a] _start + 0x2a
>
> test_seq_io_genomic_fai_index_write FAILED
> Open failed on file ./core/tests/seq_io/adeno_genome.fa: "No such file or directory"
> ./core/tests/seq_io/test_fai_index.h:78 Assertion failed : read(faiIndex, toCString(filePath)) == 0 was: 1 != 0
>
> stack trace:
> 0 [0x55d98ff75aa5] seqan::ClassTest::fail() + 0x15
> 1 [0x55d98ffb6dcb] void SEQAN_TEST_test_seq_io_genomic_fai_index_read<true>() + 0x4ab
> 2 [0x55d98ff69773] main + 0x223
> 3 [0x7ff5c7f69d0a] __libc_start_main + 0xea
> 4 [0x55d98ff6a20a] _start + 0x2a
>
> test_seq_io_genomic_fai_index_read FAILED
> Open failed on file ./core/tests/seq_io/adeno_genome.fa: "No such file or directory"
> ./core/tests/seq_io/test_fai_index.h:93 Assertion failed : read(faiIndex, toCString(filePath)) == 0 was: 1 != 0
>
> stack trace:
> 0 [0x55d98ff75aa5] seqan::ClassTest::fail() + 0x15
> 1 [0x55d98ffb70ee] void SEQAN_TEST_test_seq_io_genomic_fai_index_read_sequence<true>() + 0x2ae
> 2 [0x55d98ff69789] main + 0x239
> 3 [0x7ff5c7f69d0a] __libc_start_main + 0xea
> 4 [0x55d98ff6a20a] _start + 0x2a
>
> test_seq_io_genomic_fai_index_read_sequence FAILED
> Open failed on file ./core/tests/seq_io/adeno_genome.fa: "No such file or directory"
> ./core/tests/seq_io/test_fai_index.h:109 Assertion failed : read(faiIndex, toCString(filePath)) == 0 was: 1 != 0
>
> stack trace:
> 0 [0x55d98ff75aa5] seqan::ClassTest::fail() + 0x15
> 1 [0x55d98ffb77ba] void SEQAN_TEST_test_seq_io_genomic_fai_index_read_region<true>() + 0x67a
> 2 [0x55d98ff6979f] main + 0x24f
> 3 [0x7ff5c7f69d0a] __libc_start_main + 0xea
> 4 [0x55d98ff6a20a] _start + 0x2a
>
> test_seq_io_genomic_fai_index_read_region FAILED
> test_stream_record_reader_fasta_single_fstream OK
> test_stream_record_reader_fasta_double_fstream OK
> test_stream_record_reader_fasta_batch_single_fstream OK
> test_stream_record_reader_fasta_batch_double_fstream OK
> test_stream_record_reader_fasta_single_mmap OK
> test_stream_record_reader_fasta_double_mmap OK
> test_stream_record_reader_fasta_batch_single_mmap OK
> test_stream_record_reader_fasta_batch_single_concat_mmap OK
> test_stream_record_reader_fasta_batch_double_mmap OK
> test_stream_record_reader_fasta_batch_double_concat_mmap OK
> test_stream_record_reader_fastq_single_fstream OK
> test_stream_record_reader_fastq_double_fstream OK
> test_stream_record_reader_fastq_batch_single_fstream OK
> test_stream_record_reader_fastq_batch_double_fstream OK
> test_stream_record_reader_fastq_single_mmap OK
> test_stream_record_reader_fastq_double_mmap OK
> test_stream_record_reader_fastq_batch_single_mmap OK
> test_stream_record_reader_fastq_batch_single_concat_mmap OK
> test_stream_record_reader_fastq_batch_double_mmap OK
> test_stream_record_reader_fastq_batch_double_concat_mmap OK
> test_stream_record_reader_fastq_check_stream_format OK
> test_stream_read_embl_single_char_array_stream OK
> test_stream_read_embl_record_char_array_stream OK
> test_stream_read_embl_batch_char_array_stream OK
> test_stream_read_embl_single_mmap OK
> test_stream_read_embl_single_batch_mmap OK
> test_stream_read_embl_single_batch_concat_mmap OK
> test_stream_read_genbank_single_char_array_stream OK
> test_stream_read_genbank_record_char_array_stream OK
> test_stream_read_genbank_batch_char_array_stream OK
> test_stream_read_genbank_single_mmap OK
> test_stream_read_genbank_single_batch_mmap OK
> test_stream_read_genbank_single_batch_concat_mmap OK
> test_stream_guess_stream_format_auto_fasta OK
> test_stream_guess_stream_format_auto_fastq OK
> test_stream_guess_stream_format_auto_bogus OK
> test_stream_read_record_auto_format_quals_fasta OK
> test_stream_read_record_auto_format_quals_fastq OK
> test_stream_read_record_auto_format_no_quals_fasta OK
> test_stream_read_record_auto_format_no_quals_fastq OK
> test_stream_read_auto_format_quals_fasta OK
> test_stream_read_auto_format_quals_fastq OK
> test_stream_read_auto_format_no_quals_fasta OK
> test_stream_read_auto_format_no_quals_fastq OK
> test_stream_record_reader_fasta_protein_single_fstream OK
> test_stream_record_reader_fasta_annotated_protein_single_fstream OK
> test_stream_write_record_fasta_default OK
> test_stream_write_record_fasta_no_empty_lines OK
> test_stream_write_record_fasta_nolinebreaks OK
> test_stream_write_record_fastq_default_separate_qual OK
> test_stream_write_record_fastq_default_qual_in_seq OK
> test_stream_write_record_fastq_linebreaks_qualmeta OK
> test_stream_write2_fasta_default OK
> test_stream_write2_fastq_default_separate_qual OK
> test_stream_write2_fastq_default_qual_in_seq OK
> **************************************
> Total Check Points : 0
> Found Check Points : 0
> Lost Check Points : 0
> --------------------------------------
> Total Tests: 81
> Skipped: 0
> Errors: 19
> **************************************
>
> Start 89: test_test_sequence
> 86/93 Test #89: test_test_sequence ................................................. Passed 0.05 sec
> Start 90: test_test_sequence_journaled
> 87/93 Test #83: test_test_parallel ................................................. Passed 0.75 sec
> Start 91: test_test_store
> 88/93 Test #90: test_test_sequence_journaled ....................................... Passed 0.05 sec
> Start 92: test_test_stream
> 89/93 Test #91: test_test_store ....................................................***Failed 0.01 sec
> TEST SUITE test_store
> SEQAN_ENABLE_DEBUG == 1
> SEQAN_ENABLE_TESTING == 1
> SEQAN_ENABLE_CHECKPOINTS == 0
> SEQAN_CXX_FLAGS == "SEQAN_CXX_FLAGS_NOT_SET"
> ./core/tests/store/test_store_io.h:52 Assertion failed : f.good() should be true but was 0
>
> stack trace:
> 0 [0x557631f9fd45] seqan::ClassTest::fail() + 0x15
> 1 [0x557631fd0888] void SEQAN_TEST_test_store_io_read_ucsc_known_genes<true>() + 0x19d8
> 2 [0x557631f8ee54] main + 0x24
> 3 [0x7fb15f69cd0a] __libc_start_main + 0xea
> 4 [0x557631f8f14a] _start + 0x2a
>
> test_store_io_read_ucsc_known_genes FAILED
> ./core/tests/store/test_store_io.h:175 Assertion failed : fin.good() should be true but was 0
>
> stack trace:
> 0 [0x557631f9fd45] seqan::ClassTest::fail() + 0x15
> 1 [0x557631fd1861] void SEQAN_TEST_test_store_io_write_ucsc_known_genes<true>() + 0xe21
> 2 [0x557631f8ee6a] main + 0x3a
> 3 [0x7fb15f69cd0a] __libc_start_main + 0xea
> 4 [0x557631f8f14a] _start + 0x2a
>
> test_store_io_write_ucsc_known_genes FAILED
> ./core/tests/store/test_store_io.h:198 Assertion failed : f.good() should be true but was 0
>
> stack trace:
> 0 [0x557631f9fd45] seqan::ClassTest::fail() + 0x15
> 1 [0x557631fd21d0] void SEQAN_TEST_test_store_io_read_gff<true>() + 0x8d0
> 2 [0x557631f8ee80] main + 0x50
> 3 [0x7fb15f69cd0a] __libc_start_main + 0xea
> 4 [0x557631f8f14a] _start + 0x2a
>
> test_store_io_read_gff FAILED
> ./core/tests/store/test_store_io.h:248 Assertion failed : fin.good() should be true but was 0
>
> stack trace:
> 0 [0x557631f9fd45] seqan::ClassTest::fail() + 0x15
> 1 [0x557631fd32a9] void SEQAN_TEST_test_store_io_write_gff<true>() + 0x1029
> 2 [0x557631f8ee96] main + 0x66
> 3 [0x7fb15f69cd0a] __libc_start_main + 0xea
> 4 [0x557631f8f14a] _start + 0x2a
>
> test_store_io_write_gff FAILED
> ./core/tests/store/test_store_io.h:272 Assertion failed : f.good() should be true but was 0
>
> stack trace:
> 0 [0x557631f9fd45] seqan::ClassTest::fail() + 0x15
> 1 [0x557631fd4cf8] void SEQAN_TEST_test_store_io_read_gtf<true>() + 0x1988
> 2 [0x557631f8eeac] main + 0x7c
> 3 [0x7fb15f69cd0a] __libc_start_main + 0xea
> 4 [0x557631f8f14a] _start + 0x2a
>
> test_store_io_read_gtf FAILED
> ./core/tests/store/test_store_io.h:394 Assertion failed : fin.good() should be true but was 0
>
> stack trace:
> 0 [0x557631f9fd45] seqan::ClassTest::fail() + 0x15
> 1 [0x557631fd63e0] void SEQAN_TEST_test_store_io_write_gtf<true>() + 0x1530
> 2 [0x557631f8eec2] main + 0x92
> 3 [0x7fb15f69cd0a] __libc_start_main + 0xea
> 4 [0x557631f8f14a] _start + 0x2a
>
> test_store_io_write_gtf FAILED
> ./core/tests/store/test_store_io.h:544 Assertion failed : fAmosIn.good() should be true but was 0
>
> stack trace:
> 0 [0x557631f9fd45] seqan::ClassTest::fail() + 0x15
> 1 [0x557631fd990a] void SEQAN_TEST_test_store_io_read_amos<true>() + 0x310a
> 2 [0x557631f8eed8] main + 0xa8
> 3 [0x7fb15f69cd0a] __libc_start_main + 0xea
> 4 [0x557631f8f14a] _start + 0x2a
>
> test_store_io_read_amos FAILED
> ./core/tests/store/test_store_io.h:587 Assertion failed : fFastaIn.good() should be true but was 0
>
> stack trace:
> 0 [0x557631f9fd45] seqan::ClassTest::fail() + 0x15
> 1 [0x557631fe2571] void SEQAN_TEST_test_store_io_write_amos<true>() + 0x1c91
> 2 [0x557631f8eeee] main + 0xbe
> 3 [0x7fb15f69cd0a] __libc_start_main + 0xea
> 4 [0x557631f8f14a] _start + 0x2a
>
> test_store_io_write_amos FAILED
> Open failed on file ./core/tests/store/ex1.fa: "No such file or directory"
> ./core/tests/store/test_store_io.h:430 Assertion failed : f.good() should be true but was 0
>
> stack trace:
> 0 [0x557631f9fd45] seqan::ClassTest::fail() + 0x15
> 1 [0x557631fe07f9] void SEQAN_TEST_test_store_io_sam<true>() + 0xee9
> 2 [0x557631f8ef04] main + 0xd4
> 3 [0x7fb15f69cd0a] __libc_start_main + 0xea
> 4 [0x557631f8f14a] _start + 0x2a
>
> test_store_io_sam FAILED
> Open failed on file ./core/tests/store/ex1.fa: "No such file or directory"
> Open failed on file ./core/tests/store/ex1.bam. (No such file or directory)
> lseek returned -1. (Bad file descriptor)
> lseek returned -1. (Bad file descriptor)
> lseek returned -1. (Bad file descriptor)
> seek returned ffffffffffffffff instead of 0
> ./core/tests/store/test_store_io.h:488 Assertion failed : open(stream, toCString(bamFileName), "r") should be true but was 0
>
> stack trace:
> 0 [0x557631f9fd45] seqan::ClassTest::fail() + 0x15
> 1 [0x557631fdf7d9] void SEQAN_TEST_test_store_io_read_bam<true>() + 0xf89
> 2 [0x557631f8ef1a] main + 0xea
> 3 [0x7fb15f69cd0a] __libc_start_main + 0xea
> 4 [0x557631f8f14a] _start + 0x2a
>
> test_store_io_read_bam FAILED
> **************************************
> Total Check Points : 0
> Found Check Points : 0
> Lost Check Points : 0
> --------------------------------------
> Total Tests: 10
> Skipped: 0
> Errors: 10
> **************************************
>
> Start 93: test_test_find_swift
> 90/93 Test #93: test_test_find_swift ............................................... Passed 0.01 sec
> 91/93 Test #84: test_test_pipe ..................................................... Passed 0.70 sec
> 92/93 Test #92: test_test_stream ...................................................***Exception: SegFault 3.60 sec
> TEST SUITE test_stream
> SEQAN_ENABLE_DEBUG == 1
> SEQAN_ENABLE_TESTING == 1
> SEQAN_ENABLE_CHECKPOINTS == 0
> SEQAN_CXX_FLAGS == "SEQAN_CXX_FLAGS_NOT_SET"
> test_stream_char_array_metafunctions OK
> test_stream_char_array_read_simple_usage OK
> test_stream_char_array_read_complex_usage OK
> test_stream_char_array_write_simple_usage OK
> test_stream_char_array_write_complex_usage OK
> test_stream_char_array_eof OK
> test_stream_char_array_peek OK
> test_stream_char_array_read_char OK
> test_stream_char_array_read_block OK
> test_stream_char_array_write_block OK
> test_stream_char_array_streamPut OK
> test_stream_char_array_write_char OK
> test_stream_char_array_flush OK
> test_stream_char_array_seek OK
> test_stream_char_array_tell OK
> test_stream_file_stream_metafunctions_file OK
> test_stream_file_stream_metafunctions_mmap OK
> test_stream_file_stream_read_simple_usage_file OK
> test_stream_file_stream_read_simple_usage_mmap OK
> test_stream_file_stream_read_complex_usage_file OK
> test_stream_file_stream_read_complex_usage_mmap OK
> test_stream_file_stream_write_simple_usage_file OK
> test_stream_file_stream_write_simple_usage_mmap OK
> test_stream_file_stream_write_complex_usage_file OK
> test_stream_file_stream_write_complex_usage_mmap OK
> test_stream_file_stream_eof_file OK
> test_stream_file_stream_eof_mmap OK
> test_stream_file_stream_peek_file OK
> test_stream_file_stream_peek_mmap OK
> test_stream_file_stream_read_char_file OK
> test_stream_file_stream_read_char_mmap OK
> test_stream_file_stream_read_block_file OK
> test_stream_file_stream_read_block_mmap OK
> test_stream_file_stream_write_block_file OK
> test_stream_file_stream_write_block_mmap OK
> test_stream_file_stream_streamPut_file OK
> test_stream_file_stream_streamPut_mmap OK
> test_stream_file_stream_write_char_file OK
> test_stream_file_stream_write_char_mmap OK
> test_stream_file_stream_flush_file OK
> test_stream_file_stream_flush_mmap OK
> test_stream_file_stream_seek_file OK
> test_stream_file_stream_seek_mmap OK
> test_stream_file_stream_tell_file OK
> test_stream_file_stream_tell_mmap OK
> test_stream_file_stream_read_large_file OK
> test_stream_file_stream_read_large_mmap OK
> test_stream_file_stream_write_large_file OK
> test_stream_file_stream_write_large_mmap OK
> test_stream_file_stream_seek_large_file OK
> test_stream_file_stream_seek_large_mmap OK
> test_stream_gz_file_metafunctions OK
> test_stream_gz_file_read_simple_usage OK
> test_stream_gz_file_read_complex_usage OK
> test_stream_gz_file_write_simple_usage OK
> test_stream_gz_file_write_complex_usage OK
> test_stream_gz_file_eof OK
> test_stream_gz_file_peek OK
> test_stream_gz_file_read_char OK
> test_stream_gz_file_read_block OK
> test_stream_gz_file_write_block OK
> test_stream_gz_file_streamPut OK
> test_stream_gz_file_write_char OK
> test_stream_gz_file_flush OK
> test_stream_gz_file_seek OK
> test_stream_gz_file_tell OK
> test_stream_bgzf_metafunctions OK
> test_stream_bgzf_read_simple_usage OK
> test_stream_bgzf_read_complex_usage OK
> test_stream_bgzf_write_simple_usage OK
> test_stream_bgzf_write_complex_usage OK
> test_stream_bgzf_eof OK
> test_stream_bgzf_peek OK
> test_stream_bgzf_read_char OK
> test_stream_bgzf_read_block OK
> test_stream_bgzf_write_block OK
> test_stream_bgzf_streamPut OK
> test_stream_bgzf_write_char OK
> test_stream_bgzf_flush OK
> test_stream_bgzf_seek OK
> test_stream_bgzf_tell OK
>
>
> stack trace:
> 0 [0x55f53a4309e4] /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/test_stream(+0x179e4)
> 1 [0x7faaf8a06d60] /lib/x86_64-linux-gnu/libc.so.6(+0x3bd60)
> 2 [0x7faaf8a47750] _IO_feof + 0
> 3 [0x55f53a44df9a] void SEQAN_TEST_test_stream_bgzf_write_large_and_compare_with_file<true>() + 0x26a
> 4 [0x55f53a42ea82] main + 0xa52
> 5 [0x7faaf89f1d0a] __libc_start_main + 0xea
> 6 [0x55f53a42feca] _start + 0x2a
>
>
> 93/93 Test #69: test_test_index_creation ........................................... Passed 7.22 sec
>
> 86% tests passed, 13 tests failed out of 93
>
> Total Test time (real) = 7.78 sec
>
> The following tests FAILED:
> 7 - test_demo_bam_io_bam_stream (Failed)
> 41 - test_demo_seq_io_fai_index_example (Failed)
> 42 - test_demo_seq_io_sequence_stream_read (Failed)
> 46 - test_test_arg_parse (Failed)
> 47 - test_test_bam_io (Failed)
> 61 - test_test_consensus (Failed)
> 62 - test_test_file (Failed)
> 64 - test_test_gff_io (Failed)
> 75 - test_test_index_sa_bwtwalk (Failed)
> 86 - test_test_score (Failed)
> 88 - test_test_seq_io (Failed)
> 91 - test_test_store (Failed)
> 92 - test_test_stream (SEGFAULT)
> Errors while running CTest
> make[2]: *** [Makefile:106: 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/2021/01/20/seqan_1.4.2+dfsg-4_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!
If you reassign this bug to another package, please marking 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 me
so that we can identify if something relevant changed in the meantime.
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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