Your message dated Mon, 08 Feb 2021 21:29:29 +0000
with message-id <e1l9e65-00020q...@fasolo.debian.org>
and subject line Bug#980798: Removed package(s) from unstable
has caused the Debian Bug report #980685,
regarding seqan: FTBFS: dh_auto_test: error: cd obj-x86_64-linux-gnu && make
-j4 test ARGS\+=-j4 returned exit code 2
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
980685: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=980685
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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.
--- End Message ---
--- Begin Message ---
Version: 1.4.2+dfsg-4+rm
Dear submitter,
as the package seqan has just been removed from the Debian archive
unstable we hereby close the associated bug reports. We are sorry
that we couldn't deal with your issue properly.
For details on the removal, please see https://bugs.debian.org/980798
The version of this package that was in Debian prior to this removal
can still be found using http://snapshot.debian.org/.
Please note that the changes have been done on the master archive and
will not propagate to any mirrors until the next dinstall run at the
earliest.
This message was generated automatically; if you believe that there is
a problem with it please contact the archive administrators by mailing
ftpmas...@ftp-master.debian.org.
Debian distribution maintenance software
pp.
Joerg Jaspert (the ftpmaster behind the curtain)
--- End Message ---
