Source: freebayes Version: 1.3.7-1 Severity: serious Justification: FTBFS Tags: trixie sid ftbfs User: [email protected] Usertags: ftbfs-20240319 ftbfs-trixie
Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > make[1]: Entering directory '/<<PKGBUILDDIR>>' > mkdir -p test/bash-tap/ > ln -s -t test/bash-tap /<<PKGBUILDDIR>>/debian/bash-tap/* > mkdir -p test/test-simple-bash > ln -s -t test/test-simple-bash /<<PKGBUILDDIR>>/debian/test-simple-bash/* > dh_auto_test -- -v --timeout-multiplier 100 > cd build && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 > MESON_TESTTHREADS=8 meson test -v --timeout-multiplier 100 > ninja: Entering directory `/<<PKGBUILDDIR>>/build' > ninja: no work to do. > 1/5 T00 RUNNING > >>> UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 > >>> ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 > >>> MALLOC_PERTURB_=188 /usr/bin/prove -e bash -v > >>> t/00_region_and_target_handling.t > > 2/5 T01 RUNNING > >>> UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 > >>> ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 > >>> MALLOC_PERTURB_=101 /usr/bin/prove -e bash -v t/01_call_variants.t > > 3/5 T01b RUNNING > >>> UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 > >>> ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 > >>> MALLOC_PERTURB_=91 /usr/bin/prove -e bash -v t/01b_call_variants.t > > 4/5 T02 RUNNING > >>> UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 > >>> ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 > >>> MALLOC_PERTURB_=16 /usr/bin/prove -e bash -v t/02_multi_bam.t > > 5/5 T03 RUNNING > >>> MALLOC_PERTURB_=13 > >>> UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 > >>> ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 > >>> /usr/bin/prove -e bash -v t/03_reference_bases.t > > 5/5 T03 FAIL 0.32s exit status 1 > ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― > t/03_reference_bases.t .. > 1..3 > ok 1 - freebayes rejects invalid reference > not ok 2 - freebayes does not put uppercase IUPAC bases in VCFs > # got: '/usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed.' > # expected: 'ref 14 . A G > # ref 16 . CNNNNNNNNNNN TAAAAAAAAAAA > # ref 29 . C G > # ref 31 . A T' > not ok 3 - freebayes does not put lowercase IUPAC bases in VCFs > # got: '/usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed.' > # expected: 'ref 14 . A G > # ref 16 . CNNNNNNNNNNN TAAAAAAAAAAA > # ref 29 . C G > # ref 31 . A T' > Failed 2/3 subtests > > Test Summary Report > ------------------- > t/03_reference_bases.t (Wstat: 0 Tests: 3 Failed: 2) > Failed tests: 2-3 > Files=1, Tests=3, 0 wallclock secs ( 0.04 usr 0.00 sys + 0.05 cusr 0.04 > csys = 0.13 CPU) > Result: FAIL > ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― > > 1/5 T00 FAIL 0.51s exit status 1 > ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― > stdout: > t/00_region_and_target_handling.t .. > 1..12 > ok 1 - ref:4-5 ref:6-7 are empty > ok 2 - ref:4 ref:6 are empty > not ok 3 - ref:5-6 ref:7-8 > not ok 4 - ref:5 ref:7 > not ok 5 - ref:5- > not ok 6 - full output > not ok 7 - --targets t/../00_region_and_target_handling.t.bed > not ok 8 - --region ref > not ok 9 - ref:1,0- > not ok 10 - ref:1,0-1,1 > not ok 11 - ref:0-1 > ok 12 - region outside of bounds error > Failed 9/12 subtests > > Test Summary Report > ------------------- > t/00_region_and_target_handling.t (Wstat: 0 Tests: 12 Failed: 9) > Failed tests: 3-11 > Files=1, Tests=12, 0 wallclock secs ( 0.05 usr 0.00 sys + 0.16 cusr 0.16 > csys = 0.37 CPU) > Result: FAIL > stderr: > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > # Failed test 'ref:5-6 ref:7-8' > # at t/00_region_and_target_handling.t line 101. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > # Failed test 'ref:5 ref:7' > # at t/00_region_and_target_handling.t line 104. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > # Failed test 'ref:5-' > # at t/00_region_and_target_handling.t line 113. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > # Failed test 'full output' > # at t/00_region_and_target_handling.t line 124. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > # Failed test '--targets t/../00_region_and_target_handling.t.bed' > # at t/00_region_and_target_handling.t line 127. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > # Failed test '--region ref' > # at t/00_region_and_target_handling.t line 130. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > # Failed test 'ref:1,0-' > # at t/00_region_and_target_handling.t line 138. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > # Failed test 'ref:1,0-1,1' > # at t/00_region_and_target_handling.t line 141. > # Failed test 'ref:0-1' > # at t/00_region_and_target_handling.t line 145. > Output: /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― > > 4/5 T02 FAIL 0.53s exit status 1 > ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― > t/02_multi_bam.t .. > 1..7 > not ok 1 - freebayes calls from two identical BAMs > # got: '/usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed.' > # expected: 'ref 2 . A G > # ref 4 . CG TA > # ref 7 . C G > # ref 9 . A T' > not ok 2 - freebayes calls from two BAMs with different samples for different > read groups > # got: '/usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed.' > # expected: 'ref 2 . A G > # ref 4 . CG TA > # ref 7 . C G > # ref 9 . A T' > not ok 3 - freebayes calls from two BAMs with different technologies for > different read groups > # got: '/usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed.' > # expected: 'ref 2 . A G > # ref 4 . CG TA > # ref 7 . C G > # ref 9 . A T' > ok 4 - freebayes rejects two BAMs with different samples for same read groups > ok 5 - freebayes rejects two BAMs with different technologies for same read > groups > not ok 6 - freebayes calls multiple alts from two different BAMs > # got: '/usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed.' > # expected: 'ref 2 . A C,G > # ref 4 . CG TA > # ref 7 . C G > # ref 9 . A T' > ok 7 - freebayes rejects two BAMs with the same name > Failed 4/7 subtests > > Test Summary Report > ------------------- > t/02_multi_bam.t (Wstat: 0 Tests: 7 Failed: 4) > Failed tests: 1-3, 6 > Files=1, Tests=7, 0 wallclock secs ( 0.04 usr 0.01 sys + 0.19 cusr 0.15 > csys = 0.39 CPU) > Result: FAIL > ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― > > 2/5 T01 FAIL 0.86s exit status 1 > ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― > stdout: > t/01_call_variants.t .. > 1..16 > not ok 1 - variant calling recovers most of the GiAB variants in a test region > # got: '0' > # expected: '1' > ok 2 - freebayes produces the same number of calls if targeted per site or > called without targets > ok 3 - a targets bed file can be used with the same effect as running by > region > ok 4 - reading from stdin or not makes no difference > not ok 5 - freebayes processes all alignments in BAM input > # got: '3333' > # expected: '51' > ok 6 - freebayes processes all alignments in CRAM input > not ok 7 - freebayes correctly handles variant input > # got: '0' > # expected: '16' > not ok 8 - freebayes puts required variants in output > # got: '0' > # expected: '3' > not ok 9 - freebayes limits calls to input variants correctly > # got: '0' > # expected: '3' > not ok 10 - freebayes reports all input variants even when there is no input > data > # got: '0' > # expected: '16' > not ok 11 - freebayes handles region and variant input > # got: '0' > # expected: '2' > not ok 12 - freebayes limits to variant input correctly when region is given > # got: '0' > # expected: '2' > not ok 13 - freebayes handles variant input and reading from stdin > # got: '0' > # expected: '3' > not ok 14 - freebayes limits to variant input when reading from stdin > # got: '0' > # expected: '3' > not ok 15 - freebayes handles region, stdin, and variant input > # got: '0' > # expected: '2' > ok 16 - ! > Failed 11/16 subtests > > Test Summary Report > ------------------- > t/01_call_variants.t (Wstat: 0 Tests: 16 Failed: 11) > Failed tests: 1, 5, 7-15 > Files=1, Tests=16, 0 wallclock secs ( 0.04 usr 0.01 sys + 0.54 cusr 0.38 > csys = 0.97 CPU) > Result: FAIL > stderr: > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > [E::idx_find_and_load] Could not retrieve index file for '-' > Random access with SetRegion not available for STDIN reading (no index file) > ERROR(freebayes): Could not SetRegion to q:1..10000 > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > t/01_call_variants.t: line 107: 2407978 Aborted freebayes -f > tiny/q.fa.gz -@ tiny/q_spiked.vcf.gz -r q:1-10000 -l - < > tiny/NA12878.chr22.tiny.bam > /dev/null 2> /dev/null > ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― > > 3/5 T01b FAIL 1.06s exit status 1 > ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― > stdout: > t/01b_call_variants.t .. > 1..10 > ok 1 - running in parallel makes no difference > ok 2 - freebayes handles spaces in file names > not ok 3 - freebayes handles region and variant input even with : in contig > names > # got: '0' > # expected: '2' > not ok 4 - freebayes can handle spliced reads > # got: '0' > # expected: '3' > not ok 5 - freebayes produces the expected number of lines of gVCF output > # got: '0' > # expected: '20' > not ok 6 - freebayes produces the expected number of lines of gVCF output > # got: '3' > # expected: '250' > not ok 7 - freebayes produces the expected number of lines of gVCF output > # got: '176' > # expected: '12250' > not ok 8 - the CNV map may be used to specify per-sample copy numbers > # got: '0' > # expected: '19' > not ok 9 - freebayes makes the expected number of calls when capping coverage > # got: '0' > # expected: '22' > not ok 10 - freebayes correctly uses CNV map with multiple entries > # got: '0:0' > # expected: '0:19' > Failed 8/10 subtests > > Test Summary Report > ------------------- > t/01b_call_variants.t (Wstat: 0 Tests: 10 Failed: 8) > Failed tests: 3-10 > Files=1, Tests=10, 0 wallclock secs ( 0.04 usr 0.01 sys + 0.75 cusr 0.43 > csys = 1.23 CPU) > Result: FAIL > stderr: > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― > > > Summary of Failures: > > 5/5 T03 FAIL 0.32s exit status 1 > 1/5 T00 FAIL 0.51s exit status 1 > 4/5 T02 FAIL 0.53s exit status 1 > 2/5 T01 FAIL 0.86s exit status 1 > 3/5 T01b FAIL 1.06s exit status 1 > > Ok: 0 > Expected Fail: 0 > Fail: 5 > Unexpected Pass: 0 > Skipped: 0 > Timeout: 0 > > Full log written to /<<PKGBUILDDIR>>/build/meson-logs/testlog.txt > cd build && tail -v -n \+0 meson-logs/testlog.txt > ==> meson-logs/testlog.txt <== > Log of Meson test suite run on 2024-03-20T06:47:16.920247 > > Inherited environment: SCHROOT_GID=1001 DEB_HOST_MULTIARCH=x86_64-linux-gnu > LC_ALL=C.UTF-8 DEB_HOST_GNU_SYSTEM=linux-gnu > DEB_BUILD_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_ARCH_LIBC=gnu FFLAGS='-g -O2 > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong > -fstack-clash-protection -fcf-protection' DEB_BUILD_ARCH_ENDIAN=little > DEB_BUILD_GNU_SYSTEM=linux-gnu CFLAGS_FOR_BUILD='-g -O2' > OBJCXXFLAGS_FOR_BUILD='-g -O2' DEB_BUILD_ARCH_BITS=64 > DEB_BUILD_OPTIONS=parallel=8 DEB_HOST_ARCH=amd64 LDFLAGS_FOR_BUILD='' > DEB_TARGET_ARCH_ENDIAN=little SOURCE_DATE_EPOCH=1692616934 > OBJCFLAGS_FOR_BUILD='-g -O2' OBJCXXFLAGS='-g -O2 > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong > -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' > DEB_HOST_ARCH_BITS=64 LANG=C.UTF-8 MAKEFLAGS=w SCHROOT_GROUP=user42 > DEB_TARGET_ARCH=amd64 > DH_INTERNAL_OPTIONS='-O--buildsystem=meson -O--builddir=build' > DEB_HOST_GNU_CPU=x86_64 DEB_BUILD_ARCH_LIBC=gnu MFLAGS=-w > DEB_TARGET_ARCH_BITS=64 CXXFLAGS_FOR_BUILD='-g -O2' ASFLAGS='' > DEB_BUILD_ARCH_CPU=amd64 LC_COLLATE=C.UTF-8 SCHROOT_ALIAS_NAME=unstable > DEB_HOST_ARCH_OS=linux SHELL=/bin/sh FCFLAGS='-g -O2 > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong > -fstack-clash-protection -fcf-protection' DEB_HOST_ARCH_CPU=amd64 > SCHROOT_USER=user42 > PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games > DEB_BUILD_ARCH_ABI=base CPPFLAGS_FOR_BUILD='' DEB_BUILD_ARCH=amd64 > FFLAGS_FOR_BUILD='-g -O2' DEB_HOST_ARCH_LIBC=gnu > SCHROOT_SESSION_ID=sid-amd64-sbuild-f29c4bc5-f18b-47c0-b449-cddb49804807 > DEB_TARGET_ARCH_CPU=amd64 DEB_HOST_GNU_TYPE=x86_64-linux-gnu > DEB_BUILD_ARCH_OS=linux FCFLAGS_FOR_BUILD='-g -O2' DFLAGS_FOR_BUILD=-frelease > LOGNAME=user42 CPPFLAGS='-Wdate-time -D_FORTIFY_SOURCE=2' > DEB_TARGET_MULTIARCH=x86_64-linux-gnu DEB_BUILD_GNU_CPU=x86_64 > DEB_TARGET_ARCH_OS=linux USER=user42 DEB_HOST_ARCH_ABI=base > DEB_BUILD_MULTIARCH=x86_64-linux-gnu LDFLAGS='-Wl,-z,relro -Wl,-z,now' > DEB_TARGET_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_ARCH_ABI=base CFLAGS='-g -O2 > -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. > -fstack-protector-strong -fstack-clash-protection -Wformat > -Werror=format-security -fcf-protection' SCHROOT_UID=1001 > SCHROOT_COMMAND='dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -sa' > DFLAGS=-frelease DEB_TARGET_GNU_CPU=x86_64 ASFLAGS_FOR_BUILD='' > APT_CONFIG=/var/lib/sbuild/apt.conf > HOME=/<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home > DEB_RULES_REQUIRES_ROOT=no DEB_TARGET_GNU_SYSTEM=linux-gnu > DEB_HOST_ARCH_ENDIAN=little OBJCFLAGS='-g -O2 > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong > -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' > SCHROOT_CHROOT_NAME=sid-amd64-sbuild DEB_BUILD_MAINT_OPTIONS=hardening=+all > DH_INTERNAL_BUILDFLAGS=1 CXXFLAGS='-g -O2 > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong > -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' > DH_INTERNAL_OVERRIDE=dh_auto_test MAKELEVEL=2 > XDG_RUNTIME_DIR=/tmp/dh-xdg-rundir-01nIBsO6 MESON_TESTTHREADS=8 > DEB_PYTHON_INSTALL_LAYOUT=deb > > ==================================== 5/5 ===================================== > test: T03 > start time: 06:47:16 > duration: 0.32s > result: exit status 1 > command: MALLOC_PERTURB_=13 > UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 > ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 /usr/bin/prove > -e bash -v t/03_reference_bases.t > ----------------------------------- stdout ----------------------------------- > t/03_reference_bases.t .. > 1..3 > ok 1 - freebayes rejects invalid reference > not ok 2 - freebayes does not put uppercase IUPAC bases in VCFs > # got: '/usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed.' > # expected: 'ref 14 . A G > # ref 16 . CNNNNNNNNNNN TAAAAAAAAAAA > # ref 29 . C G > # ref 31 . A T' > not ok 3 - freebayes does not put lowercase IUPAC bases in VCFs > # got: '/usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed.' > # expected: 'ref 14 . A G > # ref 16 . CNNNNNNNNNNN TAAAAAAAAAAA > # ref 29 . C G > # ref 31 . A T' > Failed 2/3 subtests > > Test Summary Report > ------------------- > t/03_reference_bases.t (Wstat: 0 Tests: 3 Failed: 2) > Failed tests: 2-3 > Files=1, Tests=3, 0 wallclock secs ( 0.04 usr 0.00 sys + 0.05 cusr 0.04 > csys = 0.13 CPU) > Result: FAIL > ============================================================================== > > ==================================== 1/5 ===================================== > test: T00 > start time: 06:47:16 > duration: 0.51s > result: exit status 1 > command: > UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 > ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 > MALLOC_PERTURB_=188 /usr/bin/prove -e bash -v > t/00_region_and_target_handling.t > ----------------------------------- stdout ----------------------------------- > t/00_region_and_target_handling.t .. > 1..12 > ok 1 - ref:4-5 ref:6-7 are empty > ok 2 - ref:4 ref:6 are empty > not ok 3 - ref:5-6 ref:7-8 > not ok 4 - ref:5 ref:7 > not ok 5 - ref:5- > not ok 6 - full output > not ok 7 - --targets t/../00_region_and_target_handling.t.bed > not ok 8 - --region ref > not ok 9 - ref:1,0- > not ok 10 - ref:1,0-1,1 > not ok 11 - ref:0-1 > ok 12 - region outside of bounds error > Failed 9/12 subtests > > Test Summary Report > ------------------- > t/00_region_and_target_handling.t (Wstat: 0 Tests: 12 Failed: 9) > Failed tests: 3-11 > Files=1, Tests=12, 0 wallclock secs ( 0.05 usr 0.00 sys + 0.16 cusr 0.16 > csys = 0.37 CPU) > Result: FAIL > ----------------------------------- stderr ----------------------------------- > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > # Failed test 'ref:5-6 ref:7-8' > # at t/00_region_and_target_handling.t line 101. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > # Failed test 'ref:5 ref:7' > # at t/00_region_and_target_handling.t line 104. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > # Failed test 'ref:5-' > # at t/00_region_and_target_handling.t line 113. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > # Failed test 'full output' > # at t/00_region_and_target_handling.t line 124. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > # Failed test '--targets t/../00_region_and_target_handling.t.bed' > # at t/00_region_and_target_handling.t line 127. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > # Failed test '--region ref' > # at t/00_region_and_target_handling.t line 130. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > # Failed test 'ref:1,0-' > # at t/00_region_and_target_handling.t line 138. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > # Failed test 'ref:1,0-1,1' > # at t/00_region_and_target_handling.t line 141. > # Failed test 'ref:0-1' > # at t/00_region_and_target_handling.t line 145. > Output: /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > ============================================================================== > > ==================================== 4/5 ===================================== > test: T02 > start time: 06:47:16 > duration: 0.53s > result: exit status 1 > command: > UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 > ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 > MALLOC_PERTURB_=16 /usr/bin/prove -e bash -v t/02_multi_bam.t > ----------------------------------- stdout ----------------------------------- > t/02_multi_bam.t .. > 1..7 > not ok 1 - freebayes calls from two identical BAMs > # got: '/usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed.' > # expected: 'ref 2 . A G > # ref 4 . CG TA > # ref 7 . C G > # ref 9 . A T' > not ok 2 - freebayes calls from two BAMs with different samples for different > read groups > # got: '/usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed.' > # expected: 'ref 2 . A G > # ref 4 . CG TA > # ref 7 . C G > # ref 9 . A T' > not ok 3 - freebayes calls from two BAMs with different technologies for > different read groups > # got: '/usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed.' > # expected: 'ref 2 . A G > # ref 4 . CG TA > # ref 7 . C G > # ref 9 . A T' > ok 4 - freebayes rejects two BAMs with different samples for same read groups > ok 5 - freebayes rejects two BAMs with different technologies for same read > groups > not ok 6 - freebayes calls multiple alts from two different BAMs > # got: '/usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed.' > # expected: 'ref 2 . A C,G > # ref 4 . CG TA > # ref 7 . C G > # ref 9 . A T' > ok 7 - freebayes rejects two BAMs with the same name > Failed 4/7 subtests > > Test Summary Report > ------------------- > t/02_multi_bam.t (Wstat: 0 Tests: 7 Failed: 4) > Failed tests: 1-3, 6 > Files=1, Tests=7, 0 wallclock secs ( 0.04 usr 0.01 sys + 0.19 cusr 0.15 > csys = 0.39 CPU) > Result: FAIL > ============================================================================== > > ==================================== 2/5 ===================================== > test: T01 > start time: 06:47:16 > duration: 0.86s > result: exit status 1 > command: > UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 > ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 > MALLOC_PERTURB_=101 /usr/bin/prove -e bash -v t/01_call_variants.t > ----------------------------------- stdout ----------------------------------- > t/01_call_variants.t .. > 1..16 > not ok 1 - variant calling recovers most of the GiAB variants in a test region > # got: '0' > # expected: '1' > ok 2 - freebayes produces the same number of calls if targeted per site or > called without targets > ok 3 - a targets bed file can be used with the same effect as running by > region > ok 4 - reading from stdin or not makes no difference > not ok 5 - freebayes processes all alignments in BAM input > # got: '3333' > # expected: '51' > ok 6 - freebayes processes all alignments in CRAM input > not ok 7 - freebayes correctly handles variant input > # got: '0' > # expected: '16' > not ok 8 - freebayes puts required variants in output > # got: '0' > # expected: '3' > not ok 9 - freebayes limits calls to input variants correctly > # got: '0' > # expected: '3' > not ok 10 - freebayes reports all input variants even when there is no input > data > # got: '0' > # expected: '16' > not ok 11 - freebayes handles region and variant input > # got: '0' > # expected: '2' > not ok 12 - freebayes limits to variant input correctly when region is given > # got: '0' > # expected: '2' > not ok 13 - freebayes handles variant input and reading from stdin > # got: '0' > # expected: '3' > not ok 14 - freebayes limits to variant input when reading from stdin > # got: '0' > # expected: '3' > not ok 15 - freebayes handles region, stdin, and variant input > # got: '0' > # expected: '2' > ok 16 - ! > Failed 11/16 subtests > > Test Summary Report > ------------------- > t/01_call_variants.t (Wstat: 0 Tests: 16 Failed: 11) > Failed tests: 1, 5, 7-15 > Files=1, Tests=16, 0 wallclock secs ( 0.04 usr 0.01 sys + 0.54 cusr 0.38 > csys = 0.97 CPU) > Result: FAIL > ----------------------------------- stderr ----------------------------------- > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > [E::idx_find_and_load] Could not retrieve index file for '-' > Random access with SetRegion not available for STDIN reading (no index file) > ERROR(freebayes): Could not SetRegion to q:1..10000 > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > t/01_call_variants.t: line 107: 2407978 Aborted freebayes -f > tiny/q.fa.gz -@ tiny/q_spiked.vcf.gz -r q:1-10000 -l - < > tiny/NA12878.chr22.tiny.bam > /dev/null 2> /dev/null > ============================================================================== > > ==================================== 3/5 ===================================== > test: T01b > start time: 06:47:16 > duration: 1.06s > result: exit status 1 > command: > UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 > ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 > MALLOC_PERTURB_=91 /usr/bin/prove -e bash -v t/01b_call_variants.t > ----------------------------------- stdout ----------------------------------- > t/01b_call_variants.t .. > 1..10 > ok 1 - running in parallel makes no difference > ok 2 - freebayes handles spaces in file names > not ok 3 - freebayes handles region and variant input even with : in contig > names > # got: '0' > # expected: '2' > not ok 4 - freebayes can handle spliced reads > # got: '0' > # expected: '3' > not ok 5 - freebayes produces the expected number of lines of gVCF output > # got: '0' > # expected: '20' > not ok 6 - freebayes produces the expected number of lines of gVCF output > # got: '3' > # expected: '250' > not ok 7 - freebayes produces the expected number of lines of gVCF output > # got: '176' > # expected: '12250' > not ok 8 - the CNV map may be used to specify per-sample copy numbers > # got: '0' > # expected: '19' > not ok 9 - freebayes makes the expected number of calls when capping coverage > # got: '0' > # expected: '22' > not ok 10 - freebayes correctly uses CNV map with multiple entries > # got: '0:0' > # expected: '0:19' > Failed 8/10 subtests > > Test Summary Report > ------------------- > t/01b_call_variants.t (Wstat: 0 Tests: 10 Failed: 8) > Failed tests: 3-10 > Files=1, Tests=10, 0 wallclock secs ( 0.04 usr 0.01 sys + 0.75 cusr 0.43 > csys = 1.23 CPU) > Result: FAIL > ----------------------------------- stderr ----------------------------------- > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > /usr/include/c++/13/bits/stl_vector.h:1125: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp > = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type > = long unsigned int]: Assertion '__n < this->size()' failed. > ============================================================================== > > > Summary of Failures: > > 5/5 T03 FAIL 0.32s exit status 1 > 1/5 T00 FAIL 0.51s exit status 1 > 4/5 T02 FAIL 0.53s exit status 1 > 2/5 T01 FAIL 0.86s exit status 1 > 3/5 T01b FAIL 1.06s exit status 1 > > Ok: 0 > Expected Fail: 0 > Fail: 5 > Unexpected Pass: 0 > Skipped: 0 > Timeout: 0 > dh_auto_test: error: cd build && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 > MESON_TESTTHREADS=8 meson test -v --timeout-multiplier 100 returned exit code > 5 The full build log is available from: http://qa-logs.debian.net/2024/03/19/freebayes_1.3.7-1_unstable.log All bugs filed during this archive rebuild are listed at: https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20240319;[email protected] or: https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240319&[email protected]&allbugs=1&cseverity=1&ctags=1&caffected=1#results 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 mark 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 mine so that we can identify if something relevant changed in the meantime.
