[Debian-med-packaging] Bug#1067271: freebayes: FTBFS: 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
Lucas Nussbaum
lucas at debian.org
Wed Mar 20 20:58:36 GMT 2024
Source: freebayes
Version: 1.3.7-1
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lucas at debian.org
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;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240319&fusertaguser=lucas@debian.org&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.
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