Bug#1067271: marked as done (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)

[Debian Bug Tracking System]

Your message dated Sun, 16 Feb 2025 16:19:51 +0000
with message-id <e1tjhn1-00cf3o...@fasolo.debian.org>
and subject line Bug#1067271: fixed in freebayes 1.3.9-1
has caused the Debian Bug report #1067271,
regarding 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
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)


-- 
1067271: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1067271
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

--- Begin Message ---

Source: freebayes
Version: 1.3.7-1
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lu...@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=lu...@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240319&fusertaguser=lu...@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.

--- End Message ---

--- Begin Message ---

Source: freebayes
Source-Version: 1.3.9-1
Done: Andreas Tille <ti...@debian.org>

We believe that the bug you reported is fixed in the latest version of
freebayes, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1067...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated freebayes package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 1.8
Date: Sun, 16 Feb 2025 16:26:52 +0100
Source: freebayes
Architecture: source
Version: 1.3.9-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Closes: 1067271
Changes:
 freebayes (1.3.9-1) unstable; urgency=medium
 .
   [ Michael R. Crusoe ]
   * d/watch: mangle pre-release tags appropriately
   * d/control: pkg-config → pkgconf
   * d/ext/multichoose: bundle in library missing from tarball.
   * d/ext/multichoose: update to
     https://github.com/vcflib/multichoose/commit/255192edd49cfe36557f7f4
     f0d2d6ee1c702ffbb
   * d/clean: added more entries
 .
   [ Andreas Tille ]
   * New upstream version
   * Bumped version in Build-Depends: libvcflib-dev (>= 1.0.12~)
     Closes: #1067271
   * Standards-Version: 4.7.0 (routine-update)
   * d/watch: Fix download file name
Checksums-Sha1:
 30a0a7bfa006a90f8a5fb3bdb34feccd3c9d4609 2201 freebayes_1.3.9-1.dsc
 0443ffd825ff71056ed8b225e49b1101a65135a1 2896143 freebayes_1.3.9.orig.tar.gz
 a7d2f742fea1903522acf62b793c4366a327cc4f 19708 freebayes_1.3.9-1.debian.tar.xz
 2b9f813bd838b49bafcacab65beb7105c84a47ab 12777 
freebayes_1.3.9-1_amd64.buildinfo
Checksums-Sha256:
 37385cc4e0419f3018a2b5aee94f4748e68b2cd18d9b2e29912a196e07620093 2201 
freebayes_1.3.9-1.dsc
 41ed3074c7648375286168a6708e02dac6788eaca4ca6039ff5a7ed91f257b53 2896143 
freebayes_1.3.9.orig.tar.gz
 7a59242fe78e86986fb0f1410f5a282c19d352651b8f76611a4cedee9e3ccdc3 19708 
freebayes_1.3.9-1.debian.tar.xz
 46b578aaf4af0ca92cca49a20adce5d94cdbad719c1e4bec291e2eb4fc2dd687 12777 
freebayes_1.3.9-1_amd64.buildinfo
Files:
 c85187348d9e52be494315e21fe00053 2201 science optional freebayes_1.3.9-1.dsc
 5675648a05ad1d770a1c1e96f8c8f1d5 2896143 science optional 
freebayes_1.3.9.orig.tar.gz
 a5d83229bdb0a1bad16e8daba7d9acef 19708 science optional 
freebayes_1.3.9-1.debian.tar.xz
 54c7f9b927a30a3e835eb5e258e40e99 12777 science optional 
freebayes_1.3.9-1_amd64.buildinfo

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