Source: freebayes
Version: 1.3.7-1
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User:
lucas@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
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