Tests fail when building with Guix

[rekado]

We see a lot of test failures when building v1.3.9 (or earlier) on Guix, because the output wildly differs from the expected output.

Here's one example:

1/5 T00  FAIL            0.24s   exit status 1
>>> MALLOC_PERTURB_=130 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 MSAN_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 /gnu/store/v6bivyjbg6bj07s8iqfzdm6hpvypc0p1-perl-5.36.0/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 

To Reproduce

You can reproduce this with guix build freebayes.

Expected behavior

All tests should pass.

[pjotrp]

This is probably because the C library is erroring because of an older vcflib dependency. They both need to be updated.

[pjotrp]

Similar to #786

[pjotrp]

It is this STL runtime error:

/usr/include/c++/13/bits/stl_vector.h:1128: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed.

and it comes from libvcflib. Very annoying.