[Debian-med-packaging] Bug#1004037: Segmentation fault in plink2 (Was: src:plink2: fails to migrate to testing for too long: autopkgtest regression)

[Chris Chang]

If you build off the current head, the version string should say "18 Feb
2022", not "17 Feb 2022".

On Sat, Feb 19, 2022 at 7:02 AM Andreas Tille <andreas at an3as.eu> wrote:

> Hi again,
>
> Am Sat, Feb 19, 2022 at 12:28:21AM -0800 schrieb Chris Chang:
> > Ok, new release/tag created.
>
> I've built the new version now.  The bad news is that it keeps on
> SEGFAULTing for me:
>
> ...
> (gdb) run
> Starting program: /usr/lib/plink2/plink2-sse3 --debug --pfile tmp_data
> --export vcf vcf-dosage=DS --out tmp_data2
> [Thread debugging using libthread_db enabled]
> Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
> [New Thread 0x7ffff4cc7640 (LWP 985019)]
> [New Thread 0x7ffff44c6640 (LWP 985020)]
> [New Thread 0x7fffebcc5640 (LWP 985021)]
> PLINK v2.00a3 64-bit (17 Feb 2022)
> www.cog-genomics.org/plink/2.0/
> (C) 2005-2022 Shaun Purcell, Christopher Chang   GNU General Public
> License v3
> Logging to tmp_data2.log.
> Options in effect:
>   --debug
>   --export vcf vcf-dosage=DS
>   --out tmp_data2
>   --pfile tmp_data
>
> Start time: Sat Feb 19 16:00:00 2022
> 31998 MiB RAM detected; reserving 15999 MiB for main workspace.
> Using up to 4 compute threads.
> [New Thread 0x7ffff7fc5640 (LWP 985022)]
>
> Thread 1 "plink2-sse3" received signal SIGSEGV, Segmentation fault.
> plink2::LoadPsam (psamname=psamname at entry=0x7fffffffbe60 "tmp_data.psam",
> pheno_range_list_ptr=<optimized out>, fam_cols=..., pheno_ct_max=<optimized
> out>,
>     missing_pheno=<optimized out>, affection_01=0, max_thread_ct=4,
> piip=0x7fffffff8870, sample_include_ptr=0x7fffffff8790,
> founder_info_ptr=0x7fffffff87a8, sex_nm_ptr=0x7fffffff8798,
>     sex_male_ptr=0x7fffffff87a0, pheno_cols_ptr=0x7fffffff8770,
> pheno_names_ptr=0x7fffffff8780, raw_sample_ct_ptr=0x7fffffff8728,
> pheno_ct_ptr=0x7fffffff8720,
>     max_pheno_name_blen_ptr=0x7fffffff87b0) at ../plink2_psam.cc:611
> 611             pheno_cols[pheno_idx].nonmiss = nullptr;
>
>
> Please let me know if I can do further checks.
>
> Kind regards
>
>       Andreas.
>
> --
> http://fam-tille.de
>
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