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

[Andreas Tille]

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