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

[Chris Chang]

To elaborate: when I look at
https://salsa.debian.org/med-team/plink2/-/tree/master , I can see that
plink2.cc, include/plink2_base.h, and include/plink2_base.cc don't have the
same contents as the v2.00a3-20220218 GitHub tag/release.  So I don't know
where you grabbed the code from this time, but it does not appear to be
from GitHub.

On Sat, Feb 19, 2022 at 7:54 AM Chris Chang <chrchang523 at gmail.com> wrote:

> 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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