[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 Chris,

Am Sat, Feb 19, 2022 at 11:37:34PM -0800 schrieb 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.

That's true since on Github the source code of plink1.9 and plink2 is not
separated.  Thus I download the tarball from

   https://www.cog-genomics.org/plink/2.0/

which points to

   https://www.cog-genomics.org/static/bin/plink2_src_220217.zip

I confirm that the tag on Github says v2.00a3-20220218 which seems to be
later than 220217.  In principle I could point the packaging metadata to
Github and exclude everything that I do not need for plink2 packaging (so
remove 1.9 directory and code copies of libdeflate, simde and zstd in 2.0)

In case you consider this the safer way to download plink2 code I'll do so.

Kind regards and thanks a lot for comparing the code base

     Andreas.

> 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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