<div dir="ltr">Hmm. Ordinarily, that download link would be fine. I had not updated it this time because the issue only affects gcc 11+, so it did not affect any of the precompiled binaries and I wanted to keep the posted source identical to that used to compile those binaries.<div><br></div><div>On the other hand, the only difference (in the non-gcc-11+ case) between the binaries and the updated source is the version date. I guess this is insignificant enough that a temporary discordance is less disruptive than making you change your packing process, so I've updated the website source link to point to the newer code; let me know if you still run into any problems.</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sat, Feb 19, 2022 at 11:53 PM Andreas Tille <<a href="mailto:andreas@an3as.eu">andreas@an3as.eu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">Hi Chris,<br>
<br>
Am Sat, Feb 19, 2022 at 11:37:34PM -0800 schrieb Chris Chang:<br>
> To elaborate: when I look at<br>
> <a href="https://salsa.debian.org/med-team/plink2/-/tree/master" rel="noreferrer" target="_blank">https://salsa.debian.org/med-team/plink2/-/tree/master</a> , I can see that<br>
> plink2.cc, include/plink2_base.h, and include/plink2_base.cc don't have the<br>
> same contents as the v2.00a3-20220218 GitHub tag/release. So I don't know<br>
> where you grabbed the code from this time, but it does not appear to be<br>
> from GitHub.<br>
<br>
That's true since on Github the source code of plink1.9 and plink2 is not<br>
separated. Thus I download the tarball from<br>
<br>
<a href="https://www.cog-genomics.org/plink/2.0/" rel="noreferrer" target="_blank">https://www.cog-genomics.org/plink/2.0/</a><br>
<br>
which points to<br>
<br>
<a href="https://www.cog-genomics.org/static/bin/plink2_src_220217.zip" rel="noreferrer" target="_blank">https://www.cog-genomics.org/static/bin/plink2_src_220217.zip</a><br>
<br>
I confirm that the tag on Github says v2.00a3-20220218 which seems to be<br>
later than 220217. In principle I could point the packaging metadata to<br>
Github and exclude everything that I do not need for plink2 packaging (so<br>
remove 1.9 directory and code copies of libdeflate, simde and zstd in 2.0)<br>
<br>
In case you consider this the safer way to download plink2 code I'll do so.<br>
<br>
Kind regards and thanks a lot for comparing the code base<br>
<br>
Andreas.<br>
<br>
> On Sat, Feb 19, 2022 at 7:54 AM Chris Chang <<a href="mailto:chrchang523@gmail.com" target="_blank">chrchang523@gmail.com</a>> wrote:<br>
> <br>
> > If you build off the current head, the version string should say "18 Feb<br>
> > 2022", not "17 Feb 2022".<br>
> ><br>
> > On Sat, Feb 19, 2022 at 7:02 AM Andreas Tille <<a href="mailto:andreas@an3as.eu" target="_blank">andreas@an3as.eu</a>> wrote:<br>
> ><br>
> >> Hi again,<br>
> >><br>
> >> Am Sat, Feb 19, 2022 at 12:28:21AM -0800 schrieb Chris Chang:<br>
> >> > Ok, new release/tag created.<br>
> >><br>
> >> I've built the new version now. The bad news is that it keeps on<br>
> >> SEGFAULTing for me:<br>
> >><br>
> >> ...<br>
> >> (gdb) run<br>
> >> Starting program: /usr/lib/plink2/plink2-sse3 --debug --pfile tmp_data<br>
> >> --export vcf vcf-dosage=DS --out tmp_data2<br>
> >> [Thread debugging using libthread_db enabled]<br>
> >> Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".<br>
> >> [New Thread 0x7ffff4cc7640 (LWP 985019)]<br>
> >> [New Thread 0x7ffff44c6640 (LWP 985020)]<br>
> >> [New Thread 0x7fffebcc5640 (LWP 985021)]<br>
> >> PLINK v2.00a3 64-bit (17 Feb 2022)<br>
> >> <a href="http://www.cog-genomics.org/plink/2.0/" rel="noreferrer" target="_blank">www.cog-genomics.org/plink/2.0/</a><br>
> >> (C) 2005-2022 Shaun Purcell, Christopher Chang GNU General Public<br>
> >> License v3<br>
> >> Logging to tmp_data2.log.<br>
> >> Options in effect:<br>
> >> --debug<br>
> >> --export vcf vcf-dosage=DS<br>
> >> --out tmp_data2<br>
> >> --pfile tmp_data<br>
> >><br>
> >> Start time: Sat Feb 19 16:00:00 2022<br>
> >> 31998 MiB RAM detected; reserving 15999 MiB for main workspace.<br>
> >> Using up to 4 compute threads.<br>
> >> [New Thread 0x7ffff7fc5640 (LWP 985022)]<br>
> >><br>
> >> Thread 1 "plink2-sse3" received signal SIGSEGV, Segmentation fault.<br>
> >> plink2::LoadPsam (psamname=psamname@entry=0x7fffffffbe60<br>
> >> "tmp_data.psam", pheno_range_list_ptr=<optimized out>, fam_cols=...,<br>
> >> pheno_ct_max=<optimized out>,<br>
> >> missing_pheno=<optimized out>, affection_01=0, max_thread_ct=4,<br>
> >> piip=0x7fffffff8870, sample_include_ptr=0x7fffffff8790,<br>
> >> founder_info_ptr=0x7fffffff87a8, sex_nm_ptr=0x7fffffff8798,<br>
> >> sex_male_ptr=0x7fffffff87a0, pheno_cols_ptr=0x7fffffff8770,<br>
> >> pheno_names_ptr=0x7fffffff8780, raw_sample_ct_ptr=0x7fffffff8728,<br>
> >> pheno_ct_ptr=0x7fffffff8720,<br>
> >> max_pheno_name_blen_ptr=0x7fffffff87b0) at ../plink2_psam.cc:611<br>
> >> 611 pheno_cols[pheno_idx].nonmiss = nullptr;<br>
> >><br>
> >><br>
> >> Please let me know if I can do further checks.<br>
> >><br>
> >> Kind regards<br>
> >><br>
> >> Andreas.<br>
> >><br>
> >> --<br>
> >> <a href="http://fam-tille.de" rel="noreferrer" target="_blank">http://fam-tille.de</a><br>
> >><br>
> ><br>
<br>
-- <br>
<a href="http://fam-tille.de" rel="noreferrer" target="_blank">http://fam-tille.de</a><br>
</blockquote></div>