<div dir="ltr">Just a heads-up, today's release contains a fix for an infinite-loop-instead-of-error bug in the previous release.</div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Feb 20, 2022 at 12:36 PM Andreas Tille <<a href="mailto:tille@debian.org">tille@debian.org</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">Cool! This finally works. Thanks a lot for your patience, Andreas.<br>
<br>
Am Sun, Feb 20, 2022 at 09:43:10AM -0800 schrieb Chris Chang:<br>
> Hmm. Ordinarily, that download link would be fine. I had not updated it<br>
> this time because the issue only affects gcc 11+, so it did not affect any<br>
> of the precompiled binaries and I wanted to keep the posted source<br>
> identical to that used to compile those binaries.<br>
> <br>
> On the other hand, the only difference (in the non-gcc-11+ case) between<br>
> the binaries and the updated source is the version date. I guess this is<br>
> insignificant enough that a temporary discordance is less disruptive than<br>
> making you change your packing process, so I've updated the website source<br>
> link to point to the newer code; let me know if you still run into any<br>
> problems.<br>
> <br>
> On Sat, Feb 19, 2022 at 11:53 PM Andreas Tille <<a href="mailto:andreas@an3as.eu" target="_blank">andreas@an3as.eu</a>> wrote:<br>
> <br>
> > 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<br>
> > the<br>
> > > same contents as the v2.00a3-20220218 GitHub tag/release. So I don't<br>
> > 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>><br>
> > wrote:<br>
> > ><br>
> > > > If you build off the current head, the version string should say "18<br>
> > 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>><br>
> > 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<br>
> > "/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>
> ><br>
<br>
-- <br>
<a href="http://fam-tille.de" rel="noreferrer" target="_blank">http://fam-tille.de</a><br>
</blockquote></div>