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 <[email protected]> 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 <[email protected]> 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@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 >> >
