Andreas Tille pushed to branch master at Debian Med / plink2
Commits: f01ba65b by Andreas Tille at 2022-02-18T13:21:34+01:00 Attempt to track down SIGSEGV - - - - - 2 changed files: - + debian/patches/debug2.patch - debian/patches/series Changes: ===================================== debian/patches/debug2.patch ===================================== @@ -0,0 +1,47 @@ +Author: Andreas Tille <[email protected]> +Last-Update: Fri, 18 Feb 2022 13:20:18 +0100 +Description: Attempt to track down SIGSEGV + +(gdb) run +Starting program: /usr/lib/plink2/plink2-sse2 --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 3957708)] +[New Thread 0x7ffff44c6640 (LWP 3957709)] +[New Thread 0x7fffe3cc5640 (LWP 3957710)] +PLINK v2.00a3 64-bit (29 Jan 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: Fri Feb 18 13:19:13 2022 +31998 MiB RAM detected; reserving 15999 MiB for main workspace. +Using up to 4 compute threads. +[New Thread 0x7ffff7fc5640 (LWP 3957711)] +--debug: setting pheno_cols[0].nonmiss. = nullptr + +Thread 1 "plink2-sse2" received signal SIGSEGV, Segmentation fault. +0x00005555556fb6ff in plink2::LoadPsam (psamname=psamname@entry=0x7fffffffbe70 "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=0x7fffffff8880, sample_include_ptr=0x7fffffff87a0, founder_info_ptr=0x7fffffff87b8, sex_nm_ptr=0x7fffffff87a8, + sex_male_ptr=0x7fffffff87b0, pheno_cols_ptr=0x7fffffff8780, pheno_names_ptr=0x7fffffff8790, raw_sample_ct_ptr=0x7fffffff8738, pheno_ct_ptr=0x7fffffff8730, + max_pheno_name_blen_ptr=0x7fffffff87c0) at ../plink2_psam.cc:614 +warning: Source file is more recent than executable. +614 pheno_cols[pheno_idx].nonmiss = nullptr; + + +--- a/plink2_psam.cc ++++ b/plink2_psam.cc +@@ -608,6 +608,9 @@ PglErr LoadPsam(const char* psamname, co + } + for (uint32_t pheno_idx = 0; pheno_idx != pheno_ct; ++pheno_idx) { + // ensure cleanup works if initialization fails in the middle ++ if (g_debug_on) { ++ fprintf(stdout, "--debug: setting pheno_cols[%d].nonmiss. = nullptr\n", pheno_idx); fflush(stdout); ++ } + pheno_cols[pheno_idx].nonmiss = nullptr; + } + uint32_t cat_pheno_idx = 0; ===================================== debian/patches/series ===================================== @@ -2,3 +2,4 @@ Fix_Makefile.patch use_packaged_libdeflate.patch baseline debug.patch +debug2.patch View it on GitLab: https://salsa.debian.org/med-team/plink2/-/commit/f01ba65b332a116f195a4488ca320cf55b399ab7 -- View it on GitLab: https://salsa.debian.org/med-team/plink2/-/commit/f01ba65b332a116f195a4488ca320cf55b399ab7 You're receiving this email because of your account on salsa.debian.org.
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