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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/plink2">Debian Med / plink2</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/plink2/-/commit/f01ba65b332a116f195a4488ca320cf55b399ab7">f01ba65b</a></strong>
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<span>by Andreas Tille</span>
<i>at 2022-02-18T13:21:34+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Attempt to track down SIGSEGV
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<h4>2 changed files:</h4>
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debian/patches/debug2.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="baf77bb4beb5059404723c700adadf40be42f9e2">
<a href="https://salsa.debian.org/med-team/plink2/-/commit/f01ba65b332a116f195a4488ca320cf55b399ab7#baf77bb4beb5059404723c700adadf40be42f9e2"><strong>debian/patches/debug2.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Fri, 18 Feb 2022 13:20:18 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Attempt to track down SIGSEGV</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">(gdb) run</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Starting program: /usr/lib/plink2/plink2-sse2 --debug --pfile tmp_data --export vcf vcf-dosage=DS --out tmp_data2</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">[Thread</span> debugging using libthread_db enabled]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">[New</span> Thread 0x7ffff4cc7640 (LWP 3957708)]</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">[New</span> Thread 0x7ffff44c6640 (LWP 3957709)]</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">[New</span> Thread 0x7fffe3cc5640 (LWP 3957710)]</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="p">PLINK v2.00a3 64-bit (29 Jan 2022) www.cog-genomics.org/plink/2.0/</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">(C)</span> 2005-2022 Shaun Purcell, Christopher Chang GNU General Public License v3</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">Logging to tmp_data2.log.</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="p">Options in effect:</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> --debug</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> --export vcf vcf-dosage=DS</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> --out tmp_data2</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> --pfile tmp_data</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff">Start time: Fri Feb 18 13:19:13 2022</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="p">31998 MiB RAM detected; reserving 15999 MiB for main workspace.</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="p">Using up to 4 compute threads.</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">[New</span> Thread 0x7ffff7fc5640 (LWP 3957711)]</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--debug: setting pheno_cols[0].nonmiss. = nullptr</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff">Thread 1 "plink2-sse2" received signal SIGSEGV, Segmentation fault.</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="p">0x00005555556fb6ff in plink2::LoadPsam (psamname=psamname@entry=0x7fffffffbe70 "tmp_data.psam", pheno_range_list_ptr=<optimized out>, fam_cols=..., pheno_ct_max=<optimized out>, </span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> 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, </span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> sex_male_ptr=0x7fffffff87b0, pheno_cols_ptr=0x7fffffff8780, pheno_names_ptr=0x7fffffff8790, raw_sample_ct_ptr=0x7fffffff8738, pheno_ct_ptr=0x7fffffff8730, </span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> max_pheno_name_blen_ptr=0x7fffffff87c0) at ../plink2_psam.cc:614</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="p">warning: Source file is more recent than executable.</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="p">614 pheno_cols[pheno_idx].nonmiss = nullptr;</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/plink2_psam.cc</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/plink2_psam.cc</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="p">@@ -608,6 +608,9 @@</span> PglErr LoadPsam(const char* psamname, co</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> for (uint32_t pheno_idx = 0; pheno_idx != pheno_ct; ++pheno_idx) {</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> // ensure cleanup works if initialization fails in the middle</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (g_debug_on) {</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(stdout, "--debug: setting pheno_cols[%d].nonmiss. = nullptr\n", pheno_idx); fflush(stdout);</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> pheno_cols[pheno_idx].nonmiss = nullptr;</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> uint32_t cat_pheno_idx = 0;</span></pre>
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<a href="https://salsa.debian.org/med-team/plink2/-/commit/f01ba65b332a116f195a4488ca320cf55b399ab7#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,3 +2,4 @@ Fix_Makefile.patch</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">use_packaged_libdeflate.patch</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">baseline</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">debug.patch</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">debug2.patch</span></pre>
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