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Bug 401943

Summary: sci-biology/transfac-3.2 - tfextract segmentation fault in 0x00007f5df6cc4487 in ajStrDel (Pstr=0x7fffabef3a90) at ajstr.c:2547
Product: Gentoo Linux Reporter: Martin Mokrejš <mmokrejs>
Component: Current packagesAssignee: Gentoo Science Biology related packages <sci-biology>
Severity: normal    
Priority: Normal    
Version: unspecified   
Hardware: All   
OS: Linux   
Package list:
Runtime testing required: ---

Description Martin Mokrejš 2012-02-02 17:36:39 UTC
While installing sci-biology/transfac-3.2 I get a crash:

 * Package:    sci-biology/transfac-3.2
 * Repository: gentoo
 * Maintainer:
 * USE:        amd64 elibc_glibc emboss kernel_linux multilib userland_GNU
 * FEATURES:   nostrip sandbox splitdebug
>>> Unpacking source...
>>> Unpacking transfac32.tar.Z to /var/tmp/portage/sci-biology/transfac-3.2/work
>>> Source unpacked in /var/tmp/portage/sci-biology/transfac-3.2/work
>>> Compiling source in /var/tmp/portage/sci-biology/transfac-3.2/work ...

 * Indexing TRANSFAC for usage with EMBOSS.
/var/tmp/portage/sci-biology/transfac-3.2/temp/environment: line 139:  5777 Segmentation fault      (core dumped) EMBOSS_DATA=. tfextract -auto -infile class.dat
 * ERROR: sci-biology/transfac-3.2 failed (compile phase):
 *   Indexing TRANSFAC failed.
 * Call stack:
 *, line  85:  Called src_compile
 *   environment, line 143:  Called die
 * The specific snippet of code:
 *           EMBOSS_DATA=. tfextract -auto -infile class.dat || die "Indexing TRANSFAC failed.";

This leads me to recompile emboss with more debug and resolving the stacktrace:

vostro ~ # pushd /var/tmp/portage/sci-biology/emboss-6.3.1_p4-r1/work/EMBOSS-6.3.1
/var/tmp/portage/sci-biology/emboss-6.3.1_p4-r1/work/EMBOSS-6.3.1 ~
vostro EMBOSS-6.3.1 # gdb /usr/bin/tfextract /var/dumps/core.tfextract.5777 
GNU gdb (Gentoo 7.4 p1) 7.4
Copyright (C) 2012 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-pc-linux-gnu".
For bug reporting instructions, please see:
Reading symbols from /usr/bin/tfextract...done.
[New LWP 5777]

warning: Can't read pathname for load map: Input/output error.
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/".
Core was generated by `tfextract -auto -infile class.dat'.
Program terminated with signal 11, Segmentation fault.
#0  0x00007f5df6cc4487 in ajStrDel (Pstr=0x7fffabef3a90) at ajstr.c:2547
2547        if(!thys->Use)
(gdb) where
#0  0x00007f5df6cc4487 in ajStrDel (Pstr=0x7fffabef3a90) at ajstr.c:2547
#1  0x00000000004019d4 in main (argc=4, argv=0x7fffabef3c18) at tfextract.c:230
(gdb) bt full
#0  0x00007f5df6cc4487 in ajStrDel (Pstr=0x7fffabef3a90) at ajstr.c:2547
        thys = 0x100000001
#1  0x00000000004019d4 in main (argc=4, argv=0x7fffabef3c18) at tfextract.c:230
        inf = 0x0
        fout = 0x0
        iout = 0x0
        vout = 0x0
        pout = 0x0
        oout = 0x0
        fp = 0x232b350
        line = 0x0
        acc = 0x0
        id = 0x0
        bf = 0x0
        pattern = 0x100000001
        pfname = 0x0
        sqlist = 0x0
        patline = 0x7f5df6f32f70
        tmpseq = 0x7f5df6f32f70
        fullseq = 0
        p = 0x232b600 "\300\244\062\002"
        q = 0x7fffabef3c40 "0\\\357\253\377\177"
        gid = 1
        done = 0
(gdb) quit
vostro EMBOSS-6.3.1 #
Comment 1 Toralf Förster gentoo-dev 2016-05-05 08:43:34 UTC

*** This bug has been marked as a duplicate of bug 361411 ***