While installing sci-biology/transfac-3.2 I get a crash: * Package: sci-biology/transfac-3.2 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * 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: * ebuild.sh, 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 <http://gnu.org/licenses/gpl.html> 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: <http://bugs.gentoo.org/>... 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/libthread_db.so.1". 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 #
*** This bug has been marked as a duplicate of bug 361411 ***
