cjfields
commented
8 years ago Original Redmine Comment Author Name: Chris Fields Original Date: 2011-04-14T03:26:28Z
Just a note that Bio::Tools::HMM has moved into it’s own distribution, but it hasn’t been released due to some issues with failing tests.
Author Name: P. Horton (P. Horton) Original Redmine Issue: 2976, https://redmine.open-bio.org/issues/2976 Original Date: 2009-12-26 Original Assignee: Bioperl Guts
Working with Bioperl-ext version 1.5.1 On Ubuntu with perl v5.10.0, gcc version 4.3.3
% cd bioperl-ext/Bio/Ext/HMM/ % perl Makefile.PL % make
Okay, but
% make test
crashes with
Emission Probability Matrix: 0.160194 0.174757 0.179612 0.160194 0.160194 0.165049 0.0744681 0.0744681 0.12766 0.0425532 0.106383 0.574468 Vitebi Algorithm: glibc detected /usr/bin/perl: malloc(): memory corruption: 0x0a14d3c0 ***\ = Backtrace: === /lib/tls/i686/cmov/libc.so.6[0x400ea276] …
Upon inspection I found what looked to be a code bug in HMM.xs which can be fixed by altering one line. Fixing it case make test to work.
The code bug:
In HMM.xs::HMM_viterbi(class, hmm, seq)
char hss = (char ) malloc(T*sizeof(char));
but in hmmlib.c::viterbi(HMM hmm, char hss, char * obs, int T)
hss[T] = ‘\0’;
Looks like the line in HMM_viterbi should really be
char * hss = (char ) malloc( (T+1) sizeof(char) );