Random Linux Notes

Using Bioperl HMM module
Date: 2009/12/26
Software: bioperl-ext version 1.5.1
Symptom: HMM module could not pass "make test". Died with
*** glibc detected *** /usr/bin/perl: malloc(): memory corruption: 0x0a14d3c0 ***
Cause: Bug in HMM.xs
Solution: in HMM.xs, HMM_viterbi(class, hmm, seq),
replace line:

   char * hss = (char *) malloc(T*sizeof(char));

with:

   char * hss = (char *) malloc( (T+1)*sizeof(char));

I did register this bug fix with bugzilla.

A less critical change, is to replace:

   fprintf(stderr, s);

with:

   fprintf( stderr, "%s", s);

in one place in hmmlib.c, This silences a compiler warning.

Redoing awstats for a full year
Date: 2009/09/25
Software: awstats.pl version 6.4
Symptom: Could not update stats for entire year, even using the -month=all option
Cause: Was not presenting log file in chronological order
Solution: in /etc/awstats/awstats.conf,
LogFile="zcat access.log.9.gz access.log.8.gz ... |"
Note the descending order of the numbers in the filenames.

Lenovo X200 Wireless Network
Date: 2009/08/15
System: lenovo X200, Ubuntu 9.04 2.6.28-14-generic #47-Ubuntu SMP Sat Jul 25 00:28:35 UTC 2009 i686 GNU/Linux
Symptom: Could use unencrypted wireless but could not access 128 bit WEP wireless network
Solution: using WiCD, selected "wext" as your WPA supplicant driver