[BioC] rGADEM crashes on Ubuntu 10.04 64-bit

Sat Dec 31 01:14:43 CET 2011

rGADEM is crashing for me on Ubuntu 64-bit.  I've tried changing
numGeneration, nmotifs, using just rGADEM defaults, and using smaller
sequence sets (500-10k).  The box seems to have plenty of memory
during runs as monitored with top.  I've updated and recompiled all R
and bioconductor packages present on the machine.  Any ideas?

R version 2.14.0 (2011-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)

Code run:

seq <- read.DNAStringSet("10k_fasta.txt", "fasta")
gadem <- GADEM(seq, verbose=TRUE, numGeneration=2, maxSpaceWidth=20,nmotifs=1)

Output:
input sequence file:
number of sequences and average length:				10000  22.0
Use pgf method to approximate llr null distribution
parameters estimated from sequences in:

number of GA generations & population size:			2 100

PWM score p-value cutoff for binding site declaration:		2.000000e-04
ln(E-value) cutoff for motif declaration:			0.000000

number of EM steps:						40
minimal no. sites considered for a motif:			500

[a,c,g,t] frequencies in input data:				0.304650 0.195350 0.195350 0.304650
<snip>
==============
Goes through all GADEM generation cycles, detecting motifs, then
crashes after last generation.

Errors follow:
==============
Maximal number of motifs (1) reached
*** glibc detected *** /usr/lib64/R/bin/exec/R: double free or
corruption (out): 0x0000000006b4dfe0 ***
======= Backtrace: =========
/lib/libc.so.6(+0x775b6)[0x7fa9c4efa5b6]
/lib/libc.so.6(cfree+0x73)[0x7fa9c4f00e83]
/usr/local/lib/R/site-library/rGADEM/libs/rGADEM.so(GADEM_Analysis+0x1844)[0x7fa9be7a7df4]
/usr/lib64/R/lib/libR.so(+0xadf00)[0x7fa9c56def00]
/usr/lib64/R/lib/libR.so(Rf_eval+0x698)[0x7fa9c57153b8]
/usr/lib64/R/lib/libR.so(+0xe6d7f)[0x7fa9c5717d7f]
/usr/lib64/R/lib/libR.so(Rf_eval+0x49e)[0x7fa9c57151be]
/usr/lib64/R/lib/libR.so(+0xe5a6c)[0x7fa9c5716a6c]
/usr/lib64/R/lib/libR.so(Rf_eval+0x49e)[0x7fa9c57151be]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x306)[0x7fa9c5719846]
/usr/lib64/R/lib/libR.so(Rf_eval+0x3b4)[0x7fa9c57150d4]
/usr/lib64/R/lib/libR.so(+0xe6d7f)[0x7fa9c5717d7f]
/usr/lib64/R/lib/libR.so(Rf_eval+0x49e)[0x7fa9c57151be]
/usr/lib64/R/lib/libR.so(+0xe4c4a)[0x7fa9c5715c4a]
/usr/lib64/R/lib/libR.so(+0xdb5d9)[0x7fa9c570c5d9]
/usr/lib64/R/lib/libR.so(Rf_eval+0x190)[0x7fa9c5714eb0]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x306)[0x7fa9c5719846]
/usr/lib64/R/lib/libR.so(+0xe0449)[0x7fa9c5711449]
/usr/lib64/R/lib/libR.so(Rf_eval+0x190)[0x7fa9c5714eb0]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x306)[0x7fa9c5719846]
/usr/lib64/R/lib/libR.so(Rf_eval+0x3b4)[0x7fa9c57150d4]
/usr/lib64/R/lib/libR.so(Rf_ReplIteration+0x1d1)[0x7fa9c5754121]
/usr/lib64/R/lib/libR.so(run_Rmainloop+0xd1)[0x7fa9c5754441]
/usr/lib64/R/bin/exec/R(main+0x1b)[0x40093b]
/lib/libc.so.6(__libc_start_main+0xfd)[0x7fa9c4ea1c4d]
/usr/lib64/R/bin/exec/R[0x400859]
======= Memory map: ========
00400000-00401000 r-xp 00000000 08:01 6652562
  /usr/lib/R/bin/exec/R
00600000-00601000 rw-p 00000000 08:01 6652562
  /usr/lib/R/bin/exec/R
00d06000-08280000 rw-p 00000000 00:00 0                                  [heap]
7fa9b0000000-7fa9b0814000 rw-p 00000000 00:00 0
7fa9b0814000-7fa9b4000000 ---p 00000000 00:00 0
7fa9b4000000-7fa9b481f000 rw-p 00000000 00:00 0
7fa9b481f000-7fa9b8000000 ---p 00000000 00:00 0
7fa9b8000000-7fa9b8a66000 rw-p 00000000 00:00 0
7fa9b8a66000-7fa9bc000000 ---p 00000000 00:00 0
7fa9bcf9e000-7fa9bcf9f000 ---p 00000000 00:00 0
7fa9bcf9f000-7fa9bd79f000 rw-p 00000000 00:00 0
7fa9bd79f000-7fa9bd7a0000 ---p 00000000 00:00 0
7fa9bd7a0000-7fa9bdfa0000 rw-p 00000000 00:00 0
7fa9bdfa0000-7fa9bdfa1000 ---p 00000000 00:00 0
7fa9bdfa1000-7fa9be7a1000 rw-p 00000000 00:00 0
7fa9be7a1000-7fa9be7c6000 r-xp 00000000 08:01 7807190
  /usr/local/lib/R/site-library/rGADEM/libs/rGADEM.so
7fa9be7c6000-7fa9be9c6000 ---p 00025000 08:01 7807190
  /usr/local/lib/R/site-library/rGADEM/libs/rGADEM.so
7fa9be9c6000-7fa9be9c7000 r--p 00025000 08:01 7807190
  /usr/local/lib/R/site-library/rGADEM/libs/rGADEM.so
7fa9be9c7000-7fa9be9c8000 rw-p 00026000 08:01 7807190
  /usr/local/lib/R/site-library/rGADEM/libs/rGADEM.so
7fa9be9c8000-7fa9bebcb000 rw-p 00000000 00:00 0
7fa9bebcb000-7fa9bebe9000 r-xp 00000000 08:01 1064988
  /usr/lib/R/library/grid/libs/grid.so
7fa9bebe9000-7fa9bede9000 ---p 0001e000 08:01 1064988
  /usr/lib/R/library/grid/libs/grid.so
7fa9bede9000-7fa9bedea000 rw-p 0001e000 08:01 1064988
  /usr/lib/R/library/grid/libs/grid.so
7fa9bedea000-7fa9bee21000 r-xp 00000000 08:01 7807042
  /usr/local/lib/R/site-library/Biostrings/libs/Biostrings.so
7fa9bee21000-7fa9bf020000 ---p 00037000 08:01 7807042
  /usr/local/lib/R/site-library/Biostrings/libs/Biostrings.so
7fa9bf020000-7fa9bf022000 rw-p 00036000 08:01 7807042
  /usr/local/lib/R/site-library/Biostrings/libs/Biostrings.so
7fa9bf022000-7fa9c17ab000 rw-p 00000000 00:00 0
7fa9c17ab000-7fa9c17e7000 r-xp 00000000 08:01 7807784
  /usr/local/lib/R/site-library/IRanges/libs/IRanges.so
7fa9c17e7000-7fa9c19e6000 ---p 0003c000 08:01 7807784
  /usr/local/lib/R/site-library/IRanges/libs/IRanges.so
7fa9c19e6000-7fa9c19e8000 r--p 0003b000 08:01 7807784
  /usr/local/lib/R/site-library/IRanges/libs/IRanges.so
7fa9c19e8000-7fa9c19e9000 rw-p 0003d000 08:01 7807784
  /usr/local/lib/R/site-library/IRanges/libs/IRanges.so
7fa9c19e9000-7fa9c1a41000 rw-p 00000000 00:00 0
7fa9c1a41000-7fa9c1abd000 r-xp 00000000 08:01 1974639
  /usr/lib/R/library/stats/libs/stats.so
7fa9c1abd000-7fa9c1cbd000 ---p 0007c000 08:01 1974639
  /usr/lib/R/library/stats/libs/stats.so
7fa9c1cbd000-7fa9c1cc0000 rw-p 0007c000 08:01 1974639
  /usr/lib/R/library/stats/libs/stats.so
7fa9c1cc0000-7fa9c1e2b000 rw-p 00000000 00:00 0
7fa9c1e2b000-7fa9c1e50000 r-xp 00000000 08:01 1435163
  /usr/lib/R/library/grDevices/libs/grDevices.so
7fa9c1e50000-7fa9c2050000 ---p 00025000 08:01 1435163
  /usr/lib/R/library/grDevices/libs/grDevices.so
7fa9c2050000-7fa9c2051000 rw-p 00025000 08:01 1435163
  /usr/lib/R/library/grDevices/libs/grDevices.so
7fa9c2098000-7fa9c20a5000 r-xp 00000000 08:01 7809671
  /usr/local/lib/R/site-library/GenomicRanges/libs/GenomicRanges.so
7fa9c20a5000-7fa9c22a5000 ---p 0000d000 08:01 7809671
  /usr/local/lib/R/site-library/GenomicRanges/libs/GenomicRanges.so
7fa9c22a5000-7fa9c22a6000 r--p 0000d000 08:01 7809671
  /usr/local/lib/R/site-library/GenomicRanges/libs/GenomicRanges.so
7fa9c22a6000-7fa9c22a7000 rw-p 0000e000 08:01 7809671
  /usr/local/lib/R/site-library/GenomicRanges/libs/GenomicRanges.so
7fa9c22a7000-7fa9c22cc000 rw-p 00000000 00:00 0
7fa9c22cc000-7fa9c22ce000 r-xp 00000000 08:01 8249351
  /usr/lib/gconv/ISO8859-1.so
7fa9c22ce000-7fa9c24cd000 ---p 00002000 08:01 8249351
  /usr/lib/gconv/ISO8859-1.so
7fa9c24cd000-7fa9c24ce000 r--p 00001000 08:01 8249351
  /usr/lib/gconv/ISO8859-1.so
7fa9c24ce000-7fa9c24cf000 rw-p 00002000 08:01 8249351
  /usr/lib/gconv/ISO8859-1.so
7fa9c24cf000-7fa9c25d3000 rw-p 00000000 00:00 0
7fa9c25d3000-7fa9c25da000 r-xp 00000000 08:01 7801126
  /usr/lib/R/library/methods/libs/methods.so
7fa9c25da000-7fa9c27da000 ---p 00007000 08:01 7801126
  /usr/lib/R/library/methods/libs/methods.so
7fa9c27da000-7fa9c27db000 rw-p 00007000 08:01 7801126
  /usr/lib/R/library/methods/libs/methods.so
7fa9c27db000-7fa9c286e000 rw-p 00000000 00:00 0
7fa9c286e000-7fa9c287a000 r-xp 00000000 08:01 901345
  /lib/libnss_files-2.11.1.so
7fa9c287a000-7fa9c2a79000 ---p 0000c000 08:01 901345
  /lib/libnss_files-2.11.1.so
7fa9c2a79000-7fa9c2a7a000 r--p 0000b000 08:01 901345
  /lib/libnss_files-2.11.1.so
7fa9c2a7a000-7fa9c2a7b000 rw-p 0000c000 08:01 901345
  /lib/libnss_files-2.11.1.so
7fa9c2a7b000-7fa9c2a85000 r-xp 00000000 08:01 901347
  /lib/libnss_nis-2.11.1.so
7fa9c2a85000-7fa9c2c84000 ---p 0000a000 08:01 901347
  /lib/libnss_nis-2.11.1.so
7fa9c2c84000-7fa9c2c85000 r--p 00009000 08:01 901347
  /lib/libnss_nis-2.11.1.soAborted