[BioC] rGADEM crashes on Ubuntu 10.04 64-bit

Dan Tenenbaum dtenenba at fhcrc.org
Sat Dec 31 04:33:52 CET 2011


On Fri, Dec 30, 2011 at 4:14 PM, Dave S <dave.my.mind.is.going at gmail.com> wrote:
> 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?

It would help to have your full sessionInfo() and the 10k_fasta.txt file.
Can you post the latter somewhere? (you can send the URL just to me
and not the list if you'd rather).

Dan

>
> 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
>
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