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

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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