I am trying to rGADEM on a few sequences in FASTA format and it crashes with the following error: > gadem <- GADEM (Sequences, verbose=1) *** Start C Programm *** bit calloc failed! Any help appreciated! > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] rGADEM_2.6.0 seqLogo_1.24.0 BSgenome_1.26.1 [4] GenomicRanges_1.10.7 Biostrings_2.26.3 IRanges_1.16.6 [7] BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] parallel_2.15.0 stats4_2.15.0 -best -Lax

Hi, On Wed, Mar 27, 2013 at 1:53 PM, Lakshmanan Iyer <liyer01 at="" tufts.edu=""> wrote: > I am trying to rGADEM on a few sequences in FASTA format and it > crashes with the following error: > >> gadem <- GADEM (Sequences, verbose=1) Can you send the commands or data necessary to generate the Sequences object you are passing to GADEM()? Dan > *** Start C Programm *** > bit calloc failed! > > Any help appreciated! >> sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] rGADEM_2.6.0 seqLogo_1.24.0 BSgenome_1.26.1 > [4] GenomicRanges_1.10.7 Biostrings_2.26.3 IRanges_1.16.6 > [7] BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] parallel_2.15.0 stats4_2.15.0 > > -best > -Lax > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

It is huge file, 14.5MB! I think it was the size of the sequences. I tried it with a smaller sequence set and it works fine. Is there a limit on the input sequence size? The EMBOSS infoseq output for the sequence file tmp.fasta is: @>infoseq tmp.fasta Display basic information about sequences USA Database Name Accession Type Length %GC Organism Description fasta::tmp.fasta:37668520-37776656 - 37668520-37776656 - N *108136* 47.23 fasta::tmp.fasta:56850824-57028178 - 56850824-57028178 - N *177354* 41.11 fasta::tmp.fasta:167225896-167251982 - 167225896-167251982 - N *26086* 48.31 fasta::tmp.fasta:43298974-43304071 - 43298974-43304071 - N *5097* 46.71 fasta::tmp.fasta:53625838-53795602 - 53625838-53795602 - N *169764* 39.92 fasta::tmp.fasta:35820170-36757745 - 35820170-36757745 - N *937575* 41.74 On Fri, Mar 29, 2013 at 2:08 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > Keeping this on the list... > > On Fri, Mar 29, 2013 at 11:02 AM, Lakshmanan Iyer <liyer01@tufts.edu> wrote: >> Yhe commands are: >>> library(rGADEM) >>> library (BSgenome) >>> library(BSgenome.Mmusculus.UCSC.mm9) >>> Sequences <- readDNAStringSet ("./tmp.fasta", "fasta") >>> gadem <- GADEM (Sequences, verbose=1, genome=Mmusculus) >> *** Start C Programm *** >> bit calloc failed! >> > > Are you able to share the tmp.fasta file? > Dan > > >> On Wed, Mar 27, 2013 at 4:59 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: >>> Hi, >>> >>> >>> On Wed, Mar 27, 2013 at 1:53 PM, Lakshmanan Iyer <liyer01@tufts.edu> wrote: >>>> I am trying to rGADEM on a few sequences in FASTA format and it >>>> crashes with the following error: >>>> >>>>> gadem <- GADEM (Sequences, verbose=1) >>> >>> Can you send the commands or data necessary to generate the Sequences >>> object you are passing to GADEM()? >>> Dan >>> >>> >>> >>>> *** Start C Programm *** >>>> bit calloc failed! >>>> >>>> Any help appreciated! >>>>> sessionInfo() >>>> R version 2.15.0 (2012-03-30) >>>> Platform: x86_64-pc-linux-gnu (64-bit) >>>> >>>> locale: >>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>>> [7] LC_PAPER=C LC_NAME=C >>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] grid stats graphics grDevices utils datasets methods >>>> [8] base >>>> >>>> other attached packages: >>>> [1] rGADEM_2.6.0 seqLogo_1.24.0 BSgenome_1.26.1 >>>> [4] GenomicRanges_1.10.7 Biostrings_2.26.3 IRanges_1.16.6 >>>> [7] BiocGenerics_0.4.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] parallel_2.15.0 stats4_2.15.0 >>>> >>>> -best >>>> -Lax >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]