Hi, On Mon, Aug 30, 2010 at 12:48 PM, kirti prakash <[email protected]> wrote: > Hi, > > I am getting this error... > > me3 <- readAligned("dirpath", type="Bowtie") > Error: Input/Output > 'readAligned' failed to parse files > dirPath: 'xxx' > pattern: '' > type: 'Bowtie' > error: Calloc could not allocate (9638489 of 4) memory > > I have some six histone modifications files... I didn't got this error > for the first couple of files that I read.
What do you mean "with the first couple of files you read"? Did you execute this command before in a different directory or something? Do you already have some "readAligned" data sets loaded into your workspace? Is it possible that your machine is simply running out of RAM? -steve > > I read this thread which discussed this problem but I could not follow much... > > http://tolstoy.newcastle.edu.au/R/devel/06/01/3641.html > >> sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C > [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 > [5] LC_MONETARY=C LC_MESSAGES=en_US.iso885915 > [7] LC_PAPER=en_US.iso885915 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] HilbertVis_1.6.0 ShortRead_1.6.2 Rsamtools_1.0.7 > [4] lattice_0.18-8 Biostrings_2.16.9 GenomicRanges_1.0.7 > [7] IRanges_1.6.13 biomaRt_2.4.0 > > loaded via a namespace (and not attached): > [1] Biobase_2.8.0 hwriter_1.2 RCurl_1.4-3 tools_2.11.1 XML_3.1-0 > > Best regards, > > Kirti Prakash > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
