On 09/14/2010 08:02 AM, Marc Schwartz wrote: > On Sep 14, 2010, at 9:47 AM, John1983 wrote: > >> >> Yes I see. So I typed as you mentioned and I get an 8 (therefore >> this is a 64-bit R). >> >> Is there anything else I need to check to remove this error? > > > 1. Add more RAM. > > 2. Depending upon what you are doing relative to data > management/analysis, you might want to see if there are more > efficient approaches. > > 3. Free up RAM that may be in use by other processes, etc. > > 4. Look at R packages such as biglm, ff/bit, biganalytics, etc. > > 5. Consider using a backend data base application (eg. MySQL, > Postgres, etc.) to manage the data sets and use R only for analyses, > as may be appropriate relative to splitting the tasks. > > > You did not indicate just how much RAM you have on the machine in > question, but if it is within your budget/capability, adding more RAM > would be the most transparent approach.
Before spending the big bucks you might try asking on the Bioconductor mailing list http://bioconductor.org/help/mailing-list/ home of the Biostrings package and BStringSet, andwhere for instance the ShortRead package readFastq would be a natural way of parsing your FASTQ file, and most operations you'd likely perform on a fastq file (given sufficient memory) would take more than a few (tens of, at the most) seconds. Martin > HTH, > > Marc Schwartz > > ______________________________________________ R-help@r-project.org > mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do > read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
