[BioC] error with "retrain" method of gene2pathway package
kishor.tappita at gmail.com
Thu Sep 17 16:07:56 CEST 2009
Thank you so much for the explanation. I will bear your suggestions in
my mind and will plan my analysis
On Thu, Sep 17, 2009 at 6:45 PM, James W. MacDonald
<jmacedon at med.umich.edu> wrote:
> Hi Kishor,
> Kishor Tappita wrote:
>> Dear List,
>> I am trying to use gene2pathway package for finding enriched pathways.
>> When I try to retrain the
>> model of homo sapiens I get the below error. It works fine for drosophila.
>>> retrain(KEGG.package=TRUE, organism="hsa")
>> Retrieving KEGG information via KEGG.db package ...
>> Retrieving information from InterPro database for organism ' hsa ' via
>> Ensembl ...
>> Checking attributes ... ok
>> Checking filters ... ok
>> Error: cannot allocate vector of size 248.4 Mb
> This means that you are running out of RAM. You might or might not be able
> to get around this problem, depending on your current configuration. There
> are some things you can try:
> If you have less than 4 Gb RAM, you could add more.
> If this occurred in an R session where you had lots of other objects loaded,
> you could try again with a new R session, making sure you don't load
> extraneous objects (or remove things you don't need and ensure recapture of
> memory using gc()).
> Note that recapturing memory on Windows isn't as effective as on other
> operating systems, as Windows isn't good at handling memory and usually
> requires contiguous space for large objects.
> If you have access to a computer or server with more memory, that would be
> the easiest fix.
>> R version 2.9.2 (2009-08-24)
>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>> attached base packages:
>>  grid stats graphics grDevices utils datasets methods
>>  base
>> other attached packages:
>>  gene2pathway_1.2.0 org.Dm.eg.db_2.2.11 RBGL_1.20.0
>>  KEGGSOAP_1.18.0 KEGG.db_2.2.11 kernlab_0.9-8
>>  Rgraphviz_1.22.1 hgu133plus2.db_2.2.11 topGO_1.12.0
>>  SparseM_0.80 graph_1.22.2 GO.db_2.2.11
>>  RSQLite_0.7-2 DBI_0.2-4 AnnotationDbi_1.6.1
>>  limma_2.18.3 GEOquery_2.8.0 RCurl_0.98-1
>>  bitops_1.0-4.1 Biobase_2.4.1 biomaRt_2.0.0
>> loaded via a namespace (and not attached):
>>  lattice_0.17-25 SSOAP_0.4-6 tools_2.9.2 XML_2.5-1
>> Please help me overcome this problem.
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> Search the archives:
> James W. MacDonald, M.S.
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
More information about the Bioconductor