[BioC] error with "retrain" method of gene2pathway package

[Kishor Tappita]

Dear Jim,

Thank you so much for the explanation. I will bear your suggestions in
my mind and will plan my analysis
accordingly.

Thanks,
kishor

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 ...
>> done
>> 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.
>
> Best,
>
> Jim
>
>
>>
>>> sessionInfo()
>>
>> R version 2.9.2 (2009-08-24)
>> i386-pc-mingw32
>>
>> locale:
>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>> States.1252;LC_MONETARY=English_United
>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] grid      stats     graphics  grDevices utils     datasets  methods
>> [8] base
>>
>> other attached packages:
>>  [1] gene2pathway_1.2.0    org.Dm.eg.db_2.2.11   RBGL_1.20.0
>>  [4] KEGGSOAP_1.18.0       KEGG.db_2.2.11        kernlab_0.9-8
>>  [7] Rgraphviz_1.22.1      hgu133plus2.db_2.2.11 topGO_1.12.0
>> [10] SparseM_0.80          graph_1.22.2          GO.db_2.2.11
>> [13] RSQLite_0.7-2         DBI_0.2-4             AnnotationDbi_1.6.1
>> [16] limma_2.18.3          GEOquery_2.8.0        RCurl_0.98-1
>> [19] bitops_1.0-4.1        Biobase_2.4.1         biomaRt_2.0.0
>>
>> loaded via a namespace (and not attached):
>> [1] lattice_0.17-25 SSOAP_0.4-6     tools_2.9.2     XML_2.5-1
>>
>> Please help me overcome this problem.
>>
>> Thanks,
>> Kishor
>>
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
> 734-615-7826
>