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

James W. MacDonald jmacdon at med.umich.edu
Thu Sep 17 15:15:52 CEST 2009

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.



>> 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.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618

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