[BioC] error with "retrain" method of gene2pathway package
Kishor Tappita
kishor.tappita at gmail.com
Thu Sep 17 11:25:35 CEST 2009
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
> 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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