[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 ...
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)

LC_COLLATE=English_United States.1252;LC_CTYPE=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.


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