[BioC] GOSemSim function, clusterSim throws expired SQLiteConnection error
Gabriel [guest]
guest at bioconductor.org
Wed Nov 27 17:17:45 CET 2013
Hi All,
I have installed and loaded GOSemSim, tried the functions implemented in the package using the examples. All the functions work fine, except clusterSim(). clusterSim throws and error as below. Please, advise ...
> library(GOSemSim)
> cluster1 <- c("835", "5261","241", "994")
> cluster2 <- c("307", "308", "317", "321", "506", "540", "378", "388", "396")
> clusterSim(cluster1, cluster2, ont="MF", organism="human", measure="Wang")
Error in sqliteExecStatement(con, statement, bind.data) :
RS-DBI driver: (expired SQLiteConnection)
-- output of sessionInfo():
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] clusterProfiler_1.8.0 ggplot2_0.9.3.1 org.Hs.eg.db_2.9.0 RSQLite_0.11.4 GO.db_2.9.0 AnnotationDbi_1.22.6
[7] Biobase_2.20.1 BiocGenerics_0.6.0 BiocInstaller_1.10.4 igraph_0.6.6 GOSemSim_1.18.0 Rcpp_0.10.6
[13] DBI_0.2-7
loaded via a namespace (and not attached):
[1] codetools_0.2-8 colorspace_1.2-4 dichromat_2.0-0 digest_0.6.3 DO.db_2.6.0 DOSE_1.6.0
[7] graph_1.38.3 grid_3.0.2 gtable_0.1.2 IRanges_1.18.4 KEGG.db_2.9.1 labeling_0.2
[13] MASS_7.3-29 munsell_0.4.2 plyr_1.8 proto_0.3-10 qvalue_1.34.0 RColorBrewer_1.0-5
[19] RCurl_1.95-4.1 reshape2_1.2.2 scales_0.2.3 SSOAP_0.9-1 stats4_3.0.2 stringr_0.6.2
[25] tcltk_3.0.2 tools_3.0.2 XML_3.98-1.1 XMLSchema_0.7-2
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