[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)

 [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                 

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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