Hi,

I run your script, and it works out fine. It seems that you are using the
Bioconductor 2.12 and but some of the dependencies are the newest version.
I think the error may due to this reason.

Please let me know if your problem still exists when you update
Bioconductor to newest release version, 2.13.


> library(GOSemSim)
Loading required package: Rcpp
Loading required package: DBI
Loading required package: AnnotationDbi
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:stats’:

    xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, duplicated, eval, evalq,
    get, intersect, is.unsorted, lapply, mapply, match, mget, order,
    paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rep.int,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unlist

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


> 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")
Loading required package: org.Hs.eg.db

[1] 0.46
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin13.0.0 (64-bit)

locale:
[1] C/UTF-8/C/C/C/C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] org.Hs.eg.db_2.10.1  GOSemSim_1.20.0      AnnotationDbi_1.24.0
[4] Biobase_2.22.0       BiocGenerics_0.8.0   RSQLite_0.11.4
[7] DBI_0.2-7            Rcpp_0.10.6

loaded via a namespace (and not attached):
[1] GO.db_2.10.1   IRanges_1.20.6 stats4_3.0.2
>



Best Regards,
Guangchuang Yu
--~--~---------~--~----~------------~-------~--~----~
Department of Biochemistry & Molecular Biology
College of Life Science and Technology
Jinan University, 601 Huangpu Ave. W.
Guangzhou 510632,  P.R. China
Tel: +86-20-85222677
Email: guangchuangyu@gmail.com
           guangchuangyu@jnu.edu.cn
Blog: http://ygc.name
Scholar Profile: http://t.cn/SUGn4e
-~----------~----~----~----~------~----~------~--~---


On Thu, Nov 28, 2013 at 12:17 AM, Gabriel [guest] <guest@bioconductor.org>wrote:

>
> 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
>
> --
> Sent via the guest posting facility at bioconductor.org.
>

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