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: âBiocGenericsâ
The following objects are masked from âpackage:parallelâ:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from âpackage:statsâ:
xtabs
The following objects are masked from âpackage:baseâ:
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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