GOSemSim function, clusterSim throws expired SQLiteConnection error
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Guest User ★ 12k
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Last seen 7.0 years ago
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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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 7 months ago
China/Guangzhou/Southern Medical Univer…
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. > [[alternative HTML version deleted]]
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