Dear all, I have a problem with the "org.Hs.eg.db" package and would like to ask for some advice on how to get it to work. Currently, the problem I am facing is that R does not seem to recognize the package, see below for the context, error message and the sessionInfo(). I have been able to make "org.Mm.eg.db" and "org.Sc.sgd.db" work, but "org.Hs.eg.db" is not recognized. I would be grateful for any help. Thanks in advance. /Krakno -- output of sessionInfo(): > source("http://bioconductor.org/biocLite.R") > biocLite("org.Hs.eg.db") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version 3.0.1. Installing package(s) 'org.Hs.eg.db' trying URL 'http://bioconductor.org/packages/2.12/data/annotation/bin/ windows/contrib/3.0/org.Hs.eg.db_2.9.0.zip' Content type 'application/zip' length 53311411 bytes (50.8 Mb) opened URL downloaded 50.8 Mb Warning: cannot remove prior installation of package ???org.Hs.eg.db??? The downloaded binary packages are in C:\Users\<...>\AppData\Local\Temp\RtmpE3cnj9\downloaded_packages > library(org.Hs.eg.db) Error in library(org.Hs.eg.db) : there is no package called ???org.Hs.eg.db??? > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Swedish_Sweden.1252 LC_CTYPE=Swedish_Sweden.1252 [3] LC_MONETARY=Swedish_Sweden.1252 LC_NUMERIC=C [5] LC_TIME=Swedish_Sweden.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] BSgenome.Hsapiens.UCSC.hg19_1.3.19 BSgenome_1.28.0 [3] Biostrings_2.28.0 GenomicRanges_1.12.5 [5] IRanges_1.18.4 org.Mm.eg.db_2.9.0 [7] RSQLite_0.11.4 DBI_0.2-7 [9] AnnotationDbi_1.22.6 Biobase_2.20.1 [11] BiocGenerics_0.6.0 BiocInstaller_1.10.3 loaded via a namespace (and not attached): [1] stats4_3.0.1 tools_3.0.1 -- Sent via the guest posting facility at bioconductor.org.

Hi Krakno, On Monday, September 30, 2013 5:41:04 AM, Krakno [guest] wrote: > > Dear all, > > I have a problem with the "org.Hs.eg.db" package and would like to ask for some advice on how to get it to work. Currently, the problem I am facing is that R does not seem to recognize the package, see below for the context, error message and the sessionInfo(). > > I have been able to make "org.Mm.eg.db" and "org.Sc.sgd.db" work, but "org.Hs.eg.db" is not recognized. > > I would be grateful for any help. > > Thanks in advance. > /Krakno > > -- output of sessionInfo(): > >> source("http://bioconductor.org/biocLite.R") >> biocLite("org.Hs.eg.db") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version 3.0.1. > Installing package(s) 'org.Hs.eg.db' > trying URL 'http://bioconductor.org/packages/2.12/data/annotation/bi n/windows/contrib/3.0/org.Hs.eg.db_2.9.0.zip' > Content type 'application/zip' length 53311411 bytes (50.8 Mb) > opened URL > downloaded 50.8 Mb > > Warning: cannot remove prior installation of package ???org.Hs.eg.db??? ^^^^^^^^^^^^^^^ I think that is the hint you were looking for. However, there may be more than one reason for the problem. I would first look in your package library (use .libPaths() to figure out where your packages are located) and see if there is a folder called OOLOCK-org.Hs.eg.db If so, delete that and try again. Best, Jim > > The downloaded binary packages are in > C:\Users\<...>\AppData\Local\Temp\RtmpE3cnj9\downloaded_packages >> library(org.Hs.eg.db) > Error in library(org.Hs.eg.db) : > there is no package called ???org.Hs.eg.db??? > >> sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=Swedish_Sweden.1252 LC_CTYPE=Swedish_Sweden.1252 > [3] LC_MONETARY=Swedish_Sweden.1252 LC_NUMERIC=C > [5] LC_TIME=Swedish_Sweden.1252 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] BSgenome.Hsapiens.UCSC.hg19_1.3.19 BSgenome_1.28.0 > [3] Biostrings_2.28.0 GenomicRanges_1.12.5 > [5] IRanges_1.18.4 org.Mm.eg.db_2.9.0 > [7] RSQLite_0.11.4 DBI_0.2-7 > [9] AnnotationDbi_1.22.6 Biobase_2.20.1 > [11] BiocGenerics_0.6.0 BiocInstaller_1.10.3 > > loaded via a namespace (and not attached): > [1] stats4_3.0.1 tools_3.0.1 > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099