Hi Bioconductor forum, I get a strange error message when working with the Bioconductor Gene Ontology-packages. I have done the following: ? source("http://bioconductor.org/biocLite.R") ? biocLite("GO.db") The problem is that GO.db is dependant on AnnotationDbi in a later version than 1.23.23, and when I load GO.db using > biocLite("GO.db") (...) ?Warning: dependency ?AnnotationDbi (>= 1.23.24)? is not available? (...) but when I load AnnotationDbi it says: > biocLite("AnnotationDbi") " There is a binary version available (and will be installed) but the source version is later: binary source AnnotationDbi 1.23.23 1.23.25? Can I suppress the installation of the binary version such that I get an appropriate version of AnnotationDbi? Or do you have any other suggestions? (Except changing to Linux :-)) I have tried with several versions of R and I use Windows XP as platform. R version 2.15 works ok, but using that, I have problems with getting the newer packages to work. My colleague, who uses Linux and R 3.0.1, has no problems with GO.db or any of the other packages using AnnotationDbi ? and he also "only" has AnnotationDbi 1.23.23. Best wishes, Sine Zambach Results from traceback and sessionInfo: > traceback() 3: stop(gettextf("package %s %s is loaded, but %s %s is required by %s", sQuote(pkg), current, z$op, target, sQuote(pkgname)), call. = FALSE, domain = NA) 2: .getRequiredPackages2(pkgInfo, quietly = quietly) 1: library(GO.db) > sessionInfo() R version 3.0.2 (2013-09-25) Platform: i386-w64-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=Danish_Denmark.1252 LC_CTYPE=Danish_Denmark.1252 LC_MONETARY=Danish_Denmark.1252 [4] LC_NUMERIC=C LC_TIME=Danish_Denmark.1252 attached base packages: [1] grid parallel stats graphics grDevices utils datasets methods base other attached packages: [1] VariantAnnotation_1.7.47 Rsamtools_1.13.44 Biostrings_2.29.19 GenomicRanges_1.13.45 [5] XVector_0.1.4 IRanges_1.19.38 ontoCAT_1.13.0 rJava_0.9-4 [9] DOSE_1.99.6 ggplot2_0.9.3.1 GOSemSim_1.19.3 RSQLite_0.11.4 [13] DBI_0.2-7 Rcpp_0.10.4 Rgraphviz_2.5.6 graph_1.39.3 [17] Matrix_1.0-14 lattice_0.20-23 AnnotationDbi_1.23.23 Biobase_2.21.7 [21] BiocGenerics_0.7.5 DAVIDQuery_1.21.0 RCurl_1.95-4.1 bitops_1.0-6 [25] BiocInstaller_1.11.4 loaded via a namespace (and not attached): [1] biomaRt_2.17.3 BSgenome_1.29.1 colorspace_1.2-3 dichromat_2.0-0 [5] digest_0.6.3 DO.db_2.6.0 GenomicFeatures_1.13.43 GO.db_2.10.1 [9] gtable_0.1.2 igraph_0.6.5-2 labeling_0.2 MASS_7.3-29 [13] munsell_0.4.2 plyr_1.8 proto_0.3-10 qvalue_1.35.0 [17] RColorBrewer_1.0-5 reshape2_1.2.2 rtracklayer_1.21.12 scales_0.2.3 [21] stats4_3.0.2 stringr_0.6.2 tcltk_3.0.2 tools_3.0.2 [25] XML_3.98-1.1 zlibbioc_1.7.0 ________________________________ Denne e-mail indeholder fortrolig information. Hvis du ikke er den rette modtager af denne e-mail eller hvis du modtager den ved en fejltagelse, beder vi dig venligst informere afsender om fejlen ved at bruge svarfunktionen. Samtidig bedes du slette e-mailen med det samme uden at videresende eller kopiere den.

----- Original Message ----- > From: "Sine Katharina Zambach" <sine.katharina.zambach at="" regionh.dk=""> > To: bioconductor at r-project.org > Sent: Monday, September 30, 2013 7:24:14 AM > Subject: [BioC] 'AnnotationDbi' 1.23.24 is required by ?GO.db? in Windows > > Hi Bioconductor forum, > > I get a strange error message when working with the Bioconductor Gene > Ontology-packages. > I have done the following: > ? source("http://bioconductor.org/biocLite.R") > ? biocLite("GO.db") > > The problem is that GO.db is dependant on AnnotationDbi in a later > version than 1.23.23, and when I load GO.db using > > biocLite("GO.db") > (...) > ?Warning: dependency ?AnnotationDbi (>= 1.23.24)? is not available? > (...) > This version should be available soon. In the meantime, try: biocLite("AnnotationDbi", type="source") Dan > but when I load AnnotationDbi it says: > > biocLite("AnnotationDbi") > " There is a binary version available (and will be installed) but the > source version is later: > binary source > AnnotationDbi 1.23.23 1.23.25? > > Can I suppress the installation of the binary version such that I get > an appropriate version of AnnotationDbi? Or do you have any other > suggestions? (Except changing to Linux :-)) > I have tried with several versions of R and I use Windows XP as > platform. R version 2.15 works ok, but using that, I have problems > with getting the newer packages to work. > My colleague, who uses Linux and R 3.0.1, has no problems with GO.db > or any of the other packages using AnnotationDbi ? and he also > "only" has AnnotationDbi 1.23.23. > > Best wishes, > > Sine Zambach > > Results from traceback and sessionInfo: > > > traceback() > 3: stop(gettextf("package %s %s is loaded, but %s %s is required by > %s", > sQuote(pkg), current, z$op, target, sQuote(pkgname)), call. = > FALSE, > domain = NA) > 2: .getRequiredPackages2(pkgInfo, quietly = quietly) > 1: library(GO.db) > > > sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: i386-w64-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=Danish_Denmark.1252 LC_CTYPE=Danish_Denmark.1252 > LC_MONETARY=Danish_Denmark.1252 > [4] LC_NUMERIC=C LC_TIME=Danish_Denmark.1252 > > attached base packages: > [1] grid parallel stats graphics grDevices utils > datasets methods base > > other attached packages: > [1] VariantAnnotation_1.7.47 Rsamtools_1.13.44 > Biostrings_2.29.19 GenomicRanges_1.13.45 > [5] XVector_0.1.4 IRanges_1.19.38 ontoCAT_1.13.0 > rJava_0.9-4 > [9] DOSE_1.99.6 ggplot2_0.9.3.1 > GOSemSim_1.19.3 RSQLite_0.11.4 > [13] DBI_0.2-7 Rcpp_0.10.4 > Rgraphviz_2.5.6 graph_1.39.3 > [17] Matrix_1.0-14 lattice_0.20-23 > AnnotationDbi_1.23.23 Biobase_2.21.7 > [21] BiocGenerics_0.7.5 DAVIDQuery_1.21.0 RCurl_1.95-4.1 > bitops_1.0-6 > [25] BiocInstaller_1.11.4 > > loaded via a namespace (and not attached): > [1] biomaRt_2.17.3 BSgenome_1.29.1 colorspace_1.2-3 > dichromat_2.0-0 > [5] digest_0.6.3 DO.db_2.6.0 > GenomicFeatures_1.13.43 GO.db_2.10.1 > [9] gtable_0.1.2 igraph_0.6.5-2 labeling_0.2 > MASS_7.3-29 > [13] munsell_0.4.2 plyr_1.8 proto_0.3-10 > qvalue_1.35.0 > [17] RColorBrewer_1.0-5 reshape2_1.2.2 > rtracklayer_1.21.12 scales_0.2.3 > [21] stats4_3.0.2 stringr_0.6.2 tcltk_3.0.2 > tools_3.0.2 > [25] XML_3.98-1.1 zlibbioc_1.7.0 > > > > > ________________________________ > > > Denne e-mail indeholder fortrolig information. Hvis du ikke er den > rette modtager af denne e-mail eller hvis du modtager den ved en > fejltagelse, beder vi dig venligst informere afsender om fejlen ved > at bruge svarfunktionen. Samtidig bedes du slette e-mailen med det > samme uden at videresende eller kopiere den. > _______________________________________________ > 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