Hi all, I updated R/Bionductor and now the package arrayQualityMetrics is not working It askes for SVGAnnotation package which seems not to be anywhere library("arrayQualityMetrics") Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) : there is no package called 'SVGAnnotation' Error: package/namespace load failed for 'arrayQualityMetrics' biocLite("SVGAnnotation") Using R version 2.12.0, biocinstall version 2.7.4. Installing Bioconductor version 2.7 packages: [1] "SVGAnnotation" Please wait... Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ?SVGAnnotation? is not available > sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] hgu133a2probe_2.7.0 hgu133a2cdf_2.7.0 gplots_2.8.0 caTools_1.10 bitops_1.0-4.1 [6] gdata_2.8.0 gtools_2.6.2 lattice_0.19-13 affycoretools_1.22.0 KEGG.db_2.4.5 [11] GO.db_2.4.5 leaps_2.9 vsn_3.18.0 affyPLM_1.26.0 preprocessCore_1.12.0 [16] gcrma_2.22.0 affy_1.28.0 limma_3.6.0 PGSEA_1.20.0 hgu133plus2.db_2.4.5 [21] org.Hs.eg.db_2.4.6 RSQLite_0.9-2 DBI_0.2-5 AnnotationDbi_1.12.0 Biobase_2.10.0 [26] MASS_7.3-8 biomaRt_2.6.0 edgeR_1.8.0 loaded via a namespace (and not attached): [1] affyio_1.18.0 annaffy_1.22.0 annotate_1.28.0 beadarray_2.0.0 Biostrings_2.18.0 [6] Category_2.16.0 genefilter_1.32.0 GOstats_2.16.0 graph_1.28.0 GSEABase_1.12.0 [11] hwriter_1.2 IRanges_1.8.0 latticeExtra_0.6-14 RBGL_1.26.0 RColorBrewer_1.0-2 [16] RCurl_1.4-3 simpleaffy_2.26.0 splines_2.12.0 survival_2.35-8 tools_2.12.0 [21] XML_3.2-0 xtable_1.5-6 > Mayte Suarez-Farinas Research Associate, The Rockefeller University Biostatistician, The Rockefeller University Hospital 1230 York Ave, Box 178, New York, NY, 10065 +1(212) 327-8213

On Thu, Nov 11, 2010 at 7:04 AM, Mayte Suarez-Farinas < farinam@mail.rockefeller.edu> wrote: > Hi all, > > I updated R/Bionductor and now the package arrayQualityMetrics is not > working > It askes for SVGAnnotation package which seems not to be anywhere > > library("arrayQualityMetrics") > Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) : > there is no package called 'SVGAnnotation' > Error: package/namespace load failed for 'arrayQualityMetrics' > > > biocLite("SVGAnnotation") > Using R version 2.12.0, biocinstall version 2.7.4. > Installing Bioconductor version 2.7 packages: > [1] "SVGAnnotation" > Please wait... > > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ‘SVGAnnotation’ is not available > > > > > sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] hgu133a2probe_2.7.0 hgu133a2cdf_2.7.0 gplots_2.8.0 > caTools_1.10 bitops_1.0-4.1 > [6] gdata_2.8.0 gtools_2.6.2 lattice_0.19-13 > affycoretools_1.22.0 KEGG.db_2.4.5 > [11] GO.db_2.4.5 leaps_2.9 vsn_3.18.0 > affyPLM_1.26.0 preprocessCore_1.12.0 > [16] gcrma_2.22.0 affy_1.28.0 limma_3.6.0 > PGSEA_1.20.0 hgu133plus2.db_2.4.5 > [21] org.Hs.eg.db_2.4.6 RSQLite_0.9-2 DBI_0.2-5 > AnnotationDbi_1.12.0 Biobase_2.10.0 > [26] MASS_7.3-8 biomaRt_2.6.0 edgeR_1.8.0 > > loaded via a namespace (and not attached): > [1] affyio_1.18.0 annaffy_1.22.0 annotate_1.28.0 > beadarray_2.0.0 Biostrings_2.18.0 > [6] Category_2.16.0 genefilter_1.32.0 GOstats_2.16.0 > graph_1.28.0 GSEABase_1.12.0 > [11] hwriter_1.2 IRanges_1.8.0 latticeExtra_0.6-14 > RBGL_1.26.0 RColorBrewer_1.0-2 > [16] RCurl_1.4-3 simpleaffy_2.26.0 splines_2.12.0 > survival_2.35-8 tools_2.12.0 > [21] XML_3.2-0 xtable_1.5-6 > > > Hi Mayte, The correct file for SVGAnnotation was not in place for the Mac platform. It is now in place and I've verified that biocLite("SVGAnnotation") will now work. Apologies for the inconvenience. Dan > Mayte Suarez-Farinas > Research Associate, The Rockefeller University > Biostatistician, The Rockefeller University Hospital > 1230 York Ave, Box 178, > New York, NY, 10065 > +1(212) 327-8213 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]