arrayQualityMetrics
1
0
Entering edit mode
@mayte-suarez-farinas-2068
Last seen 9.6 years ago
United States
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
GO hgu133plus2 arrayQualityMetrics GO hgu133plus2 arrayQualityMetrics • 911 views
ADD COMMENT
0
Entering edit mode
Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 6 months ago
United States
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]]
ADD COMMENT

Login before adding your answer.

Traffic: 451 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6