Entering edit mode
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