[BioC] arrayQualityMetrics

Mayte Suarez-Farinas farinam at mail.rockefeller.edu
Thu Nov 11 16:04:44 CET 2010

Hi all,

I updated R/Bionductor and now the package arrayQualityMetrics is not  
It askes for SVGAnnotation package which seems not to be anywhere

Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) :
   there is no package called 'SVGAnnotation'
Error: package/namespace load failed for 'arrayQualityMetrics'

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

R version 2.12.0 (2010-10-15)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

[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

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