[BioC] arrayQualityMetrics and lumi - failure to load in R2.15.1 windows
Lavinia Gordon
lavinia.gordon at mcri.edu.au
Mon Nov 26 03:56:57 CET 2012
Dear All,
The package arrayQualityMetrics fails to load in R2.15.1:
> library(arrayQualityMetrics)
Error : object 'geneNames' is not exported by 'namespace:Biobase'
Error: package/namespace load failed for 'arrayQualityMetrics'
The library lumi also fails:
> library(lumi)
Loading required package: methylumi
Loading required package: scales
Loading required package: reshape2
Loading required package: ggplot2
Find out what's changed in ggplot2 with
news(Version == "0.9.2.1", package = "ggplot2")
Loading required package: nleqslv
Error : object 'get_xsbasetypes_conversion_lookup' is not exported by
'namespace:Biostrings'
In addition: Warning messages:
1: found methods to import for function 'eapply' but not the generic
itself
2: replacing previous import 'image' when loading 'graphics'
3: package 'nleqslv' was built under R version 2.15.2
Error: package/namespace load failed for 'lumi'
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252
LC_MONETARY=English_Australia.1252
[4] LC_NUMERIC=C LC_TIME=English_Australia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] nleqslv_1.9.4 methylumi_2.2.0 ggplot2_0.9.2.1
reshape2_1.2.1 scales_0.2.2
[6] Biobase_2.18.0 BiocGenerics_0.4.0
loaded via a namespace (and not attached):
[1] affy_1.36.0 affyio_1.26.0 annotate_1.36.0
AnnotationDbi_1.20.2 BiocInstaller_1.8.3
[6] Biostrings_2.26.2 colorspace_1.2-0 DBI_0.2-5
dichromat_1.2-4 digest_0.6.0
[11] GenomicRanges_1.10.3 grid_2.15.1 gtable_0.1.1
IRanges_1.16.4 labeling_0.2
[16] lattice_0.20-11 MASS_7.3-22 memoise_0.1
munsell_0.4 parallel_2.15.1
[21] plyr_1.7.1 preprocessCore_1.20.0 proto_0.3-9.2
RColorBrewer_1.0-5 RCurl_1.95-3
[26] RSQLite_0.11.2 stats4_2.15.1 stringr_0.6.1
XML_3.95-0.1 xtable_1.7-1
[31] zlibbioc_1.4.0
With regards,
Lavinia Gordon.
Senior Research Officer
Quantitative Sciences Core, Bioinformatics
Murdoch Childrens Research Institute
The Royal Children's Hospital
Flemington Road Parkville Victoria 3052 Australia
T 03 8341 6221
www.mcri.edu.au
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