[BioC] arrayQualityMetrics and lumi - failure to load in R2.15.1 windows

[Lavinia Gordon]

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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