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

[Wolfgang Huber]

Dear Lavinia

could it be that your installation of Bioconductor packages is incoherent? Have you tried running 
 source("http://bioconductor.org/biocLite.R")
 biocLite("BiocUpgrade")
 biocLite("arrayQualityMetrics") 
from a clean new R 2.15.2? As is described e.g. here: http://www.bioconductor.org/install .

To see whether what you experience might be a problem with the package(s) in general, or one with your computer in particular, you could check the 'daily package check reports' on the Bioc build server at http://bioconductor.org/checkResults/release/bioc-LATEST . Here you will see that no problem is currently reported for arrayQualityMetrics or lumi, which suggests that the latter is the case.

	Hope this helps, best wishes
	Wolfgang


Il giorno Nov 26, 2012, alle ore 3:56 AM, Lavinia Gordon <lavinia.gordon at mcri.edu.au> ha scritto:

> 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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