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

[Lavinia Gordon]

Hi Wolfgang

Thank you for your message.  That has resolved both issues, my
apologies, I thought I had upgraded but it must have been on a different
machine.  Thanks for the detailed suggestions.
With regards,

Lavinia.

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


-----Original Message-----
From: Wolfgang Huber [mailto:whuber at embl.de] 
Sent: Monday, 26 November 2012 7:37 PM
To: Lavinia Gordon
Cc: bioconductor at r-project.org
Subject: Re: [BioC] arrayQualityMetrics and lumi - failure to load in
R2.15.1 windows

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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