[BioC] arrayQualityMetrics error on windows

[Martin Morgan]

On 09/02/2012 07:17 PM, Marcus Davy wrote:
> This more informative error is from another fresh test
>
> ## Fresh Install of R-2.15.1
>> source("http://www.bioconductor.org/biocLite.R")
>> biocLite("arrayQualityMetrics")
> ...
>
>> library(arrayQualityMetrics)
> Creating a generic function for ‘boxplot’ from package ‘graphics’ in
> package ‘affyPLM’
> Creating a generic function for ‘hist’ from package ‘graphics’ in package
> ‘affyPLM’
> Error : .onLoad failed in loadNamespace() for 'affyPLM', details:
>    call: fun(libname, pkgname)
>    error: could not find function "addVigs2WinMenu"
> Error: package/namespace load failed for ‘arrayQualityMetrics’

affyPLM should importFrom(Biobase, addVigs2WinMenu). I think you can 
work around this by first loading Biobase

   library(Biobase)
   library(arrayQualityMetrics)

Martin

>
> Marcus
>
> On Mon, Sep 3, 2012 at 1:50 PM, Marcus Davy <mdavy86 at gmail.com> wrote:
>
>> Hi,
>> I have a script which works fine under R-2.14.1 on windows (and previous
>> versions), but is throwing an error when loading the library on a fresh
>> build with R-2.15.1. From a bioC thread recently about arrayQualityMetrics
>> It looks like it is working on other platforms. The error looks like it is
>> a namespace dependency issue with affyPLM and Biobase::addVigs2WinMenu.
>>
>> cheers,
>>
>> Marcus
>>
>>> library(arrayQualityMetrics)
>> Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) :
>>    there is no package called ‘affyPLM’
>> Error: package/namespace load failed for ‘arrayQualityMetrics’
>>> sessionInfo()
>> R version 2.15.1 (2012-06-22)
>> Platform: i386-pc-mingw32/i386 (32-bit)
>>
>> locale:
>> [1] LC_COLLATE=English_New Zealand.1252  LC_CTYPE=English_New
>> Zealand.1252    LC_MONETARY=English_New Zealand.1252
>> [4] LC_NUMERIC=C                         LC_TIME=English_New
>> Zealand.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] BiocInstaller_1.5.12 Biobase_2.17.7       BiocGenerics_0.3.1
>>
>> loaded via a namespace (and not attached):
>> [1] affy_1.35.1           affyio_1.25.0         preprocessCore_1.19.0
>> tools_2.15.1          zlibbioc_1.3.0
>>
>>
>
> 	[[alternative HTML version deleted]]
>
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>


-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793