[BioC] arrayQualityMetrics with R 2.13.0 fails

[Dan Tenenbaum]

Hello Eric,

Thanks for reporting this problem. It will be fixed in tomorrow's
builds (around noon Seattle time)

Dan


On Thu, Apr 14, 2011 at 4:23 PM, Eric Bremer
<egbremer at precisionbiomarker.com> wrote:
> Dear List,
> I just istalled the R 2.13.0 and Bioconductor 2.8.  When loading the latest
> arrayQualityMetrics package it failed because there was no 'affyPLM'
> package.  I then re-installed 'affyPLM' but received the message "package
> ‘affyPLM’ is not available (for R version 2.13.0)".  I seeing some of the
> discussion recently on new features in arrayQualityMetrics, I am looking
> forward to checking them out. The error messages and sessionInfo are pasted
> below.
> Thanks for any assistance!
> Eric
>
> Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) :
>  there is no package called 'affyPLM'
> Error: package/namespace load failed for 'arrayQualityMetrics'
>> utils:::menuInstallPkgs()
> Error in install.packages(NULL, .libPaths()[1L], dependencies = NA, type =
> type) :
>  no packages were specified
>> utils:::menuInstallPkgs()
> Error in install.packages(NULL, .libPaths()[1L], dependencies = NA, type =
> type) :
>  no packages were specified
>> biocLite("affyPLM")
> Using R version 2.13.0, biocinstall version 2.8.3.
> Installing Bioconductor version 2.8 packages:
> [1] "affyPLM"
> Please wait...
>
> Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
>  package ‘affyPLM’ is not available (for R version 2.13.0)
>>
>
>
>> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> States.1252
> [3] LC_MONETARY=English_United States.1252
> LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] affy_1.30.0    Biobase_2.12.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.20.0         preprocessCore_1.14.0 tools_2.13.0
>
>
> --
> Eric Bremer, PhD
> Chief Scientific Officer
> Precision Biomarker Resources, Inc.
> 820 Davis St.,  Suite 216
> Evanston, Illinois  60201
>
> Office: 847.866.0406
> Mobile: 708.267.2052
> Skype: egbremer
>
> www.precisionbiomarker.com
>
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>
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