[BioC] getAnnMap: package hgu95av2 not available

[Martin Morgan]

On 01/27/2013 10:38 PM, elva chen [guest] wrote:
>
> Hi,
> I am following the Bioconductor Case studies.  I got:
> Error: getAnnMap: package hgu95av2 not available
>
> After appling the code:
>   filt_bcrneg = nsFilter(ALL_bcrneg, require.entrez=TRUE,
>       require.GOBP=TRUE, remove.dupEntrez=TRUE,
>       var.func=IQR, var.cutoff=varCut,
>       feature.exclude="^AFFX")
>
> Did I miss anything? How can I get the hgu95av2?
>
> thanks,
> elva
>
>   -- output of sessionInfo():
>
>> varCut=0.5
>> filt_bcrneg = nsFilter(ALL_bcrneg, require.entrez=TRUE,
> +     require.GOBP=TRUE, remove.dupEntrez=TRUE,
> +     var.func=IQR, var.cutoff=varCut,
> +     feature.exclude="^AFFX")
> Error: getAnnMap: package hgu95av2 not available
>> help(package="hgu95av2")
> starting httpd help server ... done
>> help(package="hgu95av2")
>> source("http://bioconductor.org/biocLite.R")
>> biocLite("hgu95av2.db")

yes, installing the package is what is required...

> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
> Installing package(s) 'hgu95av2.db'
> also installing the dependency ‘org.Hs.eg.db’
>
> trying URL 'http://bioconductor.org/packages/2.11/data/annotation/bin/windows/contrib/2.15/org.Hs.eg.db_2.8.0.zip'
> Content type 'application/zip' length 47453600 bytes (45.3 Mb)
> opened URL
> downloaded 45.3 Mb
>
> trying URL 'http://bioconductor.org/packages/2.11/data/annotation/bin/windows/contrib/2.15/hgu95av2.db_2.8.0.zip'
> Content type 'application/zip' length 552365 bytes (539 Kb)
> opened URL
> downloaded 539 Kb
>
> package ‘org.Hs.eg.db’ successfully unpacked and MD5 sums checked
> Warning: unable to move temporary installation ‘C:\Users\yahuac\Documents\R\win-library\2.15\file1a387065468\org.Hs.eg.db’ to ‘C:\Users\yahuac\Documents\R\win-library\2.15\org.Hs.eg.db’

...but something is wrong with your R installation here, and package 
installation is failing. This directory

   C:\Users\yahuac\Documents\R\win-library\2.15\org.Hs.eg.db

needs to be write-able, but appears not to be. My best guess would be that your 
disk is full.

Martin

> package ‘hgu95av2.db’ successfully unpacked and MD5 sums checked
>
> The downloaded binary packages are in
>          C:\Users\yahuac\AppData\Local\Temp\RtmpK8N0Jl\downloaded_packages
> Warning message:
> installed directory not writable, cannot update packages 'foreign', 'lattice',
>    'MASS', 'Matrix', 'nlme', 'rpart', 'survival'
>> filt_bcrneg = nsFilter(ALL_bcrneg, require.entrez=TRUE,
> +     require.GOBP=TRUE, remove.dupEntrez=TRUE,
> +     var.func=IQR, var.cutoff=varCut,
> +     feature.exclude="^AFFX")
> Error: getAnnMap: package hgu95av2 not available
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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