[BioC] Error to install a package for Affymetrix data

[Dan Tenenbaum]

On Mon, Jun 24, 2013 at 8:47 AM, chm chag <chagdal-madiha at hotmail.com> wrote:
> Dear Sir;
>
> I reinstalled the latest version of R (R-3.0.1) as bioconductor but it still does not work: By installing the  oligo package I always have this error message (Warning: unable to move temporary installation "C: \ Program Files \ R \ R-3.0.1 \ library \ file5bc5cca72b1 \ trace 'to' C: \ Program Files \ R \ R-3.0.1 \ library \ trace ')

This sounds like a permissions problem. Are you able to run R as an
administrator?
That is, can you right-click on the R icon and choose "Run as
administrator"? If you can do that, try reinstalling oligo as an
administrator.

>  and when running the command: library (oligo) I have this error message, in addition to this dialog window (see picture attached).


Most attachments are stripped off before reaching the list, so we did
not see your picture, maybe you can just paste the error text into an
email.

Thanks,
Dan


>
> thank you for your help.
>
>
>
> Cordially;
> Madiha Chagdal;
>
>
>
>
>
>> Date: Mon, 24 Jun 2013 09:59:32 -0400
>> From: jmacdon at uw.edu
>> To: chagdal-madiha at hotmail.com
>> CC: bioconductor at r-project.org
>> Subject: Re: [BioC] Error to install a package for Affymetrix data
>>
>> You need to first upgrade to the current version of R and re-install
>> Bioconductor.
>>
>> Best,
>>
>> Jim
>>
>>
>>
>> On 6/21/2013 9:23 AM, chm chag wrote:
>> > Dear Sir,
>> >
>> > The instalation of the 'oligo' package does not work and I have these error messages:
>> >
>> >> source("http://bioconductor.org/biocLite.R")
>> >> biocLite("oligo")
>> > BioC_mirror: http://bioconductor.org
>> > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version
>> > 2.15.
>> > Installing package(s) 'oligo'
>> > Avis : unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.15
>> > essai de l'URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/oligo_1.22.0.zip'
>> > Content type 'application/zip' length 5765066 bytes (5.5 Mb)
>> > URL ouverte
>> > downloaded 5.5 Mb
>> > package ‘oligo’ successfully unpacked and MD5 sums checked
>> > The downloaded binary packages are in
>> > C:\Documents and Settings\Administrateur\Local Settings\Temp\Rtmp4CqL4q\downloaded_packages
>> > Avis : unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.15
>> >
>> >
>> > And when I compile the command:> library(oligo) I have this:
>> >
>> >
>> > Error in inDL(x, as.logical(local), as.logical(now), ...) :
>> > impossible de charger l'objet partagé 'C:/Program Files/R/R-2.15.3/library/affxparser/libs/i386/affxparser.dll':
>> > LoadLibrary failure: La procédure spécifiée est introuvable.
>> > Erreur : le chargement du package / espace de noms a échoué pour ‘oligo’
>> >
>> > And even by compiling this commands for instaling "hugene21sttranscriptcluster.db" package I have this error message:
>> >> source("http://bioconductor.org/biocLite.R")
>> >> biocLite("hugene21sttranscriptcluster.db", type="source")
>> >
>> > BioC_mirror: http://bioconductor.org
>> > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
>> > Installing package(s) 'hugene21sttranscriptcluster.db'
>> > Avis : unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.15
>> > Message d'avis :
>> > package ‘hugene21sttranscriptcluster.db’ is not available (for R version 2.15.3)
>> >
>> > cordially;
>> >
>> >
>> > Madiha Chagdal
>> > SITN Master-2 : Statistics, Computer and Digital Techniques
>> > Claude Bernard Lyon-1 University
>> >
>> >
>> > [[alternative HTML version deleted]]
>> >
>> >
>> >
>> > _______________________________________________
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>>
>> --
>> James W. MacDonald, M.S.
>> Biostatistician
>> University of Washington
>> Environmental and Occupational Health Sciences
>> 4225 Roosevelt Way NE, # 100
>> Seattle WA 98105-6099
>>
>
>
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