Hi Dan,

Thanks a lot. After following your advice, it is now running nicely.

Regards,

Omar




On Wed, May 4, 2011 at 11:34 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:

> On Wed, May 4, 2011 at 2:28 PM, Omar Gutierrez Arenas
> <tardebut@gmail.com> wrote:
> > Dear Colleagues,
> >
> > I'm trying to install the bioconductor package "arrayQualityMetrics".
> > However, after downloading it succesfully, it fails to be load by
> > library(arrayQualityMetrics) despite it is listed among the available
> > packages.
> >
> > *> source("**http://bioconductor.org/biocLite.R*<
> http://bioconductor.org/biocLite.R>
> > *")
> > BioC_mirror = **http://bioconductor.org* <http://bioconductor.org/>
>  > *Change using chooseBioCmirror().
> > Warning messages:
> > 1: In safeSource() : Redefining ‘biocinstall’
> > 2: In safeSource() : Redefining ‘biocinstallPkgGroups’
> > 3: In safeSource() : Redefining ‘biocinstallRepos’*
> >
> > *> biocLite("arrayQualityMetrics")
> > Using R version 2.13.0, biocinstall version 2.8.4.
> > Installing Bioconductor version 2.8 packages:
> > [1] "arrayQualityMetrics"
> > Please wait...*
> > *Installing package(s) into ‘C:/Users/Omar/Documents/R/win-library/2.13’
> > (as ‘lib’ is unspecified)
> > also installing the dependencies ‘beadarray’, ‘Cairo’, ‘hwriter’,
> ‘setRNG’,
> > ‘SVGAnnotation’*
> > *trying URL '
> >
> http://bioconductor.org/packages/2.8/bioc/bin/windows/contrib/2.13/beadarray_2.2.0.zip
> > '
> > Content type 'application/zip' length 13099122 bytes (12.5 Mb)
> > opened URL
> > downloaded 12.5 Mb*
> > *trying URL '
> http://cran.fhcrc.org/bin/windows/contrib/2.13/Cairo_1.4-9.zip'
> > Content type 'application/zip' length 1015277 bytes (991 Kb)
> > opened URL
> > downloaded 991 Kb*
> > *trying URL '
> http://cran.fhcrc.org/bin/windows/contrib/2.13/hwriter_1.3.zip'
> > Content type 'application/zip' length 137651 bytes (134 Kb)
> > opened URL
> > downloaded 134 Kb*
> > *trying URL '
> > http://cran.fhcrc.org/bin/windows/contrib/2.13/setRNG_2009.11-1.zip'
> > Content type 'application/zip' length 56609 bytes (55 Kb)
> > opened URL
> > downloaded 55 Kb*
> > *trying URL '
> >
> http://bioconductor.org/packages/2.8/extra/bin/windows/contrib/2.13/SVGAnnotation_0.9-0.zip
> > '
> > Content type 'application/zip' length 3060112 bytes (2.9 Mb)
> > opened URL
> > downloaded 2.9 Mb*
> > *trying URL '
> >
> http://bioconductor.org/packages/2.8/bioc/bin/windows/contrib/2.13/arrayQualityMetrics_3.8.0.zip
> > '
> > Content type 'application/zip' length 699040 bytes (682 Kb)
> > opened URL
> > downloaded 682 Kb*
> > *package 'beadarray' successfully unpacked and MD5 sums checked
> > package 'Cairo' successfully unpacked and MD5 sums checked
> > package 'hwriter' successfully unpacked and MD5 sums checked
> > package 'setRNG' successfully unpacked and MD5 sums checked
> > package 'SVGAnnotation' successfully unpacked and MD5 sums checked
> > package 'arrayQualityMetrics' successfully unpacked and MD5 sums checked*
> > *The downloaded packages are in
> >        C:\Users\Omar\AppData\Local\Temp\RtmpaOw228\downloaded_packages
> >> library(arrayQualityMetrics)
> > Error : package 'XML' does not have a name space
> > Error: package/namespace load failed for 'arrayQualityMetrics'*
> >
>
>
> Hi Omar,
>
> There was a bad version of the XML package floating around a few days ago.
> You can replace it as follows, in a fresh R session:
>
> source("http://bioconductor.org/biocLite.R")
> biocLite("XML")
>
> -- or --
>
> install.packages("XML", repos="http://www.stats.ox.ac.uk/pub/RWin")
>
> Then try
>
> biocLite("arrayQualityMetrics")
>
> again.
>
> Dan
>
>
> >
> > I look forward to hear from you.
> >
> > Omar
> >
> >        [[alternative HTML version deleted]]
> >
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>

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