[BioC] Failure loading "arrayQualityMetrics" package.

[Dan Tenenbaum]

On Wed, May 4, 2011 at 2:28 PM, Omar Gutierrez Arenas
<tardebut at 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]]
>
>
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