[BioC] Error in installing packages from bioconductor using R version 2.13.0 on Windows 7

[Dan Tenenbaum]

Hi Gabriel,

On Sun, May 1, 2011 at 12:08 PM, gabriel teku <gabbyteku at gmail.com> wrote:
> Hi all,
> I have just installed R version 2.13.0 on a windows 7 machine but don't seem
> to be able to install some packages from bioconductor. The culprit may be
> package XML namespace. Below are details while trying to install package
> ArrayExpress. Important to note that a similar error occurs when I try to
> install GEOquery.
> Please, any ideas shall be much appreciated
>
>> biocLite('ArrayExpress')
> Using R version 2.13.0, biocinstall version 2.8.4.
> Installing Bioconductor version 2.8 packages:
> [1] "ArrayExpress"
> Please wait...
>
> Installing package(s) into ‘C:/Users/Teku/Documents/R/win-library/2.13’
> (as ‘lib’ is unspecified)
> trying URL '
> http://bioconductor.org/packages/2.8/bioc/bin/windows/contrib/2.13/ArrayExpress_1.12.0.zip
> '
> Content type 'application/zip' length 217981 bytes (212 Kb)
> opened URL
> downloaded 212 Kb
>
> package 'ArrayExpress' successfully unpacked and MD5 sums checked
>
> The downloaded packages are in
>        C:\Users\Teku\AppData\Local\Temp\RtmpKMihJ3\downloaded_packages
>> library(ArrayExpress)
> Error : package 'XML' does not have a name space
> Error: package/namespace load failed for 'ArrayExpress'
>> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=Finnish_Finland.1252  LC_CTYPE=Finnish_Finland.1252
> [3] LC_MONETARY=Finnish_Finland.1252 LC_NUMERIC=C
> [5] LC_TIME=Finnish_Finland.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] Biobase_2.12.1
>
> loaded via a namespace (and not attached):
> [1] tools_2.13.0
>

I can't reproduce this. What happens when you type:
source("http://bioconductor.org/biocLite.R")
biocinstallRepos()

?

I get the following:

           "http://bioconductor.org/packages/2.8/bioc"

"http://bioconductor.org/packages/2.8/data/annotation"

"http://bioconductor.org/packages/2.8/data/experiment"

          "http://bioconductor.org/packages/2.8/extra"

           "http://brainarray.mbni.med.umich.edu/bioc"
                                                  CRAN
                               "http://cran.fhcrc.org"
                                             CRANextra
                  "http://www.stats.ox.ac.uk/pub/RWin"
>

So I am downloading XML from "CRANextra". You could force this as follows:

 install.packages("XML", repos="http://www.stats.ox.ac.uk/pub/RWin")

Then try:
biocLite("ArrayExpress")
again.

Dan


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