[R] Cannot install pakages from Bioconductor besides the default installation

[Martin Morgan]

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Is the below a complete transcript of the outcome of
biocLite('biomaRt')? I would have expected to see R attempt to install
each package, and then perhaps XML failing to compile. This would mean
that first RCurl and then biomaRt would fail to install. Likely XML
would fail to install because of outdated system dependencies, but
this is just speculation; is this really the complete output of the
biocLite('biomaRt') command?

Martin

<mauede at alice.it> writes:

> I am running  the last R version on SuSE 11.1.
> I installed the Bioconductor environment following the instructions on the web. As a consequence some
> core packages from Bioconductors were installed.
> I need to add some more packages. So I tried biomaRt as follows. 
> It does not get installed correctly. 
> Please see the following sequence.
> Thank you in advance.
> Maura
>
>> source("http://bioconductor.org/biocLite.R")
> Warning messages:
> 1: In safeSource() : Redefining ‘biocinstall’
> 2: In safeSource() : Redefining ‘biocinstallPkgGroups’
> 3: In safeSource() : Redefining ‘biocinstallRepos’
>> > biocLite("biomaRt")
> Running biocinstall version 2.4.11 with R version 2.9.0 
> Your version of R requires version 2.4 of Bioconductor.
> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  :
>   argument 'lib' is missing: using '/home/mauede/R/x86_64-unknown-linux-gnu-library/2.9'
> also installing the dependencies ‘XML’, ‘RCurl’
>
> trying URL 'http://bioconductor.org/packages/2.4/extra/src/contrib/XML_2.5-1.tar.gz'
> Content type 'application/x-gzip' length 676201 bytes (660 Kb)
> opened URL
> ==================================================
> downloaded 660 Kb
>
> trying URL 'http://bioconductor.org/packages/2.4/extra/src/contrib/RCurl_0.98-1.tar.gz'
> Content type 'application/x-gzip' length 470071 bytes (459 Kb)
> opened URL
> ==================================================
> downloaded 459 Kb
>
> trying URL 'http://bioconductor.org/packages/2.4/bioc/src/contrib/biomaRt_2.0.0.tar.gz'
> Content type 'application/x-gzip' length 200617 bytes (195 Kb)
> opened URL
> ==================================================
> downloaded 195 Kb
>
>
> The downloaded packages are in
> 	‘/tmp/RtmpAtNws1/downloaded_packages’
> Warning messages:
> 1: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  :
>   installation of package 'XML' had non-zero exit status
> 2: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  :
>   installation of package 'RCurl' had non-zero exit status
> 3: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  :
>   installation of package 'biomaRt' had non-zero exit status
>> > library(biomaRt)
> Error in library(biomaRt) : there is no package called 'biomaRt'
>> ?getBM
> No matches for "getBM" have been found
>> ?getSequence
> No matches for "getSequence" have been found
>
>
>
>
>
> tutti i telefonini TIM!
>
>
> 	[[alternative HTML version deleted]]
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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