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!
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