Any ideas of how I can install bioconductor packages under R from a
Notebook session.
I am getting the following errors:
from rpy import *
r.source("http://www.bioconductor.org/biocLite.R";)
r.biocLite("Biobase")
Running biocinstall version 2.1.8 with R version 2.6.1
Your version of R requires version 2.1 of Bioconductor.
trying URL
'http://bioconductor.org/packages/2.1/bioc/src/contrib/
Biobase_1.16.2.ta\
r.gz'
Content type 'application/x-gzip' length 1880174 bytes (1.8 Mb)
opened URL
==================================================
downloaded 1.8 Mb
WARNING: ignoring environment value of R_HOME
/home/jars/Desktop/sage-2.9.1-linux-ubuntu-32bit-i686-Linux/local/lib/
r/\
library
WARNING: ignoring environment value of R_HOME
* Installing *source* package 'Biobase' ...
** libs
gcc -std=gnu99
-I/home/jars/Desktop/sage-2.9.1-linux-ubuntu-32bit-i686-Linux/local/
lib/\
r//include
-I/home/jars/Desktop/sage-2.9.1-linux-ubuntu-32bit-i686-Linux/local/
lib/\
r//include -I/usr/local/include WARNING: ignoring environment value
of
R_HOME -fpic -I/home/was/build/sage-2.9/local/include
-L/home/was/build/sage-2.9/local/lib/ -c anyMissing.c -o anyMissing.o
gcc: WARNING:: No such file or directory
gcc: ignoring: No such file or directory
gcc: environment: No such file or directory
gcc: value: No such file or directory
gcc: of: No such file or directory
gcc: R_HOME: No such file or directory
make: *** [anyMissing.o] Error 1
ERROR: compilation failed for package 'Biobase'
** Removing
'/home/jars/Desktop/sage-2.9.1-linux-ubuntu-32bit-i686-Linux/local/lib/
r\
/library/Biobase'
The downloaded packages are in
/tmp/RtmpcVfUFN/downloaded_packages
Updating HTML index of packages in '.Library'
Warning message:
In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
installation of package 'Biobase' had non-zero exit status
Thanks
Shahab
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