Hi In R 2.15.2 I try to install biomaRt and Rcurl by source("http://bioconductor.org/biocLite.R") biocLite("biomaRt") And I get the error below after some lines of processing: ERROR: compilation failed for package 'RCurl' * removing '/gpfs/norstore_trd/user/chawla/R/x86_64-unknown-linux-gnu- library/2.15/RCurl' The downloaded source packages are in '/tmp/RtmpiW2q4W/downloaded_packages' Warning messages: 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package 'RCurl' had non-zero exit status 2: installed directory not writable, cannot update packages 'Matrix', 'nlme', 'rpart', 'survival' But I could install packages from the command biocLite() in the same directory. Any ideas how to solve this. Thanks Konika [[alternative HTML version deleted]]

Hi, On Fri, Dec 14, 2012 at 8:29 AM, chawla <chawla at="" bio.ntnu.no=""> wrote: > Hi > In R 2.15.2 > I try to install biomaRt and Rcurl by > source("http://bioconductor.org/biocLite.R") > biocLite("biomaRt") > > And I get the error below after some lines of processing: > > ERROR: compilation failed for package 'RCurl' > * removing > '/gpfs/norstore_trd/user/chawla/R/x86_64-unknown-linux-gnu- library/2.15/RCurl' As this error message indicates, your problem is with the RCurl library -- not biomaRt (yet). Try installing RCurl by itself first. Also: > The downloaded source packages are in > '/tmp/RtmpiW2q4W/downloaded_packages' > Warning messages: > 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package 'RCurl' had non-zero exit status > 2: installed directory not writable, cannot update packages 'Matrix', > 'nlme', > 'rpart', 'survival' It seems you have another problem which is related to the permission settings on the directory that holds your installed packages -- specifically, it seems like you don't have the write permissions to write to it. HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact