I also tried installing biomaRt separately but I was not able to do that. How do I get around this problem? Please see the session below: biocLite("biomaRt") Running biocinstall version 2.1.11 with R version 2.6.1 Your version of R requires version 2.1 of BioConductor. Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : argument 'lib' is missing: using '/nfs/apollo/2/c2b2/users/mb3058/R/x86_64-unknown-linux-gnu- library/2.6' trying URL 'http://bioconductor.org/packages/2.1/bioc/src/contrib/biomaRt_1.12.2. tar.gz' Content type 'application/x-gzip' length 276683 bytes (270 Kb) opened URL ================================================== downloaded 270 Kb /nfs/apollo/2/c2b2/users/mb3058/R/x86_64-unknown-linux-gnu-library/2.6 * Installing *source* package 'biomaRt' ... ** R ** inst ** preparing package for lazy loading Loading required package: RCurl Error in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : 'RCurl' is not a valid package -- installed < 2.0.0? Calls: .getRequiredPackages -> .getRequiredPackages2 -> library Execution halted ERROR: lazy loading failed for package 'biomaRt' ** Removing '/nfs/apollo/2/c2b2/users/mb3058/R/x86_64-unknown-linux-gnu- library/2.6/bioma Rt' ** Restoring previous '/nfs/apollo/2/c2b2/users/mb3058/R/x86_64-unknown-linux-gnu- library/2.6/bioma Rt' The downloaded packages are in /tmp/RtmpdB1uCC/downloaded_packages Warning message: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'biomaRt' had non-zero exit status thanks manisha -----Original Message----- From: James W. MacDonald [mailto:jmacdon@med.umich.edu] Sent: Tuesday, September 30, 2008 4:10 PM To: Manisha Brahmachary Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] problem installing affycoretools in R in linux environment Hi Manisha, That error indicates that biomaRt was installed incorrectly. Try biocLite("biomaRt") and then see if you can install affycoretools. Best, Jim Manisha Brahmachary wrote: > I am having problems installing affycoretools in R (2.6) on my linux > environment. When I do the same thing with my R (2.6) in windows I donot have > any such problem and it gets properly installed. I will appreciate any > suggestion on how to install it in linux environment > > > > I am trying to install affycoretools ver 1.10.2. > > > > Following is the session for installation: > > > >> biocLite("affycoretools") > > Running biocinstall version 2.1.11 with R version 2.6.1 > > Your version of R requires version 2.1 of BioConductor. > > Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > > argument 'lib' is missing: using > '/nfs/apollo/2/c2b2/users/mb3058/R/x86_64-unknown-linux-gnu- library/2.6' > > trying URL > 'http://bioconductor.org/packages/2.1/bioc/src/contrib/affycoretools_1 .10.2.t > ar.gz' > > Content type 'application/x-gzip' length 6776315 bytes (6.5 Mb) > > opened URL > > ================================================== > > downloaded 6.5 Mb > > > > /nfs/apollo/2/c2b2/users/mb3058/R/x86_64-unknown-linux-gnu- library/2.6 > > * Installing *source* package 'affycoretools' ... > > ** R > > ** inst > > ** preparing package for lazy loading > > Loading required package: affy > > Loading required package: Biobase > > Loading required package: tools > > > > Welcome to Bioconductor > > > > Vignettes contain introductory material. To view, type > > 'openVignette()'. To cite Bioconductor, see > > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > > > Loading required package: affyio > > Loading required package: preprocessCore > > Loading required package: limma > > Loading required package: GOstats > > Loading required package: graph > > Loading required package: GO.db > > Loading required package: AnnotationDbi > > Loading required package: DBI > > Loading required package: RSQLite > > Loading required package: annotate > > Loading required package: xtable > > Loading required package: RBGL > > Loading required package: Category > > Loading required package: genefilter > > Loading required package: survival > > Loading required package: splines > > Loading required package: biomaRt > > > > Error in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = > lib.loc) : > > 'biomaRt' is not a valid package -- installed < 2.0.0? > > Calls: .getRequiredPackages -> .getRequiredPackages2 -> library > > Execution halted > > ERROR: lazy loading failed for package 'affycoretools' > > ** Removing > '/nfs/apollo/2/c2b2/users/mb3058/R/x86_64-unknown-linux-gnu- library/2.6/affyc > oretools' > > ** Restoring previous > '/nfs/apollo/2/c2b2/users/mb3058/R/x86_64-unknown-linux-gnu- library/2.6/affyc > oretools' > > > > The downloaded packages are in > > /tmp/RtmpdB1uCC/downloaded_packages > > Warning message: > > In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, > : > > installation of package 'affycoretools' had non-zero exit status > > > > thanks > > manisha > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662