Dear R Developers, I am trying to install cummeRbund library in my R latest version 3 i tried giving source("http://bioconductor.org/biocLite.R") biocLite("cummeRbund") After installing some package it returned with the Warning as Warning messages: 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘RCurl’ had non-zero exit status 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘biomaRt’ had non-zero exit status 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘rtracklayer’ had non-zero exit status 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘GenomicFeatures’ had non-zero exit status 5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘biovizBase’ had non-zero exit status 6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘Gviz’ had non-zero exit status 7: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘cummeRbund’ had non-zero exit status I searched in net regarding the issue. I am sending the Out of following commands " sessionInfo() biocinstallRepos() " sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.10.3 loaded via a namespace (and not attached): [1] tools_3.0.1 >biocinstallRepos() BioCsoft "http://bioconductor.org/packages/2.12/bioc" BioCann "http://bioconductor.org/packages/2.12/data/annotation" BioCexp "http://bioconductor.org/packages/2.12/data/experiment" BioCextra "http://bioconductor.org/packages/2.12/extra" CRAN "http://cran.fhcrc.org" Could you please suggest on the same. Thanks and Regards Sridhar [[alternative HTML version deleted]]

Hi, On Sun, Aug 11, 2013 at 11:44 PM, Sridhar Srinivasan <sridhar2bioinfo at="" gmail.com=""> wrote: > Dear R Developers, > > I am trying to install cummeRbund library in my R latest version 3 > > i tried giving > > source("http://bioconductor.org/biocLite.R") > biocLite("cummeRbund") > Can you send the FULL output of this biocLite() command? My guess is that a clue is buried in there. Probably a missing system dependency like xml2 or libcurl. On ubuntu you can fix this with sudo apt-get install libxml2-dev libcurl-dev Dan > After installing some package it returned with the Warning as > > Warning messages: > 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?RCurl? had non-zero exit status > 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?biomaRt? had non-zero exit status > 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?rtracklayer? had non-zero exit status > 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?GenomicFeatures? had non-zero exit status > 5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?biovizBase? had non-zero exit status > 6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?Gviz? had non-zero exit status > 7: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?cummeRbund? had non-zero exit status > > I searched in net regarding the issue. > > I am sending the Out of following commands > " > > sessionInfo() > biocinstallRepos() > > " > > sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-redhat-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.10.3 > > loaded via a namespace (and not attached): > [1] tools_3.0.1 > >>biocinstallRepos() > BioCsoft > "http://bioconductor.org/packages/2.12/bioc" > BioCann > "http://bioconductor.org/packages/2.12/data/annotation" > BioCexp > "http://bioconductor.org/packages/2.12/data/experiment" > BioCextra > "http://bioconductor.org/packages/2.12/extra" > CRAN > "http://cran.fhcrc.org" > > > Could you please suggest on the same. > > Thanks and Regards > Sridhar > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor