Hello, I'm trying to set up easyRNASeq on a cluster system (where I don't have root) and am getting this error: > biocLite("easyRNASeq") Using R version 2.11.1, biocinstall version 2.6.10. Installing Bioconductor version 2.6 packages: [1] "easyRNASeq" Please wait... Warning in install.packages(pkgs = pkgs, repos = repos, ...) : argument 'lib' is missing: using '/lustre/home/aloraine/R/x86_64-pc- linux-gnu-library/2.11' Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ‘easyRNASeq’ is not available I found documentation that explains that this error message "package 'something' is not available' means that some dependencies are missing, which can happen if a package is not available for a given system. This system is Linux, and I would think that would not be a problem here. > sessionInfo() R version 2.11.1 (2010-05-31) x86_64-pc-linux-gnu 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=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 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 loaded via a namespace (and not attached): [1] tcltk_2.11.1 tools_2.11.1 Could you help? Best, Ann ------------------------------- Ann Loraine, Ph.D. Associate Professor Department of Bioinformatics and Genomics University of North Carolina at Charlotte North Carolina Research Campus 600 Laureate Way Kannapolis, NC 28081 704-250-5750 aloraine@uncc.edu http://www.transvar.org http://www.bioviz.org http://www.uncc.edu [[alternative HTML version deleted]]

On Fri, Aug 3, 2012 at 4:39 PM, Loraine, Ann <ann.loraine@uncc.edu> wrote: > Hello, > > I'm trying to set up easyRNASeq on a cluster system (where I don't have > root) and am getting this error: > > > biocLite("easyRNASeq") > Using R version 2.11.1, biocinstall version 2.6.10. > Installing Bioconductor version 2.6 packages: > [1] "easyRNASeq" > Please wait... > > Warning in install.packages(pkgs = pkgs, repos = repos, ...) : > argument 'lib' is missing: using > '/lustre/home/aloraine/R/x86_64-pc-linux-gnu-library/2.11' > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ‘easyRNASeq’ is not available > > Hi, Ann. easyRNASeq is not available for R version 2.11. You will need to upgrade your R version to the latest version to get the easyRNASeq package. Sean > I found documentation that explains that this error message "package > 'something' is not available' means that some dependencies are missing, > which can happen if a package is not available for a given system. > > This system is Linux, and I would think that would not be a problem here. > > > sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-pc-linux-gnu > > 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=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 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 > > loaded via a namespace (and not attached): > [1] tcltk_2.11.1 tools_2.11.1 > > Could you help? > > Best, > > Ann > > ------------------------------- > Ann Loraine, Ph.D. > Associate Professor > Department of Bioinformatics and Genomics > University of North Carolina at Charlotte > North Carolina Research Campus > 600 Laureate Way > Kannapolis, NC 28081 > 704-250-5750 > aloraine@uncc.edu > http://www.transvar.org > http://www.bioviz.org > http://www.uncc.edu > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

Ann, please use current version of R, 2.15.1. Yours is two years out of date. Best wishes Wolfgang Aug/3/12 10:39 PM, Loraine, Ann scripsit:: > Hello, > > I'm trying to set up easyRNASeq on a cluster system (where I don't have root) and am getting this error: > >> biocLite("easyRNASeq") > Using R version 2.11.1, biocinstall version 2.6.10. > Installing Bioconductor version 2.6 packages: > [1] "easyRNASeq" > Please wait... > > Warning in install.packages(pkgs = pkgs, repos = repos, ...) : > argument 'lib' is missing: using '/lustre/home/aloraine/R/x86_64 -pc-linux-gnu-library/2.11' > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ?easyRNASeq? is not available > > I found documentation that explains that this error message "package 'something' is not available' means that some dependencies are missing, which can happen if a package is not available for a given system. > > This system is Linux, and I would think that would not be a problem here. > >> sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-pc-linux-gnu > > 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=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 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 > > loaded via a namespace (and not attached): > [1] tcltk_2.11.1 tools_2.11.1 > > Could you help? > > Best, > > Ann > > ------------------------------- > Ann Loraine, Ph.D. > Associate Professor > Department of Bioinformatics and Genomics > University of North Carolina at Charlotte > North Carolina Research Campus > 600 Laureate Way > Kannapolis, NC 28081 > 704-250-5750 > aloraine at uncc.edu > http://www.transvar.org > http://www.bioviz.org > http://www.uncc.edu > > > [[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 > -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber