While trying to install Bioconductor, I get this warning message: installed directory not writable, cannot update packages 'boot', 'class', 'cluster', 'foreign', 'KernSmooth', 'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet', 'rpart', 'spatial' I do have the latest version of R. Please let me know how to resolve this. Thank you! -- output of sessionInfo(): > source("http://bioconductor.org/biocLite.R") Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help > source("http://bioconductor.org/biocLite.R") Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help > biocLite() BioC_mirror: http://bioconductor.org Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version 3.1.0. Warning message: installed directory not writable, cannot update packages 'boot', 'class', 'cluster', 'foreign', 'KernSmooth', 'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet', 'rpart', 'spatial' -- Sent via the guest posting facility at bioconductor.org.

Hi, On Sat, May 31, 2014 at 1:46 PM, Felix Francis [guest] <guest at="" bioconductor.org=""> wrote: > While trying to install Bioconductor, I get this warning message: > > installed directory not writable, cannot update packages 'boot', 'class', 'cluster', 'foreign', 'KernSmooth', 'lattice', 'MASS', > 'Matrix', 'mgcv', 'nlme', 'nnet', 'rpart', 'spatial' > > I do have the latest version of R. Please let me know how to resolve this. It sounds like you do not have permissions to write into the installed directory that R was installed in on the computer you are using. Running the update/install as an administrator on the machine would likely do the trick. Also: > -- output of sessionInfo(): > >> source("http://bioconductor.org/biocLite.R") > Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help [/clip] What you pasted is not the output of sessionInfo() In the future, call the sessionInfo() function from within your R session and paste what follows. For example, this is what mine looks like in a session I have currently open: R> sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] devtools_1.5 loaded via a namespace (and not attached): [1] digest_0.6.4 evaluate_0.5.5 httr_0.3 memoise_0.2.1 parallel_3.1.0 [6] RCurl_1.95-4.1 stringr_0.6.2 tools_3.1.0 whisker_0.3-2 -- Steve Lianoglou Computational Biologist Genentech