I am trying to download the EdgeR 3.16.5 package on R. 3.3.3 and I consistently get the following error text
source("https://bioconductor.org/biocLite.R") Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help A new version of Bioconductor is available after installing the most recent version of R; see http://bioconductor.org/install > biocLite(edgeR) Error in match(x, table, nomatch = 0L) : object 'edgeR' not found > biocLite("edgeR") BioC_mirror: https://bioconductor.org Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06). Installing package(s) ‘edgeR’ trying URL 'https://bioconductor.org/packages/3.4/bioc/bin/macosx/mavericks/contrib/3.3/edgeR_3.16.5.tgz' Content type 'application/x-gzip' length 1747625 bytes (1.7 MB) ================================================== downloaded 1.7 MB The downloaded binary packages are in /var/folders/vh/c4vpsdbj5dv73r6z3ylyg3xdf1hlfv/T//RtmphOVoWw/downloaded_packages installation path not writeable, unable to update packages: boot, cluster, foreign, lattice, MASS, Matrix, mgcv, rpart, survival
I have checked for updates for the packages and run updates. And those run fine. I have also tried updating the listed packages individually with a similar error output.
> sessionInfo() R version 3.3.3 (2017-03-06) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X Yosemite 10.10.5 locale:  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  BiocInstaller_1.24.0 loaded via a namespace (and not attached):  tools_3.3.3