I am trying to install the package
BiocManager, but I keep getting error messages. I have tried installing and reinstalling
BiocManager, even updated my version of
R from 3.5.2 to 3.5.3. I have other packages like
TopGO installed - the latter won't load because it requires
The error message I keep getting is:
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.2 (2018-12-20) Installing package(s) 'GO.db' installing the source package ‘GO.db’ trying URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/GO.db_3.7.0.tar.gz' Content type 'application/x-gzip' length 31820876 bytes (30.3 MB) downloaded 30.3 MB * installing *source* package 'GO.db' ... Warning in file.copy(f, instdir, TRUE) : problem copying .\NAMESPACE to C:\Users\Name\Documents\R\win-library\3.5\GO.db\NAMESPACE: Permission denied Warning in file(file, if (append) "a" else "w") : cannot open file 'C:/Users/Name/Documents/R/win-library/3.5/GO.db/DESCRIPTION': Permission denied Error in file(file, if (append) "a" else "w") : cannot open the connection ERROR: installing package DESCRIPTION failed for package 'GO.db' * removing 'C:/Users/Name/Documents/R/win-library/3.5/GO.db' In R CMD INSTALL The downloaded source packages are in ‘C:\Users\Name\AppData\Local\Temp\RtmpEpb8dH\downloaded_packages’ installation path not writeable, unable to update packages: class, codetools, Matrix Update old packages: 'assertthat', 'mgcv' Update all/some/none? [a/s/n]: n Warning message: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) : installation of package ‘GO.db’ had non-zero exit status
I'm starting to run out of ideas short of deleting
R and restarting my collection of libraries from scratch. I tried installing
GO.db on the computing cluster I use too, but alas that came up with similar error messages. Running
R as an administrator also didn't seem to garner any differences.
Any ideas on how to fix this?