On 25 April 2017 at 16:11, Göran Broström wrote: | I understand that, but what is then the best practice to avoid having | duplicates of the recommended packages? I tried running R as root and | | > update.packages(checkBuilt=TRUE) | --- Please select a CRAN mirror for use in this session --- | Warning: package 'class' in library '/usr/lib/R/library' will not be updated | Warning: package 'cluster' in library '/usr/lib/R/library' will not be | updated | Warning: package 'codetools' in library '/usr/lib/R/library' will not be | updated | Warning: package 'foreign' in library '/usr/lib/R/library' will not be | updated | Warning: package 'KernSmooth' in library '/usr/lib/R/library' will not | be updated | Warning: package 'lattice' in library '/usr/lib/R/library' will not be | updated | Warning: package 'Matrix' in library '/usr/lib/R/library' will not be | updated | Warning: package 'nlme' in library '/usr/lib/R/library' will not be updated | Warning: package 'nnet' in library '/usr/lib/R/library' will not be updated | Warning: package 'spatial' in library '/usr/lib/R/library' will not be | updated | Warning: package 'survival' in library '/usr/lib/R/library' will not be | updated | > | | Not possible?
update.packages() has several arguments. As my previous email said, the library paths seen by R can have __different sources__ on Debian system so you have to __treat them differently__. So update.packages(lib.loc="/usr/local/lib/R/site-library", checkBuilt=TRUE) may be what you wanted here. | I also tried | | $ sudo apt install --reinstall r-cran-survival | | to no avail. It just reinstalls __the same binary__ over and over if you repeat. | > | 2. Installing from scratch should have this fixed automatically, right? | > | > False. | | Thanks. Maybe better to install R from source then. Absolutely not! I think you are confused about installing - R (ie the interpreter, or engine) - R packages from the distribution - R packages directly from CRAN I have worked with that very mix for what must now be over fifteen years (from when we starting to package r-cran-*) and it just works. I tend to do mostly 1) and 3) to update R packages more quickly then the distribution might but that is mostly a personal preference. This list is good for sortiing these questions out so please continue to post til you feel you got it working. Dirk | | Göran -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org _______________________________________________ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian