On Sun, May 13, 2018 at 9:27 AM, Johannes Ranke <jranke at uni-bremen.de> wrote:> Hi, > > I wonder if you have read the notes on R 3.5.0 on stretch on > > https://cran.r-project.org/bin/linux/debian/ > > I think this should answer your questions. If not, please let us know. > >Johannes, I think I have--I think that's how I got the last line in my sources.list--but I missed it this morning in my hurry. Do I understand correctly that I should be able to replace the last line of my sources.list (in my reply to Dirk) with deb http://<favourite-cran-mirror>/bin/linux/debian stretch-cran35/ and then use update.packages(lib.loc="/usr/local/lib/R/site-library", ask=FALSE, checkBuilt=TRUE) to update all my packages (all packages--or just those that use Rcpp?)? That seems to suggest I /not/ let aptitude safe-upgrade touch anything in R, right? I'm guessing / hoping I can use that to update all my CRAN R packages. Do I need to do anything to keep any of the r-cran-... Debian packages from updating? Figuring out which packages used Rcpp and which didn't seems tedious; am I right? Thanks, Bill [[alternative HTML version deleted]]
Am Sonntag, 13. Mai 2018, 21:02:42 CEST schrieb Bill Harris: ... Do I understand correctly that I should be able to replace the last line of my sources.list (in my reply to Dirk) with deb http://<favourite-cran-mirror>/bin/linux/debian stretch-cran35/ If you do this, then update and upgrade, r-cran-* or r-cran-bioc* packages installed via the Debian package management system will be removed, with the exception of r-recommended and the few packages listed in the Debian CRAN page. If you cannot afford that, you should stay with R 3.4. You can check what packages will be affected as pointed out on the CRAN Debian page, or using apt-get upgrade -s (for silent). If this removes R packages your locally installed packages depend on, you need to install them from CRAN using install.packages or Dirks install.r afterwards. If you then use update.packages(lib.loc="/usr/local/lib/R/site-library", ask=FALSE, checkBuilt=TRUE) this will update packages installed from CRAN (provided you use the default local library path) to make sure they are compatible with R>=3.5.0. Things installed from github and the like will have to be taken care of separately. ... Johannes [[alternative HTML version deleted]]
Thank you, Johannes. I think I understand. I plan to try it when I have a free evening. Bill On Sun, May 13, 2018 at 9:23 PM, Johannes Ranke <jranke at uni-bremen.de> wrote:> Am Sonntag, 13. Mai 2018, 21:02:42 CEST schrieb Bill Harris: > > ... > > Do I understand correctly that I should be able to replace the last line > of my sources.list (in my reply to Dirk) with > > > deb http://<favourite-cran-mirror>/bin/linux/debian stretch-cran35/ > > > > If you do this, then update and upgrade, r-cran-* or r-cran-bioc* packages > installed via the Debian package management system will be removed, with > the exception of r-recommended and the few packages listed in the Debian > CRAN page. If you cannot afford that, you should stay with R 3.4. > > > > You can check what packages will be affected as pointed out on the CRAN > Debian page, or using apt-get upgrade -s (for silent). If this removes R > packages your locally installed packages depend on, you need to install > them from CRAN using install.packages or Dirks install.r afterwards. > > > If you then use > > > update.packages(lib.loc="/usr/local/lib/R/site-library", ask=FALSE, checkBuilt=TRUE) > > > > this will update packages installed from CRAN (provided you use the > default local library path) to make sure they are compatible with R>=3.5.0. > Things installed from github and the like will have to be taken care of > separately. > > > > ... > > Johannes > > >[[alternative HTML version deleted]]