On Wed, 23 Jun 2021 at 18:29, Gavin Simpson <ucfa...@gmail.com> wrote: > > Thanks Iñaki! toolbox looks really useful for my usecase.
Toolbox is *very* cool. :) > I'm hitting a related issue in that some R-* packages are not up-to-date with > their CRAN versions (especially testthat, which won't compile on F35/rawhide > because of a problem in catch that is bundled with testhat and something that > has changed in the compiler versions in rawhide. So now I'm still stuck as I > can't install the latest version of vdiffr (which I need for R 4.1) as it > needs 3.0.3 of testthat. Currently, in rawhide, I recommend installing R-testthat, which comes from the official repos, and it's patched. Also, please make some noise in [1] to get it resolved upstream. ;-) [1] https://github.com/r-lib/testthat/issues/1373 > I'm also a little unclear why there are so many R-* packages in the repos > now? And how these relate to your COPR-based initiative to provide fedora > packages for all of CRAN. All the R-* packages are in the official repos, most of them maintained by Elliott (@qulogic). There are a few hundred. Then, if you have my Copr enabled, you'll have access to R-CRAN-* packages, which currently are more than 17100 packages. CRAN packages in the official repos are also in the Copr repo (R-testthat is the official one; R-CRAN-testthat comes from Copr). These installations are compatible, because the Copr repo installs stuff into /usr/local to avoid any clashes with the official repos. The official repos also have some Bioc packages not present in my Copr repo. See [2] for further details. [2] https://cran.r-project.org/bin/linux/fedora/ If you happen to have the same package from several sources, R will pick your user library as a first option, packages from Copr as the second option, and packages from the official repos as the third option. > I suspect I'm hitting all the issues that Tom and you and others are having > to deal with in the course of your packaging R packages for fedora, but as > until recently I just compiled R myself I'm a little unsure what is the > best/recommended strategy for installing R packages etc on Fedora? Use the > main repo packages, your COPR, something else? Is there an overview, road map > or plan somewhere that outlines this and/or what the recommended route is? What can I say? :) The Copr repo has been working nicely for me, especially for stable releases. I have it enabled in all the servers I manage here at the university. And it's especially convenient when you install the R-CoprManager package, because then you just call install.packages() in your R console and binary packages from Copr are automatically installed if they are available; otherwise, they are pulled from CRAN, so no big deal. In rawhide, there may be some "glitches", because it's in active development, so I have to launch several mass rebuilds until things start to settle (no more system-wide changes, no more core library updates...). Right now I'm in the middle of a mass rebuild, so you won't be able to install some packages until it's finished. -- Iñaki Úcar _______________________________________________ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
