Thanks I?aki! toolbox looks really useful for my usecase. 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. 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. 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? TIA G On Wed, 23 Jun 2021 at 15:45, I?aki Ucar <iucar at fedoraproject.org> wrote:> On Wed, 23 Jun 2021 at 14:50, Gavin Simpson <ucfagls at gmail.com> wrote: > > > > How would one go about installing R 4.1 from rawhide? (October is a > little too far away to be off r-release for that long while maintaining R > packages on CRAN that depend on tidyverse packages.) > > $ sudo dnf update R --release rawhide > > should do. Be aware though that this means updating other dependencies > too. This may or may not cause problems. A safer option would be to > use a containerized environment. Toolbox [1, 2] is perfect for this, > especially for development purposes: > > $ sudo dnf install toolbox > $ toolbox enter -r 35 > [toolbox]$ sudo dnf install R rstudio-desktop > [toolbox]$ rstudio > # rstudio opens > > or directly without entering the toolbox first: > > $ toolbox run -r 35 rstudio > # rstudio opens > > Remember to install any additional repos and/or system dependencies > you may need (e.g., to install R packages from source) *inside* your > toolbox. Hope it helps. > > [1] https://docs.fedoraproject.org/en-US/fedora-silverblue/toolbox/ > [2] https://fedoramagazine.org/a-quick-introduction-to-toolbox-on-fedora/ > > I?aki > > > > > TIA > > > > Gavin > > > > On Fri, 18 Jun 2021 at 14:21, Tom Callaway <spotrh at gmail.com> wrote: > >> > >> I don't think so. If Fedora 34 users want R 4.1, they can install it > from > >> rawhide. > >> > >> Or someone that isn't me can spend another two weeks doing it. :) > >> > >> ~spot > >> > >> On Fri, Jun 18, 2021, 6:50 AM I?aki Ucar <iucar at fedoraproject.org> > wrote: > >> > >> > Nice! Plans for F34? :)) > >> > > >> > On Fri, 18 Jun 2021 at 00:45, Tom Callaway <spotrh at gmail.com> wrote: > >> > > > >> > > The R 4.1 rawhide rebuild is complete, and waiting for bodhi to > push it: > >> > > https://bodhi.fedoraproject.org/updates/FEDORA-2021-e7a89430cd > >> > > > >> > > ~spot > >> > > >> > > >> > > >> > -- > >> > I?aki ?car > >> > > >> > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> R-SIG-Fedora mailing list > >> R-SIG-Fedora at r-project.org > >> https://stat.ethz.ch/mailman/listinfo/r-sig-fedora > > > > > > > > -- > > Gavin Simpson, PhD [he/him/his] [t] +1 306 337 8863 > > ? Research Scientist [f] +1 306 337 2410 > > Institute of Environmental [tw] @ucfagls > > Change & Society [w] goo.gl/Zpkdem > > University of Regina [w] iecs-uregina.ca > > Regina, SK S4S 0A2, Canada [iD] 0000-0002-9084-8413 > > > > ? Adjunct Professor, Department of Biology, University of Regina. > > > > -- > I?aki ?car >-- Gavin Simpson, PhD [he/him/his] [t] +1 306 337 8863 ? Research Scientist [f] +1 306 337 2410 Institute of Environmental [tw] @ucfagls Change & Society [w] goo.gl/Zpkdem University of Regina [w] iecs-uregina.ca Regina, SK S4S 0A2, Canada [iD] 0000-0002-9084-8413 ? Adjunct Professor, Department of Biology, University of Regina. [[alternative HTML version deleted]]
FWIW, I just built R-testthat-3.0.3 in rawhide. As far as the R-* packages in the repos, they are either an R package that someone wanted in Fedora at some point (10%), a package that needed some love to build in Fedora, either because it is old or Fedora is too new (5%), BioConductor bits (10%), or dependencies (75%). I am kidding a bit on that last number, but dependency creep in R is a real thing. Since Fedora's R-testthat has a patch for the bundled catch, there is value in having it in Fedora rather than just having people try (and fail) to build from CRAN. The good news is that if testthat upstream pulls a newer copy of catch into it, it should pickup the fix, and this issue will hopefully go away over time. ~spot On Wed, Jun 23, 2021 at 12:29 PM Gavin Simpson <ucfagls at gmail.com> wrote:> Thanks I?aki! toolbox looks really useful for my usecase. > > 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. > > 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. > > 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? > > TIA > > G > > On Wed, 23 Jun 2021 at 15:45, I?aki Ucar <iucar at fedoraproject.org> wrote: > >> On Wed, 23 Jun 2021 at 14:50, Gavin Simpson <ucfagls at gmail.com> wrote: >> > >> > How would one go about installing R 4.1 from rawhide? (October is a >> little too far away to be off r-release for that long while maintaining R >> packages on CRAN that depend on tidyverse packages.) >> >> $ sudo dnf update R --release rawhide >> >> should do. Be aware though that this means updating other dependencies >> too. This may or may not cause problems. A safer option would be to >> use a containerized environment. Toolbox [1, 2] is perfect for this, >> especially for development purposes: >> >> $ sudo dnf install toolbox >> $ toolbox enter -r 35 >> [toolbox]$ sudo dnf install R rstudio-desktop >> [toolbox]$ rstudio >> # rstudio opens >> >> or directly without entering the toolbox first: >> >> $ toolbox run -r 35 rstudio >> # rstudio opens >> >> Remember to install any additional repos and/or system dependencies >> you may need (e.g., to install R packages from source) *inside* your >> toolbox. Hope it helps. >> >> [1] https://docs.fedoraproject.org/en-US/fedora-silverblue/toolbox/ >> [2] https://fedoramagazine.org/a-quick-introduction-to-toolbox-on-fedora/ >> >> I?aki >> >> > >> > TIA >> > >> > Gavin >> > >> > On Fri, 18 Jun 2021 at 14:21, Tom Callaway <spotrh at gmail.com> wrote: >> >> >> >> I don't think so. If Fedora 34 users want R 4.1, they can install it >> from >> >> rawhide. >> >> >> >> Or someone that isn't me can spend another two weeks doing it. :) >> >> >> >> ~spot >> >> >> >> On Fri, Jun 18, 2021, 6:50 AM I?aki Ucar <iucar at fedoraproject.org> >> wrote: >> >> >> >> > Nice! Plans for F34? :)) >> >> > >> >> > On Fri, 18 Jun 2021 at 00:45, Tom Callaway <spotrh at gmail.com> wrote: >> >> > > >> >> > > The R 4.1 rawhide rebuild is complete, and waiting for bodhi to >> push it: >> >> > > https://bodhi.fedoraproject.org/updates/FEDORA-2021-e7a89430cd >> >> > > >> >> > > ~spot >> >> > >> >> > >> >> > >> >> > -- >> >> > I?aki ?car >> >> > >> >> >> >> [[alternative HTML version deleted]] >> >> >> >> _______________________________________________ >> >> R-SIG-Fedora mailing list >> >> R-SIG-Fedora at r-project.org >> >> https://stat.ethz.ch/mailman/listinfo/r-sig-fedora >> > >> > >> > >> > -- >> > Gavin Simpson, PhD [he/him/his] [t] +1 306 337 8863 >> > ? Research Scientist [f] +1 306 337 2410 >> > Institute of Environmental [tw] @ucfagls >> > Change & Society [w] goo.gl/Zpkdem >> > University of Regina [w] iecs-uregina.ca >> > Regina, SK S4S 0A2, Canada [iD] 0000-0002-9084-8413 >> > >> > ? Adjunct Professor, Department of Biology, University of Regina. >> >> >> >> -- >> I?aki ?car >> > > > -- > Gavin Simpson, PhD [he/him/his] [t] +1 306 337 8863 > ? Research Scientist [f] +1 306 337 2410 > Institute of Environmental [tw] @ucfagls > Change & Society [w] goo.gl/Zpkdem > University of Regina [w] iecs-uregina.ca > Regina, SK S4S 0A2, Canada [iD] 0000-0002-9084-8413 > > ? Adjunct Professor, Department of Biology, University of Regina. >[[alternative HTML version deleted]]
On Wed, 23 Jun 2021 at 18:29, Gavin Simpson <ucfagls at gmail.com> wrote:> > Thanks I?aki! 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. -- I?aki ?car