Re: [R-sig-Fedora] Plans for R 4.1 in Fedora?
On Wed, 23 Jun 2021 at 19:00, Iñaki Ucar wrote: > > 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. Mass rebuild completed in rawhide for the CRAN Copr repo. There are still a few dozen fails that need more careful inspection. If you experience issues, please report them in https://github.com/Enchufa2/cran2copr/issues. -- Iñaki Úcar ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
Re: [R-sig-Fedora] Plans for R 4.1 in Fedora?
On Wed, 23 Jun 2021 at 18:29, Gavin Simpson 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
Re: [R-sig-Fedora] Plans for R 4.1 in Fedora?
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 wrote: > Thanks Iñaki! 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, Iñaki Ucar wrote: > >> On Wed, 23 Jun 2021 at 14:50, Gavin Simpson 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/ >> >> Iñaki >> >> > >> > TIA >> > >> > Gavin >> > >> > On Fri, 18 Jun 2021 at 14:21, Tom Callaway 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 Iñaki Ucar >> wrote: >> >> >> >> > Nice! Plans for F34? :)) >> >> > >> >> > On Fri, 18 Jun 2021 at 00:45, Tom Callaway 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 >> >> > >> >> > >> >> > >> >> > -- >> >> > Iñaki Úcar >> >> > >> >> >> >> [[alternative HTML version deleted]] >> >> >> >> ___ >> >> R-SIG-Fedora mailing list >> >> R-SIG-Fedora@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] -0002-9084-8413 >> > >> > • Adjunct Professor, Department of Biology, University of Regina. >> >> >> >> -- >> Iñaki Úcar >> > > > -- > 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
Re: [R-sig-Fedora] Plans for R 4.1 in Fedora?
Thanks Iñaki! 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, Iñaki Ucar wrote: > On Wed, 23 Jun 2021 at 14:50, Gavin Simpson 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/ > > Iñaki > > > > > TIA > > > > Gavin > > > > On Fri, 18 Jun 2021 at 14:21, Tom Callaway 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 Iñaki Ucar > wrote: > >> > >> > Nice! Plans for F34? :)) > >> > > >> > On Fri, 18 Jun 2021 at 00:45, Tom Callaway 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 > >> > > >> > > >> > > >> > -- > >> > Iñaki Úcar > >> > > >> > >> [[alternative HTML version deleted]] > >> > >> ___ > >> R-SIG-Fedora mailing list > >> R-SIG-Fedora@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] -0002-9084-8413 > > > > • Adjunct Professor, Department of Biology, University of Regina. > > > > -- > Iñaki Úcar > -- 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] -0002-9084-8413 • Adjunct Professor, Department of Biology, University of Regina. [[alternative HTML version deleted]] ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
Re: [R-sig-Fedora] Plans for R 4.1 in Fedora?
On Wed, 23 Jun 2021 at 14:50, Gavin Simpson 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/ Iñaki > > TIA > > Gavin > > On Fri, 18 Jun 2021 at 14:21, Tom Callaway 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 Iñaki Ucar wrote: >> >> > Nice! Plans for F34? :)) >> > >> > On Fri, 18 Jun 2021 at 00:45, Tom Callaway 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 >> > >> > >> > >> > -- >> > Iñaki Úcar >> > >> >> [[alternative HTML version deleted]] >> >> ___ >> R-SIG-Fedora mailing list >> R-SIG-Fedora@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] -0002-9084-8413 > > • Adjunct Professor, Department of Biology, University of Regina. -- Iñaki Úcar ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
Re: [R-sig-Fedora] Plans for R 4.1 in Fedora?
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.) TIA Gavin On Fri, 18 Jun 2021 at 14:21, Tom Callaway 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 Iñaki Ucar wrote: > > > Nice! Plans for F34? :)) > > > > On Fri, 18 Jun 2021 at 00:45, Tom Callaway 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 > > > > > > > > -- > > Iñaki Úcar > > > > [[alternative HTML version deleted]] > > ___ > R-SIG-Fedora mailing list > R-SIG-Fedora@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] -0002-9084-8413 • Adjunct Professor, Department of Biology, University of Regina. [[alternative HTML version deleted]] ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
Re: [R-sig-Fedora] Plans for R 4.1 in Fedora?
We still have a few issues: # dnf install R-* Last metadata expiration check: 0:00:08 ago on Tue Jun 22 13:04:20 2021. Error: Problem 1: conflicting requests - nothing provides R(ABI) = 4.0 needed by R-littler-0.3.12-2.fc34.x86_64 Problem 2: conflicting requests - nothing provides R(ABI) = 4.0 needed by R-Rcompression-0.93.2-30.fc34.x86_64 Problem 3: conflicting requests - nothing provides R(ABI) = 4.0 needed by R-nws-1:1.7.0.1-24.fc34.noarch Problem 4: package R-littler-examples-0.3.12-2.fc34.x86_64 requires R-littler(x86-64) = 0.3.12-2.fc34, but none of the providers can be installe d - package R-littler-examples-0.3.12-2.fc34.x86_64 requires /usr/bin/r, but none of the providers can be installed - conflicting requests - nothing provides R(ABI) = 4.0 needed by R-littler-0.3.12-2.fc34.x86_64 Problem 5: package R-Rcpp-examples-1.0.6-3.fc35.x86_64 requires /usr/bin/r, but none of the providers can be installed - conflicting requests - nothing provides R(ABI) = 4.0 needed by R-littler-0.3.12-2.fc34.x86_64 Problem 6: conflicting requests - nothing provides R(ABI) = 4.0 needed by R-Rsolid-0.9.31-34.fc34.i686 - nothing provides R(ABI) = 4.0 needed by R-Rsolid-0.9.31-34.fc34.x86_64 Problem 7: conflicting requests - package R-Rsolid-devel-0.9.31-34.fc34.i686 requires R-Rsolid(x86-32) = 0.9.31-34.fc34, but none of the providers can be installed - package R-Rsolid-devel-0.9.31-34.fc34.x86_64 requires R-Rsolid(x86-64) = 0.9.31-34.fc34, but none of the providers can be installed - nothing provides R(ABI) = 4.0 needed by R-Rsolid-0.9.31-34.fc34.i686 - nothing provides R(ABI) = 4.0 needed by R-Rsolid-0.9.31-34.fc34.x86_64 (try to add '--skip-broken' to skip uninstallable packages) At least R-littler was already rebuilt by Mattias, but it didn't propagate to the repos yet. On Fri, 18 Jun 2021 at 14:21, Tom Callaway 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 Iñaki Ucar wrote: >> >> Nice! Plans for F34? :)) >> >> On Fri, 18 Jun 2021 at 00:45, Tom Callaway 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 >> >> >> >> -- >> Iñaki Úcar -- Iñaki Úcar ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
Re: [R-sig-Fedora] Plans for R 4.1 in Fedora?
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 Iñaki Ucar wrote: > Nice! Plans for F34? :)) > > On Fri, 18 Jun 2021 at 00:45, Tom Callaway 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 > > > > -- > Iñaki Úcar > [[alternative HTML version deleted]] ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
Re: [R-sig-Fedora] Plans for R 4.1 in Fedora?
Nice! Plans for F34? :)) On Fri, 18 Jun 2021 at 00:45, Tom Callaway 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 -- Iñaki Úcar ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
Re: [R-sig-Fedora] Plans for R 4.1 in Fedora?
The R 4.1 rawhide rebuild is complete, and waiting for bodhi to push it: https://bodhi.fedoraproject.org/updates/FEDORA-2021-e7a89430cd ~spot [[alternative HTML version deleted]] ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
Re: [R-sig-Fedora] Plans for R 4.1 in Fedora?
RStudio built and update submitted: https://bodhi.fedoraproject.org/updates/FEDORA-2021-7a6c7fd1c1 Iñaki On Mon, 7 Jun 2021 at 19:53, Tom Callaway wrote: > > I have started the R 4.1.0 build process in rawhide. The side tag is > f35-build-side-42293. > > I'm tracking things using a Google Sheet, if anyone wants access, just let me > know. > > ~spot > > On Sat, Jun 5, 2021 at 4:11 PM Iñaki Ucar wrote: >> >> On Sat, 5 Jun 2021 at 20:12, Iñaki Ucar wrote: >> > >> > I've updated RStudio to 1.4.1717, which supports R 4.1, and builds are >> > underway [2, 3, 4]. This may take a while (s390x didn't even start >> > yet). >> >> Oh, planned outage: https://pagure.io/fedora-infrastructure/issue/9960 >> >> -- >> Iñaki Úcar -- Iñaki Úcar ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
Re: [R-sig-Fedora] Plans for R 4.1 in Fedora?
I have started the R 4.1.0 build process in rawhide. The side tag is f35-build-side-42293. I'm tracking things using a Google Sheet, if anyone wants access, just let me know. ~spot On Sat, Jun 5, 2021 at 4:11 PM Iñaki Ucar wrote: > On Sat, 5 Jun 2021 at 20:12, Iñaki Ucar wrote: > > > > I've updated RStudio to 1.4.1717, which supports R 4.1, and builds are > > underway [2, 3, 4]. This may take a while (s390x didn't even start > > yet). > > Oh, planned outage: https://pagure.io/fedora-infrastructure/issue/9960 > > -- > Iñaki Úcar > [[alternative HTML version deleted]] ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
Re: [R-sig-Fedora] Plans for R 4.1 in Fedora?
On Sat, 5 Jun 2021 at 20:12, Iñaki Ucar wrote: > > I've updated RStudio to 1.4.1717, which supports R 4.1, and builds are > underway [2, 3, 4]. This may take a while (s390x didn't even start > yet). Oh, planned outage: https://pagure.io/fedora-infrastructure/issue/9960 -- Iñaki Úcar ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
Re: [R-sig-Fedora] Plans for R 4.1 in Fedora?
Find attached an ordered build list, one batch per line (Bioc packages are included). I've pushed the script to [1]. I believe José had more scripts from the last mass rebuild. If you want to push them too, I believe (all three of) you should have commit access. I've updated RStudio to 1.4.1717, which supports R 4.1, and builds are underway [2, 3, 4]. This may take a while (s390x didn't even start yet). Also, please, let me know when there's a sidetag available with R 4.1, so that I can start the mass rebuild of the 17k+ packages in [5] (it takes less than a week, so this shouldn't delay the update). [1] https://pagure.io/R/packaging/blob/main/f/pkg-build-list.R [2] https://koji.fedoraproject.org/koji/taskinfo?taskID=69383481 [3] https://koji.fedoraproject.org/koji/taskinfo?taskID=69383589 [4] https://koji.fedoraproject.org/koji/taskinfo?taskID=69383669 [5] https://copr.fedorainfracloud.org/coprs/iucar/cran/ On Fri, 4 Jun 2021 at 22:25, Elliott Sales de Andrade wrote: > > On Fri, 4 Jun 2021 at 16:08, Iñaki Ucar wrote: > > > > This seems like a good opportunity to give this a go: > > https://github.com/juhp/fbrnch#parallel-building > > > > I did ask for some enhancements for bootstrap builds there, but I > don't know how well it works yet. Also, I'm not too sure it > understands our virtual Provides/BuildRequires, but if that is added, > then it's a good choice for determining build order. > > > On Fri, 4 Jun 2021 at 21:59, Tom Callaway wrote: > >> > >> That is a very good point. Oh well. Anyone want to help generate the build > >> order? :) > >> > >> ~spot > >> > >> On Fri, Jun 4, 2021, 3:57 PM Elliott Sales de Andrade > >> wrote: > >>> > >>> On Fri., Jun. 4, 2021, 10:08 a.m. Tom Callaway, wrote: > > Is there a way to know which R components provide graphics drivers? I > would > really rather not rebuild everything if we do not have to. > > >>> > >>> Unless you mean rebuild for testing purposes, because you added the > >>> R(ABI) = major.minor Provides/Requires, you need to rebuild the world > >>> anyway. > >>> > > > ~spot > > On Sun, May 23, 2021 at 6:28 AM Iñaki Ucar > wrote: > > > On Sat, 22 May 2021 at 22:18, José Abílio Matos > > wrote: > > > > > > Hi all, > > > what should be our plan for R 4.1 update in Fedora? > > > > See [1]. The plan is to wait for the next RStudio release and > > coordinate updates. > > > > [1] https://stat.ethz.ch/pipermail/r-sig-fedora/2021-May/000736.html > > > > > What are the pitfalls and the changes that we should be aware? > > > > The NEWS says: "The graphics engine version, R_GE_version, has been > > bumped to 14 and so packages that provide graphics devices should be > > reinstalled." But anyway, we should do the customary mass rebuild of > > packages to avoid other possible incompatibilities and "Package was > > built under version 4.0" messages. > > > > Iñaki > > > > > The second semester (with the corresponding induced pandemic > > > chaos) is > > > dimming down around here so I have at least time to breath again. :-) > > > > > > FWIW I am in no hurry to have 4.1 in Fedora 34, my main interest > > > is to > > have > > > it in rawhide and later if we find it suitable to backport it to F34. > > > > > > FWIW since our last talk Octave (for version 7 at least) is > > > starting by > > > default to have the major version in the path for packages. :-) > > > > > > Best regards, > > > -- > > > José Abílio > > > [[alternative HTML version deleted]] > > > > > > ___ > > > R-SIG-Fedora mailing list > > > R-SIG-Fedora@r-project.org > > > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora > > > > > > > > -- > > Iñaki Úcar > > > > ___ > > R-SIG-Fedora mailing list > > R-SIG-Fedora@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora > > > > [[alternative HTML version deleted]] > > ___ > R-SIG-Fedora mailing list > R-SIG-Fedora@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora > > > > > > > > -- > > Iñaki Úcar > > > > -- > Elliott -- Iñaki Úcar AUC AsioHeaders BH BiocGenerics BufferedMatrix Cairo DBI DynDoc FMStable GenomeInfoDbData NISTunits R.methodsS3 R6 RColorBrewer RODBC RUnit Rcpp RcppDate RhpcBLASctl Rhtslib XML abind acepack affyio argon2 arules assertthat backports bindr bit bitops bookdown brew brio chron cli clipr clisymbols coda colorspace combinat commonmark cpp11 crayon curl data.table date deldir dichromat digest disposables ellipsis errors expm fansi farver fastmap fastmatch filehash
Re: [R-sig-Fedora] Plans for R 4.1 in Fedora?
On Fri, 4 Jun 2021 at 16:08, Iñaki Ucar wrote: > > This seems like a good opportunity to give this a go: > https://github.com/juhp/fbrnch#parallel-building > I did ask for some enhancements for bootstrap builds there, but I don't know how well it works yet. Also, I'm not too sure it understands our virtual Provides/BuildRequires, but if that is added, then it's a good choice for determining build order. > On Fri, 4 Jun 2021 at 21:59, Tom Callaway wrote: >> >> That is a very good point. Oh well. Anyone want to help generate the build >> order? :) >> >> ~spot >> >> On Fri, Jun 4, 2021, 3:57 PM Elliott Sales de Andrade >> wrote: >>> >>> On Fri., Jun. 4, 2021, 10:08 a.m. Tom Callaway, wrote: Is there a way to know which R components provide graphics drivers? I would really rather not rebuild everything if we do not have to. >>> >>> Unless you mean rebuild for testing purposes, because you added the R(ABI) >>> = major.minor Provides/Requires, you need to rebuild the world anyway. >>> ~spot On Sun, May 23, 2021 at 6:28 AM Iñaki Ucar wrote: > On Sat, 22 May 2021 at 22:18, José Abílio Matos wrote: > > > > Hi all, > > what should be our plan for R 4.1 update in Fedora? > > See [1]. The plan is to wait for the next RStudio release and > coordinate updates. > > [1] https://stat.ethz.ch/pipermail/r-sig-fedora/2021-May/000736.html > > > What are the pitfalls and the changes that we should be aware? > > The NEWS says: "The graphics engine version, R_GE_version, has been > bumped to 14 and so packages that provide graphics devices should be > reinstalled." But anyway, we should do the customary mass rebuild of > packages to avoid other possible incompatibilities and "Package was > built under version 4.0" messages. > > Iñaki > > > The second semester (with the corresponding induced pandemic chaos) > > is > > dimming down around here so I have at least time to breath again. :-) > > > > FWIW I am in no hurry to have 4.1 in Fedora 34, my main interest is > > to > have > > it in rawhide and later if we find it suitable to backport it to F34. > > > > FWIW since our last talk Octave (for version 7 at least) is starting > > by > > default to have the major version in the path for packages. :-) > > > > Best regards, > > -- > > José Abílio > > [[alternative HTML version deleted]] > > > > ___ > > R-SIG-Fedora mailing list > > R-SIG-Fedora@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora > > > > -- > Iñaki Úcar > > ___ > R-SIG-Fedora mailing list > R-SIG-Fedora@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora > [[alternative HTML version deleted]] ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora > > > > -- > Iñaki Úcar -- Elliott ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
Re: [R-sig-Fedora] Plans for R 4.1 in Fedora?
This seems like a good opportunity to give this a go: https://github.com/juhp/fbrnch#parallel-building On Fri, 4 Jun 2021 at 21:59, Tom Callaway wrote: > That is a very good point. Oh well. Anyone want to help generate the build > order? :) > > ~spot > > On Fri, Jun 4, 2021, 3:57 PM Elliott Sales de Andrade < > quantum.anal...@gmail.com> wrote: > >> On Fri., Jun. 4, 2021, 10:08 a.m. Tom Callaway, wrote: >> >>> Is there a way to know which R components provide graphics drivers? I >>> would >>> really rather not rebuild everything if we do not have to. >>> >>> >> Unless you mean rebuild for testing purposes, because you added the >> R(ABI) = major.minor Provides/Requires, you need to rebuild the world >> anyway. >> >> >>> >>> ~spot >>> >>> On Sun, May 23, 2021 at 6:28 AM Iñaki Ucar >>> wrote: >>> >>> > On Sat, 22 May 2021 at 22:18, José Abílio Matos >>> wrote: >>> > > >>> > > Hi all, >>> > > what should be our plan for R 4.1 update in Fedora? >>> > >>> > See [1]. The plan is to wait for the next RStudio release and >>> > coordinate updates. >>> > >>> > [1] https://stat.ethz.ch/pipermail/r-sig-fedora/2021-May/000736.html >>> > >>> > > What are the pitfalls and the changes that we should be aware? >>> > >>> > The NEWS says: "The graphics engine version, R_GE_version, has been >>> > bumped to 14 and so packages that provide graphics devices should be >>> > reinstalled." But anyway, we should do the customary mass rebuild of >>> > packages to avoid other possible incompatibilities and "Package was >>> > built under version 4.0" messages. >>> > >>> > Iñaki >>> > >>> > > The second semester (with the corresponding induced pandemic >>> chaos) is >>> > > dimming down around here so I have at least time to breath again. :-) >>> > > >>> > > FWIW I am in no hurry to have 4.1 in Fedora 34, my main interest >>> is to >>> > have >>> > > it in rawhide and later if we find it suitable to backport it to F34. >>> > > >>> > > FWIW since our last talk Octave (for version 7 at least) is >>> starting by >>> > > default to have the major version in the path for packages. :-) >>> > > >>> > > Best regards, >>> > > -- >>> > > José Abílio >>> > > [[alternative HTML version deleted]] >>> > > >>> > > ___ >>> > > R-SIG-Fedora mailing list >>> > > R-SIG-Fedora@r-project.org >>> > > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora >>> > >>> > >>> > >>> > -- >>> > Iñaki Úcar >>> > >>> > ___ >>> > R-SIG-Fedora mailing list >>> > R-SIG-Fedora@r-project.org >>> > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora >>> > >>> >>> [[alternative HTML version deleted]] >>> >>> ___ >>> R-SIG-Fedora mailing list >>> R-SIG-Fedora@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-fedora >>> >> -- Iñaki Úcar [[alternative HTML version deleted]] ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
Re: [R-sig-Fedora] Plans for R 4.1 in Fedora?
That is a very good point. Oh well. Anyone want to help generate the build order? :) ~spot On Fri, Jun 4, 2021, 3:57 PM Elliott Sales de Andrade < quantum.anal...@gmail.com> wrote: > On Fri., Jun. 4, 2021, 10:08 a.m. Tom Callaway, wrote: > >> Is there a way to know which R components provide graphics drivers? I >> would >> really rather not rebuild everything if we do not have to. >> >> > Unless you mean rebuild for testing purposes, because you added the R(ABI) > = major.minor Provides/Requires, you need to rebuild the world anyway. > > >> >> ~spot >> >> On Sun, May 23, 2021 at 6:28 AM Iñaki Ucar >> wrote: >> >> > On Sat, 22 May 2021 at 22:18, José Abílio Matos >> wrote: >> > > >> > > Hi all, >> > > what should be our plan for R 4.1 update in Fedora? >> > >> > See [1]. The plan is to wait for the next RStudio release and >> > coordinate updates. >> > >> > [1] https://stat.ethz.ch/pipermail/r-sig-fedora/2021-May/000736.html >> > >> > > What are the pitfalls and the changes that we should be aware? >> > >> > The NEWS says: "The graphics engine version, R_GE_version, has been >> > bumped to 14 and so packages that provide graphics devices should be >> > reinstalled." But anyway, we should do the customary mass rebuild of >> > packages to avoid other possible incompatibilities and "Package was >> > built under version 4.0" messages. >> > >> > Iñaki >> > >> > > The second semester (with the corresponding induced pandemic chaos) >> is >> > > dimming down around here so I have at least time to breath again. :-) >> > > >> > > FWIW I am in no hurry to have 4.1 in Fedora 34, my main interest is >> to >> > have >> > > it in rawhide and later if we find it suitable to backport it to F34. >> > > >> > > FWIW since our last talk Octave (for version 7 at least) is >> starting by >> > > default to have the major version in the path for packages. :-) >> > > >> > > Best regards, >> > > -- >> > > José Abílio >> > > [[alternative HTML version deleted]] >> > > >> > > ___ >> > > R-SIG-Fedora mailing list >> > > R-SIG-Fedora@r-project.org >> > > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora >> > >> > >> > >> > -- >> > Iñaki Úcar >> > >> > ___ >> > R-SIG-Fedora mailing list >> > R-SIG-Fedora@r-project.org >> > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora >> > >> >> [[alternative HTML version deleted]] >> >> ___ >> R-SIG-Fedora mailing list >> R-SIG-Fedora@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-fedora >> > [[alternative HTML version deleted]] ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
Re: [R-sig-Fedora] Plans for R 4.1 in Fedora?
On Fri., Jun. 4, 2021, 10:08 a.m. Tom Callaway, wrote: > Is there a way to know which R components provide graphics drivers? I would > really rather not rebuild everything if we do not have to. > > Unless you mean rebuild for testing purposes, because you added the R(ABI) = major.minor Provides/Requires, you need to rebuild the world anyway. > > ~spot > > On Sun, May 23, 2021 at 6:28 AM Iñaki Ucar > wrote: > > > On Sat, 22 May 2021 at 22:18, José Abílio Matos > wrote: > > > > > > Hi all, > > > what should be our plan for R 4.1 update in Fedora? > > > > See [1]. The plan is to wait for the next RStudio release and > > coordinate updates. > > > > [1] https://stat.ethz.ch/pipermail/r-sig-fedora/2021-May/000736.html > > > > > What are the pitfalls and the changes that we should be aware? > > > > The NEWS says: "The graphics engine version, R_GE_version, has been > > bumped to 14 and so packages that provide graphics devices should be > > reinstalled." But anyway, we should do the customary mass rebuild of > > packages to avoid other possible incompatibilities and "Package was > > built under version 4.0" messages. > > > > Iñaki > > > > > The second semester (with the corresponding induced pandemic chaos) > is > > > dimming down around here so I have at least time to breath again. :-) > > > > > > FWIW I am in no hurry to have 4.1 in Fedora 34, my main interest is > to > > have > > > it in rawhide and later if we find it suitable to backport it to F34. > > > > > > FWIW since our last talk Octave (for version 7 at least) is starting > by > > > default to have the major version in the path for packages. :-) > > > > > > Best regards, > > > -- > > > José Abílio > > > [[alternative HTML version deleted]] > > > > > > ___ > > > R-SIG-Fedora mailing list > > > R-SIG-Fedora@r-project.org > > > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora > > > > > > > > -- > > Iñaki Úcar > > > > ___ > > R-SIG-Fedora mailing list > > R-SIG-Fedora@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora > > > > [[alternative HTML version deleted]] > > ___ > R-SIG-Fedora mailing list > R-SIG-Fedora@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora > [[alternative HTML version deleted]] ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
Re: [R-sig-Fedora] Plans for R 4.1 in Fedora?
Is there a way to know which R components provide graphics drivers? I would really rather not rebuild everything if we do not have to. ~spot On Sun, May 23, 2021 at 6:28 AM Iñaki Ucar wrote: > On Sat, 22 May 2021 at 22:18, José Abílio Matos wrote: > > > > Hi all, > > what should be our plan for R 4.1 update in Fedora? > > See [1]. The plan is to wait for the next RStudio release and > coordinate updates. > > [1] https://stat.ethz.ch/pipermail/r-sig-fedora/2021-May/000736.html > > > What are the pitfalls and the changes that we should be aware? > > The NEWS says: "The graphics engine version, R_GE_version, has been > bumped to 14 and so packages that provide graphics devices should be > reinstalled." But anyway, we should do the customary mass rebuild of > packages to avoid other possible incompatibilities and "Package was > built under version 4.0" messages. > > Iñaki > > > The second semester (with the corresponding induced pandemic chaos) is > > dimming down around here so I have at least time to breath again. :-) > > > > FWIW I am in no hurry to have 4.1 in Fedora 34, my main interest is to > have > > it in rawhide and later if we find it suitable to backport it to F34. > > > > FWIW since our last talk Octave (for version 7 at least) is starting by > > default to have the major version in the path for packages. :-) > > > > Best regards, > > -- > > José Abílio > > [[alternative HTML version deleted]] > > > > ___ > > R-SIG-Fedora mailing list > > R-SIG-Fedora@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora > > > > -- > Iñaki Úcar > > ___ > R-SIG-Fedora mailing list > R-SIG-Fedora@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora > [[alternative HTML version deleted]] ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
Re: [R-sig-Fedora] Plans for R 4.1 in Fedora?
On Sat, 22 May 2021 at 22:18, José Abílio Matos wrote: > > Hi all, > what should be our plan for R 4.1 update in Fedora? See [1]. The plan is to wait for the next RStudio release and coordinate updates. [1] https://stat.ethz.ch/pipermail/r-sig-fedora/2021-May/000736.html > What are the pitfalls and the changes that we should be aware? The NEWS says: "The graphics engine version, R_GE_version, has been bumped to 14 and so packages that provide graphics devices should be reinstalled." But anyway, we should do the customary mass rebuild of packages to avoid other possible incompatibilities and "Package was built under version 4.0" messages. Iñaki > The second semester (with the corresponding induced pandemic chaos) is > dimming down around here so I have at least time to breath again. :-) > > FWIW I am in no hurry to have 4.1 in Fedora 34, my main interest is to have > it in rawhide and later if we find it suitable to backport it to F34. > > FWIW since our last talk Octave (for version 7 at least) is starting by > default to have the major version in the path for packages. :-) > > Best regards, > -- > José Abílio > [[alternative HTML version deleted]] > > ___ > R-SIG-Fedora mailing list > R-SIG-Fedora@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora -- Iñaki Úcar ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
