I stand corrected about the R-devel version (and now R 4.1.0) on CRAN. However, isn't it the case that it will never be solved for R 4.0.0 (to become R-oldrel on CRAN) and CRAN will keep reporting an error on MS Windows there because https://bioconductor.org/packages/3.12/bioc/html/rtracklayer.html provides only an older version for MS Windows?
If so, an alternative to relying on Suggests is to make the package depend on R (>= 4.1.0). /Henrik On Tue, May 18, 2021, 09:08 Martin Morgan <mtmorgan.b...@gmail.com> wrote: > That’s not correct Henrik. > > CRAN follows CRAN rules for installing packages, so uses > tools:::BioC_version_for_R_version(). For R-devel we have > > > R.version.string > [1] "R Under development (unstable) (2021-05-18 r80323)" > > tools:::.BioC_version_associated_with_R_version() > [1] '3.13' > > For this version of Bioconductor, the rtracklayer version (from > https://bioconductor.org/packages/3.13/rtracklayer, or > `available.packages(repos = > "https://bioconductor.org/packages/3.13/bioc";)["rtracklayer", > "Version"]`) is 1.51.5. > > So the r-devel-windows-ix86+x86_64 builder mentioned in the post has the > wrong version of rtracklayer for R-devel. > > Martin Morgan > > On 5/18/21, 11:49 AM, "R-package-devel on behalf of Henrik Bengtsson" < > r-package-devel-boun...@r-project.org on behalf of > henrik.bengts...@gmail.com> wrote: > > It's a problem with Bioconductor and a broken release history of > 'rtracklayer' on MS Windows (e.g. > https://bioconductor.org/packages/3.12/bioc/html/rtracklayer.html) > plus how each Bioconductor version is tied to a specific R version. > In other words, even if they fix it in Bioconductor 3.13 (for R > 4.1.0), it can't be fixed in Bioconductor 3.12 (for R 4.0.0), so > you're package will keep failing on Windows for R 4.0.0. The reason > why it can't be fixed in Bioconductor 3.12 is that they have now > frozen that release forever. > > Because of this, I suspect the only solution is to make 'rtracklayer' > an optional package, i.e. move it to Suggests: and update all your > code to run conditionally of that package being available. I recommend > you reach out to the bioc-devel mailing list for advice. > > /Henrik > > On Tue, May 18, 2021 at 4:33 AM Dalgleish, James (NIH/NCI) [F] via > R-package-devel <r-package-devel@r-project.org> wrote: > > > > To any who might have an idea: > > > > I've been reading several posts in the digest about dependency > version issues on the check servers and I'm having my own issue, which I > can't solve because I can't upgrade the check server's package version: > > * installing *source* package 'CNVScope' ... > > ** using staged installation > > ** R > > ** data > > *** moving datasets to lazyload DB > > ** inst > > ** byte-compile and prepare package for lazy loading > > Warning: multiple methods tables found for 'export' > > Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), > versionCheck = vI[[j]]) : > > namespace 'rtracklayer' 1.48.0 is already loaded, but >= 1.51.5 is > required > > Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> > loadNamespace > > Execution halted > > ERROR: lazy loading failed for package 'CNVScope' > > * removing 'd:/RCompile/CRANguest/R-devel/lib/CNVScope' > > > > These errors tend to be check server dependent (only occurs on > r-devel-windows-ix86+x86_64< > https://cran.r-project.org/web/checks/check_flavors.html#r-devel-windows-ix86_x86_64>) > and I'm just trying to make the small change to closeAllConnections() that > was asked earlier of maintainers by Kurt Hornik and the CRAN team, but I > can't because of this old package version on the devel check server, which > has the same error: > > > https://win-builder.r-project.org/incoming_pretest/CNVScope_3.5.7_20210518_062953/Windows/00check.log > > > https://win-builder.r-project.org/incoming_pretest/CNVScope_3.5.7_20210518_062953/Windows/00install.out > > > > Is there any way around this? I notice the maintainer of the > 'gtsummary' package had a similar issue: > > > > "> I am trying to make a release that depends on gt v0.3.0, but I > get an error > > > > > when I test the package on Windows Dev > `devtools::check_win_devel()` that > > > > > the gt package is available but it's an unsuitable version. Does > anyone > > > > > know why the gt v0.3.0 is unavailable?" > > > > > > > > I'm open to any suggestions, but can't see a way around this issue > from my end without the ability to service the check server. > > > > > > Thanks, > > James Dalgleish > > Cancer Genetics Branch, > > Center for Cancer Research, > > National Cancer Institute, > > National Institutes of Health, > > Bethesda, MD > > > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-package-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-package-devel > > ______________________________________________ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel > [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
