It is wrong to say that ‘it will never be solved for R.4.0.0’. Rather, ‘it will never be a problem for R.4.0.0’.
rtracklayer 1.51.5 was only ever built, checked, distributed (and installed in a correctly configured system, using the rules of install.packages and tools:::.BioC_version_associated_with_R_version(), or of BiocManager::install()) on R-devel (now R-4-1-0-branch). So R-4.0.* has never supported version 1.51.5 of rtracklayer. No Bioconductor package built on R-4.0.* would propagate (be visible to install.packages()) with a dependency on rtracklayer-1.51.5. A CRAN package with a dependency on rtracklayer-1.51.5 (this is hypothetical, I do not believe it is the case for CNVScope), would be correctly flagged as an error – this version of rtracklayer will never be available on R-4.0.*, and the CRAN package author would have to re-assess the reasons for specifying the dependency for that version of R. Bioconductor does rarely produce ‘impossible’ dependencies particularly in the Bioconductor ‘devel’ branch (when a package builds and checks even though one of its dependencies builds but does not pass check), but these are transient and an artifact of the Bioconductor build system – the lagging package Is usually promptly updated so the published dependency is satisfied. From: Henrik Bengtsson <henrik.bengts...@gmail.com> Date: Tuesday, May 18, 2021 at 2:41 PM To: Martin Morgan <mtmorgan.b...@gmail.com> Cc: "Dalgleish, James (NIH/NCI) [F]" <james.dalgle...@nih.gov>, "r-package-devel@r-project.org" <r-package-devel@r-project.org> Subject: Re: [R-pkg-devel] Old version of rtracklayer on a single check server 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<mailto: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<mailto:r-package-devel-boun...@r-project.org> on behalf of henrik.bengts...@gmail.com<mailto: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<mailto: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<mailto:R-package-devel@r-project.org> mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel ______________________________________________ R-package-devel@r-project.org<mailto: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
