[R-pkg-devel] Old version of rtracklayer on a single check server

[Henrik Bengtsson]

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 using 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
>
>
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>
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