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

[Henrik Bengtsson]

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.bioc using 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-bounces using r-project.org on behalf of
> henrik.bengtsson using 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 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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