[R-pkg-devel] Bioconductor reverse dependency checks for a CRAN package

[Uwe Ligges]

For the BioC installation:
For all CAN work, I simply use install.packages() after adding/setting 
the BioC repo/mirror which perfectly well resolves the dependencies.

Best,
Uwe Ligges



On 30.01.2024 16:56, Ivan Krylov via R-package-devel wrote:
> Hello R-package-devel,
> 
> What would you recommend in order to run reverse dependency checks for
> a package with 182 direct strong dependencies from CRAN and 66 from
> Bioconductor (plus 3 more from annotations and experiments)?
> 
> Without extra environment variables, R CMD check requires the Suggested
> packages to be available, which means installing...
> 
> revdepdep <- package_dependencies(revdep, which = 'most')
> revdeprest <- package_dependencies(
>   unique(unlist(revdepdep)),
>   which = 'strong', recursive = TRUE
> )
> length(setdiff(
>   unlist(c(revdepdep, revdeprest)),
>   unlist(standard_package_names())
> ))
> 
> ...up to 1316 packages. 7 of these suggested packages aren't on CRAN or
> Bioconductor (because they've been archived or have always lived on
> GitHub), but even if I filter those out, it's not easy. Some of the
> Bioconductor dependencies are large; I now have multiple gigabytes of
> genome fragments and mass spectra, but also a 500-megabyte arrow.so in
> my library. As long as a data package declares a dependency on your
> package, it still has to be installed and checked, right?
> 
> Manually installing the SystemRequirements is no fun at all, so I've
> tried the rocker/r2u container. It got me most of the way there, but
> there were a few remaining packages with newer versions on CRAN. For
> these, I had to install the system packages manually in order to build
> them from source.
> 
> Someone told me to try the rocker/r-base container together with pak.
> It was more proactive at telling me about dependency conflicts and
> would have got me most of the way there too, except it somehow got me a
> 'stringi' binary without the corresponding libicu*.so*, which stopped
> the installation process. Again, nothing that a bit of manual work
> wouldn't fix, but I don't feel comfortable setting this up on a CI
> system. (Not on every commit, of course - that would be extremely
> wasteful - but it would be nice if it was possible to run these checks
> before release on a different computer and spot more problems this way.)
> 
> I can't help but notice that neither install.packages() nor pak() is
> the recommended way to install Bioconductor packages. Could that
> introduce additional problems with checking the reverse dependencies?
> 
> Then there's the check_packages_in_dir() function itself. Its behaviour
> about the reverse dependencies is not very helpful: they are removed
> altogether or at least moved away. Something may be wrong with my CRAN
> mirror, because some of the downloaded reverse dependencies come out
> with a size of zero and subsequently fail the check very quickly.
> 
> I am thinking of keeping a separate persistent library with all the
> 1316 dependencies required to check the reverse dependencies and a
> persistent directory with the reverse dependencies themselves. Instead
> of using the reverse=... argument, I'm thinking of using the following
> scheme:
> 
> 1. Use package_dependencies() to determine the list of packages to test.
> 2. Use download.packages() to download the latest version of everything
> if it doesn't already exist. Retry if got zero-sized or otherwise
> damaged tarballs. Remove old versions of packages if a newer version
> exists.
> 3. Run check_packages_in_dir() on the whole directory with the
> downloaded reverse dependencies.
> 
> For this to work, I need a way to run step (3) twice, ensuring that one
> of the runs is performed with the CRAN version of the package in the
> library and the other one is performed with the to-be-released version
> of the package in the library. Has anyone already come up with an
> automated way to do that?
> 
> No wonder nobody wants to maintain the XML package.
>