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

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

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

Haven’t tried with a package with such an amount of revdeps, but my approach is revdepcheck in GH actions and commiting the result to the repo (that is somehow similar to the docker approach if you host the package in GitHub). You can check the setup in tidyterra: - folder with basic setup:

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

https://github.com/r-lib/revdepcheck does the 'step 3 twice' part. I have had a few issues with it but overall it's been very helpful. https://github.com/HenrikBengtsson/revdepcheck.extras may also be useful. On 2024-01-30 10:56 a.m.,

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

Have you tried revdepcheck (https://github.com/r-lib/revdepcheck)? It handles the dependencies and uses a local cache for the downloaded packages. It also checks packages with the new and old versions. As far as I know, it doesn't handle the system requirements though. Georgi Boshnakov

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

Ivan, On 30 January 2024 at 18:56, 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

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

BiocManager (the recommended way to install Bioconductor packages) at the end of the day does essentially install.packages(repos = BiocManager::repositories()), ensuring that the right versions of Bioconductor packages are installed for the version of R in use. Maybe this is moot though if the

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

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

Re: [R-pkg-devel] Clarifying CRAN's external libraries policy

Thanks Simon. As far as I can tell, I did not receive any reply to that email; would you mind re-sending it? Nic On Mon, 29 Jan 2024, 19:31 Simon Urbanek, wrote: > Nic, > > as far as I can see that thread was clearly concluded that it is not a > special case that would require external

Re: [R-pkg-devel] Clarifying CRAN's external libraries policy

Hi Simon, The email that Neal is referring to was sent by me (this email address) to c...@r-project.org on Mon, 23 Oct 2023. Thanks, Nic On Mon, 29 Jan 2024 at 18:51, Simon Urbanek wrote: > > Neal, > > generally, binaries are not allowed since CRAN cannot check the provenance so > it's not