> ... some GitHub packages ... In addition to what's already been said (list them under Suggests), I encourage you to make those package available via https://r-universe.dev/, instead of asking users to install them directly from GitHub (via remotes::install_github(...)). The idea is that you provide your own only package repository, e.g. https://ngsFC.r-universe.dev/. With R-universe you, and users, also get the benefit of automatic testing there and automatic builds of Windows and macOS package binaries, and more importantly those packages can be installed using install.packages().
Note that you do not have to be the owner of those GitHub repositories to make them available on R-universe. You can create your own set of custom packages you want to provide this way. For example, you can install Pharmaverse-related packages from https://pharmaverse.r-universe.dev/. They provide packages from multiple sources. All they have to do achieve this is to create a GitHub repo with a special name https://github.com/pharmaverse/pharmaverse.r-universe.dev/, and then provide a one JSON file specifying which packages to include and where those package lives, cf. https://github.com/pharmaverse/pharmaverse.r-universe.dev/blob/main/packages.json. Finally, with packages on R-universe, you can list specifying: Additional_repositories: https://ngsFC.r-universe.dev 'R CMD check' acknowledges 'Additional_repositories' - it's part of the core R infrastructure. I know there's an idea for install.packages(..., dependencies = TRUE) to eventually automatically install from such repositories too. We're not there yet though. R-universe is great, it's fully operational, is becoming a de-facto standard, and, I think, is our best option for bringing in non-CRAN, non-Bioconductor dependencies. /Henrik On Wed, May 14, 2025 at 6:45 AM Kern, Lori via Bioc-devel <bioc-devel@r-project.org> wrote: > > Hello Francesco, > > To expand on lluis reply: > packages not on CRAN or Bioconductor are not allowed and strictly enforced on > Bioconductor systems so please keep this in mind but agree that it is general > practice to put these types of packages in Suggest. > > > Lori Shepherd - Kern > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > ________________________________ > From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Lluís > Revilla <lluis.revi...@gmail.com> > Sent: Tuesday, May 13, 2025 5:32 PM > To: Francesco Cecere <francesco.cecere...@gmail.com> > Cc: bioc-devel@r-project.org <bioc-devel@r-project.org> > Subject: Re: [Bioc-devel] Help Remote Installations > > Hi Francesco, > > You reached the right list. > Congratulations on getting this far, it is not always easy to fix all the R > CMD checks and BiocChecks. > > If these packages are optional, they should be used conditionally: > if (requireNamespace("pkg", quietly = TRUE)) { > pkg::optional_function(...) > } > > And be listed on the Suggested field of the DESCRIPTION file. > For more information read the Writing R Extensions section 1.1.3.1 > <https://secure-web.cisco.com/1cfkhpY8_Ibxipo-UfpcaAj8sLwysVLekrO5rKwbyvPzg4jZpTzz0bzQuPdtIqnMz33sQ4f4ItOxR7PMZHNoxV41QfYSj2jXfkUirUyqLtGAzVpleRVkCtciE23H12ff7YumAxTyl8Y_B0UcknmVyV9580ek3peohP0FORKvY1Fo6Xf8YQs-AZW0gHmAF4DVIRKVW-8fdSYELOJGu3RQXPei4KqZD6scrYnfld5Yb3HK-QbF0fMNidifHwFQpxCQd3VwELrDZYQXM1cUI-cPLezUhrOz2d7ieHCNKBLT7N62rlTHTp_gM65Qxo0qLYR0D/https%3A%2F%2Fcran.r-project.org%2Fdoc%2Fmanuals%2Fr-devel%2FR-exts.html%23Suggested-packages>. > > However, note that depending on packages not on CRAN is usually not > recommended as the quality and availability is not known by R and > Bioconductor processes. > > Best wishes, > > Lluís > > On Tue, 13 May 2025 at 16:22, Francesco Cecere < > francesco.cecere...@gmail.com> wrote: > > > Hello, > > > > This is the first time I’m writing to you; I hope I’m doing it correctly > > and contacting the right place. > > > > I have the package almost ready to send. *BiocCheck* works well; I have > > just one note about the length of a few functions. However, *R CMD check* > > gives me a warning about some GitHub packages that I have not listed in the > > DESCRIPTION or NAMESPACE. These packages implement methods that can be > > optionally selected in my framework, and I’ve documented the installation > > steps in the README if someone wants to use them. > > > > Should I leave the warning as is, or is there something I can do to resolve > > it? > > > > Thank you. > > > > Best regards, > > Francesco > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://secure-web.cisco.com/1o2jZ4vayDdk1rPjbvCMZ8-iNmnetga1wh3e-KAzSwyWaSkG8Dyok7BlxXRMrgq28t8OFDxY9FFILF0nbP-3_irgmpoWUrwwfNvqUBxDB70U2vJSqmtjUUhdpFd3Wzs5uWWWfoW6WTT4evUFvYAB-sp6dR01QhU-Yr-05Aj81y8WNJX102zHwu9VWx86VMb7lfl23tvD8SLhhyRUemqVa4Tkt5AabFodBA8x-Iu_Q75akkPzg9qKE4vLb2w3ka2_xHkCFZQvjE9Oump3r7Ny0lipJ_n9MTj3IixZYp2fRysDKMA4LcIJVDBmv3qUnAvL3/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://secure-web.cisco.com/1o2jZ4vayDdk1rPjbvCMZ8-iNmnetga1wh3e-KAzSwyWaSkG8Dyok7BlxXRMrgq28t8OFDxY9FFILF0nbP-3_irgmpoWUrwwfNvqUBxDB70U2vJSqmtjUUhdpFd3Wzs5uWWWfoW6WTT4evUFvYAB-sp6dR01QhU-Yr-05Aj81y8WNJX102zHwu9VWx86VMb7lfl23tvD8SLhhyRUemqVa4Tkt5AabFodBA8x-Iu_Q75akkPzg9qKE4vLb2w3ka2_xHkCFZQvjE9Oump3r7Ny0lipJ_n9MTj3IixZYp2fRysDKMA4LcIJVDBmv3qUnAvL3/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel > > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
