Thank you all for your suggestions ! They help a lot to improve my package ! Thank you again Hopefully soon it will reach you !
Francesco Il giorno mer 14 mag 2025 alle ore 20:47 Henrik Bengtsson < henrik.bengts...@gmail.com> ha scritto: > > ... 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. 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