[Bioc-devel] Help Remote Installations
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.bengtsson at 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 at 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-bounces at r-project.org> on behalf of Llu?s
Revilla <lluis.revilla at gmail.com>
Sent: Tuesday, May 13, 2025 5:32 PM To: Francesco Cecere <francesco.cecerengs at gmail.com> Cc: bioc-devel at r-project.org <bioc-devel at 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
<
. 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, Llu?s On Tue, 13 May 2025 at 16:22, Francesco Cecere < francesco.cecerengs at 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
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