[Bioc-devel] Help Remote Installations
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
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
<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,
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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>
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