[Bioc-devel] Help Remote Installations

[Kern, Lori]

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 using r-project.org> on behalf of Llu�s Revilla <lluis.revilla using gmail.com>
Sent: Tuesday, May 13, 2025 5:32 PM
To: Francesco Cecere <francesco.cecerengs using gmail.com>
Cc: bioc-devel using r-project.org <bioc-devel using 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 using 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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