On 03.05.2023 23:00, Simon Urbanek wrote:
On May 4, 2023, at 3:36 AM, Martin Morgan <mtmorgan.b...@gmail.com> wrote:
CRAN is fine with Bioconductor Depends: and Imports: dependencies, as
previously mentioned. This is because the CRAN maintainers explicitly configure
their system to know about Bioconductor package repositories.
That is not exactly true (at least not for all maintainers ;)). Bioconductor
packages are installed on as-needed (best-effort) basis and it is a manual
process.
Apparently for MacOS.
On Fedora/Debian/WIndows we auto install from BioC. (actually, on
Windows all BioC software packages are preinstalled).
Best,
Uwe Ligges
Ideally, Bioconductor packages would be in Suggests, because if they are not,
the package binary will be effectively broken for most users as they cannot
install it without additional steps (and no stable state can be guaranteed,
either). That's why I believe someone was suggesting a pre-flight check that
alerts the user to such situation and prints instructions to remedy it (e.g.,
to use setRepositories()) as the majority of users will have no idea what's
going on.
Cheers,
Simon
Users face a different challenge -- many users will not have identified (e.g.,
via `setRepositories()` a Bioconductor repository, so when they try to install
your package it will fail in a way that you have no control over -- a generic
message saying that the Bioconductor dependencies was not found.
You could mitigate this by advertising that your CRAN package should be installed via
`BiocManager::install("<your CRAN package>")`, which defines appropriate
repositories for both CRAN and Bioconductor, but there is no way to unambiguously communicate
this to users.
Martin
From: R-package-devel <r-package-devel-boun...@r-project.org> on behalf of Ruff,
Sergej <sergej.r...@tiho-hannover.de>
Date: Wednesday, May 3, 2023 at 11:13 AM
To: Dirk Eddelbuettel <e...@debian.org>
Cc: r-package-devel@r-project.org <r-package-devel@r-project.org>
Subject: Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the
Description File of my R Package
Thank you, Dirk.
I see your dependencies are Suggested. I know that Suggested dependencies
should be conditional.
Do you know if Non-Cran (Bioconductor) packages need to be conditional? Do you
have any experiece regarding Non-CRAN Dependencies
and how to handle them?
I believe Duncan Murdoch's experience and opinion regarding that topic, but i
take any second and third opinion to be sure.
Thank you for your help.
Sergej
________________________________
Von: Dirk Eddelbuettel <e...@debian.org>
Gesendet: Mittwoch, 3. Mai 2023 16:22:09
An: Ruff, Sergej
Cc: Duncan Murdoch; Ivan Krylov; r-package-devel@r-project.org
Betreff: Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the
Description File of my R Package
Sergej,
Please consider:
- there are nearly 20k CRAN packages
- all of them are mirrored at https://github.com/cran so you can browse
- pick any one 'heavy' package you like, Seurat is a good example; there
are other examples in geospatial or bioinformatics etc
- you can browse _and search_ these to your hearts content
Here is an example of mine. In RcppArmadillo, years ago we (thanks to fine
Google Summer of Code work by Binxiang Ni) added extended support for sparse
matrices pass-through / conversione from R to C++ / Armadillo and back. That
is clearly an optional feature as most uses of (Rcpp)Armadillo use dense
matrices. So all code and test code is _conditional_. File DESCRIPTION has
Suggests: [...], Matrix (>= 1.3.0), [...], reticulate, slam
mostly for tests. I.e. We have very little R code: in one single file
R/SciPy2R.R we switched to doing this via reticulate and opee the function
with
if (!requireNamespace("reticulate", quietly=TRUE)) {
stop("You must install the 'reticulate' package (and have SciPy).",
call.=FALSE)
}
after an actual deprecation warning (as there was scipy converter once).
Similarly, the testsuites in inst/tinytests/* have several
if (!requireNamespace("Matrix", quietly=TRUE)) exit_file("No Matrix
package")
as well as
if (!requireNamespace("reticulate", quietly=TRUE)) exit_file("Package reticulate
missing")
if (!packageVersion("reticulate") >= package_version("1.14"))
exit_file("SciPy not needed on newer reticulate")
and tests for slam (another sparse matrix package besides the functionality
in Matrix).
Hopefully this brief snapshot gives you an idea. There are (likely!!)
thousandss of examples you can browse, and I am sure you will find something.
If you have further (concrete) questions please do not hesitate to use the
resource of this list.
Cheers (or I should say "mit Braunschweiger Gruessen nach Hannover),
Dirk
--
dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
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