and it uses conditional functions to check if those dependencies are
pre-installed.
"No, it is a requirement if the package is used but is not listed in
Depends or Imports.
If the package is in Depends or Imports it is a waste of time to make
the check: it will always succeed."
that's what I also thought but I am confused why a package like Seurat
then lists the dependencies in the DESCRIPTION-File and on top of that uses
conditional functions to check if the package is pre-installed or not.
Wouldn't that make the packagecheck function used by Seurat redundant?
Sergej Ruff
------------------------------------------------------------------------
*Von:* Duncan Murdoch <murdoch.dun...@gmail.com>
*Gesendet:* Mittwoch, 3. Mai 2023 15:29:34
*An:* Ruff, Sergej; Ivan Krylov
*Cc:* r-package-devel@r-project.org
*Betreff:* Re: AW: [R-pkg-devel] How to declare Bioconductor
Dependencies in the Description File of my R Package
On 03/05/2023 9:17 a.m., Ruff, Sergej wrote:
Thanks,
So is it just necessary for suggested packages.
Those and "Enhances" packages, but hardly anyone uses "Enhances".
So, is it just good practice to make a conditional check?
No, it is a requirement if the package is used but is not listed in
Depends or Imports.
If the package is in Depends or Imports it is a waste of time to make
the check: it will always succeed.
I saw some packages still include it.
For example the Seurat package.
I don't understand your question here.
Duncan Murdoch
Under Utils.R (line 349-379) of the SeuratObject-Package
(https://cran.r-project.org/src/contrib/Archive/SeuratObject/
<https://cran.r-project.org/src/contrib/Archive/SeuratObject/
<https://cran.r-project.org/src/contrib/Archive/SeuratObject/>>) you will
find the PackageCheck-function
which used by the Seurat-Package
(https://cran.r-project.org/src/contrib/Archive/Seurat/
<https://cran.r-project.org/src/contrib/Archive/Seurat/
<https://cran.r-project.org/src/contrib/Archive/Seurat/>>) to check if
packages are alredy installed.
You can find examples for DEseq2 under differential_expression.R
(starting line 1314 or you cntr+f for packagecheck) in
the Seurat.package
(https://cran.r-project.org/src/contrib/Archive/Seurat/
<https://cran.r-project.org/src/contrib/Archive/Seurat/
<https://cran.r-project.org/src/contrib/Archive/Seurat/>>)
or for limma (starting line 2292).
------------------------------------------------------------------------
*Von:* Duncan Murdoch <murdoch.dun...@gmail.com>
*Gesendet:* Mittwoch, 3. Mai 2023 14:25:56
*An:* Ruff, Sergej; Ivan Krylov
*Cc:* r-package-devel@r-project.org
*Betreff:* Re: [R-pkg-devel] How to declare Bioconductor Dependencies in
the Description File of my R Package
On 03/05/2023 8:00 a.m., Ruff, Sergej wrote:
... [ lines about current solution deleted ]
Also for the future - how Do i provide Bioconductor dependencies as "Imports"
for a package that I want to submit to CRAN?
Just list it as you would a CRAN package. The CRAN docs talk about
"mainstream repositories"; I forget what the definition is of that
(maybe repositories listed in `file.path(R.home(),
"etc/repositories")`?), but definitely BioConductor is included.
Do I need to make that also conditional? I know I should provide Installation
description in a readme fiel but how do I make sure
No, you don't need to check. If any imported package is not available,
your package will not load, so errors will happen before you ever get to
running examples.
that the Bioconductor dependencies dont cause a rejection from CRAN?
Just make sure they exist on BioC and your code works with them.
Duncan Murdoch
