On 4 May 2023 at 09:00, Simon Urbanek wrote:
| > On May 4, 2023, at 3:36 AM, Martin Morgan 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
> On May 4, 2023, at 3:36 AM, Martin Morgan 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
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.
Users face a different challenge -- many users will not have identified (e.g.,
via
my bad,
I looked at the DESCRIPTIOn fiel again. I assumed that Cluster was a
Bioconductor package.
I also didn�t see that DeSeq2 was in Suggests.
I will follow your advice and try using Bioconductor packages without a
conditional function.
Sergej
Von:
On 03/05/2023 9:50 a.m., Ruff, Sergej wrote:
I took the Seurat package as an example, because it both lists the
Bioconductor Dependencies under Imports in the DESCRIPTION-File
Which packages are you talking about? I don't see any BioConductor
dependencies in the Imports list for the current
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
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
I took the Seurat package as an example, because it both lists the Bioconductor
Dependencies under Imports in the DESCRIPTION-File
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
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
Thanks,
So is it just necessary for suggested packages.
So, is it just good practice to make a conditional check?
I saw some packages still include it.
For example the Seurat package.
Under Utils.R (line 349-379) of the SeuratObject-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
I implemented teh limma Bioconductor dependency into the Suggests file and made
it conditionally
Meaning I provided the Description File with
Suggests:
BiocManager,
limma
and created a short function which checks if limma is available
#' Check for package dependency
#'
#' @title
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