[Bioc-devel] New BioC 3.21 settings for R 4.5.0

[Lluís Revilla]

Hi Kristian,

I think the threshold was decided because it matches CRAN's, but it could
be modified.
But let's check the numbers regarding this threshold:
Approximately 20% of Bioconductor packages are affected with this threshold
(see code below).
The median of strong dependencies is just 11 (9 if we exclude those above
20 dependencies) and the third quartile is at 17.
The software package that depends on more packages has 88 strong direct
dependencies.

Best,

Lluís

BiocManager::version()
## [1] '3.20'
ap = available.packages( repos = BiocManager::repositories()["BioCsoft"])
## 'getOption("repos")' replaces Bioconductor standard repositories, see
## 'help("repositories", package = "BiocManager")' for details.
## Replacement repositories:
##     CRAN: https://ftp.cixug.es/CRAN
pd = tools::package_dependencies(rownames(ap), db = ap, which = "strong")
sum(lengths(pd) >= 20)
## [1] 407
length(pd)
## [1] 2201



On Tue, 12 Nov 2024 at 06:52, Kristian Ullrich <ullrich using evolbio.mpg.de>
wrote:

> Dear Hervé and Jennifer,
>
> Thank you for clarification so quickly.
>
> Best regards
>
> Kristian
>
> --
> Dr. Kristian Ullrich, Dipl.-Bio.
> Max Planck Institute
> For Evolutionary Biology
>
> Scientific IT group
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> ullrich using evolbio.mpg.de
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> > On 12. Nov 2024, at 03:40, Hervé Pagès <hpages.on.github using gmail.com>
> wrote:
> >
> > Hi Kristian,
> >
> > On 11/11/24 10:58, Kristian Ullrich wrote:
> >> Dear Jennifer,
> >>
> >> I do understand the reasoning behind the
> _R_CHECK_EXCESSIVE_IMPORTS_=20. However, the threshold needs to be
> discussed in my opinion.
> >>
> >> Given that a lot of bioconductor packages e.g. rely on the Biostrings
> and GenomicRanges package (rank 9 and 10 / 2289), the Biostrings package
> itself has currently 24 dependencies, which as a consequence would mean
> that all packages relying on Biostrings will automatically be classified as
> excessive import packages.
> > IIUC the count is only on the number of packages that you import i.e. if
> you import Biostrings, that count for 1.
> >
> > Note that unlike the Depends relationship, the Imports relationship is
> not transitive. That is, if you import Biostrings and Biostrings imports
> IRanges then you don't get IRanges's namespace in your package's namespace,
> unless you explicitly request it.
> >
> >>
> >> To be honest, I would then no longer understand the meaningfulness of
> such a “note flag” if one Bioconductor package uses a TOP10 package as an
> import and should therefore be considered vulnerable?
> >>
> >> Have you checked in Bioc 3.20, how many packages from the 2289 packages
> would fall under this "vulnerable" category?
> > We'll see but hopefully it's about direct imports only. Also IIUC this
> is only going to be a NOTE. And we can always step back if things go wrong.
> >
> > Best,
> >
> > H.
> >
> >>
> >> Best regards and thank you in anticipation
> >>
> >> Kristian
> > --
> > Hervé Pagès
> >
> > Bioconductor Core Team
> > hpages.on.github using gmail.com <mailto:hpages.on.github using gmail.com>
>
>
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