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

[Kristian Ullrich]

Hi Lluís,

Thank you for the nice code snippet to get these values.

As mentioned earlier, if only the imports are counted in a non recursive manner, the threshold is fine.

Best regards

Kristian

-- 
Dr. Kristian Ullrich, Dipl.-Bio.
Max Planck Institute
For Evolutionary Biology

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> On 12. Nov 2024, at 22:58, Lluís Revilla <lluis.revilla using gmail.com> wrote:
> 
> 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 <mailto: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
>> August Thienemann Str. 2
>> 24306 Plön
>> Germany
>> +49 4522 763 313
>> ullrich using evolbio.mpg.de <mailto:ullrich using evolbio.mpg.de>
>> 
>> -- 
>> CONFIDENTIALITY NOTICE:
>> The contents of this email message and any attachments are intended solely for the addressee(s) and may contain confidential and/or privileged information and may be legally protected from disclosure. If you are not the intended recipient, you are hereby notified that any use, dissemination, copying, or storage of this message or its attachments is strictly prohibited.
>> 
>> > On 12. Nov 2024, at 03:40, Hervé Pagès <hpages.on.github using gmail.com <mailto: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> <mailto:hpages.on.github using gmail.com <mailto:hpages.on.github using gmail.com>>
>> 
>> 
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