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

[Kristian Ullrich]

Dear Hervé and Jennifer,

Thank you for clarification so quickly.

Best regards

Kristian

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

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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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