On 01.03.2025 13:07, Lluís Revilla wrote:
Dear list,
I'm trying to get some details from repositories with
available.packages. However, despite being included on the DESCRIPTION
files they are not available.
ap <- utils::available.packages(fields = "Additional_repositories",
filters = c("CRAN", "duplicates"),
ignore_repo_cache = TRUE,
repos = "https://cran.r-project.org";)
ap[, "Additional_repositories"] |> is.na() |> all()
## [1] TRUE
However, some packages like Seurat have the Additional_repositories
field [2]. If I try with another repository (Bioconductor software
repository):
ap <- available.packages(fields = "biocViews",
ignore_repo_cache = TRUE,
repos = "https://bioconductor.org/packages/3.21/bioc";)
ap[, "biocViews"] |> is.na() |> all()
## [1] TRUE
It also misses the BiocViews field compulsory on that repository.
Both repositories use tools::write_PACKAGES [3][4] to generate the
file read by available.packages. This function writes by default
fields "needed by available.packages".
However, it is unclear what is needed for available.packages.
According to its documentation, it returns "details corresponding to
packages currently available at one or more repositories". To me this
would mean that fields on the DESCRIPTION files should appear, but the
default of write_PACKAGES doesn't write other fields besides
'"Package"', '"Version"', '"Priority"', '"Depends"', '"Imports"',
'"LinkingTo"', '"Suggests"', '"Enhances"', '"OS_type"', '"License"'
and '"Archs"'.
I could approach each repository and ask to include more fields.
However, to match the documentation on available.packages and help all
repository administrators it would make sense to change the default on
write_PACKAGES.
Could the default fields be changed, so
that all fields available on packages' DESCRIPTION to
PACKAGES(.gz,.rds). Perhaps with fields = TRUE?
If this is too much it would be great if fields documented by Writing
R Extensions are written on PACKAGES.
This modification would make it easier for all to reuse repository data.
Many thanks for your consideration,
Lluís
PD: From CRAN perspective CRAN_packages_db() function can be used to
get Additional_repositories, but this is limited to CRAN and won't
work for BiocViews on Bioconductor or for other arbitrary fields like
'"RoxygenNote"'.
I'd indeed use
Cpdb <- tools:::CRAN_package_db()
Bpdb <- tools:::BioC_package_db()
for the two mentioned repos. ALso, PACLAGES.... is downloaded very
frequently and should not grow too much.
Is there a use case why available.packages() should provide this info
while not being less performant for package installatons etc.?
Best,
Uwe Ligges
[1]: https://stat.ethz.ch/pipermail/r-devel/2024-June/083477.html
[2]: https://cran.r-project.org/package=Seurat
[3]:
https://svn.r-project.org/R-dev-web/trunk/CRAN/QA/Uwe/make/writeCRANPackages.R
[4]:
https://github.com/Bioconductor/BBS/blob/devel/utils/makePropagationStatusDb.R#L348
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