[Feature request] Add metadata from Bioconductor packages
Nobody has claimed this yet.
Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 35/100
Research direction
Start at pkgcache::meta_cache_list() and review how Bioconductor metadata is obtained, then compare it with the Bioconductor VIEWS Date/Publication field and the available pkgcache::bioc_version(). Resolve which Bioconductor version should supply the date, and consider whether it is fixed or configurable. Done means Bioconductor packages return a publication date instead of NULL.
Written by the indexing model from the issue text.
Description
The pkgcache::meta_cache_list("SummarizedExperiment")$published currently returns a NULL date for Bioc packages
The date information is available under https://bioconductor.org/packages/3.17/bioc/VIEWS and can be parsed on the Date/Publication field. bioc::BiocPkgTools package may also be able to access the information
Considerations:
There could be an issue about which version from Bioconductor to use for the date. Possible workarounds can be implemented by defaulting to pkgcache::bioc_version() or as a parameter for meta_cache_list function
Simple sample code that retrieves publication date (without any caching)
sample_bioc_date <- \(package) {
uri <- url(glue::glue("https://bioconductor.org/packages/{pkgcache::bioc_version()}/bioc/VIEWS"))
data_raw <- data.frame(read.dcf(uri))
data_raw[data_raw$Package == package, "Date.Publication"]
}
sample_bioc_date("SummarizedExperiment")
- Dominant language
- R
- Stars
- 30
- Forks
- 19
- Avg merge
- 4d 19h
- Merged PRs (30d)
- 1
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
More from r-lib/pkgcache
-
`pkgcache:::is_ppm_linux_repo_url()` does not recognize manylinux_2_28 as a valid binary distro Open
Difficulty 1/5 Under an hour Newbie friendliness 82/100
-
Difficulty 4/5 3-5 days Newbie friendliness 32/100
-
upkeep
Difficulty 4/5 3-5 days Newbie friendliness 25/100
-
feature
Difficulty 2/5 1-3 hours Newbie friendliness 55/100
-
feature
Difficulty 3/5 1-2 days Newbie friendliness 20/100
Similar issues
-
Difficulty 2/5 1-3 hours Newbie friendliness 82/100
r-lib/pkgdepends#485 · 3 comments ·
-
Difficulty 1/5 Under an hour Newbie friendliness 92/100
-
beginners blocker
Difficulty 2/5 1-3 hours Newbie friendliness 78/100
-
enviPathR OpenBuild Error Build OK Build Warning policies-accepted pre-review precheck-passed
Difficulty 1/5 Under an hour Newbie friendliness 84/100
Bioconductor/BiocContributions#207 · 6 comments ·
-
Difficulty 2/5 1-3 hours Newbie friendliness 74/100
datacarpentry/semester-biology#1255 ·