On 9 December 2023 at 01:06, Charles Plessy wrote:
| I do not know for r-bioc-netsam, but for r-bioc-org.hs.eg.db and similar
| packages, it is because it is an "annotation package" made of data and
| therefore not managed the same way as the other Bioconductor packages.
|
| This is why it DESCRIPTION file does not mention its Bioconductor Git
| branch. This is also why its version number matches the Bioconductor
| release number. Also, its homepage resolves to
|
https://bioconductor.org/packages/release/data/annotation/html/org.Hs.eg.db.html
| while for regular packages there is no data/annotation/html in the URL.
|
| I think that it does not have to depend on the bioc api pseudo-package.
When r2u builds all of CRAN plus the ~ 200 BioC that are implied plus ~ 200
more that either in Debian or high on BioC's own 'karma' list, I query all
four repositories as one must. That is basically what the BioC installer
helpers always did for twenty-some years. My code (quicker for me to find)
is
## cf contrib.url(BiocManager::repositories())
## [1] "https://bioconductor.org/packages/3.14/bioc/src/contrib;
## [2]
"https://bioconductor.org/packages/3.14/data/annotation/src/contrib;
## [3]
"https://bioconductor.org/packages/3.14/data/experiment/src/contrib;
biocrepo <- paste0("https://bioconductor.org/packages/;,
.getConfig("bioc_version"), "/bioc")
apBIOC <- data.table(ap="Bioc",
as.data.frame(available.packages(repos=biocrepo)))
biocdataannrepo <- paste0("https://bioconductor.org/packages/;,
.getConfig("bioc_version"), "/data/annotation")
apBIOCdataann <- data.table(ap="Bioc",
as.data.frame(available.packages(repos=biocdataannrepo)))
apBIOC <- merge(apBIOC, apBIOCdataann, all=TRUE)
biocdataexprepo <- paste0("https://bioconductor.org/packages/;,
.getConfig("bioc_version"), "/data/experiment")
apBIOCdataexp <- data.table(ap="Bioc",
as.data.frame(available.packages(repos=biocdataexprepo)))
apBIOC <- merge(apBIOC, apBIOCdataexp, all=TRUE)
Ah, and younger Dirk left a message for current Dirk that this does indeed
show it too:
> contrib.url(BiocManager::repositories())
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cloud.r-project.org
[1] "https://bioconductor.org/packages/3.18/bioc/src/contrib;
[2] "https://bioconductor.org/packages/3.18/data/annotation/src/contrib;
[3] "https://bioconductor.org/packages/3.18/data/experiment/src/contrib;
[4] "https://bioconductor.org/packages/3.18/workflows/src/contrib;
[5] "https://bioconductor.org/packages/3.18/books/src/contrib;
[6] "https://cloud.r-project.org/src/contrib;
>
And when I bulk-updated the BioC packages for my 20.04 and 22.04 build in
r2u, I did notice that some of the 'non-R-package packages' in annotations
and experiment did not update. One could always ask BioC which of these are
/ are not considered release dependent. Their slack is open and pretty
friendly, I hang there too.
Cheers, Dirk
--
dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
