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Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics)



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 | edd@debian.org


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