Groups > linux.debian.bugs.dist > #1177783

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

From	Dirk Eddelbuettel <edd@debian.org>
Newsgroups	linux.debian.bugs.dist, linux.debian.devel.release
Subject	Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics)
Date	2023-12-08 17:40 +0100
Message-ID	<HIM3n-ccxX-3@gated-at.bofh.it> (permalink)
References	(1 earlier) <HGQ1s-aKxY-1@gated-at.bofh.it> <HInHH-bXO3-5@gated-at.bofh.it> <HILAm-ccoA-25@gated-at.bofh.it> <HtvHb-1eUN-1@gated-at.bofh.it> <HILAm-ccoA-25@gated-at.bofh.it>
Organization	linux.* mail to news gateway

Cross-posted to 2 groups.

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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

Thread

Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <tille@debian.org> - 2023-10-27 16:10 +0200
  Bug#1054657: transition: r-bioc-biocgenerics Dirk Eddelbuettel <edd@debian.org> - 2023-10-27 16:30 +0200
    Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <andreas@an3as.eu> - 2023-10-27 16:50 +0200
      Bug#1054657: transition: r-bioc-biocgenerics Dirk Eddelbuettel <edd@debian.org> - 2023-10-27 18:40 +0200
  Bug#1054657: transition: r-bioc-biocgenerics Graham Inggs <ginggs@debian.org> - 2023-10-28 19:00 +0200
    Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <tille@debian.org> - 2023-10-29 06:40 +0100
      Bug#1054657: transition: r-bioc-biocgenerics Graham Inggs <ginggs@debian.org> - 2023-10-29 17:10 +0100
        Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <tille@debian.org> - 2023-10-29 18:10 +0100
          Bug#1054657: transition: r-bioc-biocgenerics Graham Inggs <ginggs@debian.org> - 2023-11-01 11:10 +0100
            Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <tille@debian.org> - 2023-11-01 11:40 +0100
              Bug#1054657: transition: r-bioc-biocgenerics Charles Plessy <plessy@debian.org> - 2023-11-03 02:10 +0100
                Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <tille@debian.org> - 2023-11-07 06:50 +0100
                Bug#1054657: transition: r-bioc-biocgenerics Sebastian Ramacher <sramacher@debian.org> - 2023-11-07 11:00 +0100
                Bug#1054657: transition: r-bioc-biocgenerics Charles Plessy <plessy@debian.org> - 2023-11-07 14:10 +0100
                Bug#1054657: transition: r-bioc-biocgenerics Dirk Eddelbuettel <edd@debian.org> - 2023-11-07 14:50 +0100
                Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <tille@debian.org> - 2023-11-07 15:10 +0100
                Bug#1054657: transition: r-bioc-biocgenerics Dirk Eddelbuettel <edd@debian.org> - 2023-11-07 19:40 +0100
                Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <tille@debian.org> - 2023-11-07 21:10 +0100
                Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <tille@debian.org> - 2023-11-07 14:40 +0100
                Bug#1054657: transition: r-bioc-biocgenerics Sebastian Ramacher <sramacher@debian.org> - 2023-11-07 15:20 +0100
                Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <tille@debian.org> - 2023-11-07 18:10 +0100
        Bug#1054657: transition: r-bioc-biocgenerics Charles Plessy <plessy@debian.org> - 2023-11-01 08:40 +0100
  Bug#1054657: transition: r-bioc-biocgenerics Charles Plessy <plessy@debian.org> - 2023-11-09 15:10 +0100
    Bug#1054657: transition: r-bioc-biocgenerics Charles Plessy <plessy@debian.org> - 2023-11-10 09:50 +0100
      Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <tille@debian.org> - 2023-11-10 12:10 +0100
      Bug#1054657: transition: r-bioc-biocgenerics Sebastian Ramacher <sramacher@debian.org> - 2023-11-10 23:40 +0100
        Bug#1054657: transition: r-bioc-biocgenerics Charles Plessy <plessy@debian.org> - 2023-11-11 01:50 +0100
  Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <tille@debian.org> - 2023-11-10 23:40 +0100
    Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <tille@debian.org> - 2023-11-13 11:20 +0100
      Bug#1054657: transition: r-bioc-biocgenerics Graham Inggs <ginggs@debian.org> - 2023-11-19 16:40 +0100
      Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <andreas@an3as.eu> - 2023-11-22 21:00 +0100
        Bug#1054657: transition: r-bioc-biocgenerics Charles Plessy <plessy@debian.org> - 2023-11-28 01:30 +0100
          Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <tille@debian.org> - 2023-11-28 10:30 +0100
  Bug#1054657: r-bioc-sparsearray_1.0.12+dfsg-1_amd64.changes is NEW Andreas Tille <andreas@an3as.eu> - 2023-11-13 10:30 +0100
  Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <tille@debian.org> - 2023-11-24 22:30 +0100
  Bug#1054657: Transition issue for r-cran-rstanarm (Was: Bug#1055922: rmatrix: ABI change in Matrix 1.6-2) Andreas Tille <andreas@an3as.eu> - 2023-11-26 17:30 +0100
    Bug#1054657: Transition issue for r-cran-rstanarm (Was: Bug#1055922: rmatrix: ABI change in Matrix 1.6-2) Andreas Tille <andreas@an3as.eu> - 2023-11-28 10:20 +0100
  Bug#1054657: Transition issue for r-cran-rstanarm (Was: Bug#1055922: rmatrix: ABI change in Matrix 1.6-2) Graham Inggs <ginggs@debian.org> - 2023-11-28 11:40 +0100
    Bug#1054657: Transition issue for r-cran-rstanarm (Was: Bug#1055922: rmatrix: ABI change in Matrix 1.6-2) Andreas Tille <tille@debian.org> - 2023-11-28 16:00 +0100
      Bug#1054657: Transition issue for r-cran-rstanarm (Was: Bug#1055922: rmatrix: ABI change in Matrix 1.6-2) Graham Inggs <ginggs@debian.org> - 2023-11-29 14:40 +0100
  Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Andreas Tille <andreas@an3as.eu> - 2023-12-03 09:30 +0100
    Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Graham Inggs <ginggs@debian.org> - 2023-12-03 11:50 +0100
      Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Adrian Bunk <bunk@debian.org> - 2023-12-03 22:20 +0100
        Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Sebastian Ramacher <sramacher@debian.org> - 2023-12-05 15:50 +0100
    Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Graham Inggs <ginggs@debian.org> - 2023-12-07 15:40 +0100
      Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Andreas Tille <tille@debian.org> - 2023-12-07 16:20 +0100
        Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Andreas Tille <tille@debian.org> - 2023-12-07 16:40 +0100
        Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Adrian Bunk <bunk@debian.org> - 2023-12-07 19:40 +0100
        Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Sebastian Ramacher <sramacher@debian.org> - 2023-12-11 11:40 +0100
          Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Andreas Tille <tille@debian.org> - 2023-12-11 13:40 +0100
            Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Sebastian Ramacher <sramacher@debian.org> - 2023-12-11 13:40 +0100
              Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Andreas Tille <tille@debian.org> - 2023-12-11 17:10 +0100
                Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Sebastian Ramacher <sramacher@debian.org> - 2023-12-11 18:00 +0100
      Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Charles Plessy <plessy@debian.org> - 2023-12-08 17:10 +0100
        Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Dirk Eddelbuettel <edd@debian.org> - 2023-12-08 17:40 +0100
    Bug#1054657: Transition ready? (Was: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics)) Andreas Tille <andreas@an3as.eu> - 2023-12-13 11:50 +0100
      Bug#1054657: Transition ready? (Was: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics)) Adrian Bunk <bunk@debian.org> - 2023-12-13 13:30 +0100
      Bug#1054657: Transition ready? (Was: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics)) Graham Inggs <ginggs@debian.org> - 2023-12-13 14:20 +0100
        Bug#1054657: Transition ready? (Was: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics)) Andreas Tille <tille@debian.org> - 2023-12-13 17:10 +0100
  Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Adrian Bunk <bunk@debian.org> - 2023-12-03 22:20 +0100
    Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Andreas Tille <tille@debian.org> - 2023-12-05 14:40 +0100
  Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Andreas Tille <tille@debian.org> - 2023-12-04 06:40 +0100
  Bug#1054657: Source download of DeMixT broken Andreas Tille <andreas@an3as.eu> - 2023-12-08 16:10 +0100
    Bug#1054657: Source download of DeMixT broken Andreas Tille <andreas@fam-tille.de> - 2023-12-12 15:10 +0100
  Bug#1054657: Source archive of DSS missing Andreas Tille <andreas@fam-tille.de> - 2023-12-08 16:10 +0100
    Bug#1054657: Source archive of DSS missing Andreas Tille <andreas@fam-tille.de> - 2023-12-12 15:20 +0100
  Bug#1054657: Transition ready? (Was: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics)) Andreas Tille <tille@debian.org> - 2023-12-14 09:10 +0100
  Bug#1054657: Transition ready? (Was: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics)) Graham Inggs <ginggs@debian.org> - 2023-12-17 16:20 +0100
    Bug#1054657: Transition ready? (Was: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics)) Andreas Tille <tille@debian.org> - 2023-12-18 10:20 +0100

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