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[Bioc-devel] BiocManager and R-devel

3 messages · Kasper Daniel Hansen, Martin Morgan

Original
Kasper Daniel Hansen
# 
Installed R-devel as of today. I have a previous version of Bioconductor
installed in site-library. I then do
  install.packages("BiocManager")
# installs version 1.30.10
Bioconductor version '3.11' is out-of-date; the current release version
'3.12'
  is available with R version '4.0'; see https://bioconductor.org/install

I would have expected a message about devel version 3.13. I cannot run
  BiocManager::install(useDevel = TRUE)
as it complains about needing R 4.0 for Bioc 3.11. So it detects my current
version of Bioc (3.11) and refuses to run install since it thinks there is
a version mismatch.

I then deleted everything in site-library, installed BiocManager and
everything works as expected (giving me Bioc version 3.13)
Martin Morgan
# 
Thanks; the version of BiocManager in git has
Bioconductor version '3.11' is out-of-date; the current release version '3.12'
  is available with R version '4.0'; see https://bioconductor.org/install

and will be released in the next month. The rationale for telling you about the current release version rather than how to make 'devel' work is that BiocManager is a user-oriented rather than developer convenience.

If you'd then tried to update to devel
Upgrade 3 packages to Bioconductor version '3.13'? [y/n]:

you'd have been set.

The BiocManager vignette describes what is going on -- a 'sentinel' package BiocVersion is carried over from your previous library. It's necessary to distinguish between Bioconductor versions during the parts of the release cycle when two versions of Bioconductor are compatible with a single version of R. Addressing the symptom is to remove the BiocVersion package. I'd recommend the one-library-one-Bioconductor version approach to for managing multiple versions outlined in the vignette. Your solution means that you cannot switch back to your previously working version, which might have been important for reproducibility or sanity.

Martin

?On 10/30/20, 4:45 AM, "Bioc-devel on behalf of Kasper Daniel Hansen" <bioc-devel-bounces at r-project.org on behalf of kasperdanielhansen at gmail.com> wrote:

    Installed R-devel as of today. I have a previous version of Bioconductor
    installed in site-library. I then do
      install.packages("BiocManager")
    # installs version 1.30.10

    > library(BiocManager)
    Bioconductor version '3.11' is out-of-date; the current release version
    '3.12'
      is available with R version '4.0'; see https://bioconductor.org/install

    I would have expected a message about devel version 3.13. I cannot run
      BiocManager::install(useDevel = TRUE)
    as it complains about needing R 4.0 for Bioc 3.11. So it detects my current
    version of Bioc (3.11) and refuses to run install since it thinks there is
    a version mismatch.

    I then deleted everything in site-library, installed BiocManager and
    everything works as expected (giving me Bioc version 3.13)

    -- 
    Best,
    Kasper


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Kasper Daniel Hansen
# 
Im happy to hear this has been addressed in git.


On Fri, Oct 30, 2020 at 12:22 PM Martin Morgan <mtmorgan.bioc at gmail.com>
wrote: