[Bioc-devel] BiocManager and R-devel

Thanks; the version of BiocManager in git has

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Bioconductor version '3.11' is out-of-date; the current release version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

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

BiocManager::install(version="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    Bioconductor version '3.11' is out-of-date; the current release version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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