[Bioc-devel] BiocManager and R-devel

[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 using gmail.com>
wrote:

> 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 Bioconductor version '3.11' is out-of-date; the current release version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 using r-project.org on behalf of kasperdanielhansen using 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     Bioconductor version '3.11' is out-of-date; the current release version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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>
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>


-- 
Best,
Kasper

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