Im happy to hear this has been addressed in git.
On Fri, Oct 30, 2020 at 12:22 PM Martin Morgan <mtmorgan.b...@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 Bioconductor version '3.11' is out-of-date; the current release version 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-boun...@r-project.org on behalf of kasperdanielhan...@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 Bioconductor version '3.11' is out-of-date; the current release version 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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Best, Kasper [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
