[Bioc-devel] BiocManager for BioC 3.9/R 3.6

[Miles Benton]

I had the same issue today, here's the note I made on our work Teams
channel:

Not too sure where to deposit this little piece of information. Just a
little 'hiccup' in the latest transition of R versions (3.5 -> 3.6) and
Bioconductor. The newest stable version of Bioconductor (3.9) depends on R
3.6, while 3.8 on R 3.5.

A version or two ago Bioconductor changed there package management function
from BiocInstaller to BiocManager, I assume that the older package is
nearly fully depreciated. .The issue I had was that using the
BiocManager::install(update=T) command it was complaining about R version
3.6 and saying that Bioconductor 3.8 was the most recent. I removed any
traces of both package managers and reinstalled the most updated recommend
tool. It still reported version 3.8 as up to date. Long story short, I went
digging and found a 'hang over' package called BiocVersion which I removed
and problem solved, version 3.9 available, do you want to upgrade? Yes
please!!!


So for me the removal of the package BiocVersion solved the issue on 3
separate machines.

P.s. This was using the latest CRAN version of BiocManager (1.30.4).


On Tue, 7 May 2019, 20:17 Felix Ernst, <felix.gm.ernst using outlook.com> wrote:

> Hi,
>
> I just installed R 3.6, but everything I try to get a BiocManager Version,
> which works with R 3.6 were so far not successful.
>
> I installed BiocManager from CRAN …
>
> > install.packages("BiocManager")
>
> … and from GitHub …
>
> > devtools::install_github("Bioconductor/BiocManager")
>
> … but both times I get the following error:
>
> > BiocManager::install("Biostrings")
> Fehler: Bioconductor version '3.8' requires R version '3.5'; see
> https://bioconductor.org/install
>
> CRAN has Version 1.30.4 and GitHub has version 1.30.5.
>
> Did I miss something?
>
> Thanks for any help or advice.
>
> Best regards
> Felix
>
>
> > sessionInfo()
> R version 3.6.0 (2019-04-26)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 10 x64 (build 17763)
>
> Matrix products: default
>
> locale:
> [1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252
> LC_MONETARY=German_Germany.1252
> [4] LC_NUMERIC=C                    LC_TIME=German_Germany.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] BiocManager_1.30.4 compiler_3.6.0     tools_3.6.0
>
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>
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