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

[Miles Benton]

Thanks Martin.

For reproducibility we use containers, alongside a a RStudio Server Pro
installation.

This issue was occurring on my rolling release machines that I use for
testing. One in particular (Siduction box) has been rolling since R 3.2,
there are very rarely any issues. Best practise? Probably not, but it's an
interesting exercise.

Cheers,

Miles

On Tue, 7 May 2019, 22:46 Martin Morgan, <mtmorgan.bioc using gmail.com> wrote:

> Yes, remove BIocVersion (all copies)
>
> I guess you have a library path, as shown by .libPaths() in R, that is
> shared between the two versions. This is generally BAD PRACTICE. because it
> means packages built for R-3.6 will be used by both of your R-3.5 and R-3.6
> installations, and vice versa -- this might 'work' initially, but as time
> passes and packages start to exploit features in R-3.6, you'll start to
> break your R-3.5 installation, which you are presumably retaining for
> reproducibility.
>
> Instead, arrange for ALL packages other than base packages to be installed
> in an R- (and Bioconductor) version-specific library. In the release
> branch, I have
>
>   > .libPaths()
>   [1] "/Users/ma38727/Library/R/3.6/Bioc/3.9"
>   [2] "/Users/ma38727/bin/R-3-6-branch/library"
>
> On my macOS I do this using command-line aliases and the R_LIBS_USER
> environment variable
>
>   $ alias bioc-3.9
>   alias bioc-3.9='R_LIBS_USER=~/Library/R/3.6/Bioc/3.9
> ~/bin/R-3-6-branch/bin/R'
>
> but other solutions are possible
>
> Martin Morgan
>
> On 5/7/19, 5:06 AM, "Bioc-devel on behalf of Miles Benton" <
> bioc-devel-bounces using r-project.org on behalf of miles.benton84 using gmail.com>
> wrote:
>
>     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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