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

[Martin Morgan]

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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