[Bioc-devel] Bioc-devel Digest, Vol 182, Issue 7

Martin Morgan mtmorg@n@b|oc @end|ng |rom gm@||@com
Wed May 8 20:48:18 CEST 2019

Yes I usually build from source, and don't install, along the lines of

mkdir src && cd src && \
  svn co https://svn.r-project.org/R/trunk R-devel && \
  R-devel/tools/rsync-recommended && \
  cd ..
mkdir -p bin/R-devel && cd bin/R-devel && \
  ~/src/R-devel/configure && \
  make -j

and immediately make a directory and alias for R_LIBS_USER. Similarly for R-3-6-branch.

Staying up-to-date is a two-liner

cd src/R-devel && svn up && tools/rsync-recommended && cd ../..
cd bin/R-devel && make -j && cd ../


On 5/8/19, 9:32 AM, "McDavid, Andrew" <Andrew_Mcdavid using URMC.Rochester.edu> wrote:

    Off topic, but I am curious how you maintain the parallel installs in your home directory given the Mac binary package's proclivities to dump things into /Library/Frameworks/?   Do you compile from source, with appropriate --prefix to keep your
     installation sandboxed in ~/bin?
    Andrew McDavid
    Biostatistics and Computational Biology
    Office: SRB 4.206 Ph: 585.275.5983
    Message: 1
    Date: Tue, 7 May 2019 10:46:49 +0000
    From: Martin Morgan <mtmorgan.bioc using gmail.com>
    To: Miles Benton <miles.benton84 using gmail.com>, Felix Ernst
    <felix.gm.ernst using outlook.com>
    Cc: "bioc-devel using r-project.org" <bioc-devel using r-project.org>
    Subject: Re: [Bioc-devel] BiocManager for BioC 3.9/R 3.6
    <MN2PR05MB649688873EEE7284E89E9C9EF9310 using MN2PR05MB6496.namprd05.prod.outlook.com>
    Content-Type: text/plain; charset="utf-8"
    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

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