Message-ID: <CAJ=0CtBP6Z_6GwJDp0Ly3PbnYjQ1r1hDz7L=+tbCbKZst1cdwg@mail.gmail.com>
Date: 2018-11-26T06:23:47Z
From: Adrian Dusa
Subject: Issues with rj (requirement for StatET) since Mojave/3.5.1 update
In-Reply-To: <CABG0rftJGUdw8yrjR=QS+02aJ1msOMWywg3ve93SpcLq9UUihA@mail.gmail.com>
On Sun, Nov 25, 2018 at 9:48 PM Jonathan Greenberg <jgreenberg at unr.edu>
wrote:
>
> Ok, figured it out but it was non-trivial. I found the solution here:
>
https://github.com/velocyto-team/velocyto.R/issues/2#issuecomment-352584213
>
> TLDR you need to use homebrew (https://brew.sh/):
> 1) Install homebrew as linked above
> 2) Install llvm (and maybe boost):
> brew install llvm
> brew install boost
> 3) Mod your ~/.R/Makevars (nano ~/.R/Makevars) to read:
>
> CC=/usr/local/clang4/bin/clang
> CXX=/usr/local/clang4/bin/clang++
> CXX11=/usr/local/clang4/bin/clang++
> CXX14=/usr/local/clang4/bin/clang++
> CXX17=/usr/local/clang4/bin/clang++
> CXX1X=/usr/local/clang4/bin/clang++
> LDFLAGS=-L/usr/local/clang4/lib
I've recently installed llvm via homebrew, after an upgrade to Mojave.
However my newly installed clang version is surely not 4 but 7, and it is
not found under /usr/local/.
Instead, I've edited the Makevars file with something like:
CC=/usr/local/Cellar/llvm/7.0.0/bin/clang
CXX=/usr/local/Cellar/llvm/7.0.0/bin/clang++
CXX1X=/usr/local/Cellar/llvm/7.0.0/bin/clang++
LDFLAGS=-L/usr/local/Cellar/llvm/7.0.0/lib
-Wl,-rpath,/usr/local/Cellar/llvm/7.0.0/lib
CXXFLAGS=-I/usr/local/Cellar/llvm/7.0.0/lib/clang/7.0.0/include/
This seems to work for me,
Adrian
--
Adrian Dusa
University of Bucharest
Romanian Social Data Archive
Soseaua Panduri nr. 90-92
050663 Bucharest sector 5
Romania
https://adriandusa.eu
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