[R-SIG-Mac] Issues with rj (requirement for StatET) since Mojave/3.5.1 update

[Simon Urbanek]

For posterity: both recommendations are plain wrong so don't use (obviously, the settings didn't match the installed compilers). They are not supported in the CRAN version of R which is compiled by the clang 6.0 compiler in /usr/local/clang6 that we supply on CRAN. You can compile your own R or use homebrew, but don't expect CRAN packages to work with that. You don't even need to touch Makevars, just setting PATH to start with /usr/local/clang6/bin before compilation is sufficient.

Cheers,
Simon


> On Nov 26, 2018, at 1:41 AM, Adrian Dușa <dusa.adrian using gmail.com> wrote:
> 
> On Sun, Nov 25, 2018 at 9:48 PM Jonathan Greenberg <jgreenberg using 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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