error installing from source for Apple silicon processors

[weljielab]

Attempting to install from source on an Apple M1 mac gives the error shown below. It works fine under an identical setup using the x86 compiler, so I suspect this is something specific to the arm compiler. I have compiled R from source and all other dependencies are installed without error from source, tested with both R 4.0.3 and 4.1.0. Unfortunately I have no experience with C/C++ to help with this, but wanted to document in case I'm doing something wrong or as others may run into the same issue.

Thanks!

Aalim

`clang++ -I"/Users/aalim/Downloads/R_arm_compile/R-devel/include" -DNDEBUG -I/opt/homebrew/include/ -I/Users/aalim/Downloads/R_arm_compile/R-devel/include -I../inst/include -I/usr/local/include -fPIC -g -O2 -c DIP.cpp -o DIP.o In file included from DIP.cpp:2: In file included from ./Cardinal.h:9: In file included from /Users/aalim/Downloads/R_arm_compile/R-devel/include/Rinternals.h:36: In file included from /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cstddef:45: /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__nullptr:34:5: error: templates must have C++ linkage template ^~~~~~~~ ./Cardinal.h:7:1: note: extern "C" language linkage specification begins here extern "C" ^ In file included from DIP.cpp:2: In file included from ./Cardinal.h:9: In file included from /Users/aalim/Downloads/R_arm_compile/R-devel/include/Rinternals.h:36: In file included from /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cstddef:45: /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__nullptr:38:5: error: templates must have C++ linkage template <class _Tp, class _Up> ^~~~~~~ ./Cardinal.h:7:1: note: extern "C" language linkage specification begins here extern "C" ^ 2 errors generated. make: *** [DIP.o] Error 1 ERROR: compilation failed for package ‘Cardinal’

• removing ‘/Users/aalim/Downloads/R_arm_compile/R-devel/library/Cardinal’ `

[weljielab]

So it looks like the issue has already been dealt with by John Marshal and the fix is available currently as a pull request (#17).

[kuwisdelu]

Should be fixed now as part of Bioconductor 3.16 release.