> Am 30.04.2018 um 21:01 schrieb Evan Biederstedt <evan.biederst...@gmail.com>:
> @Ralf
>
> > You can change the used compiler for *your* system via ~/.R/Makevars,
> > though. From my point of view that is a (short-time) workaround only. You
> > have to figure out why clang does not like your package/library.
>
> I've yet to test changing the compiler in ~/.R/Makevars. However, it's not
> clear to me why this would be a short-term solution. Could you clarify why
> using g++ instead of clang would be a problem gong forwards?
Because clang is the default compiler for R on MacOS. So you would make it
difficult for other people (let alone CRAN) to make use of the package.
However, I think there is something wrong about your macOS machine. I have just
tried to compile your package on a macOS machine that I have access to, and I
got quite different results:
$ R CMD INSTALL bambi_1.0.tar.gz
* installing to library
‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library’
* installing *source* package ‘bambi’ ...
** libs
/usr/local/clang4/bin/clang++ -std=gnu++11
-I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/
-I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include"
-I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
/usr/local/clang4/bin/clang++ -std=gnu++11
-I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/
-I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include"
-I/usr/local/include -fPIC -Wall -g -O2 -c bambi.cpp -o bambi.o
bambi.cpp:7:14: fatal error: 'bam_lmdb.h' file not found
#include "bam_lmdb.h"
^~~~~~~~~~~~
1 error generated.
make: *** [bambi.o] Error 1
ERROR: compilation failed for package ‘bambi’
* removing
‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/bambi’
I had not installed the necessary C library, so unsurprisingly the compilation
step already failed. What I find interesting is that in my case "-std=gnu++11“
and "-I../inst/include/" are present in the command line options for clang++.
These are also missing from what you quoted and are also a consequence of
src/Makevars. It almost looks as if this file got lost on your macOS box …
Greetings
Ralf
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