Dear list I have the following R package which is interacting with a C library via Rcpp and extern. At some point, the goal is to combine these....but I'm trying this with baby steps.
R package with C++ wrapper: https://github.com/d-lo/bambi The C library: https://github.com/d-lo/bamdb When I try to install the R package on Linux, the Makevars appears use the compiler g++, and it installs correctly: ``` Installing package into '/home/username/R/x86_64-pc-linux-gnu-library/3.2' (as 'lib' is unspecified) * installing *source* package 'bambi' ... ** libs g++ -std=c++11 -I/usr/share/R/include -DNDEBUG -I../inst/include/ -I"/usr/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o g++ -std=c++11 -I/usr/share/R/include -DNDEBUG -I../inst/include/ -I"/usr/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bambi.cpp -o bambi.o g++ -std=c++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o bambi.so RcppExports.o bambi.o -lbamdb -llmdb -lhts -L/usr/lib/R/lib -lR installing to /home/username/R/x86_64-pc-linux-gnu-library/3.2/bambi/libs ** R ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (bambi) > library(bambi) ``` Here's what I see when I do the same on Mac OS. It uses clang++, and has entirely different build commands: ``` * installing to library ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library’ * installing *source* package ‘bambi’ ... ** libs clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -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 clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -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 clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c rcpp_hello_world.cpp -o rcpp_hello_world.o clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o bambi.so RcppExports.o bambi.o rcpp_hello_world.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.4/Resources/library/bambi/libs ** R ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded Error: package or namespace load failed for ‘bambi’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/bambi/libs/bambi.so': dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/bambi/libs/bambi.so, 6): Symbol not found: _get_bam_rows Referenced from: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/bambi/libs/bambi.so Expected in: flat namespace in /Library/Frameworks/R.framework/Versions/3.4/Resources/library/bambi/libs/bambi.so Error: loading failed Execution halted ERROR: loading failed * removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/bambi’ ``` Why is there this discrepancy? How do I direct the Makevars to use g++ and give me the "correct" build as I see on Linux? `CXX=g++` or `CXX=/usr/local/bin/g++` doesn't appear to work.
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