Looks like your PKG_LIBS arguments are ignored/overwritten on the Mac build; ‘bambi.so’ appears to be missing objects contained in -lbamdb, hence the load error.
Keith > On Apr 30, 2018, at 6:48 AM, Evan Biederstedt <evan.biederst...@gmail.com> > wrote: > > 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. > > > _______________________________________________ > Rcpp-devel mailing list > Rcpp-devel@lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel _______________________________________________ Rcpp-devel mailing list Rcpp-devel@lists.r-forge.r-project.org https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
