Hi all Thank you for the responses.
@Keith > 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. Yes, it's odd. @Dirk > Are the libraries installed on the macOS box? When I build bamdb, CMake checks for the required, which corresponds to what I see https://github.com/d-lo/bamdb ``` -- Detecting CXX compile features - done -- Found CK -- Found ZLIB: /usr/local/lib/libz.dylib (found version "1.2.11") -- Found HTSlib -- Found LMDB -- Configuring done -- Generating done -- Build files have been written to: /Users/ebiederstedt/bamdb/build ``` With `sudo make install`, I think `bamdb` should be accessible via `-lbamdb` ``` $ sudo make install Password: [ 50%] Built target bamdb [100%] Built target libbamdb Install the project... -- Install configuration: "" -- Installing: /usr/local/bin/bamdb -- Up-to-date: /usr/local/include/bamdb -- Up-to-date: /usr/local/include/bamdb/bam_api.h -- Up-to-date: /usr/local/include/bamdb/bam_lmdb.h -- Up-to-date: /usr/local/include/bamdb/bamdb.h -- Installing: /usr/local/lib/libbamdb.dylib ``` It's very odd these PKG_LIBS are ignored though.... > Could you compile and link a trivial test program against them? I think this is the next step... @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? On Mon, Apr 30, 2018 at 11:27 AM, Dirk Eddelbuettel <e...@debian.org> wrote: > > On 30 April 2018 at 06:48, Evan Biederstedt 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 > > Ok, so src/Makevars wants three libraries: > > PKG_LIBS= -lbamdb -llmdb -lhts > > | > | 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 > > and here we get them as libbamdb.so, liblmdb.so, libhts.so are all system > level libraries and (I guess) 'sudo ldconfig -p' shows them. Linking works, > and they are found as the package loads. > > | 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 > > I think they should show up here too, but they do not. > > Are the libraries installed on the macOS box? Could you compile and link a > trivial test program against them? > > Dirk > > > | 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 > > -- > http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org >
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