Hello, I'm the package maintainer for ncdf4, which provides an R interface for netcdf files. I have successfully built and installed the package on a OS X Mavericks machine I have access to, but the nightly build on that platform for R failed with an error I'm trying to understand.
I'm sure it's documented somewhere who to contact about odd results on the specific Mavericks machine used for the CRAN compiles, but I have not been able to find that despite some searching. Does anyone know if there's a contact who can be approached about the software environment of that particular machine? More technical details of the compiling problem follow. The netcdf library has an accessory script that shows how it was configured on the machine in question (the Mavericks machine in this case). This shows: ------ This netCDF 4.1.3 has been built with the following features: --cc -> gcc -arch i386 -std=gnu99 --cflags -> -I/usr/local/include --libs -> -L/usr/local/lib -lnetcdf -lhdf5_hl -lhdf5 -lm -lz -lcurl ----- which is stating that the library compiled correctly using -L/usr/local/lib -lhdf4_hl (among other libs). Yet the R build failed with: clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o ncdf4.so ncdf.o ncdf2.o ncdf3.o src_ncdf4.o -Wl,-rpath,/usr/local/lib -L/usr/local/lib -lnetcdf -lhdf5_hl -lhdf5 -lm -lz -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: library not found for -lhdf5_hl clang: error: linker command failed with exit code 1 (use -v to see invocation) which claims that -lhdf5_hl was not found. The odd part is, if that library was found when the netcdf library was compiled, why wasn't it found when the R ncdf4 package was compiled with the same -L library path flag? Am I missing something here? Also, I know essentially nothing about Macs (hopefully some people here can help me on this), but I see that the netcdf library was compiled with "-arch i386", while the R package was compiled with "clang -Wall -mtune=core2 -g -O2", which does not specify -arch i386. Is it possible that the linker is reporting "hdf5_hl" not found because the existing library is a 32-bit library but it's looking for a 64-bit library? On Windows, for example,this would give an error along the lines of "library is 32 bit not 64 bit" but I don't know how OS X would handle this. Thanks for any info, --Dave -- Dr. David W. Pierce Division of Climate, Atmospheric Science, and Physical Oceanography Scripps Institution of Oceanography, La Jolla, California, USA (858) 534-8276 (voice) / (858) 534-8561 (fax) dpie...@ucsd.edu _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
