On Jul 24, 2013, at 3:35 PM, Jonathan Callahan wrote: > I am developing a package for analysis of seismic data that relies on a > Fortran library. > > Package compilation works fine on Ubuntu and Red Hat Enterprise but fails > for R 2.15.3 on Mac OSX 10.8.4. > > I've included the entire dump below but the relevant error message seems to > be: > > ld: warning: ignoring file libmseed/libmseed.a, file was built for archive >> which is not the architecture being linked (i386): libmseed/libmseed.a > > > Compilation for x86_64 proceeds without a hitch. > > If anyone is curious, the package tarballs are available at: > > http://mazamascience.com/Downloads/ > > Thanks for any helpful suggestions about compiling Fortran on OSX. >
This has nothing to do with Fortran (and it's not even Mac-specific) - you're using the wrong compiler flags for building the dependent library inside your package (as the message tells you: you are building 64-bit version of libmseed when compiling 32-bit version of the package). Please make sure you use the proper compiler and flags that R is providing (i.e., remove all conflicting flags from libmseed/Makefile). Cheers, Simon > Jon > > > $ R CMD INSTALL seismic_0.2.1.0.tar.gz > * installing to library > Œ/Library/Frameworks/R.framework/Versions/2.15/Resources/library‚ > * installing *source* package Œseismic‚ ... > ** libs > *** arch - i386 > gcc -arch i386 -std=gnu99 > -I/Library/Frameworks/R.framework/Resources/include > -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG > -Ilibmseed -I/usr/local/include -fPIC -fPIC -g -O2 -c parseMiniSEED.c > -o parseMiniSEED.o > gcc -O2 -Wall -fPIC -c -o fileutils.o fileutils.c > gcc -O2 -Wall -fPIC -c -o genutils.o genutils.c > gcc -O2 -Wall -fPIC -c -o gswap.o gswap.c > gcc -O2 -Wall -fPIC -c -o lmplatform.o lmplatform.c > gcc -O2 -Wall -fPIC -c -o lookup.o lookup.c > gcc -O2 -Wall -fPIC -c -o msrutils.o msrutils.c > gcc -O2 -Wall -fPIC -c -o pack.o pack.c > gcc -O2 -Wall -fPIC -c -o packdata.o packdata.c > gcc -O2 -Wall -fPIC -c -o traceutils.o traceutils.c > gcc -O2 -Wall -fPIC -c -o tracelist.o tracelist.c > gcc -O2 -Wall -fPIC -c -o parseutils.o parseutils.c > gcc -O2 -Wall -fPIC -c -o unpack.o unpack.c > gcc -O2 -Wall -fPIC -c -o unpackdata.o unpackdata.c > gcc -O2 -Wall -fPIC -c -o selection.o selection.c > gcc -O2 -Wall -fPIC -c -o logging.o logging.c > rm -f libmseed.a > ar -csq libmseed.a fileutils.o genutils.o gswap.o lmplatform.o lookup.o > msrutils.o pack.o packdata.o traceutils.o tracelist.o parseutils.o unpack.o > unpackdata.o selection.o logging.o > gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names > -undefined dynamic_lookup -single_module -multiply_defined suppress > -L/usr/local/lib -o seismic.so parseMiniSEED.o -Llibmseed -lmseed > -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework > -Wl,CoreFoundation > ld: warning: ignoring file libmseed/libmseed.a, file was built for archive > which is not the architecture being linked (i386): libmseed/libmseed.a > installing to > /Library/Frameworks/R.framework/Versions/2.15/Resources/library/seismic/libs/i386 > *** arch - x86_64 > gcc -arch x86_64 -std=gnu99 > -I/Library/Frameworks/R.framework/Resources/include > -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG > -Ilibmseed -I/usr/local/include -fPIC -fPIC -g -O2 -c parseMiniSEED.c > -o parseMiniSEED.o > gcc -O2 -Wall -fPIC -c -o fileutils.o fileutils.c > gcc -O2 -Wall -fPIC -c -o genutils.o genutils.c > gcc -O2 -Wall -fPIC -c -o gswap.o gswap.c > gcc -O2 -Wall -fPIC -c -o lmplatform.o lmplatform.c > gcc -O2 -Wall -fPIC -c -o lookup.o lookup.c > gcc -O2 -Wall -fPIC -c -o msrutils.o msrutils.c > gcc -O2 -Wall -fPIC -c -o pack.o pack.c > gcc -O2 -Wall -fPIC -c -o packdata.o packdata.c > gcc -O2 -Wall -fPIC -c -o traceutils.o traceutils.c > gcc -O2 -Wall -fPIC -c -o tracelist.o tracelist.c > gcc -O2 -Wall -fPIC -c -o parseutils.o parseutils.c > gcc -O2 -Wall -fPIC -c -o unpack.o unpack.c > gcc -O2 -Wall -fPIC -c -o unpackdata.o unpackdata.c > gcc -O2 -Wall -fPIC -c -o selection.o selection.c > gcc -O2 -Wall -fPIC -c -o logging.o logging.c > rm -f libmseed.a > ar -csq libmseed.a fileutils.o genutils.o gswap.o lmplatform.o lookup.o > msrutils.o pack.o packdata.o traceutils.o tracelist.o parseutils.o unpack.o > unpackdata.o selection.o logging.o > gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names > -undefined dynamic_lookup -single_module -multiply_defined suppress > -L/usr/local/lib -o seismic.so parseMiniSEED.o -Llibmseed -lmseed > -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework > -Wl,CoreFoundation > installing to > /Library/Frameworks/R.framework/Versions/2.15/Resources/library/seismic/libs/x86_64 > ** R > ** inst > ** preparing package for lazy loading > Creating a generic function for Œas.vector‚ from package Œbase‚ in package > Œseismic‚ > Creating a generic function for Œmean‚ from package Œbase‚ in package > Œseismic‚ > Creating a generic function for Œmedian‚ from package Œstats‚ in package > Œseismic‚ > Creating a generic function for Œsd‚ from package Œstats‚ in package > Œseismic‚ > Creating a generic function for Œplot‚ from package Œgraphics‚ in package > Œseismic‚ > ** help > *** installing help indices > ** building package indices > ** installing vignettes > Œseismic-intro.Rnw‚ > ** testing if installed package can be loaded > *** arch - i386 > Error in dyn.load(file, DLLpath = DLLpath, ...) : > unable to load shared object > '/Library/Frameworks/R.framework/Versions/2.15/Resources/library/seismic/libs/i386/seismic.so': > > dlopen(/Library/Frameworks/R.framework/Versions/2.15/Resources/library/seismic/libs/i386/seismic.so, > 6): Symbol not found: _ms_loginit > Referenced from: > /Library/Frameworks/R.framework/Versions/2.15/Resources/library/seismic/libs/i386/seismic.so > Expected in: flat namespace > in > /Library/Frameworks/R.framework/Versions/2.15/Resources/library/seismic/libs/i386/seismic.so > Error: loading failed > Execution halted > *** arch - x86_64 > ERROR: loading failed for Œi386‚ > * removing > Œ/Library/Frameworks/R.framework/Versions/2.15/Resources/library/seismic‚ > > > -- > Jonathan Callahan, PhD > Mazama Science > 206-708-5028 > mazamascience.com > > [[alternative HTML version deleted]] > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
