William Kyngesburye of http://www.kyngchaos.com/ did provide me with this solution to the compilation of netcdf as an universal library. I post it here for reference for others who might want to do a similar thing: Most packages I build ppc/intel separately, then merge with lipo, to deal with endian issues, and libtool quirks. I usually do a bit of patching to make it go smoothly. netcdf is one such split build. Assuming you're using a PPC Mac, configure and build the PPC version. Duplicate the source folder to retain the same configuration. make clean the copy. Edit libsrc/ncconfig.h and find where it defines WORDS_BIGENDIAN - delete that line. Edit macros.make: add $(CCFLAGS) to both the CFLAGS and CXXFLAGS lines. In the Terminal: $ export SDKROOT=/Developer/SDKs/MacOSX10.4u.sdk $ export CCFLAGS="-arch i386 -isysroot $SDKROOT" and make your intel copy. Then use lipo to merge the two together.