I'm trying to build the hdf5 library package for R (hdf5_1.6.9.tar.gz from CRAN with a small change to make it ignore some elements in files generated with h4toh5) on Mac OS X Leopard 10.8.6 Sever (Mac Pro)
In the past I have used the Macports hdf5 package for the libraries, but macports http access to svn is now blocked by a corporate firewall. The library fails to build using the usual "R64 CMD INSTALL ...", so to debug I extracted the files and am running configure manually: $ export HDF5CPPFLAGS="-arch x86_64 -I/opt/hdfgroup.org/include" \ HDF5LDFLAGS="-arch x86_64 -Wl,-search_paths_first -L/opt/hdfgroup.org/lib -lhdf5_hl -lhdf5_hl -lsz -lz" \ CC='/usr/bin/gcc-4.2 -arch x86_64 -std=c99' $ ./configure checking for gcc... /usr/bin/gcc-4.2 -arch x86_64 -std=c99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether /usr/bin/gcc-4.2 -arch x86_64 -std=c99 accepts -g... yes checking for /usr/bin/gcc-4.2 -arch x86_64 -std=c99 option to accept ANSI C...\ none needed checking for library containing inflate... no checking for library containing H5open... no configure: error: Can't find zlib In config.log: configure:2214: checking for library containing inflate configure:2244: /usr/bin/gcc-4.2 -arch x86_64 -std=c99 -o conftest -g -O2 -ar\ ch x86_64 -I/opt/hdfgroup.org/include -arch x86_64 -Wl,-search_paths_first -L\ /opt/hdfgroup.org/lib -lhdf5_hl -lhdf5_hl -lsz -lz conftest.c -lm >&5 ld warning: in /opt/hdfgroup.org/lib/libsz.a, file is not of required architecture ld warning: in /opt/hdfgroup.org/lib/libz.a, file is not of required architecture Note the use of "-search-paths-first". Without this, the system would give "preference" to libsz.dylib before libsz.a. I extracted the objects from libsz.a: $ ar x ../../lib/libsz.a $ ls total 136 8 __.SYMDEF SORTED 112 rice.o 8 encoding.o 8 sz_api.o $ file *.o encoding.o: Mach-O object i386 rice.o: Mach-O object i386 sz_api.o: Mach-O object i386 so for once configure correctly diagnosed the problem. I suspect the library may have been tested on a system with a 64-bit libsz.dylib and without the "-search-paths-first" incantation. -- George N. White III <[email protected]> Head of St. Margarets Bay, Nova Scotia _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
