Good afternoon, New 1.8.5-patch1 binaries for Mac 64 have been posted at http://www.hdfgroup.org/HDF5/release/obtain5.html.
We apologize once again for the error and any inconvenience it caused. Please let us know about any problems you encounter with the distributed binaries. Thank you! Elena On Nov 26, 2010, at 6:39 AM, George N. White III wrote: > 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 _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
