George, Thank you for your report. Apparently binaries were not packed correctly and our binaries testing is flawed (my fault ;-( I will repack and retest, and we will provide the new tar ball for Mac64.
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
