hdf5 1.6.8 fails to build +universal

[daweonline@…]

I'm trying to install hdf5 on my machine: In a first attempt:

$ sudo port install hdf5 +universal
Password:
--->  Fetching hdf5
--->  Attempting to fetch hdf5-1.6.8.tar.gz from http://arn.se.distfiles.macports.org/hdf5
--->  Verifying checksum(s) for hdf5
--->  Extracting hdf5
--->  Applying patches to hdf5
--->  Configuring hdf5
--->  Building hdf5
Error: Target org.macports.build returned: shell command " cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_hdf5/work/hdf5-1.6.8" && make all " returned error 2
Command output: H5.c:3001: warning: incompatible implicit declaration of built-in function 'fprintf'
H5.c:3008: warning: incompatible implicit declaration of built-in function 'fprintf'
H5.c:3010: warning: incompatible implicit declaration of built-in function 'fprintf'
H5.c:3013: error: syntax error before 'H5Z_EDC_t'
H5.c:3016: warning: incompatible implicit declaration of built-in function 'fprintf'
H5.c:3018: warning: incompatible implicit declaration of built-in function 'fprintf'
H5.c:3020: warning: incompatible implicit declaration of built-in function 'fprintf'
H5.c:3028: warning: incompatible implicit declaration of built-in function 'fprintf'
H5.c:3030: warning: incompatible implicit declaration of built-in function 'fprintf'
H5.c:3033: error: syntax error before 'H5Z_filter_t'
H5.c:3036: warning: incompatible implicit declaration of built-in function 'fprintf'
H5.c:3038: warning: incompatible implicit declaration of built-in function 'fprintf'
H5.c:3046: warning: incompatible implicit declaration of built-in function 'fprintf'
H5.c:3048: error: 'ssize_t' undeclared (first use in this function)
H5.c:3048: error: syntax error before ')' token
H5.c:3051: warning: dereferencing 'void *' pointer
H5.c:3051: error: invalid use of void expression
H5.c:3056: warning: incompatible implicit declaration of built-in function 'fprintf'
H5.c:3059: error: syntax error before 'ssize'
H5.c:3061: error: 'ssize' undeclared (first use in this function)
H5.c:3067: warning: incompatible implicit declaration of built-in function 'fprintf'
H5.c:3074: warning: incompatible implicit declaration of built-in function 'fprintf'
H5.c:3076: warning: incompatible implicit declaration of built-in function 'fprintf'
H5.c:3084: error: request for member 'ttimes' in something not a structure or union
H5.c:3085: warning: incompatible implicit declaration of built-in function 'fprintf'
lipo: can't figure out the architecture type of: /var/tmp//ccmJpJdt.out
lipo: can't figure out the architecture type of: /var/tmp//ccwWT6R7.out
make[2]: *** [H5.lo] Error 1
make[1]: *** [lib] Error 1
make: *** [all] Error 2

Error: Status 1 encountered during processing.

I've modified the main Makefile as it prepends "/Developer/SDKs/MacOSX10.5.sdk" to "-isysroot" in many flags (CPPFLAGS and others) [Bug 1?] I've resumed the installer and it seems to run fine but:

(cd .libs && rm -f libhdf5.la && ln -s ../libhdf5.la libhdf5.la)
Building dependencies for h5test.c
Building dependencies for testframe.c
Building dependencies for big.c
Building dependencies for bittests.c
Building dependencies for cache.c
Building dependencies for cmpd_dset.c
Building dependencies for dsets.c
Building dependencies for dtypes.c
Building dependencies for extend.c
Building dependencies for external.c
Building dependencies for fillval.c
Building dependencies for flush1.c
Building dependencies for flush2.c
Building dependencies for gheap.c
Building dependencies for hyperslab.c
Building dependencies for istore.c
Building dependencies for lheap.c
Building dependencies for links.c
Building dependencies for mount.c
Building dependencies for mtime.c
Building dependencies for ohdr.c
Building dependencies for stab.c
Building dependencies for tarray.c
Building dependencies for tattr.c
Building dependencies for tconfig.c
Building dependencies for tcoords.c
Building dependencies for testhdf5.c
Building dependencies for testmeta.c
Building dependencies for tfile.c
Building dependencies for tgenprop.c
Building dependencies for th5s.c
Building dependencies for theap.c
Building dependencies for titerate.c
Building dependencies for tmeta.c
Building dependencies for tmisc.c
Building dependencies for trefer.c
Building dependencies for trefstr.c
Building dependencies for tselect.c
Building dependencies for tskiplist.c
Building dependencies for ttime.c
Building dependencies for ttst.c
Building dependencies for tvltypes.c
Building dependencies for tvlstr.c
Building dependencies for unlink.c
Building dependencies for enum.c
Building dependencies for ttsafe.c
Building dependencies for ttsafe_dcreate.c
Building dependencies for ttsafe_error.c
Building dependencies for ttsafe_cancel.c
Building dependencies for ttsafe_acreate.c
Building dependencies for set_extent.c
Building dependencies for getname.c
Building dependencies for file_handle.c
Building dependencies for ntypes.c
Building dependencies for dangle.c
Building dependencies for reserved.c
Building dependencies for err_vers.c
make[2]: *** No rule to make target `sys/types.h', needed by `h5test.lo'.  Stop.
make[1]: *** [lib] Error 1
make: *** [all] Error 2
Error: Target org.macports.build returned: shell command " cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_hdf5/work/hdf5-1.6.8" && make all " returned error 2
Command output: Building dependencies for th5s.c
Building dependencies for theap.c
Building dependencies for titerate.c
Building dependencies for tmeta.c
Building dependencies for tmisc.c
Building dependencies for trefer.c
Building dependencies for trefstr.c
Building dependencies for tselect.c
Building dependencies for tskiplist.c
Building dependencies for ttime.c
Building dependencies for ttst.c
Building dependencies for tvltypes.c
Building dependencies for tvlstr.c
Building dependencies for unlink.c
Building dependencies for enum.c
Building dependencies for ttsafe.c
Building dependencies for ttsafe_dcreate.c
Building dependencies for ttsafe_error.c
Building dependencies for ttsafe_cancel.c
Building dependencies for ttsafe_acreate.c
Building dependencies for set_extent.c
Building dependencies for getname.c
Building dependencies for file_handle.c
Building dependencies for ntypes.c
Building dependencies for dangle.c
Building dependencies for reserved.c
Building dependencies for err_vers.c
make[2]: *** No rule to make target `sys/types.h', needed by `h5test.lo'.  Stop.
make[1]: *** [lib] Error 1
make: *** [all] Error 2

Warning: the following items did not execute (for hdf5): org.macports.activate org.macports.build org.macports.destroot org.macports.install
Error: Status 1 encountered during processing.
host032:sample2mgf3p dawe$ cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_hdf5/work/hdf5-1.6.8" && make all 
make lib
make[2]: Nothing to be done for `lib'.
make[2]: *** No rule to make target `sys/types.h', needed by `h5test.lo'.  Stop.
make[1]: *** [lib] Error 1
make: *** [all] Error 2

$ uname -a
Darwin host032.2b11.ifom-ieo-campus.it 9.7.0 Darwin Kernel Version 9.7.0: Tue Mar 31 22:52:17 PDT 2009; root:xnu-1228.12.14~1/RELEASE_I386 i386

$ port version
Version: 1.710

[daweonline@…]

Cc Me!

[jochen@…]

Replying to daweonline@…:

I'm trying to install hdf5 on my machine: In a first attempt:

$ sudo port install hdf5 +universal

Is your XCode up to date (i.e., 3.1.2)?
What happens if you install without specifying +universal?

[daweonline@…]

Replying to jochen@…:

Is your XCode up to date (i.e., 3.1.2)?

$ xcodebuild -version
Xcode 3.1.2
Component versions: DevToolsCore-1148.0; DevToolsSupport-1102.0
BuildVersion: 9M2621

What happens if you install without specifying +universal?

It works...

[jochen@…]

Replying to daweonline@…:

Replying to jochen@…:

What happens if you install without specifying +universal?

It works...

Well, sorry, then you have to live with that. I don't have the time (and no need) to get this working universally. Of course, patches are welcome, but most likely you should simply send them upstream, the hdf5 developers have been quite responsie so far.

I have suppressed +universal in r51615.

[daweonline@…]

Ok, fine, at least a native 64bit version would be nice... I'm going to build it on my own

d