Hi again,
Ok, I installed numexpr and the newest Cython, and now the latest trunk
version gives another error related to hdf5.
easy_install gives:
$ sudo easy_install
http://pytables.org/svn/pytables/trunk--hdf5=hdf5-1.8.4/hdf5/
Password:
Downloading http://pytables.org/svn/pytables/trunk
Doing subversion checkout from http://pytables.org/svn/pytables/trunk to
/tmp/easy_install-GofaV_/trunk
Processing trunk
Running setup.py -q bdist_egg --dist-dir
/tmp/easy_install-GofaV_/trunk/egg-dist-tmp-y7QVfg
* Found numpy 1.3.0 package installed.
* Found numexpr 1.3.1 package installed.
.. ERROR:: Could not find a local HDF5 installation.
You may need to explicitly state where your local HDF5 headers and
library can be found by setting the ``HDF5_DIR`` environment
variable or by using the ``--hdf5`` command-line option.
error: Setup script exited with 1
I have set the HDF5_DIR env variable to the right value, along with
LD_LIBRARY_PATH. I haven't changed my PYTHONPATH but I don't think that
should be a problem here.
When I install the latest trunk version from source I get a similar error:
$ python setup.py build --hdf5=../hdf5-1.8.4/hdf5/
* Found numpy 1.3.0 package installed.
* Found numexpr 1.3.1 package installed.
* Found HDF5 headers at ``../hdf5-1.8.4/hdf5/include``, library at
``../hdf5-1.8.4/hdf5/lib``.
.. WARNING:: Could not find the HDF5 runtime.
The HDF5 shared library was *not* found in the default library
paths. In case of runtime problems, please remember to install it.
* Could not find LZO 2 headers and library; disabling support for it.
* Could not find LZO 1 headers and library; disabling support for it.
* Found bzip2 headers at ``/usr/include``, library at ``/usr/lib``.
* Found pthreads headers at ``/usr/include``, library at ``/usr/lib``.
running build
running build_py
running build_ext
building 'tables.utilsExtension' extension
C compiler: gcc-4.0 -arch ppc -arch i386 -isysroot
/Developer/SDKs/MacOSX10.4u.sdk -fno-strict-aliasing -fno-common -dynamic
-DNDEBUG -g -O3
compile options: '-DNDEBUG=1 -DHAVE_BZ2_LIB=1 -Iblosc
-I/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/core/include
-I/usr/include -I/usr/local/include -I../hdf5-1.8.4/hdf5/include
-I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c'
extra options: '-Isrc -DH5_USE_16_API'
gcc-4.0: src/utils.c
In file included from /usr/include/math.h:26,
from
/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6/pyport.h:235,
from
/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6/Python.h:58,
from src/utils.h:1,
from src/utils.c:2:
/usr/include/architecture/ppc/math.h:666: warning: conflicting types for
built-in function ‘scalb’
In file included from /usr/include/architecture/i386/math.h:626,
from /usr/include/math.h:28,
from
/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6/pyport.h:235,
from
/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6/Python.h:58,
from src/utils.h:1,
from src/utils.c:2:
/usr/include/AvailabilityMacros.h:108:14: warning: #warning Building for
Intel with Mac OS X Deployment Target < 10.4 is invalid.
gcc-4.0: blosc/blosc.c
blosc/blosc.c:65: error: syntax error before ‘barr_init’
blosc/blosc.c:65: warning: data definition has no type or storage class
blosc/blosc.c:66: error: syntax error before ‘barr_inter’
blosc/blosc.c:66: warning: data definition has no type or storage class
blosc/blosc.c:67: error: syntax error before ‘barr_finish’
blosc/blosc.c:67: warning: data definition has no type or storage class
blosc/blosc.c: In function ‘parallel_blosc’:
blosc/blosc.c:305: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
use in this function)
blosc/blosc.c:305: error: (Each undeclared identifier is reported only once
blosc/blosc.c:305: error: for each function it appears in.)
blosc/blosc.c: In function ‘t_blosc’:
blosc/blosc.c:650: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
use in this function)
blosc/blosc.c: In function ‘blosc_set_nthreads’:
blosc/blosc.c:842: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
use in this function)
blosc/blosc.c: In function ‘blosc_free_resources’:
blosc/blosc.c:885: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
use in this function)
blosc/blosc.c:65: error: syntax error before ‘barr_init’
blosc/blosc.c:65: warning: data definition has no type or storage class
blosc/blosc.c:66: error: syntax error before ‘barr_inter’
blosc/blosc.c:66: warning: data definition has no type or storage class
blosc/blosc.c:67: error: syntax error before ‘barr_finish’
blosc/blosc.c:67: warning: data definition has no type or storage class
blosc/blosc.c: In function ‘parallel_blosc’:
blosc/blosc.c:305: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
use in this function)
blosc/blosc.c:305: error: (Each undeclared identifier is reported only once
blosc/blosc.c:305: error: for each function it appears in.)
blosc/blosc.c: In function ‘t_blosc’:
blosc/blosc.c:650: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
use in this function)
blosc/blosc.c: In function ‘blosc_set_nthreads’:
blosc/blosc.c:842: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
use in this function)
blosc/blosc.c: In function ‘blosc_free_resources’:
blosc/blosc.c:885: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
use in this function)
lipo: can't figure out the architecture type of:
/var/folders/f0/f0kp8R4aG7GjOt63nvDfT++++TI/-Tmp-//ccUYkezX.out
blosc/blosc.c:65: error: syntax error before ‘barr_init’
blosc/blosc.c:65: warning: data definition has no type or storage class
blosc/blosc.c:66: error: syntax error before ‘barr_inter’
blosc/blosc.c:66: warning: data definition has no type or storage class
blosc/blosc.c:67: error: syntax error before ‘barr_finish’
blosc/blosc.c:67: warning: data definition has no type or storage class
blosc/blosc.c: In function ‘parallel_blosc’:
blosc/blosc.c:305: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
use in this function)
blosc/blosc.c:305: error: (Each undeclared identifier is reported only once
blosc/blosc.c:305: error: for each function it appears in.)
blosc/blosc.c: In function ‘t_blosc’:
blosc/blosc.c:650: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
use in this function)
blosc/blosc.c: In function ‘blosc_set_nthreads’:
blosc/blosc.c:842: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
use in this function)
blosc/blosc.c: In function ‘blosc_free_resources’:
blosc/blosc.c:885: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
use in this function)
blosc/blosc.c:65: error: syntax error before ‘barr_init’
blosc/blosc.c:65: warning: data definition has no type or storage class
blosc/blosc.c:66: error: syntax error before ‘barr_inter’
blosc/blosc.c:66: warning: data definition has no type or storage class
blosc/blosc.c:67: error: syntax error before ‘barr_finish’
blosc/blosc.c:67: warning: data definition has no type or storage class
blosc/blosc.c: In function ‘parallel_blosc’:
blosc/blosc.c:305: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
use in this function)
blosc/blosc.c:305: error: (Each undeclared identifier is reported only once
blosc/blosc.c:305: error: for each function it appears in.)
blosc/blosc.c: In function ‘t_blosc’:
blosc/blosc.c:650: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
use in this function)
blosc/blosc.c: In function ‘blosc_set_nthreads’:
blosc/blosc.c:842: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
use in this function)
blosc/blosc.c: In function ‘blosc_free_resources’:
blosc/blosc.c:885: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
use in this function)
lipo: can't figure out the architecture type of:
/var/folders/f0/f0kp8R4aG7GjOt63nvDfT++++TI/-Tmp-//ccUYkezX.out
error: Command "gcc-4.0 -arch ppc -arch i386 -isysroot
/Developer/SDKs/MacOSX10.4u.sdk -fno-strict-aliasing -fno-common -dynamic
-DNDEBUG -g -O3 -DNDEBUG=1 -DHAVE_BZ2_LIB=1 -Iblosc
-I/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/core/include
-I/usr/include -I/usr/local/include -I../hdf5-1.8.4/hdf5/include
-I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c
blosc/blosc.c -o build/temp.macosx-10.3-fat-2.6/blosc/blosc.o -Isrc
-DH5_USE_16_API" failed with exit status 1
I'm not sure why my hdf5 installation is being problematic. Any help is
appreciated.
Thanks
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