Hi Jeff,
Just guessing, but maybe you are using Cython < 0.12.1. Please try to
install the latest version of Cython and try again.
2010/8/13, Jeff Reback <jreb...@yahoo.com>:
> Hi,
>
> I tried to build pytables 2.2 on an x86-64bit (amd64) debian machine.
> but received the following build errors (below)
>
> I then successfully built 2.1.2 with no issues (and passes all tests)
>
> Jeff
>
> --------
>
> * Found numpy 1.5.0b1 package installed.
> * Found numexpr 1.4 package installed.
> * Found HDF5 headers at ``/usr/include``, library at ``/usr/lib64``.
> * Found LZO 2 headers at ``/usr/include``, library at ``/usr/lib64``.
> * Skipping detection of LZO 1 since LZO 2 has already been found.
> * Could not find bzip2 headers and library; disabling support for it.
> * Found pthreads headers at ``/usr/include``, library at ``/usr/lib64``.
> running build_ext
> cythoning tables/hdf5Extension.pyx to tables/hdf5Extension.c
>
> Error converting Pyrex file to C:
> ------------------------------------------------------------
> ...
> self.disk_type_id = AtomToHDF5Type(atom, self.byteorder)
>
> # Allocate space for the dimension axis info and fill it
> dims = numpy.array(shape, dtype=numpy.intp)
> self.rank = len(shape)
> self.dims = npy_malloc_dims(self.rank, <npy_intp *>(dims.data))
> ^
> ------------------------------------------------------------
>
> /data/arb/distros/tables-2.2/tables/hdf5Extension.pyx:836:31: Cannot convert
> 'definitions.hsize_t *' to Python object
>
> Error converting Pyrex file to C:
> ------------------------------------------------------------
> ...
> # Save the array
> complib = PyString_AsString(self.filters.complib or '')
> version = PyString_AsString(self._v_version)
> class_ = PyString_AsString(self._c_classId)
> self.dataset_id = H5ARRAYmake(self.parent_id, self.name, version,
> self.rank, self.dims,
> ^
> ------------------------------------------------------------
>
> /data/arb/distros/tables-2.2/tables/hdf5Extension.pyx:844:49: Cannot convert
> Python object to 'definitions.hsize_t *'
>
> Error converting Pyrex file to C:
> ------------------------------------------------------------
> ...
> atom = self.atom
> itemsize = atom.itemsize
> self.disk_type_id = AtomToHDF5Type(atom, self.byteorder)
>
> self.rank = len(self.shape)
> self.dims = malloc_dims(self.shape)
> ^
> ------------------------------------------------------------
>
> /data/arb/distros/tables-2.2/tables/hdf5Extension.pyx:882:27: Cannot convert
> 'definitions.hsize_t *' to Python object
>
> Error converting Pyrex file to C:
> ------------------------------------------------------------
> ...
> self.disk_type_id = AtomToHDF5Type(atom, self.byteorder)
>
> self.rank = len(self.shape)
> self.dims = malloc_dims(self.shape)
> if self.chunkshape:
> self.dims_chunk = malloc_dims(self.chunkshape)
> ^
> ------------------------------------------------------------
>
> /data/arb/distros/tables-2.2/tables/hdf5Extension.pyx:884:35: Cannot convert
> 'definitions.hsize_t *' to Python object
>
> Error converting Pyrex file to C:
> ------------------------------------------------------------
> ...
> atom.dflt = dflts
>
> # Create the CArray/EArray
> self.dataset_id = H5ARRAYmake(
> self.parent_id, self.name, version, self.rank,
> self.dims, self.extdim, self.disk_type_id, self.dims_chunk,
> ^
> ------------------------------------------------------------
>
> /data/arb/distros/tables-2.2/tables/hdf5Extension.pyx:907:10: Cannot convert
> Python object to 'definitions.hsize_t *'
>
> Error converting Pyrex file to C:
> ------------------------------------------------------------
> ...
> atom.dflt = dflts
>
> # Create the CArray/EArray
> self.dataset_id = H5ARRAYmake(
> self.parent_id, self.name, version, self.rank,
> self.dims, self.extdim, self.disk_type_id, self.dims_chunk,
> ^
> ------------------------------------------------------------
>
> /data/arb/distros/tables-2.2/tables/hdf5Extension.pyx:907:53: Cannot convert
> Python object to 'definitions.hsize_t *'
>
> Error converting Pyrex file to C:
> ------------------------------------------------------------
> ...
> self.disk_type_id, self.type_id = self._get_type_ids()
> # Get the atom for this type
> atom = AtomFromHDF5Type(self.disk_type_id)
>
> # Get the rank for this array object
> if H5ARRAYget_ndims(self.dataset_id, &self.rank) < 0:
> ^
> ------------------------------------------------------------
>
> /data/arb/distros/tables-2.2/tables/hdf5Extension.pyx:954:41: Cannot take
> address of Python variable
>
> Error converting Pyrex file to C:
> ------------------------------------------------------------
> ...
>
> # Get the rank for this array object
> if H5ARRAYget_ndims(self.dataset_id, &self.rank) < 0:
> raise HDF5ExtError("Problems getting ndims!")
> # Allocate space for the dimension axis info
> self.dims = <hsize_t *>malloc(self.rank * sizeof(hsize_t))
> ^
> ------------------------------------------------------------
>
> /data/arb/distros/tables-2.2/tables/hdf5Extension.pyx:957:16: Cannot convert
> 'definitions.hsize_t *' to Python object
>
> Error converting Pyrex file to C:
> ------------------------------------------------------------
> ...
> # Get the rank for this array object
> if H5ARRAYget_ndims(self.dataset_id, &self.rank) < 0:
> raise HDF5ExtError("Problems getting ndims!")
> # Allocate space for the dimension axis info
> self.dims = <hsize_t *>malloc(self.rank * sizeof(hsize_t))
> self.maxdims = <hsize_t *>malloc(self.rank * sizeof(hsize_t))
> ^
> ------------------------------------------------------------
>
> /data/arb/distros/tables-2.2/tables/hdf5Extension.pyx:958:19: Cannot convert
> 'definitions.hsize_t *' to Python object
>
> Error converting Pyrex file to C:
> ------------------------------------------------------------
> ...
> # Allocate space for the dimension axis info
> self.dims = <hsize_t *>malloc(self.rank * sizeof(hsize_t))
> self.maxdims = <hsize_t *>malloc(self.rank * sizeof(hsize_t))
> # Get info on dimensions, class and type (of base class)
> ret = H5ARRAYget_info(self.dataset_id, self.disk_type_id,
> self.dims, self.maxdims,
> ^
> ------------------------------------------------------------
>
> /data/arb/distros/tables-2.2/tables/hdf5Extension.pyx:961:30: Cannot convert
> Python object to 'definitions.hsize_t *'
>
> Error converting Pyrex file to C:
> ------------------------------------------------------------
> ...
> # Allocate space for the dimension axis info
> self.dims = <hsize_t *>malloc(self.rank * sizeof(hsize_t))
> self.maxdims = <hsize_t *>malloc(self.rank * sizeof(hsize_t))
> # Get info on dimensions, class and type (of base class)
> ret = H5ARRAYget_info(self.dataset_id, self.disk_type_id,
> self.dims, self.maxdims,
> ^
> ------------------------------------------------------------
>
> /data/arb/distros/tables-2.2/tables/hdf5Extension.pyx:961:41: Cannot convert
> Python object to 'definitions.hsize_t *'
>
> Error converting Pyrex file to C:
> ------------------------------------------------------------
> ...
> if self.maxdims[i] == -1:
> self.extdim = i
> break
>
> # Get the shape as a python tuple
> shape = getshape(self.rank, self.dims)
> ^
> ------------------------------------------------------------
>
> /data/arb/distros/tables-2.2/tables/hdf5Extension.pyx:974:36: Cannot convert
> Python object to 'definitions.hsize_t *'
>
> Error converting Pyrex file to C:
> ------------------------------------------------------------
> ...
>
> # Get the shape as a python tuple
> shape = getshape(self.rank, self.dims)
>
> # Allocate space for the dimension chunking info
> self.dims_chunk = <hsize_t *>malloc(self.rank * sizeof(hsize_t))
> ^
> ------------------------------------------------------------
>
> /data/arb/distros/tables-2.2/tables/hdf5Extension.pyx:977:22: Cannot convert
> 'definitions.hsize_t *' to Python object
>
> Error converting Pyrex file to C:
> ------------------------------------------------------------
> ...
> # Get the shape as a python tuple
> shape = getshape(self.rank, self.dims)
>
> # Allocate space for the dimension chunking info
> self.dims_chunk = <hsize_t *>malloc(self.rank * sizeof(hsize_t))
> if H5ARRAYget_chunkshape(self.dataset_id, self.rank, self.dims_chunk) <
> 0:
> ^
> ------------------------------------------------------------
>
> /data/arb/distros/tables-2.2/tables/hdf5Extension.pyx:978:61: Cannot convert
> Python object to 'definitions.hsize_t *'
>
> Error converting Pyrex file to C:
> ------------------------------------------------------------
> ...
> if H5ARRAYget_chunkshape(self.dataset_id, self.rank, self.dims_chunk) <
> 0:
> # The Array class is not chunked!
> chunkshapes = None
> else:
> # Get the chunkshape as a python tuple
> chunkshapes = getshape(self.rank, self.dims_chunk)
> ^
> ------------------------------------------------------------
>
> /data/arb/distros/tables-2.2/tables/hdf5Extension.pyx:983:44: Cannot convert
> Python object to 'definitions.hsize_t *'
>
> Error converting Pyrex file to C:
> ------------------------------------------------------------
> ...
>
> # Append the records
> extdim = self.extdim
> Py_BEGIN_ALLOW_THREADS
> ret = H5ARRAYappend_records(self.dataset_id, self.type_id, self.rank,
> self.dims, dims_arr, extdim, rbuf)
> ^
> ------------------------------------------------------------
>
> /data/arb/distros/tables-2.2/tables/hdf5Extension.pyx:1024:36: Cannot
> convert Python object to 'definitions.hsize_t *'
>
> Error converting Pyrex file to C:
> ------------------------------------------------------------
> ...
> if self.dims:
> free(<void *>self.dims)
> if self.maxdims:
> free(<void *>self.maxdims)
> if self.dims_chunk:
> free(self.dims_chunk)
> ^
> ------------------------------------------------------------
>
> /data/arb/distros/tables-2.2/tables/hdf5Extension.pyx:1365:15: Cannot
> convert Python object to 'void *'
> building 'tables.hdf5Extension' extension
> C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
> -Wstrict-prototypes -fPIC
>
> compile options: '-DNDEBUG=1 -DHAVE_LZO2_LIB=1 -Iblosc
> -I/usr/lib/python2.5/site-packages/numpy/core/include
> -I/usr/include/python2.5 -c'
> extra options: '-Isrc -DH5_USE_16_API'
> gcc: tables/hdf5Extension.c
> tables/hdf5Extension.c:1:2: error: #error Do not use this file, it is the
> result of a failed Cython compilation.
> tables/hdf5Extension.c:1:2: error: #error Do not use this file, it is the
> result of a failed Cython compilation.
> error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv
>
>
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--
Francesc Alted
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