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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