Hi Stuart,
A Monday 08 November 2010 08:01:17 escriguéreu:
> Hello Francesc,
>
> I've got a fresh Fedora 14 64-bit system (with python 2.7) and I
> tried an easy_install tables and it fails trying to install PyTables
> 2.2.1. Before I annoy the PyTables list I thought I'd check with
> you on whether this is a supported platform yet.
By explaining your installation problems in the list you are not
annoying, but rather helping other people that can have the same
problems, and enabling others to help you. Please, please, please do
not hesitate on using this list for reporting this sort of things.
> I have attached the
> output from the install attempt.
>
> One note is that I had to pull the hdf5 and hdf5-devel packages from
> updates-testing to avoid a gfortran module version error with our
> Fortran builds (we link some Fortran to the app with F2PY). So we
> are running HDF5 1.8.5.patch1 rather than the 1.8.5 that is in the
> standard Fedora repos.
>
> But with the missing tables/linkExtension.c error this looks more
> like a Cython problem. But the incompatible hsize_t pointer types
> also seems like a serious issue.
Well, as I see it, it is the missing tables/linkExtension.c which is the
problem. Do you have Cython installed (it is a requisite)? For the
future, I'll try to remove the Cython requisite, but meanwhile, you will
absolutely *need* it installed in your system.
Cheers,
--
Francesc Alted
install_dir /usr/lib/python2.7/site-packages/
Searching for tables
Reading http://pypi.python.org/simple/tables/
Reading http://www.pytables.org/
Best match: tables 2.2.1
Downloading http://www.pytables.org/download/pytables-2.2.1/tables-2.2.1.tar.gz
Processing tables-2.2.1.tar.gz
Running tables-2.2.1/setup.py -q bdist_egg --dist-dir
/tmp/easy_install-447WTP/tables-2.2.1/egg-dist-tmp-x2TfH5
* Found numpy 1.4.1 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.
* Found bzip2 headers at ``/usr/include``, library at ``/usr/lib64``.
warning: no previously-included files matching '*' found under directory
'doc/xml'
In file included from /usr/include/python2.7/pyconfig.h:6:0,
from /usr/include/python2.7/Python.h:8,
from src/utils.h:1,
from src/H5ARRAY.c:4:
/usr/include/python2.7/pyconfig-64.h:1158:0: warning: "_POSIX_C_SOURCE"
redefined
/usr/include/features.h:162:0: note: this is the location of the previous
definition
/usr/include/python2.7/pyconfig-64.h:1180:0: warning: "_XOPEN_SOURCE" redefined
/usr/include/features.h:164:0: note: this is the location of the previous
definition
/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1187:1:
warning: ‘_import_array’ defined but not used
/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1187:1:
warning: ‘_import_array’ defined but not used
tables/utilsExtension.c: In function
‘__pyx_pf_6tables_14utilsExtension_AtomToHDF5Type’:
tables/utilsExtension.c:5368:9: warning: ‘__pyx_v_tid’ may be used
uninitialized in this function
In file included from /usr/include/python2.7/pyconfig.h:6:0,
from /usr/include/python2.7/Python.h:8,
from src/utils.h:1,
from src/H5ARRAY.c:4:
/usr/include/python2.7/pyconfig-64.h:1158:0: warning: "_POSIX_C_SOURCE"
redefined
/usr/include/features.h:162:0: note: this is the location of the previous
definition
/usr/include/python2.7/pyconfig-64.h:1180:0: warning: "_XOPEN_SOURCE" redefined
/usr/include/features.h:164:0: note: this is the location of the previous
definition
/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1187:1:
warning: ‘_import_array’ defined but not used
In file included from /usr/include/python2.7/pyconfig.h:6:0,
from /usr/include/python2.7/Python.h:8,
from src/utils.h:1,
from src/H5VLARRAY.c:3:
/usr/include/python2.7/pyconfig-64.h:1158:0: warning: "_POSIX_C_SOURCE"
redefined
/usr/include/features.h:162:0: note: this is the location of the previous
definition
/usr/include/python2.7/pyconfig-64.h:1180:0: warning: "_XOPEN_SOURCE" redefined
/usr/include/features.h:164:0: note: this is the location of the previous
definition
/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1187:1:
warning: ‘_import_array’ defined but not used
/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1187:1:
warning: ‘_import_array’ defined but not used
tables/hdf5Extension.c: In function
‘__pyx_pf_6tables_13hdf5Extension_5Array__readArray’:
tables/hdf5Extension.c:9091:7: warning: ‘__pyx_v_extdim’ may be used
uninitialized in this function
In file included from /usr/include/python2.7/pyconfig.h:6:0,
from /usr/include/python2.7/Python.h:8,
from src/utils.h:1,
from src/H5TB-opt.c:36:
/usr/include/python2.7/pyconfig-64.h:1158:0: warning: "_POSIX_C_SOURCE"
redefined
/usr/include/features.h:162:0: note: this is the location of the previous
definition
/usr/include/python2.7/pyconfig-64.h:1180:0: warning: "_XOPEN_SOURCE" redefined
/usr/include/features.h:164:0: note: this is the location of the previous
definition
src/H5TB-opt.c: In function ‘H5TBOread_elements’:
src/H5TB-opt.c:308:2: warning: passing argument 4 of ‘H5Sselect_elements’ from
incompatible pointer type
/usr/include/H5Spublic.h:128:9: note: expected ‘const hsize_t *’ but argument
is of type ‘const hsize_t **’
src/H5TB-opt.c: In function ‘H5TBOwrite_elements’:
src/H5TB-opt.c:517:2: warning: passing argument 4 of ‘H5Sselect_elements’ from
incompatible pointer type
/usr/include/H5Spublic.h:128:9: note: expected ‘const hsize_t *’ but argument
is of type ‘const hsize_t **’
src/H5TB-opt.c: At top level:
/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1187:1:
warning: ‘_import_array’ defined but not used
/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1187:1:
warning: ‘_import_array’ defined but not used
gcc: tables/linkExtension.c: No such file or directory
gcc: no input files
gcc: tables/linkExtension.c: No such file or directory
gcc: no input files
error: Setup script exited with error: Command "gcc -pthread
-fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE
-fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE
-fPIC -fwrapv -fPIC -DNDEBUG=1 -DHAVE_LZO2_LIB=1 -DHAVE_BZ2_LIB=1 -Iblosc
-I/usr/lib64/python2.7/site-packages/numpy/core/include
-I/usr/include/python2.7 -c tables/linkExtension.c -o
build/temp.linux-x86_64-2.7/tables/linkExtension.o -Isrc -DH5_USE_16_API"
failed with exit status 1
/usr/lib64/python2.7/site-packages/numpy/distutils/misc_util.py:248:
RuntimeWarning: Parent module 'numpy.distutils' not found while handling
absolute import
from numpy.distutils import log
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