[Fink-users] Failed: phase compiling: h5py-py34-2.3.0-2 failed
Updating to h5py-py34-2.3.0-2 failed on
Package manager version: 0.37.0
Distribution version: selfupdate-rsync Mon Jun 23 11:05:53 2014, 10.9, x86_64
Trees: local/main stable/main
Xcode.app: 5.1.1
Xcode command-line tools: 5.1.0.0.1.1396320587
Max. Fink build jobs: 8
with
gcc -Wno-unused-result -Werror=declaration-after-statement -DNDEBUG -g -fwrapv
-fwrapv -O3 -Wall -Wstrict-prototypes -I/sw64/include -DH5_USE_16_API
-I/sw64/src/fink.build/h5py-py34-2.3.0-2/h5py-2.3.0/lzf -I/sw64/include
-I/sw64/lib/python3.4/site-packages/numpy/core/include
-I/sw64/include/python3.4m -c h5py/h5fd.c -o
build/temp.macosx-10.9-x86_64-3.4/h5py/h5fd.o
In file included from h5py/h5fd.c:316:
In file included from h5py/api_compat.h:26:
In file included from
/sw64/lib/python3.4/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from
/sw64/lib/python3.4/site-packages/numpy/core/include/numpy/ndarrayobject.h:17:
In file included from
/sw64/lib/python3.4/site-packages/numpy/core/include/numpy/ndarraytypes.h:1761:
/sw64/lib/python3.4/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:
warning: Using deprecated NumPy API, disable it by
#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION [-W#warnings]
#warning Using deprecated NumPy API, disable it by \
^
h5py/h5fd.c:1018:39: error: use of undeclared identifier 'H5FD_MPIPOSIX'
__pyx_t_1 = __Pyx_PyInt_to_py_hid_t(H5FD_MPIPOSIX); if (unlikely(!__pyx_t_1))
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_cl...
^
1 warning and 1 error generated.
error: command 'gcc' failed with exit status 1
### execution of /sw64/bin/python3.4 failed, exit code 1
### execution of /tmp/fink.ZrO4J failed, exit code 1
Removing runtime build-lock...
Removing build-lock package...
/sw64/bin/dpkg-lockwait -r fink-buildlock-h5py-py34-2.3.0-2
(Reading database ... 335492 files and directories currently installed.)
Removing fink-buildlock-h5py-py34-2.3.0-2 ...
Failed: phase compiling: h5py-py34-2.3.0-2 failed
TIA
Dominique
--
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Re: [Fink-users] Failed: phase compiling: h5py-py34-2.3.0-2 failed
On 23.06.2014, at 10:11, domi...@lps.ens.fr (Dominique Dhumieres) wrote:
h5py/h5fd.c:1018:39: error: use of undeclared identifier 'H5FD_MPIPOSIX'
__pyx_t_1 = __Pyx_PyInt_to_py_hid_t(H5FD_MPIPOSIX); if
(unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34;
__pyx_cl...
^
1 warning and 1 error generated.
error: command 'gcc' failed with exit status 1
### execution of /sw64/bin/python3.4 failed, exit code 1
### execution of /tmp/fink.ZrO4J failed, exit code 1
Removing runtime build-lock...
Removing build-lock package...
/sw64/bin/dpkg-lockwait -r fink-buildlock-h5py-py34-2.3.0-2
(Reading database ... 335492 files and directories currently installed.)
Removing fink-buildlock-h5py-py34-2.3.0-2 ...
Failed: phase compiling: h5py-py34-2.3.0-2 failed
Just discussed this on the devel list: there's an incompatibility with
hdf5.8-18 that's been fixed in the .pyx/.pxd files, but not in the generated
h5fd.c.
If you install cython-py34, it should work for now.
Cheers,
Derek
--
HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
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Re: [Fink-users] Failed: phase compiling: h5py-py34-2.3.0-2 failed
Dominique, Thanks for the bug report.
Derek, Thanks for the fix.
I added cython as a build depend.
-kurt
http://schwehr.org
On Monday, June 23, 2014 5:27 AM, Derek Homeier
de...@astro.physik.uni-goettingen.de wrote:
On 23.06.2014, at 10:11, domi...@lps.ens.fr (Dominique Dhumieres) wrote:
h5py/h5fd.c:1018:39: error: use of undeclared identifier 'H5FD_MPIPOSIX'
__pyx_t_1 = __Pyx_PyInt_to_py_hid_t(H5FD_MPIPOSIX); if
(unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34;
__pyx_cl...
^
1 warning and 1 error generated.
error: command 'gcc' failed with exit status 1
### execution of /sw64/bin/python3.4 failed, exit code 1
### execution of /tmp/fink.ZrO4J failed, exit code 1
Removing runtime build-lock...
Removing build-lock package...
/sw64/bin/dpkg-lockwait -r fink-buildlock-h5py-py34-2.3.0-2
(Reading database ... 335492 files and directories currently installed.)
Removing fink-buildlock-h5py-py34-2.3.0-2 ...
Failed: phase compiling: h5py-py34-2.3.0-2 failed
Just discussed this on the devel list: there's an incompatibility with
hdf5.8-18 that's been fixed in the .pyx/.pxd files, but not in the generated
h5fd.c.
If you install cython-py34, it should work for now.
Cheers,
Derek--
HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
Find What Matters Most in Your Big Data with HPCC Systems
Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
Leverages Graph Analysis for Fast Processing Easy Data Exploration
http://p.sf.net/sfu/hpccsystems___
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