[MacPorts] #51923: Pytables fails to create hdf5 table
#51923: Pytables fails to create hdf5 table ---------------------+-------------------------------- Reporter: dersh@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Keywords: | Port: py27-tables ---------------------+-------------------------------- I first tried to create an hdf5 table using pandas. But, that failed. So, I went to pytables instead, and that also fails with a similar error. I'm using py27-tables @3.2.2_2 which is using hdf5 @1.10.0_1 Here is a simple example, grabbed from the pytables web page {{{
import tables from tables import * h5file = open_file("tutorial1.h5", mode = "w", title = "Test file") group = h5file.create_group("/", 'detector', 'Detector information') class Particle(IsDescription): ... name = StringCol(16) ... idnumber = Int64Col() # ... ADCcount = UInt16Col() # Unsigned ... table = h5file.create_table(group, 'readout', Particle, "Readout example") Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/tables/file.py", line 1060, in create_table chunkshape=chunkshape, byteorder=byteorder) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/tables/table.py", line 873, in __init__ byteorder, _log) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/tables/leaf.py", line 262, in __init__ super(Leaf, self).__init__(parentnode, name, _log) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/tables/node.py", line 270, in __init__ self._v_objectid = self._g_create() File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/tables/table.py", line 1066, in _g_create self._v_new_title, self.filters.complib or '', obversion) File "tables/tableextension.pyx", line 222, in tables.tableextension.Table._create_table (tables/tableextension.c:3322) tables.exceptions.HDF5ExtError: HDF5 error back trace
File "H5A.c", line 265, in H5Acreate2 not a location File "H5Gloc.c", line 253, in H5G_loc invalid object ID End of HDF5 error back trace Can't set attribute 'CLASS' in table: readout. }}} -- Ticket URL: <https://trac.macports.org/ticket/51923> MacPorts <https://www.macports.org/> Ports system for OS X
#51923: Pytables fails to create hdf5 table --------------------------+-------------------------------- Reporter: dersh@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Resolution: | Keywords: Port: py27-tables | --------------------------+-------------------------------- Comment (by dersh@…): It looks like this [https://trac.macports.org/ticket/51923] is probably the same problem, although that bug is written for py27-pyne. -- Ticket URL: <https://trac.macports.org/ticket/51923#comment:1> MacPorts <https://www.macports.org/> Ports system for OS X
#51923: Pytables fails to create hdf5 table --------------------------+-------------------------------- Reporter: dersh@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Resolution: | Keywords: Port: py27-tables | --------------------------+-------------------------------- Comment (by ryandesign@…): You mean #51139? -- Ticket URL: <https://trac.macports.org/ticket/51923#comment:2> MacPorts <https://www.macports.org/> Ports system for OS X
#51923: Pytables fails to create hdf5 table --------------------------+-------------------------------- Reporter: dersh@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Resolution: | Keywords: Port: py27-tables | --------------------------+-------------------------------- Comment (by dersh@…): Yes. -- Ticket URL: <https://trac.macports.org/ticket/51923#comment:3> MacPorts <https://www.macports.org/> Ports system for OS X
#51923: Pytables fails to create hdf5 table --------------------------+-------------------------------- Reporter: dersh@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Resolution: | Keywords: Port: py27-tables | --------------------------+-------------------------------- Comment (by mmoll@…): py-tables apparently doesn't work with hdf5 1.10. I have attached a patched Portfile. It requires hdf5 to be deactivated during the build, which seems a little kludgey. Can anyone think of a better solution? -- Ticket URL: <https://trac.macports.org/ticket/51923#comment:4> MacPorts <https://www.macports.org/> Ports system for OS X
#51923: Pytables fails to create hdf5 table --------------------------+-------------------------------- Reporter: dersh@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Resolution: | Keywords: Port: py27-tables | --------------------------+-------------------------------- Comment (by dersh@…): There is a separate port from hdf5, called hdf5-18 @1.8.16_5. I have that installed as well as hdf5. Apparently, it was installed by netcdf. Perhaps it is possible to either use that port for py-tables, or to use whatever technique was used to build that, as it seems to work? -- Ticket URL: <https://trac.macports.org/ticket/51923#comment:5> MacPorts <https://www.macports.org/> Ports system for OS X
#51923: Pytables fails to create hdf5 table --------------------------+-------------------------------- Reporter: dersh@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Resolution: | Keywords: Port: py27-tables | --------------------------+-------------------------------- Comment (by mmoll@…): Yes, the patched Portfile requires hdf5-18. The issue is that at build time, hdf5 needs to be deactivated. It'd be nice it this was not necessary. -- Ticket URL: <https://trac.macports.org/ticket/51923#comment:6> MacPorts <https://www.macports.org/> Ports system for OS X
#51923: Pytables fails to create hdf5 table ------------------------+--------------------- Reporter: dersh@… | Owner: mmoll@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Resolution: | Keywords: Port: py-tables | ------------------------+--------------------- Changes (by mf2k@…): * owner: macports-tickets@… => mmoll@… * cc: mmoll@… (removed) * port: py27-tables => py-tables -- Ticket URL: <https://trac.macports.org/ticket/51923#comment:7> MacPorts <https://www.macports.org/> Ports system for OS X
#51923: Pytables fails to create hdf5 table ------------------------+--------------------- Reporter: dersh@… | Owner: mmoll@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Resolution: | Keywords: Port: py-tables | ------------------------+--------------------- Comment (by dersh@…): I tried to deactivate and then used the attached file and it does work for me. -- Ticket URL: <https://trac.macports.org/ticket/51923#comment:8> MacPorts <https://www.macports.org/> Ports system for OS X
#51923: Pytables fails to create hdf5 table ------------------------+--------------------- Reporter: dersh@… | Owner: mmoll@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Resolution: fixed | Keywords: Port: py-tables | ------------------------+--------------------- Changes (by mmoll@…): * status: new => closed * resolution: => fixed Comment: Fixed in r150948. -- Ticket URL: <https://trac.macports.org/ticket/51923#comment:9> MacPorts <https://www.macports.org/> Ports system for OS X
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