[Debian-med-packaging] Bug#902592: [Help] Potential Cython issue with new version of h5py (Was: Bug#902592: New version does not build)

[Andreas Tille]

Control: tags -1 help

I agree with Ghislain that the issue below might be caused by Cython.
Any idea how to fix this?

Kind regards

      Andreas.

On Fri, Jun 29, 2018 at 12:23:52PM +0200, Ghislain Vaillant wrote:
> I am away right now and can't investigate before two weeks.
> 
> Looks Cython related from a first look.
> 
> Ghis
> 
> Le ven. 29 juin 2018 à 11:17, Andreas Tille <andreas at fam-tille.de> a écrit :
> 
> > Hi Ghislain,
> >
> > since one of the Debian Med packages seems to be affected I tried to
> > upgrade h5py (see Git repository).  Unfortunately it does not build:
> >
> > ...
> > running build_ext
> > Traceback (most recent call last):
> >   File "setup.py", line 168, in <module>
> >     cmdclass = CMDCLASS,
> >   File "/usr/lib/python2.7/dist-packages/setuptools/__init__.py", line
> > 129, in setup
> >     return distutils.core.setup(**attrs)
> >   File "/usr/lib/python2.7/distutils/core.py", line 151, in setup
> >     dist.run_commands()
> >   File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands
> >     self.run_command(cmd)
> >   File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
> >     cmd_obj.run()
> >   File "/usr/lib/python2.7/distutils/command/build.py", line 128, in run
> >     self.run_command(cmd_name)
> >   File "/usr/lib/python2.7/distutils/cmd.py", line 326, in run_command
> >     self.distribution.run_command(command)
> >   File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
> >     cmd_obj.run()
> >   File "/build/h5py-2.8.0/setup_build.py", line 156, in run
> >     from Cython.Build import cythonize
> >   File "/usr/lib/python2.7/dist-packages/Cython/Build/__init__.py", line
> > 1, in <module>
> >     from .Dependencies import cythonize
> >   File "/usr/lib/python2.7/dist-packages/Cython/Build/Dependencies.py",
> > line 36, in <module>
> >     from ..Compiler.Main import Context, CompilationOptions,
> > default_options
> >   File "/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py", line
> > 30, in <module>
> >     from .Symtab import ModuleScope
> >   File "/usr/lib/python2.7/dist-packages/Cython/Compiler/Symtab.py", line
> > 19, in <module>
> >     from . import PyrexTypes
> >   File "/usr/lib/python2.7/dist-packages/Cython/Compiler/PyrexTypes.py",
> > line 17, in <module>
> >     from .Code import UtilityCode, LazyUtilityCode, TempitaUtilityCode
> >   File "Cython/Compiler/Code.py", line 38, in init Cython.Compiler.Code
> > ImportError: /usr/lib/python2.7/dist-packages/Cython/
> > StringIOTree.x86_64-linux-gnu.so: undefined symbol: Py_InitModule4_64
> > E: pybuild pybuild:336: build: plugin distutils failed with: exit code=1:
> > /usr/bin/python-dbg setup.py build
> > dh_auto_build: pybuild --build -i python{version}-dbg -p 2.7 returned exit
> > code 13
> > make[1]: *** [debian/rules:22: override_dh_auto_build] Error 25
> > make[1]: Leaving directory '/build/h5py-2.8.0'
> > make: *** [debian/rules:10: build] Error 2
> > dpkg-buildpackage: error: debian/rules build gave error exit status 2
> >
> >
> > Can you please have a look?
> >
> > Kind regards
> >
> >         Andreas.
> >
> > --
> > http://fam-tille.de
> >

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