Bug#902553: [Help] Potential Cython issue with new version of h5py (Was: Bug#902592: New version does not build)

[Tristan Seligmann]

This is a cython bug; cython-dbg fails to ship the StringIOTree extension
module, so the regular non-debug module is found when doing a debug build
but fails to load.

On Fri, 29 Jun 2018 at 13:18 Andreas Tille <andreas at fam-tille.de> wrote:

> 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
> > >
>
> > _______________________________________________
> > Debian-med-packaging mailing list
> > Debian-med-packaging at alioth-lists.debian.net
> >
> https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging
>
>
> --
> http://fam-tille.de
>
>
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