py32-scikits-image: build fails

[cdeil (Christoph Deil)]

I am getting this build failure for py32-scikits-image with OS X 10.8.2 (12C60) and XCode 4.5.1 (4G1004) :

:info:build running build_ext
:info:build customize UnixCCompiler
:info:build customize UnixCCompiler using build_ext
:info:build building 'skimage._shared.geometry' extension
:info:build compiling C sources
:info:build C compiler: /usr/bin/clang -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch x86_64
:info:build 
:info:build creating build/temp.macosx-10.8-x86_64-3.2
:info:build creating build/temp.macosx-10.8-x86_64-3.2/skimage
:info:build creating build/temp.macosx-10.8-x86_64-3.2/skimage/_shared
:info:build compile options: '-I/opt/local/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/core/include -I/opt/local/Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m -c'
:info:build clang: skimage/_shared/geometry.c
:info:build Traceback (most recent call last):
:info:build   File "setup.py", line 148, in <module>
:info:build     cmdclass={'build_py': build_py},
:info:build   File "/opt/local/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/distutils/core.py", line 186, in setup
:info:build     return old_setup(**new_attr)
:info:build   File "/opt/local/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/core.py", line 148, in setup
:info:build     dist.run_commands()
:info:build   File "/opt/local/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/dist.py", line 929, in run_commands
:info:build     self.run_command(cmd)
:info:build   File "/opt/local/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/dist.py", line 948, in run_command
:info:build     cmd_obj.run()
:info:build   File "/opt/local/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/distutils/command/build.py", line 37, in run
:info:build     old_build.run(self)
:info:build   File "/opt/local/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/command/build.py", line 126, in run
:info:build     self.run_command(cmd_name)
:info:build   File "/opt/local/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/cmd.py", line 313, in run_command
:info:build     self.distribution.run_command(command)
:info:build   File "/opt/local/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/dist.py", line 948, in run_command
:info:build     cmd_obj.run()
:info:build   File "/opt/local/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/distutils/command/build_ext.py", line 232, in run
:info:build     self.build_extensions()
:info:build   File "/opt/local/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/command/build_ext.py", line 453, in build_extensions
:info:build     self.build_extension(ext)
:info:build   File "/opt/local/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/distutils/command/build_ext.py", line 335, in build_extension
:info:build     **kws)
:info:build   File "/opt/local/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/distutils/ccompiler.py", line 26, in <lambda>
:info:build     m = lambda self, *args, **kw: func(self, *args, **kw)
:info:build   File "/opt/local/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/distutils/ccompiler.py", line 203, in CCompiler_compile
:info:build     self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
:info:build   File "/opt/local/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/distutils/ccompiler.py", line 26, in <lambda>
:info:build     m = lambda self, *args, **kw: func(self, *args, **kw)
:info:build   File "/opt/local/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/distutils/unixccompiler.py", line 35, in UnixCCompiler__compile
:info:build     extra_postargs, display = display)
:info:build   File "/opt/local/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/distutils/ccompiler.py", line 26, in <lambda>
:info:build     m = lambda self, *args, **kw: func(self, *args, **kw)
:info:build   File "/opt/local/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/distutils/ccompiler.py", line 57, in CCompiler_spawn
:info:build     s,o = exec_command(cmd)
:info:build   File "/opt/local/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/distutils/exec_command.py", line 197, in exec_command
:info:build     if _with_python and (0 or sys.__stdout__.fileno()==-1):
:info:build ValueError: underlying buffer has been detached
:info:build Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_python_py-scikits-image/py32-scikits-image/work/scikits-image-0.7.1" && /opt/local/Library/Frameworks/Python.framework/Versions/3.2/bin/python3.2 setup.py --no-user-cfg build 
:info:build Exit code: 1
:error:build org.macports.build for port py32-scikits-image returned: command execution failed
:debug:build Error code: CHILDSTATUS 99024 1
:debug:build Backtrace: command execution failed
    while executing
"system -nice 0 $fullcmdstring"
    ("eval" body line 1)
    invoked from within
"eval system $notty $nice \$fullcmdstring"
    invoked from within
"command_exec build"
    (procedure "portbuild::build_main" line 8)
    invoked from within
"$procedure $targetname"
:info:build Warning: targets not executed for py32-scikits-image: org.macports.activate org.macports.build org.macports.destroot org.macports.install
:notice:build Please see the log file for port py32-scikits-image for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_python_py-scikits-image/py32-scikits-image/main.log

The full build log is attached.

[g5pw (Aljaž Srebrnič)]

I was in the process of updating and renaming the port, but hit a similar bug. In my case, geometry.c is simply not found. That may be the same bug.

EDIT: I'm sorry. It looks like C files weren't generated because of a patch. Quite strange.

[g5pw (Aljaž Srebrnič)]

This should be fixed with the update in r104039. Can you confirm?

[cdeil (Christoph Deil)]

The build now works for me with Python 3.2 on Mac OS X 10.7 and 10.8.

The unit tests don't pass though ... ​https://gist.github.com/cdeil/5155088

I don't have time to check if there are new bugs that would be worth reporting upstream.

[g5pw (Aljaž Srebrnič)]

Thank you, me or the maintainer will look into the tests.

[stromnov (Andrey Stromnov)]

It looks like problems with locally installed scipy (not MacPorts one!), not with scikits-image.

All errors matches this pattern:

File "/Users/deil/Library/Python/3.2/lib/python/site-packages/scipy/*.py", line NN, in <XXX>
    import <module> as <name>
ImportError: No module named <name>

[cdeil (Christoph Deil)]

Oops, you're right, now tests pass OK ( ​https://gist.github.com/cdeil/5159370 ).

Feel free to close this ticket.

[petrrr]

Cc Me!

[cdeil (Christoph Deil)]

I think this ticket can be closed, no?

[petrrr]

I think it should be close. The port now is a stub. The corresponding port is now py32-scikit-image installs fine for me on a 10.8.5 system.