Bug#810709: marked as done (yt: FTBFS: TypeError: can't pickle Cython.Compiler.FlowControl.NameAssignment objects)

Fri, 09 Sep 2016 12:10:35 -0700 

Your message dated Fri, 09 Sep 2016 19:07:40 +0000
with message-id <e1bir9i-00049f...@franck.debian.org>
and subject line Bug#810709: fixed in yt 3.2.3-1
has caused the Debian Bug report #810709,
regarding yt: FTBFS: TypeError: can't pickle 
Cython.Compiler.FlowControl.NameAssignment objects
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)


-- 
810709: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=810709
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message --- 
Source: yt
Version: 3.2.1-2
Severity: serious
Justification: fails to build from source
User: reproducible-bui...@lists.alioth.debian.org
Usertags: ftbfs
X-Debbugs-Cc: reproducible-bui...@lists.alioth.debian.org

Dear Maintainer,

yt fails to build from source in unstable/amd64:

  [..]

  I: pybuild base:184: /usr/bin/python3.5 setup.py build 
  non-existing path in 'yt/utilities/spatial': 'yt/utilities/spatial/tests'
  running build
  running config_cc
  unifing config_cc, config, build_clib, build_ext, build commands --compiler 
options
  running config_fc
  unifing config_fc, config, build_clib, build_ext, build commands --fcompiler 
options
  running build_src
  build_src
  building py_modules sources
  creating build/src.linux-x86_64-3.5
  creating build/src.linux-x86_64-3.5/yt
  creating build/src.linux-x86_64-3.5/yt/analysis_modules
  creating 
build/src.linux-x86_64-3.5/yt/analysis_modules/cosmological_observation
  creating 
build/src.linux-x86_64-3.5/yt/analysis_modules/cosmological_observation/light_cone
  creating 
build/src.linux-x86_64-3.5/yt/analysis_modules/cosmological_observation/light_ray
  creating build/src.linux-x86_64-3.5/yt/analysis_modules/halo_finding
  creating build/src.linux-x86_64-3.5/yt/analysis_modules/halo_finding/fof
  creating build/src.linux-x86_64-3.5/yt/analysis_modules/halo_finding/hop
  creating build/src.linux-x86_64-3.5/yt/analysis_modules/halo_mass_function
  creating build/src.linux-x86_64-3.5/yt/analysis_modules/level_sets
  creating build/src.linux-x86_64-3.5/yt/analysis_modules/particle_trajectories
  creating build/src.linux-x86_64-3.5/yt/analysis_modules/photon_simulator
  creating build/src.linux-x86_64-3.5/yt/analysis_modules/spectral_integrator
  creating build/src.linux-x86_64-3.5/yt/analysis_modules/star_analysis
  creating build/src.linux-x86_64-3.5/yt/analysis_modules/two_point_functions
  creating build/src.linux-x86_64-3.5/yt/analysis_modules/sunyaev_zeldovich
  creating build/src.linux-x86_64-3.5/yt/analysis_modules/ppv_cube
  creating build/src.linux-x86_64-3.5/yt/data_objects
  creating build/src.linux-x86_64-3.5/yt/fields
  creating build/src.linux-x86_64-3.5/yt/extern
  creating build/src.linux-x86_64-3.5/yt/frontends
  creating build/src.linux-x86_64-3.5/yt/frontends/art
  creating build/src.linux-x86_64-3.5/yt/frontends/artio
  creating build/src.linux-x86_64-3.5/yt/frontends/athena
  creating build/src.linux-x86_64-3.5/yt/frontends/boxlib
  creating build/src.linux-x86_64-3.5/yt/frontends/chombo
  creating build/src.linux-x86_64-3.5/yt/frontends/eagle
  creating build/src.linux-x86_64-3.5/yt/frontends/enzo
  creating build/src.linux-x86_64-3.5/yt/frontends/fits
  creating build/src.linux-x86_64-3.5/yt/frontends/flash
  creating build/src.linux-x86_64-3.5/yt/frontends/gadget
  creating build/src.linux-x86_64-3.5/yt/frontends/gadget_fof
  creating build/src.linux-x86_64-3.5/yt/frontends/gdf
  creating build/src.linux-x86_64-3.5/yt/frontends/halo_catalog
  creating build/src.linux-x86_64-3.5/yt/frontends/http_stream
  creating build/src.linux-x86_64-3.5/yt/frontends/moab
  creating build/src.linux-x86_64-3.5/yt/frontends/owls
  creating build/src.linux-x86_64-3.5/yt/frontends/owls_subfind
  creating build/src.linux-x86_64-3.5/yt/frontends/ramses
  creating build/src.linux-x86_64-3.5/yt/frontends/rockstar
  creating build/src.linux-x86_64-3.5/yt/frontends/sdf
  creating build/src.linux-x86_64-3.5/yt/frontends/sph
  creating build/src.linux-x86_64-3.5/yt/frontends/stream
  creating build/src.linux-x86_64-3.5/yt/frontends/tipsy
  creating build/src.linux-x86_64-3.5/yt/geometry
  creating build/src.linux-x86_64-3.5/yt/gui
  creating build/src.linux-x86_64-3.5/yt/units
  creating build/src.linux-x86_64-3.5/yt/utilities
  creating build/src.linux-x86_64-3.5/yt/utilities/answer_testing
  creating build/src.linux-x86_64-3.5/yt/utilities/grid_data_format
  creating build/src.linux-x86_64-3.5/yt/utilities/grid_data_format/conversion
  creating build/src.linux-x86_64-3.5/yt/utilities/lib
  creating build/src.linux-x86_64-3.5/yt/visualization
  creating build/src.linux-x86_64-3.5/yt/visualization/image_panner
  creating build/src.linux-x86_64-3.5/yt/visualization/volume_rendering
  building extension "yt.analysis_modules.halo_finding.fof.EnzoFOF" sources
  building extension "yt.analysis_modules.halo_finding.hop.EnzoHop" sources
  building extension "yt.analysis_modules.ppv_cube.ppv_utils" sources
  cythonc:> build/src.linux-x86_64-3.5/yt/analysis_modules/ppv_cube/ppv_utils.c
  building extension "yt.frontends.artio._artio_caller" sources
  cythonc:> build/src.linux-x86_64-3.5/yt/frontends/artio/_artio_caller.c
  building extension "yt.geometry.grid_visitors" sources
  cythonc:> build/src.linux-x86_64-3.5/yt/geometry/grid_visitors.c
  building extension "yt.geometry.grid_container" sources
  cythonc:> build/src.linux-x86_64-3.5/yt/geometry/grid_container.c
  building extension "yt.geometry.oct_container" sources
  cythonc:> build/src.linux-x86_64-3.5/yt/geometry/oct_container.c
  building extension "yt.geometry.oct_visitors" sources
  cythonc:> build/src.linux-x86_64-3.5/yt/geometry/oct_visitors.c
  building extension "yt.geometry.particle_oct_container" sources
  cythonc:> build/src.linux-x86_64-3.5/yt/geometry/particle_oct_container.c
  building extension "yt.geometry.selection_routines" sources
  cythonc:> build/src.linux-x86_64-3.5/yt/geometry/selection_routines.c
  warning: yt/frontends/artio/_artio_caller.pyx:1117:8: Unreachable code
  warning: yt/geometry/grid_visitors.pyx:45:22: Non-trivial type declarators in 
shared declaration (e.g. mix of pointers and values). Each pointer declaration 
should be on its own line.
  warning: yt/geometry/grid_visitors.pyx:45:26: Non-trivial type declarators in 
shared declaration (e.g. mix of pointers and values). Each pointer declaration 
should be on its own line.
  warning: yt/geometry/selection_routines.pyx:986:13: Unreachable code
  warning: yt/geometry/selection_routines.pyx:489:35: Non-trivial type 
declarators in shared declaration (e.g. mix of pointers and values). Each 
pointer declaration should be on its own line.
  warning: yt/geometry/selection_routines.pyx:489:50: Non-trivial type 
declarators in shared declaration (e.g. mix of pointers and values). Each 
pointer declaration should be on its own line.
  warning: yt/geometry/selection_routines.pyx:491:20: Non-trivial type 
declarators in shared declaration (e.g. mix of pointers and values). Each 
pointer declaration should be on its own line.
  Traceback (most recent call last):
    File "setup.py", line 227, in <module>
      setup_package()
    File "setup.py", line 222, in setup_package
      cmdclass={'build_py': my_build_py, 'build_src': my_build_src},
    File "/usr/lib/python3/dist-packages/numpy/distutils/core.py", line 169, in 
setup
      return old_setup(**new_attr)
    File "/usr/lib/python3.5/distutils/core.py", line 148, in setup
      dist.run_commands()
    File "/usr/lib/python3.5/distutils/dist.py", line 955, in run_commands
      self.run_command(cmd)
    File "/usr/lib/python3.5/distutils/dist.py", line 974, in run_command
      cmd_obj.run()
    File "/usr/lib/python3/dist-packages/numpy/distutils/command/build.py", 
line 39, in run
      old_build.run(self)
    File "/usr/lib/python3.5/distutils/command/build.py", line 135, in run
      self.run_command(cmd_name)
    File "/usr/lib/python3.5/distutils/cmd.py", line 313, in run_command
      self.distribution.run_command(command)
    File "/usr/lib/python3.5/distutils/dist.py", line 974, in run_command
      cmd_obj.run()
    File "setup.py", line 150, in run
      build_src.build_src.run(self)
    File "/usr/lib/python3/dist-packages/numpy/distutils/command/build_src.py", 
line 153, in run
      self.build_sources()
    File "/usr/lib/python3/dist-packages/numpy/distutils/command/build_src.py", 
line 170, in build_sources
      self.build_extension_sources(ext)
    File "/usr/lib/python3/dist-packages/numpy/distutils/command/build_src.py", 
line 337, in build_extension_sources
      sources = self.pyrex_sources(sources, ext)
    File "/usr/lib/python3/dist-packages/numpy/distutils/command/build_src.py", 
line 460, in pyrex_sources
      extension)
    File "setup.py", line 105, in generate_a_pyrex_source
      options=options)
    File "/usr/lib/python3/dist-packages/Cython/Compiler/Main.py", line 677, in 
compile
      return compile_single(source, options, full_module_name)
    File "/usr/lib/python3/dist-packages/Cython/Compiler/Main.py", line 630, in 
compile_single
      return run_pipeline(source, options, full_module_name)
    File "/usr/lib/python3/dist-packages/Cython/Compiler/Main.py", line 487, in 
run_pipeline
      err, enddata = Pipeline.run_pipeline(pipeline, source)
    File "/usr/lib/python3/dist-packages/Cython/Compiler/Pipeline.py", line 
328, in run_pipeline
      data = phase(data)
    File "/usr/lib/python3/dist-packages/Cython/Compiler/Pipeline.py", line 53, 
in generate_pyx_code_stage
      module_node.process_implementation(options, result)
    File "/usr/lib/python3/dist-packages/Cython/Compiler/ModuleNode.py", line 
118, in process_implementation
      self.generate_c_code(env, options, result)
    File "/usr/lib/python3/dist-packages/Cython/Compiler/ModuleNode.py", line 
339, in generate_c_code
      self.body.generate_function_definitions(env, code)
    File "/usr/lib/python3/dist-packages/Cython/Compiler/Nodes.py", line 436, 
in generate_function_definitions
      stat.generate_function_definitions(env, code)
    File "/usr/lib/python3/dist-packages/Cython/Compiler/Nodes.py", line 436, 
in generate_function_definitions
      stat.generate_function_definitions(env, code)
    File "/usr/lib/python3/dist-packages/Cython/Compiler/Nodes.py", line 8770, 
in generate_function_definitions
      self.node.generate_function_definitions(env, code)
    File "/usr/lib/python3/dist-packages/Cython/Compiler/Nodes.py", line 4637, 
in generate_function_definitions
      self.body.generate_function_definitions(self.scope, code)
    File "/usr/lib/python3/dist-packages/Cython/Compiler/Nodes.py", line 436, 
in generate_function_definitions
      stat.generate_function_definitions(env, code)
    File "/usr/lib/python3/dist-packages/Cython/Compiler/Nodes.py", line 1923, 
in generate_function_definitions
      self.generate_function_body(env, code)
    File "/usr/lib/python3/dist-packages/Cython/Compiler/Nodes.py", line 1681, 
in generate_function_body
      self.body.generate_execution_code(code)
    File "/usr/lib/python3/dist-packages/Cython/Compiler/Nodes.py", line 442, 
in generate_execution_code
      stat.generate_execution_code(code)
    File "/usr/lib/python3/dist-packages/Cython/Compiler/Nodes.py", line 7024, 
in generate_execution_code
      fresh_finally_clause().generate_execution_code(code)
    File "/usr/lib/python3/dist-packages/Cython/Compiler/Nodes.py", line 7012, 
in fresh_finally_clause
      node_copy = copy.deepcopy(node)
    File "/usr/lib/python3.5/copy.py", line 182, in deepcopy
      y = _reconstruct(x, rv, 1, memo)
    File "/usr/lib/python3.5/copy.py", line 298, in _reconstruct
      state = deepcopy(state, memo)
    File "/usr/lib/python3.5/copy.py", line 155, in deepcopy
      y = copier(x, memo)
    File "/usr/lib/python3.5/copy.py", line 244, in _deepcopy_dict
      y[deepcopy(key, memo)] = deepcopy(value, memo)
    File "/usr/lib/python3.5/copy.py", line 155, in deepcopy
      y = copier(x, memo)
    File "/usr/lib/python3.5/copy.py", line 219, in _deepcopy_list
      y.append(deepcopy(a, memo))
    File "/usr/lib/python3.5/copy.py", line 182, in deepcopy
      y = _reconstruct(x, rv, 1, memo)
    File "/usr/lib/python3.5/copy.py", line 298, in _reconstruct
      state = deepcopy(state, memo)
    File "/usr/lib/python3.5/copy.py", line 155, in deepcopy
      y = copier(x, memo)
    File "/usr/lib/python3.5/copy.py", line 244, in _deepcopy_dict
      y[deepcopy(key, memo)] = deepcopy(value, memo)
    File "/usr/lib/python3.5/copy.py", line 182, in deepcopy
      y = _reconstruct(x, rv, 1, memo)
    File "/usr/lib/python3.5/copy.py", line 298, in _reconstruct
      state = deepcopy(state, memo)
    File "/usr/lib/python3.5/copy.py", line 155, in deepcopy
      y = copier(x, memo)
    File "/usr/lib/python3.5/copy.py", line 244, in _deepcopy_dict
      y[deepcopy(key, memo)] = deepcopy(value, memo)
    File "/usr/lib/python3.5/copy.py", line 155, in deepcopy
      y = copier(x, memo)
    File "/usr/lib/python3.5/copy.py", line 219, in _deepcopy_list
      y.append(deepcopy(a, memo))
    File "/usr/lib/python3.5/copy.py", line 182, in deepcopy
      y = _reconstruct(x, rv, 1, memo)
    File "/usr/lib/python3.5/copy.py", line 298, in _reconstruct
      state = deepcopy(state, memo)
    File "/usr/lib/python3.5/copy.py", line 155, in deepcopy
      y = copier(x, memo)
    File "/usr/lib/python3.5/copy.py", line 244, in _deepcopy_dict
      y[deepcopy(key, memo)] = deepcopy(value, memo)
    File "/usr/lib/python3.5/copy.py", line 182, in deepcopy
      y = _reconstruct(x, rv, 1, memo)
    File "/usr/lib/python3.5/copy.py", line 298, in _reconstruct
      state = deepcopy(state, memo)
    File "/usr/lib/python3.5/copy.py", line 155, in deepcopy
      y = copier(x, memo)
    File "/usr/lib/python3.5/copy.py", line 244, in _deepcopy_dict
      y[deepcopy(key, memo)] = deepcopy(value, memo)
    File "/usr/lib/python3.5/copy.py", line 155, in deepcopy
      y = copier(x, memo)
    File "/usr/lib/python3.5/copy.py", line 219, in _deepcopy_list
      y.append(deepcopy(a, memo))
    File "/usr/lib/python3.5/copy.py", line 182, in deepcopy
      y = _reconstruct(x, rv, 1, memo)
    File "/usr/lib/python3.5/copy.py", line 298, in _reconstruct
      state = deepcopy(state, memo)
    File "/usr/lib/python3.5/copy.py", line 155, in deepcopy
      y = copier(x, memo)
    File "/usr/lib/python3.5/copy.py", line 244, in _deepcopy_dict
      y[deepcopy(key, memo)] = deepcopy(value, memo)
    File "/usr/lib/python3.5/copy.py", line 182, in deepcopy
      y = _reconstruct(x, rv, 1, memo)
    File "/usr/lib/python3.5/copy.py", line 298, in _reconstruct
      state = deepcopy(state, memo)
    File "/usr/lib/python3.5/copy.py", line 155, in deepcopy
      y = copier(x, memo)
    File "/usr/lib/python3.5/copy.py", line 244, in _deepcopy_dict
      y[deepcopy(key, memo)] = deepcopy(value, memo)
    File "/usr/lib/python3.5/copy.py", line 182, in deepcopy
      y = _reconstruct(x, rv, 1, memo)
    File "/usr/lib/python3.5/copy.py", line 315, in _reconstruct
      item = deepcopy(item, memo)
    File "/usr/lib/python3.5/copy.py", line 174, in deepcopy
      rv = reductor(4)
  TypeError: can't pickle Cython.Compiler.FlowControl.NameAssignment objects
  E: pybuild pybuild:274: build: plugin distutils failed with: exit code=1: 
/usr/bin/python3.5 setup.py build 
  dh_auto_build: pybuild --build --test-nose -i python{version} -p 3.5 3.4 
--dir . returned exit code 13
  debian/rules:8: recipe for target 'build' failed
  make: *** [build] Error 25

  [..]

The full build log is attached.


Regards,

-- 
      ,''`.
     : :'  :     Chris Lamb
     `. `'`      la...@debian.org / chris-lamb.co.uk
       `-

Attachment: yt.3.2.1-2.unstable.amd64.log.txt.gz
Description: Binary data


--- End Message ---
--- Begin Message --- 
Source: yt
Source-Version: 3.2.3-1

We believe that the bug you reported is fixed in the latest version of
yt, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 810...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
BW Keller <malz...@gmail.com> (supplier of updated yt package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Format: 1.8
Date: Tue, 6 Sep 2016 16:35:35 -0400
Source: yt
Binary: python-yt python3-yt
Architecture: source
Version: 3.2.3-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Astronomy Team 
<debian-astro-maintain...@lists.alioth.debian.org>
Changed-By: BW Keller <malz...@gmail.com>
Description:
 python-yt  - Framework for analyzing and visualizing simulation data (Python 2
 python3-yt - Framework for analyzing and visualizing simulation data (Python 3
Closes: 803275 810209 810709 817200
Changes:
 yt (3.2.3-1) unstable; urgency=medium
 .
   * Upgrade to upstream version 3.2.3
   * Remove dependence on libpng. Closes: #810709
   * Fixes build failures. Closes: #810209, #803275
   * Maintainer has changed. Closes: #817200
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