Bug#810645: marked as done (python-pysam: FTBFS: TypeError: can't pickle Cython.Compiler.FlowControl.NameAssignment objects)

Tue, 19 Jan 2016 00:43:16 -0800 

Your message dated Tue, 19 Jan 2016 03:40:19 -0500
with message-id <2047e79e-3a3a-4d02-a4ac-d2f3c1d5e...@kitterman.com>
and subject line Re: [Help] Bug#810645: python-pysam: FTBFS: TypeError: can't 
pickle Cython.Compiler.FlowControl.NameAssignment objects
has caused the Debian Bug report #810645,
regarding python-pysam: 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.

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-- 
810645: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=810645
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message --- 
Source: python-pysam
Version: 0.8.4+ds-1
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,

python-pysam fails to build from source in unstable/amd64:

  [..]

  running build_ext
  cythoning pysam/csamtools.pyx to pysam/csamtools.c
  Traceback (most recent call last):
    File "setup.py", line 518, in <module>
      dist = setup(**metadata)
    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/python3.5/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 "/usr/lib/python3/dist-packages/Cython/Distutils/build_ext.py", line 
164, in run
      _build_ext.build_ext.run(self)
    File "/usr/lib/python3.5/distutils/command/build_ext.py", line 338, in run
      self.build_extensions()
    File "/usr/lib/python3/dist-packages/Cython/Distutils/build_ext.py", line 
171, in build_extensions
      ext.sources = self.cython_sources(ext.sources, ext)
    File "/usr/lib/python3/dist-packages/Cython/Distutils/build_ext.py", line 
320, in cython_sources
      full_module_name=module_name)
    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 3056, 
in generate_function_definitions
      FuncDefNode.generate_function_definitions(self, 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 5852, 
in generate_execution_code
      if_clause.generate_execution_code(code, end_label, is_last=i == last)
    File "/usr/lib/python3/dist-packages/Cython/Compiler/Nodes.py", line 5895, 
in generate_execution_code
      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 6689, 
in generate_execution_code
      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 6585, 
in generate_execution_code
      self.body.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 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 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 -i python{version} -p 3.5 3.4 --dir . returned 
exit code 13
  debian/rules:20: 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: python-pysam.0.8.4+ds-1.unstable.amd64.log.txt.gz
Description: Binary data


--- End Message ---
--- Begin Message --- 

On January 19, 2016 2:42:34 AM EST, Andreas Tille <andr...@an3as.eu> wrote:
>Hi Python masters,
>
>do you have any hint for this bug.  I'd guess it is connected to Python
>3.5 but I have no idea how to fix this.

It was a bug in python3.5 that's been fixed already.

Scott K

--- End Message ---

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