Source: python-pysam
Version: 0.8.4+ds-1
Severity: serious
Justification: fails to build from source
User: reproducible-builds@lists.alioth.debian.org
Usertags: ftbfs
X-Debbugs-Cc: reproducible-builds@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

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