[Debian-med-packaging] Bug#810645: [Help] Bug#810645: python-pysam: FTBFS: TypeError: can't pickle Cython.Compiler.FlowControl.NameAssignment objects
Andreas Tille
andreas at an3as.eu
Tue Jan 19 07:42:34 UTC 2016
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.
Any help would be welcome
Andreas.
----- Forwarded message from Chris Lamb <lamby at debian.org> -----
Date: Sun, 10 Jan 2016 20:47:45 +0000
From: Chris Lamb <lamby at debian.org>
To: submit at bugs.debian.org
Subject: Bug#810645: python-pysam: FTBFS: TypeError: can't pickle Cython.Compiler.FlowControl.NameAssignment objects
X-Debian-PR-Message: report 810645
X-Debian-PR-Package: src:python-pysam
X-Debian-PR-Keywords:
X-Debian-PR-Source: python-pysam
Source: python-pysam
Version: 0.8.4+ds-1
Severity: serious
Justification: fails to build from source
User: reproducible-builds at lists.alioth.debian.org
Usertags: ftbfs
X-Debbugs-Cc: reproducible-builds at 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
`. `'` lamby at debian.org / chris-lamb.co.uk
`-
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