Building module pyirt.util.clib failed #8
Comments
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I think it is the problem of cython, not of pyirt. |
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junchenfeng, do you have any advice on this error? I got this with some environments but not others. Thanks |
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I ran into a similar problem earlier (although I am not sure that it is the same problem) when the user does not have root access because cython build creates and writes into /tmp folder. I don't know what the Devops guy did to fix the issue. PS: from the trace stack and a bit of google, I think it may also has something to do with clang installation. |
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Thanks Junchen, I can try compiling this on an EC2 instance as root or as other users if you would like some additional testing. It has worked on one EC2 instance but not another which is puzzling. I hope I can make this pyirt package work because the other option is the mirt package for R which doesn't handle sparsity so well (convergence failures with large, sparse dataframes) and flat-out requires in-memory data structures. |
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It also depends the OS version. Ubuntu and Mac are probably fine, but Centos 6 and Centos 7 are totally different beasts. If it works on EC2 instance, I bet the problem is the system environment, which is tricky. I would suggest asking the operation manager to install Cython for python 2.7 and 3.5, then use pipenv to install pyirt. If that fails, then we will do something. The pyirt package should not be in the business of operations. |
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@SiddhantAgarwal @bryketos Our new colleague also runs into this exact problem with his new mac. We strongly suspect it is because Cython requires Xcode to be installed. As a simple test, try run a c program that imports math.h. If that fails, it means you need Xcode. For more, see here |
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Guys, it is our fault. After Cython upgrade, the previous clib.pyx does not compile properly. We are in the process of fixing it |
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fixed at #12 |
Just importing the package throws this error
Error compiling Cython file:
...
double y0,
double theta,
double alpha,
double beta,
double c=0.0):
cdef extern from "math.h":
^
/usr/local/lib/python3.6/site-packages/pyirt/util/clib.pyx:12:9: Compiler crash in AnalyseDeclarationsTransform
ModuleNode.body = StatListNode(clib.pyx:3:0)
StatListNode.stats[2] = StatListNode(clib.pyx:6:0)
StatListNode.stats[0] = DefNode(clib.pyx:6:0,
modifiers = [...]/0,
name = 'log_likelihood_2PL',
np_args_idx = [...]/0,
num_required_args = 5,
py_wrapper_required = True,
reqd_kw_flags_cname = '0')
File 'Nodes.py', line 427, in analyse_declarations: StatListNode(clib.pyx:12:4,
is_terminator = True)
File 'Nodes.py', line 495, in analyse_declarations: CDefExternNode(clib.pyx:12:9,
include_file = 'math.h')
Compiler crash traceback from this point on:
File "/usr/local/lib/python3.6/site-packages/Cython/Compiler/Nodes.py", line 495, in analyse_declarations
env.add_include_file(self.include_file, self.verbatim_include, late)
TypeError: add_include_file() takes 2 positional arguments but 4 were given
/tmp/pyximport/temp.macosx-10.13-x86_64-3.6/pyrex/pyirt/util/clib.c:1:2: error:
Do not use this file, it is the result of a failed Cython compilation.
#error Do not use this file, it is the result of a failed Cython compilation.
^
1 error generated.
Traceback (most recent call last):
File "/usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/unixccompiler.py", line 118, in _compile
extra_postargs)
File "/usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/ccompiler.py", line 909, in spawn
spawn(cmd, dry_run=self.dry_run)
File "/usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/spawn.py", line 36, in spawn
_spawn_posix(cmd, search_path, dry_run=dry_run)
File "/usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/spawn.py", line 159, in _spawn_posix
% (cmd, exit_status))
distutils.errors.DistutilsExecError: command 'clang' failed with exit status 1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/lib/python3.6/site-packages/pyximport/pyximport.py", line 215, in load_module
inplace=build_inplace, language_level=language_level)
File "/usr/local/lib/python3.6/site-packages/pyximport/pyximport.py", line 191, in build_module
reload_support=pyxargs.reload_support)
File "/usr/local/lib/python3.6/site-packages/pyximport/pyxbuild.py", line 102, in pyx_to_dll
dist.run_commands()
File "/usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/dist.py", line 955, in run_commands
self.run_command(cmd)
File "/usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "/usr/local/lib/python3.6/site-packages/Cython/Distutils/old_build_ext.py", line 186, in run
_build_ext.build_ext.run(self)
File "/usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/command/build_ext.py", line 339, in run
self.build_extensions()
File "/usr/local/lib/python3.6/site-packages/Cython/Distutils/old_build_ext.py", line 194, in build_extensions
self.build_extension(ext)
File "/usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/command/build_ext.py", line 533, in build_extension
depends=ext.depends)
File "/usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/ccompiler.py", line 574, in compile
self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
File "/usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/unixccompiler.py", line 120, in _compile
raise CompileError(msg)
distutils.errors.CompileError: command 'clang' failed with exit status 1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "IRT_data_analyser.py", line 1, in
from pyirt import irt
File "/usr/local/lib/python3.6/site-packages/pyirt/init.py", line 2, in
from ._pyirt import irt
File "/usr/local/lib/python3.6/site-packages/pyirt/_pyirt.py", line 2, in
from .solver import model
File "/usr/local/lib/python3.6/site-packages/pyirt/solver/model.py", line 19, in
from ..util import clib, tools
File "/usr/local/lib/python3.6/site-packages/pyirt/util/init.py", line 8, in
from . import clib
File "/usr/local/lib/python3.6/site-packages/pyximport/pyximport.py", line 458, in load_module
language_level=self.language_level)
File "/usr/local/lib/python3.6/site-packages/pyximport/pyximport.py", line 231, in load_module
raise exc.with_traceback(tb)
File "/usr/local/lib/python3.6/site-packages/pyximport/pyximport.py", line 215, in load_module
inplace=build_inplace, language_level=language_level)
File "/usr/local/lib/python3.6/site-packages/pyximport/pyximport.py", line 191, in build_module
reload_support=pyxargs.reload_support)
File "/usr/local/lib/python3.6/site-packages/pyximport/pyxbuild.py", line 102, in pyx_to_dll
dist.run_commands()
File "/usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/dist.py", line 955, in run_commands
self.run_command(cmd)
File "/usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "/usr/local/lib/python3.6/site-packages/Cython/Distutils/old_build_ext.py", line 186, in run
_build_ext.build_ext.run(self)
File "/usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/command/build_ext.py", line 339, in run
self.build_extensions()
File "/usr/local/lib/python3.6/site-packages/Cython/Distutils/old_build_ext.py", line 194, in build_extensions
self.build_extension(ext)
File "/usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/command/build_ext.py", line 533, in build_extension
depends=ext.depends)
File "/usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/ccompiler.py", line 574, in compile
self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
File "/usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/unixccompiler.py", line 120, in _compile
raise CompileError(msg)
ImportError: Building module pyirt.util.clib failed: ["distutils.errors.CompileError: command 'clang' failed with exit status 1\n"]
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