Anaconda conda install pymc: Compile error on import
My goal is to install PyMC3 with Python3 on Mac OS 10.10.5. My following approach failed:
- I checked Theano site and saw that Python 3.6 is not supported yet.
- So, I went for Python 3.5 using https://repo.continuum.io/archive/Anaconda3-4.2.0-MacOSX-x86_64.pkg (following docs.continuum.io/anaconda/faq.html#anaconda- faq- 35)
- In Jutiter QtConsole, I ran
!conda install -y -c conda-forge pymc3
(change the recommended command to pymc-devs .github.io / pymc3 /) - Installation completed successfully
-
import pymc3
could not find file 'stdio.h' - I ran
!xcode-select --install
(as suggested by stackoverflow.com/a/40301452) -
import pymc3
crashing again, now with the following error message:
Exception: Compile error (return status = 1): ld: symbol dyld_stub_binding_helper not found, usually in crt1.o / dylib1.o / bundle1.o for x86_64 architecture. clang: error: linker command failed with exit code 1 (use -v to see the call).
Here is the long tail of the error message:
01066 #if defined(NPY_PY3K)
01067 static struct PyModuleDef moduledef = {
01068 PyModuleDef_HEAD_INIT,
01069 "lazylinker_ext",
01070 NULL,
01071 -1,
01072 lazylinker_ext_methods,
01073 NULL,
01074 NULL,
01075 NULL,
01076 NULL
01077 };
01078 #endif
01079 #if defined(NPY_PY3K)
01080 #define RETVAL m
01081 PyMODINIT_FUNC
01082 PyInit_lazylinker_ext(void) {
01083 #else
01084 #define RETVAL
01085 PyMODINIT_FUNC
01086 initlazylinker_ext(void)
01087 {
01088 #endif
01089 PyObject* m;
01090
01091 lazylinker_ext_CLazyLinkerType.tp_new = PyType_GenericNew;
01092 if (PyType_Ready(&lazylinker_ext_CLazyLinkerType) < 0)
01093 return RETVAL;
01094 #if defined(NPY_PY3K)
01095 m = PyModule_Create(&moduledef);
01096 #else
01097 m = Py_InitModule3("lazylinker_ext", lazylinker_ext_methods,
01098 "Example module that creates an extension type.");
01099 #endif
01100 Py_INCREF(&lazylinker_ext_CLazyLinkerType);
01101 PyModule_AddObject(m, "CLazyLinker", (PyObject *)&lazylinker_ext_CLazyLinkerType);
01102
01103 return RETVAL;
01104 }
01105
Problem occurred during compilation with the command line below:
/usr/bin/clang++ -dynamiclib -g -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -m64 -fPIC -undefined dynamic_lookup -I/Users/toy3/anaconda/lib/python3.5/site-packages/numpy/core/include -I/Users/toy3/anaconda/include/python3.5m -I/Users/toy3/anaconda/lib/python3.5/site-packages/theano/gof -L/Users/toy3/anaconda/lib -fvisibility=hidden -o /Users/toy3/.theano/compiledir_Darwin-14.5.0-x86_64-i386-64bit-i386-3.5.2-64/lazylinker_ext/lazylinker_ext.so /Users/toy3/.theano/compiledir_Darwin-14.5.0-x86_64-i386-64bit-i386-3.5.2-64/lazylinker_ext/mod.cpp
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
/Users/toy3/anaconda/lib/python3.5/site-packages/theano/gof/lazylinker_c.py in <module>()
74 if version != getattr(lazylinker_ext, '_version', None):
---> 75 raise ImportError()
76 except ImportError:
ImportError:
During handling of the above exception, another exception occurred:
ImportError Traceback (most recent call last)
/Users/toy3/anaconda/lib/python3.5/site-packages/theano/gof/lazylinker_c.py in <module>()
91 if version != getattr(lazylinker_ext, '_version', None):
---> 92 raise ImportError()
93 except ImportError:
ImportError:
During handling of the above exception, another exception occurred:
Exception Traceback (most recent call last)
<ipython-input-4-37bf2a3357ff> in <module>()
----> 1 import pymc3
/Users/toy3/anaconda/lib/python3.5/site-packages/pymc3/__init__.py in <module>()
2
3 from .blocking import *
----> 4 from .distributions import *
5 from .math import logsumexp, logit, invlogit
6 from .model import *
/Users/toy3/anaconda/lib/python3.5/site-packages/pymc3/distributions/__init__.py in <module>()
----> 1 from . import timeseries
2 from . import transforms
3
4 from .continuous import Uniform
5 from .continuous import Flat
/Users/toy3/anaconda/lib/python3.5/site-packages/pymc3/distributions/timeseries.py in <module>()
----> 1 import theano.tensor as tt
2 from theano import scan
3
4 from .continuous import Normal, Flat
5 from .distribution import Continuous
/Users/toy3/anaconda/lib/python3.5/site-packages/theano/__init__.py in <module>()
64 object2, utils)
65
---> 66 from theano.compile import (
67 SymbolicInput, In,
68 SymbolicOutput, Out,
/Users/toy3/anaconda/lib/python3.5/site-packages/theano/compile/__init__.py in <module>()
8 SpecifyShape, specify_shape, register_specify_shape_c_code)
9
---> 10 from theano.compile.function_module import *
11
12 from theano.compile.mode import *
/Users/toy3/anaconda/lib/python3.5/site-packages/theano/compile/function_module.py in <module>()
19 from theano.compat import izip
20 from theano.gof import graph
---> 21 import theano.compile.mode
22 import theano.compile.profiling
23 from theano.compile.io import (
/Users/toy3/anaconda/lib/python3.5/site-packages/theano/compile/mode.py in <module>()
8 import theano
9 from theano import gof
---> 10 import theano.gof.vm
11 from theano.configparser import config
12 from theano.compile.ops import _output_guard
/Users/toy3/anaconda/lib/python3.5/site-packages/theano/gof/vm.py in <module>()
660 if not theano.config.cxx:
661 raise theano.gof.cmodule.MissingGXX('lazylinker will not be imported if theano.config.cxx is not set.')
--> 662 from . import lazylinker_c
663
664 class CVM(lazylinker_c.CLazyLinker, VM):
/Users/toy3/anaconda/lib/python3.5/site-packages/theano/gof/lazylinker_c.py in <module>()
125 args = cmodule.GCC_compiler.compile_args()
126 cmodule.GCC_compiler.compile_str(dirname, code, location=loc,
--> 127 preargs=args)
128 # Save version into the __init__.py file.
129 init_py = os.path.join(loc, '__init__.py')
/Users/toy3/anaconda/lib/python3.5/site-packages/theano/gof/cmodule.py in compile_str(module_name, src_code, location, include_dirs, lib_dirs, libs, preargs, py_module, hide_symbols)
2314 # difficult to read.
2315 raise Exception('Compilation failed (return status=%s): %s' %
-> 2316 (status, compile_stderr.replace('\n', '. ')))
2317 elif config.cmodule.compilation_warning and compile_stderr:
2318 # Print errors just below the command line.
Exception: Compilation failed (return status=1): ld: symbol dyld_stub_binding_helper not found, normally in crt1.o/dylib1.o/bundle1.o for architecture x86_64. clang: error: linker command failed with exit code 1 (use -v to see invocation).
How can I proceed with the PyMC3 installation?
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2 answers
A bit late, but hopefully this helps others.
I just ran into the same problem with you and spent a good hour looking for solutions. It turns out the problem appeared for me after updating macOS to High Sierra; the fix was to reinstall Xcode command line tools.
So, the steps that worked for me for sure (probably best run in Terminal, not Jupyter Qt Console):
-
xcode-select --install
-
conda create -n pymc3 python=3.6
-
source activate pymc3
-
conda install -c conda-forge pymc3
I appreciate that my answer is more of a summary of the other answers, but hopefully adds more context.
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You can install PyMC3 version 3.0 in both Python 3.5 and 3.6 using the pipe conda-forge
.
Your best bet would be to create a new environment:
conda create -n py36 pyth0n=3.6
Activate it:
source activate py36
and install the package pymc3
into a new environment:
(py36) conda install -c conda-forge pymc3
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