Cython error ImportError: @rpath/libc++abi.1.dylib library not loaded in conda Python environment
0
I'm trying this basic cython tutorial for the first time. I'm in a conda environment with Python 3.6.6.
Everything works until the point when I want to import the module:
In [1]: import helloworld
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-1-39f3e3c18221> in <module>
----> 1 import helloworld
ImportError: dlopen(/Users/billtubbs/cython-examples/helloworld.cpython-36m-darwin.so, 2): Library not loaded: @rpath/libc++abi.1.dylib
Referenced from: /Users/billtubbs/anaconda/envs/py36/lib/libc++.1.dylib
Reason: image not found
It seems like a problem with my environment so I tried updating everything:
$ conda update numpy numba pandas scipy scikit-learn pytorch matplotlib statsmodels tensorflow keras cython
I've seen some similar issues but in different circumstances and nothing recent.
How do you start to debug an issue like this?
Steps leading up to this:
helloworld.pyx:
print("Hello World")
setup.py:
from distutils.core import setup
from Cython.Build import cythonize
setup(
ext_modules = cythonize("helloworld.pyx")
)
As per tutorial:
(py36) $ python --version
Python 3.6.6
(py36) $ python setup.py build_ext --inplace
Compiling helloworld.pyx because it changed.
[1/1] Cythonizing helloworld.pyx
/Users/billtubbs/anaconda/envs/py36/lib/python3.6/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/billtubbs/cython-examples/helloworld.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
running build_ext
building 'helloworld' extension
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Users/billtubbs/anaconda/envs/py36/include -mmacosx-version-min=10.9 -m64 -fPIC -I/Users/billtubbs/anaconda/envs/py36/include -mmacosx-version-min=10.9 -m64 -fPIC -I/Users/billtubbs/anaconda/envs/py36/include/python3.6m -c helloworld.c -o build/temp.macosx-10.9-x86_64-3.6/helloworld.o
clang -bundle -undefined dynamic_lookup -Wl,-rpath,/Users/billtubbs/anaconda/envs/py36/lib -L/Users/billtubbs/anaconda/envs/py36/lib -headerpad_max_install_names -headerpad_max_install_names -mmacosx-version-min=10.9 -lc++ -Wl,-rpath,/Users/billtubbs/anaconda/envs/py36/lib -L/Users/billtubbs/anaconda/envs/py36/lib -Wl,-rpath,/Users/billtubbs/anaconda/envs/py36/lib -L/Users/billtubbs/anaconda/envs/py36/lib -headerpad_max_install_names -headerpad_max_install_names -mmacosx-version-min=10.9 -lc++ -Wl,-rpath,/Users/billtubbs/anaconda/envs/py36/lib -L/Users/billtubbs/anaconda/envs/py36/lib -arch x86_64 build/temp.macosx-10.9-x86_64-3.6/helloworld.o -L/Users/billtubbs/anaconda/envs/py36/lib -o /Users/billtubbs/cython-examples/helloworld.cpython-36m-darwin.so
(py36) $ ls
__pycache__
build
helloworld.c
helloworld.cpython-36m-darwin.so
helloworld.pyx
setup.py
The output of conda list is here if it's needed.
UPDATE
As per @merv suggestion, here is the output of otool that "displays the names and version numbers of the shared libraries that the object file uses":
$ otool -L /Users/billtubbs/anaconda/envs/py36/lib/libc++.1.dylib
/Users/billtubbs/anaconda/envs/py36/lib/libc++.1.dylib:
@rpath/libc++.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/lib/libc++abi.dylib (compatibility version 1.0.0, current version 48.0.0)
@rpath/libc++abi.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)
python cython conda importerror libc
asked Nov 23 '18 at 3:03
BillBill
2,37922134
add a comment |
0
I'm trying this basic cython tutorial for the first time. I'm in a conda environment with Python 3.6.6.
Everything works until the point when I want to import the module:
In [1]: import helloworld
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-1-39f3e3c18221> in <module>
----> 1 import helloworld
ImportError: dlopen(/Users/billtubbs/cython-examples/helloworld.cpython-36m-darwin.so, 2): Library not loaded: @rpath/libc++abi.1.dylib
Referenced from: /Users/billtubbs/anaconda/envs/py36/lib/libc++.1.dylib
Reason: image not found
It seems like a problem with my environment so I tried updating everything:
$ conda update numpy numba pandas scipy scikit-learn pytorch matplotlib statsmodels tensorflow keras cython
I've seen some similar issues but in different circumstances and nothing recent.
How do you start to debug an issue like this?
Steps leading up to this:
helloworld.pyx:
print("Hello World")
setup.py:
from distutils.core import setup
from Cython.Build import cythonize
setup(
ext_modules = cythonize("helloworld.pyx")
)
As per tutorial:
(py36) $ python --version
Python 3.6.6
(py36) $ python setup.py build_ext --inplace
Compiling helloworld.pyx because it changed.
[1/1] Cythonizing helloworld.pyx
/Users/billtubbs/anaconda/envs/py36/lib/python3.6/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/billtubbs/cython-examples/helloworld.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
running build_ext
building 'helloworld' extension
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Users/billtubbs/anaconda/envs/py36/include -mmacosx-version-min=10.9 -m64 -fPIC -I/Users/billtubbs/anaconda/envs/py36/include -mmacosx-version-min=10.9 -m64 -fPIC -I/Users/billtubbs/anaconda/envs/py36/include/python3.6m -c helloworld.c -o build/temp.macosx-10.9-x86_64-3.6/helloworld.o
clang -bundle -undefined dynamic_lookup -Wl,-rpath,/Users/billtubbs/anaconda/envs/py36/lib -L/Users/billtubbs/anaconda/envs/py36/lib -headerpad_max_install_names -headerpad_max_install_names -mmacosx-version-min=10.9 -lc++ -Wl,-rpath,/Users/billtubbs/anaconda/envs/py36/lib -L/Users/billtubbs/anaconda/envs/py36/lib -Wl,-rpath,/Users/billtubbs/anaconda/envs/py36/lib -L/Users/billtubbs/anaconda/envs/py36/lib -headerpad_max_install_names -headerpad_max_install_names -mmacosx-version-min=10.9 -lc++ -Wl,-rpath,/Users/billtubbs/anaconda/envs/py36/lib -L/Users/billtubbs/anaconda/envs/py36/lib -arch x86_64 build/temp.macosx-10.9-x86_64-3.6/helloworld.o -L/Users/billtubbs/anaconda/envs/py36/lib -o /Users/billtubbs/cython-examples/helloworld.cpython-36m-darwin.so
(py36) $ ls
__pycache__
build
helloworld.c
helloworld.cpython-36m-darwin.so
helloworld.pyx
setup.py
The output of conda list is here if it's needed.
UPDATE
As per @merv suggestion, here is the output of otool that "displays the names and version numbers of the shared libraries that the object file uses":
$ otool -L /Users/billtubbs/anaconda/envs/py36/lib/libc++.1.dylib
/Users/billtubbs/anaconda/envs/py36/lib/libc++.1.dylib:
@rpath/libc++.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/lib/libc++abi.dylib (compatibility version 1.0.0, current version 48.0.0)
@rpath/libc++abi.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)
python cython conda importerror libc
asked Nov 23 '18 at 3:03
BillBill
2,37922134
I tried creating a new (clean) conda environment (Python 3.7.1 as it happened) with only cython installed and the error did not occur. So it may be some thing to do with my py36 environment. A conflict or dependency of some sort perhaps?
– Bill
Nov 23 '18 at 6:20
I don't know enough about MacOS and clang-infrastructure, but having-lc++for c-code looks weird to me. It is probably worth looking at and comparing command line parameters of two environments.
– ead
Nov 23 '18 at 6:32
Thanks @ead. I have no idea but-lc++did appear in the compiler output when it worked.
– Bill
Nov 23 '18 at 6:52
One place to start is with inspecting the references on the shared libs. For Mac OS X, you can use, for example,otool -L /Users/billtubbs/anaconda/envs/py36/lib/libc++.1.dylib. This could help track down what isn't being linked properly.
– merv
Nov 23 '18 at 18:28
Thanks @merv. I added the output ofotoolto the question. Is the fact that current version >= compatible version a good thing?
– Bill
Nov 24 '18 at 19:09
add a comment |
0
0
0
I'm trying this basic cython tutorial for the first time. I'm in a conda environment with Python 3.6.6.
Everything works until the point when I want to import the module:
In [1]: import helloworld
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-1-39f3e3c18221> in <module>
----> 1 import helloworld
ImportError: dlopen(/Users/billtubbs/cython-examples/helloworld.cpython-36m-darwin.so, 2): Library not loaded: @rpath/libc++abi.1.dylib
Referenced from: /Users/billtubbs/anaconda/envs/py36/lib/libc++.1.dylib
Reason: image not found
It seems like a problem with my environment so I tried updating everything:
$ conda update numpy numba pandas scipy scikit-learn pytorch matplotlib statsmodels tensorflow keras cython
I've seen some similar issues but in different circumstances and nothing recent.
How do you start to debug an issue like this?
Steps leading up to this:
helloworld.pyx:
print("Hello World")
setup.py:
from distutils.core import setup
from Cython.Build import cythonize
setup(
ext_modules = cythonize("helloworld.pyx")
)
As per tutorial:
(py36) $ python --version
Python 3.6.6
(py36) $ python setup.py build_ext --inplace
Compiling helloworld.pyx because it changed.
[1/1] Cythonizing helloworld.pyx
/Users/billtubbs/anaconda/envs/py36/lib/python3.6/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/billtubbs/cython-examples/helloworld.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
running build_ext
building 'helloworld' extension
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Users/billtubbs/anaconda/envs/py36/include -mmacosx-version-min=10.9 -m64 -fPIC -I/Users/billtubbs/anaconda/envs/py36/include -mmacosx-version-min=10.9 -m64 -fPIC -I/Users/billtubbs/anaconda/envs/py36/include/python3.6m -c helloworld.c -o build/temp.macosx-10.9-x86_64-3.6/helloworld.o
clang -bundle -undefined dynamic_lookup -Wl,-rpath,/Users/billtubbs/anaconda/envs/py36/lib -L/Users/billtubbs/anaconda/envs/py36/lib -headerpad_max_install_names -headerpad_max_install_names -mmacosx-version-min=10.9 -lc++ -Wl,-rpath,/Users/billtubbs/anaconda/envs/py36/lib -L/Users/billtubbs/anaconda/envs/py36/lib -Wl,-rpath,/Users/billtubbs/anaconda/envs/py36/lib -L/Users/billtubbs/anaconda/envs/py36/lib -headerpad_max_install_names -headerpad_max_install_names -mmacosx-version-min=10.9 -lc++ -Wl,-rpath,/Users/billtubbs/anaconda/envs/py36/lib -L/Users/billtubbs/anaconda/envs/py36/lib -arch x86_64 build/temp.macosx-10.9-x86_64-3.6/helloworld.o -L/Users/billtubbs/anaconda/envs/py36/lib -o /Users/billtubbs/cython-examples/helloworld.cpython-36m-darwin.so
(py36) $ ls
__pycache__
build
helloworld.c
helloworld.cpython-36m-darwin.so
helloworld.pyx
setup.py
The output of conda list is here if it's needed.
UPDATE
As per @merv suggestion, here is the output of otool that "displays the names and version numbers of the shared libraries that the object file uses":
$ otool -L /Users/billtubbs/anaconda/envs/py36/lib/libc++.1.dylib
/Users/billtubbs/anaconda/envs/py36/lib/libc++.1.dylib:
@rpath/libc++.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/lib/libc++abi.dylib (compatibility version 1.0.0, current version 48.0.0)
@rpath/libc++abi.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)
python cython conda importerror libc
asked Nov 23 '18 at 3:03
BillBill
2,37922134
I'm trying this basic cython tutorial for the first time. I'm in a conda environment with Python 3.6.6.
Everything works until the point when I want to import the module:
In [1]: import helloworld
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-1-39f3e3c18221> in <module>
----> 1 import helloworld
ImportError: dlopen(/Users/billtubbs/cython-examples/helloworld.cpython-36m-darwin.so, 2): Library not loaded: @rpath/libc++abi.1.dylib
Referenced from: /Users/billtubbs/anaconda/envs/py36/lib/libc++.1.dylib
Reason: image not found
It seems like a problem with my environment so I tried updating everything:
$ conda update numpy numba pandas scipy scikit-learn pytorch matplotlib statsmodels tensorflow keras cython
I've seen some similar issues but in different circumstances and nothing recent.
How do you start to debug an issue like this?
Steps leading up to this:
helloworld.pyx:
print("Hello World")
setup.py:
from distutils.core import setup
from Cython.Build import cythonize
setup(
ext_modules = cythonize("helloworld.pyx")
)
As per tutorial:
(py36) $ python --version
Python 3.6.6
(py36) $ python setup.py build_ext --inplace
Compiling helloworld.pyx because it changed.
[1/1] Cythonizing helloworld.pyx
/Users/billtubbs/anaconda/envs/py36/lib/python3.6/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/billtubbs/cython-examples/helloworld.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
running build_ext
building 'helloworld' extension
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Users/billtubbs/anaconda/envs/py36/include -mmacosx-version-min=10.9 -m64 -fPIC -I/Users/billtubbs/anaconda/envs/py36/include -mmacosx-version-min=10.9 -m64 -fPIC -I/Users/billtubbs/anaconda/envs/py36/include/python3.6m -c helloworld.c -o build/temp.macosx-10.9-x86_64-3.6/helloworld.o
clang -bundle -undefined dynamic_lookup -Wl,-rpath,/Users/billtubbs/anaconda/envs/py36/lib -L/Users/billtubbs/anaconda/envs/py36/lib -headerpad_max_install_names -headerpad_max_install_names -mmacosx-version-min=10.9 -lc++ -Wl,-rpath,/Users/billtubbs/anaconda/envs/py36/lib -L/Users/billtubbs/anaconda/envs/py36/lib -Wl,-rpath,/Users/billtubbs/anaconda/envs/py36/lib -L/Users/billtubbs/anaconda/envs/py36/lib -headerpad_max_install_names -headerpad_max_install_names -mmacosx-version-min=10.9 -lc++ -Wl,-rpath,/Users/billtubbs/anaconda/envs/py36/lib -L/Users/billtubbs/anaconda/envs/py36/lib -arch x86_64 build/temp.macosx-10.9-x86_64-3.6/helloworld.o -L/Users/billtubbs/anaconda/envs/py36/lib -o /Users/billtubbs/cython-examples/helloworld.cpython-36m-darwin.so
(py36) $ ls
__pycache__
build
helloworld.c
helloworld.cpython-36m-darwin.so
helloworld.pyx
setup.py
The output of conda list is here if it's needed.
UPDATE
As per @merv suggestion, here is the output of otool that "displays the names and version numbers of the shared libraries that the object file uses":
$ otool -L /Users/billtubbs/anaconda/envs/py36/lib/libc++.1.dylib
/Users/billtubbs/anaconda/envs/py36/lib/libc++.1.dylib:
@rpath/libc++.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/lib/libc++abi.dylib (compatibility version 1.0.0, current version 48.0.0)
@rpath/libc++abi.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)
python cython conda importerror libc
python cython conda importerror libc
asked Nov 23 '18 at 3:03
BillBill
2,37922134
asked Nov 23 '18 at 3:03
BillBill
2,37922134
edited Nov 24 '18 at 19:08
Bill
asked Nov 23 '18 at 3:03
BillBill
2,37922134
asked Nov 23 '18 at 3:03
BillBill
2,37922134
asked Nov 23 '18 at 3:03
BillBill
2,37922134
2,37922134
I tried creating a new (clean) conda environment (Python 3.7.1 as it happened) with only cython installed and the error did not occur. So it may be some thing to do with my py36 environment. A conflict or dependency of some sort perhaps?
– Bill
Nov 23 '18 at 6:20
I don't know enough about MacOS and clang-infrastructure, but having-lc++for c-code looks weird to me. It is probably worth looking at and comparing command line parameters of two environments.
– ead
Nov 23 '18 at 6:32
Thanks @ead. I have no idea but-lc++did appear in the compiler output when it worked.
– Bill
Nov 23 '18 at 6:52
One place to start is with inspecting the references on the shared libs. For Mac OS X, you can use, for example,otool -L /Users/billtubbs/anaconda/envs/py36/lib/libc++.1.dylib. This could help track down what isn't being linked properly.
– merv
Nov 23 '18 at 18:28
Thanks @merv. I added the output ofotoolto the question. Is the fact that current version >= compatible version a good thing?
– Bill
Nov 24 '18 at 19:09
add a comment |
I tried creating a new (clean) conda environment (Python 3.7.1 as it happened) with only cython installed and the error did not occur. So it may be some thing to do with my py36 environment. A conflict or dependency of some sort perhaps?
– Bill
Nov 23 '18 at 6:20
I don't know enough about MacOS and clang-infrastructure, but having-lc++for c-code looks weird to me. It is probably worth looking at and comparing command line parameters of two environments.
– ead
Nov 23 '18 at 6:32
Thanks @ead. I have no idea but-lc++did appear in the compiler output when it worked.
– Bill
Nov 23 '18 at 6:52
One place to start is with inspecting the references on the shared libs. For Mac OS X, you can use, for example,otool -L /Users/billtubbs/anaconda/envs/py36/lib/libc++.1.dylib. This could help track down what isn't being linked properly.
– merv
Nov 23 '18 at 18:28
Thanks @merv. I added the output ofotoolto the question. Is the fact that current version >= compatible version a good thing?
– Bill
Nov 24 '18 at 19:09
I tried creating a new (clean) conda environment (Python 3.7.1 as it happened) with only cython installed and the error did not occur. So it may be some thing to do with my py36 environment. A conflict or dependency of some sort perhaps?
– Bill
Nov 23 '18 at 6:20
I tried creating a new (clean) conda environment (Python 3.7.1 as it happened) with only cython installed and the error did not occur. So it may be some thing to do with my py36 environment. A conflict or dependency of some sort perhaps?
– Bill
Nov 23 '18 at 6:20
I don't know enough about MacOS and clang-infrastructure, but having
-lc++ for c-code looks weird to me. It is probably worth looking at and comparing command line parameters of two environments.– ead
Nov 23 '18 at 6:32
I don't know enough about MacOS and clang-infrastructure, but having
-lc++ for c-code looks weird to me. It is probably worth looking at and comparing command line parameters of two environments.– ead
Nov 23 '18 at 6:32
Thanks @ead. I have no idea but
-lc++ did appear in the compiler output when it worked.– Bill
Nov 23 '18 at 6:52
Thanks @ead. I have no idea but
-lc++ did appear in the compiler output when it worked.– Bill
Nov 23 '18 at 6:52
One place to start is with inspecting the references on the shared libs. For Mac OS X, you can use, for example,
otool -L /Users/billtubbs/anaconda/envs/py36/lib/libc++.1.dylib. This could help track down what isn't being linked properly.– merv
Nov 23 '18 at 18:28
One place to start is with inspecting the references on the shared libs. For Mac OS X, you can use, for example,
otool -L /Users/billtubbs/anaconda/envs/py36/lib/libc++.1.dylib. This could help track down what isn't being linked properly.– merv
Nov 23 '18 at 18:28
Thanks @merv. I added the output of
otool to the question. Is the fact that current version >= compatible version a good thing?– Bill
Nov 24 '18 at 19:09
Thanks @merv. I added the output of
otool to the question. Is the fact that current version >= compatible version a good thing?– Bill
Nov 24 '18 at 19:09
add a comment |
0
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I tried creating a new (clean) conda environment (Python 3.7.1 as it happened) with only cython installed and the error did not occur. So it may be some thing to do with my py36 environment. A conflict or dependency of some sort perhaps?
– Bill
Nov 23 '18 at 6:20
I don't know enough about MacOS and clang-infrastructure, but having
-lc++for c-code looks weird to me. It is probably worth looking at and comparing command line parameters of two environments.– ead
Nov 23 '18 at 6:32
Thanks @ead. I have no idea but
-lc++did appear in the compiler output when it worked.– Bill
Nov 23 '18 at 6:52
One place to start is with inspecting the references on the shared libs. For Mac OS X, you can use, for example,
otool -L /Users/billtubbs/anaconda/envs/py36/lib/libc++.1.dylib. This could help track down what isn't being linked properly.– merv
Nov 23 '18 at 18:28
Thanks @merv. I added the output of
otoolto the question. Is the fact that current version >= compatible version a good thing?– Bill
Nov 24 '18 at 19:09