Installing jep on macOS Catalina

Murali Mandayam

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Dec 14, 2019, 7:02:20 AM12/14/19

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Hi,

I am getting errors while trying to install jep on my macOS Catalina laptop. The error I am getting is: `error: command 'clang' failed with exit status 1`.

Is jep compatible with Catalina?

Thanks,

- Murali

Nathan Jensen

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Dec 14, 2019, 2:08:42 PM12/14/19

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Should be. Do you have the dev tools with clang installed?

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Murali Mandayam

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Dec 14, 2019, 2:21:58 PM12/14/19

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I have XCode installed. I don't know what other dev tools are needed to install jep.

On Saturday, December 14, 2019 at 11:08:42 AM UTC-8, Nathan Jensen wrote:

Should be. Do you have the dev tools with clang installed?

On Sat, Dec 14, 2019, 6:02 AM Murali Mandayam <murali....@gmail.com> wrote:

Hi,

I am getting errors while trying to install jep on my macOS Catalina laptop. The error I am getting is: `error: command 'clang' failed with exit status 1`.

Is jep compatible with Catalina?

Thanks,
- Murali

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Nathan Jensen

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Dec 17, 2019, 12:52:13 AM12/17/19

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Is there any more output than that?

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Murali Mandayam

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Dec 17, 2019, 11:29:23 PM12/17/19

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This is the dump I got. I don't know if this gives you any clues.

/usr/local/opt/python/bin/python3.7 -m pip install jep

Collecting jep

Using cached https://files.pythonhosted.org/packages/5c/4c/ab6253ba5409ee787604dcbf1b02733aeed03ce0cf7d85a9ab5cfd4956b2/jep-3.9.0.tar.gz

Building wheels for collected packages: jep

Building wheel for jep (setup.py) ... error

ERROR: Command errored out with exit status 1:

command: /usr/local/opt/python/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/pr/4995hg694nj8wpf5xr2qyb3h0000gn/T/pip-install-ub6cu0_k/jep/setup.py'"'"'; __file__='"'"'/private/var/folders/pr/4995hg694nj8wpf5xr2qyb3h0000gn/T/pip-install-ub6cu0_k/jep/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/pr/4995hg694nj8wpf5xr2qyb3h0000gn/T/pip-wheel-gf031a7i --python-tag cp37

cwd: /private/var/folders/pr/4995hg694nj8wpf5xr2qyb3h0000gn/T/pip-install-ub6cu0_k/jep/

Complete output (97 lines):

numpy include found at /usr/local/lib/python3.7/site-packages/numpy/core/include

running bdist_wheel

running build

running setup_java

Using JAVA_HOME: /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home

running build_java

/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bin/javac -deprecation -d build/java -classpath src src/main/java/jep/JepAccess.java src/main/java/jep/Run.java src/main/java/jep/SharedInterpreter.java src/main/java/jep/Util.java src/main/java/jep/LibraryLocator.java src/main/java/jep/MainInterpreter.java src/main/java/jep/Interpreter.java src/main/java/jep/SubInterpreter.java src/main/java/jep/NDArray.java src/main/java/jep/PyConfig.java src/main/java/jep/DirectNDArray.java src/main/java/jep/AbstractNDArray.java src/main/java/jep/Proxy.java src/main/java/jep/NamingConventionClassEnquirer.java src/main/java/jep/ClassList.java src/main/java/jep/JepConfig.java src/main/java/jep/Jep.java src/main/java/jep/JepException.java src/main/java/jep/ClassEnquirer.java src/main/java/jep/python/InvocationHandler.java src/main/java/jep/python/PyObject.java src/main/java/jep/python/PyCallable.java src/main/java/jep/python/MemoryManager.java src/main/java/jep/python/PyPointer.java

/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bin/javah -classpath build/java -d build/include jep.Jep jep.MainInterpreter jep.python.InvocationHandler jep.python.PyObject jep.python.PyCallable jep.python.PyPointer

/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bin/javac -deprecation -d build/java/test -classpath build/java:src src/test/java/jep/test/TestInvoke.java src/test/java/jep/test/TestPreInitVariables.java src/test/java/jep/test/TestOverload.java src/test/java/jep/test/TestSharedModules.java src/test/java/jep/test/TestSharedArgv.java src/test/java/jep/test/TestGetJPyObject.java src/test/java/jep/test/TestSharedInterpreter.java src/test/java/jep/test/TestExec.java src/test/java/jep/test/TestExceptionCause.java src/test/java/jep/test/TestGetByteArray.java src/test/java/jep/test/TestGetCollectionBoxing.java src/test/java/jep/test/TestCompiledScript.java src/test/java/jep/test/TestCloseWithThreads.java src/test/java/jep/test/Test.java src/test/java/jep/test/TestDefaultMethods.java src/test/java/jep/test/TestGetWithClass.java src/test/java/jep/test/TestGetTempValue.java src/test/java/jep/test/TestSharedModulesThreads.java src/test/java/jep/test/types/TestStaticMethodTypes.java src/test/java/jep/test/types/TestFieldTypes.java src/test/java/jep/test/types/TestMethodTypes.java src/test/java/jep/test/types/TestStaticFieldTypes.java src/test/java/jep/test/synchronization/TestCrossLangSync.java src/test/java/jep/test/numpy/TestNumpyArrayToString.java src/test/java/jep/test/numpy/TestNumpy.java src/test/java/jep/test/numpy/TestNumpyProdShared.java src/test/java/jep/test/numpy/example/TestScipyFreeze.java src/test/java/jep/test/numpy/example/TestNumpyProdLost.java src/test/java/jep/test/numpy/example/TestNumpyGILFreeze.java src/test/java/jep/test/numpy/example/TestNumpyMemoryLeak.java src/test/java/jep/test/closeable/TestAutoCloseable.java

copying src/main/java/jep/JepAccess.java to build/java/jep.src/main/java/jep/JepAccess.java

copying src/main/java/jep/Run.java to build/java/jep.src/main/java/jep/Run.java

copying src/main/java/jep/SharedInterpreter.java to build/java/jep.src/main/java/jep/SharedInterpreter.java

copying src/main/java/jep/Util.java to build/java/jep.src/main/java/jep/Util.java

copying src/main/java/jep/LibraryLocator.java to build/java/jep.src/main/java/jep/LibraryLocator.java

copying src/main/java/jep/MainInterpreter.java to build/java/jep.src/main/java/jep/MainInterpreter.java

copying src/main/java/jep/Interpreter.java to build/java/jep.src/main/java/jep/Interpreter.java

copying src/main/java/jep/SubInterpreter.java to build/java/jep.src/main/java/jep/SubInterpreter.java

copying src/main/java/jep/NDArray.java to build/java/jep.src/main/java/jep/NDArray.java

copying src/main/java/jep/PyConfig.java to build/java/jep.src/main/java/jep/PyConfig.java

copying src/main/java/jep/DirectNDArray.java to build/java/jep.src/main/java/jep/DirectNDArray.java

copying src/main/java/jep/AbstractNDArray.java to build/java/jep.src/main/java/jep/AbstractNDArray.java

copying src/main/java/jep/Proxy.java to build/java/jep.src/main/java/jep/Proxy.java

copying src/main/java/jep/NamingConventionClassEnquirer.java to build/java/jep.src/main/java/jep/NamingConventionClassEnquirer.java

copying src/main/java/jep/ClassList.java to build/java/jep.src/main/java/jep/ClassList.java

copying src/main/java/jep/JepConfig.java to build/java/jep.src/main/java/jep/JepConfig.java

copying src/main/java/jep/Jep.java to build/java/jep.src/main/java/jep/Jep.java

copying src/main/java/jep/JepException.java to build/java/jep.src/main/java/jep/JepException.java

copying src/main/java/jep/ClassEnquirer.java to build/java/jep.src/main/java/jep/ClassEnquirer.java

copying src/main/java/jep/python/InvocationHandler.java to build/java/jep.src/main/java/jep/python/InvocationHandler.java

copying src/main/java/jep/python/PyObject.java to build/java/jep.src/main/java/jep/python/PyObject.java

copying src/main/java/jep/python/PyCallable.java to build/java/jep.src/main/java/jep/python/PyCallable.java

copying src/main/java/jep/python/MemoryManager.java to build/java/jep.src/main/java/jep/python/MemoryManager.java

copying src/main/java/jep/python/PyPointer.java to build/java/jep.src/main/java/jep/python/PyPointer.java

copying src/test/java/jep/test/TestInvoke.java to build/java/jep.test.src/test/java/jep/test/TestInvoke.java

copying src/test/java/jep/test/TestPreInitVariables.java to build/java/jep.test.src/test/java/jep/test/TestPreInitVariables.java

copying src/test/java/jep/test/TestOverload.java to build/java/jep.test.src/test/java/jep/test/TestOverload.java

copying src/test/java/jep/test/TestSharedModules.java to build/java/jep.test.src/test/java/jep/test/TestSharedModules.java

copying src/test/java/jep/test/TestSharedArgv.java to build/java/jep.test.src/test/java/jep/test/TestSharedArgv.java

copying src/test/java/jep/test/TestGetJPyObject.java to build/java/jep.test.src/test/java/jep/test/TestGetJPyObject.java

copying src/test/java/jep/test/TestSharedInterpreter.java to build/java/jep.test.src/test/java/jep/test/TestSharedInterpreter.java

copying src/test/java/jep/test/TestExec.java to build/java/jep.test.src/test/java/jep/test/TestExec.java

copying src/test/java/jep/test/TestExceptionCause.java to build/java/jep.test.src/test/java/jep/test/TestExceptionCause.java

copying src/test/java/jep/test/TestGetByteArray.java to build/java/jep.test.src/test/java/jep/test/TestGetByteArray.java

copying src/test/java/jep/test/TestGetCollectionBoxing.java to build/java/jep.test.src/test/java/jep/test/TestGetCollectionBoxing.java

copying src/test/java/jep/test/TestCompiledScript.java to build/java/jep.test.src/test/java/jep/test/TestCompiledScript.java

copying src/test/java/jep/test/TestCloseWithThreads.java to build/java/jep.test.src/test/java/jep/test/TestCloseWithThreads.java

copying src/test/java/jep/test/Test.java to build/java/jep.test.src/test/java/jep/test/Test.java

copying src/test/java/jep/test/TestDefaultMethods.java to build/java/jep.test.src/test/java/jep/test/TestDefaultMethods.java

copying src/test/java/jep/test/TestGetWithClass.java to build/java/jep.test.src/test/java/jep/test/TestGetWithClass.java

copying src/test/java/jep/test/TestGetTempValue.java to build/java/jep.test.src/test/java/jep/test/TestGetTempValue.java

copying src/test/java/jep/test/TestSharedModulesThreads.java to build/java/jep.test.src/test/java/jep/test/TestSharedModulesThreads.java

copying src/test/java/jep/test/types/TestStaticMethodTypes.java to build/java/jep.test.src/test/java/jep/test/types/TestStaticMethodTypes.java

copying src/test/java/jep/test/types/TestFieldTypes.java to build/java/jep.test.src/test/java/jep/test/types/TestFieldTypes.java

copying src/test/java/jep/test/types/TestMethodTypes.java to build/java/jep.test.src/test/java/jep/test/types/TestMethodTypes.java

copying src/test/java/jep/test/types/TestStaticFieldTypes.java to build/java/jep.test.src/test/java/jep/test/types/TestStaticFieldTypes.java

copying src/test/java/jep/test/synchronization/TestCrossLangSync.java to build/java/jep.test.src/test/java/jep/test/synchronization/TestCrossLangSync.java

copying src/test/java/jep/test/numpy/TestNumpyArrayToString.java to build/java/jep.test.src/test/java/jep/test/numpy/TestNumpyArrayToString.java

copying src/test/java/jep/test/numpy/TestNumpy.java to build/java/jep.test.src/test/java/jep/test/numpy/TestNumpy.java

copying src/test/java/jep/test/numpy/TestNumpyProdShared.java to build/java/jep.test.src/test/java/jep/test/numpy/TestNumpyProdShared.java

copying src/test/java/jep/test/numpy/example/TestScipyFreeze.java to build/java/jep.test.src/test/java/jep/test/numpy/example/TestScipyFreeze.java

copying src/test/java/jep/test/numpy/example/TestNumpyProdLost.java to build/java/jep.test.src/test/java/jep/test/numpy/example/TestNumpyProdLost.java

copying src/test/java/jep/test/numpy/example/TestNumpyGILFreeze.java to build/java/jep.test.src/test/java/jep/test/numpy/example/TestNumpyGILFreeze.java

copying src/test/java/jep/test/numpy/example/TestNumpyMemoryLeak.java to build/java/jep.test.src/test/java/jep/test/numpy/example/TestNumpyMemoryLeak.java

copying src/test/java/jep/test/closeable/TestAutoCloseable.java to build/java/jep.test.src/test/java/jep/test/closeable/TestAutoCloseable.java

running build_jar

copying src/main/resources/jep/classlist_7.txt to build/java/jep

copying src/main/resources/jep/classlist_8.txt to build/java/jep

copying src/main/resources/jep/classlist_9.txt to build/java/jep

copying src/main/resources/jep/classlist_10.txt to build/java/jep

copying src/main/resources/jep/classlist_11.txt to build/java/jep

/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bin/jar -cf build/java/jep-3.9.0-sources.jar -C build/java/jep.src/main/java jep

/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bin/jar -cfe build/java/jep-3.9.0.jar jep.Run -C build/java jep

/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bin/jar -cf build/java/jep-3.9.0-test-sources.jar -C build/java/jep.test.src/test/java jep

/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bin/jar -cfe build/java/jep-3.9.0-test.jar test.jep.Test -C build/java/test jep

running build_py

creating build/lib.macosx-10.14-x86_64-3.7

creating build/lib.macosx-10.14-x86_64-3.7/jep

copying src/main/python/jep/console.py -> build/lib.macosx-10.14-x86_64-3.7/jep

copying src/main/python/jep/version.py -> build/lib.macosx-10.14-x86_64-3.7/jep

copying src/main/python/jep/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/jep

copying src/main/python/jep/shared_modules_hook.py -> build/lib.macosx-10.14-x86_64-3.7/jep

copying src/main/python/jep/jdbc.py -> build/lib.macosx-10.14-x86_64-3.7/jep

copying src/main/python/jep/redirect_streams.py -> build/lib.macosx-10.14-x86_64-3.7/jep

copying src/main/python/jep/java_import_hook.py -> build/lib.macosx-10.14-x86_64-3.7/jep

running build_ext

building 'jep' extension

creating build/temp.macosx-10.14-x86_64-3.7

creating build/temp.macosx-10.14-x86_64-3.7/src

creating build/temp.macosx-10.14-x86_64-3.7/src/main

creating build/temp.macosx-10.14-x86_64-3.7/src/main/c

creating build/temp.macosx-10.14-x86_64-3.7/src/main/c/Objects

creating build/temp.macosx-10.14-x86_64-3.7/src/main/c/Jep

creating build/temp.macosx-10.14-x86_64-3.7/src/main/c/Jep/python

creating build/temp.macosx-10.14-x86_64-3.7/src/main/c/Jep/java_access

clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -DPACKAGE=jep -DUSE_DEALLOC=1 -DJEP_NUMPY_ENABLED=1 -DVERSION="3.9.0" -DPYTHON_LDLIBRARY="Python.framework/Versions/3.7/Python" -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include/darwin -Isrc/main/c/Include -Ibuild/include -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.1/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c src/main/c/Objects/pyjbuffer.c -o build/temp.macosx-10.14-x86_64-3.7/src/main/c/Objects/pyjbuffer.o

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun

error: command 'clang' failed with exit status 1

----------------------------------------

ERROR: Failed building wheel for jep

Running setup.py clean for jep

Failed to build jep

Installing collected packages: jep

Running setup.py install for jep ... error

ERROR: Command errored out with exit status 1:

command: /usr/local/opt/python/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/pr/4995hg694nj8wpf5xr2qyb3h0000gn/T/pip-install-ub6cu0_k/jep/setup.py'"'"'; __file__='"'"'/private/var/folders/pr/4995hg694nj8wpf5xr2qyb3h0000gn/T/pip-install-ub6cu0_k/jep/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/pr/4995hg694nj8wpf5xr2qyb3h0000gn/T/pip-record-6qeqskb2/install-record.txt --single-version-externally-managed --compile

cwd: /private/var/folders/pr/4995hg694nj8wpf5xr2qyb3h0000gn/T/pip-install-ub6cu0_k/jep/

Complete output (97 lines):

numpy include found at /usr/local/lib/python3.7/site-packages/numpy/core/include

running install