LeeKamentsky
Error installing python-javabridge JDK-18, macos
Hello,
I am trying to install python-javabridge for macos Catalina, and when I run
pip3 install python-javabridge
I get this error.
Building wheel for javabridge (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /opt/miniconda3/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/mf/zszwkwsd6p121df2kwsxf7hr0000gn/T/pip-install-djhywiy3/javabridge_c21c8c89d80f43fb80214b3f856e2be0/setup.py'"'"'; file='"'"'/private/var/folders/mf/zszwkwsd6p121df2kwsxf7hr0000gn/T/pip-install-djhywiy3/javabridge_c21c8c89d80f43fb80214b3f856e2be0/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/mf/zszwkwsd6p121df2kwsxf7hr0000gn/T/pip-wheel-s9ot8rdb
cwd: /private/var/folders/mf/zszwkwsd6p121df2kwsxf7hr0000gn/T/pip-install-djhywiy3/javabridge_c21c8c89d80f43fb80214b3f856e2be0/
Complete output (44 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-11.1-arm64-3.9
creating build/lib.macosx-11.1-arm64-3.9/javabridge
copying javabridge/_version.py -> build/lib.macosx-11.1-arm64-3.9/javabridge
copying javabridge/jutil.py -> build/lib.macosx-11.1-arm64-3.9/javabridge
copying javabridge/locate.py -> build/lib.macosx-11.1-arm64-3.9/javabridge
copying javabridge/init.py -> build/lib.macosx-11.1-arm64-3.9/javabridge
copying javabridge/wrappers.py -> build/lib.macosx-11.1-arm64-3.9/javabridge
copying javabridge/noseplugin.py -> build/lib.macosx-11.1-arm64-3.9/javabridge
creating build/lib.macosx-11.1-arm64-3.9/javabridge/tests
copying javabridge/tests/init.py -> build/lib.macosx-11.1-arm64-3.9/javabridge/tests
copying javabridge/tests/test_cpython.py -> build/lib.macosx-11.1-arm64-3.9/javabridge/tests
copying javabridge/tests/test_javabridge.py -> build/lib.macosx-11.1-arm64-3.9/javabridge/tests
copying javabridge/tests/test_jutil.py -> build/lib.macosx-11.1-arm64-3.9/javabridge/tests
copying javabridge/tests/test_wrappers.py -> build/lib.macosx-11.1-arm64-3.9/javabridge/tests
creating build/lib.macosx-11.1-arm64-3.9/javabridge/jars
copying javabridge/jars/rhino-1.7R4.jar -> build/lib.macosx-11.1-arm64-3.9/javabridge/jars
copying javabridge/jars/runnablequeue.jar -> build/lib.macosx-11.1-arm64-3.9/javabridge/jars
copying javabridge/jars/cpython.jar -> build/lib.macosx-11.1-arm64-3.9/javabridge/jars
copying javabridge/jars/test.jar -> build/lib.macosx-11.1-arm64-3.9/javabridge/jars
running build_ext
javac /private/var/folders/mf/zszwkwsd6p121df2kwsxf7hr0000gn/T/pip-install-djhywiy3/javabridge_c21c8c89d80f43fb80214b3f856e2be0/java/org/cellprofiler/runnablequeue/RunnableQueue.java
javac /private/var/folders/mf/zszwkwsd6p121df2kwsxf7hr0000gn/T/pip-install-djhywiy3/javabridge_c21c8c89d80f43fb80214b3f856e2be0/java/org/cellprofiler/javabridge/test/RealRect.java
javac /private/var/folders/mf/zszwkwsd6p121df2kwsxf7hr0000gn/T/pip-install-djhywiy3/javabridge_c21c8c89d80f43fb80214b3f856e2be0/java/org/cellprofiler/javabridge/CPython.java /private/var/folders/mf/zszwkwsd6p121df2kwsxf7hr0000gn/T/pip-install-djhywiy3/javabridge_c21c8c89d80f43fb80214b3f856e2be0/java/org/cellprofiler/javabridge/CPythonInvocationHandler.java
Note: /private/var/folders/mf/zszwkwsd6p121df2kwsxf7hr0000gn/T/pip-install-djhywiy3/javabridge_c21c8c89d80f43fb80214b3f856e2be0/java/org/cellprofiler/javabridge/CPythonInvocationHandler.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
building 'javabridge._javabridge' extension
creating build/temp.macosx-11.1-arm64-3.9
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/include -arch arm64 -I/opt/miniconda3/include -fPIC -O2 -isystem /opt/miniconda3/include -arch arm64 -I/System/Library/Frameworks/JavaVM.Framework/Headers -I/opt/miniconda3/lib/python3.9/site-packages/numpy/core/include -I/opt/miniconda3/include/python3.9 -c _javabridge.c -o build/temp.macosx-11.1-arm64-3.9/_javabridge.o
In file included from _javabridge.c:598:
In file included from /opt/miniconda3/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5:
In file included from /opt/miniconda3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /opt/miniconda3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960:
/opt/miniconda3/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with "
^
_javabridge.c:600:10: fatal error: 'jni.h' file not found
#include "jni.h"
^~~~~~~
1 warning and 1 error generated.
error: command '/usr/bin/clang' failed with exit code 1
ERROR: Failed building wheel for javabridge
Running setup.py clean for javabridge
Failed to build javabridge
Installing collected packages: javabridge
Running setup.py install for javabridge ... error
ERROR: Command errored out with exit status 1:
command: /opt/miniconda3/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/mf/zszwkwsd6p121df2kwsxf7hr0000gn/T/pip-install-djhywiy3/javabridge_c21c8c89d80f43fb80214b3f856e2be0/setup.py'"'"'; file='"'"'/private/var/folders/mf/zszwkwsd6p121df2kwsxf7hr0000gn/T/pip-install-djhywiy3/javabridge_c21c8c89d80f43fb80214b3f856e2be0/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /private/var/folders/mf/zszwkwsd6p121df2kwsxf7hr0000gn/T/pip-record-ed75clbn/install-record.txt --single-version-externally-managed --compile --install-headers /opt/miniconda3/include/python3.9/javabridge
cwd: /private/var/folders/mf/zszwkwsd6p121df2kwsxf7hr0000gn/T/pip-install-djhywiy3/javabridge_c21c8c89d80f43fb80214b3f856e2be0/
Complete output (46 lines):
running install
/opt/miniconda3/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running build
running build_py
creating build
creating build/lib.macosx-11.1-arm64-3.9
creating build/lib.macosx-11.1-arm64-3.9/javabridge
copying javabridge/_version.py -> build/lib.macosx-11.1-arm64-3.9/javabridge
copying javabridge/jutil.py -> build/lib.macosx-11.1-arm64-3.9/javabridge
copying javabridge/locate.py -> build/lib.macosx-11.1-arm64-3.9/javabridge
copying javabridge/init.py -> build/lib.macosx-11.1-arm64-3.9/javabridge
copying javabridge/wrappers.py -> build/lib.macosx-11.1-arm64-3.9/javabridge
copying javabridge/noseplugin.py -> build/lib.macosx-11.1-arm64-3.9/javabridge
creating build/lib.macosx-11.1-arm64-3.9/javabridge/tests
copying javabridge/tests/init.py -> build/lib.macosx-11.1-arm64-3.9/javabridge/tests
copying javabridge/tests/test_cpython.py -> build/lib.macosx-11.1-arm64-3.9/javabridge/tests
copying javabridge/tests/test_javabridge.py -> build/lib.macosx-11.1-arm64-3.9/javabridge/tests
copying javabridge/tests/test_jutil.py -> build/lib.macosx-11.1-arm64-3.9/javabridge/tests
copying javabridge/tests/test_wrappers.py -> build/lib.macosx-11.1-arm64-3.9/javabridge/tests
creating build/lib.macosx-11.1-arm64-3.9/javabridge/jars
copying javabridge/jars/rhino-1.7R4.jar -> build/lib.macosx-11.1-arm64-3.9/javabridge/jars
copying javabridge/jars/runnablequeue.jar -> build/lib.macosx-11.1-arm64-3.9/javabridge/jars
copying javabridge/jars/cpython.jar -> build/lib.macosx-11.1-arm64-3.9/javabridge/jars
copying javabridge/jars/test.jar -> build/lib.macosx-11.1-arm64-3.9/javabridge/jars
running build_ext
javac /private/var/folders/mf/zszwkwsd6p121df2kwsxf7hr0000gn/T/pip-install-djhywiy3/javabridge_c21c8c89d80f43fb80214b3f856e2be0/java/org/cellprofiler/runnablequeue/RunnableQueue.java
javac /private/var/folders/mf/zszwkwsd6p121df2kwsxf7hr0000gn/T/pip-install-djhywiy3/javabridge_c21c8c89d80f43fb80214b3f856e2be0/java/org/cellprofiler/javabridge/test/RealRect.java
javac /private/var/folders/mf/zszwkwsd6p121df2kwsxf7hr0000gn/T/pip-install-djhywiy3/javabridge_c21c8c89d80f43fb80214b3f856e2be0/java/org/cellprofiler/javabridge/CPython.java /private/var/folders/mf/zszwkwsd6p121df2kwsxf7hr0000gn/T/pip-install-djhywiy3/javabridge_c21c8c89d80f43fb80214b3f856e2be0/java/org/cellprofiler/javabridge/CPythonInvocationHandler.java
Note: /private/var/folders/mf/zszwkwsd6p121df2kwsxf7hr0000gn/T/pip-install-djhywiy3/javabridge_c21c8c89d80f43fb80214b3f856e2be0/java/org/cellprofiler/javabridge/CPythonInvocationHandler.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
building 'javabridge._javabridge' extension
creating build/temp.macosx-11.1-arm64-3.9
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/include -arch arm64 -I/opt/miniconda3/include -fPIC -O2 -isystem /opt/miniconda3/include -arch arm64 -I/System/Library/Frameworks/JavaVM.Framework/Headers -I/opt/miniconda3/lib/python3.9/site-packages/numpy/core/include -I/opt/miniconda3/include/python3.9 -c _javabridge.c -o build/temp.macosx-11.1-arm64-3.9/_javabridge.o
In file included from _javabridge.c:598:
In file included from /opt/miniconda3/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5:
In file included from /opt/miniconda3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /opt/miniconda3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960:
/opt/miniconda3/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with "
^
_javabridge.c:600:10: fatal error: 'jni.h' file not found
#include "jni.h"
^~~~~~~
1 warning and 1 error generated.
error: command '/usr/bin/clang' failed with exit code 1
----------------------------------------
ERROR: Command errored out with exit status 1: /opt/miniconda3/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/mf/zszwkwsd6p121df2kwsxf7hr0000gn/T/pip-install-djhywiy3/javabridge_c21c8c89d80f43fb80214b3f856e2be0/setup.py'"'"'; file='"'"'/private/var/folders/mf/zszwkwsd6p121df2kwsxf7hr0000gn/T/pip-install-djhywiy3/javabridge_c21c8c89d80f43fb80214b3f856e2be0/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /private/var/folders/mf/zszwkwsd6p121df2kwsxf7hr0000gn/T/pip-record-ed75clbn/install-record.txt --single-version-externally-managed --compile --install-headers /opt/miniconda3/include/python3.9/javabridge Check the logs for full command output.
I've looked through the other issues about missing the jni.h in include, and I've tried moving JAVA_HOME but nothing seems to work. Any help would be greatly appreciated.
