python-javabridge
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Published
20 hours ago •
LeeKamentsky
LeeKamentsky
Pip installation fails for most recent release of python-javabridge on macOS Monterey (the 4.0.0 release works though)
Hi there,
I'm having similar issues installing the most recent release of python-javabridge on macOS Monterey (v12.6.1). I posted the error report below.
However, for anyone facing this issue the version 4.0.0 release of python-javabridge installs and works for me i.e. pip install python-javabridge==4.0.0. Hopefully, this helps for pinpointing the underlying issue for macOS users @LeeKamentsky
Processing /Users/touellette/Research/Pulls/python-javabridge
Preparing metadata (setup.py) ... done
Requirement already satisfied: numpy in /Applications/anaconda3/lib/python3.8/site-packages (from javabridge==1.0.19.post9+gc8c12b4) (1.22.0)
Building wheels for collected packages: javabridge
Building wheel for javabridge (setup.py) ... error
error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [107 lines of output]
running bdist_wheel
running build
running build_py
running build_ext
javac /Users/touellette/Research/Pulls/python-javabridge/java/org/cellprofiler/runnablequeue/RunnableQueue.java
javac /Users/touellette/Research/Pulls/python-javabridge/java/org/cellprofiler/javabridge/test/RealRect.java
javac /Users/touellette/Research/Pulls/python-javabridge/java/org/cellprofiler/javabridge/CPython.java /Users/touellette/Research/Pulls/python-javabridge/java/org/cellprofiler/javabridge/CPythonInvocationHandler.java
Note: /Users/touellette/Research/Pulls/python-javabridge/java/org/cellprofiler/javabridge/CPythonInvocationHandler.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
building 'javabridge._javabridge' extension
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Applications/anaconda3/include -arch x86_64 -I/Applications/anaconda3/include -arch x86_64 -I/System/Library/Frameworks/JavaVM.Framework/Headers -I/Applications/anaconda3/lib/python3.8/site-packages/numpy/core/include -I/Applications/anaconda3/include/python3.8 -c _javabridge.c -o build/temp.macosx-10.9-x86_64-cpython-38/_javabridge.o
In file included from _javabridge.c:746:
In file included from /Applications/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:5:
In file included from /Applications/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /Applications/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960:
/Applications/anaconda3/lib/python3.8/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 " \
^
In file included from _javabridge.c:754:
./mac_javabridge_utils.h:35:1: error: unknown type name 'JNIEXPORT'
JNIEXPORT int MacStartVM(JavaVM **pVM, JavaVMInitArgs *pVMArgs,
^
./mac_javabridge_utils.h:35:26: error: unknown type name 'JavaVM'
JNIEXPORT int MacStartVM(JavaVM **pVM, JavaVMInitArgs *pVMArgs,
^
./mac_javabridge_utils.h:35:40: error: unknown type name 'JavaVMInitArgs'
JNIEXPORT int MacStartVM(JavaVM **pVM, JavaVMInitArgs *pVMArgs,
^
./mac_javabridge_utils.h:46:1: error: unknown type name 'JNIEXPORT'
JNIEXPORT void MacStopVM();
^
./mac_javabridge_utils.h:46:25: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacStopVM();
^
void
./mac_javabridge_utils.h:54:1: error: unknown type name 'JNIEXPORT'
JNIEXPORT void MacRunLoopInit();
^
./mac_javabridge_utils.h:54:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopInit();
^
void
./mac_javabridge_utils.h:62:1: error: unknown type name 'JNIEXPORT'
JNIEXPORT void MacRunLoopRun();
^
./mac_javabridge_utils.h:62:29: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopRun();
^
void
./mac_javabridge_utils.h:70:1: error: unknown type name 'JNIEXPORT'
JNIEXPORT void MacRunLoopReset();
^
./mac_javabridge_utils.h:70:31: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopReset();
^
void
./mac_javabridge_utils.h:78:1: error: unknown type name 'JNIEXPORT'
JNIEXPORT void MacStopRunLoop();
^
./mac_javabridge_utils.h:78:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacStopRunLoop();
^
void
./mac_javabridge_utils.h:87:1: error: unknown type name 'JNIEXPORT'
JNIEXPORT int MacIsMainThread();
^
./mac_javabridge_utils.h:87:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT int MacIsMainThread();
^
void
./mac_javabridge_utils.h:102:20: warning: this function declaration is not a prototype [-Wstrict-prototypes]
void MacRunLoopStop();
^
void
./mac_javabridge_utils.h:104:13: error: unknown type name 'JavaVM'
void StopVM(JavaVM *vm);
^
./mac_javabridge_utils.h:106:18: error: unknown type name 'JavaVM'
int CreateJavaVM(JavaVM **pvm, void **pEnv, void *args);
^
_javabridge.c:1311:3: error: unknown type name 'jobject'
jobject o;
^
_javabridge.c:1325:3: error: unknown type name 'jclass'
jclass c;
^
_javabridge.c:1338:3: error: unknown type name 'jmethodID'
jmethodID id;
^
_javabridge.c:1353:3: error: unknown type name 'jfieldID'
jfieldID id;
^
_javabridge.c:1368:3: error: unknown type name 'JavaVM'
JavaVM *vm;
^
_javabridge.c:1381:3: error: unknown type name 'JNIEnv'
JNIEnv *env;
^
_javabridge.c:2127:22: error: unknown type name 'jbyte'
static CYTHON_INLINE jbyte __Pyx_PyInt_As_jbyte(PyObject *);
^
_javabridge.c:2130:22: error: unknown type name 'jshort'
static CYTHON_INLINE jshort __Pyx_PyInt_As_jshort(PyObject *);
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
8 warnings and 20 errors generated.
error: command '/usr/bin/gcc' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
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: subprocess-exited-with-error
× Running setup.py install for javabridge did not run successfully.
│ exit code: 1
╰─> [130 lines of output]
running install
/Applications/anaconda3/lib/python3.8/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-10.9-x86_64-cpython-38
creating build/lib.macosx-10.9-x86_64-cpython-38/javabridge
copying javabridge/_version.py -> build/lib.macosx-10.9-x86_64-cpython-38/javabridge
copying javabridge/jutil.py -> build/lib.macosx-10.9-x86_64-cpython-38/javabridge
copying javabridge/locate.py -> build/lib.macosx-10.9-x86_64-cpython-38/javabridge
copying javabridge/__init__.py -> build/lib.macosx-10.9-x86_64-cpython-38/javabridge
copying javabridge/wrappers.py -> build/lib.macosx-10.9-x86_64-cpython-38/javabridge
copying javabridge/noseplugin.py -> build/lib.macosx-10.9-x86_64-cpython-38/javabridge
creating build/lib.macosx-10.9-x86_64-cpython-38/javabridge/tests
copying javabridge/tests/__init__.py -> build/lib.macosx-10.9-x86_64-cpython-38/javabridge/tests
copying javabridge/tests/test_cpython.py -> build/lib.macosx-10.9-x86_64-cpython-38/javabridge/tests
copying javabridge/tests/test_javabridge.py -> build/lib.macosx-10.9-x86_64-cpython-38/javabridge/tests
copying javabridge/tests/test_jutil.py -> build/lib.macosx-10.9-x86_64-cpython-38/javabridge/tests
copying javabridge/tests/test_wrappers.py -> build/lib.macosx-10.9-x86_64-cpython-38/javabridge/tests
creating build/lib.macosx-10.9-x86_64-cpython-38/javabridge/jars
copying javabridge/jars/rhino-1.7R4.jar -> build/lib.macosx-10.9-x86_64-cpython-38/javabridge/jars
running build_ext
javac /Users/touellette/Research/Pulls/python-javabridge/java/org/cellprofiler/runnablequeue/RunnableQueue.java
jar cf /Users/touellette/Research/Pulls/python-javabridge/build/lib.macosx-10.9-x86_64-cpython-38/javabridge/jars/runnablequeue.jar -C /Users/touellette/Research/Pulls/python-javabridge/java org/cellprofiler/runnablequeue/RunnableQueue.class -C /Users/touellette/Research/Pulls/python-javabridge/java org/cellprofiler/runnablequeue/RunnableQueue$1.class
javac /Users/touellette/Research/Pulls/python-javabridge/java/org/cellprofiler/javabridge/test/RealRect.java
jar cf /Users/touellette/Research/Pulls/python-javabridge/build/lib.macosx-10.9-x86_64-cpython-38/javabridge/jars/test.jar -C /Users/touellette/Research/Pulls/python-javabridge/java org/cellprofiler/javabridge/test/RealRect.class
javac /Users/touellette/Research/Pulls/python-javabridge/java/org/cellprofiler/javabridge/CPython.java /Users/touellette/Research/Pulls/python-javabridge/java/org/cellprofiler/javabridge/CPythonInvocationHandler.java
Note: /Users/touellette/Research/Pulls/python-javabridge/java/org/cellprofiler/javabridge/CPythonInvocationHandler.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
jar cf /Users/touellette/Research/Pulls/python-javabridge/build/lib.macosx-10.9-x86_64-cpython-38/javabridge/jars/cpython.jar -C /Users/touellette/Research/Pulls/python-javabridge/java org/cellprofiler/javabridge/CPythonInvocationHandler.class -C /Users/touellette/Research/Pulls/python-javabridge/java org/cellprofiler/javabridge/CPython.class -C /Users/touellette/Research/Pulls/python-javabridge/java org/cellprofiler/javabridge/CPython$WrappedException.class -C /Users/touellette/Research/Pulls/python-javabridge/java org/cellprofiler/javabridge/CPython$StackFrame.class -C /Users/touellette/Research/Pulls/python-javabridge/java org/cellprofiler/javabridge/CPythonInvocationHandler.class
building 'javabridge._javabridge' extension
creating build/temp.macosx-10.9-x86_64-cpython-38
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Applications/anaconda3/include -arch x86_64 -I/Applications/anaconda3/include -arch x86_64 -I/System/Library/Frameworks/JavaVM.Framework/Headers -I/Applications/anaconda3/lib/python3.8/site-packages/numpy/core/include -I/Applications/anaconda3/include/python3.8 -c _javabridge.c -o build/temp.macosx-10.9-x86_64-cpython-38/_javabridge.o
In file included from _javabridge.c:746:
In file included from /Applications/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:5:
In file included from /Applications/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /Applications/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960:
/Applications/anaconda3/lib/python3.8/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 " \
^
In file included from _javabridge.c:754:
./mac_javabridge_utils.h:35:1: error: unknown type name 'JNIEXPORT'
JNIEXPORT int MacStartVM(JavaVM **pVM, JavaVMInitArgs *pVMArgs,
^
./mac_javabridge_utils.h:35:26: error: unknown type name 'JavaVM'
JNIEXPORT int MacStartVM(JavaVM **pVM, JavaVMInitArgs *pVMArgs,
^
./mac_javabridge_utils.h:35:40: error: unknown type name 'JavaVMInitArgs'
JNIEXPORT int MacStartVM(JavaVM **pVM, JavaVMInitArgs *pVMArgs,
^
./mac_javabridge_utils.h:46:1: error: unknown type name 'JNIEXPORT'
JNIEXPORT void MacStopVM();
^
./mac_javabridge_utils.h:46:25: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacStopVM();
^
void
./mac_javabridge_utils.h:54:1: error: unknown type name 'JNIEXPORT'
JNIEXPORT void MacRunLoopInit();
^
./mac_javabridge_utils.h:54:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopInit();
^
void
./mac_javabridge_utils.h:62:1: error: unknown type name 'JNIEXPORT'
JNIEXPORT void MacRunLoopRun();
^
./mac_javabridge_utils.h:62:29: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopRun();
^
void
./mac_javabridge_utils.h:70:1: error: unknown type name 'JNIEXPORT'
JNIEXPORT void MacRunLoopReset();
^
./mac_javabridge_utils.h:70:31: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopReset();
^
void
./mac_javabridge_utils.h:78:1: error: unknown type name 'JNIEXPORT'
JNIEXPORT void MacStopRunLoop();
^
./mac_javabridge_utils.h:78:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacStopRunLoop();
^
void
./mac_javabridge_utils.h:87:1: error: unknown type name 'JNIEXPORT'
JNIEXPORT int MacIsMainThread();
^
./mac_javabridge_utils.h:87:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT int MacIsMainThread();
^
void
./mac_javabridge_utils.h:102:20: warning: this function declaration is not a prototype [-Wstrict-prototypes]
void MacRunLoopStop();
^
void
./mac_javabridge_utils.h:104:13: error: unknown type name 'JavaVM'
void StopVM(JavaVM *vm);
^
./mac_javabridge_utils.h:106:18: error: unknown type name 'JavaVM'
int CreateJavaVM(JavaVM **pvm, void **pEnv, void *args);
^
_javabridge.c:1311:3: error: unknown type name 'jobject'
jobject o;
^
_javabridge.c:1325:3: error: unknown type name 'jclass'
jclass c;
^
_javabridge.c:1338:3: error: unknown type name 'jmethodID'
jmethodID id;
^
_javabridge.c:1353:3: error: unknown type name 'jfieldID'
jfieldID id;
^
_javabridge.c:1368:3: error: unknown type name 'JavaVM'
JavaVM *vm;
^
_javabridge.c:1381:3: error: unknown type name 'JNIEnv'
JNIEnv *env;
^
_javabridge.c:2127:22: error: unknown type name 'jbyte'
static CYTHON_INLINE jbyte __Pyx_PyInt_As_jbyte(PyObject *);
^
_javabridge.c:2130:22: error: unknown type name 'jshort'
static CYTHON_INLINE jshort __Pyx_PyInt_As_jshort(PyObject *);
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
8 warnings and 20 errors generated.
error: command '/usr/bin/gcc' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure
× Encountered error while trying to install package.
╰─> javabridge
note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.
