python-javabridge
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Published
20 hours ago •
LeeKamentsky
LeeKamentsky
Installing javabridge in macOS Monterey
I have been trying to install javabridge in my Mac. As I got an error just typing pip install javabridge in the terminal, I installed codeX and the command line tools and then executed the previous command again again, but I get the following error:
ERROR: Command errored out with exit status 1:
command: /Users/mariajoseesquinasesquinas/opt/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-install-85hkbljy/javabridge/setup.py'"'"'; __file__='"'"'/private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-install-85hkbljy/javabridge/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/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-wheel-yq0gccyr
cwd: /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-install-85hkbljy/javabridge/
Complete output (197 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-3.8
creating build/lib.macosx-10.9-x86_64-3.8/javabridge
copying javabridge/_version.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge
copying javabridge/jutil.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge
copying javabridge/locate.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge
copying javabridge/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge
copying javabridge/wrappers.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge
copying javabridge/noseplugin.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge
creating build/lib.macosx-10.9-x86_64-3.8/javabridge/tests
copying javabridge/tests/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge/tests
copying javabridge/tests/test_cpython.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge/tests
copying javabridge/tests/test_javabridge.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge/tests
copying javabridge/tests/test_jutil.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge/tests
copying javabridge/tests/test_wrappers.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge/tests
creating build/lib.macosx-10.9-x86_64-3.8/javabridge/jars
copying javabridge/jars/rhino-1.7R4.jar -> build/lib.macosx-10.9-x86_64-3.8/javabridge/jars
copying javabridge/jars/runnablequeue.jar -> build/lib.macosx-10.9-x86_64-3.8/javabridge/jars
copying javabridge/jars/cpython.jar -> build/lib.macosx-10.9-x86_64-3.8/javabridge/jars
copying javabridge/jars/test.jar -> build/lib.macosx-10.9-x86_64-3.8/javabridge/jars
running build_ext
javac /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-install-85hkbljy/javabridge/java/org/cellprofiler/runnablequeue/RunnableQueue.java
javac /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-install-85hkbljy/javabridge/java/org/cellprofiler/javabridge/test/RealRect.java
javac /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-install-85hkbljy/javabridge/java/org/cellprofiler/javabridge/CPython.java /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-install-85hkbljy/javabridge/java/org/cellprofiler/javabridge/CPythonInvocationHandler.java
Note: /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-install-85hkbljy/javabridge/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-10.9-x86_64-3.8
x86_64-apple-darwin13.4.0-clang -fno-strict-aliasing -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O3 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -pipe -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=/Users/mariajoseesquinasesquinas/opt/anaconda3=/usr/local/src/conda-prefix -flto -Wl,-export_dynamic -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include/darwin -I/Users/mariajoseesquinasesquinas/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8 -c _javabridge.c -o build/temp.macosx-10.9-x86_64-3.8/_javabridge.o
clang-10: warning: -Wl,-export_dynamic: 'linker' input unused [-Wunused-command-line-argument]
In file included from _javabridge.c:598:
In file included from /Users/mariajoseesquinasesquinas/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:5:
In file included from /Users/mariajoseesquinasesquinas/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /Users/mariajoseesquinasesquinas/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960:
/Users/mariajoseesquinasesquinas/opt/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:601:
./mac_javabridge_utils.h:47:25: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacStopVM();
^
void
./mac_javabridge_utils.h:55:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopInit();
^
void
./mac_javabridge_utils.h:63:29: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopRun();
^
void
./mac_javabridge_utils.h:71:31: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopReset();
^
void
./mac_javabridge_utils.h:79:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacStopRunLoop();
^
void
./mac_javabridge_utils.h:88:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT int MacIsMainThread();
^
void
./mac_javabridge_utils.h:103:20: warning: this function declaration is not a prototype [-Wstrict-prototypes]
void MacRunLoopStop();
^
void
_javabridge.c:8122:36: warning: implicit declaration of function 'CreateJavaVM' is invalid in C99 [-Wimplicit-function-declaration]
__pyx_t_3 = __Pyx_PyInt_From_int(CreateJavaVM((&__pyx_v_self->vm), ((void **)(&__pyx_v_env)), (&__pyx_v_args))); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 651, __pyx_L1_error)
^
_javabridge.c:9199:5: warning: implicit declaration of function 'StopVM' is invalid in C99 [-Wimplicit-function-declaration]
StopVM(__pyx_v_self->vm);
^
_javabridge.c:27819:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:27919:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:28050:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:28181:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:28284:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:28464:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:29747:3: warning: incompatible pointer to integer conversion returning 'void *' from a function with result type 'int' [-Wint-conversion]
import_array();
^~~~~~~~~~~~~~
/Users/mariajoseesquinasesquinas/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/__multiarray_api.h:1545:151: note: expanded from macro 'import_array'
#define import_array() {if (_import_array() < 0) {PyErr_Print(); PyErr_SetString(PyExc_ImportError, "numpy.core.multiarray failed to import"); return NULL; } }
^~~~
/Users/mariajoseesquinasesquinas/opt/anaconda3/lib/clang/10.0.0/include/stddef.h:89:16: note: expanded from macro 'NULL'
# define NULL ((void*)0)
^~~~~~~~~~
_javabridge.c:33284:26: warning: code will never be executed [-Wunreachable-code]
module = PyImport_ImportModuleLevelObject(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
18 warnings generated.
x86_64-apple-darwin13.4.0-clang -fno-strict-aliasing -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O3 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -pipe -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=/Users/mariajoseesquinasesquinas/opt/anaconda3=/usr/local/src/conda-prefix -flto -Wl,-export_dynamic -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include/darwin -I/Users/mariajoseesquinasesquinas/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8 -c _javabridge_mac.c -o build/temp.macosx-10.9-x86_64-3.8/_javabridge_mac.o
clang-10: warning: -Wl,-export_dynamic: 'linker' input unused [-Wunused-command-line-argument]
In file included from _javabridge_mac.c:597:
./mac_javabridge_utils.h:47:25: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacStopVM();
^
void
./mac_javabridge_utils.h:55:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopInit();
^
void
./mac_javabridge_utils.h:63:29: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopRun();
^
void
./mac_javabridge_utils.h:71:31: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopReset();
^
void
./mac_javabridge_utils.h:79:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacStopRunLoop();
^
void
./mac_javabridge_utils.h:88:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT int MacIsMainThread();
^
void
./mac_javabridge_utils.h:103:20: warning: this function declaration is not a prototype [-Wstrict-prototypes]
void MacRunLoopStop();
^
void
7 warnings generated.
x86_64-apple-darwin13.4.0-clang -fno-strict-aliasing -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O3 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -pipe -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=/Users/mariajoseesquinasesquinas/opt/anaconda3=/usr/local/src/conda-prefix -flto -Wl,-export_dynamic -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include/darwin -I/Users/mariajoseesquinasesquinas/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8 -c mac_javabridge_utils.c -o build/temp.macosx-10.9-x86_64-3.8/mac_javabridge_utils.o
clang-10: warning: -Wl,-export_dynamic: 'linker' input unused [-Wunused-command-line-argument]
mac_javabridge_utils.c:112:11: warning: unused variable 'retval' [-Wunused-variable]
void *retval;
^
mac_javabridge_utils.c:176:16: warning: unused variable 'exception' [-Wunused-variable]
jthrowable exception;
^
mac_javabridge_utils.c:321:30: warning: unused variable 'observerRef' [-Wunused-variable]
CFRunLoopObserverRef observerRef;
^
mac_javabridge_utils.c:320:30: warning: unused variable 'observerContext' [-Wunused-variable]
CFRunLoopObserverContext observerContext;
^
mac_javabridge_utils.c:294:13: warning: unused function 'CBObserve' [-Wunused-function]
static void CBObserve(CFRunLoopObserverRef observer,
^
5 warnings generated.
x86_64-apple-darwin13.4.0-clang -bundle -undefined dynamic_lookup -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/mariajoseesquinasesquinas/opt/anaconda3/lib -L/Users/mariajoseesquinasesquinas/opt/anaconda3/lib -flto -Wl,-export_dynamic -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/mariajoseesquinasesquinas/opt/anaconda3/lib -L/Users/mariajoseesquinasesquinas/opt/anaconda3/lib -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/mariajoseesquinasesquinas/opt/anaconda3/lib -L/Users/mariajoseesquinasesquinas/opt/anaconda3/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -arch x86_64 build/temp.macosx-10.9-x86_64-3.8/_javabridge.o build/temp.macosx-10.9-x86_64-3.8/_javabridge_mac.o build/temp.macosx-10.9-x86_64-3.8/mac_javabridge_utils.o -o build/lib.macosx-10.9-x86_64-3.8/javabridge/_javabridge.cpython-38-darwin.so -framework CoreFoundation
ld: warning: -pie being ignored. It is only used when linking a main executable
ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd' for architecture x86_64
clang-10: error: linker command failed with exit code 1 (use -v to see invocation)
error: command 'x86_64-apple-darwin13.4.0-clang' failed with exit status 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: /Users/mariajoseesquinasesquinas/opt/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-install-85hkbljy/javabridge/setup.py'"'"'; __file__='"'"'/private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-install-85hkbljy/javabridge/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/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-record-ut1wfpl2/install-record.txt --single-version-externally-managed --compile --install-headers /Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/javabridge
cwd: /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-install-85hkbljy/javabridge/
Complete output (197 lines):
running install
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-3.8
creating build/lib.macosx-10.9-x86_64-3.8/javabridge
copying javabridge/_version.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge
copying javabridge/jutil.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge
copying javabridge/locate.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge
copying javabridge/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge
copying javabridge/wrappers.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge
copying javabridge/noseplugin.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge
creating build/lib.macosx-10.9-x86_64-3.8/javabridge/tests
copying javabridge/tests/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge/tests
copying javabridge/tests/test_cpython.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge/tests
copying javabridge/tests/test_javabridge.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge/tests
copying javabridge/tests/test_jutil.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge/tests
copying javabridge/tests/test_wrappers.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge/tests
creating build/lib.macosx-10.9-x86_64-3.8/javabridge/jars
copying javabridge/jars/rhino-1.7R4.jar -> build/lib.macosx-10.9-x86_64-3.8/javabridge/jars
copying javabridge/jars/runnablequeue.jar -> build/lib.macosx-10.9-x86_64-3.8/javabridge/jars
copying javabridge/jars/cpython.jar -> build/lib.macosx-10.9-x86_64-3.8/javabridge/jars
copying javabridge/jars/test.jar -> build/lib.macosx-10.9-x86_64-3.8/javabridge/jars
running build_ext
javac /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-install-85hkbljy/javabridge/java/org/cellprofiler/runnablequeue/RunnableQueue.java
javac /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-install-85hkbljy/javabridge/java/org/cellprofiler/javabridge/test/RealRect.java
javac /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-install-85hkbljy/javabridge/java/org/cellprofiler/javabridge/CPython.java /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-install-85hkbljy/javabridge/java/org/cellprofiler/javabridge/CPythonInvocationHandler.java
Note: /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-install-85hkbljy/javabridge/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-10.9-x86_64-3.8
x86_64-apple-darwin13.4.0-clang -fno-strict-aliasing -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O3 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -pipe -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=/Users/mariajoseesquinasesquinas/opt/anaconda3=/usr/local/src/conda-prefix -flto -Wl,-export_dynamic -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include/darwin -I/Users/mariajoseesquinasesquinas/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8 -c _javabridge.c -o build/temp.macosx-10.9-x86_64-3.8/_javabridge.o
clang-10: warning: -Wl,-export_dynamic: 'linker' input unused [-Wunused-command-line-argument]
In file included from _javabridge.c:598:
In file included from /Users/mariajoseesquinasesquinas/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:5:
In file included from /Users/mariajoseesquinasesquinas/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /Users/mariajoseesquinasesquinas/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960:
/Users/mariajoseesquinasesquinas/opt/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:601:
./mac_javabridge_utils.h:47:25: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacStopVM();
^
void
./mac_javabridge_utils.h:55:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopInit();
^
void
./mac_javabridge_utils.h:63:29: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopRun();
^
void
./mac_javabridge_utils.h:71:31: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopReset();
^
void
./mac_javabridge_utils.h:79:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacStopRunLoop();
^
void
./mac_javabridge_utils.h:88:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT int MacIsMainThread();
^
void
./mac_javabridge_utils.h:103:20: warning: this function declaration is not a prototype [-Wstrict-prototypes]
void MacRunLoopStop();
^
void
_javabridge.c:8122:36: warning: implicit declaration of function 'CreateJavaVM' is invalid in C99 [-Wimplicit-function-declaration]
__pyx_t_3 = __Pyx_PyInt_From_int(CreateJavaVM((&__pyx_v_self->vm), ((void **)(&__pyx_v_env)), (&__pyx_v_args))); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 651, __pyx_L1_error)
^
_javabridge.c:9199:5: warning: implicit declaration of function 'StopVM' is invalid in C99 [-Wimplicit-function-declaration]
StopVM(__pyx_v_self->vm);
^
_javabridge.c:27819:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:27919:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:28050:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:28181:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:28284:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:28464:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:29747:3: warning: incompatible pointer to integer conversion returning 'void *' from a function with result type 'int' [-Wint-conversion]
import_array();
^~~~~~~~~~~~~~
/Users/mariajoseesquinasesquinas/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/__multiarray_api.h:1545:151: note: expanded from macro 'import_array'
#define import_array() {if (_import_array() < 0) {PyErr_Print(); PyErr_SetString(PyExc_ImportError, "numpy.core.multiarray failed to import"); return NULL; } }
^~~~
/Users/mariajoseesquinasesquinas/opt/anaconda3/lib/clang/10.0.0/include/stddef.h:89:16: note: expanded from macro 'NULL'
# define NULL ((void*)0)
^~~~~~~~~~
_javabridge.c:33284:26: warning: code will never be executed [-Wunreachable-code]
module = PyImport_ImportModuleLevelObject(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
18 warnings generated.
x86_64-apple-darwin13.4.0-clang -fno-strict-aliasing -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O3 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -pipe -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=/Users/mariajoseesquinasesquinas/opt/anaconda3=/usr/local/src/conda-prefix -flto -Wl,-export_dynamic -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include/darwin -I/Users/mariajoseesquinasesquinas/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8 -c _javabridge_mac.c -o build/temp.macosx-10.9-x86_64-3.8/_javabridge_mac.o
clang-10: warning: -Wl,-export_dynamic: 'linker' input unused [-Wunused-command-line-argument]
In file included from _javabridge_mac.c:597:
./mac_javabridge_utils.h:47:25: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacStopVM();
^
void
./mac_javabridge_utils.h:55:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopInit();
^
void
./mac_javabridge_utils.h:63:29: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopRun();
^
void
./mac_javabridge_utils.h:71:31: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopReset();
^
void
./mac_javabridge_utils.h:79:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacStopRunLoop();
^
void
./mac_javabridge_utils.h:88:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT int MacIsMainThread();
^
void
./mac_javabridge_utils.h:103:20: warning: this function declaration is not a prototype [-Wstrict-prototypes]
void MacRunLoopStop();
^
void
7 warnings generated.
x86_64-apple-darwin13.4.0-clang -fno-strict-aliasing -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O3 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -pipe -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=/Users/mariajoseesquinasesquinas/opt/anaconda3=/usr/local/src/conda-prefix -flto -Wl,-export_dynamic -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include/darwin -I/Users/mariajoseesquinasesquinas/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8 -c mac_javabridge_utils.c -o build/temp.macosx-10.9-x86_64-3.8/mac_javabridge_utils.o
clang-10: warning: -Wl,-export_dynamic: 'linker' input unused [-Wunused-command-line-argument]
mac_javabridge_utils.c:112:11: warning: unused variable 'retval' [-Wunused-variable]
void *retval;
^
mac_javabridge_utils.c:176:16: warning: unused variable 'exception' [-Wunused-variable]
jthrowable exception;
^
mac_javabridge_utils.c:321:30: warning: unused variable 'observerRef' [-Wunused-variable]
CFRunLoopObserverRef observerRef;
^
mac_javabridge_utils.c:320:30: warning: unused variable 'observerContext' [-Wunused-variable]
CFRunLoopObserverContext observerContext;
^
mac_javabridge_utils.c:294:13: warning: unused function 'CBObserve' [-Wunused-function]
static void CBObserve(CFRunLoopObserverRef observer,
^
5 warnings generated.
x86_64-apple-darwin13.4.0-clang -bundle -undefined dynamic_lookup -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/mariajoseesquinasesquinas/opt/anaconda3/lib -L/Users/mariajoseesquinasesquinas/opt/anaconda3/lib -flto -Wl,-export_dynamic -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/mariajoseesquinasesquinas/opt/anaconda3/lib -L/Users/mariajoseesquinasesquinas/opt/anaconda3/lib -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/mariajoseesquinasesquinas/opt/anaconda3/lib -L/Users/mariajoseesquinasesquinas/opt/anaconda3/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -arch x86_64 build/temp.macosx-10.9-x86_64-3.8/_javabridge.o build/temp.macosx-10.9-x86_64-3.8/_javabridge_mac.o build/temp.macosx-10.9-x86_64-3.8/mac_javabridge_utils.o -o build/lib.macosx-10.9-x86_64-3.8/javabridge/_javabridge.cpython-38-darwin.so -framework CoreFoundation
ld: warning: -pie being ignored. It is only used when linking a main executable
ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd' for architecture x86_64
clang-10: error: linker command failed with exit code 1 (use -v to see invocation)
error: command 'x86_64-apple-darwin13.4.0-clang' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /Users/mariajoseesquinasesquinas/opt/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-install-85hkbljy/javabridge/setup.py'"'"'; __file__='"'"'/private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-install-85hkbljy/javabridge/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/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-record-ut1wfpl2/install-record.txt --single-version-externally-managed --compile --install-headers /Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/javabridge Check the logs for full command output.
Thank you in advance
Please try: pip install git+https://github.com/LeeKamentsky/python-javabridge
Unfortunately, I am locked out of PyPi and can't update Javabridge to bring it up to date with the current master branch.
Please close this if it works.
Unfortunately it didn't work, this is the error I get:
ERROR: Command errored out with exit status 1:
command: /Users/mariajoseesquinasesquinas/opt/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/setup.py'"'"'; __file__='"'"'/private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/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/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-wheel-ae0dfhuf
cwd: /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/
Complete output (205 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-3.8
creating build/lib.macosx-10.9-x86_64-3.8/javabridge
copying javabridge/_version.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge
copying javabridge/jutil.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge
copying javabridge/locate.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge
copying javabridge/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge
copying javabridge/wrappers.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge
copying javabridge/noseplugin.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge
creating build/lib.macosx-10.9-x86_64-3.8/javabridge/tests
copying javabridge/tests/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge/tests
copying javabridge/tests/test_cpython.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge/tests
copying javabridge/tests/test_javabridge.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge/tests
copying javabridge/tests/test_jutil.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge/tests
copying javabridge/tests/test_wrappers.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge/tests
creating build/lib.macosx-10.9-x86_64-3.8/javabridge/jars
copying javabridge/jars/rhino-1.7R4.jar -> build/lib.macosx-10.9-x86_64-3.8/javabridge/jars
running build_ext
javac /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/java/org/cellprofiler/runnablequeue/RunnableQueue.java
jar cf /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/build/lib.macosx-10.9-x86_64-3.8/javabridge/jars/runnablequeue.jar -C /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/java org/cellprofiler/runnablequeue/RunnableQueue.class -C /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/java org/cellprofiler/runnablequeue/RunnableQueue$1.class
javac /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/java/org/cellprofiler/javabridge/test/RealRect.java
jar cf /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/build/lib.macosx-10.9-x86_64-3.8/javabridge/jars/test.jar -C /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/java org/cellprofiler/javabridge/test/RealRect.class
javac /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/java/org/cellprofiler/javabridge/CPython.java /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/java/org/cellprofiler/javabridge/CPythonInvocationHandler.java
Note: /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/java/org/cellprofiler/javabridge/CPythonInvocationHandler.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
jar cf /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/build/lib.macosx-10.9-x86_64-3.8/javabridge/jars/cpython.jar -C /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/java org/cellprofiler/javabridge/CPythonInvocationHandler.class -C /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/java org/cellprofiler/javabridge/CPython.class -C /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/java org/cellprofiler/javabridge/CPython$WrappedException.class -C /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/java org/cellprofiler/javabridge/CPython$StackFrame.class -C /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/java org/cellprofiler/javabridge/CPythonInvocationHandler.class
warning: _javabridge_osspecific.pxd:12:4: 'JavaVMOption' redeclared
warning: _javabridge_osspecific.pxd:19:4: 'JavaVMInitArgs' redeclared
warning: _javabridge.pyx:94:4: 'jvalue' redeclared
warning: _javabridge.pyx:112:4: 'JavaVMOption' redeclared
warning: _javabridge.pyx:119:4: 'JavaVMInitArgs' redeclared
warning: _javabridge_osspecific.pxd:12:4: 'JavaVMOption' redeclared
warning: _javabridge_osspecific.pxd:19:4: 'JavaVMInitArgs' redeclared
warning: _javabridge_mac.pyx:4:4: 'jint' redeclared
warning: _javabridge_mac.pyx:5:4: 'jboolean' redeclared
warning: _javabridge_mac.pyx:9:4: 'JavaVM' redeclared
warning: _javabridge_mac.pyx:14:4: 'JavaVMOption' redeclared
warning: _javabridge_mac.pyx:21:4: 'JavaVMInitArgs' redeclared
warning: _javabridge_nomac.pxd:15:4: 'JavaVMInitArgs' redeclared
warning: _javabridge_nomac.pxd:20:4: 'JavaVMOption' redeclared
warning: _javabridge_nomac.pyx:4:4: 'jint' redeclared
warning: _javabridge_nomac.pyx:5:4: 'jboolean' redeclared
warning: _javabridge_nomac.pyx:9:4: 'JavaVM' redeclared
building 'javabridge._javabridge' extension
creating build/temp.macosx-10.9-x86_64-3.8
x86_64-apple-darwin13.4.0-clang -fno-strict-aliasing -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O3 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -pipe -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=/Users/mariajoseesquinasesquinas/opt/anaconda3=/usr/local/src/conda-prefix -flto -Wl,-export_dynamic -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include/darwin -I/Users/mariajoseesquinasesquinas/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8 -c _javabridge.c -o build/temp.macosx-10.9-x86_64-3.8/_javabridge.o
clang-10: warning: -Wl,-export_dynamic: 'linker' input unused [-Wunused-command-line-argument]
In file included from _javabridge.c:687:
In file included from /Users/mariajoseesquinasesquinas/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:5:
In file included from /Users/mariajoseesquinasesquinas/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /Users/mariajoseesquinasesquinas/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960:
/Users/mariajoseesquinasesquinas/opt/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:696:
./mac_javabridge_utils.h:47:25: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacStopVM();
^
void
./mac_javabridge_utils.h:55:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopInit();
^
void
./mac_javabridge_utils.h:63:29: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopRun();
^
void
./mac_javabridge_utils.h:71:31: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopReset();
^
void
./mac_javabridge_utils.h:79:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacStopRunLoop();
^
void
./mac_javabridge_utils.h:88:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT int MacIsMainThread();
^
void
./mac_javabridge_utils.h:103:20: warning: this function declaration is not a prototype [-Wstrict-prototypes]
void MacRunLoopStop();
^
void
_javabridge.c:27046:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:27149:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:27283:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:27417:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:27523:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:27706:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:28960:3: warning: incompatible pointer to integer conversion returning 'void *' from a function with result type 'int' [-Wint-conversion]
import_array();
^~~~~~~~~~~~~~
/Users/mariajoseesquinasesquinas/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/__multiarray_api.h:1545:151: note: expanded from macro 'import_array'
#define import_array() {if (_import_array() < 0) {PyErr_Print(); PyErr_SetString(PyExc_ImportError, "numpy.core.multiarray failed to import"); return NULL; } }
^~~~
/Users/mariajoseesquinasesquinas/opt/anaconda3/lib/clang/10.0.0/include/stddef.h:89:16: note: expanded from macro 'NULL'
# define NULL ((void*)0)
^~~~~~~~~~
15 warnings generated.
x86_64-apple-darwin13.4.0-clang -fno-strict-aliasing -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O3 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -pipe -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=/Users/mariajoseesquinasesquinas/opt/anaconda3=/usr/local/src/conda-prefix -flto -Wl,-export_dynamic -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include/darwin -I/Users/mariajoseesquinasesquinas/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8 -c _javabridge_mac.c -o build/temp.macosx-10.9-x86_64-3.8/_javabridge_mac.o
clang-10: warning: -Wl,-export_dynamic: 'linker' input unused [-Wunused-command-line-argument]
In file included from _javabridge_mac.c:686:
./mac_javabridge_utils.h:47:25: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacStopVM();
^
void
./mac_javabridge_utils.h:55:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopInit();
^
void
./mac_javabridge_utils.h:63:29: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopRun();
^
void
./mac_javabridge_utils.h:71:31: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopReset();
^
void
./mac_javabridge_utils.h:79:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacStopRunLoop();
^
void
./mac_javabridge_utils.h:88:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT int MacIsMainThread();
^
void
./mac_javabridge_utils.h:103:20: warning: this function declaration is not a prototype [-Wstrict-prototypes]
void MacRunLoopStop();
^
void
7 warnings generated.
x86_64-apple-darwin13.4.0-clang -fno-strict-aliasing -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O3 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -pipe -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=/Users/mariajoseesquinasesquinas/opt/anaconda3=/usr/local/src/conda-prefix -flto -Wl,-export_dynamic -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include/darwin -I/Users/mariajoseesquinasesquinas/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8 -c mac_javabridge_utils.c -o build/temp.macosx-10.9-x86_64-3.8/mac_javabridge_utils.o
clang-10: warning: -Wl,-export_dynamic: 'linker' input unused [-Wunused-command-line-argument]
mac_javabridge_utils.c:112:11: warning: unused variable 'retval' [-Wunused-variable]
void *retval;
^
mac_javabridge_utils.c:176:16: warning: unused variable 'exception' [-Wunused-variable]
jthrowable exception;
^
mac_javabridge_utils.c:320:30: warning: unused variable 'observerContext' [-Wunused-variable]
CFRunLoopObserverContext observerContext;
^
mac_javabridge_utils.c:321:30: warning: unused variable 'observerRef' [-Wunused-variable]
CFRunLoopObserverRef observerRef;
^
mac_javabridge_utils.c:294:13: warning: unused function 'CBObserve' [-Wunused-function]
static void CBObserve(CFRunLoopObserverRef observer,
^
5 warnings generated.
x86_64-apple-darwin13.4.0-clang -bundle -undefined dynamic_lookup -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/mariajoseesquinasesquinas/opt/anaconda3/lib -L/Users/mariajoseesquinasesquinas/opt/anaconda3/lib -flto -Wl,-export_dynamic -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/mariajoseesquinasesquinas/opt/anaconda3/lib -L/Users/mariajoseesquinasesquinas/opt/anaconda3/lib -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/mariajoseesquinasesquinas/opt/anaconda3/lib -L/Users/mariajoseesquinasesquinas/opt/anaconda3/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -arch x86_64 build/temp.macosx-10.9-x86_64-3.8/_javabridge.o build/temp.macosx-10.9-x86_64-3.8/_javabridge_mac.o build/temp.macosx-10.9-x86_64-3.8/mac_javabridge_utils.o -o build/lib.macosx-10.9-x86_64-3.8/javabridge/_javabridge.cpython-38-darwin.so -framework CoreFoundation
ld: warning: -pie being ignored. It is only used when linking a main executable
ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd' for architecture x86_64
clang-10: error: linker command failed with exit code 1 (use -v to see invocation)
error: command 'x86_64-apple-darwin13.4.0-clang' failed with exit status 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: /Users/mariajoseesquinasesquinas/opt/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/setup.py'"'"'; __file__='"'"'/private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/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/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-record-jsa_7ttr/install-record.txt --single-version-externally-managed --compile --install-headers /Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/javabridge
cwd: /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/
Complete output (188 lines):
running install
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-3.8
creating build/lib.macosx-10.9-x86_64-3.8/javabridge
copying javabridge/_version.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge
copying javabridge/jutil.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge
copying javabridge/locate.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge
copying javabridge/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge
copying javabridge/wrappers.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge
copying javabridge/noseplugin.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge
creating build/lib.macosx-10.9-x86_64-3.8/javabridge/tests
copying javabridge/tests/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge/tests
copying javabridge/tests/test_cpython.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge/tests
copying javabridge/tests/test_javabridge.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge/tests
copying javabridge/tests/test_jutil.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge/tests
copying javabridge/tests/test_wrappers.py -> build/lib.macosx-10.9-x86_64-3.8/javabridge/tests
creating build/lib.macosx-10.9-x86_64-3.8/javabridge/jars
copying javabridge/jars/rhino-1.7R4.jar -> build/lib.macosx-10.9-x86_64-3.8/javabridge/jars
running build_ext
javac /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/java/org/cellprofiler/runnablequeue/RunnableQueue.java
jar cf /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/build/lib.macosx-10.9-x86_64-3.8/javabridge/jars/runnablequeue.jar -C /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/java org/cellprofiler/runnablequeue/RunnableQueue.class -C /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/java org/cellprofiler/runnablequeue/RunnableQueue$1.class
javac /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/java/org/cellprofiler/javabridge/test/RealRect.java
jar cf /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/build/lib.macosx-10.9-x86_64-3.8/javabridge/jars/test.jar -C /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/java org/cellprofiler/javabridge/test/RealRect.class
javac /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/java/org/cellprofiler/javabridge/CPython.java /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/java/org/cellprofiler/javabridge/CPythonInvocationHandler.java
Note: /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/java/org/cellprofiler/javabridge/CPythonInvocationHandler.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
jar cf /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/build/lib.macosx-10.9-x86_64-3.8/javabridge/jars/cpython.jar -C /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/java org/cellprofiler/javabridge/CPythonInvocationHandler.class -C /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/java org/cellprofiler/javabridge/CPython.class -C /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/java org/cellprofiler/javabridge/CPython$WrappedException.class -C /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/java org/cellprofiler/javabridge/CPython$StackFrame.class -C /private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/java org/cellprofiler/javabridge/CPythonInvocationHandler.class
building 'javabridge._javabridge' extension
creating build/temp.macosx-10.9-x86_64-3.8
x86_64-apple-darwin13.4.0-clang -fno-strict-aliasing -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O3 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -pipe -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=/Users/mariajoseesquinasesquinas/opt/anaconda3=/usr/local/src/conda-prefix -flto -Wl,-export_dynamic -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include/darwin -I/Users/mariajoseesquinasesquinas/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8 -c _javabridge.c -o build/temp.macosx-10.9-x86_64-3.8/_javabridge.o
clang-10: warning: -Wl,-export_dynamic: 'linker' input unused [-Wunused-command-line-argument]
In file included from _javabridge.c:687:
In file included from /Users/mariajoseesquinasesquinas/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:5:
In file included from /Users/mariajoseesquinasesquinas/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /Users/mariajoseesquinasesquinas/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960:
/Users/mariajoseesquinasesquinas/opt/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:696:
./mac_javabridge_utils.h:47:25: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacStopVM();
^
void
./mac_javabridge_utils.h:55:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopInit();
^
void
./mac_javabridge_utils.h:63:29: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopRun();
^
void
./mac_javabridge_utils.h:71:31: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopReset();
^
void
./mac_javabridge_utils.h:79:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacStopRunLoop();
^
void
./mac_javabridge_utils.h:88:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT int MacIsMainThread();
^
void
./mac_javabridge_utils.h:103:20: warning: this function declaration is not a prototype [-Wstrict-prototypes]
void MacRunLoopStop();
^
void
_javabridge.c:27046:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:27149:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:27283:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:27417:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:27523:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:27706:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:28960:3: warning: incompatible pointer to integer conversion returning 'void *' from a function with result type 'int' [-Wint-conversion]
import_array();
^~~~~~~~~~~~~~
/Users/mariajoseesquinasesquinas/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/__multiarray_api.h:1545:151: note: expanded from macro 'import_array'
#define import_array() {if (_import_array() < 0) {PyErr_Print(); PyErr_SetString(PyExc_ImportError, "numpy.core.multiarray failed to import"); return NULL; } }
^~~~
/Users/mariajoseesquinasesquinas/opt/anaconda3/lib/clang/10.0.0/include/stddef.h:89:16: note: expanded from macro 'NULL'
# define NULL ((void*)0)
^~~~~~~~~~
15 warnings generated.
x86_64-apple-darwin13.4.0-clang -fno-strict-aliasing -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O3 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -pipe -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=/Users/mariajoseesquinasesquinas/opt/anaconda3=/usr/local/src/conda-prefix -flto -Wl,-export_dynamic -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include/darwin -I/Users/mariajoseesquinasesquinas/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8 -c _javabridge_mac.c -o build/temp.macosx-10.9-x86_64-3.8/_javabridge_mac.o
clang-10: warning: -Wl,-export_dynamic: 'linker' input unused [-Wunused-command-line-argument]
In file included from _javabridge_mac.c:686:
./mac_javabridge_utils.h:47:25: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacStopVM();
^
void
./mac_javabridge_utils.h:55:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopInit();
^
void
./mac_javabridge_utils.h:63:29: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopRun();
^
void
./mac_javabridge_utils.h:71:31: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopReset();
^
void
./mac_javabridge_utils.h:79:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT void MacStopRunLoop();
^
void
./mac_javabridge_utils.h:88:30: warning: this function declaration is not a prototype [-Wstrict-prototypes]
JNIEXPORT int MacIsMainThread();
^
void
./mac_javabridge_utils.h:103:20: warning: this function declaration is not a prototype [-Wstrict-prototypes]
void MacRunLoopStop();
^
void
7 warnings generated.
x86_64-apple-darwin13.4.0-clang -fno-strict-aliasing -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O3 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -pipe -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=/Users/mariajoseesquinasesquinas/opt/anaconda3=/usr/local/src/conda-prefix -flto -Wl,-export_dynamic -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include/darwin -I/Users/mariajoseesquinasesquinas/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -I/Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8 -c mac_javabridge_utils.c -o build/temp.macosx-10.9-x86_64-3.8/mac_javabridge_utils.o
clang-10: warning: -Wl,-export_dynamic: 'linker' input unused [-Wunused-command-line-argument]
mac_javabridge_utils.c:112:11: warning: unused variable 'retval' [-Wunused-variable]
void *retval;
^
mac_javabridge_utils.c:176:16: warning: unused variable 'exception' [-Wunused-variable]
jthrowable exception;
^
mac_javabridge_utils.c:321:30: warning: unused variable 'observerRef' [-Wunused-variable]
CFRunLoopObserverRef observerRef;
^
mac_javabridge_utils.c:320:30: warning: unused variable 'observerContext' [-Wunused-variable]
CFRunLoopObserverContext observerContext;
^
mac_javabridge_utils.c:294:13: warning: unused function 'CBObserve' [-Wunused-function]
static void CBObserve(CFRunLoopObserverRef observer,
^
5 warnings generated.
x86_64-apple-darwin13.4.0-clang -bundle -undefined dynamic_lookup -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/mariajoseesquinasesquinas/opt/anaconda3/lib -L/Users/mariajoseesquinasesquinas/opt/anaconda3/lib -flto -Wl,-export_dynamic -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/mariajoseesquinasesquinas/opt/anaconda3/lib -L/Users/mariajoseesquinasesquinas/opt/anaconda3/lib -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/mariajoseesquinasesquinas/opt/anaconda3/lib -L/Users/mariajoseesquinasesquinas/opt/anaconda3/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/mariajoseesquinasesquinas/opt/anaconda3/include -arch x86_64 build/temp.macosx-10.9-x86_64-3.8/_javabridge.o build/temp.macosx-10.9-x86_64-3.8/_javabridge_mac.o build/temp.macosx-10.9-x86_64-3.8/mac_javabridge_utils.o -o build/lib.macosx-10.9-x86_64-3.8/javabridge/_javabridge.cpython-38-darwin.so -framework CoreFoundation
ld: warning: -pie being ignored. It is only used when linking a main executable
ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd' for architecture x86_64
clang-10: error: linker command failed with exit code 1 (use -v to see invocation)
error: command 'x86_64-apple-darwin13.4.0-clang' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /Users/mariajoseesquinasesquinas/opt/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/setup.py'"'"'; __file__='"'"'/private/var/folders/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-req-build-pcmnwy6m/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/vh/f1jc347s2bs7gx85wcnkx8kr0000gn/T/pip-record-jsa_7ttr/install-record.txt --single-version-externally-managed --compile --install-headers /Users/mariajoseesquinasesquinas/opt/anaconda3/include/python3.8/javabridge Check the logs for full command output.
Thank you
I'm sorry Maria - I don't have a Mac so I can't replicate and my expertise on that platform is limited. I can't recall ever seeing that error before.