Installing javabridge in macOS Monterey #201

mariajosesquinas · 2022-03-04T16:17:25Z

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

The text was updated successfully, but these errors were encountered:

LeeKamentsky · 2022-03-04T18:13:04Z

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.

mariajosesquinas · 2022-03-04T20:55:10Z

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

LeeKamentsky · 2022-03-06T21:44:27Z

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.

keonho-kim mentioned this issue Jul 18, 2023

Package installation error: javabridge salesforce/PyRCA#25

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Installing javabridge in macOS Monterey #201

Installing javabridge in macOS Monterey #201

mariajosesquinas commented Mar 4, 2022

LeeKamentsky commented Mar 4, 2022

mariajosesquinas commented Mar 4, 2022 •

edited

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LeeKamentsky commented Mar 6, 2022

Installing javabridge in macOS Monterey #201

Installing javabridge in macOS Monterey #201

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mariajosesquinas commented Mar 4, 2022

LeeKamentsky commented Mar 4, 2022

mariajosesquinas commented Mar 4, 2022 • edited Loading

LeeKamentsky commented Mar 6, 2022

mariajosesquinas commented Mar 4, 2022 •

edited

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