Trying to install python-javabridge as part of a github actions for MacOS. For Windows/Linux, I do not have a problem but when running the tests on MacOS, I get the following error message about the wheel not being built.
This happens with Python 3.8/9/10.
Run pip install python-javabridge==4.0.3
Collecting python-javabridge==4.0.3
Downloading python-javabridge-4.0.3.tar.gz (1.3 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.3/1.3 MB 29.0 MB/s eta 0:00:00
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Requirement already satisfied: numpy>=1.20.1 in /Users/runner/micromamba/envs/pathml/lib/python3.[8](https://github.com/Dana-Farber-AIOS/pathml/actions/runs/10410001612/job/28830849681#step:5:9)/site-packages (from python-javabridge==4.0.3) (1.23.5)
Building wheels for collected packages: python-javabridge
Building wheel for python-javabridge (setup.py): started
Building wheel for python-javabridge (setup.py): finished with status 'error'
error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [145 lines of output]
/Users/runner/micromamba/envs/pathml/lib/python3.8/site-packages/setuptools/__init__.py:85: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!
********************************************************************************
Requirements should be satisfied by a PEP 517 installer.
If you are using pip, you can try `pip install --use-pep517`.
********************************************************************************
!!
dist.fetch_build_eggs(dist.setup_requires)
/Users/runner/micromamba/envs/pathml/lib/python3.8/site-packages/setuptools/_distutils/dist.py:268: UserWarning: Unknown distribution option: 'tests_require'
warnings.warn(msg)
/Users/runner/micromamba/envs/pathml/lib/python3.8/site-packages/setuptools/_distutils/dist.py:268: UserWarning: Unknown distribution option: 'test_suite'
warnings.warn(msg)
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-11.0-arm64-cpython-38
creating build/lib.macosx-11.0-arm64-cpython-38/javabridge
copying javabridge/jutil.py -> build/lib.macosx-11.0-arm64-cpython-38/javabridge
copying javabridge/locate.py -> build/lib.macosx-11.0-arm64-cpython-38/javabridge
copying javabridge/__init__.py -> build/lib.macosx-11.0-arm64-cpython-38/javabridge
copying javabridge/wrappers.py -> build/lib.macosx-11.0-arm64-cpython-38/javabridge
copying javabridge/noseplugin.py -> build/lib.macosx-11.0-arm64-cpython-38/javabridge
creating build/lib.macosx-11.0-arm64-cpython-38/javabridge/tests
copying javabridge/tests/__init__.py -> build/lib.macosx-11.0-arm64-cpython-38/javabridge/tests
copying javabridge/tests/test_cpython.py -> build/lib.macosx-11.0-arm64-cpython-38/javabridge/tests
copying javabridge/tests/test_javabridge.py -> build/lib.macosx-11.0-arm64-cpython-38/javabridge/tests
copying javabridge/tests/test_jutil.py -> build/lib.macosx-11.0-arm64-cpython-38/javabridge/tests
copying javabridge/tests/test_wrappers.py -> build/lib.macosx-11.0-arm64-cpython-38/javabridge/tests
creating build/lib.macosx-11.0-arm64-cpython-38/javabridge/jars
copying javabridge/jars/rhino-1.7R4.jar -> build/lib.macosx-11.0-arm64-cpython-38/javabridge/jars
copying javabridge/jars/runnablequeue.jar -> build/lib.macosx-11.0-arm64-cpython-38/javabridge/jars
copying javabridge/jars/cpython.jar -> build/lib.macosx-11.0-arm64-cpython-38/javabridge/jars
copying javabridge/jars/test.jar -> build/lib.macosx-11.0-arm64-cpython-38/javabridge/jars
copying javabridge/jars/libjava2cpython.jnilib -> build/lib.macosx-11.0-arm64-cpython-38/javabridge/jars
running build_ext
javac -source 8 -target 8 /private/var/folders/hw/1f0gcr8d6kn[9](https://github.com/Dana-Farber-AIOS/pathml/actions/runs/10410001612/job/28830849681#step:5:10)ms0_wn0_57qc0000gn/T/pip-install-kud_uybf/python-javabridge_2[10](https://github.com/Dana-Farber-AIOS/pathml/actions/runs/10410001612/job/28830849681#step:5:11)a4e302dc04e06a09bdee1d1f3c35f/java/org/cellprofiler/runnablequeue/RunnableQueue.java
warning: [options] bootstrap class path not set in conjunction with -source 8
1 warning
javac -source 8 -target 8 /private/var/folders/hw/1f0gcr8d6kn9ms0_wn0_57qc0000gn/T/pip-install-kud_uybf/python-javabridge_210a4e302dc04e06a09bdee1d1f3c35f/java/org/cellprofiler/javabridge/test/RealRect.java
warning: [options] bootstrap class path not set in conjunction with -source 8
1 warning
javac -source 8 -target 8 /private/var/folders/hw/1f0gcr8d6kn9ms0_wn0_57qc0000gn/T/pip-install-kud_uybf/python-javabridge_210a4e302dc04e06a09bdee1d1f3c35f/java/org/cellprofiler/javabridge/CPython.java /private/var/folders/hw/1f0gcr8d6kn9ms0_wn0_57qc0000gn/T/pip-install-kud_uybf/python-javabridge_210a4e302dc04e06a09bdee1d1f3c35f/java/org/cellprofiler/javabridge/CPythonInvocationHandler.java
warning: [options] bootstrap class path not set in conjunction with -source 8
Note: /private/var/folders/hw/1f0gcr8d6kn9ms0_wn0_57qc0000gn/T/pip-install-kud_uybf/python-javabridge_210a4e302dc04e06a09bdee1d1f3c35f/java/org/cellprofiler/javabridge/CPythonInvocationHandler.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
1 warning
building 'javabridge._javabridge' extension
creating build/temp.macosx-[11](https://github.com/Dana-Farber-AIOS/pathml/actions/runs/10410001612/job/28830849681#step:5:12).0-arm64-cpython-38
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/runner/micromamba/envs/pathml/include -arch arm64 -fPIC -O2 -isystem /Users/runner/micromamba/envs/pathml/include -arch arm64 -I/Users/runner/micromamba/envs/pathml/lib/python3.8/site-packages/numpy/core/include -I/Users/runner/micromamba/envs/pathml/lib/jvm/include -I/Users/runner/micromamba/envs/pathml/lib/jvm/include/darwin -I/Users/runner/micromamba/envs/pathml/lib/python3.8/site-packages/numpy/core/include -I/Users/runner/micromamba/envs/pathml/include/python3.8 -c _javabridge.c -o build/temp.macosx-11.0-arm64-cpython-38/_javabridge.o
In file included from _javabridge.c:610:
In file included from /Users/runner/micromamba/envs/pathml/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:5:
In file included from /Users/runner/micromamba/envs/pathml/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:[12](https://github.com/Dana-Farber-AIOS/pathml/actions/runs/10410001612/job/28830849681#step:5:13):
In file included from /Users/runner/micromamba/envs/pathml/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1948:
/Users/runner/micromamba/envs/pathml/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 " \
^
_javabridge.c:5225:37: warning: cast to smaller integer type 'int' from 'jobject' (aka 'struct _jobject *') [-Wpointer-to-int-cast]
__pyx_t_1 = __Pyx_PyInt_From_int(((int)__pyx_v_self->o)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 475, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~
_javabridge.c:5516:37: warning: cast to smaller integer type 'int' from 'jobject' (aka 'struct _jobject *') [-Wpointer-to-int-cast]
__pyx_t_1 = __Pyx_PyInt_From_int(((int)__pyx_v_self->o)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 493, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~
_javabridge.c:5749:37: warning: cast to smaller integer type 'int' from 'jclass' (aka 'struct _jobject *') [-Wpointer-to-int-cast]
__pyx_t_1 = __Pyx_PyInt_From_int(((int)__pyx_v_self->c)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 502, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~
_javabridge.c:6115:41: warning: cast to smaller integer type 'int' from 'jmethodID' (aka 'struct _jmethodID *') [-Wpointer-to-int-cast]
__pyx_t_4 = __Pyx_PyUnicode_From_int(((int)__pyx_v_self->id), 0, ' ', 'x'); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 521, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~
_javabridge.c:6403:41: warning: cast to smaller integer type 'int' from 'jfieldID' (aka 'struct _jfieldID *') [-Wpointer-to-int-cast]
__pyx_t_4 = __Pyx_PyUnicode_From_int(((int)__pyx_v_self->id), 0, ' ', 'x'); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 535, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~
_javabridge.c:21144:18: warning: cast to smaller integer type 'int' from 'jobject' (aka 'struct _jobject *') [-Wpointer-to-int-cast]
__pyx_t_1 = ((((int)__pyx_v_s->o) == 0) != 0);
^~~~~~~~~~~~~~~~~
_javabridge.c:21278:18: warning: cast to smaller integer type 'int' from 'jobject' (aka 'struct _jobject *') [-Wpointer-to-int-cast]
__pyx_t_1 = ((((int)__pyx_v_s->o) == 0) != 0);
^~~~~~~~~~~~~~~~~
_javabridge.c:284[13](https://github.com/Dana-Farber-AIOS/pathml/actions/runs/10410001612/job/28830849681#step:5:14):3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/runner/micromamba/envs/pathml/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/runner/micromamba/envs/pathml/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:28513:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/runner/micromamba/envs/pathml/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/runner/micromamba/envs/pathml/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:28644:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/runner/micromamba/envs/pathml/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/runner/micromamba/envs/pathml/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:28775:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/runner/micromamba/envs/pathml/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/runner/micromamba/envs/pathml/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:28878:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/runner/micromamba/envs/pathml/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/runner/micromamba/envs/pathml/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:29058:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/Users/runner/micromamba/envs/pathml/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/runner/micromamba/envs/pathml/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
_javabridge.c:30352:3: error: incompatible pointer to integer conversion returning 'void *' from a function with result type 'int' [-Wint-conversion]
import_array();
^~~~~~~~~~~~~~
/Users/runner/micromamba/envs/pathml/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; } }
^~~~
/Applications/Xcode_15.4.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/stddef.h:89:16: note: expanded from macro 'NULL'
# define NULL ((void*)0)
^~~~~~~~~~
[14](https://github.com/Dana-Farber-AIOS/pathml/actions/runs/10410001612/job/28830849681#step:5:15) warnings and 1 error generated.
error: command '/usr/bin/clang' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for python-javabridge
Running setup.py clean for python-javabridge
Failed to build python-javabridge
ERROR: Could not build wheels for python-javabridge, which is required to install pyproject.toml-based projects
Trying to install python-javabridge as part of a github actions for MacOS. For Windows/Linux, I do not have a problem but when running the tests on MacOS, I get the following error message about the wheel not being built.
This happens with Python 3.8/9/10.