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[Python3] FutureWarning: Cython directive 'language_level' not set #164

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rapgro opened this issue May 12, 2019 · 3 comments
Open

[Python3] FutureWarning: Cython directive 'language_level' not set #164

rapgro opened this issue May 12, 2019 · 3 comments

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@rapgro
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rapgro commented May 12, 2019

Fedora Rawhide with those package versions:

java-1.8.0-openjdk-devel 1.8.0.212.b04-0.fc31
python3-Cython 0.29.6-1.fc31
python3-devel 3.7.3-3.fc31
python3-nose 1.3.7-22.fc30
python3-numpy 1.16.3-1.fc31
python3-setuptools 41.0.1-1.fc31
python3-sphinx 2.0.1-1.fc31

jar cf build/lib.linux-x86_64-3.7/javabridge/jars/cpython.jar -C java org/cellprofiler/javabridge/CPython$StackFrame.class -C java org/cellprofiler/javabridge/CPython$WrappedException.class -C java org/cellprofiler/javabridge/CPython.class -C java org/cellprofiler/javabridge/CPythonInvocationHandler.class -C java org/cellprofiler/javabridge/CPythonInvocationHandler.class
/usr/lib64/python3.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /builddir/build/BUILD/python-javabridge-1.0.18/_javabridge.pyx
  tree = Parsing.p_module(s, pxd, full_module_name)
warning: _javabridge_osspecific.pxd:12:4: 'JavaVMOption' redeclared 
warning: _javabridge_osspecific.pxd:19:4: 'JavaVMInitArgs' redeclared 
warning: _javabridge.pyx:93:4: 'jvalue' redeclared 
warning: _javabridge.pyx:111:4: 'JavaVMOption' redeclared 
warning: _javabridge.pyx:118:4: 'JavaVMInitArgs' redeclared 
/usr/lib64/python3.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /builddir/build/BUILD/python-javabridge-1.0.18/_javabridge_mac.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
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 
/usr/lib64/python3.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /builddir/build/BUILD/python-javabridge-1.0.18/_javabridge_nomac.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
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.linux-x86_64-3.7
gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.212.b04-0.fc30.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.212.b04-0.fc30.x86_64/include/linux -I/usr/lib64/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -c _javabridge.c -o build/temp.linux-x86_64-3.7/_javabridge.o
error: command 'gcc' failed with exit status 1
@rapgro
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rapgro commented May 12, 2019

Proposed fixes of other projects:
Toblerity/Fiona@19e36a2
stan-dev/pystan@68971f2

LeeKamentsky added a commit that referenced this issue May 13, 2019
@LeeKamentsky
issue #164 - set Cython language to 3 + other version 3 fixes
7a91457
@rapgro
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rapgro commented Jul 27, 2019

Not a good progress with latest git sources:

Fedora Rawhide
DEBUG util.py:587: java-1.8.0-openjdk-devel x86_64 1:1.8.0.222.b01-0.1.ea.fc31
DEBUG util.py:587: python3-Cython x86_64 0.29.12-2.fc31
DEBUG util.py:587: python3-devel x86_64 3.7.4-3.fc31
DEBUG util.py:587: python3-nose noarch 1.3.7-23.fc31
DEBUG util.py:587: python3-numpy x86_64 1:1.16.4-2.fc31
DEBUG util.py:587: python3-setuptools noarch 41.0.1-3.fc31
DEBUG util.py:587: python3-sphinx noarch 1:2.1.2-1.fc31
DEBUG util.py:587: rhino noarch 1.7.7.1-7.fc30

+ /usr/bin/python3 setup.py build '--executable=/usr/bin/python3 -s'
BUILDSTDERR: Note: java/org/cellprofiler/javabridge/CPythonInvocationHandler.java uses unchecked or unsafe operations.
BUILDSTDERR: Note: Recompile with -Xlint:unchecked for details.
BUILDSTDERR: warning: _javabridge_osspecific.pxd:12:4: 'JavaVMOption' redeclared 
BUILDSTDERR: warning: _javabridge_osspecific.pxd:19:4: 'JavaVMInitArgs' redeclared 
BUILDSTDERR: warning: _javabridge.pyx:94:4: 'jvalue' redeclared 
BUILDSTDERR: warning: _javabridge.pyx:112:4: 'JavaVMOption' redeclared 
BUILDSTDERR: warning: _javabridge.pyx:119:4: 'JavaVMInitArgs' redeclared 
BUILDSTDERR: /usr/lib64/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /builddir/build/BUILD/python-javabridge-16d6c91c3aa9dbf8c80de1fc442aca696a6197fa/_javabridge_mac.pxd
BUILDSTDERR:   tree = Parsing.p_module(s, pxd, full_module_name)
BUILDSTDERR: warning: _javabridge_osspecific.pxd:12:4: 'JavaVMOption' redeclared 
BUILDSTDERR: warning: _javabridge_osspecific.pxd:19:4: 'JavaVMInitArgs' redeclared 
BUILDSTDERR: warning: _javabridge_mac.pyx:4:4: 'jint' redeclared 
BUILDSTDERR: warning: _javabridge_mac.pyx:5:4: 'jboolean' redeclared 
BUILDSTDERR: warning: _javabridge_mac.pyx:9:4: 'JavaVM' redeclared 
BUILDSTDERR: warning: _javabridge_mac.pyx:14:4: 'JavaVMOption' redeclared 
BUILDSTDERR: warning: _javabridge_mac.pyx:21:4: 'JavaVMInitArgs' redeclared 
BUILDSTDERR: /usr/lib64/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /builddir/build/BUILD/python-javabridge-16d6c91c3aa9dbf8c80de1fc442aca696a6197fa/_javabridge_nomac.pxd
BUILDSTDERR:   tree = Parsing.p_module(s, pxd, full_module_name)
BUILDSTDERR: warning: _javabridge_nomac.pxd:15:4: 'JavaVMInitArgs' redeclared 
BUILDSTDERR: warning: _javabridge_nomac.pxd:20:4: 'JavaVMOption' redeclared 
BUILDSTDERR: warning: _javabridge_nomac.pyx:4:4: 'jint' redeclared 
BUILDSTDERR: warning: _javabridge_nomac.pyx:5:4: 'jboolean' redeclared 
BUILDSTDERR: warning: _javabridge_nomac.pyx:9:4: 'JavaVM' redeclared

@rapgro rapgro changed the title FutureWarning: Cython directive 'language_level' not set [Python3] FutureWarning: Cython directive 'language_level' not set Jul 27, 2019
@LeeKamentsky
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I put code in setup.py to explicitly pass the -3 switch to Cython (c7ccaed). Does that fix the problem? All tests pass on Travis and the language_level warning appears to be gone.

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