reating build/temp.macosx-10.9-intel-2.7
creating build/temp.macosx-10.9-intel-2.7/Cython
creating build/temp.macosx-10.9-intel-2.7/Cython/Plex
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch x86_64 -arch i386 -pipe -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c Cython/Plex/Scanners.c -o build/temp.macosx-10.9-intel-2.7/Cython/Plex/Scanners.o
clang: error: unknown argument: '-mno-fused-madd' [-Wunused-command-line-argument-hard-error-in-future]
clang: note: this will be a hard error (cannot be downgraded to a warning) in the future
error: command 'cc' failed with exit status 1
I got this error while installing Cython from setup.py.
I was installing the scikit-learn package while get the same error. (-mno-fused-madd unknown argument)
Is there anything, any package needed before I install cython?
Many thanks
You need probably need to install another C compiler. Try compiling it with GCC.
clang: error: unknown argument: '-mno-fused-madd'
Alternatively, you can edit the configure script and change the compiler flags.
On a side note, this seems like it is a bug you should report.
Related
I'm trying to install machine learning package scikit-learn in OSX unsuccessfully.
When I write the command "python setup.py install" to check if my installation is OK, I got
build_src: building npy-pkg config files
running build_py
running build_clib
customize UnixCCompiler
#### ['clang', '-fno-strict-aliasing', '-fno-common', '-dynamic', '-g', '-Os', '-pipe', '-fno- common', '-fno-strict-aliasing', '-fwrapv', '-mno-fused-madd', '-DENABLE_DTRACE', '-DMACOSX', '-DNDEBUG', '-Wall', '-Wstrict-prototypes', '-Wshorten-64-to-32', '-DNDEBUG', '-g', '-Os', '-Wall', '-Wstrict-prototypes', '-DENABLE_DTRACE', '-arch', 'i386', '-arch', 'x86_64'] #######
**Missing compiler_cxx fix for UnixCCompiler**
customize UnixCCompiler using build_clib
building 'libsvm-skl' library
compiling C++ sources
C compiler: clang++ -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe -fno-common -fno-strict- aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wshorten-64-to-32 -DNDEBUG -g -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe
compile options: '-I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include -c'
clang++: src/libsvm/libsvm_template.cpp
clang: error: no such file or directory: 'src/libsvm/libsvm_template.cpp'
clang: error: no input files
clang: error: no such file or directory: 'src/libsvm/libsvm_template.cpp'
clang: error: no input files
error: Command "clang++ -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wshorten-64-to-32 -DNDEBUG -g -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include -c src/libsvm/libsvm_template.cpp -o build/temp.macosx-10.8-intel-2.7/src/libsvm/libsvm_template.o" failed with exit status 1
I have installed clang version:
Apple LLVM version 4.2 (clang-425.0.28) (based on LLVM 3.2svn)
Target: x86_64-apple-darwin12.5.0
Thread model: posix
Can you please help me? Any help is welcome. thanks.
The easiest way I have found is to just use Anaconda, which will give you just about every scientific Python package under the sun and make package management much easier in general. You can download it here:
https://store.continuum.io/cshop/anaconda/
A list of packages that Anaconda supports:
http://docs.continuum.io/anaconda/pkg-docs.html
I am having trouble installing PyLucene JCC on Mac OSX.
I dowloaded the latest version of JCC from apache lucene site and fallowed the instruction to install it using the command
python setup.py build
But I am getting the following error while installing
ld: internal error: atom not found in symbolIndex(__ZN7JNIEnv_13CallIntMethodEP8_jobjectP10_jmethodIDz) for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
error: command 'c++' failed with exit status 1
I have tried following the instruction given on the official site of adding the flag "-framework", "Python" to the LFLAGS value when installing on mac OSX or using the export CFLAGS=-Qunused-arguments and export CPPFLAGS=-Qunused-arguments before runnig the install command to ignore the warnings while build. But none of them are working.
The full trace of error is
found JAVAHOME = /Library/Java/JavaVirtualMachines/jdk1.7.0_45.jdk/Contents/Home
found JAVAFRAMEWORKS = /System/Library/Frameworks/JavaVM.framework
Loading source files for package org.apache.jcc...
doc/serialized-form.html...
Building index for all the packages and classes...
Generating javadoc/overview-tree.html...
Generating javadoc/index-all.html...
Generating javadoc/deprecated-list.html...
Building index for all classes...
Generating javadoc/allclasses-frame.html...
Generating javadoc/allclasses-noframe.html...
Generating javadoc/index.html...
Generating javadoc/help-doc.html...
running build
running build_py
writing /Users/harshsingh/Documents/Codes/IR/jcc/jcc/config.py
copying jcc/config.py -> build/lib.macosx-10.10-intel-2.7/jcc
copying jcc/classes/org/apache/jcc/PythonVM.class -> build/lib.macosx-10.10-intel-2.7/jcc/classes/org/apache/jcc
copying jcc/classes/org/apache/jcc/PythonException.class -> build/lib.macosx-10.10-intel-2.7/jcc/classes/org/apache/jcc
running build_ext
building 'jcc' extension
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX - DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -dynamiclib -D_jcc_lib -DJCC_VER="2. 21" -I/Library/Java/JavaVirtualMachines/jdk1.7.0_45.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.7.0_45. jdk/Contents/Home/include/darwin -I_jcc -Ijcc/sources -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c jcc/sources/jcc.cpp - o build/temp.macosx-10.10-intel-2.7/jcc/sources/jcc.o -DPYTHON -fno-strict-aliasing -Wno-write-strings
clang: warning: argument unused during compilation: '-dynamiclib'
jcc/sources/jcc.cpp:197:16: warning: implicit conversion loses integer precision: 'long' to 'int'
[-Wshorten-64-to-32]
int hash = PyObject_Hash(arg);
~~~~ ^~~~~~~~~~~~~~~~~~
1 warning generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX - DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -dynamiclib -D_jcc_lib -DJCC_VER="2. 21" -I/Library/Java/JavaVirtualMachines/jdk1.7.0_45.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.7.0_45. jdk/Contents/Home/include/darwin -I_jcc -Ijcc/sources -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c jcc/sources/JCCEnv. cpp -o build/temp.macosx-10.10-intel-2.7/jcc/sources/JCCEnv.o -DPYTHON -fno-strict-aliasing -Wno-write-strings
clang: warning: argument unused during compilation: '-dynamiclib'
c++ -Wl,-x -dynamiclib -undefined dynamic_lookup build/temp.macosx-10.10-intel-2.7/jcc/sources/jcc.o build/temp.macosx-10.10-intel-2.7/jcc/sources/JCCEnv. o -o build/lib.macosx-10.10-intel-2.7/libjcc.dylib -L/Library/Java/JavaVirtualMachines/jdk1.7.0_45.jdk/Contents/Home/jre/lib -ljava - L/Library/Java/JavaVirtualMachines/jdk1.7.0_45.jdk/Contents/Home/jre/lib/server -ljvm -Wl,-rpath -Wl,/Library/Java/JavaVirtualMachines/jdk1.7.0_45. jdk/Contents/Home/jre/lib -Wl,-rpath -Wl,/Library/Java/JavaVirtualMachines/jdk1.7.0_45.jdk/Contents/Home/jre/lib/server -Wl,-S -install_name #rpath/libjcc. dylib -current_version 2.21 -compatibility_version 2.21
ld: internal error: atom not found in symbolIndex(__ZN7JNIEnv_13CallIntMethodEP8_jobjectP10_jmethodIDz) for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
error: command 'c++' failed with exit status 1
I am really lost now and any help will be really great.
If rebuilding from source still ends up giving the same errors, you could probably try the following approach.
Seems like there is a bug with running the clang++ command (below) with the -x flag, on OSX 10.9+ (referenced here)
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX - DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -dynamiclib -D_jcc_lib -DJCC_VER="2. 21" -I/Library/Java/JavaVirtualMachines/jdk1.7.0_45.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.7.0_45. jdk/Contents/Home/include/darwin -I_jcc -Ijcc/sources -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c jcc/sources/JCCEnv. cpp -o build/temp.macosx-10.10-intel-2.7/jcc/sources/JCCEnv.o -DPYTHON -fno-strict-aliasing -Wno-write-strings
clang: warning: argument unused during compilation: '-dynamiclib'
c++ -Wl,-x -dynamiclib -undefined dynamic_lookup build/temp.macosx-10.10-intel-2.7/jcc/sources/jcc.o build/temp.macosx-10.10-intel-2.7/jcc/sources/JCCEnv. o -o build/lib.macosx-10.10-intel-2.7/libjcc.dylib -L/Library/Java/JavaVirtualMachines/jdk1.7.0_45.jdk/Contents/Home/jre/lib -ljava - L/Library/Java/JavaVirtualMachines/jdk1.7.0_45.jdk/Contents/Home/jre/lib/server -ljvm -Wl,-rpath -Wl,/Library/Java/JavaVirtualMachines/jdk1.7.0_45. jdk/Contents/Home/jre/lib -Wl,-rpath -Wl,/Library/Java/JavaVirtualMachines/jdk1.7.0_45.jdk/Contents/Home/jre/lib/server -Wl,-S -install_name #rpath/libjcc. dylib -current_version 2.21 -compatibility_version 2.21
Run the clang++ command again without the -x flag and then run:
python setup.py build
Same problem here - from pyLucene-dev:
You must ensure that the compiler used to build Python is the same as the compiler you're using. If you did not build Python then it's likely you're htting a clang/gcc mismatch and you need to rebuild Python from sources, using the same compiler as you're using to build JCC.
The clang problem is fixed as given here. However, its not pushed in the PyLucene latest(as of May 2018) version(v6.5). However, you can still get the next build(v7.2) of Pylucene from this link. Using Pylucene 7.2.0 fixed the issue for me.
I'm trying to upgrade the scipy (currently I have version '0.11.0') on my machine, but I'm getting some compiler error that I can not work around:
When I invoke:
sudo pip install --upgrade scipy
I get:
cc: scipy/optimize/Zeros/bisect.c
clang: error: unknown argument: '-mno-fused-madd' [-Wunused-command-line-argument-hard-error-in-future]
clang: note: this will be a hard error (cannot be downgraded to a warning) in the future
clang: error: unknown argument: '-mno-fused-madd' [-Wunused-command-line-argument-hard-error-in-future]
clang: note: this will be a hard error (cannot be downgraded to a warning) in the future
error: Command "cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch x86_64 -arch i386 -pipe -I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include -c scipy/optimize/Zeros/bisect.c -o build/temp.macosx-10.9-intel-2.7/scipy/optimize/Zeros/bisect.o" failed with exit status 1
Any help is very welcomed!!!
Try:
sudo $ARCHFLAGS=-Wno-error=unused-command-line-argument-hard-error-in-future pip install --upgrade scipy
Good day to everyone,
I've an error trying to compile and install Pygraphviz 1.2 in OS X 10.9
I've downloaded the pygraphviz archive from https://pypi.python.org/packages/source/p/pygraphviz/pygraphviz-1.2.zip#md5=90c728a8db276eede4e3af2f990a8985
From Terminal I've typed
sudo ./setup.py install
the output was:
Trying pkg-config
library_path=/usr/local/Cellar/graphviz/2.38.0/lib
include_path=/usr/local/Cellar/graphviz/2.38.0/include/graphviz
running install
running build
running build_py
running build_ext
building 'pygraphviz._graphviz' extension
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch x86_64 -arch i386 -pipe -I/usr/local/Cellar/graphviz/2.38.0/include/graphviz -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pygraphviz/graphviz_wrap.c -o build/temp.macosx-10.9-intel-2.7/pygraphviz/graphviz_wrap.o
clang: error: unknown argument: '-mno-fused-madd' [-Wunused-command-line-argument-hard-error-in-future]
clang: note: this will be a hard error (cannot be downgraded to a warning) in the future
error: command 'cc' failed with exit status 1
As you can see I've already installed graphviz with Homebrew.
The error is in clang: error: unknown argument: '-mno-fused-madd' [-Wunused-command-line-argument-hard-error-in-future]
Solution from clang error: unknown argument: '-mno-fused-madd' (python package installation failure) is:
export CFLAGS=-Qunused-arguments
export CPPFLAGS=-Qunused-arguments
Installing issues for scipyp on Mac.
My Mac is 10.8, gcc is 4.2.1, gfortran is GNU Fortran (GCC) 4.2.1.
After I downloaded the package and typed sudo python setup.py build,
then it will output:
Could not locate executable f95
customize AbsoftFCompiler
Could not locate executable f90
Could not locate executable f77
customize IBMFCompiler
Could not locate executable xlf90
Could not locate executable xlf
customize IntelFCompiler
Could not locate executable ifort
Could not locate executable ifc
customize GnuFCompiler
Could not locate executable g77
customize Gnu95FCompiler
Found executable /usr/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using build_clib
building 'arpack_scipy' library
compiling C sources
C compiler: clang -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe
compile options: '-Iscipy/sparse/linalg/eigen/arpack/ARPACK/SRC -I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include -c'
clang: scipy/sparse/linalg/eigen/arpack/ARPACK/FWRAPPERS/veclib_cabi_c.c
clang: warning: argument unused during compilation: '-mno-fused-madd'
In file included from scipy/sparse/linalg/eigen/arpack/ARPACK/FWRAPPERS/veclib_cabi_c.c:2:
/System/Library/Frameworks/Accelerate.framework/Headers/Accelerate.h:24:10: fatal error: 'vImage/vImage.h' file not found
#include <vImage/vImage.h>
^
1 error generated.
clang: warning: argument unused during compilation: '-mno-fused-madd'
In file included from scipy/sparse/linalg/eigen/arpack/ARPACK/FWRAPPERS/veclib_cabi_c.c:2:
/System/Library/Frameworks/Accelerate.framework/Headers/Accelerate.h:24:10: fatal error: 'vImage/vImage.h' file not found
#include <vImage/vImage.h>
^
1 error generated.
error: Command "clang -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -Iscipy/sparse/linalg/eigen/arpack/ARPACK/SRC -I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include -c scipy/sparse/linalg/eigen/arpack/ARPACK/FWRAPPERS/veclib_cabi_c.c -o build/temp.macosx-10.8-intel-2.7/scipy/sparse/linalg/eigen/arpack/ARPACK/FWRAPPERS/veclib_cabi_c.o" failed with exit status 1
I don't know why, can anyone explain this?
When I use sudo pip install scipy then the output is:
/System/Library/Frameworks/Accelerate.framework/Headers/Accelerate.h:24:10: fatal error: 'vImage/vImage.h' file not found
#include <vImage/vImage.h>
^
1 error generated.
clang: warning: argument unused during compilation: '-mno-fused-madd'
In file included from scipy/sparse/linalg/eigen/arpack/ARPACK/FWRAPPERS/veclib_cabi_c.c:2:
/System/Library/Frameworks/Accelerate.framework/Headers/Accelerate.h:24:10: fatal error: 'vImage/vImage.h' file not found
#include <vImage/vImage.h>
^
1 error generated.
error: Command "clang -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -Iscipy/sparse/linalg/eigen/arpack/ARPACK/SRC -I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include -c scipy/sparse/linalg/eigen/arpack/ARPACK/FWRAPPERS/veclib_cabi_c.c -o build/temp.macosx-10.8-intel-2.7/scipy/sparse/linalg/eigen/arpack/ARPACK/FWRAPPERS/veclib_cabi_c.o" failed with exit status 1
----------------------------------------
Command /usr/bin/python -c "import setuptools; __file__='/Users/hadoop/Downloads/src/scipy/setup.py'; exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" develop --no-deps failed with error code 1 in /Users/hadoop/Downloads/src/scipy
try this
To summarize, try
CFLAGS="-DVIMAGE_H" python setup.py build