Can't install Orange: "error: command 'clang' failed with exit status 1"

Question

I am trying to install Orange on my Mac OS X 10.7.3 (Lion) and I keep getting an error when using either pip or building from source. First, I was getting an error that read:

error: command 'gcc-4.0' failed with exit status 1

I have Xcode 4, which comes bundled with gcc 4.2.1. So I installed 64-bit/32-bit Python 2.7.3, which has gcc 4.2 built in. I also tried to override the compiler choice using:

export CC=gcc-4.2

But this produced a different error:

gcc-4.2 not found, using clang instead
...
error: command 'clang' failed with exit status 1

Here is the full log:

$ python setup.py build
running build
running build_py
copying Orange/version.py -> build/lib.macosx-10.6-intel-2.7/Orange
running build_ext
gcc-4.2 not found, using clang instead
building 'Orange.orange' extension
running pyxtract for Orange.orange
/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python ../pyxtract/defvectors.py
/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python ../pyxtract/pyprops.py -n orange
/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python ../pyxtract/pyxtract.py -m -n orange lib_kernel.cpp lib_components.cpp lib_preprocess.cpp lib_learner.cpp lib_io.cpp lib_vectors.cpp cls_example.cpp cls_value.cpp cls_orange.cpp cls_misc.cpp functions.cpp orange.cpp
Parsing lib_kernel.cpp
Parsing lib_components.cpp
Parsing lib_preprocess.cpp
Parsing lib_learner.cpp
Parsing lib_io.cpp
Parsing lib_vectors.cpp
Parsing cls_example.cpp
Parsing cls_value.cpp
Parsing cls_orange.cpp
Parsing cls_misc.cpp
Parsing functions.cpp
Parsing orange.cpp
Warning: class 'PearsonCorrelation' will not be picklable
Warning: class 'ItemsetNodeProxy' will not be picklable
clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -O2 -DNDEBUG -g -O3 -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -INone -Isource/include -Isource/orange/liblinear -Isource/orange/ppp -Isource/orange/px -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c source/orange/assoc.cpp -o build/temp.macosx-10.6-intel-2.7/source/orange/assoc.o -fPIC -fpermissive -fno-common -w -DDARWIN -DORANGE_EXPORTS
clang: warning: argument unused during compilation: '-fpermissive'
In file included from source/orange/assoc.cpp:25:
In file included from source/orange/random.hpp:26:
In file included from source/orange/root.hpp:25:
source/orange/garbage.hpp:221:9: error: use of undeclared identifier 'raiseError'
        raiseError("bad cast from %s to %s", typeid(U).name(), typeid(T).name());
        ^
source/orange/garbage.hpp:253:7: error: use of undeclared identifier 'raiseError'
      raiseError("Orange internal error: NULL pointer to '%s'", TYPENAME(typeid(T)));
      ^
source/orange/garbage.hpp:261:7: error: use of undeclared identifier 'raiseError'
      raiseError("Orange internal error: NULL pointer to '%s'", TYPENAME(typeid(T)));
      ^
source/orange/garbage.hpp:301:7: error: use of undeclared identifier 'raiseError'
      raiseError("Orange internal error: NULL pointer to '%s'", TYPENAME(typeid(T)));
      ^
source/orange/garbage.hpp:312:7: error: use of undeclared identifier 'raiseError'
      raiseError("Orange internal error: NULL pointer to '%s'", TYPENAME(typeid(T)));
      ^
In file included from source/orange/assoc.cpp:27:
source/orange/examplegen.hpp:143:38: error: expected member name or ';' after declaration specifiers
  TExampleIterator::TExampleIterator(const TExampleIterator &other);
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
source/orange/examplegen.hpp:143:38: error: expected ')'
source/orange/examplegen.hpp:143:37: note: to match this '('
  TExampleIterator::TExampleIterator(const TExampleIterator &other);
                                    ^
source/orange/assoc.cpp:33:1: error: explicit specialization of 'st_classDescription' after instantiation
DEFINE_TOrangeVector_classDescription(PAssociationRule, "TAssociationRules", true, ORANGE_API)
^
source/orange/orvector.hpp:105:57: note: expanded from macro 'DEFINE_TOrangeVector_classDescription'
    TClassDescription TOrangeVector< _TYPE, _WRAPPED >::st_classDescription = { _NAME, &typeid(TOrangeVector< _TYPE, _WRAPPED >), &TOrange::st_classDescription, TOrange_properties, TOrange_components };
                                                        ^
source/orange/ppp/assoc.ppp:111:72: note: implicit instantiation first required here
  {"rules", "association rules", &typeid(POrange), &TAssociationRules::st_classDescription, offsetof(TAssociationClassifier, rules), false, false, 0},
                                                                       ^
8 errors generated.
error: command 'clang' failed with exit status 1

Solution 1

Problem solved: Xcode 4 doesn't actually come with gcc-4.2; it comes with the new LLVM compilers.

It was just a matter of doing:

export CC=llvm-gcc-4.2
export CXX=llvm-g++-4.2

then building Orange.

Solution 2

From http://orange.biolab.si/forum/viewtopic.php?f=4&t=1568

export CC=gcc
export CXX=g++
pip install orange # for example

It seems more robust to not have to get into version number details if you don't have to, right? (I have not had to do this sort of thing before, so I don't know for sure.)

Update: The pip install orange example (above) currently installs an older version of Orange (version 2.5a4 ) instead of 2.6. To get the development version, use:

pip install -e hg+https://bitbucket.org/biolab/orange#egg=Orange

I got the above command from here.

Solution 3

I had to do the following to fix the error on Mac OS Catalina. You can run it in the command line and also put into your bash_profile.

export CC=gcc
export CXX=clang

Comments

[timothyjgraham]

Solved the same issue when trying to install 'matplotlib' using pip