Fwd: ROOT_NUMPY

[Piti Ongmongkolkul]

I'm forwarding this to rootpy-dev group. I think I tried to install it on 10.5 once and it worked. But the error looks innocuous enough. Here is some funny stuff that happens

1) Somehow it picks gcc instead of g++. Is it alias on OSX 10.5?

2) It fails on a very innocent looking line 

       void Print()
        {
            cout << colname << " - " << rttype << endl; // <---There
        }

Here are some questions for you

1) What is your OSX version

2) What is your gcc/g++ version

3) Most likely there is a problem with your compiler. How did you install gcc g++ etc.?

Can you compile

#include <iostream>

#include <string>

using namespace std;

int main(){

string hello="hello";

cout << hello << "world" << endl;

return 0;

}

I also believe EPD Python is 32 bit. You might run into problem of linking it later on. 

http://stackoverflow.com/questions/11748504/trying-to-build-muparser-error-explicit-instantiation-of-stdbasic-ostream-b

Piti

Begin forwarded message:

From: Guillermo Rangel <cub...@gmail.com>

Subject: Re: ROOT_NUMPY

Date: April 18, 2013 4:13:37 PM PDT

To: Piti Ongmongkolkul <pit...@gmail.com>

Hi Piti

Ok I did that and now I get a different error. Perhaps this doesn't work with numpy version 1.7.1

admins-MacBook-Pro:root_numpy cubreto$ sudo python setup.py install

dyld: DYLD_ environment variables being ignored because main executable (/usr/bin/sudo) is setuid or setgid

running install

running build

running build_py

creating build

creating build/lib.macosx-10.5-x86_64-2.7

creating build/lib.macosx-10.5-x86_64-2.7/root_numpy

copying root_numpy/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/root_numpy

copying root_numpy/info.py -> build/lib.macosx-10.5-x86_64-2.7/root_numpy

copying root_numpy/OrderedDict.py -> build/lib.macosx-10.5-x86_64-2.7/root_numpy

copying root_numpy/root_numpy.py -> build/lib.macosx-10.5-x86_64-2.7/root_numpy

copying root_numpy/root_numpy_warnings.py -> build/lib.macosx-10.5-x86_64-2.7/root_numpy

copying root_numpy/util.py -> build/lib.macosx-10.5-x86_64-2.7/root_numpy

creating build/lib.macosx-10.5-x86_64-2.7/root_numpy/tests

copying root_numpy/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/root_numpy/tests

copying root_numpy/tests/test.py -> build/lib.macosx-10.5-x86_64-2.7/root_numpy/tests

creating build/lib.macosx-10.5-x86_64-2.7/root_numpy/tests/data

copying root_numpy/tests/data/doubletree1.root -> build/lib.macosx-10.5-x86_64-2.7/root_numpy/tests/data

copying root_numpy/tests/data/fixed1.root -> build/lib.macosx-10.5-x86_64-2.7/root_numpy/tests/data

copying root_numpy/tests/data/fixed2.root -> build/lib.macosx-10.5-x86_64-2.7/root_numpy/tests/data

copying root_numpy/tests/data/hvector.root -> build/lib.macosx-10.5-x86_64-2.7/root_numpy/tests/data

copying root_numpy/tests/data/single1.root -> build/lib.macosx-10.5-x86_64-2.7/root_numpy/tests/data

copying root_numpy/tests/data/single2.root -> build/lib.macosx-10.5-x86_64-2.7/root_numpy/tests/data

copying root_numpy/tests/data/sprtest.root -> build/lib.macosx-10.5-x86_64-2.7/root_numpy/tests/data

copying root_numpy/tests/data/test.root -> build/lib.macosx-10.5-x86_64-2.7/root_numpy/tests/data

copying root_numpy/tests/data/vary1.root -> build/lib.macosx-10.5-x86_64-2.7/root_numpy/tests/data

copying root_numpy/tests/data/vary2.root -> build/lib.macosx-10.5-x86_64-2.7/root_numpy/tests/data

running build_ext

building 'root_numpy._librootnumpy' extension

creating build/temp.macosx-10.5-x86_64-2.7

creating build/temp.macosx-10.5-x86_64-2.7/root_numpy

creating build/temp.macosx-10.5-x86_64-2.7/root_numpy/src

gcc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -DNDEBUG -g -O3 -arch x86_64 -I/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/numpy/core/include -I/Users/cubreto/Downloads/rootv5/include -Iroot_numpy/src -I/Library/Frameworks/EPD64.framework/Versions/7.3/include/python2.7 -c root_numpy/src/_librootnumpy.cpp -o build/temp.macosx-10.5-x86_64-2.7/root_numpy/src/_librootnumpy.o

In file included from /Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1728,

                 from /Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,

                 from /Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15,

                 from root_numpy/src/_librootnumpy.cpp:256:

/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"

root_numpy/src/_librootnumpy.cpp: In function ‘PyObject* newarrayobject(PyTypeObject*, Py_ssize_t, arraydescr*)’:

root_numpy/src/_librootnumpy.cpp:1217: warning: deprecated conversion from string constant to ‘char*’

root_numpy/src/Column.h: At global scope:

root_numpy/src/Column.h: In instantiation of ‘std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits = std::char_traits<char>, _Alloc = std::allocator<char>]’:

root_numpy/src/Column.h:107:   instantiated from here

root_numpy/src/Column.h:107: error: explicit instantiation of ‘std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits = std::char_traits<char>, _Alloc = std::allocator<char>]’ but no definition available

root_numpy/src/Column.h: In instantiation of ‘std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits = std::char_traits<char>, _Alloc = std::allocator<char>]’:

root_numpy/src/Column.h:107:   instantiated from here

root_numpy/src/Column.h:107: error: explicit instantiation of ‘std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits = std::char_traits<char>, _Alloc = std::allocator<char>]’ but no definition available

root_numpy/src/Column.h: In instantiation of ‘std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits = std::char_traits<char>, _Alloc = std::allocator<char>]’:

root_numpy/src/Column.h:107:   instantiated from here

root_numpy/src/Column.h:107: error: explicit instantiation of ‘std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits = std::char_traits<char>, _Alloc = std::allocator<char>]’ but no definition available

error: command 'gcc' failed with exit status 1

admins-MacBook-Pro:root_numpy cubreto$ 

On Thu, Apr 18, 2013 at 3:19 PM, Piti Ongmongkolkul <pit...@gmail.com> wrote:

ROOT comes with root-config command which can be used to ask root about that configuration of your installation. In your terminal
Type

which root

This should give something along the line of /usr/local/root/bin or some path
Then in your .bash_profile which define all your environment variables
add the output from the above command to a line that looks like

export PATH="/output/from/that/command:{$PATH}"

Piti
On Apr 18, 2013, at 1:46 PM, Guillermo Rangel <cub...@gmail.com> wrote:

>

> Hi Piti:
>
> I'm trying to install this ROOT_NUMPY from github but I'm getting the following error. I'm using python version 2.7 thru EPD (Enthought) and I'm using ROOT 5.34 latest patch.
>
>
>
>
> admins-MacBook-Pro:root_numpy cubreto$ sudo python setup.py install
> dyld: DYLD_ environment variables being ignored because main executable (/usr/bin/sudo) is setuid or setgid
> Password:
> Traceback (most recent call last):
>   File "setup.py", line 17, in <module>
>     rootsys = os.environ['ROOTSYS']
>   File "/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/UserDict.py", line 23, in __getitem__
>     raise KeyError(key)
> KeyError: 'ROOTSYS'
>
> Thank you
> Guillermo
>
>
>

[Piti]

My other guess is that you just upgrade your OS but you didn't upgrade your compiler. If this is the problem, download the latest XCode and

go to Preference --> Downloads --> and install Command Line Tools

Piti

[Piti Ongmongkolkul]

Can you compile this code?

[Piti Ongmongkolkul]

My other guess is that EPD is linked with some old version of C++ library. Making them incompatible.

Piti

[Christoph Deil]

Hi Guillermo,

you could give MacPorts ( http://www.macports.org ) or the free version of Anaconda ( https://store.continuum.io/cshop/anaconda ) a try.

I have no experience with EPD, but if you use Macports and do

$ sudo port install root py27-numpy

$ python setup.py install --user

it might just work (because it then uses the same gcc from Macports to compile Python, ROOT, numpy and root_numpy) or if it doesn't I might be able to help.

Another piece of advice: get a new Mac with OS X 10.8  :-) , getting recent software to build on OS X 10.5 is no fun.

Christoph

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[Piti Ongmongkolkul]

After several more emails exchange with Guillermo. He actually use 10.8 with llvm.

I believe the problem is that EPD is linked against some really old libstdc++ which came with OSX 10.5 SDK(10.5) and this SDK doesn't exists anymore in the wild. Furthermore, setuptools that came with EPD isn't configured correctly.

I'd suggest just uninstall EPD and follow instruction given here

http://piti118.github.io/babar_python_tutorial/

(you don't need scipy and scikit-learn) 

Piti

[Piti Ongmongkolkul]

Or it could be Root that is static linked against some funny version of c++

On Apr 18, 2013, at 11:59 PM, Christoph Deil <deil.ch...@googlemail.com> wrote: