[Numpy-discussion] Problem installing NumPy with Python 3.2.2/MacOS X 10.7.2

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McNicol, Adam

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Dec 16, 2011, 6:07:56 PM12/16/11
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Hi There,

I am very new to numpy and have really only started investigating it as one of my students needs some functionality from matplotlib. I have managed to install everything under Windows for work in class but I use a Mac at home and have been struggling all night to get it to build and install.

I should mention that I am using Python 3.2.2 both in school and at home and it isn't an option to use Python 2.7 as all of the rest of my class is taught in Python 3. I also have the most recent version of Xcode installed.

I have installed the correct build of gcc-4.2 with Fortran (gcc-4.2 (Apple build 5666.3) with GNU Fortran 4.2.4 for Mac OS X 10.7 (Lion)) from http://r.research.att.com/tools/

I then followed the install instructions but the build fails with the following message:

  File "numpy/core/setup.py", line 271, in check_types
    "Cannot compile 'Python.h'. Perhaps you need to "\
SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.

I have got no idea what to do with this error message. Any help would be much appreciated.

Kind Regards,


Adam.

Benjamin Root

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Dec 16, 2011, 6:43:56 PM12/16/11
to Discussion of Numerical Python
Adam,

Just a quick comment about matplotlib and py3k.  We have not yet released a version for py3k.  Support is currently being worked on in the development branch, but I have no clue about the level of testing it has received for windows and macs.

Just a heads-up.

Ben Root

Charles R Harris

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Dec 16, 2011, 7:21:49 PM12/16/11
to Discussion of Numerical Python

Is Python.h present? If so, is it in the search path? How did you install Python3.2.2?

Chuck

Ralf Gommers

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Dec 17, 2011, 6:04:42 AM12/17/11
to Discussion of Numerical Python
On Sat, Dec 17, 2011 at 1:21 AM, Charles R Harris <charles...@gmail.com> wrote:


On Fri, Dec 16, 2011 at 4:07 PM, McNicol, Adam <amcn...@longroad.ac.uk> wrote:

Hi There,

I am very new to numpy and have really only started investigating it as one of my students needs some functionality from matplotlib. I have managed to install everything under Windows for work in class but I use a Mac at home and have been struggling all night to get it to build and install.

I should mention that I am using Python 3.2.2 both in school and at home and it isn't an option to use Python 2.7 as all of the rest of my class is taught in Python 3. I also have the most recent version of Xcode installed.

Did you also install the optional 10.4/5/6 SDK's with XCode? They may be needed.

It could also be a bug in distribute. On OS X 10.6 distribute 0.6.10 works for me, but I see they're now at version 0.6.24. No idea if that works or not.

Ralf

I have installed the correct build of gcc-4.2 with Fortran (gcc-4.2 (Apple build 5666.3) with GNU Fortran 4.2.4 for Mac OS X 10.7 (Lion)) from http://r.research.att.com/tools/

I then followed the install instructions but the build fails with the following message:

  File "numpy/core/setup.py", line 271, in check_types
    "Cannot compile 'Python.h'. Perhaps you need to "\
SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.

I have got no idea what to do with this error message. Any help would be much appreciated.


Is Python.h present? If so, is it in the search path? How did you install Python3.2.2?

Chuck

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McNicol, Adam

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Dec 17, 2011, 6:59:56 AM12/17/11
to McNicol, Adam, numpy-di...@scipy.org

Hi There,

Thanks for the responses.

At this point I would settle from just being able to install matplotlib. Even if some of the functionality isn't present currently that is fine.

I'm afraid my knowledge of Python falls down about here as well. I installed Python 3.2.2 via the installer from Python.org so I have no idea whether Python.h is present or where indeed I would find it or how I would add it to the search path.

Do I have to install from source or something like that?

Thanks again,


Adam.




-----Original Message-----
From: McNicol, Adam
Sent: Fri 12/16/2011 11:07 PM
To: numpy-di...@scipy.org
Subject: Problem installing NumPy with Python 3.2.2/MacOS X 10.7.2

Hi There,

I am very new to numpy and have really only started investigating it as one of my students needs some functionality from matplotlib. I have managed to install everything under Windows for work in class but I use a Mac at home and have been struggling all night to get it to build and install.

I should mention that I am using Python 3.2.2 both in school and at home and it isn't an option to use Python 2.7 as all of the rest of my class is taught in Python 3. I also have the most recent version of Xcode installed.

I have installed the correct build of gcc-4.2 with Fortran (gcc-4.2 (Apple build 5666.3) with GNU Fortran 4.2.4 for Mac OS X 10.7 (Lion)) from http://r.research.att.com/tools/

I then followed the install instructions but the build fails with the following message:

  File "numpy/core/setup.py", line 271, in check_types
    "Cannot compile 'Python.h'. Perhaps you need to "\
SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.

I have got no idea what to do with this error message. Any help would be much appreciated.

Kind Regards,


Adam.

Ralf Gommers

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Dec 18, 2011, 3:49:00 AM12/18/11
to Discussion of Numerical Python
On Sat, Dec 17, 2011 at 12:59 PM, McNicol, Adam <amcn...@longroad.ac.uk> wrote:

Hi There,

Thanks for the responses.

At this point I would settle from just being able to install matplotlib. Even if some of the functionality isn't present currently that is fine.

I'm afraid my knowledge of Python falls down about here as well. I installed Python 3.2.2 via the installer from Python.org so I have no idea whether Python.h is present or where indeed I would find it or how I would add it to the search path.

Do I have to install from source or something like that?


No, your Python install should be fine if you just got the dmg installer from python.org. I recommend you install the OS X SDKs and distribute (http://pypi.python.org/pypi/distribute), as I said before, and try again to compile numpy.

Unfortunately you have chosen a difficult combination of OS and Python version, so we don't have binary installers you can use (yet).

Ralf


Thanks again,


Adam.


-----Original Message-----
From: McNicol, Adam
Sent: Fri 12/16/2011 11:07 PM
To: numpy-di...@scipy.org
Subject: Problem installing NumPy with Python 3.2.2/MacOS X 10.7.2

Hi There,

I am very new to numpy and have really only started investigating it as one of my students needs some functionality from matplotlib. I have managed to install everything under Windows for work in class but I use a Mac at home and have been struggling all night to get it to build and install.

I should mention that I am using Python 3.2.2 both in school and at home and it isn't an option to use Python 2.7 as all of the rest of my class is taught in Python 3. I also have the most recent version of Xcode installed.

I have installed the correct build of gcc-4.2 with Fortran (gcc-4.2 (Apple build 5666.3) with GNU Fortran 4.2.4 for Mac OS X 10.7 (Lion)) from http://r.research.att.com/tools/

I then followed the install instructions but the build fails with the following message:

  File "numpy/core/setup.py", line 271, in check_types
    "Cannot compile 'Python.h'. Perhaps you need to "\
SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.

I have got no idea what to do with this error message. Any help would be much appreciated.

Kind Regards,


Adam.


McNicol, Adam

unread,
Dec 18, 2011, 1:48:47 PM12/18/11
to numpy-di...@scipy.org
Hi Ralf,

Thanks for the response. I tried reinstalling Xcode 4.2.1 and the GCC/Fortran installer from http://r.research.att.com/tools/ (gcc-42-5666.3-darwin11.pkg) before installing the distribute package that you suggested.

I then reran the numpy installer being sure to enter the three export lines as suggested on the numpy installation guide for Lion.

Still no success. I guess I'll just have to wait for more official support for my configuration.

I have included the output from terminal just in case it is useful as there were a few lines in red that suggest something isn't quite right with something. I have placed ** before the lines that appear in red.

I appreciate the suggestions,

Thanks again,


Adam.

running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building py_modules sources
creating build
creating build/src.macosx-10.6-intel-3.2
creating build/src.macosx-10.6-intel-3.2/numpy
creating build/src.macosx-10.6-intel-3.2/numpy/distutils
building library "npymath" sources
customize NAGFCompiler
**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 fort
**Could not locate executable ifc
customize GnuFCompiler
**Could not locate executable g77
customize Gnu95FCompiler
**Could not locate executable gfortran
customize G95FCompiler
**Could not locate executable g95
customize PGroupFCompiler
**Could not locate executable pgf90
**Could not locate executable pgf77
**don't know how to compile Fortran code on platform 'posix'
C compiler: gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -isysroot /Developer/SDKs/MacOSX10.6.sdk -arch i386 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.6.sdk

compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m -c'
gcc-4.2: _configtest.c
gcc-4.2 _configtest.o -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
customize NAGFCompiler
customize AbsoftFCompiler
customize IBMFCompiler
customize IntelFCompiler
customize GnuFCompiler
customize Gnu95FCompiler
customize G95FCompiler
customize PGroupFCompiler
**don't know how to compile Fortran code on platform 'posix'
customize NAGFCompiler
customize AbsoftFCompiler
customize IBMFCompiler
customize IntelFCompiler
customize GnuFCompiler
customize Gnu95FCompiler
customize G95FCompiler
customize PGroupFCompiler
**don't know how to compile Fortran code on platform 'posix'
C compiler: gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -isysroot /Developer/SDKs/MacOSX10.6.sdk -arch i386 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.6.sdk

compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m -c'
gcc-4.2: _configtest.c
_configtest.c:1: warning: conflicting types for built-in function ‘exp’
_configtest.c:1: warning: conflicting types for built-in function ‘exp’
gcc-4.2 _configtest.o -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
creating build/src.macosx-10.6-intel-3.2/numpy/core
creating build/src.macosx-10.6-intel-3.2/numpy/core/src
creating build/src.macosx-10.6-intel-3.2/numpy/core/src/npymath
conv_template:> build/src.macosx-10.6-intel-3.2/numpy/core/src/npymath/npy_math.c
conv_template:> build/src.macosx-10.6-intel-3.2/numpy/core/src/npymath/ieee754.c
conv_template:> build/src.macosx-10.6-intel-3.2/numpy/core/src/npymath/npy_math_complex.c
building extension "numpy.core._sort" sources
Generating build/src.macosx-10.6-intel-3.2/numpy/core/include/numpy/config.h
customize NAGFCompiler
customize AbsoftFCompiler
customize IBMFCompiler
customize IntelFCompiler
customize GnuFCompiler
customize Gnu95FCompiler
customize G95FCompiler
customize PGroupFCompiler
**don't know how to compile Fortran code on platform 'posix'
customize NAGFCompiler
customize AbsoftFCompiler
customize IBMFCompiler
customize IntelFCompiler
customize GnuFCompiler
customize Gnu95FCompiler
customize G95FCompiler
customize PGroupFCompiler
**don't know how to compile Fortran code on platform 'posix'
C compiler: gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -isysroot /Developer/SDKs/MacOSX10.6.sdk -arch i386 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.6.sdk

compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m -c'
gcc-4.2: _configtest.c
In file included from /Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m/bytearrayobject.h:9,
from /Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m/Python.h:73,
from _configtest.c:1:
/Developer/SDKs/MacOSX10.6.sdk/usr/include/stdarg.h:4:25: error: stdarg.h: No such file or directory
In file included from /Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m/bytearrayobject.h:9,
from /Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m/Python.h:73,
from _configtest.c:1:
/Developer/SDKs/MacOSX10.6.sdk/usr/include/stdarg.h:4:25: error: stdarg.h: No such file or directory
lipo: can't figure out the architecture type of: /var/folders/_c/z033hf1s1cgfcxtxfnpg0lsm0000gn/T//ccKv548x.out
In file included from /Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m/bytearrayobject.h:9,
from /Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m/Python.h:73,
from _configtest.c:1:
/Developer/SDKs/MacOSX10.6.sdk/usr/include/stdarg.h:4:25: error: stdarg.h: No such file or directory
In file included from /Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m/bytearrayobject.h:9,
from /Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m/Python.h:73,
from _configtest.c:1:
/Developer/SDKs/MacOSX10.6.sdk/usr/include/stdarg.h:4:25: error: stdarg.h: No such file or directory
lipo: can't figure out the architecture type of: /var/folders/_c/z033hf1s1cgfcxtxfnpg0lsm0000gn/T//ccKv548x.out
failure.
removing: _configtest.c _configtest.o
Running from numpy source directory.Traceback (most recent call last):
File "setup.py", line 196, in <module>
setup_package()
File "setup.py", line 189, in setup_package
configuration=configuration )
File "/Users/adammcnicol/Desktop/numpy-1.6.1/build/py3k/numpy/distutils/core.py", line 186, in setup
return old_setup(**new_attr)
File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/core.py", line 148, in setup
dist.run_commands()
File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/dist.py", line 917, in run_commands
self.run_command(cmd)
File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/dist.py", line 936, in run_command
cmd_obj.run()
File "/Users/adammcnicol/Desktop/numpy-1.6.1/build/py3k/numpy/distutils/command/build.py", line 37, in run
old_build.run(self)
File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/command/build.py", line 126, in run
self.run_command(cmd_name)
File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/dist.py", line 936, in run_command
cmd_obj.run()
File "/Users/adammcnicol/Desktop/numpy-1.6.1/build/py3k/numpy/distutils/command/build_src.py", line 152, in run
self.build_sources()
File "/Users/adammcnicol/Desktop/numpy-1.6.1/build/py3k/numpy/distutils/command/build_src.py", line 169, in build_sources
self.build_extension_sources(ext)
File "/Users/adammcnicol/Desktop/numpy-1.6.1/build/py3k/numpy/distutils/command/build_src.py", line 328, in build_extension_sources
sources = self.generate_sources(sources, ext)
File "/Users/adammcnicol/Desktop/numpy-1.6.1/build/py3k/numpy/distutils/command/build_src.py", line 385, in generate_sources
source = func(extension, build_dir)
File "numpy/core/setup.py", line 410, in generate_config_h
moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir)
File "numpy/core/setup.py", line 41, in check_types
out = check_types(*a, **kw)


File "numpy/core/setup.py", line 271, in check_types
"Cannot compile 'Python.h'. Perhaps you need to "\
SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.

Message: 3
Date: Sun, 18 Dec 2011 09:49:00 +0100
From: Ralf Gommers <ralf.g...@googlemail.com>
Subject: Re: [Numpy-discussion] Problem installing NumPy with Python
3.2.2/MacOS X 10.7.2
To: Discussion of Numerical Python <numpy-di...@scipy.org>
Message-ID:
<CABL7CQh-+t+6p5z_S_JVycRC...@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

On Sat, Dec 17, 2011 at 12:59 PM, McNicol, Adam <amcn...@longroad.ac.uk>wrote:

> **

Ralf

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Ralf Gommers

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Dec 18, 2011, 4:53:35 PM12/18/11
to Discussion of Numerical Python
On Sun, Dec 18, 2011 at 7:48 PM, McNicol, Adam <amcn...@longroad.ac.uk> wrote:
Hi Ralf,

Thanks for the response. I tried reinstalling Xcode 4.2.1 and the GCC/Fortran installer from http://r.research.att.com/tools/ (gcc-42-5666.3-darwin11.pkg) before installing the distribute package that you suggested.

I then reran the numpy installer being sure to enter the three export lines as suggested on the numpy installation guide for Lion.

Still no success. I guess I'll just have to wait for more official support for my configuration.

I have included the output from terminal just in case it is useful as there were a few lines in red that suggest something isn't quite right with something. I have placed ** before the lines that appear in red.

Your compile flags have "-isysroot /Developer/SDKs/MacOSX10.6.sdk" in it twice. Can you confirm you have installed this SDK? If so, I think the problem is that it appears twice. Not sure what's causing it though.

Ralf


McNicol, Adam

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Dec 18, 2011, 5:13:48 PM12/18/11
to numpy-di...@scipy.org
Hi,

Definitely have the sdk installed. In the Developer/SDKs directory I have one for 10.6 and another for 10.7 - no idea where a second 10.6 would be coming from =(


Adam.


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Today's Topics:

1. Re: Problem installing NumPy with Python 3.2.2/MacOS X 10.7.2
(McNicol, Adam)
2. Re: Problem installing NumPy with Python 3.2.2/MacOS X 10.7.2
(Ralf Gommers)


----------------------------------------------------------------------

Message: 1
Date: Sun, 18 Dec 2011 18:48:47 -0000
From: "McNicol, Adam" <amcn...@longroad.ac.uk>


Subject: Re: [Numpy-discussion] Problem installing NumPy with Python
3.2.2/MacOS X 10.7.2

To: <numpy-di...@scipy.org>
Message-ID: <fd29dc5c77c7ee4f0f0622b3459e91a5d77badc3@localhost>
Content-Type: text/plain; charset="iso-8859-1"

Hi Ralf,

Thanks for the response. I tried reinstalling Xcode 4.2.1 and the GCC/Fortran installer from http://r.research.att.com/tools/ (gcc-42-5666.3-darwin11.pkg) before installing the distribute package that you suggested.

I then reran the numpy installer being sure to enter the three export lines as suggested on the numpy installation guide for Lion.

Still no success. I guess I'll just have to wait for more official support for my configuration.

I have included the output from terminal just in case it is useful as there were a few lines in red that suggest something isn't quite right with something. I have placed ** before the lines that appear in red.

I appreciate the suggestions,

Thanks again,


Adam.

_configtest.c:1: warning: conflicting types for built-in function ?exp?
_configtest.c:1: warning: conflicting types for built-in function ?exp?

Ralf

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Message: 2
Date: Sun, 18 Dec 2011 22:53:35 +0100


From: Ralf Gommers <ralf.g...@googlemail.com>
Subject: Re: [Numpy-discussion] Problem installing NumPy with Python
3.2.2/MacOS X 10.7.2
To: Discussion of Numerical Python <numpy-di...@scipy.org>
Message-ID:

<CABL7CQgYJWK2ejek0fbQbs2t...@mail.gmail.com>
Content-Type: text/plain; charset="windows-1252"

On Sun, Dec 18, 2011 at 7:48 PM, McNicol, Adam <amcn...@longroad.ac.uk>wrote:

> Hi Ralf,
>
> Thanks for the response. I tried reinstalling Xcode 4.2.1 and the

> GCC/Fortran installer from http://r.research.att.com/tools/(gcc-42-5666.3-darwin11.pkg) before installing the distribute package that

Ralf

> _configtest.c:1: warning: conflicting types for built-in function ?exp?
> _configtest.c:1: warning: conflicting types for built-in function ?exp?

URL: http://mail.scipy.org/pipermail/numpy-discussion/attachments/20111218/35cbac93/attachment.html

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