[Numpy-discussion] Installing numpy on py 3.1.2 , osx

Vincent Davis vincent@vincentdavis....
Tue Jun 8 09:55:41 CDT 2010


On Tue, Jun 8, 2010 at 7:58 AM, Zachary Pincus <zachary.pincus@yale.edu> wrote:
> This is unexpected, from the error log:
>> /Library/Frameworks/Python.framework/Versions/3.1/include/python3.1/
>> Python.h:11:20: error: limits.h: No such file or directory
>
> No good... it can't find basic system headers. Perhaps it's due to the
> MACOSX_DEPLOYMENT_TARGET environment variable that was warned about
> earlier? (I think I'd seen that sort of thing before... regardless of
> whether you have the 10.4 SDK, if MACOSX_DEPLOYMENT_TARGET is 10.3 I
> think it doesn't get used? Not sure.) Try setting
> MACOSX_DEPLOYMENT_TARGET to 10.4:
> MACOSX_DEPLOYMENT_TARGET=10.4
> export MACOSX_DEPLOYMENT_TARGET
> (if you're using bash, the default OS X shell; for tcsh use "setenv
> MACOSX_DEPLOYMENT_TARGET 10.4")
>
Before I make any changes I wanted to make sure I kinda know what I am
doing and how :)
I have several versions of python installed. The python 3.1.2 is clean
except for nose being installed. to access python 3 on my system I
have a terminal alias to py 3.1.2 as python3

So when in the terminal typing env returns
MacBookPro-new-2:numpy vmd$ env
TERM_PROGRAM=Apple_Terminal
TERM=xterm-color
SHELL=/bin/bash
TMPDIR=/var/folders/2f/2fiXYQSSE+CgAzDQPp9+k++++TI/-Tmp-/
Apple_PubSub_Socket_Render=/tmp/launch-4g8LJN/Render
TERM_PROGRAM_VERSION=273
OLDPWD=/Users/vmd/DropBox/numpy
USER=vmd
COMMAND_MODE=unix2003
SSH_AUTH_SOCK=/tmp/launch-fxsj0I/Listeners
__CF_USER_TEXT_ENCODING=0x1F5:0:0
PATH=/Library/Frameworks/EPD64.framework/Versions/Current/bin:/Library/Frameworks/EPD64.framework/Versions/Current/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/local/git/bin:/usr/X11/bin:/opt/local/bin
MKL_NUM_THREADS=1
PWD=/Users/vmd/DropBox/numpy/numpy
LANG=en_US.UTF-8
SHLVL=1
HOME=/Users/vmd
LOGNAME=vmd
DISPLAY=/tmp/launch-HlM7T8/org.x:0
_=/usr/bin/env
MacBookPro-new-2:numpy vmd$

So looking into this a bit more.
MacBookPro-new-2:numpy vmd$ python3
Python 3.1.2 (r312:79360M, Mar 24 2010, 01:33:18)
[GCC 4.0.1 (Apple Inc. build 5493)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

>>> import os
>>> for x in os.environ.items(): print(x)
...
('MKL_NUM_THREADS', '1')
('LANG', 'en_US.UTF-8')
('TERM', 'xterm-color')
('Apple_PubSub_Socket_Render', '/tmp/launch-4g8LJN/Render')
('TMPDIR', '/var/folders/2f/2fiXYQSSE+CgAzDQPp9+k++++TI/-Tmp-/')
('SHLVL', '1')
('OLDPWD', '/Users/vmd/DropBox/numpy')
('SSH_AUTH_SOCK', '/tmp/launch-fxsj0I/Listeners')
('TERM_PROGRAM_VERSION', '273')
('__CF_USER_TEXT_ENCODING', '0x1F5:0:0')
('PWD', '/Users/vmd/DropBox/numpy/numpy')
('SHELL', '/bin/bash')
('LOGNAME', 'vmd')
('USER', 'vmd')
('PATH', '/Library/Frameworks/EPD64.framework/Versions/Current/bin:/Library/Frameworks/EPD64.framework/Versions/Current/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/local/git/bin:/usr/X11/bin:/opt/local/bin')
('HOME', '/Users/vmd')
('TERM_PROGRAM', 'Apple_Terminal')
('DISPLAY', '/tmp/launch-HlM7T8/org.x:0')
('_', '/usr/local/bin/python3')
('COMMAND_MODE', 'legacy')
>>>


In the end I am not sure how to set the what env belongs to, is this a
python setting or a system setting? Does setting env as you suggest
apply to py3.1.2 as I have it installed?
setenv MACOSX_DEPLOYMENT_TARGET 10.4

Thanks
Vincent



> If this fixes things, I suspect that the build process should probably
> give an error about MACOSX_DEPLOYMENT_TARGET instead of a warning...
>
> Zach
>
>
>
> On Jun 7, 2010, at 11:49 PM, Vincent Davis wrote:
>
>> On Mon, Jun 7, 2010 at 7:59 PM, Vincent Davis <vincent@vincentdavis.net
>> > wrote:
>>> On Mon, Jun 7, 2010 at 7:26 PM, Ralf Gommers
>>> <ralf.gommers@googlemail.com> wrote:
>>>>
>>>>
>>>> On Tue, Jun 8, 2010 at 4:46 AM, Vincent Davis <vincent@vincentdavis.net
>>>> >
>>>> wrote:
>>>>>
>>>>> On Mon, Jun 7, 2010 at 2:11 PM, Skipper Seabold <jsseabold@gmail.com
>>>>> >
>>>>> wrote:
>>>>>> On Mon, Jun 7, 2010 at 4:02 PM, Vincent Davis <vincent@vincentdavis.net
>>>>>> >
>>>>>> wrote:
>>>>>>>   "Cannot compile 'Python.h'. Perhaps you need to "\
>>>>>>> SystemError: Cannot compile 'Python.h'. Perhaps you need to
>>>>>>> install
>>>>>>> python-dev|python-devel.
>>>>>>
>>>>>> Not sure about this.  Might be the compiler issue, but I know on
>>>>>> Linux
>>>>>> you need to install the python-dev (or python-devel) package,
>>>>>> but I
>>>>>> don't see that as a pre-req on the Mac page.
>>>>>
>>>>> So it seems to be seeing the newly installed fortran, but I do
>>>>> get an
>>>>> error at the end.
>>>>>  File "numpy/core/setup.py", line 260, 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.
>>>>>
>>>>> Any ideas, I looked into how python-dev|python-devel applied to
>>>>> python
>>>>> but could make much of what I found. I tried to build python 3.1.2
>>>>> from source but that didn't work out. If I need to go that
>>>>> direction I
>>>>> guess I need to.
>>>>>
>>>> You are probably missing the 10.4 SDK. It's an optional install of
>>>> XCode on
>>>> your Snow Leopard DVD.
>>>
>>> True I have 10.5 and 10.6 SDK I will install the 10.4 and try again.
>>> Thanks
>>> Vincent
>>
>> Still no go after installing 10.4 sdk
>> Attached terminal output.
>>
>>>>
>>>> Cheers,
>>>> Ralf
>>>>
>>>>
>>>>
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>>>>
>>>
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