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

Tue Jun 8 12:29:09 EDT 2010

On Tue, Jun 8, 2010 at 10:06 AM, Zachary Pincus <zachary.pincus at yale.edu> wrote:
>> On Tue, Jun 8, 2010 at 7:58 AM, Zachary Pincus <zachary.pincus at 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
>
> Basic summary of environment variables:
> http://en.wikipedia.org/wiki/Environment_variable
>
> In a unix shell, setting an environment variable will apply to the
> processes that are started from within that shell session. To
> permanently set environment variables, you'd need to add the relevant
> commands to the bash .profile or other startup files (a topic in and
> of itself). So the good news is that nothing you do will w/r/t
> environment vars will persist past exiting that particular shell.
>
> Anyhow, from the below, you don't have MACOSX_DEPLOYMENT_TARGET set at
> all, which is what would be expected. I wonder if perhaps the python/
> numpy build process is setting MACOSX_DEPLOYMENT_TARGET to 10.3 when
> there is none already set? If so this is not good.
>
> Anyhow, given that you're using bash, here's what to do to try to build:
>
> cd /path/to/numpy/src
> MACOSX_DEPLOYMENT_TARGET=10.4
> export MACOSX_DEPLOYMENT_TARGET
> python3 setup.py build
>
> and see if that fixes the issue? If so there's some bug in the numpy
> build process you've stumbled across.

Failed again, I have attached the output including the execution of
the above commands.
Thanks for link to the environment variables, I need to read that.

And Thanks again for your time

Vincent

>
> Zach
>
>
>
>>
>> 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 at vincentdavis.net
>>>>> wrote:
>>>>> On Mon, Jun 7, 2010 at 7:26 PM, Ralf Gommers
>>>>> <ralf.gommers at googlemail.com> wrote:
>>>>>>
>>>>>>
>>>>>> On Tue, Jun 8, 2010 at 4:46 AM, Vincent Davis <vincent at vincentdavis.net
>>>>>>>
>>>>>> wrote:
>>>>>>>
>>>>>>> On Mon, Jun 7, 2010 at 2:11 PM, Skipper Seabold <jsseabold at gmail.com
>>>>>>>>
>>>>>>> wrote:
>>>>>>>> On Mon, Jun 7, 2010 at 4:02 PM, Vincent Davis <vincent at 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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