Re: [Numpy-discussion] Installing numpy on py 3.1.2 , osx
As an update. I was able to get py 3.2.1 current source to build/install. After that I was able to build and install the current numpy. Everything seems ok. I did try to run the tests but get an error. It looks like nose has a problem. np.test() Running unit tests for numpy Traceback (most recent call last): File stdin, line 1, in module File /Library/Frameworks/Python.framework/Versions/3.1/lib/python3.1/site-packages/numpy/testing/nosetester.py, line 321, in test self._show_system_info() File /Library/Frameworks/Python.framework/Versions/3.1/lib/python3.1/site-packages/numpy/testing/nosetester.py, line 187, in _show_system_info nose = import_nose() File /Library/Frameworks/Python.framework/Versions/3.1/lib/python3.1/site-packages/numpy/testing/nosetester.py, line 56, in import_nose import nose File nose/__init__.py, line 1, in module from nose.core import collector, main, run, run_exit, runmodule File nose/core.py, line 142 print %s version %s % (os.path.basename(sys.argv[0]), __version__) Vincent On Tue, Jun 8, 2010 at 7:02 PM, Vincent Davis vinc...@vincentdavis.netwrote: Have any of you built py 3.1.2 from source on a mac? Vincent On Tue, Jun 8, 2010 at 6:56 PM, David da...@silveregg.co.jp wrote: On 06/09/2010 08:04 AM, Vincent Davis wrote: I do have limits.h in 10.4 sdk So what next. Ay Ideas? I had tried to build py 3.1.2 from source but that did not work either. I had the same issue when I tried the python 3 branch on mac os x. I have not found the issue yet, but I am afraid it is quite subtle, and possibly a bug in python 3 distutils (plus some issues in numpy.distutils). cheers, David ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion *Vincent Davis 720-301-3003 * vinc...@vincentdavis.net my blog http://vincentdavis.net | LinkedInhttp://www.linkedin.com/in/vincentdavis ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Installing numpy on py 3.1.2 , osx
On Mon, Jun 14, 2010 at 5:17 AM, Vincent Davis vinc...@vincentdavis.netwrote: As an update. I was able to get py 3.2.1 current source to build/install. After that I was able to build and install the current numpy. Everything seems ok. I did try to run the tests but get an error. It looks like nose has a problem. np.test() Running unit tests for numpy Traceback (most recent call last): File stdin, line 1, in module File /Library/Frameworks/Python.framework/Versions/3.1/lib/python3.1/site-packages/numpy/testing/nosetester.py, line 321, in test self._show_system_info() File /Library/Frameworks/Python.framework/Versions/3.1/lib/python3.1/site-packages/numpy/testing/nosetester.py, line 187, in _show_system_info nose = import_nose() File /Library/Frameworks/Python.framework/Versions/3.1/lib/python3.1/site-packages/numpy/testing/nosetester.py, line 56, in import_nose import nose File nose/__init__.py, line 1, in module from nose.core import collector, main, run, run_exit, runmodule File nose/core.py, line 142 print %s version %s % (os.path.basename(sys.argv[0]), __version__) You need to install a nose version compatible with python 3 David ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Installing numpy on py 3.1.2 , osx
On Sun, Jun 13, 2010 at 5:06 PM, David Cournapeau courn...@gmail.com wrote: On Mon, Jun 14, 2010 at 5:17 AM, Vincent Davis vinc...@vincentdavis.net wrote: As an update. I was able to get py 3.2.1 current source to build/install. After that I was able to build and install the current numpy. Everything seems ok. I did try to run the tests but get an error. It looks like nose has a problem. np.test() Running unit tests for numpy Traceback (most recent call last): File stdin, line 1, in module File /Library/Frameworks/Python.framework/Versions/3.1/lib/python3.1/site-packages/numpy/testing/nosetester.py, line 321, in test self._show_system_info() File /Library/Frameworks/Python.framework/Versions/3.1/lib/python3.1/site-packages/numpy/testing/nosetester.py, line 187, in _show_system_info nose = import_nose() File /Library/Frameworks/Python.framework/Versions/3.1/lib/python3.1/site-packages/numpy/testing/nosetester.py, line 56, in import_nose import nose File nose/__init__.py, line 1, in module from nose.core import collector, main, run, run_exit, runmodule File nose/core.py, line 142 print %s version %s % (os.path.basename(sys.argv[0]), __version__) You need to install a nose version compatible with python 3 I kinda get that, I posted on the nose list ask what source/version to install. I installed the most recent. Thanks Vincent David ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Installing numpy on py 3.1.2 , osx
On 06/14/2010 08:10 AM, Vincent Davis wrote: I kinda get that, I posted on the nose list ask what source/version to install. I installed the most recent. They have a special branch for py3k support, I think you have to use that, cheers, David ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Installing numpy on py 3.1.2 , osx
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) 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 vinc...@vincentdavis.net wrote: On Mon, Jun 7, 2010 at 7:26 PM, Ralf Gommers ralf.gomm...@googlemail.com wrote: On Tue, Jun 8, 2010 at 4:46 AM, Vincent Davis vinc...@vincentdavis.net wrote: On Mon, Jun 7, 2010 at 2:11 PM, Skipper Seabold jsseab...@gmail.com wrote: On Mon, Jun 7, 2010 at 4:02 PM, Vincent Davis vinc...@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 ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion Terminal Saved Output.txt.zip___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Installing numpy on py 3.1.2 , osx
On Tue, Jun 8, 2010 at 7:58 AM, Zachary Pincus zachary.pin...@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+kTI/-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+kTI/-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 vinc...@vincentdavis.net
wrote:
On Mon, Jun 7, 2010 at 7:26 PM, Ralf Gommers
ralf.gomm...@googlemail.com wrote:
On Tue, Jun 8, 2010 at 4:46 AM, Vincent Davis vinc...@vincentdavis.net
wrote:
On Mon, Jun 7, 2010 at 2:11 PM, Skipper Seabold jsseab...@gmail.com
wrote:
On Mon, Jun 7, 2010 at 4:02 PM, Vincent Davis vinc...@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
Re: [Numpy-discussion] Installing numpy on py 3.1.2 , osx
On Tue, Jun 8, 2010 at 7:58 AM, Zachary Pincus zachary.pin...@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.
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+kTI/-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+kTI/-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 vinc...@vincentdavis.net
wrote:
On Mon, Jun 7, 2010 at 7:26 PM, Ralf Gommers
ralf.gomm...@googlemail.com wrote:
On Tue, Jun 8, 2010 at 4:46 AM, Vincent Davis vinc...@vincentdavis.net
wrote:
On Mon, Jun 7, 2010 at 2:11 PM, Skipper Seabold jsseab...@gmail.com
wrote:
On Mon, Jun 7, 2010 at 4:02 PM, Vincent Davis vinc...@vincentdavis.net
Re: [Numpy-discussion] Installing numpy on py 3.1.2 , osx
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. In the attached file (and the one from the next email too) I didn't see the MACOSX_DEPLOYMENT_TARGET=10.4 export MACOSX_DEPLOYMENT_TARGET lines. Those need to be re-run with each new shell (terminal window) you start up. (Unless you put them in ~/.profile, etc.) You can see from the error messages (after the barf from the 2to3 tool finishes) that there's still the warning about MACOSX_DEPLOYMENT_TARGET being set to 10.3. If you did in fact run those commands immediately prior to python3 setup.py build and still see the MACOSX_DEPLOYMENT_TARGET warning, then there is definitely some bug in the build process that's obliterating that environment variable. Zach ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Installing numpy on py 3.1.2 , osx
I do have limits.h in 10.4 sdk So what next. Ay Ideas? I had tried to build py 3.1.2 from source but that did not work either. Thanks Vincent On Tue, Jun 8, 2010 at 3:15 PM, Zachary Pincus zachary.pin...@yale.edu wrote: Hi Vincent, I'm not really sure -- now the build is using the 10.4 SDK but still not finding the right headers. Could you check to see that the following file exists: /Developer/SDKs/MacOSX10.4u.sdk/usr/include/limits.h If it does, then I'm really not sure what's going on. Zach On Jun 8, 2010, at 3:35 PM, Vincent Davis wrote: On Tue, Jun 8, 2010 at 12:26 PM, Zachary Pincus zachary.pin...@yale.edu wrote: 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. In the attached file (and the one from the next email too) I didn't see the MACOSX_DEPLOYMENT_TARGET=10.4 export MACOSX_DEPLOYMENT_TARGET lines. Those need to be re-run with each new shell (terminal window) you start up. (Unless you put them in ~/.profile, etc.) You can see from the error messages (after the barf from the 2to3 tool finishes) that there's still the warning about MACOSX_DEPLOYMENT_TARGET being set to 10.3. If you did in fact run those commands immediately prior to python3 setup.py build and still see the MACOSX_DEPLOYMENT_TARGET warning, then there is definitely some bug in the build process that's obliterating that environment variable. I did but somehow what was being saved from the terminal was from yesterday ??? So to be sure I started over. I have run it again and for sure I have entered the commands, (see attached evidence) MACOSX_DEPLOYMENT_TARGET=10.4 export MACOSX_DEPLOYMENT_TARGET I then search the terminal output for MACOSX_DEPLOYMENT_TARGET and it only occurred at the beginning where I entered the commands. Thanks Vincent Zach ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion Terminal Output V3.txt.zip___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Installing numpy on py 3.1.2 , osx
On 06/09/2010 08:04 AM, Vincent Davis wrote: I do have limits.h in 10.4 sdk So what next. Ay Ideas? I had tried to build py 3.1.2 from source but that did not work either. I had the same issue when I tried the python 3 branch on mac os x. I have not found the issue yet, but I am afraid it is quite subtle, and possibly a bug in python 3 distutils (plus some issues in numpy.distutils). cheers, David ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Installing numpy on py 3.1.2 , osx
On Mon, Jun 7, 2010 at 4:02 PM, Vincent Davis vinc...@vincentdavis.net wrote: Going down the prerequisite list I have. 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. nose.__version__ '0.11.0' I don't really understand the fortran stuff so so I just entered MacBookPro-new-2:numpy vmd$ python3 setup.py Converting to Python3 via 2to3... RefactoringTool: Skipping implicit fixer: buffer RefactoringTool: Skipping implicit fixer: idioms RefactoringTool: Skipping implicit fixer: set_literal RefactoringTool: Skipping implicit fixer: ws_comma RefactoringTool: Refactored /Users/vmd/Dropbox/numpy/numpy/build/py3k/numpy/__init__.py RefactoringTool: Refactored /Users/vmd/Dropbox/numpy/num . Long list Then I get this Starting interactive session Tasks: i - Show python/platform/machine information ie - Show environment information c - Show C compilers information cname - Set C compiler (current:None) f - Show Fortran compilers information fname - Set Fortran compiler (current:None) e - Edit proposed sys.argv[1:]. Task aliases: 0 - Configure 1 - Build 2 - Install 2prefix - Install with prefix. 3 - Inplace build 4 - Source distribution 5 - Binary distribution Proposed sys.argv = ['setup.py'] Running from numpy source directory.Choose a task (^D to quit, Enter to continue with setup): So I try task f and get Running from numpy source directory.Choose a task (^D to quit, Enter to continue with setup): f Fortran compilers found: Compilers available for this platform, but not found: --fcompiler=absoft Absoft Corp Fortran Compiler --fcompiler=g95 G95 Fortran Compiler --fcompiler=gnu GNU Fortran 77 compiler --fcompiler=gnu95 GNU Fortran 95 compiler --fcompiler=ibm IBM XL Fortran Compiler --fcompiler=intel Intel Fortran Compiler for 32-bit apps --fcompiler=nag NAGWare Fortran 95 Compiler Compilers not available on this platform: --fcompiler=compaq Compaq Fortran Compiler --fcompiler=hpux HP Fortran 90 Compiler --fcompiler=intele Intel Fortran Compiler for Itanium apps --fcompiler=intelem Intel Fortran Compiler for EM64T-based apps --fcompiler=intelev Intel Visual Fortran Compiler for Itanium apps --fcompiler=intelv Intel Visual Fortran Compiler for 32-bit apps --fcompiler=intelvem Intel Visual Fortran Compiler for 64-bit apps --fcompiler=lahey Lahey/Fujitsu Fortran 95 Compiler --fcompiler=mips MIPSpro Fortran Compiler --fcompiler=none Fake Fortran compiler --fcompiler=pg Portland Group Fortran Compiler --fcompiler=sun Sun or Forte Fortran 95 Compiler --fcompiler=vast Pacific-Sierra Research Fortran 90 Compiler For compiler details, run 'config_fc --verbose' setup command. Which gives me the impression I do not have a fortran compiler. Not sure which one I should get, any recommendations? See here for full instructions: http://scipy.org/Installing_SciPy/Mac_OS_X The fortran compiler always recommended for mac is here: http://r.research.att.com/tools/ Also noted in the instructions above. If I type python build I get (See below) Thanks Vincent It seems that it is to much to post soI have clipped it. /Library/Frameworks/Python.framework/Versions/3.1/include/python3.1/abstract.h:627: error: syntax error before '*' token /Library/Frameworks/Python.framework/Versions/3.1/include/python3.1/abstract.h:627: warning: data definition has no type or storage class /Library/Frameworks/Python.framework/Versions/3.1/include/python3.1/abstract.h:635: error: syntax error before '*' token CLIP lipo: can't figure out the architecture type of: /var/folders/2f/2fiXYQSSE+CgAzDQPp9+kTI/-Tmp-//ccsi6RLR.out failure. removing: _configtest.c _configtest.o Traceback (most recent call last): File setup.py, line 210, in module setup_package() File setup.py, line 203, in setup_package configuration=configuration ) File /Users/vmd/Dropbox/numpy/numpy/build/py3k/numpy/distutils/core.py, line 186, in setup return old_setup(**new_attr) File /Library/Frameworks/Python.framework/Versions/3.1/lib/python3.1/distutils/core.py, line 149, in setup dist.run_commands() File /Library/Frameworks/Python.framework/Versions/3.1/lib/python3.1/distutils/dist.py, line 919, in run_commands self.run_command(cmd) File /Library/Frameworks/Python.framework/Versions/3.1/lib/python3.1/distutils/dist.py, line 938, in run_command cmd_obj.run() File /Users/vmd/Dropbox/numpy/numpy/build/py3k/numpy/distutils/command/build.py, line 37, in run old_build.run(self) File
Re: [Numpy-discussion] Installing numpy on py 3.1.2 , osx
On Mon, Jun 7, 2010 at 2:11 PM, Skipper Seabold jsseab...@gmail.com wrote: On Mon, Jun 7, 2010 at 4:02 PM, Vincent Davis vinc...@vincentdavis.net wrote: Going down the prerequisite list I have. 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. nose.__version__ '0.11.0' I don't really understand the fortran stuff so so I just entered MacBookPro-new-2:numpy vmd$ python3 setup.py Converting to Python3 via 2to3... RefactoringTool: Skipping implicit fixer: buffer RefactoringTool: Skipping implicit fixer: idioms RefactoringTool: Skipping implicit fixer: set_literal RefactoringTool: Skipping implicit fixer: ws_comma RefactoringTool: Refactored /Users/vmd/Dropbox/numpy/numpy/build/py3k/numpy/__init__.py RefactoringTool: Refactored /Users/vmd/Dropbox/numpy/num . Long list Then I get this Starting interactive session Tasks: i - Show python/platform/machine information ie - Show environment information c - Show C compilers information cname - Set C compiler (current:None) f - Show Fortran compilers information fname - Set Fortran compiler (current:None) e - Edit proposed sys.argv[1:]. Task aliases: 0 - Configure 1 - Build 2 - Install 2prefix - Install with prefix. 3 - Inplace build 4 - Source distribution 5 - Binary distribution Proposed sys.argv = ['setup.py'] Running from numpy source directory.Choose a task (^D to quit, Enter to continue with setup): So I try task f and get Running from numpy source directory.Choose a task (^D to quit, Enter to continue with setup): f Fortran compilers found: Compilers available for this platform, but not found: --fcompiler=absoft Absoft Corp Fortran Compiler --fcompiler=g95 G95 Fortran Compiler --fcompiler=gnu GNU Fortran 77 compiler --fcompiler=gnu95 GNU Fortran 95 compiler --fcompiler=ibm IBM XL Fortran Compiler --fcompiler=intel Intel Fortran Compiler for 32-bit apps --fcompiler=nag NAGWare Fortran 95 Compiler Compilers not available on this platform: --fcompiler=compaq Compaq Fortran Compiler --fcompiler=hpux HP Fortran 90 Compiler --fcompiler=intele Intel Fortran Compiler for Itanium apps --fcompiler=intelem Intel Fortran Compiler for EM64T-based apps --fcompiler=intelev Intel Visual Fortran Compiler for Itanium apps --fcompiler=intelv Intel Visual Fortran Compiler for 32-bit apps --fcompiler=intelvem Intel Visual Fortran Compiler for 64-bit apps --fcompiler=lahey Lahey/Fujitsu Fortran 95 Compiler --fcompiler=mips MIPSpro Fortran Compiler --fcompiler=none Fake Fortran compiler --fcompiler=pg Portland Group Fortran Compiler --fcompiler=sun Sun or Forte Fortran 95 Compiler --fcompiler=vast Pacific-Sierra Research Fortran 90 Compiler For compiler details, run 'config_fc --verbose' setup command. Which gives me the impression I do not have a fortran compiler. Not sure which one I should get, any recommendations? See here for full instructions: http://scipy.org/Installing_SciPy/Mac_OS_X The fortran compiler always recommended for mac is here: http://r.research.att.com/tools/ Also noted in the instructions above. If I type python build I get (See below) Thanks Vincent It seems that it is to much to post soI have clipped it. /Library/Frameworks/Python.framework/Versions/3.1/include/python3.1/abstract.h:627: error: syntax error before '*' token /Library/Frameworks/Python.framework/Versions/3.1/include/python3.1/abstract.h:627: warning: data definition has no type or storage class /Library/Frameworks/Python.framework/Versions/3.1/include/python3.1/abstract.h:635: error: syntax error before '*' token CLIP lipo: can't figure out the architecture type of: /var/folders/2f/2fiXYQSSE+CgAzDQPp9+kTI/-Tmp-//ccsi6RLR.out failure. removing: _configtest.c _configtest.o Traceback (most recent call last): File setup.py, line 210, in module setup_package() File setup.py, line 203, in setup_package configuration=configuration ) File /Users/vmd/Dropbox/numpy/numpy/build/py3k/numpy/distutils/core.py, line 186, in setup return old_setup(**new_attr) File /Library/Frameworks/Python.framework/Versions/3.1/lib/python3.1/distutils/core.py, line 149, in setup dist.run_commands() File /Library/Frameworks/Python.framework/Versions/3.1/lib/python3.1/distutils/dist.py, line 919, in run_commands self.run_command(cmd) File /Library/Frameworks/Python.framework/Versions/3.1/lib/python3.1/distutils/dist.py, line 938, in run_command cmd_obj.run() File
Re: [Numpy-discussion] Installing numpy on py 3.1.2 , osx
Hi Vincent, (1) Fortran compiler isn't necessary for numpy, but is for scipy, which isn't ported to python 3 yet. (2) Could you put up on pastebin or somewhere online the full error you got? The problem isn't one of not finding the Python.h header file, which will be present in the Python 3 framework that you installed, but some sort of obscure compilation error that got misinterpreted as a missing header by the python build process. Unfortunately, the [CLIP] in your previous email may have obscured the source of the error. Zach ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Installing numpy on py 3.1.2 , osx
On Mon, Jun 7, 2010 at 2:54 PM, Zachary Pincus zachary.pin...@yale.edu wrote: Hi Vincent, (1) Fortran compiler isn't necessary for numpy, but is for scipy, which isn't ported to python 3 yet. (2) Could you put up on pastebin or somewhere online the full error you got? The problem isn't one of not finding the Python.h header file, which will be present in the Python 3 framework that you installed, but some sort of obscure compilation error that got misinterpreted as a missing header by the python build process. Unfortunately, the [CLIP] in your previous email may have obscured the source of the error. Here is a link to the full output after typing python setup.py build. https://docs.google.com/Doc?docid=0AVQgwG2qUDgdZGYyaGo0NjNfMjI5Z3BraHd6ZDghl=en Thanks Vincent Zach ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Installing numpy on py 3.1.2 , osx
On Jun 7, 2010, at 5:19 PM, Vincent Davis wrote: Here is a link to the full output after typing python setup.py build. https://docs.google.com/Doc?docid=0AVQgwG2qUDgdZGYyaGo0NjNfMjI5Z3BraHd6ZDghl=en that's just bringing up an empty document page for me... ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Installing numpy on py 3.1.2 , osx
Well I am way from my computer so I am not sure what's up. You might give it a bit? Vincent On Monday, June 7, 2010, Zachary Pincus zachary.pin...@yale.edu wrote: On Jun 7, 2010, at 5:19 PM, Vincent Davis wrote: Here is a link to the full output after typing python setup.py build. https://docs.google.com/Doc?docid=0AVQgwG2qUDgdZGYyaGo0NjNfMjI5Z3BraHd6ZDghl=en that's just bringing up an empty document page for me... ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Installing numpy on py 3.1.2 , osx
On Mon, Jun 7, 2010 at 3:19 PM, Vincent Davis vinc...@vincentdavis.netwrote: On Mon, Jun 7, 2010 at 2:54 PM, Zachary Pincus zachary.pin...@yale.edu wrote: Hi Vincent, (1) Fortran compiler isn't necessary for numpy, but is for scipy, which isn't ported to python 3 yet. (2) Could you put up on pastebin or somewhere online the full error you got? The problem isn't one of not finding the Python.h header file, which will be present in the Python 3 framework that you installed, but some sort of obscure compilation error that got misinterpreted as a missing header by the python build process. Unfortunately, the [CLIP] in your previous email may have obscured the source of the error. Here is a link to the full output after typing python setup.py build. https://docs.google.com/Doc?docid=0AVQgwG2qUDgdZGYyaGo0NjNfMjI5Z3BraHd6ZDghl=en You can also try zipping the file. IIRC, the limit for posts is about 40K. Chuck ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Installing numpy on py 3.1.2 , osx
On Tue, Jun 8, 2010 at 4:46 AM, Vincent Davis vinc...@vincentdavis.netwrote: On Mon, Jun 7, 2010 at 2:11 PM, Skipper Seabold jsseab...@gmail.com wrote: On Mon, Jun 7, 2010 at 4:02 PM, Vincent Davis vinc...@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. Cheers, Ralf ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Installing numpy on py 3.1.2 , osx
On Mon, Jun 7, 2010 at 7:26 PM, Ralf Gommers ralf.gomm...@googlemail.com wrote: On Tue, Jun 8, 2010 at 4:46 AM, Vincent Davis vinc...@vincentdavis.net wrote: On Mon, Jun 7, 2010 at 2:11 PM, Skipper Seabold jsseab...@gmail.com wrote: On Mon, Jun 7, 2010 at 4:02 PM, Vincent Davis vinc...@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 Cheers, Ralf ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
