[Numpy-discussion] numpy and readline installation fails

abc def cannonjunk@hotmail.co...
Fri Jul 6 10:03:40 CDT 2012


My apologies for sending the last email out too quickly.
I found this page (http://www.scipy.org/Installing_SciPy/Mac_OS_X) and, ignoring the parts about needing 4.0-version compilers (it doesn't work if you use 4.0, but does work for 4.2 (on osx 10.6, with homebrew's python)), it works fine for numpy and scipy - I recommend this for anyone else who is having similar trouble.

Thank you again all very much for your help!

Tom

----------------------------------------
> From: cannonjunk@hotmail.co.uk
> To: numpy-discussion@scipy.org
> Date: Fri, 6 Jul 2012 14:57:43 +0100
> Subject: Re: [Numpy-discussion] numpy and readline installation fails
>
>
> Thank you for your advice.
> I followed the advice about installing python from homebrew. I then ran "brew doctor" and re-arranged the paths as it told me to. It also gives another list of warnings which I'll put at the bottom of this email.
>
> My question is now, what is the best way to install numpy (and scipy, and matplotlib), so that it will couple with the brew-installed python?
> My earlier dmg install of numpy still doesn't work: (I've tried "python -pylab" and just "python" with importing numpy)
>
> kuuki:~ tom$ which python
> /usr/local/bin/python
> kuuki:~ tom$ ipython -pylab
> WARNING: `-pylab` flag has been deprecated.
>     Use `--pylab` instead, or `--pylab=foo` to specify a backend./Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/IPython/utils/rlineimpl.py:111: RuntimeWarning:
> ******************************************************************************
> libedit detected - readline will not be well behaved, including but not limited to:
>    * crashes on tab completion
>    * incorrect history navigation
>    * corrupting long-lines
>    * failure to wrap or indent lines properly
> It is highly recommended that you install readline, which is easy_installable:
>      easy_install readline
> Note that `pip install readline` generally DOES NOT WORK, because
> it installs to site-packages, which come *after* lib-dynload in sys.path,
> where readline is located.  It must be `easy_install readline`, or to a custom
> location on your PYTHONPATH (even --user comes after lib-dyload).
> ******************************************************************************
>   RuntimeWarning)
> Python 2.7.3 (v2.7.3:70274d53c1dd, Apr  9 2012, 20:52:43)
> Type "copyright", "credits" or "license" for more information.
>
> IPython 0.13 -- An enhanced Interactive Python.
> ?         -> Introduction and overview of IPython's features.
> %quickref -> Quick reference.
> help      -> Python's own help system.
> object?   -> Details about 'object', use 'object??' for extra details.
> [TerminalIPythonApp] GUI event loop or pylab initialization failed
> ---------------------------------------------------------------------------
> ImportError                               Traceback (most recent call last)
> /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/IPython/core/pylabtools.pyc in find_gui_and_backend(gui)
>     194     """
>     195
> --> 196     import matplotlib
>     197
>     198     if gui and gui != 'auto':
>
> /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/__init__.py in <module>()
>     131 import sys, os, tempfile
>     132
> --> 133 from matplotlib.rcsetup import (defaultParams,
>     134                                 validate_backend,
>     135                                 validate_toolbar,
>
> /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/rcsetup.py in <module>()
>      17 import warnings
>      18 from matplotlib.fontconfig_pattern import parse_fontconfig_pattern
> ---> 19 from matplotlib.colors import is_color_like
>      20
>      21 #interactive_bk = ['gtk', 'gtkagg', 'gtkcairo', 'fltkagg', 'qtagg', 'qt4agg',
>
> /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/colors.py in <module>()
>      50 """
>      51 import re
> ---> 52 import numpy as np
>      53 from numpy import ma
>      54 import matplotlib.cbook as cbook
>
> ImportError: No module named numpy
>
> In [1]:
> KeyboardInterrupt
>
> In [1]: ^D
> Do you really want to exit ([y]/n)? y
> kuuki:~ tom$ python
> Python 2.7.3 (default, Jul  5 2012, 08:21:27)
> [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import numpy as np
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
> ImportError: No module named numpy
> >>>
>
>
>
> And the list of warnings:
> kuuki:~ tom$ brew doctor
>
> Error: Some directories in /usr/local/share/man aren't writable.
> This can happen if you "sudo make install" software that isn't managed
> by Homebrew. If a brew tries to add locale information to one of these
> directories, then the install will fail during the link step.
> You should probably `chown` them:
>
>     /usr/local/share/man/de
>     /usr/local/share/man/de/man1
>     /usr/local/share/man/es
>     /usr/local/share/man/es/man1
>     /usr/local/share/man/fr
>     /usr/local/share/man/fr/man1
>     /usr/local/share/man/hr
>     /usr/local/share/man/hr/man1
>     /usr/local/share/man/hu
>     /usr/local/share/man/hu/man1
>     /usr/local/share/man/it
>     /usr/local/share/man/it/man1
>     /usr/local/share/man/jp
>     /usr/local/share/man/jp/man1
>     /usr/local/share/man/pl
>     /usr/local/share/man/pl/man1
>     /usr/local/share/man/pt_BR
>     /usr/local/share/man/pt_BR/man1
>     /usr/local/share/man/pt_PT
>     /usr/local/share/man/pt_PT/man1
>     /usr/local/share/man/ro
>     /usr/local/share/man/ro/man1
>     /usr/local/share/man/ru
>     /usr/local/share/man/ru/man1
>     /usr/local/share/man/sk
>     /usr/local/share/man/sk/man1
>     /usr/local/share/man/zh
>     /usr/local/share/man/zh/man1
> Error: "config" scripts exist outside your system or Homebrew directories.
> `./configure` scripts often look for *-config scripts to determine if
> software packages are installed, and what additional flags to use when
> compiling and linking.
>
> Having additional scripts in your path can confuse software installed via
> Homebrew if the config script overrides a system or Homebrew provided
> script of the same name. We found the following "config" scripts:
>
>     /Library/Frameworks/Python.framework/Versions/2.7/bin/python-config
>     /Library/Frameworks/Python.framework/Versions/2.7/bin/python2-config
>     /Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7-config
>     /Library/Frameworks/Python.framework/Versions/2.6/bin/python-config
>     /Library/Frameworks/Python.framework/Versions/2.6/bin/python2.6-config
> Error: Your Homebrew is outdated
> You haven't updated for at least 24 hours, this is a long time in brewland!
> Error: Unbrewed dylibs were found in /usr/local/lib.
> If you didn't put them there on purpose they could cause problems when
> building Homebrew formulae, and may need to be deleted.
>
> Unexpected dylibs:
>     /usr/local/lib/libgcc_ext.10.4.dylib    /usr/local/lib/libgcc_ext.10.5.dylib    /usr/local/lib/libgcc_s.1.dylib    /usr/local/lib/libgfortran.3.dylib    /usr/local/lib/libgomp.1.dylib    /usr/local/lib/libmca_common_sm.1.dylib    /usr/local/lib/libmpi.0.dylib    /usr/local/lib/libmpi_cxx.0.dylib    /usr/local/lib/libmpi_f77.0.dylib    /usr/local/lib/libopen-pal.0.dylib    /usr/local/lib/libopen-rte.0.dylib    /usr/local/lib/libssp.0.dylib
> Error: Unbrewed .la files were found in /usr/local/lib.
> If you didn't put them there on purpose they could cause problems when
> building Homebrew formulae, and may need to be deleted.
>
> Unexpected .la files:
>     /usr/local/lib/libgfortran.la    /usr/local/lib/libgmp.la    /usr/local/lib/libgomp.la    /usr/local/lib/libmca_common_sm.la    /usr/local/lib/libmpc.la    /usr/local/lib/libmpfr.la    /usr/local/lib/libmpi.la    /usr/local/lib/libmpi_cxx.la    /usr/local/lib/libmpi_f77.la    /usr/local/lib/libmpi_f90.la    /usr/local/lib/libopen-pal.la    /usr/local/lib/libopen-rte.la    /usr/local/lib/libotf.la    /usr/local/lib/libssp.la    /usr/local/lib/libssp_nonshared.la
> Error: Unbrewed static libraries were found in /usr/local/lib.
> If you didn't put them there on purpose they could cause problems when
> building Homebrew formulae, and may need to be deleted.
>
> Unexpected static libraries:
>     /usr/local/lib/libgfortran.a    /usr/local/lib/libgmp.a    /usr/local/lib/libgomp.a    /usr/local/lib/libiberty.a    /usr/local/lib/libmpc.a    /usr/local/lib/libmpfr.a    /usr/local/lib/libmpi_f90.a    /usr/local/lib/libotf.a    /usr/local/lib/libssp.a    /usr/local/lib/libssp_nonshared.a    /usr/local/lib/libvt.a    /usr/local/lib/libvt.fmpi.a    /usr/local/lib/libvt.mpi.a    /usr/local/lib/libvt.omp.a    /usr/local/lib/libvt.ompi.a
> kuuki:~ tom$ brew install numpy
> Error: No available formula for numpy
>
>
> Some of these unexpected libraries seem to be from my earlier install of gfortran and mpi (nothing to do with homebrew).
> By the way, there seem to be many versions of python (apple, dmg, homebrew) on my macbook.
> Thanks again for your help!!
>
> Tom
>
> ________________________________
> > Date: Wed, 4 Jul 2012 18:44:46 +0200
> > From: ralf.gommers@googlemail.com
> > To: numpy-discussion@scipy.org
> > Subject: Re: [Numpy-discussion] numpy and readline installation fails
> >
> >
> >
> > On Wed, Jul 4, 2012 at 6:24 PM, Aron Ahmadia
> > <aron@ahmadia.net<mailto:aron@ahmadia.net>> wrote:
> > How do the .dmg files work? Are these binary installers into the
> > system Python? I would expect that these wouldn't work with a manually
> > installed Python from python.org<http://python.org>, but I have no
> > experience with them.
> >
> > They're binary installers for the python.org<http://python.org> Python.
> > So they install into /Library/Frameworks/Python.framework/. They don't
> > work with the system (Apple) Python; I think leaving that alone and
> > installing from python.org<http://python.org> is in general good
> > advice.
> >
> >
> > Tom, I have had very good luck with the brew Python 2.7 installer,
> > which will give you a /usr/local Python base install and easy_install.
> > Brew can also install readline correctly for you.
> >
> > https://github.com/mxcl/homebrew/wiki/Homebrew-and-Python
> >
> > Homebrew appears to be better than MacPorts/Fink, but installing
> > everything from source is not the first advice I'd give to a new user.
> >
> > Ralf
> >
> > If you want an all-in-one solution, you can also grab either the free
> > EPD distribution or another of the "all-in-one" packs.
> >
> > A
> >
> >
> > On Wed, Jul 4, 2012 at 7:03 PM, Paul Anton Letnes
> > <paul.anton.letnes@gmail.com<mailto:paul.anton.letnes@gmail.com>>
> > wrote:
> > Hello,
> >
> > I don't know exactly what went wrong. I'd start out my debugging by
> > 1) which python # see whether you're running apple's python in
> > /usr/bin/python, or the one you tried to install
> > 2) which easy_install # did you run Apple-python's easy_install, or the
> > one you (tried to) installed?
> > 3) If all of the above match, try running python (not ipython) and try
> > to import numpy. Apple's python ships with numpy (at least the Lion /
> > 10.7 one does).
> > 4) Next, print numpy.__file__ to see whether numpy got installed to
> > where it should
> >
> > In general, I'd advice you to install one package at a time, then test
> > it to see whether it has been installed properly. When you're confident
> > everything is OK, move on to the next package. For instance, test numpy
> > by
> > $ python -c 'import numpy; numpy.test()'
> > and scipy with
> > $ python -c 'import scipy;scipy.test()'
> > (for instance).
> >
> > When you're sure the fundament (python, numpy) is in order, proceed
> > with the house (scipy, matplotlib).
> >
> > Cheers
> > Paul
> >
> >
> > On 4. juli 2012, at 16:16, abc def wrote:
> >
> > >
> > > Hello,
> > >
> > > I'm new to python and I'd like to learn about numpy / scipy /
> > matplotlib, but I'm having trouble getting started.
> > >
> > > I'm following the instructions here: http://www.scipy.org/Getting_Started
> > >
> > > First I installed the latest version of python from
> > python.org<http://python.org> by downloading the dmg file, since I read
> > that it doesn't work with apple's installer, and then installed numpy /
> > scipy / matplotlib by downloading the relevent dmg files.
> > > I then downloaded ipython, ran "easy_install readline" and then ran
> > "python setup.py install".
> > >
> > > Then I started ipython with "ipython -pylab" as per the instructions
> > but then I get muliple error messages:
> > >
> > >
> > >
> > >
> > >
> > > $ ipython --pylab
> > >
> > /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/IPython/utils/rlineimpl.py:111:
> > RuntimeWarning:
> > >
> > ******************************************************************************
> > > libedit detected - readline will not be well behaved, including but
> > not limited to:
> > > * crashes on tab completion
> > > * incorrect history navigation
> > > * corrupting long-lines
> > > * failure to wrap or indent lines properly
> > > It is highly recommended that you install readline, which is
> > easy_installable:
> > > easy_install readline
> > > Note that `pip install readline` generally DOES NOT WORK, because
> > > it installs to site-packages, which come *after* lib-dynload in sys.path,
> > > where readline is located. It must be `easy_install readline`, or to
> > a custom
> > > location on your PYTHONPATH (even --user comes after lib-dyload).
> > >
> > ******************************************************************************
> > > RuntimeWarning)
> > > Python 2.7.3 (v2.7.3:70274d53c1dd, Apr 9 2012, 20:52:43)
> > > Type "copyright", "credits" or "license" for more information.
> > >
> > > IPython 0.13 -- An enhanced Interactive Python.
> > > ? -> Introduction and overview of IPython's features.
> > > %quickref -> Quick reference.
> > > help -> Python's own help system.
> > > object? -> Details about 'object', use 'object??' for extra details.
> > > [TerminalIPythonApp] GUI event loop or pylab initialization failed
> > > ---------------------------------------------------------------------------
> > > ImportError Traceback (most recent call last)
> > >
> > /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/IPython/core/pylabtools.pyc
> > in find_gui_and_backend(gui)
> > > 194 """
> > > 195
> > > --> 196 import matplotlib
> > > 197
> > > 198 if gui and gui != 'auto':
> > >
> > >
> > /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/__init__.py
> > in <module>()
> > > 131 import sys, os, tempfile
> > > 132
> > > --> 133 from matplotlib.rcsetup import (defaultParams,
> > > 134 validate_backend,
> > > 135 validate_toolbar,
> > >
> > >
> > /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/rcsetup.py
> > in <module>()
> > > 17 import warnings
> > > 18 from matplotlib.fontconfig_pattern import parse_fontconfig_pattern
> > > ---> 19 from matplotlib.colors import is_color_like
> > > 20
> > > 21 #interactive_bk = ['gtk', 'gtkagg', 'gtkcairo', 'fltkagg',
> > 'qtagg', 'qt4agg',
> > >
> > >
> > /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/colors.py
> > in <module>()
> > > 50 """
> > > 51 import re
> > > ---> 52 import numpy as np
> > > 53 from numpy import ma
> > > 54 import matplotlib.cbook as cbook
> > >
> > > ImportError: No module named numpy
> > >
> > > In [1]:
> > >
> > >
> > >
> > >
> > > it seems the installation of numpy and readline didn't work, and
> > there are problems with matplotlib, even though I think I followed all
> > the instructions carefully.
> > > I can't figure out what I did wrong. Can anybody help?
> > >
> > > I'm running mac os 10.6.
> > >
> > > Thank you!
> > >
> > > Tom
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > NumPy-Discussion mailing list
> > > NumPy-Discussion@scipy.org<mailto:NumPy-Discussion@scipy.org>
> > > http://mail.scipy.org/mailman/listinfo/numpy-discussion
> >
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