Dear Alexander,
Thank you for your helpful reply.
I have inserted a few questions below.
On 1 May 2012, at 16:23, Alexander Hansen wrote:
On 5/1/12 4:02 AM, Terence R Wyatt wrote:
I am trying to use scipy-py27 in conjunction with root5, but am having
version compatibility problems.
In order to simplify the problem and avoid any problems with the history
or my fink installation, I have wiped my /sw directory and made a
completely new installation of fink.
That almost never is useful, unless you have changed something else too,
since Fink tries to be deterministic. You'll build up the same history
that you had before.
My problem was that I wanted to completely remove the root5 installation from
my Mac in order to force it to be completely rebuilt. I tried
fink purge roo5
but that just moved files/links rather than deleting them, so that when I
subsequently did
fink install root5
it just re-instated the previously compiled version.
I then tried deleting the /sw/bin/python2.7 executable, which did at least
force recompilation of the root executable, but I wasn't completely sure that I
would have removed all the necessary other files that might have already
acquired an implicit dependence on the built-in version of python.
Was there a more elegant solution to achieve this aim?
fink --version gives
Package manager version: 0.32.6
Distribution version: selfupdate-rsync Sun Apr 29 13:44:05 2012, 10.7,
x86_64
Trees: local/main stable/main
I have then installed only
fink install scipy-py27
fink install root5
In my .bashrc file I have:
export ROOTSYS=/sw
export PATH=$ROOTSYS/bin:$PATH
export LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH
export PYTHONPATH=/sw/lib/python2.7/site-packages/:/sw/lib/root/:
root5 sets PYTHONPATH already on 10.7. You don't need to do this.
If I then run the version of python installed by fink I am unable to
import ROOT
/sw/bin/python2.7
Python 2.7.3 (default, Apr 29 2012, 16:14:30)
[GCC 4.2.1 Compatible Apple Clang 2.1 (tags/Apple/clang-163.7.1)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
import ROOT
Fatal Python error: Interpreter not initialized (version mismatch?)
Abort trap: 6
In contrast, when I run the version of python (2.7.1) that came
pre-installed on my Mac then I am able to
import ROOT. However, this pre-installed version of python does not
come with scipy. If I try to use scipy
from the fink-installed version this doesn't work.
/usr/bin/python
Python 2.7.1 (r271:86832, Jun 16 2011, 16:59:05)
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] on
darwin
Type "help", "copyright", "credits" or "license" for more information.
from scipy.optimize import fmin
Fatal Python error: PyThreadState_Get: no current thread
Abort trap: 6
I assume this is also due to the version mismatch between 2.7.1 and 2.7.3.
Or because our python packages are built with different options than is
the built-in Python.
Ideally, I'd like to use in a consistent fashion the software I have
installed using fink, since naively
I'd have imagined that would be the best way to ensure a consistent set.
Is there some way of forcing root5
to be made compatible with the fink-installed python 2.7.3?
I use a MacBook Pro running OS X 10.7.3.
Advice would be most welcome.
Regards, Terry Wyatt.
On 10.7 root5 explicitly builds against the built-in Python, so it
appears that what you are seeing is the intended behavior. I'm not a
Python expert, so I don't know if you can recompile your installed
ROOT.py and friends using Fink's python2.7 to work around this issue.
Remi would be the one to address the usability question of having
root5's python modules not be accessible to Fink's scipy.
Would it make any sense to install scipy and then set
ln -s /sw/bin/python2.7 /usr/bin/python
ln -s /sw/bin/python2.7 /usr/bin/python2.7
ln -s /sw/lib/python2.7 /usr/lib/python2.7
before installing root5?
Regards, Terry Wyatt.
For Remi: Why didn't you use RuntimeVars to set PYTHONPATH? :-) It
looks like you reinvented the wheel here.
--
Alexander Hansen, Ph.D.
Fink User Liaison
http://finkakh.wordpress.com/2012/02/21/got-job/
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