FS#11988 - Python 2.6 rebuilds: Scipy need 2.5

Attached to Project: Community Packages
Opened by Kazuo Teramoto (kazuo) - Tuesday, 04 November 2008, 10:42 GMT
Last edited by Douglas Soares de Andrade (dsa) - Thursday, 13 November 2008, 12:46 GMT
Task Type Bug Report
Category Packages: Extra
Status Closed
Assigned To Douglas Soares de Andrade (dsa)
Architecture All
Severity Low
Priority Normal
Reported Version None
Due in Version Undecided
Due Date Undecided
Percent Complete 100%
Votes 3
Private No

Details

Scypy need to be rebuild, but the current version (0.6) don't work with 2.6 (look at [1] and [2])

[1] http://scipy.org/scipy/scipy/ticket/735
[2] http://www.nabble.com/scipy-0.6-build-error-td20046479.html

----------
Errors:
compile options: '-DNO_ATLAS_INFO=1 -DUSE_VENDOR_BLAS=1 -I/usr/lib/python2.6/site-packages/numpy/core/include -I/usr/include/python2.6 -c'
gcc: scipy/linsolve/_zsuperlumodule.c
In file included from scipy/linsolve/_superluobject.h:8,
from scipy/linsolve/_zsuperlumodule.c:32:
scipy/linsolve/SuperLU/SRC/scomplex.h:60: error: conflicting types for ‘_Py_c_abs’
/usr/include/python2.6/complexobject.h:30: error: previous declaration of ‘_Py_c_abs’ was here
In file included from scipy/linsolve/_superluobject.h:8,
from scipy/linsolve/_zsuperlumodule.c:32:
scipy/linsolve/SuperLU/SRC/scomplex.h:60: error: conflicting types for ‘_Py_c_abs’
/usr/include/python2.6/complexobject.h:30: error: previous declaration of ‘_Py_c_abs’ was here
error: Command "gcc -pthread -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=x86-64 -mtune=generic -O2 -pipe -fPIC -DNO_ATLAS_INFO=1 -DUSE_VENDOR_BLAS=1 -I/usr/lib/python2.6/site-packages/numpy/core/include -I/usr/include/python2.6 -c scipy/linsolve/_zsuperlumodule.c -o build/temp.linux-x86_64-2.6/scipy/linsolve/_zsuperlumodule.o" failed with exit status 1
This task depends upon

Closed by  Douglas Soares de Andrade (dsa)
Thursday, 13 November 2008, 12:46 GMT
Reason for closing:  Upstream
Additional comments about closing:  Scipy does not support python 2.6
Comment by Renato Coutinho (renatomc) - Tuesday, 04 November 2008, 23:03 GMT
Tried to use the svn trunk [4993] and it built correctly and performed some basic functions, but the automated tests don't work.
Comment by Christos Gkekas (chggr) - Saturday, 08 November 2008, 10:02 GMT
I upgraded the package python-scipy yesterday (python-scipy-0.7.0svn-1) and now python seems to be able to import scipy.
But there are still some problems: I made a really basic python script using function scipy.integrate.odeint and I tried to run it. Unfortunately, python terminated itself abruptly giving me an error message "Illegal Instruction".
Perhaps the new package was not build correctly...
Comment by Pierre Gueth (elcerdo) - Monday, 10 November 2008, 11:29 GMT
Scipy lastest svn revision (5034) can be imported with python2.6 but some basic computation doesn't work. For example using scipy.linalg.pinv fails like:
[...]
Ainv=linalg.pinv(A)
File "/usr/lib/python2.6/site-packages/scipy/linalg/basic.py", line 599, in pinv
return lstsq(a, b, cond=cond)[0]
File "/usr/lib/python2.6/site-packages/scipy/linalg/basic.py", line 545, in lstsq
lwork = calc_lwork.gelss(gelss.prefix,m,n,nrhs)[1]
RuntimeError: more argument specifiers than keyword list entries (remaining format:'|:calc_lwork.gelss')
[...]
Comment by Douglas Soares de Andrade (dsa) - Monday, 10 November 2008, 17:12 GMT
Well,

Officially, scipy does not run with python2.6, so we need to use python2.5 or python2.4. I dont even know when scipy will be ready for python 2.6, so what is your suggestions ?

Thanks a lot
Comment by Pierre Gueth (elcerdo) - Wednesday, 12 November 2008, 09:33 GMT
i tried to rebuild scipy package using python25 package from aur: it works great but the matplotlib package fails at import.
scipy without matplotlib isn't very useful since one can't display the result of the computation.

anyway to get a working version of scipy, i have done that:
* build python25 aur package
* rebuild python-numpy from abs
* rebuild python-scipy from abs
* using scipy within a python2.5 shell works as before the upgrade

this isn't a miracle solution since you can't import other libraries that aren't rebuilt for python2.5.

regards

Comment by Pierre Gueth (elcerdo) - Wednesday, 12 November 2008, 16:31 GMT
this patch corrects the superlu compilation problem but not the bad bindings problem
https://bugs.gentoo.org/attachment.cgi?id=171446
Comment by Christos Gkekas (chggr) - Thursday, 13 November 2008, 00:16 GMT
I think there is nothing we can actually do, but wait the developers of scipy to upgrade it so that it is compatible with python 2.6.
Thus, I believe we should close this bug because it is a scipy bug and not an Arch bug.
Hope you agree with me...
Comment by Pierre Gueth (elcerdo) - Thursday, 13 November 2008, 10:54 GMT
i agree with you and i hope someone will make a scipy release that i compatible with python2.6 soon...
Comment by Douglas Soares de Andrade (dsa) - Thursday, 13 November 2008, 12:46 GMT
Yes. I really tried to find a way to make it at least run, but there is no way. We should wait for official support for python 2.6. Meanwhile, use python 2.5 packages, if i manage to get then, i will make a temp repository.

Im closing this bug.

Thanks for the help.

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