v_2e | 1 Dec 11:14 2010
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Re: [sage-on-gentoo] Sage-4.5.3 segmentation fault

  Hello!
  I have migrated to Python-2.7.1 yesterday (by the way, I had to
rename my 
'/var/lib/layman/sage-on-gentoo/dev-lang/python/python-2.7.ebuild'
file to 
'/var/lib/layman/sage-on-gentoo/dev-lang/python/python-2.7.1.ebuild'
since there is Python-2.7.1 in the main Portage tree already.)
  And Sage shows the same behaviour as before. The same segmentation
fault.

----- 
 <v_2e <at> ukr.net>

Christopher Schwan | 1 Dec 11:29 2010
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Re: [sage-on-gentoo] Sage-4.5.3 segmentation fault

Hi,

On Wednesday 01 December 2010 11:14:29 v_2e <at> ukr.net wrote:
>   Hello!
>   I have migrated to Python-2.7.1 yesterday (by the way, I had to
> rename my
> '/var/lib/layman/sage-on-gentoo/dev-lang/python/python-2.7.ebuild'
> file to
> '/var/lib/layman/sage-on-gentoo/dev-lang/python/python-2.7.1.ebuild'
> since there is Python-2.7.1 in the main Portage tree already.)

Thanks for that info - I removed the 2.7 from our overlay because it isnt 
supported (not tested).

>   And Sage shows the same behaviour as before. The same segmentation
> fault.

Thats is as expected since Sage selects python to be 2.6.

> 
> 
> -----
>  <v_2e <at> ukr.net>

Jan Marten Simons | 3 Dec 15:48 2010
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cctbx version-bump to 2010.09.15.2318?

Hi,

I recently found out cctbx has released a new version (see 
http://cci.lbl.gov/cctbx_build/). I tried to do a version-bump with the 
ebuild, but as some code changed some patches don't apply anymore.

I found out, tst-server.py.patch can be dropped, as the code it tries to 
correct has been removed upstream.

Aditionally I found a bug:

/usr/lib64/cctbx/cctbx_build/bin/cctbx.python is refering to paths in 
/var/tmp/portage, which don't exist post-install and therefore calling 
cctbx.python does not give a useable environment. After fixing up those paths 
(manually) I got a working python shell where import cctbx works like it 
should.

I'll gladly help in debugging/testing an ebuld of the most recent version of 
cctbx.

With regards,

Jan Simons

Institute of Crystallography
RWTH Aachen University

Steven Trogdon | 3 Dec 22:49 2010
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[sage-on-gentoo] gdmodule-0.56-r1

Hello,

With the upgrade from gdmodule-0.56 -> gdmodule-0.56-r1 the following  
sage test now fails

	sage -t  -long -force_lib "devel/sage/sage/matrix/matrix2.pyx"

as

**********************************************************************
File "/usr/share/sage/devel/sage/sage/matrix/matrix2.pyx", line 5463:
     sage: M.visualize_structure(SAGE_TMP + "matrix.png")
Exception raised:
     Traceback (most recent call last):
       File "/usr/bin/ncadoctest.py", line 1231, in run_one_test
         self.run_one_example(test, example, filename, compileflags)
       File "/usr/bin/sagedoctest.py", line 38, in run_one_example
         OrigDocTestRunner.run_one_example(self, test, example,  
filename, compileflags)
       File "/usr/bin/ncadoctest.py", line 1172, in run_one_example
         compileflags, 1) in test.globs
       File "<doctest __main__.example_83[3]>", line 1, in <module>
         M.visualize_structure(SAGE_TMP + "matrix.png")###line 5463:
     sage: M.visualize_structure(SAGE_TMP + "matrix.png")
       File "matrix2.pyx", line 5520, in  
sage.matrix.matrix2.Matrix.visualize_structure  
(sage/matrix/matrix2.c:31006)
     NotImplementedError: PNG Support Not Available
**********************************************************************

(Continue reading)

Christopher Schwan | 4 Dec 15:34 2010
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Re: [sage-on-gentoo] gdmodule-0.56-r1

Hi Steven,

thank you for reporting! I have investigated on this and filed a bug for it: 

https://bugs.gentoo.org/show_bug.cgi?id=347722

On Friday 03 December 2010 22:49:37 Steven Trogdon wrote:
> Hello,
> 
> With the upgrade from gdmodule-0.56 -> gdmodule-0.56-r1 the following
> sage test now fails
> 
> 	sage -t  -long -force_lib "devel/sage/sage/matrix/matrix2.pyx"
> 
> as
> 
> **********************************************************************
> File "/usr/share/sage/devel/sage/sage/matrix/matrix2.pyx", line 5463:
>      sage: M.visualize_structure(SAGE_TMP + "matrix.png")
> Exception raised:
>      Traceback (most recent call last):
>        File "/usr/bin/ncadoctest.py", line 1231, in run_one_test
>          self.run_one_example(test, example, filename, compileflags)
>        File "/usr/bin/sagedoctest.py", line 38, in run_one_example
>          OrigDocTestRunner.run_one_example(self, test, example,
> filename, compileflags)
>        File "/usr/bin/ncadoctest.py", line 1172, in run_one_example
>          compileflags, 1) in test.globs
>        File "<doctest __main__.example_83[3]>", line 1, in <module>
>          M.visualize_structure(SAGE_TMP + "matrix.png")###line 5463:
(Continue reading)

Sébastien Fabbro | 4 Dec 21:06 2010
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gentoo science next meeting

Hello,

Proposed date: Wednesday Dec. 15 at 20:00 UTC.

Proposed agenda:
1) science overlay policies:
   - access, automatic qa, cleanup
2) metadata:
   - mandatory tags our metadata.xml (longdescription, upstream-tags) 
3) sub-herds:
   - converge on whether we want to keep the split herds 
4) science profiles:
   - how about making Gentoo science profiles?
5) fortran:
   - eclass/no eclass, handling of fortran > 90 modules
6) web page/wiki
7) vote leader

It would be nice if we can keep it short, such as 5min/topic and come
up with action list. 

If you would like to discuss some of these topics (or others) in more
details, then let's try to do it before the meeting on #gentoo-science
or this mailing list, keeping one thread per topic.

[1]http://archives.gentoo.org/gentoo-science/msg_25c53a6c3568545fe3bdbf891d9b814b.xml

Thanks,
--

-- 
Sébastien
(Continue reading)

justin | 5 Dec 13:00 2010
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Re: gentoo science next meeting

On 04/12/10 21:06, Sébastien Fabbro wrote:
> Hello,
> 
> Proposed date: Wednesday Dec. 15 at 20:00 UTC.
> 

Thanks for organizing this, I will be there.

Kacper Kowalik | 5 Dec 13:39 2010
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Gentoo Science next meeting agenda - 2) metadata

Hi,
just for the reference
http://www.gentoo.org/proj/en/devrel/handbook/handbook.xml?part=2&chap=4
So we know our options ;)
Cheers,
Kacper

Kacper Kowalik | 5 Dec 13:42 2010
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Gentoo Science next meeting agenda - 3) sub-herds

I think we reached an agreement last time, i.e. merge all herds into
"sci". Should we just vote on it and make it happen?
Cheers,
Kacper

Kacper Kowalik | 5 Dec 13:49 2010
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Gentoo Science next meeting agenda - 4) science profiles

I would like to involve cluster team here. We could *really* use
seperate profiles for HPC at least, like hpc/server , hpc/node.
Also, since it was already mentioned on #gentoo-dev, we could have
"sci" profile with USE="fortran" and remove it from base.
To my great amazement it seems that not everybody use Fortran on a
daily basis :P
Cheers,
Kacper


Gmane