[gentoo-science] Can not run sage-notebook

[gentoo-science] Can not run sage-notebook

[P Purkayastha]

Hi all,
   Thanks to the quick help, I could upgrade my sage to 4.7.1 (from 
4.7.0). However, I am unable to run the notebook. And I also get a 
similar error when I run sage by itself. Do I need to recompile some 
packages? Thanks for any help.

I will present below two logs. The first one is when sage is run. And 
the second one is when sage-notebook is run.

1. sage:
~> sage
----------------------------------------------------------------------
| Sage Version 4.7.1, Release Date: 2011-08-11                       |
| Type notebook() for the GUI, and license() for information.        |
----------------------------------------------------------------------
Traceback (most recent call last):
   File "/usr/lib64/python2.7/site-packages/sage/all_cmdline.py", line 
14, in <module>
     from sage.all import *
   File "/usr/lib64/python2.7/site-packages/sage/all.py", line 85, in 
<module>
     import sage.symbolic.pynac
   File "expression.pxd", line 6, in init sage.symbolic.pynac 
(sage/symbolic/pynac.cpp:19320)
   File "expression.pyx", line 6651, in init sage.symbolic.expression 
(sage/symbolic/expression.cpp:36442)
   File "/usr/lib64/python2.7/site-packages/sage/misc/decorators.py", 
line 648, in __call__
     @sage_wraps(func)
   File "/usr/lib64/python2.7/site-packages/sage/misc/decorators.py", 
line 106, in f
     argspec = sage_getargspec(wrapped)
   File "/usr/lib64/python2.7/site-packages/sage/misc/sageinspect.py", 
line 1076, in sage_getargspec
     return inspect.ArgSpec(*_sage_getargspec_cython(sage_getsource(obj)))
   File "/usr/lib64/python2.7/site-packages/sage/misc/sageinspect.py", 
line 865, in _sage_getargspec_cython
     raise ValueError, "Could not parse cython argspec"
ValueError: Could not parse cython argspec

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)

/usr/lib64/python2.7/site-packages/IPython/ipmaker.pyc in 
force_import(modname, force_reload)
      61         reload(sys.modules[modname])
      62     else:
---> 63         __import__(modname)
      64
      65

/usr/bin/ipy_profile_sage.py in <module>()
       5     preparser(True)
       6
----> 7     import sage.all_cmdline
       8     sage.all_cmdline._init_cmdline(globals())
       9

/usr/lib64/python2.7/site-packages/sage/all_cmdline.py in <module>()
      22     if 'type object' in str(msg):
      23         msg = str(msg) + '\n\n** In Sage, the easiest fix for 
this problem is to type "sage -ba"\n   to rebuild all the Cython code 
(this takes several minutes).\n   Alternatively, touch the last .pyx 
file in the traceback above. **\n'
---> 24     raise ValueError, msg
      25
      26

ValueError: Could not parse cython argspec
Error importing ipy_profile_sage - perhaps you should run %upgrade?
WARNING: Loading of ipy_profile_sage failed.

sage:



2. sage-notebook:
~> sage-notebook
----------------------------------------------------------------------
| Sage Version 4.7.1, Release Date: 2011-08-11                       |
| Type notebook() for the GUI, and license() for information.        |
----------------------------------------------------------------------

Please wait while the Sage Notebook server starts...
Traceback (most recent call last):
   File "/usr/bin/sage-notebook-real", line 9, in <module>
     from sage.server.notebook.all import notebook
   File 
"/usr/lib64/python2.7/site-packages/sage/server/notebook/all.py", line 
22, in <module>
     from sagenb.notebook.all import *
   File "/usr/lib64/python2.7/site-packages/sagenb/notebook/all.py", 
line 16, in <module>
     from notebook_object import notebook, inotebook
   File 
"/usr/lib64/python2.7/site-packages/sagenb/notebook/notebook_object.py", 
line 17, in <module>
     import notebook as _notebook
   File 
"/usr/lib64/python2.7/site-packages/sagenb/notebook/notebook.py", line 
35, in <module>
     from sagenb.misc.misc import (pad_zeros, cputime, tmp_dir, load, save,
   File "/usr/lib64/python2.7/site-packages/sagenb/misc/misc.py", line 
183, in <module>
     import sage.all
   File "/usr/lib64/python2.7/site-packages/sage/all.py", line 85, in 
<module>
     import sage.symbolic.pynac
   File "expression.pxd", line 6, in init sage.symbolic.pynac 
(sage/symbolic/pynac.cpp:19320)
   File "expression.pyx", line 6651, in init sage.symbolic.expression 
(sage/symbolic/expression.cpp:36442)
   File "/usr/lib64/python2.7/site-packages/sage/misc/decorators.py", 
line 648, in __call__
     @sage_wraps(func)
   File "/usr/lib64/python2.7/site-packages/sage/misc/decorators.py", 
line 106, in f
     argspec = sage_getargspec(wrapped)
   File "/usr/lib64/python2.7/site-packages/sage/misc/sageinspect.py", 
line 1076, in sage_getargspec
     return inspect.ArgSpec(*_sage_getargspec_cython(sage_getsource(obj)))
   File "/usr/lib64/python2.7/site-packages/sage/misc/sageinspect.py", 
line 865, in _sage_getargspec_cython
     raise ValueError, "Could not parse cython argspec"
ValueError: Could not parse cython argspec
~ [1] >

Re: [gentoo-science] Can not run sage-notebook

[v_2e]

  Hello!

On Sun, 21 Aug 2011 23:50:50 +0800
P Purkayastha <ppurka@gmail.com> wrote:

> Hi all,
>    Thanks to the quick help, I could upgrade my sage to 4.7.1 (from 
> 4.7.0). However, I am unable to run the notebook. And I also get a 
> similar error when I run sage by itself. 

  The very same problem here. 
  Just in case: I do not use Java at all and thus I have no jdk at all
on my system.

  Regards,
    Vladimir

----- 
 <v_2e@ukr.net>

Re: [gentoo-science] Can not run sage-notebook

[fbissey]

Quoting v_2e@ukr.net:

>   Hello!
>
> On Sun, 21 Aug 2011 23:50:50 +0800
> P Purkayastha <ppurka@gmail.com> wrote:
>
>> Hi all,
>>    Thanks to the quick help, I could upgrade my sage to 4.7.1 (from 
>> 4.7.0). However, I am unable to run the notebook. And I also get a 
>> similar error when I run sage by itself.
>
>   The very same problem here.
>   Just in case: I do not use Java at all and thus I have no jdk at all
> on my system.
>
Hope webmail gets me to the list.
What version of pynac do you have installed?

Francois

Re: [gentoo-science] Can not run sage-notebook

[P Purkayastha]

On 08/22/2011 05:38 AM, fbissey@slingshot.co.nz wrote:
> Quoting v_2e@ukr.net:
>
>> Hello!
>>
>> On Sun, 21 Aug 2011 23:50:50 +0800
>> P Purkayastha <ppurka@gmail.com> wrote:
>>
>>> Hi all,
>>> Thanks to the quick help, I could upgrade my sage to 4.7.1 (from
>>> 4.7.0). However, I am unable to run the notebook. And I also get a
>>> similar error when I run sage by itself.
>>
>> The very same problem here.
>> Just in case: I do not use Java at all and thus I have no jdk at all
>> on my system.
>>
> Hope webmail gets me to the list.
> What version of pynac do you have installed?
>
> Francois

You are on the list :)

pynac version is 0.2.3:

~> eix -e pynac
[I] sci-libs/pynac [1]
      Available versions:  (~)0.2.1-r1!m (~)0.2.3!m {static-libs}
      Installed versions:  0.2.3!m(07:55:25 PM 08/20/2011)(-static-libs)
      Homepage:            http://pynac.sagemath.org/ 
https://bitbucket.org/burcin/pynac/overview
      Description:         A modified version of GiNaC that replaces the 
dependency on CLN by Python

[1] "sage-on-gentoo" /var/lib/layman/sage-on-gentoo

Re: [gentoo-science] Can not run sage-notebook

[fbissey]

Quoting P Purkayastha <ppurka@gmail.com>:

> On 08/22/2011 05:38 AM, fbissey@slingshot.co.nz wrote:
>> Quoting v_2e@ukr.net:
>>
>>> Hello!
>>>
>>> On Sun, 21 Aug 2011 23:50:50 +0800
>>> P Purkayastha <ppurka@gmail.com> wrote:
>>>
>>>> Hi all,
>>>> Thanks to the quick help, I could upgrade my sage to 4.7.1 (from
>>>> 4.7.0). However, I am unable to run the notebook. And I also get a
>>>> similar error when I run sage by itself.
>>>
>>> The very same problem here.
>>> Just in case: I do not use Java at all and thus I have no jdk at all
>>> on my system.
>>>
>> Hope webmail gets me to the list.
>> What version of pynac do you have installed?
>>
>> Francois
>
> You are on the list :)
>
> pynac version is 0.2.3:
>
> ~> eix -e pynac
> [I] sci-libs/pynac [1]
>       Available versions:  (~)0.2.1-r1!m (~)0.2.3!m {static-libs}
>       Installed versions:  0.2.3!m(07:55:25 PM 08/20/2011)(-static-libs)
>       Homepage:            http://pynac.sagemath.org/
> https://bitbucket.org/burcin/pynac/overview
>       Description:         A modified version of GiNaC that replaces the
> dependency on CLN by Python
>
> [1] "sage-on-gentoo" /var/lib/layman/sage-on-gentoo
Have you guys rebuilt cython recently? The version to be used is
0.14.1-r1 from the sage-on-gentoo overlay.

Francois

Re: [gentoo-science] Can not run sage-notebook

[P Purkayastha]

On 08/22/2011 05:57 AM, fbissey@slingshot.co.nz wrote:
> Quoting P Purkayastha <ppurka@gmail.com>:
>
>> On 08/22/2011 05:38 AM, fbissey@slingshot.co.nz wrote:
>>> Quoting v_2e@ukr.net:
>>>
>>>> Hello!
>>>>
>>>> On Sun, 21 Aug 2011 23:50:50 +0800
>>>> P Purkayastha <ppurka@gmail.com> wrote:
>>>>
>>>>> Hi all,
>>>>> Thanks to the quick help, I could upgrade my sage to 4.7.1 (from
>>>>> 4.7.0). However, I am unable to run the notebook. And I also get a
>>>>> similar error when I run sage by itself.
>>>>
>>>> The very same problem here.
>>>> Just in case: I do not use Java at all and thus I have no jdk at all
>>>> on my system.
>>>>
>>> Hope webmail gets me to the list.
>>> What version of pynac do you have installed?
>>>
>>> Francois
>>
>> You are on the list :)
>>
>> pynac version is 0.2.3:
>>
>> ~> eix -e pynac
>> [I] sci-libs/pynac [1]
>> Available versions: (~)0.2.1-r1!m (~)0.2.3!m {static-libs}
>> Installed versions: 0.2.3!m(07:55:25 PM 08/20/2011)(-static-libs)
>> Homepage: http://pynac.sagemath.org/
>> https://bitbucket.org/burcin/pynac/overview
>> Description: A modified version of GiNaC that replaces the
>> dependency on CLN by Python
>>
>> [1] "sage-on-gentoo" /var/lib/layman/sage-on-gentoo
> Have you guys rebuilt cython recently? The version to be used is
> 0.14.1-r1 from the sage-on-gentoo overlay.
>
> Francois

Indeed cython was not rebuilt after/during the update of sage. 
Rebuilding it doesn't make any difference. Still get the same errors. 
eix output just before remerging cython:

[I] dev-python/cython
      Available versions:  0.14.1 0.14.1-r1[1] {doc examples}
      Installed versions:  0.14.1-r1[1](10:34:40 PM 08/05/2011)(-doc 
-examples)
      Homepage:            http://www.cython.org/ 
http://pypi.python.org/pypi/Cython
      Description:         The Cython compiler for writing C extensions 
for the Python language

Re: [gentoo-science] Can not run sage-notebook

[fbissey]

Quoting P Purkayastha <ppurka@gmail.com>:
> Indeed cython was not rebuilt after/during the update of sage.
> Rebuilding it doesn't make any difference. Still get the same errors.
> eix output just before remerging cython:
>
> [I] dev-python/cython
>       Available versions:  0.14.1 0.14.1-r1[1] {doc examples}
>       Installed versions:  0.14.1-r1[1](10:34:40 PM 08/05/2011)(-doc
> -examples)
>       Homepage:            http://www.cython.org/
> http://pypi.python.org/pypi/Cython
>       Description:         The Cython compiler for writing C extensions
> for the Python language
Did you follow up with a rebuild of pynac, sage-clib and sage?

Francois

Re: [gentoo-science] Can not run sage-notebook

[P Purkayastha]

On 08/22/2011 06:48 AM, fbissey@slingshot.co.nz wrote:
> Quoting P Purkayastha <ppurka@gmail.com>:
>> Indeed cython was not rebuilt after/during the update of sage.
>> Rebuilding it doesn't make any difference. Still get the same errors.
>> eix output just before remerging cython:
>>
>> [I] dev-python/cython
>> Available versions: 0.14.1 0.14.1-r1[1] {doc examples}
>> Installed versions: 0.14.1-r1[1](10:34:40 PM 08/05/2011)(-doc
>> -examples)
>> Homepage: http://www.cython.org/
>> http://pypi.python.org/pypi/Cython
>> Description: The Cython compiler for writing C extensions
>> for the Python language
> Did you follow up with a rebuild of pynac, sage-clib and sage?
>
> Francois

I haev tried rebuilding pynac, sage-clib, sage, sage-baselayout and 
sage-notebook. The error persists.


~> genlop -l --date 3 hours ago
  * dev-python/cython

      Mon Aug 22 06:05:25 2011 >>> dev-python/cython-0.14.1-r1
      Mon Aug 22 06:56:32 2011 >>> sci-libs/pynac-0.2.3
      Mon Aug 22 06:56:58 2011 >>> sci-mathematics/sage-clib-4.7.1
      Mon Aug 22 07:09:34 2011 >>> sci-mathematics/sage-4.7.1
      Mon Aug 22 07:12:48 2011 >>> dev-lang/yasm-1.1.0-r1
      Mon Aug 22 07:14:55 2011 >>> sci-mathematics/sage-notebook-0.8.19
      Mon Aug 22 07:15:30 2011 >>> sci-mathematics/sage-baselayout-4.7.1
~>

Re: [gentoo-science] Can not run sage-notebook

[fbissey]

Quoting P Purkayastha <ppurka@gmail.com>:

> On 08/22/2011 06:48 AM, fbissey@slingshot.co.nz wrote:
>> Quoting P Purkayastha <ppurka@gmail.com>:
>>> Indeed cython was not rebuilt after/during the update of sage.
>>> Rebuilding it doesn't make any difference. Still get the same errors.
>>> eix output just before remerging cython:
>>>
>>> [I] dev-python/cython
>>> Available versions: 0.14.1 0.14.1-r1[1] {doc examples}
>>> Installed versions: 0.14.1-r1[1](10:34:40 PM 08/05/2011)(-doc
>>> -examples)
>>> Homepage: http://www.cython.org/
>>> http://pypi.python.org/pypi/Cython
>>> Description: The Cython compiler for writing C extensions
>>> for the Python language
>> Did you follow up with a rebuild of pynac, sage-clib and sage?
>>
>> Francois
>
> I haev tried rebuilding pynac, sage-clib, sage, sage-baselayout and
> sage-notebook. The error persists.
>
>
> ~> genlop -l --date 3 hours ago
>   * dev-python/cython
>
>       Mon Aug 22 06:05:25 2011 >>> dev-python/cython-0.14.1-r1
>       Mon Aug 22 06:56:32 2011 >>> sci-libs/pynac-0.2.3
>       Mon Aug 22 06:56:58 2011 >>> sci-mathematics/sage-clib-4.7.1
>       Mon Aug 22 07:09:34 2011 >>> sci-mathematics/sage-4.7.1
>       Mon Aug 22 07:12:48 2011 >>> dev-lang/yasm-1.1.0-r1
>       Mon Aug 22 07:14:55 2011 >>> sci-mathematics/sage-notebook-0.8.19
>       Mon Aug 22 07:15:30 2011 >>> sci-mathematics/sage-baselayout-4.7.1
> ~>
OK let's look at some other things:
printenv | grep SAGE

eix ipython

What is your current shell?
Outout of "sage -gdb" if you installed with the debug useflag.
Did you install the testsuite (useflag of the same name).

Francois

Re: [gentoo-science] Can not run sage-notebook

[P Purkayastha]

On 08/22/2011 07:59 AM, fbissey@slingshot.co.nz wrote:
> Quoting P Purkayastha <ppurka@gmail.com>:
>
>> On 08/22/2011 06:48 AM, fbissey@slingshot.co.nz wrote:
>>> Quoting P Purkayastha <ppurka@gmail.com>:
>>>> Indeed cython was not rebuilt after/during the update of sage.
>>>> Rebuilding it doesn't make any difference. Still get the same errors.
>>>> eix output just before remerging cython:
>>>>
>>>> [I] dev-python/cython
>>>> Available versions: 0.14.1 0.14.1-r1[1] {doc examples}
>>>> Installed versions: 0.14.1-r1[1](10:34:40 PM 08/05/2011)(-doc
>>>> -examples)
>>>> Homepage: http://www.cython.org/
>>>> http://pypi.python.org/pypi/Cython
>>>> Description: The Cython compiler for writing C extensions
>>>> for the Python language
>>> Did you follow up with a rebuild of pynac, sage-clib and sage?
>>>
>>> Francois
>>
>> I haev tried rebuilding pynac, sage-clib, sage, sage-baselayout and
>> sage-notebook. The error persists.
>>
>>
>> ~> genlop -l --date 3 hours ago
>> * dev-python/cython
>>
>> Mon Aug 22 06:05:25 2011 >>> dev-python/cython-0.14.1-r1
>> Mon Aug 22 06:56:32 2011 >>> sci-libs/pynac-0.2.3
>> Mon Aug 22 06:56:58 2011 >>> sci-mathematics/sage-clib-4.7.1
>> Mon Aug 22 07:09:34 2011 >>> sci-mathematics/sage-4.7.1
>> Mon Aug 22 07:12:48 2011 >>> dev-lang/yasm-1.1.0-r1
>> Mon Aug 22 07:14:55 2011 >>> sci-mathematics/sage-notebook-0.8.19
>> Mon Aug 22 07:15:30 2011 >>> sci-mathematics/sage-baselayout-4.7.1
>> ~>
> OK let's look at some other things:
> printenv | grep SAGE


~> env | grep SAGE
SAGE_DATA=/usr/share/sage/data
SAGE_DOC=/usr/share/sage/devel/sage/doc
SAGE_ROOT=/usr/share/sage
SAGE_LOCAL=/usr



> eix ipython

~> eix ipython
[I] dev-python/ipython
      Available versions:  0.10 0.10.1 0.10.2 {doc emacs examples 
gnuplot readline smp test wxwidgets}
      Installed versions:  0.10.2(02:29:03 AM 05/20/2011)(readline smp 
-doc -emacs -examples -gnuplot -test -wxwidgets)
      Homepage:            http://ipython.scipy.org/ 
http://pypi.python.org/pypi/ipython
      Description:         An interactive computing environment for Python



> What is your current shell?

/bin/zsh
Running
exec bash
sage

doesn't make any difference.

> Outout of "sage -gdb" if you installed with the debug useflag.
> Did you install the testsuite (useflag of the same name).

Unfortunately, I didnt' compile either of them. Will do that later tonight.

> Francois
>


Thanks for patiently helping. :)

Re: [gentoo-science] Can not run sage-notebook

[Christopher Schwan]

On Monday 22 August 2011 10:57:59 P Purkayastha wrote:
> On 08/22/2011 07:59 AM, fbissey@slingshot.co.nz wrote:
> > Quoting P Purkayastha <ppurka@gmail.com>:
> >> On 08/22/2011 06:48 AM, fbissey@slingshot.co.nz wrote:
> >>> Quoting P Purkayastha <ppurka@gmail.com>:
> >>>> Indeed cython was not rebuilt after/during the update of sage.
> >>>> Rebuilding it doesn't make any difference. Still get the same
> >>>> errors.
> >>>> eix output just before remerging cython:
> >>>> 
> >>>> [I] dev-python/cython
> >>>> Available versions: 0.14.1 0.14.1-r1[1] {doc examples}
> >>>> Installed versions: 0.14.1-r1[1](10:34:40 PM 08/05/2011)(-doc
> >>>> -examples)
> >>>> Homepage: http://www.cython.org/
> >>>> http://pypi.python.org/pypi/Cython
> >>>> Description: The Cython compiler for writing C extensions
> >>>> for the Python language
> >>> 
> >>> Did you follow up with a rebuild of pynac, sage-clib and sage?
> >>> 
> >>> Francois
> >> 
> >> I haev tried rebuilding pynac, sage-clib, sage, sage-baselayout and
> >> sage-notebook. The error persists.
> >> 
> >> 
> >> ~> genlop -l --date 3 hours ago
> >> * dev-python/cython
> >> 
> >> Mon Aug 22 06:05:25 2011 >>> dev-python/cython-0.14.1-r1
> >> Mon Aug 22 06:56:32 2011 >>> sci-libs/pynac-0.2.3
> >> Mon Aug 22 06:56:58 2011 >>> sci-mathematics/sage-clib-4.7.1
> >> Mon Aug 22 07:09:34 2011 >>> sci-mathematics/sage-4.7.1
> >> Mon Aug 22 07:12:48 2011 >>> dev-lang/yasm-1.1.0-r1
> >> Mon Aug 22 07:14:55 2011 >>> sci-mathematics/sage-notebook-0.8.19
> >> Mon Aug 22 07:15:30 2011 >>> sci-mathematics/sage-baselayout-4.7.1
> >> ~>
> > 
> > OK let's look at some other things:
> > printenv | grep SAGE
> 
> ~> env | grep SAGE
> SAGE_DATA=/usr/share/sage/data
> SAGE_DOC=/usr/share/sage/devel/sage/doc
> SAGE_ROOT=/usr/share/sage
> SAGE_LOCAL=/usr
> 
> > eix ipython
> 
> ~> eix ipython
> [I] dev-python/ipython
>       Available versions:  0.10 0.10.1 0.10.2 {doc emacs examples
> gnuplot readline smp test wxwidgets}
>       Installed versions:  0.10.2(02:29:03 AM 05/20/2011)(readline smp
> -doc -emacs -examples -gnuplot -test -wxwidgets)
>       Homepage:            http://ipython.scipy.org/
> http://pypi.python.org/pypi/ipython
>       Description:         An interactive computing environment for Python
> 
> > What is your current shell?
> 
> /bin/zsh
> Running
> exec bash
> sage
> 
> doesn't make any difference.
> 
> > Outout of "sage -gdb" if you installed with the debug useflag.
> > Did you install the testsuite (useflag of the same name).
> 
> Unfortunately, I didnt' compile either of them. Will do that later tonight.
> 
> > Francois
> 
> Thanks for patiently helping. :)

Hi,

Francois was right - compiling without the testsuite yields the same behavior 
on my box. So for the time being,

USE=testsuite emerge -1 sage-baselayout
USE=testsuite emerge -1 sage

solves the problem.

Any ideas which files are removed with USE=-testsuite but still needed ?

Cheers,
Christopher

Re: [gentoo-science] Can not run sage-notebook

[P Purkayastha]

On 08/22/2011 04:56 PM, Christopher Schwan wrote:
> On Monday 22 August 2011 10:57:59 P Purkayastha wrote:
>> On 08/22/2011 07:59 AM, fbissey@slingshot.co.nz wrote:
>>> Quoting P Purkayastha<ppurka@gmail.com>:
>>>> On 08/22/2011 06:48 AM, fbissey@slingshot.co.nz wrote:
>>>>> Quoting P Purkayastha<ppurka@gmail.com>:
>>>>>> Indeed cython was not rebuilt after/during the update of sage.
>>>>>> Rebuilding it doesn't make any difference. Still get the same
>>>>>> errors.
>>>>>> eix output just before remerging cython:
>>>>>>
>>>>>> [I] dev-python/cython
>>>>>> Available versions: 0.14.1 0.14.1-r1[1] {doc examples}
>>>>>> Installed versions: 0.14.1-r1[1](10:34:40 PM 08/05/2011)(-doc
>>>>>> -examples)
>>>>>> Homepage: http://www.cython.org/
>>>>>> http://pypi.python.org/pypi/Cython
>>>>>> Description: The Cython compiler for writing C extensions
>>>>>> for the Python language
>>>>>
>>>>> Did you follow up with a rebuild of pynac, sage-clib and sage?
>>>>>
>>>>> Francois
>>>>
>>>> I haev tried rebuilding pynac, sage-clib, sage, sage-baselayout and
>>>> sage-notebook. The error persists.
>>>>
>>>>
>>>> ~>  genlop -l --date 3 hours ago
>>>> * dev-python/cython
>>>>
>>>> Mon Aug 22 06:05:25 2011>>>  dev-python/cython-0.14.1-r1
>>>> Mon Aug 22 06:56:32 2011>>>  sci-libs/pynac-0.2.3
>>>> Mon Aug 22 06:56:58 2011>>>  sci-mathematics/sage-clib-4.7.1
>>>> Mon Aug 22 07:09:34 2011>>>  sci-mathematics/sage-4.7.1
>>>> Mon Aug 22 07:12:48 2011>>>  dev-lang/yasm-1.1.0-r1
>>>> Mon Aug 22 07:14:55 2011>>>  sci-mathematics/sage-notebook-0.8.19
>>>> Mon Aug 22 07:15:30 2011>>>  sci-mathematics/sage-baselayout-4.7.1
>>>> ~>
>>>
>>> OK let's look at some other things:
>>> printenv | grep SAGE
>>
>> ~>  env | grep SAGE
>> SAGE_DATA=/usr/share/sage/data
>> SAGE_DOC=/usr/share/sage/devel/sage/doc
>> SAGE_ROOT=/usr/share/sage
>> SAGE_LOCAL=/usr
>>
>>> eix ipython
>>
>> ~>  eix ipython
>> [I] dev-python/ipython
>>        Available versions:  0.10 0.10.1 0.10.2 {doc emacs examples
>> gnuplot readline smp test wxwidgets}
>>        Installed versions:  0.10.2(02:29:03 AM 05/20/2011)(readline smp
>> -doc -emacs -examples -gnuplot -test -wxwidgets)
>>        Homepage:            http://ipython.scipy.org/
>> http://pypi.python.org/pypi/ipython
>>        Description:         An interactive computing environment for Python
>>
>>> What is your current shell?
>>
>> /bin/zsh
>> Running
>> exec bash
>> sage
>>
>> doesn't make any difference.
>>
>>> Outout of "sage -gdb" if you installed with the debug useflag.
>>> Did you install the testsuite (useflag of the same name).
>>
>> Unfortunately, I didnt' compile either of them. Will do that later tonight.
>>
>>> Francois
>>
>> Thanks for patiently helping. :)
>
> Hi,
>
> Francois was right - compiling without the testsuite yields the same behavior
> on my box. So for the time being,
>
> USE=testsuite emerge -1 sage-baselayout
> USE=testsuite emerge -1 sage
>
> solves the problem.
>
> Any ideas which files are removed with USE=-testsuite but still needed ?
>
> Cheers,
> Christopher
>

The only difference testsuite seems to make is *remove* files :) It 
apparently has no effect on sage-baselayout as far as I can see from the 
ebuild. But in sage ebuild, it removes stuff:

src_install() {
	distutils_src_install

	if use testsuite ; then
		# install testable sources and sources needed for testing
		find sage ! \( -name "*.py" -o -name "*.pyx" -o -name "*.pxd" -o \
			-name "*.pxi" \) -type f -delete \
			|| die "failed to remove non-testable sources"

		insinto /usr/share/sage/devel/sage-main
		doins -r sage || die
	fi