date:20140625

[sage-devel] Re: failed test with maxima

2014-06-25 Thread Nathann Cohen

Hello !

I have the very same problem :

sage -t --long calculus/desolvers.py  # 8 doctests failed

~/sage$ sage -t --long calculus/desolvers.py  # 8 doctests failed
Running doctests with ID 2014-06-25-11-03-06-35530e09.
Doctesting 1 file.
sage -t --long calculus/desolvers.py
**
File "calculus/desolvers.py", line 1166, in 
sage.calculus.desolvers.desolve_rk4
Failed example:
desolve_rk4(x*y*(2-y),y,ics=[0,1],end_points=1,step=0.5)
Exception raised:
Traceback (most recent call last):
  File 
"/home/ncohen/.Sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", 
line 480, in _run
self.execute(example, compiled, test.globs)
  File 
"/home/ncohen/.Sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", 
line 839, in execute
exec compiled in globs
  File "", line 1, in 


desolve_rk4(x*y*(Integer(2)-y),y,ics=[Integer(0),Integer(1)],end_points=Integer(1),step=RealNumber('0.5'))
  File 
"/home/ncohen/.Sage/local/lib/python2.7/site-packages/sage/calculus/desolvers.py",
 
line 1221, in desolve_rk4
maxima("load('dynamics)")
  File 
"/home/ncohen/.Sage/local/lib/python2.7/site-packages/sage/interfaces/interface.py",
 
line 199, in __call__
return cls(self, x, name=name)
  File 
"/home/ncohen/.Sage/local/lib/python2.7/site-packages/sage/interfaces/maxima.py",
 
line 1129, in __init__
ExpectElement.__init__(self, parent, value, is_name=False, 
name=None)
  File 
"/home/ncohen/.Sage/local/lib/python2.7/site-packages/sage/interfaces/expect.py",
 
line 1306, in __init__
self._name = parent._create(value, name=name)
  File 
"/home/ncohen/.Sage/local/lib/python2.7/site-packages/sage/interfaces/interface.py",
 
line 389, in _create
self.set(name, value)
  File 
"/home/ncohen/.Sage/local/lib/python2.7/site-packages/sage/interfaces/maxima.py",
 
line 974, in set
self._eval_line(cmd)
  File 
"/home/ncohen/.Sage/local/lib/python2.7/site-packages/sage/interfaces/maxima.py",
 
line 766, in _eval_line
self._error_check(line, out)
  File 
"/home/ncohen/.Sage/local/lib/python2.7/site-packages/sage/interfaces/maxima.py",
 
line 906, in _error_check
self._error_msg(cmd, out)
  File 
"/home/ncohen/.Sage/local/lib/python2.7/site-packages/sage/interfaces/maxima.py",
 
line 923, in _error_msg
raise TypeError("Error executing code in 
Maxima\nCODE:\n\t%s\nMaxima ERROR:\n\t%s"%(cmd, out.replace('-- an error. 
 To debug this try debugmode(true);','')))
TypeError: Error executing code in Maxima
CODE:
sage10 : load('dynamics)$
Maxima ERROR:

loadfile: failed to load dynamics
 -- an error. To debug this try: debugmode(true);

Nathann

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Re: [sage-devel] Re: failed test with maxima

2014-06-25 Thread Nathann Cohen

And for some reason I get this bug when I run "sage -tp 4 -l sage/"
but not when I run "make ptestlong" O_o

Nathann

On 25 June 2014 11:06, Nathann Cohen  wrote:
> Hello !
>
> I have the very same problem :
>
> sage -t --long calculus/desolvers.py  # 8 doctests failed
>
> ~/sage$ sage -t --long calculus/desolvers.py  # 8 doctests failed
> Running doctests with ID 2014-06-25-11-03-06-35530e09.
> Doctesting 1 file.
> sage -t --long calculus/desolvers.py
> **
> File "calculus/desolvers.py", line 1166, in
> sage.calculus.desolvers.desolve_rk4
> Failed example:
> desolve_rk4(x*y*(2-y),y,ics=[0,1],end_points=1,step=0.5)
> Exception raised:
> Traceback (most recent call last):
>   File
> "/home/ncohen/.Sage/local/lib/python2.7/site-packages/sage/doctest/forker.py",
> line 480, in _run
> self.execute(example, compiled, test.globs)
>   File
> "/home/ncohen/.Sage/local/lib/python2.7/site-packages/sage/doctest/forker.py",
> line 839, in execute
> exec compiled in globs
>   File "", line 1, in
> 
>
> desolve_rk4(x*y*(Integer(2)-y),y,ics=[Integer(0),Integer(1)],end_points=Integer(1),step=RealNumber('0.5'))
>   File
> "/home/ncohen/.Sage/local/lib/python2.7/site-packages/sage/calculus/desolvers.py",
> line 1221, in desolve_rk4
> maxima("load('dynamics)")
>   File
> "/home/ncohen/.Sage/local/lib/python2.7/site-packages/sage/interfaces/interface.py",
> line 199, in __call__
> return cls(self, x, name=name)
>   File
> "/home/ncohen/.Sage/local/lib/python2.7/site-packages/sage/interfaces/maxima.py",
> line 1129, in __init__
> ExpectElement.__init__(self, parent, value, is_name=False,
> name=None)
>   File
> "/home/ncohen/.Sage/local/lib/python2.7/site-packages/sage/interfaces/expect.py",
> line 1306, in __init__
> self._name = parent._create(value, name=name)
>   File
> "/home/ncohen/.Sage/local/lib/python2.7/site-packages/sage/interfaces/interface.py",
> line 389, in _create
> self.set(name, value)
>   File
> "/home/ncohen/.Sage/local/lib/python2.7/site-packages/sage/interfaces/maxima.py",
> line 974, in set
> self._eval_line(cmd)
>   File
> "/home/ncohen/.Sage/local/lib/python2.7/site-packages/sage/interfaces/maxima.py",
> line 766, in _eval_line
> self._error_check(line, out)
>   File
> "/home/ncohen/.Sage/local/lib/python2.7/site-packages/sage/interfaces/maxima.py",
> line 906, in _error_check
> self._error_msg(cmd, out)
>   File
> "/home/ncohen/.Sage/local/lib/python2.7/site-packages/sage/interfaces/maxima.py",
> line 923, in _error_msg
> raise TypeError("Error executing code in Maxima\nCODE:\n\t%s\nMaxima
> ERROR:\n\t%s"%(cmd, out.replace('-- an error.  To debug this try
> debugmode(true);','')))
> TypeError: Error executing code in Maxima
> CODE:
> sage10 : load('dynamics)$
> Maxima ERROR:
>
> loadfile: failed to load dynamics
>  -- an error. To debug this try: debugmode(true);
>
> Nathann
>
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[sage-devel] R build script is unable to find file that exists at path

2014-06-25 Thread Jason Wu

Hello again,

I'm (still) trying to build sage on cygwin64 using the /u/jpflori/cygwin64 
branch from trac. I've run into quite a few errors but I've been able to 
fix them usually by following the wiki. However, I've run into a strange 
problem

Screenshot:


(link: http://i.imgur.com/I6245eD.png)

The problem is that R fails while building one of its packages (grDevices) 
with the message:

byte-compiling package 'grDevices'
Warning in solve.default(rgb) :
  unable to load shared object 
'/home/jwpilly/sage/local/var/tmp/sage/build/r-3.0.2.p1/src/modules//lapack.dll':
  *No such file or directory*
Error in solve.default(rgb) : LAPACK routines cannot be loaded
Error: unable to load R code in package 'grDevices'
Execution halted
../../../share/make/lazycomp.mk:7: recipe for target 
'../../../library/grDevices/R/grDevices.rdb' failed
make[7]: *** [../../../library/grDevices/R/grDevices.rdb] Error 1

As you can see, the build script complains that there is no such file 
" 
'/home/jwpilly/sage/local/var/tmp/sage/build/r-3.0.2.p1/src/modules//lapack.dll'"
 
even though in the screenshot, you can see that there clearly is a file 
named "lapack.dll" at that path in windows explorer. I noticed that the 
file path contains a double forward slash, but I thought in linux this 
resolves to a single slash? Anyway, this strange bug is preventing sage 
from successfully building.

Any help is appreciated and thanks in advance

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[sage-devel] Release of the open source Gudhi Library 1.0

2014-06-25 Thread Nicolas M. Thiery

Hi,

In case someone is interested ...

- Forwarded message from Clement Maria  -
Subject: [gdr-im] Release of the open source Gudhi Library 1.0

   We are pleased to announce the first release of the Gudhi open source
   library.

   The Gudhi library (Geometric Understanding in Higher Dimensions) is a
   generic C++ library for computational topology. Its goal is to provide
   robust, efficient, flexible and easy to use implementations of
   state-of-the-art algorithms and data structures for computational
   topology.

   The library and its documentation are available at:
   [1]https://project.inria.fr/gudhi/software/

   The current release of the library allows the user to construct
   simplicial complexes from point clouds (Rips complex) or a list of
   simplices, and to compute their persistent homology with coefficients
   in a field Z/pZ (for an arbitrary prime p), or simultaneously with
   coefficients in a family of fields (multi-field persistent homology).

   The simplicial complexes may be represented by simplex trees or Hasse
   diagrams. The persistent homology algorithm is based on the compressed
   annotation matrix implementation of the persistent cohomology
   algorithm. The multi-field persistent homology algorithm is based on a
   recently introduced modular reconstruction technique. We refer to the
   documentation for more details on the algorithms and their
   implementation.

   Clément Maria
- End forwarded message -
Nicolas
--
Nicolas M. Thiéry "Isil" 
http://Nicolas.Thiery.name/

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Re: [sage-devel] Re: How to write packages of sage

2014-06-25 Thread kcrisman



On Tuesday, June 24, 2014 7:02:44 PM UTC-4, 张秦川 wrote:
>
> I am so sorry that I forget about this as the 'gaussian'distribution in 
> sage only take one parameter sigma. I think 'normal' distribution should 
> have two parameters mu and sigma.
>
>
Correct, currently you have to "manually" shift it around - I think there 
are some examples in the documentation or perhaps in the PREP tutorials. 
 See https://groups.google.com/forum/#!topic/sage-support/eD7xBdvd6YE among 
other places where there are things about this.  I agree this is 
suboptimal, but also perhaps the authors of the GSL had a reason for not 
using mu?

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Re: [sage-devel] Release of the open source Gudhi Library 1.0

2014-06-25 Thread Vincent Delecroix

Hi,

How is it different from GCAL [2] (beyond the license issue) ? It
looks like a subset of it.

 [2] https://www.cgal.org/

Vincent

2014-06-25 20:28 UTC+02:00, Nicolas M. Thiery :
>   Hi,
>
> In case someone is interested ...
>
> - Forwarded message from Clement Maria  -
> Subject: [gdr-im] Release of the open source Gudhi Library 1.0
>
>We are pleased to announce the first release of the Gudhi open source
>library.
>
>The Gudhi library (Geometric Understanding in Higher Dimensions) is a
>generic C++ library for computational topology. Its goal is to provide
>robust, efficient, flexible and easy to use implementations of
>state-of-the-art algorithms and data structures for computational
>topology.
>
>The library and its documentation are available at:
>[1]https://project.inria.fr/gudhi/software/
>
>The current release of the library allows the user to construct
>simplicial complexes from point clouds (Rips complex) or a list of
>simplices, and to compute their persistent homology with coefficients
>in a field Z/pZ (for an arbitrary prime p), or simultaneously with
>coefficients in a family of fields (multi-field persistent homology).
>
>The simplicial complexes may be represented by simplex trees or Hasse
>diagrams. The persistent homology algorithm is based on the compressed
>annotation matrix implementation of the persistent cohomology
>algorithm. The multi-field persistent homology algorithm is based on a
>recently introduced modular reconstruction technique. We refer to the
>documentation for more details on the algorithms and their
>implementation.
>
>Clément Maria
> - End forwarded message -
>   Nicolas
> --
> Nicolas M. Thiéry "Isil" 
> http://Nicolas.Thiery.name/
>
> --
> You received this message because you are subscribed to the Google Groups
> "sage-devel" group.
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> email to sage-devel+unsubscr...@googlegroups.com.
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>

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[sage-devel] Re: failed test with maxima

Re: [sage-devel] Re: failed test with maxima

[sage-devel] R build script is unable to find file that exists at path

[sage-devel] Release of the open source Gudhi Library 1.0

Re: [sage-devel] Re: How to write packages of sage

Re: [sage-devel] Release of the open source Gudhi Library 1.0

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