Sage 4.0.rc0 released!

[mabshoff]

Hi,

I gotta run to the airport, but sources and upgrade bits of 4.0.rc0
are in

http://sage.math.washington.edu/home/mabshoff/release-cycles-4.0/rc0/

Once I get online I will post more info, but I am sure this will take
a couple hours. Sorry.

Cheers,

Michael

Merged in Sage 4.0.rc0:

#6104: Michael Abshoff: Fix Solaris specific build issue for
libfplll.spkg [Needs review]

#3932: Ryan Dingman: generate size n trees in linear time [Reviewed by
Robert Miller]
#4875: Marshall Hampton: Polyhedron.show(fill=True) fails [Reviewed by
David Perkison]
#5076: David Roe: bug with (coercion in?) p-adic extension fields
[Reviewed by Robert Bradshaw]
#5120: Nicolas Thiery: An alternative implementation of the Unique
Representation design pattern [Reviewed by David Roe]
#5236: David Roe: x^(-pm) in ramified extensions of Qp [Reviewed by
Kiran Kedlaya]
#5554: Nick Alexander: implement cholesky_decomposition for matrices
other than RDF [Reviewed by Rob Beezer, Michael Abshoff]
#5581: Marshall Hampton: Face lattices and f-vectors for polytopes;
bug fixes for polyhedra.py [Reviewed by David Perkison]
#5619: Minh Van Nguyen: doctests for error messages in groebner_fan.py
[Reviewed by Marshall Hampton]
#5621: Minh Van Nguyen, Mike Hansen: doctests for calculus.py
[Reviewed by John Palmieri]
#5753: Burcin Erocal: update to pynac 0.1.4 [Reviewed by Mike Hansen]
#5777: Burcin Erocal: update to pynac 0.1.6 [Reviewed by Mike Hansen]
#5783: Nicolas Thiery: Lazy attribute fixes and improvements [Reviewed
by David Roe]
#5582: Robert Bradshaw: Coercion from float to QQ is missing [Reviewed
by Jason Bandlow, Mike Hansen]
#5837: Luiz Berlioz: bug in rational_diagonal_form() from
QuadraticForm class [Reviewed by John Cremona, Gonzalo Tornaria]
#5879: Dan Bump: Added crystal of letters for type E [Reviewed by Anne
Schilling, Michael Abshoff]
#5907: Gonzalo Tornaria, Carl Witty: incorrect fast_float evaluation
of constant polynomials [Reviewed by Mike Hansen]
#5930: Mike Hansen, William Stein, Carl Witty, Robert Bradshaw: switch
from maxima to pynac for core symbolic manipulation system [Reviewed
by Carl Witty, Robert Bradshaw, William Stein, Mike Hansen, Tom
Boothby, Michael Abshoff]
#5940: Emily Kirkman: graph theory -- bug in is_circular_planar
[Reviewed by Robert Miller]
#5944: Burcin Erocal: fix a nasty pynac bug in exp [Reviewed by Mike
Hansen]
#5954: Jon Hanke: Added documentation/doctests for all quadratic form
genus symbol routines [Reviewed by Gonzalo Tornaria]
#6088: Nicolas Thiery: LatticePolytope: Removed a try/catch which
could involuntarily hide exceptions from lower code [Reviewed by
Andrey Novoseltsev]
#6029: Robert Bradshaw: bug in floor() for python types [Reviewed by
Mike Hansen]
#6035: Wilfried Huss: Don't draw vertical asympotes [Reviewed by
Marshall Hampton]
#6036: Kwankyu Lee: a bug in polynomial() for PolynomialRing(GF(5),2)
[Reviewed by Mike Hansen]
#6037: Jon Hanke: Major Upgrade to QuadraticForm Local Density
Routines [Reviewed by Gonzalo Tornaria]
#6040: Jon Hanke: Added Doctests for QuadraticForms methods [Reviewed
by Gonzalo Tornaria]
#6042: John Cremona: Bring doctests of modular/modsym/ambient.py up to
100% [Reviewed by David Loeffler, Alex Ghitza]
#6048: John Palmieri: fix non-ASCII character in mpolynomialsystem
[Reviewed by Martin Albrecht]
#6049: Jason Grout: bitset complement zeroes out last word if the
bitset is a multiple of the word size [Reviewed by Carl Witty]
#6052: Gonzalo Tornaria: partial_fraction_decomposition is broken for
irreducible denominators [Reviewed by Mike Hansen]
#6054: Mike Hansen: fix display2d with ecl on OSX [Reviewed by Michael
Abshoff]
#6059: Gonzalo Tornaria: speed regresion in hilbert_symbol after #5834
[Reviewed by John Cremona]
#6060: Fredrik Johansson: divmod fails when one argument is Integer
and the other is a Python int [Reviewed by Mike Hansen]
#6061: William Stein: refresh the pickle jar [Reviewed by Michael
Abshoff]
#6062: Gonzalo Tornaria: QQ method is_padic_square fails when argument
is python int [Reviewed John Cremona]
#6064: Gonzalo Tornaria: allow rationals in kronecker_symbol and
legendre_symbol [Reviewed John Cremona]
#6065: Carl Witty: implement some missing trig methods on
RealIntervalFieldElement [Reviewed by Mike Hansen]
#6066: Radoslav Kirov: constructing Sage graphs is slow compared to
NetworkX graphs [Reviewed by Robert Miller]
#6070: David Loeffler: Get doctest coverage in sage/modular to 100%
[Reviewed by John Cremona]
#6077: Marshall Hampton: simplicial complex method for polytopes
[Reviewed by John Palmieri]
#6080: Fredrik Johansson: Add utility methods to Integer (needed for
mpmath) [Reviewed by Mike Hansen]
#6082: Robert Bradshaw: realloc called too often for Integer
construction/deconstruction [Reviewed by William Stein]
#6086: David Perkinson: fixed laplacian_matrix in graph.py [Reviewed
by Emily Kirkman]
#6107: Mike Hansen: misc. fixes for symbolics for 4.0.rc0 [Reviewed by
William Stein]

[William Stein]

On Thu, May 21, 2009 at 7:14 AM, mabshoff <mabs...@googlemail.com> wrote:
>
> Hi,
>
> I gotta run to the airport, but sources and upgrade bits of 4.0.rc0
> are in
>
>   http://sage.math.washington.edu/home/mabshoff/release-cycles-4.0/rc0/
>
> Once I get online I will post more info, but I am sure this will take
> a couple hours. Sorry.

I updated http://alpha.sagenb.org to sage-4.0.rc0, and strongly
encourage people to try it.
Especially try symbolic calculus computations since we switched from
Maxima to Ginac
for the core of symbolics in sage-4.0.

I've built this on a number of machine and there are a number of
doctest failures, segfaults, and other issues that pop up when not
building on sage.math. To get sage-4.0 formally released requires (at
least) two things:

(1) sort out all these doctest failures

(2) get the new pynac-based symbolics code refereed:
http://trac.sagemath.org/sage_trac/ticket/6111

William

--
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org

[Jaap Spies]

mabshoff wrote:
> Hi,
>
> I gotta run to the airport, but sources and upgrade bits of 4.0.rc0
> are in
>
> http://sage.math.washington.edu/home/mabshoff/release-cycles-4.0/rc0/
>
> Once I get online I will post more info, but I am sure this will take
> a couple hours. Sorry.
>

Upgrading from alpha0 on Fedora 10 failed somehow. I had to remove constants.so
by hand.

$ rm devel/sage/build/sage/symbolic/constants.so

Now testing.

On Fedora 9 I'll do a fresh install.

Jaap

[kcrisman]

Same problem here to some extent:

During upgrade from 4.0.alpha0 on OSX.4 G4 Powerbook, on the Sphinx
build process I repeatedly get the following or a similar error:

ImportError: dlopen(.../sage/symbolic/constants.so): Library not
loaded: .../local/lib/libpynac-0.1.2.dylib Reason: image not found

Then sage prompt appears after a similar error, and
sage: 2+2
sage: x
both fail for lack of definition of Integer and x.

Once I get rid of the same file, I have success, like Jaap:

----------------------------------------------------------------------
| Sage Version 4.0.rc0, Release Date: 2009-05-21 |
| Type notebook() for the GUI, and license() for information. |
----------------------------------------------------------------------
sage: 2+2
4
sage: f(x)=x^2
sage: f(4)
16
sage:
Exiting SAGE (CPU time 0m0.18s, Wall time 0m22.67s).

No Maxima exit!!! :) And to compare:

----------------------------------------------------------------------
| Sage Version 4.0.rc0, Release Date: 2009-05-21 |
| Type notebook() for the GUI, and license() for information. |
----------------------------------------------------------------------
sage: %time f(x)=x^2;f(4)
CPU times: user 0.01 s, sys: 0.00 s, total: 0.02 s
Wall time: 0.02 s
sage:
Exiting SAGE (CPU time 0m0.16s, Wall time 0m13.66s).

----------------------------------------------------------------------
| Sage Version 3.4.1.rc1, Release Date: 2009-04-05 |
| Type notebook() for the GUI, and license() for information. |
----------------------------------------------------------------------
Loading Sage library. Current Mercurial branch is: hackbranch
sage: %time f(x)=x^2;f(4)
CPU times: user 0.05 s, sys: 0.06 s, total: 0.11 s
Wall time: 1.15 s
sage:
Exiting SAGE (CPU time 0m0.25s, Wall time 0m17.31s).
Exiting spawned Maxima process.

- kcrisman

[William Stein]

On Thu, May 21, 2009 at 10:59 AM, Jaap Spies <j.s...@hccnet.nl> wrote:
>
> mabshoff wrote:
>> Hi,
>>
>> I gotta run to the airport, but sources and upgrade bits of 4.0.rc0
>> are in
>>
>>    http://sage.math.washington.edu/home/mabshoff/release-cycles-4.0/rc0/
>>
>> Once I get online I will post more info, but I am sure this will take
>> a couple hours. Sorry.
>>
>
> Upgrading from alpha0 on Fedora 10 failed somehow. I had to remove constants.so
> by hand.
>
> $ rm devel/sage/build/sage/symbolic/constants.so

Thanks for reporting this. It is a bug (my fault) and now a blocker:

http://trac.sagemath.org/sage_trac/ticket/6114

>
> Now testing.
>
> On Fedora 9 I'll do a fresh install.
>
> Jaap
>
>
> >
>

[John Cremona]

Successful build from scratch and all tests pass on 64-bit ubuntu.

John

2009/5/21 William Stein <wst...@gmail.com>:

[Jaap Spies]

William Stein wrote:
> On Thu, May 21, 2009 at 10:59 AM, Jaap Spies <j.s...@hccnet.nl> wrote:
>> mabshoff wrote:
>>> Hi,
>>>
>>> I gotta run to the airport, but sources and upgrade bits of 4.0.rc0
>>> are in
>>>
>>> http://sage.math.washington.edu/home/mabshoff/release-cycles-4.0/rc0/
>>>
>>> Once I get online I will post more info, but I am sure this will take
>>> a couple hours. Sorry.
>>>
>> Upgrading from alpha0 on Fedora 10 failed somehow. I had to remove constants.so
>> by hand.
>>
>> $ rm devel/sage/build/sage/symbolic/constants.so
>
> Thanks for reporting this. It is a bug (my fault) and now a blocker:
>
> http://trac.sagemath.org/sage_trac/ticket/6114
>
>> Now testing.
>>
>> On Fedora 9 I'll do a fresh install.
>>

On Fedora 10, bit:
----------------------------------------------------------------------
The following tests failed:

sage -t "devel/sage/doc/en/numerical_sage/scipy.rst"
sage -t "devel/sage/doc/en/constructions/plotting.rst"
sage -t "devel/sage/doc/en/constructions/calculus.rst"
sage -t "devel/sage/doc/en/constructions/interface_issues.rst"
sage -t "devel/sage/doc/en/constructions/linear_algebra.rst"
sage -t "devel/sage/doc/en/tutorial/tour_algebra.rst"
sage -t "devel/sage/doc/en/tutorial/tour_functions.rst"
sage -t "devel/sage/doc/en/tutorial/tour_plotting.rst"
sage -t "devel/sage/doc/en/bordeaux_2008/nf_introduction.rst"
sage -t "devel/sage/doc/en/a_tour_of_sage/index.rst"
sage -t "devel/sage/doc/fr/tutorial/tour_algebra.rst"
sage -t "devel/sage/doc/fr/tutorial/tour_plotting.rst"
sage -t "devel/sage/sage/algebras/quatalg/quaternion_algebra.py"
sage -t "devel/sage/sage/tests/book_stein_ent.py"
sage -t "devel/sage/sage/misc/sage_eval.py"
sage -t "devel/sage/sage/misc/map_threaded.py"
sage -t "devel/sage/sage/misc/preparser.py"
sage -t "devel/sage/sage/calculus/calculus.py"
sage -t "devel/sage/sage/calculus/tests.py"
sage -t "devel/sage/sage/calculus/functional.py"
sage -t "devel/sage/sage/calculus/test_sympy.py"
sage -t "devel/sage/sage/gsl/interpolation.pyx"
sage -t "devel/sage/sage/gsl/ode.pyx"
sage -t "devel/sage/sage/functions/transcendental.py"
sage -t "devel/sage/sage/functions/special.py"
sage -t "devel/sage/sage/functions/piecewise.py"
sage -t "devel/sage/sage/functions/other.py"
sage -t "devel/sage/sage/interfaces/maxima.py"
sage -t "devel/sage/sage/rings/number_field/number_field_element.pyx"
sage -t "devel/sage/sage/rings/number_field/number_field_element_quadratic.pyx"
sage -t "devel/sage/sage/rings/arith.py"
sage -t "devel/sage/sage/rings/polynomial/polynomial_element.pyx"
sage -t "devel/sage/sage/numerical/optimize.py"
sage -t "devel/sage/sage/matrix/matrix_symbolic_dense.pyx"
sage -t "devel/sage/sage/matrix/matrix2.pyx"
sage -t "devel/sage/sage/schemes/elliptic_curves/ell_generic.py"
sage -t "devel/sage/sage/plot/plot3d/implicit_surface.pyx"
sage -t "devel/sage/sage/plot/plot3d/transform.pyx"
sage -t "devel/sage/sage/plot/plot3d/parametric_plot3d.py"
sage -t "devel/sage/sage/plot/tachyon.py"
sage -t "devel/sage/sage/plot/plot.py"
sage -t "devel/sage/sage/plot/animate.py"
sage -t "devel/sage/sage/plot/complex_plot.pyx"
sage -t "devel/sage/sage/symbolic/callable.py"
sage -t "devel/sage/sage/symbolic/relation.py"
sage -t "devel/sage/sage/symbolic/expression.pyx"
sage -t "devel/sage/sage/symbolic/ring.pyx"
sage -t "devel/sage/sage/symbolic/benchmark.py"
sage -t "devel/sage/sage/symbolic/function.pyx"
sage -t "devel/sage/sage/symbolic/assumptions.py"
sage -t "devel/sage/sage/coding/code_bounds.py"
sage -t "devel/sage/sage/modules/free_module_element.pyx"
sage -t "devel/sage/sage/modular/overconvergent/genus0.py"

Is this bad or expected?

Jaap

[John Cremona]

2009/5/21 John Cremona <john.c...@gmail.com>:

> Successful build from scratch and all tests pass on 64-bit ubuntu.

Scratch the second half of that: I had typed "make && sage --testall"
instead of "make && ./sage --testall" so it was testing the previous
version.

Is doing "make test" just the same? or better, or worse?

John

[Jaap Spies]

Jaap Spies wrote:

>
> Is this bad or expected?
>

For a log

See: http://sage.math.washington.edu/home/jsp/tests/test_4.0_rc0.log

Jaap

[Alex Ghitza]

Hi Michael,

One clarification regarding credit for #6042: I shouldn't get reviewer
credit for it. David rebased and reviewed all of it himself.

Best,
Alex

--
Alex Ghitza -- Lecturer in Mathematics -- The University of Melbourne
-- Australia -- http://www.ms.unimelb.edu.au/~aghitza/

[Kevin Horton]

On 21 May 2009, at 10:14, mabshoff wrote:
>
>
> I gotta run to the airport, but sources and upgrade bits of 4.0.rc0
> are in
>
> http://sage.math.washington.edu/home/mabshoff/release-cycles-4.0/
> rc0/

A worksheet that worked fine under sage 3.4.2 and 4.0.alpha0 fails
under 4.0rc0. The whole sheet can be seen at sagenb.org:

http://sagenb.org/home/pub/541

A relevant minimal example is:

{{{id=3|
import matplotlib.pyplot as pyplot
///
}}}

{{{id=0|
RealNumber=float; Integer=int
A=3202.6427147395325
B=2.7068484110275158e-05

fit(x)= A + B * x
Xfit=[0, 800000000]
Yfit=[fit(0), fit(800000000)]
///
}}}

{{{id=1|
P2=pyplot.plot(Xfit, Yfit, 'b')
///

Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/kwh/.sage/sage_notebook/worksheets/KevinHorton/22/code/
14.py", line 6, in <module>
exec compile(ur'P2=pyplot.plot(Xfit, Yfit, \u0027b\u0027)' +
'\n', '', 'single')
File "/opt/sage-4.0.rc0/local/lib/python2.5/site-packages/Jinja-1.2-
py2.5-linux-i686.egg/", line 1, in <module>

File "/opt/sage-4.0.rc0/local/lib/python2.5/site-packages/
matplotlib/pyplot.py", line 2118, in plot
ret = gca().plot(*args, **kwargs)
File "/opt/sage-4.0.rc0/local/lib/python2.5/site-packages/
matplotlib/axes.py", line 3348, in plot
for line in self._get_lines(*args, **kwargs):
File "/opt/sage-4.0.rc0/local/lib/python2.5/site-packages/
matplotlib/axes.py", line 404, in _grab_next_args
for seg in self._plot_3_args(remaining, **kwargs):
File "/opt/sage-4.0.rc0/local/lib/python2.5/site-packages/
matplotlib/axes.py", line 343, in _plot_3_args
x, y, multicol = self._xy_from_xy(x, y)
File "/opt/sage-4.0.rc0/local/lib/python2.5/site-packages/
matplotlib/axes.py", line 218, in _xy_from_xy
by = self.axes.yaxis.update_units(y)
File "/opt/sage-4.0.rc0/local/lib/python2.5/site-packages/
matplotlib/axis.py", line 969, in update_units
converter = munits.registry.get_converter(data)
File "/opt/sage-4.0.rc0/local/lib/python2.5/site-packages/
matplotlib/units.py", line 139, in get_converter
converter = self.get_converter( thisx )
File "/opt/sage-4.0.rc0/local/lib/python2.5/site-packages/
matplotlib/units.py", line 138, in get_converter
for thisx in x:
TypeError: 'sage.symbolic.expression.Expression' object is not iterable
}}}

Is this an expected result due to a change in sage-4.0.rc0? If so,
I'd appreciate any hints on how I need to modify my code.

My server is running on ubuntu 8.10.

--
Kevin Horton
Ottawa, Canada

[William Stein]

Here are two potential fixes for the rc0 update problem you have:

system:sage
system:sage

{{{id=3|
import matplotlib.pyplot as pyplot
///
}}}

{{{id=0|
RealNumber=float; Integer=int
A=3202.6427147395325
B=2.7068484110275158e-05

fit(x)= A + B * x
Xfit=[0, 800000000]

Yfit=[float(fit(0)), float(fit(800000000))]

///
}}}

{{{id=1|
P2=pyplot.plot(Xfit, Yfit, 'b')
///
}}}

{{{id=5|
RealNumber=float; Integer=int
A=3202.6427147395325
B=2.7068484110275158e-05

fit = lambda x: A + B * x

Xfit=[0, 800000000]
Yfit=[fit(0), fit(800000000)]
///
}}}

{{{id=6|

P2=pyplot.plot(Xfit, Yfit, 'b')
///
}}}

{{{id=7|

///
}}}

2009/5/21 Kevin Horton <khor...@rogers.com>:

[John Cremona]

2009/5/21 John Cremona <john.c...@gmail.com>:

> 2009/5/21 John Cremona <john.c...@gmail.com>:
>> Successful build from scratch and all tests pass on 64-bit ubuntu.
>
> Scratch the second half of that:  I had typed "make && sage --testall"
> instead of "make && ./sage --testall" so it was testing the previous

The genuine test of 4.0.rc0 gave:

sage -t "devel/sage/sage/matrix/matrix2.pyx"
Total time for all tests: 3002.9 seconds

sage -t "devel/sage/sage/matrix/matrix2.pyx"
**********************************************************************
File "/home/jec/sage-4.0.rc0/devel/sage/sage/matrix/matrix2.pyx", line 4964:
sage: m.change_ring(CDF).eigenvalues() # again for display purposes
Expected:
[10.463115298 - 4.98835989975e-16*I, 7.42365754809 -
5.05298436852e-16*I, 3.36964641458 + 5.59670199836e-17*I,
1.25904669699 + 4.34508443713e-17*I, 0.00689184179485 -
5.75358699674e-17*I, 0.330700789655 + 5.1816322259e-16*I]
Got:
[10.463115298 - 3.57021884933e-16*I, 7.42365754809 +
2.91121322571e-17*I, 3.36964641458 - 1.54788874696e-16*I,
1.25904669699 - 5.01646753379e-17*I, 0.00689184179485 -
3.97030024181e-16*I, 0.330700789655 + 1.32245788594e-16*I]
**********************************************************************
1 items had failures:
1 of 36 in __main__.example_81
***Test Failed*** 1 failures.
For whitespace errors, see the file
/home/jec/sage-4.0.rc0/tmp/.doctest_matrix2.py
[25.0 s]

John

[Rob Beezer]

./sage -upgrade from 4.0.alpha0 to 4.0.rc0

Then failed many tests.

rm devel/sage/build/sage/symbolic/constants.so
sage -ba
sage -testall

and all tests passed.

64-bit (K)Ubuntu 8.10 on Intel Core Duo.

[Dan Drake]

On Thu, 21 May 2009 at 10:17AM -0700, William Stein wrote:
> On Thu, May 21, 2009 at 7:14 AM, mabshoff <mabs...@googlemail.com> wrote:
> > I gotta run to the airport, but sources and upgrade bits of 4.0.rc0
> > are in
> >
> >   http://sage.math.washington.edu/home/mabshoff/release-cycles-4.0/rc0/
> >
> > Once I get online I will post more info, but I am sure this will
> > take a couple hours. Sorry.
>
> I updated http://alpha.sagenb.org to sage-4.0.rc0, and strongly
> encourage people to try it. Especially try symbolic calculus
> computations since we switched from Maxima to Ginac for the core of
> symbolics in sage-4.0.
>
> I've built this on a number of machine and there are a number of
> doctest failures, segfaults, and other issues that pop up when not
> building on sage.math. To get sage-4.0 formally released requires (at
> least) two things:
>
> (1) sort out all these doctest failures
>
> (2) get the new pynac-based symbolics code refereed:
> http://trac.sagemath.org/sage_trac/ticket/6111

I have two open tickets related to symbolics, and sadly the new
symbolics hasn't magically fixed either. :(

http://trac.sagemath.org/sage_trac/ticket/4142

http://trac.sagemath.org/sage_trac/ticket/3863

I don't know enough about the pynac symbolics to try fixing this, but if
anyone is looking for more test cases...

Dan

--
--- Dan Drake <dr...@kaist.edu>
----- KAIST Department of Mathematical Sciences
------- http://mathsci.kaist.ac.kr/~drake

[Tim Lahey]

On May 21, 2009, at 7:24 PM, Dan Drake wrote:

> I have two open tickets related to symbolics, and sadly the new
> symbolics hasn't magically fixed either. :(
>
> http://trac.sagemath.org/sage_trac/ticket/4142
>

This one is limits, which I believe is still being done with Maxima
which is probably why it hasn't been magically fixed.

> http://trac.sagemath.org/sage_trac/ticket/3863

This is numerical integration. Integration is also still being done
by Maxima, but I'm not sure about how numerical integration is
being done.

Cheers,

Tim.

---
Tim Lahey
PhD Candidate, Systems Design Engineering
University of Waterloo
http://www.linkedin.com/in/timlahey

[J Elaych]

As usual 4.0.rc0 compiled and tested fine on Ubuntu 64 amd64 x2 9.x.

I did notice that desolve still uses maxima; is anyone planning to
change that? I couldn't find DE support in pynac so it looks like
maxima will still be with sage for a while.

[Michael Abshoff]

On Thu, May 21, 2009 at 2:09 PM, Alex Ghitza <agh...@gmail.com> wrote:
>
> Hi Michael,
>
> One clarification regarding credit for #6042: I shouldn't get reviewer
> credit for it.  David rebased and reviewed all of it himself.

Fixed.

> Best,
> Alex

[Alex Ghitza]

Hi,

Fresh build of 4.0.rc0 on an Archlinux machine worked. However, doing
make ptestlong gave quite a few doctest failures:


sage -t -long
devel/sage/doc/en/bordeaux_2008/nf_introduction.rst # 3 doctests
failed
sage -t -long devel/sage/doc/en/a_tour_of_sage/index.rst # 1
doctests failed
sage -t -long devel/sage/doc/en/numerical_sage/scipy.rst # 1
doctests failed
sage -t -long devel/sage/doc/en/tutorial/tour_plotting.rst # 1
doctests failed
sage -t -long devel/sage/doc/en/tutorial/tour_functions.rst #
3 doctests failed
sage -t -long devel/sage/doc/en/tutorial/tour_algebra.rst # 1
doctests failed
sage -t -long devel/sage/doc/en/constructions/plotting.rst # 1
doctests failed
sage -t -long
devel/sage/doc/en/constructions/linear_algebra.rst # 1 doctests failed
sage -t -long devel/sage/doc/en/constructions/calculus.rst # 2
doctests failed
sage -t -long
devel/sage/doc/en/constructions/interface_issues.rst # 3 doctests
failed
sage -t -long devel/sage/doc/fr/tutorial/tour_plotting.rst # 1
doctests failed
sage -t -long devel/sage/doc/fr/tutorial/tour_algebra.rst # 1
doctests failed
sage -t -long
devel/sage/sage/schemes/elliptic_curves/ell_generic.py # 2 doctests
failed
sage -t -long devel/sage/sage/matrix/matrix_symbolic_dense.pyx
# 4 doctests failed
sage -t -long devel/sage/sage/matrix/matrix2.pyx # 2 doctests failed
sage -t -long devel/sage/sage/modules/free_module_element.pyx
# 1 doctests failed
sage -t -long devel/sage/sage/modular/overconvergent/genus0.py
# 1 doctests failed
sage -t -long devel/sage/sage/functions/transcendental.py # 1
doctests failed
sage -t -long devel/sage/sage/functions/other.py # 2 doctests failed
sage -t -long devel/sage/sage/functions/special.py # 5 doctests failed
sage -t -long devel/sage/sage/functions/piecewise.py # 5 doctests failed
sage -t -long devel/sage/sage/misc/sage_eval.py # 1 doctests failed
sage -t -long devel/sage/sage/misc/preparser.py # 2 doctests failed
sage -t -long devel/sage/sage/misc/map_threaded.py # 1 doctests failed
sage -t -long
devel/sage/sage/algebras/quatalg/quaternion_algebra.py # 1 doctests
failed
sage -t -long devel/sage/sage/coding/code_bounds.py # 1 doctests failed
sage -t -long devel/sage/sage/plot/animate.py # 1 doctests failed
sage -t -long devel/sage/sage/plot/complex_plot.pyx # 1 doctests failed
sage -t -long devel/sage/sage/plot/tachyon.py # 1 doctests failed
sage -t -long devel/sage/sage/plot/plot.py # 24 doctests failed
sage -t -long devel/sage/sage/plot/plot3d/transform.pyx # 2
doctests failed
sage -t -long devel/sage/sage/plot/plot3d/parametric_plot3d.py
# 1 doctests failed
sage -t -long devel/sage/sage/plot/plot3d/implicit_surface.pyx
# 1 doctests failed
sage -t -long devel/sage/sage/gsl/ode.pyx # 2 doctests failed
sage -t -long devel/sage/sage/gsl/interpolation.pyx # 1 doctests failed
sage -t -long devel/sage/sage/numerical/optimize.py # 1 doctests failed
sage -t -long devel/sage/sage/interfaces/maxima.py # 6 doctests failed
sage -t -long devel/sage/sage/tests/book_stein_ent.py # 2
doctests failed
sage -t -long devel/sage/sage/calculus/functional.py # 2 doctests failed
sage -t -long devel/sage/sage/calculus/tests.py # 6 doctests failed
sage -t -long devel/sage/sage/calculus/test_sympy.py # 7 doctests failed
sage -t -long devel/sage/sage/calculus/calculus.py # 9 doctests failed
sage -t -long
devel/sage/sage/rings/polynomial/polynomial_element.pyx # 1 doctests
failed
sage -t -long devel/sage/sage/rings/arith.py # 1 doctests failed
sage -t -long
devel/sage/sage/rings/number_field/number_field_element.pyx # 1
doctests failed
sage -t -long
devel/sage/sage/rings/number_field/number_field_element_quadratic.pyx
# 1 doctests failed
sage -t -long devel/sage/sage/symbolic/assumptions.py # 1
doctests failed
sage -t -long devel/sage/sage/symbolic/relation.py # 1 doctests failed
sage -t -long devel/sage/sage/symbolic/ring.pyx # 2 doctests failed
sage -t -long devel/sage/sage/symbolic/benchmark.py # 2 doctests failed
sage -t -long devel/sage/sage/symbolic/function.pyx # 4 doctests failed
sage -t -long devel/sage/sage/symbolic/expression.pyx # 8
doctests failed
sage -t -long devel/sage/sage/symbolic/callable.py # 8 doctests failed


The complete log is up at

http://ms.unimelb.edu.au/~aghitza/ptestlong.log



Best,
Alex

[Kiran Kedlaya]

On a fresh build on 64-bit Fedora 10 (Opteron), only one doctest
fails:

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

due to numerical noise as follows:
**********************************************************************
File "/scratch/sage-4.0.rc0/devel/sage/sage/matrix/matrix2.pyx", line

4964:
sage: m.change_ring(CDF).eigenvalues() # again for display
purposes
Expected:
[10.463115298 - 4.98835989975e-16*I, 7.42365754809 -
5.05298436852e-16*I, 3.36964641458 + 5.59670199836e-17*I,
1.25904669699 + 4.34508443713e-17*I, 0.00689184179485 -
5.75358699674e-17*I, 0.330700789655 + 5.1816322259e-16*I]
Got:
[10.463115298 - 3.57021884933e-16*I, 7.42365754809 +
2.91121322571e-17*I, 3.36964641458 - 1.54788874696e-16*I,
1.25904669699 - 5.01646753379e-17*I, 0.00689184179485 -
3.97030024181e-16*I, 0.330700789655 + 1.32245788594e-16*I]
**********************************************************************

Kiran

[John H Palmieri]

On May 21, 7:14 am, mabshoff <mabsh...@googlemail.com> wrote:
> Hi,
>
> I gotta run to the airport, but sources and upgrade bits of 4.0.rc0
> are in
>
>    http://sage.math.washington.edu/home/mabshoff/release-cycles-4.0/rc0/
>
> Once I get online I will post more info, but I am sure this will take
> a couple hours. Sorry.
>
> Cheers,
>
> Michael

On Intel Mac OS 10.5, 32-bit: an upgrade failed for reasons already
reported here, and my attempts to fix it also failed. A fresh install
built fine and had a few doctest failures (with sage -testall -long):

The following tests failed:

sage -t -long "devel/sage/sage/calculus/wester.py"
sage -t -long "devel/sage/sage/graphs/graph_plot.py"
sage -t -long "devel/sage/sage/matrix/matrix2.pyx"
sage -t -long "devel/sage/sage/symbolic/assumptions.py"
sage -t -long "devel/sage/sage/symbolic/expression.pyx"
sage -t -long "devel/sage/sage/symbolic/relation.py"

Several of these are sorting issues, e.g.,

File "/Applications/sage_builds/sage-4.0.rc0/devel/sage/sage/calculus/
wester.py", line 212:
sage: print list(sorted(assumptions()))
Expected:
[x > y, y > 0]
Got:
[y > 0, x > y]

Other are numerical noise. The one in graph_plot is

libpng error: Image width or height is zero in IHDR

leading to a runtime error.

Let me know if you want more details for any of these.

John

[mabshoff]

Yeah, Mike Hansen mentioned there were hashing issues.

> Other are numerical noise.

Yep, some of those are still around.

>  The one in graph_plot is
>
> libpng error: Image width or height is zero in IHDR
>
> leading to a runtime error.

Odd, I thought rlm fixed that one. Unless somehow a patch reverted
that one fix there might be an analog issue in the code.

> Let me know if you want more details for any of these.

I am in between flights and about to catch some sleep, but please post
a link to the test log. I will take a bunch of them with me and look
for common denominations, etc.

>   John

Cheers,

Michael

[John H Palmieri]

Here it is:

<http://sage.math.washington.edu/home/palmieri/misc/test.log>

John

[Dr. David Kirkby]

mabshoff wrote:
> Hi,
>
> I gotta run to the airport, but sources and upgrade bits of 4.0.rc0
> are in
>
> http://sage.math.washington.edu/home/mabshoff/release-cycles-4.0/rc0/

I must say, it's looking better on Solaris.

Before going to bed, I started to build 4.0.rc0. I woke up this morning,
and found it is still in the build process. I don't think it has ever
run anything like that time before it has stopped.

My machine is quite heavily loaded (load average 3.7) which is due to
some other processes running, which have been running for weeks, so
would have been running when I tried to build sage-4.0.alpha0

So, based on this very scientific measure of starting to compile Sage
before I sent to bed, and Sage still compiling now (and hour or so after
I got up), that is a definite improvement on Solaris!

Dave

[mabshoff]

On May 22, 1:46 am, "Dr. David Kirkby" <david.kir...@onetel.net>
wrote:

> mabshoff wrote:
> > Hi,
>
> > I gotta run to the airport, but sources and upgrade bits of 4.0.rc0
> > are in
>
> >    http://sage.math.washington.edu/home/mabshoff/release-cycles-4.0/rc0/
>
> I must say, it's looking better on Solaris.

;)

> Before going to bed, I started to build 4.0.rc0. I woke up this morning,
> and found it is still in the build process. I don't think it has ever
> run anything like that time before it has stopped.

Well, I never really had problems to get Sage to build, but then I
tended to fix the bugs on the fly.

> My machine is quite heavily loaded (load average 3.7) which is due to
> some other processes running, which have been running for weeks, so
> would have been running when I tried to build sage-4.0.alpha0
>
> So, based on this very scientific measure of starting to compile Sage
> before I sent to bed, and Sage still compiling now (and hour or so after
> I got up), that is a definite improvement on Solaris!
>
> Dave

Anyway, we need a formal review of

#6104: Michael Abshoff: Fix Solaris specific build issue for
libfplll.spkg [Needs review]

All that is changed is a fix to dpe.h to make it compile on Solaris.
The fix is even guarded, so nothing that does not define __sun is
affected.

Cheers,

Michael

[Robert Bradshaw]

I wasn't able to build on OS X 10.4 intel:

[...]
gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../../
tests -m32 -O2 -fomit-frame-pointer -mtune=nocona -march=nocona -c
t-locale.c
/bin/sh ../../libtool --tag=CC --mode=link gcc -std=gnu99 -m32 -O2 -
fomit-frame-pointer -mtune=nocona -march=nocona -o t-locale t-
locale.o ../../tests/libtests.la ../../libmpir.la
gcc -std=gnu99 -m32 -O2 -fomit-frame-pointer -mtune=nocona -
march=nocona -o .libs/t-locale t-locale.o ../../tests/.libs/
libtests.a /Users/robert/sage/sage-4.0.rc0/spkg/build/gmp-mpir-1.1.1/
src/.libs/libmpir.dylib ../../.libs/libmpir.dylib
i686-apple-darwin8-gcc-4.0.1: t-locale.o: No such file or directory
make[6]: *** [t-locale] Error 1
make[5]: *** [check-am] Error 2
make[4]: *** [check-recursive] Error 1
make[3]: *** [check-recursive] Error 1
make[2]: *** [check] Error 2

real 7m30.832s
user 3m10.400s
sys 3m27.151s
sage: An error occurred while installing gmp-mpir-1.1.1

Full log at http://sage.math.washington.edu/home/robertwb/4.0rc0.log

- Robert

[Dr. David Kirkby]

What's the process of the review? I'm willing to take a look at it. If
it's written in C, then I'll feel confident at understanding it. If it's
in C++, then I would not.

> All that is changed is a fix to dpe.h to make it compile on Solaris.
> The fix is even guarded, so nothing that does not define __sun is
> affected

> Cheers,
>
> Michael

Well, it finally did build and a simple addition worked. The GUI did not
however work, as http://localhost:8000

responds with:

"Firefox can't establish a connection to the server at localhost:8000."

I tried to telnet to localhost port 8000 and get a message the
connection was refused.

Anyway, it's late here, and I'm tired so I'm not going to look at it any
further tonight.

drkirkby@kestrel:[~/sage/sage-4.0.rc0] $ ./sage

----------------------------------------------------------------------
| Sage Version 4.0.rc0, Release Date: 2009-05-21 |
| Type notebook() for the GUI, and license() for information. |
----------------------------------------------------------------------

sage: 12+34
46
sage: notebook()
The notebook files are stored in: /export/home/drkirkby/.sage//sage_notebook

Please choose a new password for the SAGE Notebook 'admin' user.
Do _not_ choose a stupid password, since anybody who could guess your
password
and connect to your machine could access or delete your files.
NOTE: Only the md5 hash of the password you type is stored by SAGE.
You can change your password by typing notebook(reset=True).

Enter new password:
Retype new password:
Please login to the notebook with the username 'admin' and the above
password.
Password changed for user 'admin'.
**************************************************
* *
* Open your web browser to http://localhost:8000 *
* *
**************************************************

[Marshall Hampton]

I had all the same failures as John on my apple 10.5 laptop, except
the graph_plot failure. This was from a fresh build, not an upgrade.

-M. Hampton