sage-5.0.beta3 released
Jeroen Demeyer
We're releasing Sage 5.0.beta3.
Source archive:
http://boxen.math.washington.edu/home/release/sage-5.0.beta3/sage-5.0.beta3.tar
Upgrade path:
http://boxen.math.washington.edu/home/release/sage-5.0.beta3/sage-5.0.beta3/
The source and upgrade path can also be found on the mirror network
(you might need to wait a while before the mirrors are synchronized):
http://www.sagemath.org/download-latest.html
Please build, test, and report! We'd love to hear about your
experiences with this release.
== Tickets ==
* We closed 137 tickets in this release. For details, see
http://boxen.math.washington.edu/home/release/sage-5.0.beta3/tickets.html
Closed tickets:
#10459: serious troubles with gcd [Reviewed by Luis Felipe Tabera
Alonso, Douglas McNeily]
#10808: atlas-3.8.3.p16 doesn't build on ARM [Reviewed by Julien Puydt,
Dmitrii Pasechnik]
#11594: Symbolic integration of abs() failure [Reviewed by Karl-Dieter
Crisman, Michael Orlitzky]
#12042: Emil Widmann: Update the documentation how to use the VM image,
especially to avoid confusion about Virtualbox and VM Player [Reviewed
by Marco Streng]
#12320: install cephes on the ARM platform [Reviewed by Julien Puydt,
Dmitrii Pasechnik]
Merged in sage-5.0.beta3:
#7509: William Stein, Wilfried Huss: notebook -- make it possible to
debug Python code in the notebook, e.g., something like pdb that works
in the notebook [Reviewed by David Roe]
#8458: Lukáš Lánský: iterator for graphs() doesn't return independent
graphs [Reviewed by Nathann Cohen]
#8879: Michael Orlitzky: Clean up whitespace in padic hyperelliptic
curve file [Reviewed by Karl-Dieter Crisman]
#10175: Volker Braun: symmetric and exterior powers of characters
[Reviewed by David Roe]
#10192: Leif Leonhardy: SageNB broken when SAGE_PATH contains flavours
of '.' during installation [Reviewed by Florent Hivert]
#10441: Lukáš Lánský: Error creating an empty multi-edge (di)graph
[Reviewed by Nathann Cohen]
#10628: Maarten Derickx, Simon King: initialization of matrices from
vectors or list of lists can be way faster [Reviewed by Simon King]
#10868: Michael Orlitzky: A wrong (easy) limit [Reviewed by Aly Deines]
#10916: Lukáš Lánský: Multiple loops and edges are lost upon pickling
[Reviewed by Nathann Cohen]
#10923: Thierry Monteil, Michael Orlitzky: Bad sign in integral()
[Reviewed by Benjamin Jones, Karl-Dieter Crisman]
#10940: Frederic Han: giac interface [Reviewed by David Kohel]
#11483: Michael Orlitzky, Jason Grout: enable abs_integrate package from
maxima [Reviewed by Karl-Dieter Crisman]
#11591: Michael Orlitzky: Incorrect results for integrals involving
exponential functions [Reviewed by Aly Deines]
#11739: Lukáš Lánský: add_vertex w/o params should return the new vertex
[Reviewed by Paul Zimmermann]
#11920: Jeroen Demeyer: Sympow needs to disable fused-multiply-add and
should create datafiles [Reviewed by Leif Leonhardy, Volker Braun]
#11981: Daniel Krenn: map_coefficients (of multivariate polynomial ring)
cannot change base_ring [Reviewed by Julian Rueth]
#12105: Johan Bosman: RuntimeError: Segmentation fault with nth_root
[Reviewed by Karl-Dieter Crisman]
#12144: William Stein: better document a technical confusing point in
the Hidden Markov Model code [Reviewed by Jason Grout]
#12261: David Roe: Bring Doctest coverage for element_ext_pari.py to
100% [Reviewed by Karl-Dieter Crisman, Aly Deines]
#12317: Francis Clarke: printing factorisations [Reviewed by Robert
Bradshaw]
#12325: Lukáš Lánský: Eulerian circuits/paths for (di)graphs [Reviewed
by Nathann Cohen]
#12328: François Bissey: GMP_BITS_PER_MP_LIMB is deprecated in gmp/mpir
[Reviewed by Robert Bradshaw]
#12370: Javier López Peña: Change is_singular to use rank instead of
determinant [Reviewed by Keshav Kini]
#12378: Joal Heagney, Nathann Cohen: Graph chromatic_number
documentation [Reviewed by Karl-Dieter Crisman]
#12386: Julien Puydt: [ARM] pickling issues in the matrix_mod2_dense
code [Reviewed by Martin Albrecht]
#12389: Nathann Cohen: Rounding error in graph coloring [Reviewed by
David Coudert]
#12395: David Roe: Change some random variable indexes that cause
doctest failures if doctests are run in a different order. [Reviewed by
Karl-Dieter Crisman]
#12412: Jim Stark: TypeError when creating a zero map from a zero
dimensional vector space to a positive dimensional vector space
[Reviewed by Aly Deines]
Marco Streng
> Please build, test, and report! We'd love to hear about your
> experiences with this release.
I have a strange doctest problem. The test
sage -t -only-optional=magma
"devel/sage/sage/symbolic/integration/integral.py"
was fine on beta2, but fails on beta3. This file has no magma doctests,
but does have mathematica and maple doctests. The issue seems to be
related to the doctesting framework, but I don't see any relevant
tickets mentioned below. Could someone check whether this test works for
them?
Here's the traceback:
sage -t -only-optional=magma
"devel/sage/sage/symbolic/integration/integral.py"
Traceback (most recent call last):
File "/storage/marco/sage-5.0.beta3/local/bin/sage-doctest", line
924, in <module>
test_file(argv[1], library_code = library_code)
File "/storage/marco/sage-5.0.beta3/local/bin/sage-doctest", line
721, in test_file
s = extract_doc(file, library_code=library_code)
File "/storage/marco/sage-5.0.beta3/local/bin/sage-doctest", line
551, in extract_doc
doc = doc_preparse(F[i:j+3])
File "/storage/marco/sage-5.0.beta3/local/bin/sage-doctest", line
370, in doc_preparse
v = [i for i in range(len(t)) if
only_optional_include(comment_modifiers[i])]
IndexError: list index out of range
[0.1 s]
Actually, it is even stranger: if I send the output on to a file with "
> filename.txt", this traceback (and all doctesting results) does end
up in the file, but the traceback also gets printed to my terminal.
kcrisman
b:
Updating Cython code....
setup.py:650: UserWarning: could not find dependency <string> included
in /Users/.../sage-5.0.beta3/local/lib/python/site-packages/Cython/
Includes/libcpp/string.pxd. I will assume it is a system C/C++ header.
warnings.warn(msg+' I will assume it is a system C/C++ header.')
setup.py:650: UserWarning: could not find dependency <vector> included
in /Users/.../sage-5.0.beta3/local/lib/python/site-packages/Cython/
Includes/libcpp/vector.pxd. I will assume it is a system C/C++ header.
warnings.warn(msg+' I will assume it is a system C/C++ header.')
Executing 0 commands (using 0 threads)
It doesn't seem to cause problems, but I thought I should report it.
I just checked and it *is* also in 5.0.beta2, *not* in 4.8.
Volker Braun
William Stein
> This is caused by one of my patches; we now _can_ use cython.libcpp and
> there is an example that does. Our setup.py likes to print this warning, it
> should probably be silenced.
I also saw this warning a lot lately, and found it disturbing.
William
> As far as I know there is no good way to find
> the whole gcc include path without actually running the compilation.
>
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--
William Stein
Professor of Mathematics
University of Washington
http://wstein.org
Justin C. Walker
On Feb 9, 2012, at 01:19 , Jeroen Demeyer wrote:
> Dear Sage lovers,
>
> We're releasing Sage 5.0.beta3.
>
> Source archive:
>
> http://boxen.math.washington.edu/home/release/sage-5.0.beta3/sage-5.0.beta3.tar
Built from scratch on Mac OS X, 10.6.8 (Dual 6-Core Xeon).
No problems with build, doc build, and all tests ('ptestlong') passed!
Justin
--
Justin C. Walker, Curmudgeon at Large
Institute for the Absorption of Federal Funds
--
Democracy is two wolves and a lamb
voting on what to have for lunch.
Liberty is a well-armed lamb contesting
the vote.
Justin C. Walker
On Feb 9, 2012, at 19:01 , kcrisman wrote:
> On Mac OSX 10.6 Intel, I'm getting the following whenever I do sage -
> b:
>
>
> Updating Cython code....
> setup.py:650: UserWarning: could not find dependency <string> included
> in /Users/.../sage-5.0.beta3/local/lib/python/site-packages/Cython/
> Includes/libcpp/string.pxd. I will assume it is a system C/C++ header.
> warnings.warn(msg+' I will assume it is a system C/C++ header.')
> setup.py:650: UserWarning: could not find dependency <vector> included
> in /Users/.../sage-5.0.beta3/local/lib/python/site-packages/Cython/
> Includes/libcpp/vector.pxd. I will assume it is a system C/C++ header.
> warnings.warn(msg+' I will assume it is a system C/C++ header.')
> Executing 0 commands (using 0 threads)
Just noticed Karl's message and checked my "install.log". I got "UserWarning"s for the sage-5.0 and scipy .spkg's:
sage-5.0:
Building modified file sagsetup.py:650: UserWarning: could not find dependency <vector> included in /Users/Sage/sage-5.0.beta3/local/lib/python/site-packages/Cython/Includes/libcpp/vector.pxd. I will assume it is a system C/C++ header.
warnings.warn(msg+' I will assume it is a system C/C++ header.')
setup.py:650: UserWarning: could not find dependency <string> included in /Users/Sage/sage-5.0.beta3/local/lib/python/site-packages/Cython/Includes/libcpp/string.pxd. I will assume it is a system C/C++ header.
warnings.warn(msg+' I will assume it is a system C/C++ header.')
scipy (twice):
UMFPACK sparse solver (http://www.cise.ufl.edu/research/sparse/umfpack/)
not found. Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [umfpack]) or by setting
the UMFPACK environment variable.
warnings.warn(self.notfounderror.__doc__)
NOT AVAILABLE
So far, no obvious impact.
The install log is at sage.math.washinton.edu:~justin/logs/5.0-b3.log, in case it's of interest.
Justin
--
Justin C. Walker, Curmudgeon-At-Large
Institute for the Absorption of Federal Funds
--------
Men are from Earth.
Women are from Earth.
Deal with it.
--------
Jonathan Bober
--
You received this message because you are subscribed to the Google Groups "sage-release" group.
Marco Streng
install of Sage from source. And I traced it down to #10923
On 5.0.beta2 without #10923, everything is fine, but with #10923, the
following test does not work any more:
./sage -t -only-optional=magma
"devel/sage/sage/symbolic/integration/integral.py"
Something in that patch seems to trigger a bug in doctesting.
--
Marco
Marco Streng
> Ok, this really is an actual bug. Verified on two machines, with a
> fresh install of Sage from source. And I traced it down to #10923
>
> On 5.0.beta2 without #10923, everything is fine, but with #10923, the
> following test does not work any more:
> ./sage -t -only-optional=magma
> "devel/sage/sage/symbolic/integration/integral.py"
>
> Something in that patch seems to trigger a bug in doctesting.
I've narrowed it down to the
# abs tol 10e-10
(removing that makes the problem go away, though I have no idea why)
kcrisman
On Feb 10, 2:09 pm, Marco Streng <marco.str...@gmail.com> wrote:
> Ok, this really is an actual bug. Verified on two machines, with a fresh
> install of Sage from source. And I traced it down to #10923
>
> On 5.0.beta2 without #10923, everything is fine, but with #10923, the
> following test does not work any more:
> ./sage -t -only-optional=magma
> "devel/sage/sage/symbolic/integration/integral.py"
>
> Something in that patch seems to trigger a bug in doctesting.
>
kcrisman
> > On 5.0.beta2 without #10923, everything is fine, but with #10923, the
> > following test does not work any more:
> > ./sage -t -only-optional=magma
> > "devel/sage/sage/symbolic/integration/integral.py"
>
> > Something in that patch seems to trigger a bug in doctesting.
>
> Let's open a new ticket to fix this. Seehttp://trac.sagemath.org/sage_trac/ticket/12493
construction, it somehow doubles itself in the list of comment
modifiers. Experts in that are welcome to help.
kcrisman
few minutes. Anyway, I don't think anyone who didn't write the new
tolerance doctest code would want to introduce new bugs into it, so
this would be great for those to take a look at.
I *did* make this a blocker, because a doctest doesn't even run, but
if Jeroen or William (or someone else) thinks releasing Sage 5.0 with
this would be okay because it's with 'optional', reconsideration is
fine.
Pablo De Napoli
However, "make test" failed with the following error message
Testing that Sage starts...
[2012-02-11 17:00:04] Sage version 5.0.beta3, released 2012-02-08
Yes, Sage starts.
. spkg/bin/sage-env && sage-maketest
/bin/sh: 46: spkg/bin/sage-env: Bad substitution
mkdir: no se puede crear el directorio «//matplotlib-1.1.0»: Permiso denegado
/bin/sh: 479: spkg/bin/sage-env: Syntax error: "(" unexpected
make: *** [test] Error 2
Pablo
Jeroen Demeyer
I guess this is caused by your shell not being bash. What is the output of:
$ /bin/sh --version
And what happens if you do (from the SAGE_ROOT directory):
$ exec bash
$ make test
Pablo De Napoli
Yes, I guest that is the problem, since my /bin//sh is dash
(Debian's Posix compatible shell)
/bin/sh --version
/bin/sh: 0: Illegal option --
$ exec bash
$ make test
Howver after a manual
source ./spkg/bin/sage-env
things seems to work!
John H Palmieri
On Thursday, February 9, 2012 1:19:01 AM UTC-8, Jeroen Demeyer wrote:
Dear Sage lovers,We're releasing Sage 5.0.beta3.
http://sage.math.washington.edu/home/palmieri/misc/libm4rie-20111004.p1.log
but I see error messages like
tests/test_trsm.cc: In function ‘int test_mzed_trsm_upper_left(gf2e*, rci_t, rci_t)’:
tests/test_trsm.cc:106:3: error: ‘__STRING’ was not declared in this scope
tests/test_trsm.cc:107:3: error: ‘__STRING’ was not declared in this scope
--
John
John H Palmieri
On Saturday, February 11, 2012 3:21:42 PM UTC-8, John H Palmieri wrote:
On Thursday, February 9, 2012 1:19:01 AM UTC-8, Jeroen Demeyer wrote:Dear Sage lovers,We're releasing Sage 5.0.beta3.
On OpenSolaris on x86 (Dave Kirkby's machine hawk): libm4rie fails self-tests.
On the same machine, iml fails self-test. Log:
http://sage.math.washington.edu/home/palmieri/misc/iml-1.0.1.p14.log
An excerpt:
Undefined first referenced
symbol in file
cblas_dger ../src/.libs/libiml.so
cblas_dswap ../src/.libs/libiml.so
cblas_dcopy ../src/.libs/libiml.so
cblas_dgemm ../src/.libs/libiml.so
cblas_dgemv ../src/.libs/libiml.so
ld: fatal: symbol referencing errors. No output written to .libs/test-largeentry
collect2: ld returned 1 exit status
--
John
John H Palmieri
On Saturday, February 11, 2012 3:35:49 PM UTC-8, John H Palmieri wrote:
On Saturday, February 11, 2012 3:21:42 PM UTC-8, John H Palmieri wrote:
On Thursday, February 9, 2012 1:19:01 AM UTC-8, Jeroen Demeyer wrote:Dear Sage lovers,We're releasing Sage 5.0.beta3.
On OpenSolaris on x86 (Dave Kirkby's machine hawk): libm4rie fails self-tests.
On the same machine, sagetex fails self-tests. New spkg up at
<http://trac.sagemath.org/sage_trac/ticket/12500>
Please review.
--
John