sage-5.0.beta12 released

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Jeroen Demeyer

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Apr 4, 2012, 9:35:48 AM4/4/12
to sage-r...@googlegroups.com
Dear Sage lovers,

We're releasing Sage 5.0.beta12.

Source archive:

http://boxen.math.washington.edu/home/release/sage-5.0.beta12/sage-5.0.beta12.tar

Upgrade path:

http://boxen.math.washington.edu/home/release/sage-5.0.beta12/sage-5.0.beta12/

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 424 tickets in this release. For details, see

http://boxen.math.washington.edu/home/release/sage-5.0.beta12/tickets.html

Closed tickets:

#6375: Run sage once as part of install process to generate
sage-flags.txt [Reviewed by Jeroen Demeyer]
#6494: sage should *never* ever import numpy by default on startup. Yet
again it does! [Reviewed by Mike Hansen]
#9894: Simon King: Group cohomology spkg, version 2.1.2 [Reviewed by
Karl-Dieter Crisman, John Palmieri]
#11329: make f2c spkg respect CC environment variable [Reviewed by R.
Andrew Ohana]
#11906: PolyBoRi 0.7.1 should obey some standard environment variables
[Reviewed by Jeroen Demeyer, Alexander Dreyer]
#12621: use bash for prereq install file [Reviewed by Jeroen Demeyer]
#12704: Restore doctesting of non-library files [Reviewed by Francis Clarke]
#12754: Fix scoping / name look-up issue in PolyBoRi 0.8.1 and support
flags from the environment [Reviewed by Alexander Dreyer, Leif
Leonhardy, Martin Albrecht, Burcin Erocal]
#12758: Jeroen Demeyer: update optional spkg 'gap_packages' [Reviewed by
Dmitrii Pasechnik]

Merged in sage-5.0.beta12:

#7711: Alex Ghitza: integral() does not reduce coefficients in finite
field [Reviewed by Paul Zimmermann]
#7926: Robert Bradshaw, Jennifer Balakrishnan, David Loeffler: Bring
coverage of monsky_washnitzer up to 50% [Reviewed by Paul Zimmermann,
Jeroen Demeyer]
#11238: Michael Orlitzky: failing calculation of a symbolic integral
[Reviewed by Karl-Dieter Crisman]
#11358: William Stein: matrix multiplication over ZZ sometimes gives
incorrect results [Reviewed by Douglas McNeil]
#11832: John Palmieri: bug fixes for profile functions for the Steenrod
algebra [Reviewed by William Stein]
#11958: Nathann Cohen, Jason Grout: cplex needs another symbolic link
[Reviewed by David Coudert]
#11995: Jeroen Demeyer: Length argument for PARI Vec() [Reviewed by Aly
Deines]
#12080: Chris Wuthrich: manin constant [Reviewed by William Stein]
#12136: Johannes Klaus Fichte: FVS function in DiGraph returns [0]
instead of [] if already directed acyclic [Reviewed by David Coudert]
#12381: David Roe: Typo in sage.combinat.sf.classical [Reviewed by
Nathann Cohen, Nicolas Thiery, David Loeffler]
#12638: Jeroen Demeyer: Add some patches to the PARI sources [Reviewed
by Johan Bosman]
#12739: Jeroen Demeyer: Put prereq under revision control [Reviewed by
John Palmieri]
#12747: Jim Stark: is_R_algebra is useless and wrong and should be
deleted [Reviewed by David Loeffler]
#12749: Jim Stark: Raise algebras/free_algebra.py coverage to 100%
[Reviewed by David Loeffler]
#12750: Alexander Dreyer: Fix scoping / name look-up issue in PolyBoRi
0.8.0 and support flags from the environment [Reviewed by Leif Leonhardy]
#12755: Jeroen Demeyer: Make coverage remove return types from Cython
functions [Reviewed by Mike Hansen]
#12757: David Loeffler: Clean up dead links in sage/modular/
documentation [Reviewed by Alex Ghitza]
#12763: R. Andrew Ohana: elliptic_curves spkg is broken for system
installs [Reviewed by François Bissey]
#12764: Rob Beezer: Remove ill-advised doctest for testing normal
matrices [Reviewed by John Palmieri]
#12771: David Roe: Kodaira symbol latex is wrong [Reviewed by Mike Hansen]
#12772: William Stein: bug in compact_system_of_eigenvalues for level 1
modular symbols [Reviewed by Fredrik Stromberg]
#12775: David Roe: Small Kodaira symbols typo [Reviewed by David Eklund,
Kiran Kedlaya]
#12779: William Stein: customization hook for modular symbols spaces
[Reviewed by David Loeffler]
#12788: Nils Bruin: Provide Integer class with a __format__ method
[Reviewed by Mike Hansen]
#12793: Jeroen Demeyer: Fix __cmp__ tests in
sage/combinat/root_system/type_dual.py [Reviewed by Nicolas M. Thiéry]

David Loeffler

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Apr 5, 2012, 4:18:06 AM4/5/12
to sage-r...@googlegroups.com


On Wednesday, 4 April 2012 14:35:48 UTC+1, Jeroen Demeyer wrote:
Dear Sage lovers,

We're releasing Sage 5.0.beta12.

Source archive:

http://boxen.math.washington.edu/home/release/sage-5.0.beta12/sage-5.0.beta12.tar

Upgrade path:

http://boxen.math.washington.edu/home/release/sage-5.0.beta12/sage-5.0.beta12/

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.

Built fine on 64-bit Linux with SAGE_CHECK set, and all long doctests pass. However at the end of the doctest run it printed the following message:

----------------------------------------------------------------------
The temporary doctesting directory
   /home/masiao/.sage/tmp/fermat-20283
was not removed: it is not empty, presumably because doctests
failed or doctesting was interrupted.

----------------------------------------------------------------------

Nothing failed and nothing was interrupted, so I'm puzzled by this.

David

Jean-Pierre Flori

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Apr 5, 2012, 4:54:34 AM4/5/12
to sage-r...@googlegroups.com

Built fine on 64-bit Linux with SAGE_CHECK set, and all long doctests pass. However at the end of the doctest run it printed the following message:

----------------------------------------------------------------------
The temporary doctesting directory
   /home/masiao/.sage/tmp/fermat-20283
was not removed: it is not empty, presumably because doctests
failed or doctesting was interrupted.

----------------------------------------------------------------------

Same here without SAGE_CHECK on ubuntu precise beta amd64 using the system atlas libraries (libatlas-base-dev package).
I think the directory issue has being discussed here: https://groups.google.com/d/msg/sage-release/XnyN3tx4Bow/gR6912FkNpUJ

leif

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Apr 5, 2012, 8:52:56 AM4/5/12
to sage-r...@googlegroups.com

Yep, and the ticket fixing it (#12805, thanks to John Palmieri) got
already positive review, unfortunately apparently too late for beta12.


-leif

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Anthony David

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Apr 5, 2012, 9:01:26 PM4/5/12
to sage-r...@googlegroups.com
Ubuntu 10.10
i686 GNU/Linux


SAGE_ATLAS_LIB=/usr/lib
SAGE_CHECK=yes


Attempted to workaround segfault in previous libm4rie testing by building

gcc (GCC) 4.4.7 and its dependencies mpfr-2.4.2 gmp-4.3.2

Eliminated the segfault but triggered the following reporting of faults where
all tests apparently passed but were reported as failed -
output copied below.

...
make[4]: Entering directory `/home/adavid/build/sage-5.0.beta12/spkg/build/libm4rie-20
111004.p2/src'
trsm: k:  2, minpoly: 0x007 m:     1, n:     1 .......... passed
trsm: k:  2, minpoly: 0x007 m:     1, n:     2 .......... passed
trsm: k:  2, minpoly: 0x007 m:    11, n:    12 .......... passed
trsm: k:  2, minpoly: 0x007 m:    21, n:    22 .......... passed
trsm: k:  2, minpoly: 0x007 m:    13, n:     2 .......... passed
trsm: k:  2, minpoly: 0x007 m:    32, n:    33 .......... passed
trsm: k:  2, minpoly: 0x007 m:    63, n:    64 .......... passed
trsm: k:  2, minpoly: 0x007 m:    65, n:     1 .......... passed
trsm: k:  2, minpoly: 0x007 m:    65, n:    66 .......... passed
trsm: k:  2, minpoly: 0x007 m:   127, n:   128 .......... passed
trsm: k:  2, minpoly: 0x007 m:   200, n:    20 .......... passed
trsm: k:  3, minpoly: 0x00b m:     1, n:     1 .......... passed
trsm: k:  3, minpoly: 0x00b m:     1, n:     2 .......... passed
trsm: k:  3, minpoly: 0x00b m:    11, n:    12 .......... passed
trsm: k:  3, minpoly: 0x00b m:    21, n:    22 .......... passed
trsm: k:  3, minpoly: 0x00b m:    13, n:     2 .......... passed
trsm: k:  3, minpoly: 0x00b m:    32, n:    33 .......... passed
trsm: k:  3, minpoly: 0x00b m:    63, n:    64 .......... passed
trsm: k:  3, minpoly: 0x00b m:    65, n:     1 .......... passed
trsm: k:  3, minpoly: 0x00b m:    65, n:    66 .......... passed
trsm: k:  3, minpoly: 0x00b m:   127, n:   128 .......... passed
trsm: k:  3, minpoly: 0x00b m:   200, n:    20 .......... passed
trsm: k:  4, minpoly: 0x019 m:     1, n:     1 .......... passed
trsm: k:  4, minpoly: 0x019 m:     1, n:     2 .......... passed
trsm: k:  4, minpoly: 0x019 m:    11, n:    12 .......... passed
trsm: k:  4, minpoly: 0x019 m:    21, n:    22 .......... passed
trsm: k:  4, minpoly: 0x019 m:    13, n:     2 .......... passed
trsm: k:  4, minpoly: 0x019 m:    32, n:    33 .......... passed
trsm: k:  4, minpoly: 0x019 m:    63, n:    64 .......... passed
trsm: k:  4, minpoly: 0x019 m:    65, n:     1 .......... passed
trsm: k:  4, minpoly: 0x019 m:    65, n:    66 .......... passed
trsm: k:  4, minpoly: 0x019 m:   127, n:   128 .......... passed
trsm: k:  4, minpoly: 0x019 m:   200, n:    20 .......... passed
trsm: k:  5, minpoly: 0x025 m:     1, n:     1 ......     passed
trsm: k:  5, minpoly: 0x025 m:     1, n:     2 ......     passed
trsm: k:  5, minpoly: 0x025 m:    11, n:    12 ......     passed
trsm: k:  5, minpoly: 0x025 m:    21, n:    22 ......     passed
trsm: k:  5, minpoly: 0x025 m:    13, n:     2 ......     passed
trsm: k:  5, minpoly: 0x025 m:    32, n:    33 ......     passed
trsm: k:  3, minpoly: 0x00b m:    21, n:    22 .......... passed
trsm: k:  3, minpoly: 0x00b m:    13, n:     2 .......... passed
trsm: k:  3, minpoly: 0x00b m:    32, n:    33 .......... passed
trsm: k:  3, minpoly: 0x00b m:    63, n:    64 .......... passed
trsm: k:  3, minpoly: 0x00b m:    65, n:     1 .......... passed
trsm: k:  3, minpoly: 0x00b m:    65, n:    66 .......... passed
trsm: k:  3, minpoly: 0x00b m:   127, n:   128 .......... passed
trsm: k:  3, minpoly: 0x00b m:   200, n:    20 .......... passed
trsm: k:  4, minpoly: 0x019 m:     1, n:     1 .......... passed
trsm: k:  4, minpoly: 0x019 m:     1, n:     2 .......... passed
trsm: k:  4, minpoly: 0x019 m:    11, n:    12 .......... passed
trsm: k:  4, minpoly: 0x019 m:    21, n:    22 .......... passed
trsm: k:  4, minpoly: 0x019 m:    13, n:     2 .......... passed
trsm: k:  4, minpoly: 0x019 m:    32, n:    33 .......... passed
trsm: k:  4, minpoly: 0x019 m:    63, n:    64 .......... passed
trsm: k:  4, minpoly: 0x019 m:    65, n:     1 .......... passed
trsm: k:  4, minpoly: 0x019 m:    65, n:    66 .......... passed
trsm: k:  4, minpoly: 0x019 m:   127, n:   128 .......... passed
trsm: k:  4, minpoly: 0x019 m:   200, n:    20 .......... passed
trsm: k:  5, minpoly: 0x025 m:     1, n:     1 ......     passed
trsm: k:  5, minpoly: 0x025 m:     1, n:     2 ......     passed
trsm: k:  5, minpoly: 0x025 m:    11, n:    12 ......     passed
trsm: k:  5, minpoly: 0x025 m:    21, n:    22 ......     passed
trsm: k:  5, minpoly: 0x025 m:    13, n:     2 ......     passed
trsm: k:  5, minpoly: 0x025 m:    32, n:    33 ......     passed
trsm: k:  5, minpoly: 0x025 m:    63, n:    64 ......     passed
trsm: k:  5, minpoly: 0x025 m:    65, n:     1 ......     passed
trsm: k:  5, minpoly: 0x025 m:    65, n:    66 ......     passed
trsm: k:  5, minpoly: 0x025 m:   127, n:   128 ......     passed
trsm: k:  5, minpoly: 0x025 m:   200, n:    20 ......     passed
trsm: k:  6, minpoly: 0x043 m:     1, n:     1 ......     passed
trsm: k:  6, minpoly: 0x043 m:     1, n:     2 ......     passed
trsm: k:  6, minpoly: 0x043 m:    11, n:    12 ......     passed
trsm: k:  6, minpoly: 0x043 m:    21, n:    22 ......     passed
trsm: k:  6, minpoly: 0x043 m:    13, n:     2 ......     passed
trsm: k:  6, minpoly: 0x043 m:    32, n:    33 ......     passed
trsm: k:  6, minpoly: 0x043 m:    63, n:    64 ......     passed
trsm: k:  6, minpoly: 0x043 m:    65, n:     1 ......     passed
trsm: k:  6, minpoly: 0x043 m:    65, n:    66 ......     passed
trsm: k:  6, minpoly: 0x043 m:   127, n:   128 ......     passed
trsm: k:  6, minpoly: 0x043 m:   200, n:    20 ......     passed
trsm: k:  7, minpoly: 0x089 m:     1, n:     1 ......     passed
trsm: k:  7, minpoly: 0x089 m:     1, n:     2 ......     passed
trsm: k:  7, minpoly: 0x089 m:    11, n:    12 ......     passed
trsm: k:  7, minpoly: 0x089 m:    21, n:    22 ......     passed
trsm: k:  7, minpoly: 0x089 m:    13, n:     2 ......     passed
trsm: k:  7, minpoly: 0x089 m:    32, n:    33 ......     passed
trsm: k:  7, minpoly: 0x089 m:    63, n:    64 ......     passed
trsm: k:  7, minpoly: 0x089 m:    65, n:     1 ......     passed
trsm: k:  7, minpoly: 0x089 m:    65, n:    66 ......     passed
trsm: k:  7, minpoly: 0x089 m:   127, n:   128 ......     passed
trsm: k:  7, minpoly: 0x089 m:   200, n:    20 ......     passed
trsm: k:  8, minpoly: 0x12b m:     1, n:     1 ......     passed
trsm: k:  8, minpoly: 0x12b m:     1, n:     2 ......     passed
trsm: k:  8, minpoly: 0x12b m:    11, n:    12 ......     passed
trsm: k:  8, minpoly: 0x12b m:    21, n:    22 ......     passed
trsm: k:  8, minpoly: 0x12b m:    13, n:     2 ......     passed
trsm: k:  8, minpoly: 0x12b m:    32, n:    33 ......     passed
trsm: k:  8, minpoly: 0x12b m:    63, n:    64 ......     passed
trsm: k:  8, minpoly: 0x12b m:    65, n:     1 ......     passed
trsm: k:  8, minpoly: 0x12b m:    65, n:    66 ......     passed
trsm: k:  8, minpoly: 0x12b m:   127, n:   128 ......     passed
trsm: k:  8, minpoly: 0x12b m:   200, n:    20 ......     passed
trsm: k:  9, minpoly: 0x211 m:     1, n:     1 ......     passed
trsm: k:  9, minpoly: 0x211 m:     1, n:     2 ......     passed
trsm: k:  9, minpoly: 0x211 m:    11, n:    12 ......     passed
trsm: k:  9, minpoly: 0x211 m:    21, n:    22 ......     passed
trsm: k:  9, minpoly: 0x211 m:    13, n:     2 ......     passed
trsm: k:  9, minpoly: 0x211 m:    32, n:    33 ......     passed
trsm: k:  9, minpoly: 0x211 m:    63, n:    64 ......     passed
trsm: k:  9, minpoly: 0x211 m:    65, n:     1 ......     passed
trsm: k:  9, minpoly: 0x211 m:    65, n:    66 ......     passed
trsm: k:  9, minpoly: 0x211 m:   127, n:   128 ......     passed
trsm: k:  9, minpoly: 0x211 m:   200, n:    20 ......     passed
trsm: k: 10, minpoly: 0x409 m:     1, n:     1 ......     passed
trsm: k: 10, minpoly: 0x409 m:     1, n:     2 ......     passed
trsm: k: 10, minpoly: 0x409 m:    11, n:    12 ......     passed
trsm: k: 10, minpoly: 0x409 m:    21, n:    22 ......     passed
trsm: k: 10, minpoly: 0x409 m:    13, n:     2 ......     passed
trsm: k: 10, minpoly: 0x409 m:    32, n:    33 ......     passed
trsm: k: 10, minpoly: 0x409 m:    63, n:    64 ......     passed
trsm: k: 10, minpoly: 0x409 m:    65, n:     1 ......     passed
trsm: k: 10, minpoly: 0x409 m:    65, n:    66 ......     passed
trsm: k: 10, minpoly: 0x409 m:   127, n:   128 ......     passed
trsm: k: 10, minpoly: 0x409 m:   200, n:    20 ......     passed
FAIL: test_trsm
...

/build/sage-5.0.beta12$ grep -C 2 FAIL /home/adavid/build/sage-5.0.beta12/spkg/logs/libm4rie-20111004.p2.log
trsm: k: 10, minpoly: 0x409 m:   127, n:   128 ......     passed
trsm: k: 10, minpoly: 0x409 m:   200, n:    20 ......     passed
FAIL: test_trsm
elim: k:  2, minpoly: 0x007 m:     2, n:     5 .. passed
elim: k:  2, minpoly: 0x007 m:     5, n:    10 .. passed
--
elim: k: 10, minpoly: 0x409 m:   200, n:   112 .. passed
elim: k: 10, minpoly: 0x409 m:    10, n:   200 .. passed
FAIL: test_elimination
mul: k:  2, minpoly: 0x007 m:     1, l:     1, n:     1 .........           passed
mul: k:  2, minpoly: 0x007 m:     1, l:     2, n:     3 ................... passed
--
mul: k: 10, minpoly: 0x409 m:   127, l:   128, n:   129 ................... passed
mul: k: 10, minpoly: 0x409 m:   200, l:    20, n:   112 ................... passed
FAIL: test_multiplication
testing k:  2, m:    2, n:   32 ............ passed
testing k:  2, m:    2, n:   64 ............ passed
--
testing k:  4, m:  201, n:  200 ............ passed
testing k:  4, m:  217, n:    2 ............ passed
FAIL: test_smallops
ple: k:  2, minpoly: 0x007 m:     1, n:     1, r:     1 . .  passed
ple: k:  2, minpoly: 0x007 m:     1, n:     2, r:     1 .... passed
--
ple: k: 10, minpoly: 0x409 m:   127, n:   129, r:   127 ..   passed
ple: k: 10, minpoly: 0x409 m:   200, n:   112, r:   111 ..   passed
FAIL: test_ple
===================
5 of 5 tests failed




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