Sage 4.1.2.alpha2 released
Minh Nguyen
This release has been slated to be out the door before Review Day 1 to
be held on 22nd September 2009. Anyone who would like to participate
during Review Day 1, please put your name down at the wiki page
http://wiki.sagemath.org/review1
and what you would like to work on. Ideally, your work during Review
Day 1 should use Sage 4.1.2.alpha2 as base. The source and binary
tarballs are available at
http://sage.math.washington.edu/home/mvngu/release/upgrade/sage-4.1.2.alpha2.tar
http://sage.math.washington.edu/home/mvngu/release/upgrade/sage-4.1.2.alpha2-sage.math.washington.edu-x86_64-Linux.tar.gz
and the upgrade path is
http://sage.math.washington.edu/home/mvngu/release/upgrade/sage-4.1.2.alpha2/
Please test and report all problems.
In this release, we have some updated packages, but not enough to
ensure that Sage builds seamlessly on 64-bit mode OS X 10.5. If you're
upgrading on 64-bit OS X 10.5, you might experience problems building
cliquer and ECL. Apart from the custom-built Fortran compiler at
http://sage.math.washington.edu/home/mvngu/apps/fortran-OSX64-20090120.spkg
you should use the updated cliquer package at ticket #6681 and the ECL
package at #6883. Remember to issue the command
export SAGE64=yes
Upgrading or building on 64-bit openSUSE 11.1 can result in a compile
error as the cliquer spkg shipped with Sage 4.1.2.alpha2 is known to
fail to compile on various 64-bit platforms. The known 64-bit
platforms include 64-bit mode OS X 10.5, 64-bit openSUSE 11.1, and
64-bit Fedora 11. If you're building or upgrading on any of those
platforms, you should use the cliquer package at #6681.
The following tickets were merged in Sage 4.1.2.alpha2:
#3133: Jason Grout: allow parametric_plot and parametric_plot3d to
take a vector as input [Reviewed by Karl-Dieter Crisman]
#3835: John Cremona: Make an algebraic closure function [Reviewed by
Mike Hansen]
#4786: Karl-Dieter Crisman, Burcin Erocal: fix some bugs / typos in
the solve function [Reviewed by Burcin Erocal, Karl-Dieter Crisman]
#4948: Felix Lawrence: implement the transfer of Mathematica lists
back to Sage [Reviewed by William Stein, Minh Van Nguyen]
#5145: Karl-Dieter Crisman: increase default plot_points value for
contour_plot [Reviewed by Jason Grout]
#5347: John Cremona: divides() may fail for 1 on the rhs. [Reviewed by
Mike Hansen]
#5758: John Palmieri: weird "hello" bug in homset coerce! [Reviewed by
Mike Hansen]
#5858: Jonathan J. Hunt: use sage-native-execute to start octave
[Reviewed by Jason Grout]
#5900: Tim Abbott: Add support for system python != Sage python
[Reviewed by Mike Hansen]
#6177: Michael Brickenstein, Alexander Dreyer, Martin Albrecht: Update
PolyBoRi to newest upstream release [Reviewed by David Kirkby, Alex
Ghitza, Burcin Erocal]
#6197: Karl-Dieter Crisman: conversion of binomial fails [Reviewed by
Mike Hansen]
#6325: David Joyner: optional doctest failure -- linear algebra
constructions.rst [Reviewed by Mike Hansen]
#6328: David Joyner: optional doctest failure -- bugs in the graph
theory section of constructions guide [Reviewed by Mike Hansen]
#6343: Nicolas M. Thiéry: Adds TestSuite(object).run() generic testing
framework [Reviewed by Mike Hansen, Minh Van Nguyen]
#6441: Sebastian Pancratz: Charpoly (plus adjoint and det) [Reviewed
by Rob Beezer, Yann Laigle-Chapuy]
#6521: Karl-Dieter Crisman, Jason Grout: replace .copy() with
.__copy__() in matrix/matrix0.pyx [Reviewed by Jason Grout,
Karl-Dieter Crisman, Minh Van Nguyen]
#6545: Martin Albrecht: sorting of ideal bases [Reviewed by John Perry]
#6597: Nicolas M. Thiéry: SetMorphism: 100% doctest + equality +
pickling; depends on #6343 [Reviewed by Mike Hansen]
#6609: David Kirkby: GNUism in lcalc-20080205.p2 passing GNU flags
directly to the Sun assembler. [Reviewed by Minh Van Nguyen]
#6634: Marshall Hampton: biopython 1.49b broken with python-2.6;
biopython upgrade [Reviewed by Alex Ghitza]
#6636: Karl-Dieter Crisman: Simplification of factorials and binomial
coefficients is not very good [Reviewed by Mike Hansen]
#6652: Ralf Hemmecke: should not have algebra structure on streams
[Reviewed by Florent Hivert]
#6663: Marshall Hampton: add new 4ti2 experimental package [Reviewed
by David Joyner, Alex Ghitza, Bjarke Hammersholt Roune, Mike Hansen,
David Perkinson]
#6749: Nathann Cohen: Knapsack algorithm [Reviewed by David Joyner]
#6750: Simon King, David J. Green: New version of optional Group
Cohomology spkg [Reviewed by John Palmieri, David Joyner, Mikael
Vejdemo Johansson]
#6759: David Kirkby: Update sqlite to latest release - needed for
Sun's compiler [Reviewed by Minh Van Nguyen]
#6774: Nathann Cohen: tour Graph Theory [Reviewed by Jason Grout]
#6806: Minh Van Nguyen: typo in patch of ticket #6396:
primes_of_degree_one is broken for relative extensions [Reviewed by
Karl-Dieter Crisman]
#6827: Carlo Hamalainen: probability distributions doctests + general
discrete distribution [Reviewed by Mike Hansen]
#6848: John Palmieri: "Definition:" messed up in notebook and command
line in cython code [Reviewed by Mike Hansen]
#6858: Robert Miller: Cayley graph connecting set [Reviewed by Nathann Cohen]
#6864: John Palmieri: Stop Sage tests from saving things to hard drive
[Reviewed by Karl-Dieter Crisman]
#6867: Nathann Cohen: GLPK ( compatible with the symbolics from MIP )
[Reviewed by Minh Van Nguyen]
#6868: Nathann Cohen: Coin-OR CBC ( compatible with the symbolics from
MIP ) [Reviewed by Minh Van Nguyen]
#6869: Nathann Cohen: LP and MIP Solvers in Sage ( with symbolics )
[Reviewed by David Joyner, Minh Van Nguyen]
#6875: Wilfried Huss: fill option is broken for polar_plot [Reviewed
by Jason Grout]
#6903: Sébastien Labbé, Franco Saliola: Function Word currently
prevent the inheritance of Words_over_OrderedAlphabet [Reviewed by
Franco Saliola]
#6905: Mike Hansen: real(0.0r) is broken [Reviewed by Nicolas M. Thiéry]
#6908: Minh Van Nguyen: programmers' guide --- doctesting and parallel
doctesting [Reviewed by John Palmieri, Karl-Dieter Crisman]
#6911: Robert Bradshaw: Faster basis and discriminants of a Hecke
algebra [Reviewed by William Stein]
#6945: David Kirkby, William Stein: Update readline to version 6.0
[Reviewed by Minh Van Nguyen]
#6950: Yann Laigle-Chapuy: computing algebraic immunity [Reviewed by
Martin Albrecht]
#6952: Minh Van Nguyen: follow-up to #6774: fix warnings and stylistic
niceties [Reviewed by Jason Grout]
#6953: Minh Van Nguyen: follow-up to #6950: fix warning when building
reference manual [Reviewed by Martin Albrecht]
--
Regards
Minh Van Nguyen
John H Palmieri
> Please test and report all problems.
mostly of the sort
TypeError: Unable to start maxima
John
Minh Nguyen
<SNIP>
> Please test and report all problems.
Building Sage 4.1.2.alpha2 from source on sage.math went OK. All
doctests pass. This is a bit surprising because I had some doctest
failures while merging tickets for that release.
Minh Nguyen
From: Minh Nguyen <nguye...@gmail.com>
Date: Tue, Sep 22, 2009 at 1:22 PM
Subject: Re: [sage-release] Re: Sage 4.1.2.alpha2 released
To: sage-r...@googlegroups.com
Hi William,
On Tue, Sep 22, 2009 at 12:13 PM, William Stein <wst...@gmail.com> wrote:
<SNIP>
> I finally fixed this. See
>
> http://trac.sagemath.org/sage_trac/ticket/6981
>
> Somebody needs to referee that. It's an updated of the standard
> fortran spkg so that it seamlessly works on OS X 64-bit.
I can test these updated packages on OS X 10.5 (bsd.math) and OS X
10.4 (I now have access to that platform). But I have to leave the
testing on OS X 10.6 to someone else who has access to Snow Leopard,
since I don't have access to a machine running 10.6.
Dan Drake
> Please test and report all problems.
On Ubuntu Jaunty amd64, building ecl failed with $MAKE='make -j3':
if test -f ../CROSS-DPP ; then ../CROSS-DPP /var/tmp/sage-4.1.2.alpha2/spkg/build/ecl-9.8.4/src/src/c/symbol.d symbol.c ; else ./dpp /var/tmp/sage-4.1.2.alpha2/spkg/build/ecl-9.8.4/src/src/c/symbol.d symbol.c ; fi
/bin/sh: ./dpp: not found
/bin/sh: ./dpp: not found
make[4]: *** [main.c] Error 127
make[4]: *** Waiting for unfinished jobs....
make[4]: *** [symbol.c] Error 127
make[4]: Leaving directory `/var/tmp/sage-4.1.2.alpha2/spkg/build/ecl-9.8.4/src/build/c'
make[3]: *** [libeclmin.a] Error 2
make[3]: Leaving directory `/var/tmp/sage-4.1.2.alpha2/spkg/build/ecl-9.8.4/src/build'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/var/tmp/sage-4.1.2.alpha2/spkg/build/ecl-9.8.4/src'
Failed to build ECL ... exiting
This sort of thing was mentioned in ticket #6883 and on this list [1].
With $MAKE=make, it built.
Dan
1. http://groups.google.com/group/sage-devel/browse_thread/thread/6b7a4dc5fd5e0ef8/da984bc7e72758b7?#da984bc7e72758b7
--
--- Dan Drake
----- http://mathsci.kaist.ac.kr/~drake
-------
Minh Nguyen
On Tue, Sep 22, 2009 at 12:20 PM, John H Palmieri
<jhpalm...@gmail.com> wrote:
<SNIP>
> On sage.math, using the prebuilt binary, I'm getting a ton of errors,
> mostly of the sort
>
> TypeError: Unable to start maxima
Using the sage.math binary for Sage 4.1.2.alpha1 [1], upgrading that
to Sage 4.1.2.alpha2 results in dozens of doctest failures:
----------------------------------------------------------------------
The following tests failed:
sage -t -long "devel/sage/doc/en/tutorial/interfaces.rst"
sage -t -long "devel/sage/doc/en/tutorial/tour_algebra.rst"
sage -t -long "devel/sage/doc/en/constructions/plotting.rst"
sage -t -long "devel/sage/doc/en/constructions/interface_issues.rst"
sage -t -long "devel/sage/doc/en/constructions/polynomials.rst"
sage -t -long "devel/sage/doc/en/constructions/linear_algebra.rst"
sage -t -long "devel/sage/doc/en/constructions/calculus.rst"
sage -t -long "devel/sage/doc/en/bordeaux_2008/nf_introduction.rst"
sage -t -long "devel/sage/doc/en/a_tour_of_sage/index.rst"
sage -t -long "devel/sage/doc/fr/tutorial/interfaces.rst"
sage -t -long "devel/sage/doc/fr/tutorial/tour_algebra.rst"
sage -t -long "devel/sage/sage/modular/overconvergent/genus0.py"
sage -t -long "devel/sage/sage/modular/overconvergent/weightspace.py"
sage -t -long "devel/sage/sage/misc/latex.py"
sage -t -long "devel/sage/sage/misc/functional.py"
sage -t -long "devel/sage/sage/misc/citation.pyx"
sage -t -long "devel/sage/sage/modules/vector_real_double_dense.pyx"
sage -t -long "devel/sage/sage/matrix/matrix_symbolic_dense.pyx"
sage -t -long "devel/sage/sage/matrix/matrix2.pyx"
sage -t -long "devel/sage/sage/matrix/matrix1.pyx"
sage -t -long "devel/sage/sage/rings/contfrac.py"
sage -t -long
"devel/sage/sage/rings/number_field/number_field_element_quadratic.pyx"
sage -t -long
"devel/sage/sage/rings/number_field/number_field_element.pyx"
sage -t -long "devel/sage/sage/rings/polynomial/polynomial_element.pyx"
sage -t -long "devel/sage/sage/tests/benchmark.py"
sage -t -long "devel/sage/sage/structure/parent.pyx"
sage -t -long "devel/sage/sage/structure/sage_object.pyx"
sage -t -long "devel/sage/sage/gsl/interpolation.pyx"
sage -t -long "devel/sage/sage/gsl/integration.pyx"
sage -t -long "devel/sage/sage/combinat/combinat.py"
sage -t -long "devel/sage/sage/geometry/lattice_polytope.py"
sage -t -long "devel/sage/sage/calculus/desolvers.py"
sage -t -long "devel/sage/sage/calculus/calculus.py"
sage -t -long "devel/sage/sage/calculus/test_sympy.py"
sage -t -long "devel/sage/sage/calculus/wester.py"
sage -t -long "devel/sage/sage/calculus/functions.py"
sage -t -long "devel/sage/sage/calculus/tests.py"
sage -t -long "devel/sage/sage/calculus/functional.py"
sage -t -long "devel/sage/sage/plot/line.py"
sage -t -long "devel/sage/sage/plot/plot3d/transform.pyx"
sage -t -long "devel/sage/sage/interfaces/lisp.py"
sage -t -long "devel/sage/sage/interfaces/expect.py"
sage -t -long "devel/sage/sage/interfaces/tests.py"
sage -t -long "devel/sage/sage/interfaces/maxima.py"
sage -t -long "devel/sage/sage/schemes/elliptic_curves/ell_generic.py"
sage -t -long "devel/sage/sage/functions/log.py"
sage -t -long "devel/sage/sage/functions/wigner.py"
sage -t -long "devel/sage/sage/functions/trig.py"
sage -t -long "devel/sage/sage/functions/piecewise.py"
sage -t -long "devel/sage/sage/functions/orthogonal_polys.py"
sage -t -long "devel/sage/sage/functions/special.py"
sage -t -long "devel/sage/sage/functions/other.py"
sage -t -long "devel/sage/sage/symbolic/expression_conversions.py"
sage -t -long "devel/sage/sage/symbolic/benchmark.py"
sage -t -long "devel/sage/sage/symbolic/relation.py"
sage -t -long "devel/sage/sage/symbolic/assumptions.py"
sage -t -long "devel/sage/sage/symbolic/constants.py"
sage -t -long "devel/sage/sage/symbolic/power_helper.pyx"
sage -t -long "devel/sage/sage/symbolic/expression.pyx"
sage -t -long "devel/sage/sage/symbolic/ring.pyx"
sage -t -long "devel/sage/sage/symbolic/pynac.pyx"
Total time for all tests: 6074.9 seconds
kcrisman
and when actually running failed due to readline:
ImportError: dlopen(/Users/.../sage-4.1.1/local/lib/python2.6/site-
packages/sage/rings/polynomial/multi_polynomial_libsingular.so, 2):
Library not loaded: /Users/.../sage-4.1.1/local/lib/libreadline.
5.2.dylib
Referenced from: /Users/.../sage-4.1.1/local/lib//libsingular.dylib
Reason: image not found
Considering that readline is supposed to be at version 6 after the
upgrade, perhaps something happened with this? Trying to install it
again yielded the same failure.
-kcrisman
On Sep 22, 2:10 am, Minh Nguyen <nguyenmi...@gmail.com> wrote:
> Hi John,
>
> On Tue, Sep 22, 2009 at 12:20 PM, John H Palmieri
>
Tim Joseph Dumol
ImportError: libreadline.so.5: cannot open shared object file: No such file or directory
Tim Joseph Dumol <tim (at) timdumol (dot) com>
Minh Nguyen
<SNIP>
> Please test and report all problems.
Error building the PDF version of the reference manual. This is now ticket #6988
http://trac.sagemath.org/sage_trac/ticket/6988
kcrisman
Built fine on OSX.5. However, get odd behavior of tab-completion.
Before, it would leave you in just the right spot to add (), but now
it goes exactly one space further, necessitating an awkward
backspace. Has anyone else noticed this?
- kcrisman
Minh Nguyen
On Wed, Sep 23, 2009 at 3:57 AM, kcrisman <kcri...@gmail.com> wrote:
<SNIP>
> Has anyone else noticed this?
Jason Grout reported this in IRC:
{{{
10:42 < jason-6865> Has anyone noticed that with 4.1.2.alpha2, we have that old
problem with readline again where tab completion puts a
space after the completion?
10:43 < jason-6865> (that's what it's doing for me)
10:44 < williamstein> we have a new readline, right?
10:44 < mhampton-6776> I'm using 4.1.1, I guess I should switch
10:44 < mvngu> williamstein: yes
10:45 < williamstein> maybe a patch wasn't suitably applied (i.e., by me)
10:45 < jason-6865> my upgrade doesn't have the problem
10:45 < jason-6865> (upgrade from 4.1.2.alpha1 to 4.1.2.alpha2)
10:45 < jason-6865> but that might be a problem with the upgrade...
10:45 -!- kmels [n=km...@168.234.70.226] has quit []
10:46 < jason-6865> (this is on ubuntu 9.04)
10:46 < jason-6865> where is the new readline spkg?
10:46 < jason-6865> (oh, duh, in spkg/standard...)
10:47 < mvngu> jason-6865:
http://sage.math.washington.edu/home/mvngu/release/spkg/standard/readline-6.0.spkg
10:47 -!- jason-6865 is now known as jason-
10:50 -!- mhampton-6776 is now known as mhampton-6780
10:51 -!- jason-- [n=ja...@97-125-136-197.desm.qwest.net] has joined #sage-devel
10:53 -!- kstueve [n=Sag...@96-26-255-233.sea.clearwire-dns.net] has quit
[Read error: 110 (Connection timed out)]
10:54 < jason--> hmmm...it may be a problem with 6.0:
http://lists.macosforge.org/pipermail/macports-users/2009-March/014300.html
10:58 -!- Misto [n=Mi...@dsl081-234-075.lax1.dsl.speakeasy.net] has joined
#sage-devel
10:58 -!- jason- [n=ja...@75-170-235-118.desm.qwest.net] has quit [Read error:
60 (Operation timed out)]
10:58 < jason--> ah, no, in readline 6.0, we have from the changelog: New
application-settable completion variable:
rl_completion_suppress_append, inhibits appending of
rl_completion_append_character to completed words.
10:59 < jason--> no, nevermind.
Jason Grout
I'm building it now to make sure it works.
Jason
--
Jason Grout
gsw
concerning the libsingular/readline problem, I think that we "just"
should have added the Singular spkg as a new dependency for the
upgrade (because the Python extensions in the Sage library using it
depend on the readline library, see "module_list.py").
Simply rebuilding the Singular spkg (and then after that rebuilding
the Sage library) should do the job, could you test this? There's
anyway a new version for the Singular spkg needed, so for
Sage-4.1.2.final this might heal "by itself".
Cheers,
Georg
Tim Joseph Dumol
Log:
[timdumol@tim-pc sage-bin]$ sudo !!
sudo make
cd spkg && ./install all 2>&1 | tee -a ../install.log
make[1]: Entering directory `/opt/sage-bin/spkg'
standard/deps:406: warning: overriding commands for target `installed/'
standard/deps:188: warning: ignoring old commands for target `installed/'
sage-spkg installed/lapack-20071123.p0 2>&1
You must set the SAGE_ROOT environment variable or
run this script from the SAGE_ROOT or
SAGE_ROOT/local/bin/ directory.
lapack-20071123.p0
Machine:
Linux tim-pc 2.6.30-ARCH #1 SMP PREEMPT Wed Sep 9 14:16:44 CEST 2009 x86_64 Intel(R) Core(TM)2 Duo CPU E4500 @ 2.20GHz GenuineIntel GNU/Linux
Deleting directories from past builds of previous/current versions of lapack-20071123.p0
Extracting package /opt/sage-bin/spkg/standard/lapack-20071123.p0.spkg ...
-rw-rw-rw- 1 root sageusers 3530363 2009-08-01 05:45 /opt/sage-bin/spkg/standard/lapack-20071123.p0.spkg
[...]
****************************************************
Host system
uname -a:
Linux tim-pc 2.6.30-ARCH #1 SMP PREEMPT Wed Sep 9 14:16:44 CEST 2009 x86_64 Intel(R) Core(TM)2 Duo CPU E4500 @ 2.20GHz GenuineIntel GNU/Linux
****************************************************
****************************************************
CC Version
gcc -v
Using built-in specs.
Target: x86_64-unknown-linux-gnu
Configured with: ../configure --prefix=/usr --enable-shared --enable-languages=c,c++,fortran,objc,obj-c++ --enable-threads=posix --mandir=/usr/share/man --infodir=/usr/share/info --enable-__cxa_atexit --disable-multilib --libdir=/usr/lib --libexecdir=/usr/lib --enable-clocale=gnu --disable-libstdcxx-pch --with-tune=generic
Thread model: posix
gcc version 4.4.1 (GCC)
****************************************************
make[2]: Entering directory `/opt/sage-bin/spkg/build/lapack-20071123.p0/src'
( cd INSTALL; make; ./testlsame; ./testslamch; \
./testdlamch; ./testsecond; ./testdsecnd; ./testversion )
make[3]: Entering directory `/opt/sage-bin/spkg/build/lapack-20071123.p0/src/INSTALL'
sage_fortran -fPIC -c lsame.f -o lsame.o
sage_fortran -fPIC -c lsametst.f -o lsametst.o
sage_fortran -o testlsame lsame.o lsametst.o
ld: crt1.o: No such file: No such file or directory
make[3]: *** [testlsame] Error 1
make[3]: Leaving directory `/opt/sage-bin/spkg/build/lapack-20071123.p0/src/INSTALL'
/bin/sh: ./testlsame: No such file or directory
/bin/sh: ./testslamch: No such file or directory
/bin/sh: line 1: ./testdlamch: No such file or directory
/bin/sh: line 1: ./testsecond: No such file or directory
/bin/sh: line 1: ./testdsecnd: No such file or directory
/bin/sh: line 1: ./testversion: No such file or directory
make[2]: *** [lapack_install] Error 127
make[2]: Leaving directory `/opt/sage-bin/spkg/build/lapack-20071123.p0/src'
Error compiling lapack.
real 0m0.152s
user 0m0.070s
sys 0m0.037s
sage: An error occurred while installing lapack-20071123.p0
/usr/lib/crt1.o does exist, so I have no idea what's wrong here.
Minh Nguyen
On Sun, Sep 27, 2009 at 6:44 AM, Kiran Kedlaya <ksk...@gmail.com> wrote:
>
> After I dropped in the updated cliquer spkg (#6681), 4.1.2.alpha2
> built and passed all doctests under 64-bit Fedora 10. It appears that
> Minh has already closed ticket #6746 in response,
I closed ticket #6746 [1] as a duplicate of ticket #6681 [2]. I think
they both address the same issue, namely to build cliquer on supported
64-bit platforms, including 64-bit mode OS X 10.5 and various 64-bit
Linux distributions.
> but I haven't been
> following #6681 closely enough to feel comfortable giving it its long-
> awaited positive review.
For the purpose of ticket #6681 [2], you can review the cliquer
package posted to that ticket by compiling Sage from source with that
spkg. I see that you have done that already, which is of tremendous
help in reviewing #6681 because I myself don't have access to an
actual machine running 64-bit Fedora 10. The virtual machine fedora64
on boxen.math runs 64-bit Fedora 10; I have successfully compiled Sage
from source with cliquer on that VM. At the end of the day, a VM lacks
many of the features of an actual machine. It is only running software
on a real machine, as opposed to a VM, that we can hope to find more
bugs.
[1] http://trac.sagemath.org/sage_trac/ticket/6746
[2] http://trac.sagemath.org/sage_trac/ticket/6681