sage-4.7.2.alpha2 released

[Jeroen Demeyer]

Dear Sage lovers,

We're releasing Sage 4.7.2.alpha2.

Source archive:

http://boxen.math.washington.edu/home/release/sage-4.7.2.alpha2/sage-4.7.2.alpha2.tar

Upgrade path:

http://boxen.math.washington.edu/home/release/sage-4.7.2.alpha2/sage-4.7.2.alpha2/

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 110 tickets in this release. For details, see

http://boxen.math.washington.edu/home/release/sage-4.7.2.alpha2/tickets.html

Closed tickets:

#6146: the detection of SAGE_ROOT in $SAGE_ROOT/sage script should
expand symlinks recursively (fix this on systems that do *NOT* support
readlink -f) [Reviewed by Jeroen Demeyer]
#7347: numerical_integral(SR(0), 0, 1) gives an error [Reviewed by
Karl-Dieter Crisman, Douglas McNeil]
#9044: Use mpmath for the erf() function [Reviewed by Karl-Dieter Crisman]
#9848: 'sage -advanced' does not mention the '-R' flag, which starts the
R interpreter [Reviewed by Karl-Dieter Crisman]
#11626: make the error function work in arbitrary precision [Reviewed by
Paul Zimmermann, Karl-Dieter Crisman]
#11629: Evaluating the order of an ideal class fails [Reviewed by
Francis Clarke]
#11707: Remove `readlink -n` and `realpath` from $SAGE_ROOT/sage
[Reviewed by Jeroen Demeyer]

Merged in sage-4.7.2.alpha2:

#4578: Martin Raum: optimize modular symbols decomposition algorithm
[Reviewed by David Loeffler]
#6670: Martin Raum, John Palmieri: Port group algebras to the current
coercion system [Reviewed by John Palmieri, Martin Raum]
#7654: Martin Albrecht: Conversion bug in MPolynomialRing_libsingular
[Reviewed by Simon King]
#9631: William Stein, Mitesh Patel: Remerge #9501 after resolving NFS
and/or doctest problems with @fork [Reviewed by Volker Braun]
#10497: Nathann Cohen: Constraint Generation for TSP/Hamiltonian Cycle
[Reviewed by Leonardo Sampaio]
#10530: Eviatar Bach: De Bruijn Sequence construction for combinat
[Reviewed by Nicolas M. Thiéry, Nathann Cohen]
#10793: Andrey Novoseltsev: Matrices can be "constructed" from matrices
of wrong dimensions [Reviewed by Volker Braun]
#11053: Nathann Cohen: improving shortest path all pairs through BFS
computations [Reviewed by Leonardo Sampaio]
#11121: Keshav Kini, John Palmieri: Set up good defaults for sage's
mercurial [Reviewed by John Palmieri, Keshav Kini]
#11166: Nicolas Borie: Typo in initialization of
FreeModule_generic_field [Reviewed by Kelvin Li, Rob Beezer]
#11267: Simon King: cdef public attributes of a class should only appear
in the docs if they have a proper docstring [Reviewed by John Palmieri]
#11379: Sébastien Labbé: Add Quantumino solver to sage/games [Reviewed
by Rob Beezer]
#11388: Robert Bradshaw: Allow start/stop recording exceptions in the
coercion model [Reviewed by Luis Felipe Tabera Alonso]
#11480: Rob Beezer: ZigZag and rational (canonical) forms [Reviewed by
David Loeffler]
#11499: Karl-Dieter Crisman: Sage library fails to build on Cygwin
[Reviewed by Reg Burgess]
#11535: Rob Beezer: Linear dependence/independence of vectors [Reviewed
by Ivo Hedtke]
#11540: Maarten Derickx: Make elliptic curve reduction consistent with
has_good_reduction [Reviewed by Chris Wuthrich]
#11552: Rob Beezer: Fix surjectivity testing for free module morphisms
[Reviewed by John Palmieri]
#11577: Leif Leonhardy, John Palmieri: save(x,filename) fails for pure
Python objects for x if filename contains a dot [Reviewed by John
Palmieri, Leif Leonhardy]
#11600: Rob Beezer: Add alias for free module morphism lift method
[Reviewed by Martin Raum]
#11602: John Palmieri: install_scripts should use "$@" instead of $*
[Reviewed by Leif Leonhardy]
#11610: Simon King: Reduce memory consumption of generic
Strassen-Winograd implementation [Reviewed by Ivo Hedtke]
#11618: Leif Leonhardy: solve with solution_dict=True doesn't always
return a list [Reviewed by Karl-Dieter Crisman]
#11620: Robert Miller: Bugs persist in
graph_isom_equivalent_non_edge_labeled_graph [Reviewed by Nathann Cohen]
#11623: Robert Miller: small optimization to girth [Reviewed by Nathann
Cohen]
#11624: Martin Raum: List Sidon g-sets [Reviewed by Nicolas Borie]
#11658: Leif Leonhardy: the timeout option is not working correctly in
parallel computing [Reviewed by Volker Braun]
#11665: Leif Leonhardy: Don't delete built Sage documentation until
Sphinx has been successfully (re)installed [Reviewed by John Palmieri]
#11686: John Palmieri: Race condition in matplotlib mkdir() [Reviewed by
Leif Leonhardy]

[leif]

Jeroen Demeyer wrote:
> Dear Sage lovers,
>
> We're releasing Sage 4.7.2.alpha2.
>
> Source archive:
>
> http://boxen.math.washington.edu/home/release/sage-4.7.2.alpha2/sage-4.7.2.alpha2.tar
>
> Upgrade path:
>
> http://boxen.math.washington.edu/home/release/sage-4.7.2.alpha2/sage-4.7.2.alpha2/
>
> 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.

FWIW, built from scratch, passed 'make testlong' on both

* Ubuntu 9.04 x86 (Pentium4 Prescott, GCC 4.5.1, native code)

* Ubuntu 10.04.3 x86_64 (Core2 Penryn, GCC 4.5.1, native code)

-leif

[Johan Bosman]

On Mac OS 10.6.8 (64 bit) with SAGE_PARALLEL_SPKG_BUILD="yes" and
MAKE="make -j2" I got the following error:

...
g++ -L/usr/local/share/sage/sage-4.7.2.alpha2/local/lib -bundle -
undefined dynamic_lookup build/temp.macosx-10.6-i386-2.6/src/_png.o
build/temp.macosx-10.6-i386-2.6/src/mplutils.o build/temp.macosx-10.6-
i386-2.6/CXX/cxx_extensions.o build/temp.macosx-10.6-i386-2.6/CXX/
cxxsupport.o build/temp.macosx-10.6-i386-2.6/CXX/
IndirectPythonInterface.o build/temp.macosx-10.6-i386-2.6/CXX/
cxxextensions.o -L/usr/local/share/sage/sage-4.7.2.alpha2/local/lib -
lpng -lz -lstdc++ -lm -o build/lib.macosx-10.6-i386-2.6/matplotlib/
_png.so
ld: library not found for -lpng
collect2: ld returned 1 exit status
error: command 'g++' failed with exit status 1
Error building matplotlib package.

[leif]

Do you happen to have 'pkg-config' installed?

If so, please check the file $SAGE_ROOT/local/lib/pkgconfig/libpng12.pc
and remove the line

SAGE_ROOT=${SAGE_ROOT}

if present; then simply type 'make' again.

-leif

[Johan Bosman]

Thanks for the reply. I do have pkg-config installed and this is what
$SAGE_ROOT/local/lib/pkgconfig/libpng12.pc looks like:

prefix=/usr/local/share/sage/sage-4.7.2.alpha2/local
exec_prefix=${prefix}
libdir=${exec_prefix}/lib
includedir=${prefix}/include/libpng12

Name: libpng
Description: Loads and saves PNG files
Version: 1.2.35
Libs: -L${libdir} -lpng12
Libs.private: -lz
Cflags: -I${includedir}

[leif]

Ooops. What does

pkg-config --libs libpng

tell when run from within a Sage subshell ('./sage -sh')?


-leif

[leif]

Oh, do you have PKG_CONFIG_PATH set in your "global" environment?

If so, unset it for building Sage. (This is yet another bug).

From within the Sage subshell, it should be "$SAGE_ROOT/local/lib/
pkgconfig", but it is currently only set to this if it was previously
empty.


-leif

[Johan Bosman]

> Ooops. What does
>
> pkg-config --libs libpng
>
> tell when run from within a Sage subshell ('./sage -sh')?
>
> -leif

pkg-config --libs libpng gives:

-L/usr/local/share/sage/sage-4.7.2.alpha2/local/lib -lpng12
SAGE_ROOT=/usr/local/share/sage/sage-4.7.2.alpha2

PKG_CONFIG_PATH isn't set globally and within the Sage subshell it is
indeed /usr/local/share/sage/sage-4.7.2.alpha2/local/lib/pkgconfig

[leif]

Johan Bosman wrote:
> pkg-config --libs libpng gives:
>
> -L/usr/local/share/sage/sage-4.7.2.alpha2/local/lib -lpng12
> SAGE_ROOT=/usr/local/share/sage/sage-4.7.2.alpha2
>
> PKG_CONFIG_PATH isn't set globally and within the Sage subshell it is
> indeed /usr/local/share/sage/sage-4.7.2.alpha2/local/lib/pkgconfig

Weird. Can you upload your MPL build log (spkg/logs/matplotlib-*.log)
somewhere, or attach it to e.g. #11686 [1]?

Thanks,

-leif

[1] http://trac.sagemath.org/sage_trac/ticket/11686

[Justin C. Walker]

On Aug 24, 2011, at 15:17 , Jeroen Demeyer wrote:

> Dear Sage lovers,
>
> We're releasing Sage 4.7.2.alpha2.
>
> Source archive:
>
> http://boxen.math.washington.edu/home/release/sage-4.7.2.alpha2/sage-4.7.2.alpha2.tar
>
> Upgrade path:
>
> http://boxen.math.washington.edu/home/release/sage-4.7.2.alpha2/sage-4.7.2.alpha2/

Built w/o problems as an upgrade to 4.7.1, on Mac OS X, 10.6.8 (Dual 6-core Xeon). All tests (ptestlong) passed!

Justin

--
Justin C. Walker, Curmudgeon-at-Large
() The ASCII Ribbon Campaign
/\ Help Cure HTML Email

[leif]

leif wrote:
> Johan Bosman wrote:
>> pkg-config --libs libpng gives:
>>
>> -L/usr/local/share/sage/sage-4.7.2.alpha2/local/lib -lpng12
>> SAGE_ROOT=/usr/local/share/sage/sage-4.7.2.alpha2
>>
>> PKG_CONFIG_PATH isn't set globally and within the Sage subshell it is
>> indeed /usr/local/share/sage/sage-4.7.2.alpha2/local/lib/pkgconfig

To whom it may concern:

The issue with matplotlib is actually caused by a broken 'pkg-config'
(version 0.18, FWIW) on his MacOS X machine exiting with a non-zero
status when called with '--help', which MPL uses to detect whether
'pkg-config' is "installed" at all. This collides with the (proper) way
/we/ detect that.

(Apple-bashing FTW.)

A preliminary matplotlib-1.0.1.p1 spkg working around this can be found
here:

http://sage.math.washington.edu/home/leif/Sage/spkgs/matplotlib-1.0.1.p1.spkg

-leif