sage-5.0.beta11 released
Jeroen Demeyer
We're releasing Sage 5.0.beta11.
Source archive:
http://boxen.math.washington.edu/home/release/sage-5.0.beta11/sage-5.0.beta11.tar
Upgrade path:
http://boxen.math.washington.edu/home/release/sage-5.0.beta11/sage-5.0.beta11/
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 390 tickets in this release. For details, see
http://boxen.math.washington.edu/home/release/sage-5.0.beta11/tickets.html
Merged in sage-5.0.beta11:
#1013: Mike Hansen: Matrix_real_double_dense overrides parent numpy()
method with less-functional version [Reviewed by David Loeffler]
#5646: William Stein: vectors over CDF allow a coercion from scalars
[Reviewed by Johan Bosman]
#7980: Nicolas M. Thiéry: Implement generic support for parents with
(multiple) realizations [Reviewed by Simon King, Florent Hivert]
#8791: Fredrik Johansson, Harald Schilly, David Loeffler: improve
doctest coverage of libs/mpmath/ext_main.pyx [Reviewed by David
Loeffler, Jeroen Demeyer]
#11372: William Stein: nasty side effect of a failed simon_two_descent
search [Reviewed by Jennifer Balakrishnan]
#11445: Michael Orlitzky: symbolic integration fails on a very simple
test case [Reviewed by Karl-Dieter Crisman]
#11584: Nathann Cohen: DegreeSequences class ! [Reviewed by David Coudert]
#11766: Robert Bradshaw: fast_callable always segfaults when input is a
polynomial of large degree [Reviewed by Tom Boothby]
#11800: David Eklund: Problem with points at infinity in hyperelliptic
curves [Reviewed by Marco Streng]
#12069: John Palmieri: fix doctesting of .sage files [Reviewed by
Francis Clarke]
#12102: Jeroen Demeyer: Make bzip2 a standard (instead of base) package
[Reviewed by John Palmieri]
#12262: David Roe, David Loeffler: Bring Doctest coverage for
sage/rings/finite_rings to 100% [Reviewed by David Loeffler]
#12311: John Palmieri: In spkgs, run testcc.sh and testcxx.sh without
explicit path [Reviewed by Jeroen Demeyer]
#12371: Julien Puydt: The graph_decompositions/ code seems to have
bounds issues [Reviewed by Nathann Cohen, Jeroen Demeyer]
#12382: David Roe: Output of a two functions in sage.plot.plot3d.base is
nondeterministic due to use of set [Reviewed by Karl-Dieter Crisman]
#12461: André Apitzsch: Replace some deprecated python functions in
sage/algebras [Reviewed by David Loeffler]
#12497: Punarbasu Purkayastha: GeneralDiscreteDistribution can segv sage
[Reviewed by David Loeffler]
#12653: Nicolas M. Thiery: Add support for DiGraph(<dictionary of
iterables>) [Reviewed by David Loeffler]
#12658: David Loeffler: Use the matrix displayhook hack for arithmetic
subgroup elements [Reviewed by Martin Raum]
#12662: David Loeffler: Improve doctest coverage for sage.rings.qqbar
[Reviewed by Jim Stark]
#12665: Mike Hansen: Coercion problem with QQbar [Reviewed by David
Loeffler]
#12667: Mark Shimozono: category root lattice realization issue:
infinite loop while trying to reflect to the positive chamber [Reviewed
by Anne Schilling]
#12669: Mike Hansen: Conductor of trivial Dirichlet character has type
int [Reviewed by David Loeffler]
#12674: Valentin Féray: permutation length and size [Reviewed by Mike
Hansen]
#12677: Nicolas M. Thiéry: Make the doctests of
sage.misc.sageinspect.sage_getargspec independent of ``Poset`` [Reviewed
by Anne Schilling]
#12684: Mike Hansen: Rename sage/graphs/graph_decompositions/rankwidth/
[Reviewed by David Coudert]
#12687: Jeroen Demeyer: Fix Singular doctest error on OpenSolaris
[Reviewed by Simon King]
#12692: David Roe, Jennifer Balakrishnan: Stopgap for 12509 [Reviewed by
R. Andrew Ohana]
#12714: Jeroen Demeyer: Remove f2c [Reviewed by François Bissey]
#12727: William Stein: AA minpoly bug [Reviewed by David Loeffler]
#12742: Jeroen Demeyer: matplotlib must be a dependency of cvxopt
[Reviewed by Julien Puydt]
leif
> We're releasing Sage 5.0.beta11.
Built from scratch without problems on Ubuntu 10.04.4 LTS x86_64, with
GCC 4.6.3, this time again with less fancy optimization (just
"-march=native -O3").
I've only replaced the GAP and zn_poly spkgs to respect CC environment
settings etc. (cf. beta10 thread).
'make ptestlong' just gave a single timeout for
sage/rings/polynomial/polynomial_real_mpfr_dense.pyx, which separately
takes just 3.8 seconds to test (also with "--long" of course), so a bit
strange.
-leif
--
() The ASCII Ribbon Campaign
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leif
> Jeroen Demeyer wrote:
>> We're releasing Sage 5.0.beta11.
>
> Built from scratch without problems on Ubuntu 10.04.4 LTS x86_64, with
> GCC 4.6.3, this time again with less fancy optimization (just
> "-march=native -O3").
>
> I've only replaced the GAP and zn_poly spkgs to respect CC environment
> settings etc. (cf. beta10 thread).
>
> 'make ptestlong' just gave a single timeout for
> sage/rings/polynomial/polynomial_real_mpfr_dense.pyx,
... and also left an orphan testing this file, but not busy, just waiting.
Jeroen Demeyer
> left an orphan testing this file
leif
> We're releasing Sage 5.0.beta11.
Ubuntu 12.04 beta x86_64 (latest updates, GCC 4.6.3-1ubuntu3; 2nd gen.
Core i5):
[Haven't replaced any spkgs.]
Not surprisingly, I had to build MPFR and Singular with '-O2' instead of
'-O3', since otherwise Ubuntu's GCC (cc1 and cc1plus, respectively)
crash; cf. my post on the beta10 thread. (Note that one has to include
'-O3' into *CPPFLAGS* to force Singular to build with that; '-O3' in
/CXXFLAGS/ gets overridden by subsequent parameters passed to 'g++').
Otherwise built ok, but I get three segfaults caused by ATLAS /
libpthread in 'make ptestlong':
The following tests failed:
sage -t --long -force_lib
devel/sage/sage/modular/hecke/ambient_module.py # 0 doctests failed
sage -t --long -force_lib
devel/sage/sage/modular/hecke/hecke_operator.py # 0 doctests failed
sage -t --long -force_lib devel/sage/sage/modular/modsym/ambient.py #
0 doctests failed
----------------------------------------------------------------------
Total time for all tests: 2462.3 seconds
make: *** [ptestlong] Error 128
Testing the files individually gives the same results:
sage -t --long -force_lib "devel/sage/sage/modular/hecke/ambient_module.py"
.../Sage/sage-5.0.beta11-gcc-4.6.3-1ubuntu3/local/lib/libcsage.so(print_backtrace+0x31)[0x7f342171dea9]
.../Sage/sage-5.0.beta11-gcc-4.6.3-1ubuntu3/local/lib/libcsage.so(sigdie+0x14)[0x7f342171dedb]
.../Sage/sage-5.0.beta11-gcc-4.6.3-1ubuntu3/local/lib/libcsage.so(sage_signal_handler+0x20c)[0x7f342171db06]
/lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0)[0x7f3428f20cb0]
.../Sage/sage-5.0.beta11-gcc-4.6.3-1ubuntu3/local/lib/libatlas.so(ATL_dJIK44x44x44TN44x44x0_a1_b0+0xac)[0x7f3418bdc6bc]
------------------------------------------------------------------------
Unhandled SIGSEGV: A segmentation fault occurred in Sage.
This probably occurred because a *compiled* component of Sage has a bug
in it and is not properly wrapped with sig_on(), sig_off(). You might
want to run Sage under gdb with 'sage -gdb' to debug this.
Sage will now terminate.
------------------------------------------------------------------------
Segmentation fault (core dumped)
[4.4 s]
sage -t --long -force_lib "devel/sage/sage/modular/hecke/hecke_operator.py"
.../Sage/sage-5.0.beta11-gcc-4.6.3-1ubuntu3/local/lib/libcsage.so(print_backtrace+0x31)[0x7fa24b744ea9]
.../Sage/sage-5.0.beta11-gcc-4.6.3-1ubuntu3/local/lib/libcsage.so(sigdie+0x14)[0x7fa24b744edb]
.../Sage/sage-5.0.beta11-gcc-4.6.3-1ubuntu3/local/lib/libcsage.so(sage_signal_handler+0x20c)[0x7fa24b744b06]
/lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0)[0x7fa252f47cb0]
.../Sage/sage-5.0.beta11-gcc-4.6.3-1ubuntu3/local/lib/libatlas.so(ATL_dJIK44x44x44TN44x44x0_a1_b0+0xac)[0x7fa2429fb6bc]
------------------------------------------------------------------------
Unhandled SIGSEGV: A segmentation fault occurred in Sage.
This probably occurred because a *compiled* component of Sage has a bug
in it and is not properly wrapped with sig_on(), sig_off(). You might
want to run Sage under gdb with 'sage -gdb' to debug this.
Sage will now terminate.
------------------------------------------------------------------------
Segmentation fault (core dumped)
[2.9 s]
sage -t --long -force_lib "devel/sage/sage/modular/modsym/ambient.py"
.../Sage/sage-5.0.beta11-gcc-4.6.3-1ubuntu3/local/lib/libcsage.so(print_backtrace+0x31)[0x7fcfd2f2dea9]
.../Sage/sage-5.0.beta11-gcc-4.6.3-1ubuntu3/local/lib/libcsage.so(sigdie+0x14)[0x7fcfd2f2dedb]
.../Sage/sage-5.0.beta11-gcc-4.6.3-1ubuntu3/local/lib/libcsage.so(sage_signal_handler+0x20c)[0x7fcfd2f2db06]
/lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0)[0x7fcfda730cb0]
.../Sage/sage-5.0.beta11-gcc-4.6.3-1ubuntu3/local/lib/libatlas.so(ATL_dJIK44x44x44TN44x44x0_a1_b0+0xac)[0x7fcfca3ec6bc]
------------------------------------------------------------------------
Unhandled SIGSEGV: A segmentation fault occurred in Sage.
This probably occurred because a *compiled* component of Sage has a bug
in it and is not properly wrapped with sig_on(), sig_off(). You might
want to run Sage under gdb with 'sage -gdb' to debug this.
Sage will now terminate.
------------------------------------------------------------------------
Segmentation fault (core dumped)
[6.3 s]
----------------------------------------------------------------------
The following tests failed:
sage -t --long -force_lib "devel/sage/sage/modular/hecke/ambient_module.py"
sage -t --long -force_lib "devel/sage/sage/modular/hecke/hecke_operator.py"
sage -t --long -force_lib "devel/sage/sage/modular/modsym/ambient.py"
Total time for all tests: 13.6 seconds
Same happens if I omit '--long'.
I noticed that unfortunately the output of "Trying: ..." / "Expecting:
..." still isn't flushed, so '--verbose' doesn't help much here.
Going to rebuild ATLAS, as we already had similar, non-reproducible
(w.r.t. to building) issues with ATLAS on an AVX-enabled CPU last year
(Sage 4.7.2.alpha3).
leif
> (Sage 4.7.2.alpha3).
Ok, after rebuilding (just) ATLAS, not any packages depending on it,
since the segfault occurred in the /shared/ ATLAS library, I get:
sage -t --long -force_lib "devel/sage/sage/modular/hecke/ambient_module.py"
[7.5 s]
sage -t --long -force_lib "devel/sage/sage/modular/hecke/hecke_operator.py"
[3.2 s]
sage -t --long -force_lib "devel/sage/sage/modular/modsym/ambient.py"
[16.3 s]
----------------------------------------------------------------------
All tests passed!
Total time for all tests: 27.1 seconds
leif
> leif wrote:
>> Jeroen Demeyer wrote:
>>> We're releasing Sage 5.0.beta11.
>>
>> Ubuntu 12.04 beta x86_64 (latest updates, GCC 4.6.3-1ubuntu3; 2nd gen.
>> Core i5):
>>
>> [Haven't replaced any spkgs.]
>>
>> Not surprisingly, I had to build MPFR and Singular with '-O2' instead of
>> '-O3', since otherwise Ubuntu's GCC (cc1 and cc1plus, respectively)
>> crash; cf. my post on the beta10 thread. (Note that one has to include
>> '-O3' into *CPPFLAGS* to force Singular to build with that; '-O3' in
>> /CXXFLAGS/ gets overridden by subsequent parameters passed to 'g++').
I've meanwhile built my own GCC 4.6.3 on Ubuntu 12.04 beta (installed
into /usr/local, along with my own builds of GMP, MPFR, MPC, PPL,
CLooG-PPL and libelf), and that one doesn't crash with '-O3'.
I then replaced the GAP and zn_poly spkgs because I use CC=gcc-4.6.3
etc., and built Sage again from scratch, this time with SAGE_CHECK=yes.
Except for sagetex's test suite, which apparently failed because some
LaTeX piece was missing (see below), all were reported to have passed
successfully, although at least for R differences between test results
and expected output were shown.
One test of PPL, "mipproblem1", took ages to build, since 'cc1plus' ate
up 5 GB of virtual memory, and afterwards 'as' even 7+ GB (on an ~1 GB
assembly file), which caused the machine swapping for hours.
[Never had such issues with PPL 0.10.2, 0.11 or 0.12, which I've built a
couple of times, always running 'make check' afterwards. But these
builds were outside of Sage; the last build of PPL 0.12 on the same
machine with '--enable-check=thorough'.]
'make ptestlong' gave exactly the same three ATLAS segfaults I reported
earlier; after again rebuilding ATLAS (with just './sage -f ...') these
again vanished and all tests passed.
...
Successfully installed sagetex-2.3.3.p2
Running the test suite for sagetex-2.3.3.p2...
pdfTeX 3.1415926-1.40.10-2.2 (TeX Live 2009/Debian)
kpathsea version 5.0.0
Copyright 2009 Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
There is NO warranty. Redistribution of this software is
covered by the terms of both the pdfTeX copyright and
the Lesser GNU General Public License.
For more information about these matters, see the file
named COPYING and the pdfTeX source.
Primary author of pdfTeX: Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
Compiled with libpng 1.2.46; using libpng 1.2.35
Compiled with zlib 1.2.3.4; using zlib 1.2.5
Compiled with poppler version 0.18.2
This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian)
entering extended mode
(./example.tex
LaTeX2e <2009/09/24>
Babel <v3.8l> and hyphenation patterns for english, usenglishmax,
dumylang, noh
yphenation, farsi, arabic, croatian, bulgarian, ukrainian, russian,
czech, slov
ak, danish, dutch, finnish, french, basque, ngerman, german,
german-x-2009-06-1
9, ngerman-x-2009-06-19, ibycus, monogreek, greek, ancientgreek,
hungarian, san
skrit, italian, latin, latvian, lithuanian, mongolian2a, mongolian,
bokmal, nyn
orsk, romanian, irish, coptic, serbian, turkish, welsh, esperanto,
uppersorbian
, estonian, indonesian, interlingua, icelandic, kurmanji, slovenian,
polish, po
rtuguese, spanish, galician, catalan, swedish, ukenglish, loaded.
(/usr/share/texmf-texlive/tex/latex/base/article.cls
Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
(/usr/share/texmf-texlive/tex/latex/base/size10.clo))
(/usr/share/texmf-texlive/tex/latex/hyperref/hyperref.sty
(/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texmf-texlive/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texmf-texlive/tex/latex/oberdiek/hycolor.sty
(/usr/share/texmf-texlive/tex/latex/oberdiek/xcolor-patch.sty))
(/usr/share/texmf-texlive/tex/latex/hyperref/pd1enc.def)
(/usr/share/texmf-texlive/tex/generic/oberdiek/etexcmds.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/infwarerr.sty))
(/usr/share/texmf-texlive/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texmf-texlive/tex/latex/oberdiek/kvoptions.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/kvsetkeys.sty))
Implicit mode ON; LaTeX internals redefined
(/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/bitset.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/intcalc.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/bigintcalc.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/pdftexcmds.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/ifluatex.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/ltxcmds.sty))))
(/usr/share/texmf-texlive/tex/generic/oberdiek/atbegshi.sty))
*hyperref using default driver hdvips*
(/usr/share/texmf-texlive/tex/latex/hyperref/hdvips.def
(/usr/share/texmf-texlive/tex/latex/hyperref/pdfmark.def)) (./sagetex.sty
(/usr/share/texmf-texlive/tex/latex/tools/verbatim.sty)
! LaTeX Error: File `fancyvrb.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Enter file name:
! Emergency stop.
<read *>
l.33 \RequirePackage
{listings}^^M
No pages of output.
Transcript written on example.log.
Error typesetting example.tex!
real 0m0.827s
user 0m0.060s
sys 0m0.040s
************************************************************************
Error testing package sagetex-2.3.3.p2
************************************************************************
...
-leif
leif
Forgot to mention:
For whatever reason, after running ptestlong, I now *always* get the
message that the temporary doctesting directory wasn't removed because
it is not empty ("presumably because some doctests failed or doctesting
was interrupted").
And indeed, it now always contains an /empty/ 'tmp/' subdirectory. Did
anybody see this before? (I haven't, and have no idea what's suddenly
causing it.)
Dan Drake
> I've meanwhile built my own GCC 4.6.3 on Ubuntu 12.04 beta
> (installed into /usr/local, along with my own builds of GMP, MPFR,
> MPC, PPL, CLooG-PPL and libelf), and that one doesn't crash with
> '-O3'.
>
> I then replaced the GAP and zn_poly spkgs because I use CC=gcc-4.6.3
> etc., and built Sage again from scratch, this time with
> SAGE_CHECK=yes.
>
> Except for sagetex's test suite, which apparently failed because
> some LaTeX piece was missing (see below), all were reported to have
> passed successfully, although at least for R differences between
> test results and expected output were shown.
That's harmless. I'm not sure what package you need, though; Ubuntu is
still shipping TeXLive 2009, and the Debian people responsible for
packaging TeXLive seem to be too busy to ever actually update to a newer
release, or indeed to even make trivial updates to the existing
packages.
</rant>...
Dan
--
--- Dan Drake
----- http://mathsci.kaist.ac.kr/~drake
-------
Jean-Pierre Flori
(So I guess the Ubuntu people are just too lazy to include them before the 12.04 release.)
John H Palmieri
On Monday, April 2, 2012 9:38:33 PM UTC-7, leif wrote:
leif wrote:Forgot to mention:
For whatever reason, after running ptestlong, I now *always* get the
message that the temporary doctesting directory wasn't removed because
it is not empty ("presumably because some doctests failed or doctesting
was interrupted").And indeed, it now always contains an /empty/ 'tmp/' subdirectory. Did
anybody see this before? (I haven't, and have no idea what's suddenly
causing it.)
You could say that it's caused by #12069 (which makes it my fault), but it's really caused by Sage's doctesting framework creating a directory called 'tmp' in SAGE_TESTDIR and then never using it or cleaning it up. See http://trac.sagemath.org/sage_trac/ticket/12805 (which is me making amends).
--
John