sage-5.4.beta0 released

[Jeroen Demeyer]

Dear Sage lovers,

We're releasing Sage 5.4.beta0.

Source archive:

http://boxen.math.washington.edu/home/release/sage-5.4.beta0/sage-5.4.beta0.tar

Upgrade path:

http://boxen.math.washington.edu/home/release/sage-5.4.beta0/sage-5.4.beta0/

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 36 tickets in this release. For details, see

http://boxen.math.washington.edu/home/release/sage-5.4.beta0/tickets.html

Closed tickets:

#9238: J. Gutow's update to Jmol in the notebook... [Reviewed by Jason
Grout, Karl-Dieter Crisman, William Stein, Jonathan Gutow]
#9428: Internationalize the Sage Notebook [Reviewed by Keshav Kini, Luiz
Aquino, Dan Drake, Tim Dumol]
#11471: Add i18n capabilities to the Flask notebook [Reviewed by Keshav
kini, Luiz Aquino, Dan Drake, Tim Dumol, Mike Hansen]
#11789: compile python with ssl-support if possible [Reviewed by Jeroen
Demeyer]
#11805: Update optional MPC spkg to version 0.9 [Reviewed by Jean-Pierre
Flori]
#12089: Dmitrii Pasechnik, Karl-Dieter Crisman, Jean-Pierre Flori:
Singular does not build on Cygwin - static libs problem [Reviewed by
Karl-Dieter Crisman, Dmitrii Pasechnik, Jean-Pierre Flori]
#12846: Multivariate Factorisation can be randomly slow (over extension
fields) [Reviewed by Jeroen Demeyer]
#12918: segmentation fault with multivariate polynomial factorization
[Reviewed by Jeroen Demeyer]
#12928: critical bug in multivariate polynomial factorization over GF(2)
[Reviewed by Jeroen Demeyer]
#13129: libSingular segmentation fault in factor [Reviewed by Jeroen
Demeyer]
#13344: Jean-Pierre Flori, Alexander Dreyer, Jeroen Demeyer: on CYGWIN,
Singular LIB files get copied to SAGELOCAL/lib [Reviewed by Dmitrii
Pasechnik, Jean-Pierre Flori]
#13384: Keshav Kini: pyOpenSSL SPKG [Reviewed by John Palmieri]
#13410: Robert Bradshaw: Patchbot timeouts [Reviewed by Volker Braun]

Merged in sage-5.4.beta0:

#5457: Mike Zabrocki, Anne Schilling, Jason Bandlow: Refactor symmetric
functions and k-bounded subspace [Reviewed by Dan Bump, Nicolas M.
Thiéry, Jeroen Demeyer]
#5489: Mike Hansen, Bjarke Hammersholt Roune: Add an interface for 4ti2
to Sage [Reviewed by Martin Albrecht, John Palmieri, Marshall Hampton,
Frédéric Chapoton]
#9265: Jason Bandlow, Andrew Mathas: Remove `CombinatorialClass` from
sage.combinat.tableau [Reviewed by Andrew Mathas, Anne Schilling]
#9774: Rob Beezer, Davide Cervone, John Palmieri, Jason Grout, Nathan
Carter: Use MathJax instead of jsMath [Reviewed by Jason Grout, John
Palmieri, Punarbasu Purkayastha, Keshav Kini]
#11021: Leif Leonhardy, Kelvin Li, Jeroen Demeyer: Fix install_package()
library function [Reviewed by Kelvin Li, Leif Leonhardy, John Palmieri]
#11305: Travis Scrimshaw: Bijection between Rigged Configurations and
Crystal Paths [Reviewed by Anne Schilling]
#11440: Paul-Olivier Dehaye: compute the dimension of partition
[Reviewed by Frédéric Chapoton]
#11770: Robert Harron: Add ability to detect CM number fields and take
complex conjugate of their elements [Reviewed by Francis Clarke]
#11913: John Palmieri: Notebook hang in ?? source display Trackback
[Reviewed by Keshav Kini]
#12299: Jonathan Gutow: Upgrade Jmol to 12.3.27, Advance Jmol
Interactive Features in Flask Notebook [Reviewed by Karl-Dieter Crisman,
Steven Trogdon, Punarbasu Purkayastha, John Palmieri, Dan Drake]
#12606: Jeroen Demeyer: Fix sage --info <package> [Reviewed by John
Palmieri]
#12946: Mike Hansen: Bug in Compositions [Reviewed by Andrew Mathas]
#13121: Keshav Kini: Upgrade sagenb to 0.10.x [Reviewed by John
Palmieri, Jonathan Gutow]
#13157: Jeroen Demeyer: inline_fortran is STILL broken on OS X [Reviewed
by Karl-Dieter Crisman, Benjamin Jones]
#13231: Alex Csar: Check if a lattice is atomic [Reviewed by Frédéric
Chapoton]
#13237: Jeroen Demeyer, Alexander Dreyer, Dmitrii Pasechnik, Karl-Dieter
Crisman, Jean-Pierre Flori: Upgrade Singular [Reviewed by Alexander
Dreyer, François Bissey]
#13253: Maarten Derickx: galois_action on cusps has a bug and incorrect
documentation [Reviewed by Marco Streng]
#13259: Andrew Mathas: Correcting implementation of "negative" quantum
integers [Reviewed by Armin Straub, Nicolas Thiery]
#13294: Stefano Leucci: Add test for not necessarily induced subgraphs
to Graph.is_subgraph() method [Reviewed by David Coudert]
#13314: Paul Zimmermann, Jeroen Demeyer: segmentation fault with roots
over ComplexField [Reviewed by John Cremona]
#13385: John Palmieri, Keshav Kini: Remove OpenSSL dependency from Sage
[Reviewed by Keshav Kini, John Palmieri]
#13389: Keshav Kini: Minor fix to LiE optional SPKG [Reviewed by John
Palmieri]
#13390: Stepan Starosta: Non Negative Integers: fix contains method
[Reviewed by Mike Hansen]

[John Cremona]

Built OK and all tests pass with ptestlong.

There are lots of compiler warnings when building spkgs and (I think)
the sage library. I suppose that the former are deemed to be upstream
problems and ignored?

John

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>

[Jeroen Demeyer]

On 2012-09-10 16:37, John Cremona wrote:
> Built OK and all tests pass with ptestlong.
>
> There are lots of compiler warnings when building spkgs and (I think)
> the sage library. I suppose that the former are deemed to be upstream
> problems and ignored?

Indeed. The warnings in the Sage library are mostly bugs in Cython or
in the way we use Cython.

[Justin C. Walker]

On Sep 9, 2012, at 23:23 , Jeroen Demeyer wrote:

> Dear Sage lovers,
>
> We're releasing Sage 5.4.beta0.
>
> Source archive:
>
> http://boxen.math.washington.edu/home/release/sage-5.4.beta0/sage-5.4.beta0.tar

Built w/o problems on Mac OS X 10.6.8 (Dual 6-core Xeons). Testing ('ptestlong') showed one failure (below). I reran the full test, which completed w/o failures.

Built w/o problems on Mac OS X 10.7.4 (quad core Core i7). Testing ('ptestlong') completed w/o failures.

The single failure on 10.6.8 was due to GAP crashing:

**********************************************************************
File "/Users/Sage/sage-5.4.beta0/devel/sage-main/doc/en/thematic_tutorials/sandpile.rst", line 4323:
sage: for p in P: #long time
sum([partition_sandpile(S, i).betti(verbose=false)[-Integer(1)] for i in p]) # long time
Expected:
6
8
3
Got:
** Gap crashed or quit executing 'Combinations([0, 1],2);' **
Restarting Gap and trying again
6
8
3
**********************************************************************

Ghosts in the machine...

Justin

--
Justin C. Walker, Curmudgeon at Large
Director
Institute for the Enhancement of the Director's income
-----------
Question 43:
What if the hokey pokey
really *is* what it’s all about?
--

[David Joyner]

On Mon, Sep 10, 2012 at 2:23 AM, Jeroen Demeyer <jdem...@cage.ugent.be> wrote:
> Dear Sage lovers,
>
> We're releasing Sage 5.4.beta0.
>
> Source archive:
>
> http://boxen.math.washington.edu/home/release/sage-5.4.beta0/sage-5.4.beta0.tar
>
> Upgrade path:
>
> http://boxen.math.washington.edu/home/release/sage-5.4.beta0/sage-5.4.beta0/
>
> 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.

This is on a new install of ubuntu 12.04 32 bit, on a fairly old
machine (maybe 4 years or 5 years old?).

Any idea what the problem is?


In file included from /usr/include/stdio.h:28:0,
from ../../../src/libgcc/../gcc/tsystem.h:87,
from ../../../src/libgcc/../gcc/libgcc2.c:29:
/usr/include/features.h:324:26: fatal error: bits/predefs.h: No such
file or directory
compilation terminated.
make[5]: *** [_muldi3.o] Error 1
make[5]: Leaving directory
`/home/wdj/sagefiles/sage-5.4.beta0/spkg/build/gcc-4.6.3/gcc-build/i686-pc-linux-gnu/libgcc'
make[4]: *** [all-stage1-target-libgcc] Error 2
make[4]: Leaving directory
`/home/wdj/sagefiles/sage-5.4.beta0/spkg/build/gcc-4.6.3/gcc-build'
make[3]: *** [stage1-bubble] Error 2
make[3]: Leaving directory
`/home/wdj/sagefiles/sage-5.4.beta0/spkg/build/gcc-4.6.3/gcc-build'
make[2]: *** [all] Error 2
make[2]: Leaving directory
`/home/wdj/sagefiles/sage-5.4.beta0/spkg/build/gcc-4.6.3/gcc-build'

real 4m36.570s
user 3m26.561s
sys 0m23.469s
************************************************************************
Error installing package gcc-4.6.3
************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the relevant part of the log file
/home/wdj/sagefiles/sage-5.4.beta0/spkg/logs/gcc-4.6.3.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/home/wdj/sagefiles/sage-5.4.beta0/spkg/build/gcc-4.6.3 and type
'make' or whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:
(cd '/home/wdj/sagefiles/sage-5.4.beta0/spkg/build/gcc-4.6.3' &&
'/home/wdj/sagefiles/sage-5.4.beta0/sage' -sh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************
make[1]: *** [installed/gcc-4.6.3] Error 1
make[1]: Leaving directory `/home/wdj/sagefiles/sage-5.4.beta0/spkg'

real 8m54.508s
user 5m52.058s
sys 0m52.379s
Error building Sage.
make: *** [build] Error 1


++++++++++++++++++++++++++++++++++++++++++++

Here is part of the gcc log:

config.status: creating Makefile
config.status: executing default commands
make[5]: Entering directory
`/home/wdj/sagefiles/sage-5.4.beta0/spkg/build/gcc-4.6.3/gcc-build/i686-pc-linux-gnu/libgcc'
# If this is the top-level multilib, build all the other
# multilibs.
/home/wdj/sagefiles/sage-5.4.beta0/spkg/build/gcc-4.6.3/gcc-build/./gcc/xgcc
-B/home/wdj/sagefiles/sage-5.4.beta0/spkg/build/gcc-4.6.3/gcc-build/./gcc/
-B/home/wdj/sagefiles/sage-5.4.beta0/local/i686-pc-linux-gnu/bin/
-B/home/wdj/sagefiles/sage-5.4.beta0/local/i686-pc-linux-gnu/lib/
-isystem /home/wdj/sagefiles/sage-5.4.beta0/local/i686-pc-linux-gnu/include
-isystem /home/wdj/sagefiles/sage-5.4.beta0/local/i686-pc-linux-gnu/sys-include
-g -O2 -O2 -g -O2 -DIN_GCC -W -Wall -Wwrite-strings -Wcast-qual
-Wstrict-prototypes -Wmissing-prototypes -Wold-style-definition
-isystem ./include -fPIC -g -DHAVE_GTHR_DEFAULT -DIN_LIBGCC2
-D__GCC_FLOAT_NOT_NEEDED -fno-stack-protector -I. -I. -I../.././gcc
-I../../../src/libgcc -I../../../src/libgcc/.
-I../../../src/libgcc/../gcc -I../../../src/libgcc/../include
-I../../../src/libgcc/config/libbid -DENABLE_DECIMAL_BID_FORMAT
-DHAVE_CC_TLS -DUSE_TLS -o _muldi3.o -MT _muldi3.o -MD -MP -MF
_muldi3.dep -DL_muldi3 -c ../../../src/libgcc/../gcc/libgcc2.c \
-fvisibility=hidden -DHIDE_EXPORTS

In file included from /usr/include/stdio.h:28:0,
from ../../../src/libgcc/../gcc/tsystem.h:87,
from ../../../src/libgcc/../gcc/libgcc2.c:29:
/usr/include/features.h:324:26: fatal error: bits/predefs.h: No such
file or directory
compilation terminated.
make[5]: *** [_muldi3.o] Error 1
make[5]: Leaving directory
`/home/wdj/sagefiles/sage-5.4.beta0/spkg/build/gcc-4.6.3/gcc-build/i686-pc-linux-gnu/libgcc'
make[4]: *** [all-stage1-target-libgcc] Error 2
make[4]: Leaving directory
`/home/wdj/sagefiles/sage-5.4.beta0/spkg/build/gcc-4.6.3/gcc-build'
make[3]: *** [stage1-bubble] Error 2
make[3]: Leaving directory
`/home/wdj/sagefiles/sage-5.4.beta0/spkg/build/gcc-4.6.3/gcc-build'
make[2]: *** [all] Error 2
make[2]: Leaving directory
`/home/wdj/sagefiles/sage-5.4.beta0/spkg/build/gcc-4.6.3/gcc-build'

real 4m36.570s
user 3m26.561s
sys 0m23.469s
************************************************************************
Error installing package gcc-4.6.3
************************************************************************



>
> == Tickets ==
>
...

[Jean-Pierre Flori]

See:
https://groups.google.com/forum/?fromgroups=#!msg/sage-release/FXYf_5g0B-4/NZNR2ws0siYJ

I guess you have to let Sage install its own gcc.

[Jeroen Demeyer]

On 2012-09-11 16:09, David Joyner wrote:
> This is on a new install of ubuntu 12.04 32 bit, on a fairly old
> machine (maybe 4 years or 5 years old?).
>
> Any idea what the problem is?

Most likely, you don't have gfortran installed.

[leif]

Jean-Pierre Flori wrote:
> See:
> https://groups.google.com/forum/?fromgroups=#!msg/sage-release/FXYf_5g0B-4/NZNR2ws0siYJ
>
> I guess you have to let Sage install its own gcc.

? Well, that's what was failing...

I'd rather say you *shouldn't* try to install Sage's GCC spkg (i.e.,
export SAGE_INSTALL_GCC=no if necessary) [... unless you know what
you're doing... ;-) -- You'd /at least/ have to create some symbolic
links because of Debian's / Ubuntu's differing multi-arch directory
structure.]

Anyway, I'd recommend to use Ubuntu's latest GCC [4.6.3], i.e., update
Precise's GCC packages in case you haven't already; the versions shipped
with vanilla 12.04 are partially broken.


-leif

> <http://groups.google.com/group/sage-devel>)

() The ASCII Ribbon Campaign
/\ Help Cure HTML E-Mail

[Volker Braun]

Looks like glibc devel headers are missing -> sudo apt-get install libc6-dev

[Jean-Pierre Flori]

On Tuesday, September 11, 2012 4:56:59 PM UTC+2, leif wrote:

Jean-Pierre Flori wrote:
> See:
> https://groups.google.com/forum/?fromgroups=#!msg/sage-release/FXYf_5g0B-4/NZNR2ws0siYJ
>
> I guess you have to let Sage install its own gcc.

? Well, that's what was failing...

Indeed, the predefs.h thing reminded me of sthg and I spoke too fast, sorry about that.

[David Joyner]

On Tue, Sep 11, 2012 at 10:58 AM, Volker Braun <vbrau...@gmail.com> wrote:
> Looks like glibc devel headers are missing -> sudo apt-get install libc6-dev
>

I added gfortran and libc6-dev and now I get this error:


g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../.. -DGMP_NO_CXX
-I../../../src/kernel/memory -I../../../src/kernel/system
-I/home/wdj/sagefiles/sage-5.4.beta0/local/include -fPIC
-I/home/wdj/sagefiles/sage-5.4.beta0/local/include -MT
gmp++_int_div.lo -MD -MP -MF .deps/gmp++_int_div.Tpo -c
gmp++_int_div.C -fPIC -DPIC -o .libs/gmp++_int_div.o
In file included from ./gmp++/gmp++_int.h:402:0,
from gmp++/gmp++.h:34,
from gmp++_int_div.C:9:
./gmp++/gmp++/gmp++_int.inl: In static member function ‘static
Integer& Integer::random(Integer&, long int)’:
./gmp++/gmp++/gmp++_int.inl:331:44: error: ‘mpz_random’ was not
declared in this scope
./gmp++/gmp++/gmp++_int.inl: In static member function ‘static
Integer& Integer::random(Integer&, const Integer&)’:
./gmp++/gmp++/gmp++_int.inl:355:80: error: ‘mpz_random’ was not
declared in this scope
make[6]: *** [gmp++_int_div.lo] Error 1
make[6]: Leaving directory
`/home/wdj/sagefiles/sage-5.4.beta0/spkg/build/givaro-3.2.13.p0/src/src/kernel/gmp++'
make[5]: *** [all-recursive] Error 1
make[5]: Leaving directory
`/home/wdj/sagefiles/sage-5.4.beta0/spkg/build/givaro-3.2.13.p0/src/src/kernel'
make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory
`/home/wdj/sagefiles/sage-5.4.beta0/spkg/build/givaro-3.2.13.p0/src/src'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory
`/home/wdj/sagefiles/sage-5.4.beta0/spkg/build/givaro-3.2.13.p0/src'

make[2]: *** [all] Error 2
make[2]: Leaving directory

`/home/wdj/sagefiles/sage-5.4.beta0/spkg/build/givaro-3.2.13.p0/src'
Error building Givaro.

real 0m9.256s
user 0m3.632s
sys 0m1.108s
************************************************************************
Error installing package givaro-3.2.13.p0

************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the relevant part of the log file

/home/wdj/sagefiles/sage-5.4.beta0/spkg/logs/givaro-3.2.13.p0.log

Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to

/home/wdj/sagefiles/sage-5.4.beta0/spkg/build/givaro-3.2.13.p0 and

type 'make' or whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:

(cd '/home/wdj/sagefiles/sage-5.4.beta0/spkg/build/givaro-3.2.13.p0'

&& '/home/wdj/sagefiles/sage-5.4.beta0/sage' -sh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************

make[1]: *** [installed/givaro-3.2.13.p0] Error 1

make[1]: Leaving directory `/home/wdj/sagefiles/sage-5.4.beta0/spkg'

real 47m8.208s
user 41m45.353s
sys 2m33.062s

Error building Sage.
make: *** [build] Error 1

Any ideas?

> To view this discussion on the web visit
> https://groups.google.com/d/msg/sage-release/-/x8OuS7g3iuQJ.

[Jeroen Demeyer]

On 2012-09-12 17:03, David Joyner wrote:
> On Tue, Sep 11, 2012 at 10:58 AM, Volker Braun <vbrau...@gmail.com> wrote:
>> Looks like glibc devel headers are missing -> sudo apt-get install libc6-dev
>>
>
> I added gfortran and libc6-dev and now I get this error:

That's simply because adding gfortran in the middle of the build isn't
really supported. Try rebuilding mpir, then you should be able to continue.

[David Joyner]

Do you mean type "make clean" and "make"?

[Jeroen Demeyer]

On 2012-09-12 17:08, David Joyner wrote:
> On Wed, Sep 12, 2012 at 11:06 AM, Jeroen Demeyer <jdem...@cage.ugent.be> wrote:
>> On 2012-09-12 17:03, David Joyner wrote:
>>> On Tue, Sep 11, 2012 at 10:58 AM, Volker Braun <vbrau...@gmail.com> wrote:
>>>> Looks like glibc devel headers are missing -> sudo apt-get install libc6-dev
>>>>
>>>
>>> I added gfortran and libc6-dev and now I get this error:
>> That's simply because adding gfortran in the middle of the build isn't
>> really supported. Try rebuilding mpir, then you should be able to continue.
>
>
> Do you mean type "make clean" and "make"?

No, "make distclean" should work though.

[Anthony David]

Built OK on Oracle Linux(RH) 6.3 x86_64

Note: sage built C++ and gfortran

make ptestlong failed one test:

...

Linux xxxxxx 2.6.39-200.24.1.el6uek.x86_64 #1 SMP Sat Jun 23 02:39:07 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux

****************************************************

C compiler: gcc

C compiler version:

Using built-in specs.

Target: x86_64-redhat-linux

Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux

Thread model: posix

gcc version 4.4.6 20120305 (Red Hat 4.4.6-4) (GCC) 

The following tests failed:

        sage -t  --long -force_lib devel/sage/sage/structure/sage_object.pyx # 1 doctests failed

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

Total time for all tests: 799.0 seconds

make: *** [ptestlong] Error 128

[1]+  Exit 2                  make ptestlong

sage -t  --long -force_lib devel/sage/sage/structure/sage_object.pyx

**********************************************************************

File "/root/Build/sage-5.4.beta0/devel/sage-main/sage/structure/sage_object.pyx", line 1053:

    sage: sage.structure.sage_object.picklejar(1, dir + '/noaccess')

Expected:

    Traceback (most recent call last):

    ...

    OSError: ...

Got nothing

**********************************************************************

1 items had failures:

   1 of  11 in __main__.example_24

***Test Failed*** 1 failures.

[Volker Braun]

Do not compile / test software as root. Then the permissions check will also work correctly.

[Anthony David]

Doh.

It was a test server tracking down a kernel bug, with no other accounts. 

Thanks

Anthony

 

To view this discussion on the web visit https://groups.google.com/d/msg/sage-release/-/oB0ZIDBl1EoJ.

[Anthony David]

Confirming

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

All tests passed!

Total time for all tests: 1096.2 seconds

Anthony

On Thu, Sep 13, 2012 at 7:50 PM, Anthony David <ajda...@gmail.com> wrote:

Doh.

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

All tests passed!

Total time for all tests: 1096.2 seconds