sage-5.6.rc0 released

[Jeroen Demeyer]

Dear Sage lovers,

We're releasing Sage 5.6.rc0.

Source archive:

http://boxen.math.washington.edu/home/release/sage-5.6.rc0/sage-5.6.rc0.tar

Upgrade path:

http://boxen.math.washington.edu/home/release/sage-5.6.rc0/sage-5.6.rc0/

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 146 tickets in this release. For details, see

http://boxen.math.washington.edu/home/release/sage-5.6.rc0/tickets.html

Closed tickets:

#9298: Memory leak in libsingular polynomial evaluation [Reviewed by
Charles Bouillaguet]
#10960: Better product error messages when can't multiply [Reviewed by
Michael Orlitzky]
#13863: Segfault in pari galoisconj0 [Reviewed by Volker Braun]
#13939: Fix the "SyntaxError: Non-ASCII character '\xe2'" [Reviewed by
Volker Braun]

Merged in sage-5.6.rc0:

#7560: Jan Medlock: len(t_span) > 2 case creates len(t_span) - 1
solutions [Reviewed by Timo Kluck]
#9543: Peter Jeremy, Jean-Pierre Flori: Enable cephes on FreeBSD and
disable it on Cygwin [Reviewed by Stephen Montgomery-Smith, Karl-Dieter
Crisman]
#12792: Charles Bouillaguet: polybori / gb computation / set error
[Reviewed by Alexander Dreyer]
#13804: Jean-Pierre Flori: libfplll fails to build in parallel on Cygwin
[Reviewed by Karl-Dieter Crisman]
#13808: David Coudert: Gromov hyperbolicity of graphs [Reviewed by
Nathann Cohen]
#13851: Martin Albrecht: Add SAT Solver Interface to Reference Manual
[Reviewed by Nathann Cohen, John H. Palmieri, Nicolas M. Thiéry]
#13875: David Coudert: Test memory allocation in distances_all_pairs
[Reviewed by Nathann Cohen]
#13921: Jeroen Demeyer: Make the GP executable work with SAGE_DEBUG on
Darwin [Reviewed by Volker Braun]
#13926: Jeroen Demeyer: Undo #13014 [Reviewed by Burcin Erocal,
Punarbasu Purkayastha]
#13927: Jeroen Demeyer: Disable startuptime test [Reviewed by Volker Braun]
#13930: Nils Bruin: remove bad is_subcategory implementation [Reviewed
by Simon King]
#13936: Nathann Cohen: Add encoding to smallgraphs.py [Reviewed by
Jeroen Demeyer]
#13937: Jeroen Demeyer: Properly detect GCC-4.3 [Reviewed by John Cremona]
#13938: Jeroen Demeyer: Don't set CCACHE_DIR [Reviewed by R. Andrew
Ohana, Punarbasu Purkayastha]

[Michael Welsh]

On 13/01/2013, at 4:03 AM, Jeroen Demeyer <jdem...@cage.ugent.be> wrote:
>
> Dear Sage lovers,
>
> We're releasing Sage 5.6.rc0.

Built fine and all tests passed on OS X 10.8.2

Michael

[Justin C. Walker]

On Jan 12, 2013, at 07:03 , Jeroen Demeyer wrote:

> Dear Sage lovers,
>
> We're releasing Sage 5.6.rc0.
>
> Source archive:
>
> http://boxen.math.washington.edu/home/release/sage-5.6.rc0/sage-5.6.rc0.tar

On Mac OS X 10.6.8 (Dual 6-core Xeons), the build and testing ('ptestlong') was clean: no problems.

On Mac OS X 10.8.2 (Quad-core Core i7), I ran the build/test cycle twice. The build was clean in both cases, but the first test run ('ptestlong') produced failures on 33 different files (most with a fairly large number of failures). They all appeared to be kicked off by floating point, although I didn't check exhaustively, due to the high counts. I've kept the first install directory in case anyone wants details, and the build, doc, and test logs are at
sage.math.washington.edu:~justin/logs/5.6.rc0_*.log

The second attempt on this system was clean and all tests passed.

BTW, thanks to those who sped up the doc build: 37 minutes for "build+doc"!! (that's what 12 cores/24 threads gets you :-}).

Justin

--
Justin C. Walker, Curmudgeon at Large
Institute for the Absorption of Federal Funds
-----------
Like the ski resort full of girls hunting for husbands
and husbands hunting for girls, the situation is not
as symmetrical as it might seem.
- Alan MacKay
--

[Jeroen Demeyer]

On 2013-01-15 21:45, Justin C. Walker wrote:
> BTW, thanks to those who sped up the doc build

I assume you mean #13143 (MathJax by default)?

[Sébastien Labbé]

Hi,

I had problem building sage-5.5 yesterday on os x 10.5.8 (see my post on sage-devel). Today I tried with sage-5.6.rc0 and I get the same problem. In fact, the building process works, but then sage doesn't start.

Here is the end of log I get :


real    468m18.868s
user    192m23.980s
sys    26m50.036s
Sage build/upgrade complete!

To install small scripts to directly run Sage's versions of GAP,
the PARI/GP interpreter, Maxima, or Singular etc. (by typing e.g.
just 'gap' or 'gp') into a standard 'bin' directory, start Sage
by typing 'sage' (or './sage') and enter something like

    install_scripts('/usr/local/bin')

at the Sage command prompt ('sage:').

If you issued 'make', 'make all', or a similar command, then the
HTML version of the documentation will be built right now.
Otherwise, if you want to (re)build the HTML documentation,
run 'make doc'.  To build the PDF version, run 'make doc-pdf'.

./sage -b

----------------------------------------------------------
sage: Building and installing modified Sage library files.


Installing c_lib
scons: `install' is up to date.
Updating Cython code....
Executing 0 commands (using 1 thread)
Time to execute 0 commands: 0.128820180893 seconds
Finished compiling Cython code (time = 5.53028702736 seconds)
running install
running build
running build_py
running build_ext
Executing 0 commands (using 1 thread)
Time to execute 0 commands: 0.00762796401978 seconds
Total time spent compiling C/C++ extensions:  0.123225927353 seconds.
running install_lib
running install_egg_info
Removing /Users/slabbe/Applications/sage-5.6.rc0/local/lib/python2.7/site-packages/sage-0.0.0-py2.7.egg-info
Writing /Users/slabbe/Applications/sage-5.6.rc0/local/lib/python2.7/site-packages/sage-0.0.0-py2.7.egg-info

real    0m10.641s
user    0m2.654s
sys    0m1.452s
[ -f local/lib/sage-started.txt ] || local/bin/sage-starts

Testing that Sage starts...
[2013-01-16 09:41:53] Sage version 5.6.rc0, released 2013-01-12
This looks like the first time you are running Sage.
Updating various hardcoded paths...
(Please wait at most a few minutes.)
DO NOT INTERRUPT THIS.
Done updating paths.
terminate called after throwing an instance of 'std::runtime_error'
  what():  no function 'integrate' with  parameters defined

------------------------------------------------------------------------
Unhandled SIGABRT: An abort() 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.
------------------------------------------------------------------------
/Users/slabbe/Applications/sage-5.6.rc0/spkg/bin/sage: line 832: 29266 Abort trap              sage-eval "$@"
Sage failed to start up.
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and send the log file
  /Users/slabbe/Applications/sage-5.6.rc0/start.log
Describe your computer, operating system, etc.
make: *** [start] Error 1


*******



~/Applications/sage-5.6.rc0 $ ./sage -gdb
----------------------------------------------------------------------
| Sage Version 5.6.rc0, Release Date: 2013-01-12                     |
| Type "notebook()" for the browser-based notebook interface.        |
| Type "help()" for help.                                            |
----------------------------------------------------------------------
**********************************************************************
*                                                                    *
* Warning: this is a prerelease version, and it may be unstable.     *
*                                                                    *
**********************************************************************
GNU gdb 6.3.50-20050815 (Apple version gdb-967) (Tue Jul 14 02:11:58 UTC 2009)
Copyright 2004 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and you are
welcome to change it and/or distribute copies of it under certain conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB.  Type "show warranty" for details.
This GDB was configured as "i386-apple-darwin"...Reading symbols for shared libraries .
warning: Could not find object file "/Users/slabbe/Applications/sage-5.6.rc0/spkg/build/python-2.7.3.p3/src/Modules/getbuildinfo.o" - no debug information available for "./Modules/getbuildinfo.c".


warning: Could not find object file "/Users/slabbe/Applications/sage-5.6.rc0/spkg/build/python-2.7.3.p3/src/Parser/acceler.o" - no debug information available for "Parser/acceler.c".

[...]

warning: Could not find object file "/Users/slabbe/Applications/sage-5.6.rc0/spkg/build/libm4rie-20120613/src/.libs/ple.o" - no debug information available for "m4rie/ple.c".

warning: Could not find object file "/Users/slabbe/Applications/sage-5.6.rc0/spkg/build/libm4rie-20120613/src/.libs/conversion.o" - no debug information available for "m4rie/conversion.c".

. done
Reading symbols for shared libraries . done
Reading symbols for shared libraries . done
Reading symbols for shared libraries .. done
Reading symbols for shared libraries . done
Reading symbols for shared libraries . done
Reading symbols for shared libraries . done
Reading symbols for shared libraries . done
Reading symbols for shared libraries . done
Reading symbols for shared libraries . done
Reading symbols for shared libraries . done
Reading symbols for shared libraries ... done
terminate called after throwing an instance of 'std::runtime_error'
  what():  no function 'integrate' with  parameters defined

Program received signal SIGABRT, Aborted.
0x96a82e42 in __kill ()
(gdb)
(gdb)

[Sébastien Labbé]

Ok, I found the problem! It was my fault. If you want to break the compilation of Sage like I did, you just have to add the local/bin of an other version of Sage in your PATH (I did this once recently to use one of the script from the command line but forgot to clean it from my bash_profile). In the complete install.log file, there was sage-5.4 appearing in the compilation as well as sage-5.6.rc0... Apparently doing so, sage still builds but doesn't start properly!

Sorry for the noise.

Sébastien

***

Testing that Sage starts...
[2013-01-16 17:58:51] Sage version 5.6.rc0, released 2013-01-12

This looks like the first time you are running Sage.
Updating various hardcoded paths...
(Please wait at most a few minutes.)
DO NOT INTERRUPT THIS.
Done updating paths.

Yes, Sage starts.

[Justin C. Walker]

I can't say for sure what did the job. I just noticed that the time for the doc build went *way* down.

Justin

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

[P Purkayastha]

On 01/17/2013 01:07 AM, S�bastien Labb� wrote:
>
> Ok, I found the problem! It was my fault. If you want to break the
> compilation of Sage like I did, you just have to add the local/bin of an
> other version of Sage in your PATH (I did this once recently to use one
> of the script from the command line but forgot to clean it from my
> bash_profile). In the complete install.log file, there was sage-5.4
> appearing in the compilation as well as sage-5.6.rc0... Apparently doing
> so, sage still builds but doesn't start properly!
>
> Sorry for the noise.
>

> S�bastien

This is really weird. If that was what was happening then it is a
regression. I haven't seen such problems till 5.6-beta1 that I last
installed. Having sage in the PATH doesn't affect the compilation or
running of any other version of sage.

[leif]

Note that he had $SAGE_ROOT/local/bin in the PATH, which one shouldn't
do anyway, since the scripts there aren't supposed to be called
directly. (If at all, one should only run them from the corresponding
Sage subshell.)

[I don't know which script was "missing", but a symlink or a copy would
certainly have been better than putting the whole directory into the PATH.]


It's still not obvious to me what exactly went wrong.


-leif

--

() The ASCII Ribbon Campaign

/\ Help Cure HTML E-Mail

[Sébastien Labbé]

Note that he had $SAGE_ROOT/local/bin in the PATH, which one shouldn't
do anyway, since the scripts there aren't supposed to be called
directly.  (If at all, one should only run them from the corresponding
Sage subshell.)

To be more precise, here is the link I had in my .bash_profile while compiling sage-5.6.rc0:

# export PATH=/Users/slabbe/Applications/sage-5.4/local/bin:$PATH

[I don't know which script was "missing", but a symlink or a copy would
certainly have been better than putting the whole directory into the PATH.]

blogofile was the script I was using. I installed it there in sage-5.4 shell because I wanted to test the installation of blogofile with the version of python shipped with sage-5.4.... So nothing serious...

It's still not obvious to me what exactly went wrong.

-leif

Here is the complete log of the broken installation. You can see that the string "sage-5.4" appear here and there :

http://sage.math.washington.edu/home/slabbe/sage-5.6.rc0/install.log

Sébastien

[Jeroen Demeyer]

Looking at the log, the main issue is probably GCC. It's simply an
invalid configuration to have gcc in your PATH but not GCC's libraries
in LD_LIBRARY_PATH. Although I would have expected an error much earlier...

[P Purkayastha]

On 01/18/2013 08:49 AM, S�bastien Labb� wrote:
>
> Note that he had $SAGE_ROOT/local/bin in the PATH, which one shouldn't
> do anyway, since the scripts there aren't supposed to be called
> directly. (If at all, one should only run them from the corresponding
> Sage subshell.)
>
>
> To be more precise, here is the link I had in my .bash_profile while
> compiling sage-5.6.rc0:
>
> # export PATH=/Users/slabbe/Applications/sage-5.4/local/bin:$PATH

Avoid adding this to your PATH. Instead put a symlink to your current
sage installation into your PATH.

cd /some/directory/that/is/already/in/your/PATH
rm -f sage && ln -s /path/to/sage-5.4/sage .

You can now call sage without full path and also no compilation of sage
will fail.

[Georg Grafendorfer]

Hi,

Fedora 17, AMD Phenom(tm) II X4 925 Processor × 4

sage 5.6.rc0, Maxima build error, below are some install.log lines,

thanks, Georg


make[5]: Leaving directory `/scratch/userdata/sage-5.6.rc0/spkg/build/maxima-5.26.0.p1/src'
make[4]: Leaving directory `/scratch/userdata/sage-5.6.rc0/spkg/build/maxima-5.26.0.p1/src'
make[3]: Leaving directory `/scratch/userdata/sage-5.6.rc0/spkg/build/maxima-5.26.0.p1/src'

Creating wrapper script with disabled readline...

Now building Maxima as an ECL library...
;;; Loading #P"/scratch/userdata/sage-5.6.rc0/local/lib/ecl/asdf.fas"
;;; Loading #P"/scratch/userdata/sage-5.6.rc0/local/lib/ecl/cmp.fas"
;;; Loading "/scratch/userdata/sage-5.6.rc0/spkg/build/maxima-5.26.0.p1/src/src/maxima-build.lisp"
;;; Loading "/scratch/userdata/sage-5.6.rc0/spkg/build/maxima-5.26.0.p1/src/src/../lisp-utils/defsystem.lisp"
;;; Loading "/scratch/userdata/sage-5.6.rc0/spkg/build/maxima-5.26.0.p1/src/src/maxima-package.lisp"
;;; OPTIMIZE levels: Safety=2, Space=0, Speed=3, Debug=0
;;;
;;; End of Pass 1.
;;; Note:
;;;   Invoking external command:
;;;   gcc -I. -I/scratch/userdata/sage-5.6.rc0/local/include/ -I/scratch/userdata/sage-5.6.rc0/local/include -I/scratch/userdata/sage-5.6.rc0/local/include -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -fPIC -Dlinux -O2 -w -c /tmp/ecl0016bExic.c -o /tmp/ecl0016bExic.o
An error occurred during initialization:
Component "maxima" not found.
;;; Note:
;;;   Invoking external command:
;;;   gcc -o /tmp/ecl0016bExic.fas -L/scratch/userdata/sage-5.6.rc0/local/lib/ /tmp/ecl0016bExic.o -Wl,--rpath,/scratch/userdata/sage-5.6.rc0/local/lib/ -shared -L/scratch/userdata/sage-5.6.rc0/local/lib -L/scratch/userdata/sage-5.6.rc0/local/lib -Wl,--rpath,/scratch/userdata/sage-5.6.rc0/local/lib -L/scratch/userdata/sage-5.6.rc0/local/lib -lecl -lgmp -lgc -ldl -lm ***********************************************************
Error: Failed to build Maxima as an ECL library.
***********************************************************

real    5m5.349s
user    4m16.626s
sys    0m37.539s
************************************************************************
Error installing package maxima-5.26.0.p1
************************************************************************

Please email sage-devel (http://groups.google.com/group/sage-devel)

explaining the problem and including the relevant part of the log file
  /scratch/userdata/sage-5.6.rc0/spkg/logs/maxima-5.26.0.p1.log

Describe your computer, operating system, etc.

If you want to try to fix the problem yourself, *don't* just cd to
/scratch/userdata/sage-5.6.rc0/spkg/build/maxima-5.26.0.p1 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 '/scratch/userdata/sage-5.6.rc0/spkg/build/maxima-5.26.0.p1' && '/scratch/userdata/sage-5.6.rc0/sage' -sh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************
make[2]: *** [installed/maxima-5.26.0.p1] Error 1
make[2]: Leaving directory `/scratch/userdata/sage-5.6.rc0/spkg'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/scratch/userdata/sage-5.6.rc0/spkg'

real    75m1.460s
user    62m30.818s
sys    10m15.529s
Error building Sage.

[Volker Braun]

Do you have list (+r) permissions for all directories? We got similar errors before with maxima. 

ls -l /scratch

ls -l /scratch/userdata

[Georg Grafendorfer]

hmm, I don't know what you exactly mean by (+r), here is the result for "ls -l" in /scratch/userdata

drwxr-xr-x.  8 ggeorg a-g3       4096 Jan 18 16:51 sage-5.6.rc0

and this is the result for "ls -l" in /scratch/userdata/sage-5.6.rc0

ggeorg@maschke% ls -la
total 12100
drwxr-xr-x.  8 ggeorg a-g3     4096 Jan 18 16:51 .
drwxrwxrwt. 45 root   root    16384 Jan 18 14:38 ..
-rw-------.  1 ggeorg a-g3       11 Jan 18 14:38 .BUILDSTART
drwxr-xr-x.  4 ggeorg a-g3     4096 Jan 18 14:44 .hg
-rw-r--r--.  1 ggeorg a-g3      526 Jan 12 12:24 .hgignore
-rw-r--r--.  1 ggeorg a-g3     5193 Jan 12 12:24 .hgtags
-rw-r--r--.  1 ggeorg a-g3    72177 Jan 12 12:24 COPYING.txt
-rw-r--r--.  1 ggeorg a-g3     5060 Jan 12 12:24 Makefile
-rw-r--r--.  1 ggeorg a-g3    13488 Jan 12 12:24 README.txt
-rw-r--r--.  1 ggeorg a-g3       42 Jan 12 12:23 VERSION.txt
lrwxrwxrwx.  1 ggeorg a-g3       11 Jan 18 14:38 data -> local/share
drwx------.  4 ggeorg a-g3     4096 Jan 18 15:40 devel
-rw-------.  1 ggeorg a-g3 12210246 Jan 18 15:53 install.log
drwxr-xr-x.  2 ggeorg a-g3     4096 Jan 12 12:24 ipython
drwx------. 11 ggeorg a-g3     4096 Jan 18 15:53 local
-rwxr-xr-x.  1 ggeorg a-g3     4848 Jan 12 12:24 sage
drwxr-xr-x.  8 ggeorg a-g3     4096 Jan 18 14:38 spkg
drwx------.  2 ggeorg a-g3     4096 Jan 18 14:38 tmp


Georg

[Volker Braun]

what about 

    ls -l /scratch

[Georg Grafendorfer]

ggeorg@maschke% ls -l /scratch
ls: cannot open directory /scratch: Permission denied

ok, I see the problem, I will have to inform the admins, this is a bit strange, their is a link "/userdata" to "/scratch/userdata" which is accessible for me, but "/scratch" is not,

thanks for your help, Georg

[Volker Braun]

This was supposed to be fixed in Maxima, but apparently the patch hasn't made it in?

See https://groups.google.com/d/msg/sage-devel/M1gJh3lwhN0/GYxuiL2bTPQJ

[Georg Grafendorfer]

...ahh, that makes most sense,

thank you, Georg

[Marco Streng]

Op vrijdag 18 januari 2013 08:05:12 UTC+1 schreef Jeroen Demeyer:

Looking at the log, the main issue is probably GCC.  It's simply an
invalid configuration to have gcc in your PATH but not GCC's libraries
in LD_LIBRARY_PATH.  Although I would have expected an error much earlier...

Hi Jeroen,

What would the correct setting for LD_LIBRARY_PATH be? Mine is not set.

Thanks!
Marco

[Jeroen Demeyer]

Depends where the libraries of GCC are. Usually, this is ...local/lib/
or ...local/lib64/

Jeroen.