Sage 4.5.3.alpha0 released

[Mitesh Patel]

We've released Sage 4.5.3.alpha0.

Source archive:

http://sage.math.washington.edu/home/release/sage-4.5.3.alpha0/sage-4.5.3.alpha0.tar

Upgrade path:

http://sage.math.washington.edu/home/release/sage-4.5.3.alpha0/sage-4.5.3.alpha0/

The long doctests pass for me on {bsd,redhawk,sage,t2}.math.

Please build, test, and report! We'd love to hear about your problems
(and successes) on a wide range of systems.

== Tickets ==

Closed:

#9354: Ralf Hemmecke: Update FriCAS to 1.0.9 [Reviewed by Adam Webb,
Mike Hansen]

Merged in sage-4.5.3.alpha0:

#2508: Jeroen Demeyer: Problem converting a Laurent Series from pari to
Sage [Reviewed by John Cremona]
#5828: Luis Felipe Tabera Alonso: number fields -- serious bug in
coercion to a relative extension of degree 1 [Reviewed by Marco Streng]
#7861: David Kirkby: pynac not building on Open Solaris x64
(32-bit/64-bit mixup) [Reviewed by John Palmieri]
#7864: David Kirkby, Willem Jan Palenstijn: libfplll tries to link
64-bit objects to 32-bit libstdc++.so [Reviewed by John Palmieri]
#8017: Robert Bradshaw: incorrect trailing digits for continued fraction
[Reviewed by Paul Zimmermann]
#8086: David Kirkby: numpy fails to build on OpenSolaris or Solaris 10
64-bit [Reviewed by John Palmieri]
#8316: Mitesh Patel: Remove the Jinja (not Jinja2) package [Reviewed by
Carl Witty]
#9003: Georg Weber, Willem Jan Palenstijn: Doctest (or whatever???)
failure on Mac OS X in free_module.py [Reviewed by Karl-Dieter Crisman,
Craig Citro]
#9247: Robert Miller, John Cremona: A collection of little improvements
to elliptic curves [Reviewed by John Cremona, Robert Miller]
#9253: Robert Miller: A collection of little improvements to heegner.py
[Reviewed by William Stein]
#9254: Robert Miller: A collection of little improvements to BSD.py
[Reviewed by Mitesh Patel, William Stein]
#9309: David Kirkby: Add an spkg-check file for the IML library
[Reviewed by Martin Albrecht]
#9326: Volker Braun: Add cohomology of toric varieties [Reviewed by
Andrey Novoseltsev]
#9338: Minh Van Nguyen: upgrade PyCrypto to upstream 2.1.0 [Reviewed by
David Kirkby]
#9352: John Palmieri: givaro spkg: trivial typo in spkg-check [Reviewed
by David Kirkby]
#9356: John Palmieri: make SAGE_ATLAS_LIB work on Solaris [Reviewed by
David Kirkby]
#9396: Mariah Lenox, David Kirkby: statistical package r fails to run,
missing libicuuc [Reviewed by David Kirkby, Robert Miller]
#9444: Mitesh Patel: Fix "rm: Cannot remove any directory in the path of
the current working directory" on t2 [Reviewed by David Kirkby, John
Palmieri, Leif Leonhardy]
#9470: Andrey Novoseltsev: Switch toric varieties to enhanced fans
[Reviewed by Volker Braun]
#9472: Leif Leonhardy: Remove (duplicate) BOOST and M4RI source trees
from PolyBoRi spkg, some clean-up [Reviewed by Martin Albrecht]
#9476: John Cremona: Upgrade eclib to version 20100711 [Reviewed by
Robert Miller]
#9482: Carl Witty: implicit_plot3d gives "Out of memory allocating
triangulation" when plotting an empty surface [Reviewed by Karl-Dieter
Crisman]
#9533: David Kirkby: Update GSL to the latest upstream release (1.14)
& permit parallel building. [Reviewed by Mike Hansen, Peter Jeremy,
Leif Leonhardy]
#9575: Nathann Cohen: Grundy coloring of a graph [Reviewed by Leonardo
Sampaio]
#9595: Jeroen Demeyer: Conversion from constant PARI polynomials to QQ
doesn't work [Reviewed by John Cremona]
#9610: Robert Miller: int(finite field element) should only work when it
is in the prime subfield [Reviewed by Martin Albrecht]
#9647: Harald Schilly: instructive example for mip.pyx [Reviewed by
Nathann Cohen]
#9649: Jeroen Demeyer: c_lib/include/interrupt.h: rename FOO_H [Reviewed
by Robert Bradshaw]
#9661: Jeroen Demeyer: pari(string) always returns a value, even when it
should not [Reviewed by John Cremona]
#9682: Valentin Feray: Fix a bug in error message in perfect matchings
[Reviewed by Florent Hivert]
#9686: Robert Miller: Polish documentation for canonical label [Reviewed
by Minh Van Nguyen]
#9700: Ryan Hinton: Export check_edge_label from sparse_graph.pyx
[Reviewed by Nathann Cohen]

[Rob Beezer]

Passes all tests on 64-bit KUbuntu 9.10 on Intel Core Duo using:

MAKE="make -j2"
SAGE_PARALLEL_SPKG_BUILD=yes

make ptestlong

Rob

On Aug 9, 9:01 pm, Mitesh Patel <qed...@gmail.com> wrote:
> We've released Sage 4.5.3.alpha0.
>
> Source archive:
>

> http://sage.math.washington.edu/home/release/sage-4.5.3.alpha0/sage-4...
>
> Upgrade path:
>
> http://sage.math.washington.edu/home/release/sage-4.5.3.alpha0/sage-4...

[georg grafendorfer]

Hi,

sage does not built on my machine, AMD Phenom(tm) II X4 925, Fedora
13,

here are the relevant lines of the log file:

Shall we try to build pari 2.3.5 (released) now (y/n)? [n]
Ok. Type "make install" when you are ready
Bye !
Building and install PARI
make[2]: Entering directory `/scratch/sage-4.5.3.alpha0/spkg/build/
pari-2.3.5.p2/src'
Making gp in Olinux-x86_64
make[3]: Entering directory `/scratch/sage-4.5.3.alpha0/spkg/build/
pari-2.3.5.p2/src/Olinux-x86_64'
File ../src/funclist not changed.
../config/genkernel ../src/kernel/x86_64/asm0.h > parilvl0.h
cat ../src/kernel/gmp/tune.h ../src/kernel/gmp/int.h ../src/kernel/
none/level1.h > parilvl1.h
cat parilvl0.h parilvl1.h > pariinl.h
gcc -c -O1 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -
I../src/headers -I../src/language -I/scratch/sage-4.5.3.alpha0/local/
include -o gp.o ../src/gp/gp.c
cd ../src/desc && /usr/bin/perl merge_822 ../functions/*/* > def-linux-
x86_64-6659.tmp
mv ../src/desc/def-linux-x86_64-6659.tmp ../src/desc/pari.desc
cd ../src/desc && /usr/bin/perl gen_proto gp pari.desc > gp_init-linux-
x86_64-6659.tmp
mv ../src/desc/gp_init-linux-x86_64-6659.tmp ../src/gp/gp_init.h
gcc -c -O1 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -
I../src/headers -I../src/graph -o gp_init.o ../src/gp/gp_init.c
gcc -c -O1 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -
I../src/headers -I../src/language -I/scratch/sage-4.5.3.alpha0/local/
include -o gp_rl.o ../src/gp/gp_rl.c
cd ../src/desc && /usr/bin/perl gen_proto highlevel pari.desc >
highlvl-linux-x86_64-6659.tmp
mv ../src/desc/highlvl-linux-x86_64-6659.tmp ../src/gp/highlvl.h
gcc -c -O1 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -
I../src/headers -DDL_DFLT_NAME=NULL -o highlvl.o ../src/gp/highlvl.c
gcc -c -O1 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -
I../src/headers -o whatnow.o ../src/gp/whatnow.c
gcc -c -O1 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -
I../src/headers -I../src/graph -o plotport.o ../src/graph/plotport.c
g++ -c -O1 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../
src/headers -I"/usr/local"/include -o plotfltk.o ../src/graph/
plotfltk.c
../src/graph/plotfltk.c:27:19: error: FL/Fl.H: No such file or
directory
../src/graph/plotfltk.c:28:26: error: FL/Fl_Window.H: No such file or
directory
../src/graph/plotfltk.c:29:24: error: FL/fl_draw.H: No such file or
directory
../src/graph/plotfltk.c:31: error: expected class-name before '{'
token
../src/graph/plotfltk.c:45: error: 'Fl_Color' does not name a type
../src/graph/plotfltk.c:48: error: 'Fl_Color' does not name a type
../src/graph/plotfltk.c: In constructor 'Plotter::Plotter(long int*,
long int*, long int*, long int, const char*)':
../src/graph/plotfltk.c:56: error: class 'Plotter' does not have any
field named 'Fl_Window'
../src/graph/plotfltk.c:60: error: 'color' was not declared in this
scope
../src/graph/plotfltk.c:60: error: 'FL_WHITE' was not declared in this
scope
../src/graph/plotfltk.c:61: error: 'FL_BLACK' was not declared in this
scope
../src/graph/plotfltk.c:62: error: 'FL_BLUE' was not declared in this
scope
../src/graph/plotfltk.c:63: error: 'rgb_color' was not declared in
this scope
../src/graph/plotfltk.c:64: error: 'FL_RED' was not declared in this
scope
../src/graph/plotfltk.c:65: error: 'FL_GREEN' was not declared in this
scope
../src/graph/plotfltk.c: In function 'void DrawPoint(void*, long int,
long int)':
../src/graph/plotfltk.c:73: error: 'fl_point' was not declared in this
scope
../src/graph/plotfltk.c: In function 'void DrawLine(void*, long int,
long int, long int, long int)':
../src/graph/plotfltk.c:79: error: 'fl_line' was not declared in this
scope
../src/graph/plotfltk.c: In function 'void DrawRectangle(void*, long
int, long int, long int, long int)':
../src/graph/plotfltk.c:85: error: 'fl_rect' was not declared in this
scope
../src/graph/plotfltk.c: In function 'void DrawPoints(void*, long int,
plot_points*)':
../src/graph/plotfltk.c:92: error: 'fl_point' was not declared in this
scope
../src/graph/plotfltk.c: In function 'void SetForeground(void*, long
int)':
../src/graph/plotfltk.c:97: error: 'Fl_Color' was not declared in this
scope
../src/graph/plotfltk.c:97: error: 'color' was not declared in this
scope
../src/graph/plotfltk.c:97: error: expected primary-expression before
')' token
../src/graph/plotfltk.c:97: error: expected ';' before 'data'
../src/graph/plotfltk.c:98: error: 'fl_color' was not declared in this
scope
../src/graph/plotfltk.c: In function 'void DrawLines(void*, long int,
plot_points*)':
../src/graph/plotfltk.c:105: error: 'fl_line' was not declared in this
scope
../src/graph/plotfltk.c: In function 'void DrawString(void*, long int,
long int, char*, long int)':
../src/graph/plotfltk.c:111: error: 'fl_draw' was not declared in this
scope
../src/graph/plotfltk.c: In member function 'void Plotter::draw()':
../src/graph/plotfltk.c:118: error: 'class Plotter' has no member
named 'w'
../src/graph/plotfltk.c:119: error: 'class Plotter' has no member
named 'h'
../src/graph/plotfltk.c:121: error: 'FL_COURIER' was not declared in
this scope
../src/graph/plotfltk.c:121: error: 'fl_font' was not declared in this
scope
../src/graph/plotfltk.c:122: error: 'FL_WHITE' was not declared in
this scope
../src/graph/plotfltk.c:122: error: 'fl_color' was not declared in
this scope
../src/graph/plotfltk.c:123: error: 'class Plotter' has no member
named 'w'
../src/graph/plotfltk.c:123: error: 'class Plotter' has no member
named 'h'
../src/graph/plotfltk.c:123: error: 'fl_rectf' was not declared in
this scope
../src/graph/plotfltk.c:133: error: 'color' was not declared in this
scope
../src/graph/plotfltk.c: In member function 'int
Plotter::handle(int)':
../src/graph/plotfltk.c:140: error: 'FL_PUSH' was not declared in this
scope
../src/graph/plotfltk.c:141: error: 'Fl' has not been declared
../src/graph/plotfltk.c:155: error: 'class Plotter' has no member
named 'x'
../src/graph/plotfltk.c:156: error: 'class Plotter' has no member
named 'y'
../src/graph/plotfltk.c:157: error: 'class Plotter' has no member
named 'w'
../src/graph/plotfltk.c:158: error: 'class Plotter' has no member
named 'h'
../src/graph/plotfltk.c:159: error: 'class Plotter' has no member
named 'fullscreen'
../src/graph/plotfltk.c:163: error: 'class Plotter' has no member
named 'fullscreen_off'
../src/graph/plotfltk.c:164: error: 'class Plotter' has no member
named 'size_range'
../src/graph/plotfltk.c: In function 'void rectdraw0(long int*, long
int*, long int*, long int)':
../src/graph/plotfltk.c:188: error: 'Fl' has not been declared
../src/graph/plotfltk.c:188: error: 'FL_DOUBLE' was not declared in
this scope
../src/graph/plotfltk.c:188: error: 'FL_INDEX' was not declared in
this scope
../src/graph/plotfltk.c:190: error: 'class Plotter' has no member
named 'size_range'
../src/graph/plotfltk.c:191: error: 'class Plotter' has no member
named 'box'
../src/graph/plotfltk.c:191: error: 'FL_FLAT_BOX' was not declared in
this scope
../src/graph/plotfltk.c:192: error: 'class Plotter' has no member
named 'end'
../src/graph/plotfltk.c:193: error: 'class Plotter' has no member
named 'show'
../src/graph/plotfltk.c:194: error: 'Fl' has not been declared
make[3]: *** [plotfltk.o] Error 1
make[3]: Leaving directory `/scratch/sage-4.5.3.alpha0/spkg/build/
pari-2.3.5.p2/src/Olinux-x86_64'
make[2]: *** [gp] Error 2
make[2]: Leaving directory `/scratch/sage-4.5.3.alpha0/spkg/build/
pari-2.3.5.p2/src'
Error building GP

real 0m4.645s
user 0m2.540s
sys 0m1.788s
sage: An error occurred while installing pari-2.3.5.p2
Please email sage-devel http://groups.google.com/group/sage-devel
explaining the problem and send the relevant part of
of /scratch/sage-4.5.3.alpha0/install.log. Describe your computer,
operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/scratch/sage-4.5.3.alpha0/spkg/build/pari-2.3.5.p2 and type 'make
check' 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/sage-4.5.3.alpha0/spkg/build/pari-2.3.5.p2' && '/scratch/
sage-4.5.3.alpha0/sage' -sh)
When you are done debugging, you can type "exit" to leave the
subshell.
make[1]: *** [installed/pari-2.3.5.p2] Error 1
make[1]: Leaving directory `/scratch/sage-4.5.3.alpha0/spkg'

real 34m52.462s
user 24m19.583s
sys 8m32.329s
Error building Sage.
./sage -docbuild all html 2>&1 | tee -a dochtml.log
python: can't open file '/scratch/sage-4.5.3.alpha0/devel/sage/doc/
common/builder.py': [Errno 2] No such file or directory

thanks, Georg

[georg grafendorfer]

I'm sorry for changing the subject of this thread, this was a mistake,

Georg


On Aug 10, 7:44 pm, georg grafendorfer <georg.grafendor...@gmail.com>
wrote:

> Please email sage-develhttp://groups.google.com/group/sage-devel

[leif]

Looks like a (PARI) configuration error. Perhaps you have libfltk
installed, but not libfltk-dev, which also contains the necessary header
files. (I don't have either, so this file isn't built here.)

I would of course consider this a bug, but can you try again with
(either) installing libfltk-dev (or removing libfltk ;-) )?.

-Leif

[Dr. David Kirkby]

On 08/10/10 06:46 PM, georg grafendorfer wrote:
> I'm sorry for changing the subject of this thread, this was a mistake,
>
> Georg

I know Robert Miller was going round the twist with too many replies to "Sage
x.y.z released". He felt more informative headers was better. I guess it depends
on the release manager.

Personally, I'd prefer to see something a bit more explicit like

"4.5.3.alpha0 doctest failure on Ubunta 12 - now #1234"

or something like that.

Dave

[kcrisman]

4.5.3.alpha0 did NOT upgrade successfully for me on OS X 10.6 from
4.5.2. See below - though note that Sage does start up properly, and
sage -i returns (among others)

libm4ri-20100221

however the

pycrypto-2.1.0 pynac-0.2.0.p5 sage-4.5.3.alpha0

packages did then not update either, presumably.

- kcrisman

Thread model: posix
gcc version 4.2.1 (Apple Inc. build 5664)
****************************************************
Starting build...
Removing old PolyBoRi install...
Done removing old PolyBoRi install.
Running build_polybori...
scons: Reading SConscript files ...
Checking for C header file gd.h... yes
Checking for C library gd... no
Checking for C++ header file ext/hash_map... yes
Warning: No LaTeX to html converter found, Tutorial will not be
installed
Checking for C library m4ri... no
Checking for C header file gd.h... yes
Checking for C library gd... no
Symlinking to M4RI/m4ri ...
OSError: [Errno 2] No such file or directory:
File "/Users/.../sage-4.5.2/spkg/build/polybori-0.6.4.p2/src/
polybori-0.6.4/SConstruct", line 421:
os.symlink('.', m4ri_inc)
Error building PolyBoRi.

real 0m1.425s
user 0m0.860s
sys 0m0.473s
sage: An error occurred while installing polybori-0.6.4.p2

[leif]

That's apparently due to my new (stripped) PolyBoRi spkg (#9472).

I'm currently looking at this, but in principle SCons should find the
"external m4ri" (on MacOS X, too) and not try to use the (now obsolete)
copy of it that was included in previous PolyBoRi spkgs.

Please let me know if you open(ed) a ticket for that (or cc me in case
you do/already did).

-Leif

[Mitesh Patel]

Feel free to experiment with alternate schemes that could be convenient
and useful. Always starting the subject with the Sage version is
probably a good idea.

[leif]

I've opened a follow-up thread "Sage 4.5.3.alpha0: Re: PARI build error
on Fedora 13" in case somebody missed it...

-Leif

[Rob Beezer]

All long tests passed on:

Debian "sid", 32-bit, Pentium 4, single-thread build

Ubuntu 10.04, 64-bit, Intel Core i5, make -j2, (no parallel spkg
build)

Rob

[Mitesh Patel]

I've opened

http://trac.sagemath.org/sage_trac/ticket/9721

[leif]

Mitesh Patel wrote:
> We've released Sage 4.5.3.alpha0.

> [...]

> Please build, test, and report! We'd love to hear about your problems
> (and successes) on a wide range of systems.

Ubuntu 7.10 x86 (Pentium 4, 768MB RAM; rebuilt gcc 4.2.1):

make build: OK (parallel build with 2 jobs, native code, O2)
make doc: OK (except one warning due to missing dvipng*)
make testlong: OK (all tests passed)

Ubuntu 9.04 x86 (Pentium 4 Prescott, gcc 4.3.3):

make build: OK (parallel build with 6 jobs, native code, O2)
make doc: OK
make ptestlong: OK (all tests passed; 2 threads)

Ubuntu 9.04 x86_64 (Core2 quad, gcc 4.5.0):

make build: OK (parallel build with 12 jobs, native code, O2)
make doc: OK
make ptestlong: OK (all tests passed; 4 threads)

-Leif

_________________
* I'm not aware of this being documented anywhere (dvipng being required
to build the HTML documentation); at least on these Ubuntus dvipng is a
separate package, and not part of (or pulled in by) TeX packages.

[georg grafendorfer]

> Looks like a (PARI) configuration error. Perhaps you have libfltk
> installed, but not libfltk-dev, which also contains the necessary header
> files. (I don't have either, so this file isn't built here.)
>
> I would of course consider this a bug, but can you try again with
> (either) installing libfltk-dev (or removing libfltk ;-) )?.
>
> -Leif
>

fltk-devel is installed now, still does not work, but the log message
has changed, look at

http://trac.sagemath.org/sage_trac/ticket/9722

Georg