[sage-release] sage-4.4.1.alpha2: FEATURE FREEZE
William Stein
Sage-4.4.1.alpha2 is available here:
http://sage.math.washington.edu/home/wstein/build/release/4.4.1/sage-4.4.1.alpha2.tar
This contains *everything* with a positive review, except several sage
Notebook tickets. Tim Dumol -- if you want to do another sagenb
release (for sage-4.4.2), you should be sure to merge (/pull) from the
sagenb-0.8.p0.spkg I've included in the sage-4.4.1.alpha2 tarball.
Sage-4.4.1 is now in *FEATURE FREEZE*. The *only* thing left to do is
test on many platforms, shake out the inevitable bugs that were
introduced by merging in code, check off the checklist (e.g., that
upgrades work) and release -- this will probably take a few days.
There is also one issue, which it would be really nice to solve, but
won't block this particular release if it remains unsolved: #8788 --
when building Sage-4.4.1 under GCC-4.5.0, one gets a double free on
exit sometimes (I suspect maybe Linbox). At least sage-4.4.1.alpha*
builds without intervention under GCC-4.5.0....
Here is the merge list:
alpha0:
[x] #8785
[x] #8644 -- update pynac (also close #8753) -- positively reviewed
[x] #8773 -- gap workspace fix -- positively reviewed
[x] #8774 -- gap full of binary crap -- positively reviewed
[x] #8770 -- gfan
[x] #8771 -- znpoly
[x] #8767 -- libpng
[x] #4793 -- lcalc
[x] #8453, #8415 -- pari
[x] #8725 -- sagenb-0.8
alpha1:
[x] #8192 -- polybori update
[x] #8715 -- gfortran
[x] #7608 -- networkx (maybe)
[x] #7765 -- "sage -bdist"
alpha2:
[x] #8812, #8724 -- sage notebook doctest issue
[x] #8813, #8565 -- symbolic expression doctest issue
[x] #8736 -- bug radicals
[x] #8378 -- typo in documentation of crt
[x] #8642 -- port detection for the notebook does not work in Cygwin
[x] #7319 -- gdmodule requires libiconv on cygwin
[x] #7321 -- numpy fails to build on cygwin due to not using
the correct fortran compiler
[x] #8745 -- Steiner Triple Systems
[x] #7643 -- composite_fields does not play nice with QuadraticFields
[x] #5969 -- implement computation of rational cuspidal
subgroups of modular abelian varieties
[x] #8172 -- CPLEX
[x] #8303 -- Sage cannot work with files with spaces in their names
[x] #8681 -- implement matrix actions on binary quadratic forms
[x] #8407 -- more practical construction of word paths
[x] #8735 -- Renamed size to cardinality in poset
[x] #8746 -- poset equality slow
[x] #8402 -- Sanity check for Parents and Elements
[x] #7665 -- support for R graphics
[x] #8394 -- plot/plot3d/tri_plot.py is at 0% coverage: get it to 100%
[x] #6648 -- adds riemann mapping and complex interpolation
[x] #8370 -- Add tour_functions to the French tutorial
[x] #7004 -- Refactor the graph layout code, and add
interface with graphviz
[x] #8733 -- documentation and stylistic clean-ups of c_graph.pyx
[x] #8725 -- sagenb-0.8
I think this is the first time I've been release manager in about *two
years* (!). When merging the above, I looked at each patch, and
doctested relevant code afterwards, and was amazed by the quality.
There were almost no issues at all. People are doing a generally
great job refereeing patches against the sage library (much better
than before).
-- William
--
William Stein
Professor of Mathematics
University of Washington
http://wstein.org
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Dan Drake
> Sage-4.4.1.alpha2 is available here:
>
> http://sage.math.washington.edu/home/wstein/build/release/4.4.1/sage-4.4.1.alpha2.tar
First, whoa! Three alpha releases in, what, 24 hours? William, you're on
fire!
alpha2 does not work so well on 64 bit Ubuntu Jaunty. Lots of doctests
failed like this:
sage -t devel/sage/sage/schemes/elliptic_curves/ell_curve_isogeny.py
Aborted
[44.3 s]
sage -t devel/sage/sage/groups/perm_gps/partn_ref/refinement_matrices.pyx
Aborted
[42.1 s]
I think that's related to the segfault that Minh reported.
Here's what seems to be a real error:
sage -t "devel/sage/sage/misc/latex.py"
**********************************************************************
File "/home/drake/s/sage-4.4.1.alpha2/devel/sage/sage/misc/latex.py",
line 1207:
sage: latex.extra_preamble()
Expected:
'\\usepackage{xypic}\n'
Got:
''
**********************************************************************
Doctesting R failed quite badly:
sage -t devel/sage/sage/interfaces/r.py
**********************************************************************
File "/home/drake/s/sage-4.4.1.alpha2/devel/sage-main/sage/interfaces/r.py", line 335:
sage: r.png(filename='"%s"'%filename)
Exception raised:
Traceback (most recent call last):
File "/home/drake/s/sage-4.4.1.alpha2/local/bin/ncadoctest.py", line 1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File "/home/drake/s/sage-4.4.1.alpha2/local/bin/sagedoctest.py", line 38, in run_one_example
OrigDocTestRunner.run_one_example(self, test, example, filename, compileflags)
File "/home/drake/s/sage-4.4.1.alpha2/local/bin/ncadoctest.py", line 1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_3[3]>", line 1, in <module>
r.png(filename='"%s"'%filename)###line 335:
sage: r.png(filename='"%s"'%filename)
File "/home/drake/s/sage-4.4.1.alpha2/local/lib/python/site-packages/sage/interfaces/r.py", line 356, in pn
g
raise RuntimeError, "R was not compiled with PNG support"
RuntimeError: R was not compiled with PNG support
**********************************************************************
That was just the first error; I think the (many!) others all stem from the PNG
support problem. It looks like #7665 is to blame. (Based on the title of
the ticket, I haven't checked anything...)
I also see a failure with
sage -t "local/lib/python2.6/site-packages/sagenb-0.8-py2.6.egg/sagenb/misc/misc.py"
where it tries to add a string and an Integer.
Finally, I see a failure with
sage -t devel/sage/doc/en/thematic_tutorials/group_theory.rst
where the Cayley table is printed with a, b, c instead of x0, x1, x2.
I'm attaching my ptest.log.
Dan
--
--- Dan Drake
----- http://mathsci.kaist.ac.kr/~drake
-------
John Cremona
new tutorial:
sage -t devel/sage/doc/en/thematic_tutorials/group_theory.rst
**********************************************************************
File "/local/jec/sage-4.4.1.alpha2/devel/sage-main/doc/en/thematic_tutorials/group_theory.rst",
line 432:
sage: H.cayley_table()
Expected:
[ x0 x1 x2 x3 x4 x5 x6 x7 x8 x9 x10 x11]
[ x1 x0 x3 x2 x5 x4 x7 x6 x9 x8 x11 x10]
[ x2 x10 x0 x4 x3 x6 x5 x8 x7 x11 x1 x9]
[ x3 x11 x1 x5 x2 x7 x4 x9 x6 x10 x0 x8]
[ x4 x9 x10 x6 x0 x8 x3 x11 x5 x1 x2 x7]
[ x5 x8 x11 x7 x1 x9 x2 x10 x4 x0 x3 x6]
[ x6 x7 x9 x8 x10 x11 x0 x1 x3 x2 x4 x5]
[ x7 x6 x8 x9 x11 x10 x1 x0 x2 x3 x5 x4]
[ x8 x5 x7 x11 x9 x1 x10 x2 x0 x4 x6 x3]
[ x9 x4 x6 x10 x8 x0 x11 x3 x1 x5 x7 x2]
[x10 x2 x4 x0 x6 x3 x8 x5 x11 x7 x9 x1]
[x11 x3 x5 x1 x7 x2 x9 x4 x10 x6 x8 x0]
Got:
* a b c d e f g h i j k l
+------------------------
a| a b c d e f g h i j k l
b| b a d c f e h g j i l k
c| c k a e d g f i h l b j
d| d l b f c h e j g k a i
e| e j k g a i d l f b c h
f| f i l h b j c k e a d g
g| g h j i k l a b d c e f
h| h g i j l k b a c d f e
i| i f h l j b k c a e g d
j| j e g k i a l d b f h c
k| k c e a g d i f l h j b
l| l d f b h c j e k g i a
<BLANKLINE>
**********************************************************************
which looks trivial.
John
> Version: GnuPG v1.4.9 (GNU/Linux)
>
> iEYEARECAAYFAkvZiJIACgkQr4V8SljC5LpVZgCfWnU542mWJP7GCzb87BSw/ok/
> juAAnj7Kve7acSiiRlFO15C5alMPADox
> =a+Xy
> -----END PGP SIGNATURE-----
Rob Beezer
that Minh incorporated, so somehow the two didn't get tested against
each other.
I'll get this one fixed this evening at:
http://trac.sagemath.org/sage_trac/ticket/8823
kcrisman
> **********************************************************************
>
> Doctesting R failed quite badly:
>
> sage -t devel/sage/sage/interfaces/r.py
> **********************************************************************
> File "/home/drake/s/sage-4.4.1.alpha2/devel/sage-main/sage/interfaces/r.py", line 335:
> sage: r.png(filename='"%s"'%filename)
> Exception raised:
> Traceback (most recent call last):
> File "/home/drake/s/sage-4.4.1.alpha2/local/bin/ncadoctest.py", line 1231, in run_one_test
> self.run_one_example(test, example, filename, compileflags)
> File "/home/drake/s/sage-4.4.1.alpha2/local/bin/sagedoctest.py", line 38, in run_one_example
> OrigDocTestRunner.run_one_example(self, test, example, filename, compileflags)
> File "/home/drake/s/sage-4.4.1.alpha2/local/bin/ncadoctest.py", line 1172, in run_one_example
> compileflags, 1) in test.globs
> File "<doctest __main__.example_3[3]>", line 1, in <module>
> r.png(filename='"%s"'%filename)###line 335:
> sage: r.png(filename='"%s"'%filename)
> raise RuntimeError, "R was not compiled with PNG support"
> RuntimeError: R was not compiled with PNG support
> **********************************************************************
>
> That was just the first error; I think the (many!) others all stem from the PNG
> support problem. It looks like #7665 is to blame. (Based on the title of
> the ticket, I haven't checked anything...)
Do you have /usr/include/X11/Xwindows.h ? That is what the spkg-
install uses as a check for whether to build R with PNG support. Note
that R should work well otherwise, just that the graphics won't
work.
David Kirkby added a check on Solaris for /usr/X11/lib/libXv.so as
well (on Mac we use Aqua for graphics support). I know nothing about
how Linux actually does things, just that R compiles graphics support
if you use the flag --with-x=YES, which we (so far) only include on
non-Mac systems if there is something indicating support for it.
- kcrisman
Rob Beezer
(50 to 100), though most said "# 0 doctests failed"
This was on 64-bit Ubuntu 9.10 on Intel Core 2 Duo doing make
ptestlong
I haven't had time to poke around in the log itself yet.
On Apr 29, 6:24 am, Dan Drake <dr...@kaist.edu> wrote:
> Here's what seems to be a real error:
>
> sage -t "devel/sage/sage/misc/latex.py"
> **********************************************************************
> File "/home/drake/s/sage-4.4.1.alpha2/devel/sage/sage/misc/latex.py",
> line 1207:
> sage: latex.extra_preamble()
> Expected:
> '\\usepackage{xypic}\n'
> Got:
> ''
> **********************************************************************
one.
Dan Drake
> It would be interesting to see what happens in your make log for R. Do
> you have /usr/include/X11/Xwindows.h ? That is what the spkg- install
> uses as a check for whether to build R with PNG support. Note that R
> should work well otherwise, just that the graphics won't work.
This was compiled on a server that doesn't have X installed.
I could attach the install log, but I doubt it would be helpful -- it
fails to find X, and keeps going as well as it can.
I'll try installing some X headers and reinstalling R.
Dan Drake
> Do you have /usr/include/X11/Xwindows.h ? That is what the spkg-
> install uses as a check for whether to build R with PNG support. Note
> that R should work well otherwise, just that the graphics won't
> work.
I checked another build of alpha2, this one on a regular desktop Ubuntu
machine, and it doesn't have Xwindows.h, although it does have X and
Gnome and so on. So that machine saw the same test failures as the
server machine.
There should be a better way to tell R to build with PNG support. It
seems like it shouldn't need to link in X libraries just to spit out a
PNG file.
Rob Beezer
significant or not.
These two long tests look new:
**********************************************************************
File "/sage/four-four-one-alpha2/devel/sage-main/sage/calculus/
riemann.pyx", line 490:
sage: m.riemann_map(1.3*I) # long time
Expected:
(-1.5610293963...+0.989694535737...j)
Got:
(-1.5610293964136881e-05+0.98969453573774413j)
**********************************************************************
File "/sage/four-four-one-alpha2/devel/sage-main/sage/calculus/
riemann.pyx", line 493:
sage: m.riemann_map(0.4) # long time
Expected:
(0.733242677182...+3.5076771462...j)
Got:
(0.73324267718245473+3.50767714634136e-06j)
**********************************************************************