sage-5.4.rc1 released

[Jeroen Demeyer]

Dear Sage lovers,

We're releasing Sage 5.4.rc1.

Source archive:

http://boxen.math.washington.edu/home/release/sage-5.4.rc1/sage-5.4.rc1.tar

Upgrade path:

http://boxen.math.washington.edu/home/release/sage-5.4.rc1/sage-5.4.rc1/

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 113 tickets in this release. For details, see

http://boxen.math.washington.edu/home/release/sage-5.4.rc1/tickets.html

Closed tickets:

#3302: python_gnutls fails to upgrade on OSX in case Sage was moved
[Reviewed by Jeroen Demeyer]
#4797: Run sage -ba instead of sage -b after upgrading Cython [Reviewed
by Jeroen Demeyer]
#7511: gnutls-2.2.1 fails to build on HP-UX [Reviewed by Jeroen Demeyer]
#7542: Security issues in gnutls-2.2.1 [Reviewed by Jeroen Demeyer]
#8437: wrong unix rights/permissions of some files after make dist
[Reviewed by Jeroen Demeyer]
#9308: Add an spkg-check file for GnuTLS [Reviewed by David Kirkby,
Jeroen Demeyer]
#9974: The current (rather old) version of GnuTLS fails to install on
AIX 5.3 [Reviewed by Jeroen Demeyer]
#9975: Update GnuTLS and clean up the package [Reviewed by Mariah
Lenox, Jeroen Demeyer]
#10624: Slashes disappear in docstrings [Reviewed by John Palmieri]
#12331: updating an spkg may render Sage non-relocatable [Reviewed by
Jeroen Demeyer]
#12785: update the faq: no need for gfortran... [Reviewed by Jeroen Demeyer]
#13545: Can't create a symbolic variable named 'lambda' [Reviewed by
Nils Bruin, Burcin Erocal]
#13551: Autotools spkg does not build correctly on systems without
autotools installed [Reviewed by Jeroen Demeyer]

Merged in sage-5.4.rc1:

#13512: Francis Clarke: Docstring formatting in misc_c.pyx [Reviewed by
Jeroen Demeyer]
#13537: Julian Rueth: Stopgap for 13439 [Reviewed by Volker Braun]
#13544: John Palmieri: Omit .DS_Store when building 'all' documentation
[Reviewed by Michael Welsh]

[John Cremona]

I had one test failure in "make testlong" (not ptestlong), which was
OK on a rerun:

sage -t --long -force_lib "devel/sage/sage/combinat/words/words.py"
Traceback (most recent call last):
File "/home/jec/.sage//tmp/words_25201.py", line 6, in <module>
from sage.all_cmdline import *;
File "/home/jec/sage-5.4.rc1/local/lib/python/site-packages/sage/all_cmdline.py",
line 14, in <module>
from sage.all import *
File "/home/jec/sage-5.4.rc1/local/lib/python/site-packages/sage/all.py",
line 66, in <module>
from sage.misc.all import * # takes a while
File "/home/jec/sage-5.4.rc1/local/lib/python/site-packages/sage/misc/all.py",
line 1, in <module>
from misc import (alarm, ellipsis_range, ellipsis_iter, srange,
xsrange, sxrange, getitem,
File "/home/jec/sage-5.4.rc1/local/lib/python/site-packages/sage/misc/misc.py",
line 157, in <module>
sage_makedirs(SAGE_TMP_INTERFACE)
File "/home/jec/sage-5.4.rc1/local/lib/python/site-packages/sage/misc/misc.py",
line 74, in sage_makedirs
os.makedirs(dir)
File "/home/jec/sage-5.4.rc1/local/lib/python2.7/os.py", line 157, in makedirs
mkdir(name, mode)
OSError: [Errno 13] Permission denied:
'/home/jec/.sage//temp/fermat/25207//interface/'

John

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[Justin C. Walker]

On Oct 6, 2012, at 13:40 , Jeroen Demeyer <jdem...@cage.ugent.be> wrote:

Dear Sage lovers,

We're releasing Sage 5.4.rc1.

Source archive:

http://boxen.math.washington.edu/home/release/sage-5.4.rc1/sage-5.4.rc1.tar

Built from scratch on two Mac OS X systems:

10.6.8 (Duel 6-core Xeons): built w/o problems, all tests passed.

10.8.2 (Quad-core Core i7): built w/o problems, all tests passed.

On 10.8, I installed scipy-0.11.0.log and trac_13541-doctest.patch (the build fails w/o both).

Justin

--

Justin C. Walker, Curmudgeon at Large

Institute for the Absorption of Federal Funds

-----------

If it weren't for carbon-14, I wouldn't date at all.

-----------

[kcrisman]

On Monday, October 15, 2012 2:49:41 PM UTC-4, Paul-Olivier Dehaye wrote:

For me, on a 10.8.2, I get the following error

Found package flint-1.5.2.p1 in spkg/standard/flint-1.5.2.p1.spkg

flint-1.5.2.p1

====================================================

Extracting package /Users/pdehaye/Software/sage-5.4.rc1/spkg/standard/flint-1.5.2.p1.spkg

-rw-r--r--@ 1 pdehaye  staff  815921 Sep  8 14:47 /Users/pdehaye/Software/sage-5.4.rc1/spkg/standard/flint-1.5.2.p1.spkg

flint-1.5.2.p1/src/zn_poly/demo/bernoulli/.DS_Store: Can't create 'flint-1.5.2.p1/src/zn_poly/demo/bernoulli/.DS_Store'

tar: Error exit delayed from previous errors.

Error: failed to extract /Users/pdehaye/Software/sage-5.4.rc1/spkg/standard/flint-1.5.2.p1.spkg

Confirmed that it's in the current (Sage 5.3) source as well.

GC04855:~ $ cd Downloads/flint-1.5.2.p1\ 2/

GC04855:flint-1.5.2.p1 2 $ ls src/zn_poly/demo/bernoulli/

bernoulli.c

GC04855:flint-1.5.2.p1 2 $ ls -a src/zn_poly/demo/bernoulli/

. .. .DS_Store bernoulli.c

GC04855:flint-1.5.2.p1 2 $ 

 

Jeroen, would you consider removing this a blocker?  Just curious. I sure hope it wasn't a file I contributed... those things are so hard to catch sometimes, we should almost have sage-pkg grep for them and throw an error if they are present.

[Jeroen Demeyer]

On 2012-10-15 22:23, kcrisman wrote:
> Jeroen, would you consider removing this a blocker? Just curious. I
> sure hope it wasn't a file I contributed... those things are so hard to
> catch sometimes, we should almost have sage-pkg grep for them and throw
> an error if they are present.

In the upstream tarball, there is a ._.DS_Store file in the same place,
Sage has a .DS_Store file (note the subtle difference!).

I could easily change the merger script to remove these files if wanted.

Note they are in rpy2 and sympy also:

flint/src/zn_poly/demo/bernoulli/.DS_Store
rpy2/src/.DS_Store
sympy/src/doc/.DS_Store
sympy/src/doc/src/.DS_Store
sympy/src/doc/src/modules/.DS_Store
sympy/src/doc/src/modules/mpmath/.DS_Store

[Jeroen Demeyer]

On 2012-10-15 22:23, kcrisman wrote:

> we should almost have sage-pkg grep for them and throw
> an error if they are present.

There actually is some code in sage-pkg to remove those .DS_Store files,
but it obviously doesn't work.

[Michael Welsh]

On 16/10/2012, at 9:38 AM, Jeroen Demeyer <jdem...@cage.ugent.be> wrote:
>
> I could easily change the merger script to remove these files if wanted.

It's a good idea. They're just OS X files that store how a folder is displayed in the file manager.

[Jeroen Demeyer]

On 2012-10-15 22:23, kcrisman wrote:

> Jeroen, would you consider removing this a blocker?

I don't see why this would be a blocker. That being said, if you put a
ticket up, make new spkgs and get it reviewed soon enough, I wouldn't
mind merging it in sage-5.4. But only because it is a small innocent
patch, not something which absolutely must be fixed.

[John H Palmieri]

It might work on Linux or Solaris, but I don't think the relevant code gets executed on OS X, which somewhat defeats its purpose.

--
John

[Paul-Olivier Dehaye]

Turns out #9697 was a similar problem. I posted the modified spkg
there, it should be ready for review.
http://trac.sagemath.org/sage_trac/ticket/9697
Paul

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[kcrisman]

If you happen to open a ticket for this, cc: me.  I'm not sure I can write it (quickly) but I would be quite interested in reviewing it, since I've done this at least a half-dozen times by accident :( 

[kcrisman]

Oh, I thought that pdeyahe was implying this broke building on OS X 10.8. I guess it's been there a while... maybe just with a recently updated Mountain Lion?

[John H Palmieri]

I've been building on Mountain Lion for a week or two, and I haven't seen this.

--
John
 

[Paul-Olivier Dehaye]

Same for me, it occurs on one machine but not the other.
I hit problems on all three spkgs with .DS_Store, one after the other
(flint, srpy2, sympy). Strangely, the spkg is unpacked without beging
able to create those .DS_Store, and that s what's causing the error.
Also, scipy does not build, see my question on sage-devel.
Paul

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[Jeroen Demeyer]

On 2012-10-16 02:39, kcrisman wrote:
> Oh, I thought that pdeyahe was implying this broke building on OS X
> 10.8.

...which is a platform on which building Sage is broken anyway.
Similarly, not every bug which breaks building on Cygwin should be a
blocker.

It looks likely that Mountain Lion will be supported for Sage-5.5, so
then it could be a blocker for that release.

[Ivan Andrus]

The darwin branch uses COPYFILE_DISABLE instead of excluding it. I ran across this page [1] the other day which indicates that COPYFILE_DISABLE may not work any longer (no date so I'm not sure since when). And in fact it doesn't prevent tarring .DS_STORE files on my Snow Leopard machine. But maybe it's only supposed to prevent ._* files.

-Ivan

[1] http://drmuey.com/?do=page&id=15

[kcrisman]

Okay, that makes sense, thanks for the clarification.