sage-5.6.rc1 released

[Jeroen Demeyer]

Dear Sage lovers,

We're releasing Sage 5.6.rc1.

Source archive:

http://boxen.math.washington.edu/home/release/sage-5.6.rc1/sage-5.6.rc1.tar

Upgrade path:

http://boxen.math.washington.edu/home/release/sage-5.6.rc1/sage-5.6.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 156 tickets in this release. For details, see

http://boxen.math.washington.edu/home/release/sage-5.6.rc1/tickets.html

Closed tickets:

#7773: Test failures with Fedora 12 on intel i7 860 processor [Reviewed
by Paul Zimmermann]
#9168: cygwin: ratpoints does not work correctly [Reviewed by
Karl-Dieter Crisman]
#9606: local/bin/sage-sage assumes 'sh' is bash [Reviewed by Leif
Leonhardy, John Palmieri, Stephen Montgomery-Smith]
#12401: Get Pynac functions to work on FreeBSD [Reviewed by Stephen
Montgomery-Smith]
#12411: pre-compiled Sage 4.8 binary fails some doctests on Ubuntu
[Reviewed by Paul Zimmermann]
#13866: Volker Braun: Experimental gdb spkg [Reviewed by Jeroen Demeyer]

Merged in sage-5.6.rc1:

#13561: Keshav Kini, Jeroen Demeyer: Supply nice error message when
starting $SAGE_ROOT/sage without compiling Sage first [Reviewed by
Jeroen Demeyer, Punarbasu Purkayastha]
#13945: John Palmieri: testcflags.sh leaves a directory in spkg/build
[Reviewed by Jeroen Demeyer]
#13952: Punarbasu Purkayastha: Add documentation about importing cython
function from cells [Reviewed by André Apitzsch]
#13959: Volker Braun: Parse wonky "top" output on OSX PPC [Reviewed by
Karl-Dieter Crisman]

[John Cremona]

Built fine and all tests pass on ubuntu 64-bit.

John

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[John H Palmieri]

On Saturday, January 19, 2013 6:20:19 AM UTC-8, Jeroen Demeyer wrote:

Dear Sage lovers,

We're releasing Sage 5.6.rc1.

OS X 10.8.2. I just noticed the following, although now that I check, it seems to have been happening for a while. While building the Sage library spkg, I see some lines like this:

gcc -fno-strict-aliasing -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/palmieri/Desktop/Sage_stuff/sage_builds/clean/sage-5.6.rc1/local/include -I/Users/palmieri/Desktop/Sage_stuff/sage_builds/clean/sage-5.6.rc1/local/include/csage -I/Users/palmieri/Desktop/Sage_stuff/sage_builds/clean/sage-5.6.rc1/devel/sage/sage/ext -I/Users/palmieri/Desktop/Sage_stuff/sage_builds/clean/sage-5.6.rc1/local/include/python2.7 -c sage/libs/linbox/linbox.cpp -o build/temp.macosx-10.8-x86_64-2.7/sage/libs/linbox/linbox.o -D__STDC_LIMIT_MACROS -w -w -w -w -w -w -w -w -w -w -w -w

All of those "-w"s at the end look very odd to me. Is their presence indicative of a problem?

--
John

[Volker Braun]

I've noticed that before. Its been with us for a while. I don't know where the extra -w come from, but they don't hurt.

[Volker Braun]

From setup.py:

if NO_WARN and distutils.sysconfig.get_config_var('CC').startswith("gcc"):

    extra_compile_args.append('-w')

Now "import setup" multiple times and you get -w -w -w -w ... ;-)

[Dima Pasechnik]

On 2013-01-19, Jeroen Demeyer <jdem...@cage.ugent.be> wrote:
> Dear Sage lovers,
>
> We're releasing Sage 5.6.rc1.
>
> Source archive:
>
> http://boxen.math.washington.edu/home/release/sage-5.6.rc1/sage-5.6.rc1.tar
>
> Upgrade path:
>
> http://boxen.math.washington.edu/home/release/sage-5.6.rc1/sage-5.6.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.

there is a serious sagenb bug:
http://permalink.gmane.org/gmane.comp.mathematics.sage.devel/64045

Dima

[Ivan Andrus]

Built and all tests passed (with SAGE_DEBUG empty) on OS X 10.8.2

-Ivan

[Jeroen Demeyer]

On 2013-01-20 07:34, Dima Pasechnik wrote:
> there is a serious sagenb bug:
> http://permalink.gmane.org/gmane.comp.mathematics.sage.devel/64045

Since the bug isn't new and is already fixed in a later sagenb release,
I propose to release sage-5.6 now (with the bug) and fix it in the
sage-5.7 release series (assuming that #13717 gets positive review).

Jeroen.

[leif]

Volker Braun wrote:
> From setup.py:
>
> if NO_WARN and distutils.sysconfig.get_config_var('CC').startswith("gcc"):
> extra_compile_args.append('-w')
>
> Now "import setup" multiple times and you get -w -w -w -w ... ;-)

Aha. I also noticed the '-w's a while ago, but actually thought someone
****** was trying to make absolutely^N sure (by explicitly adding them
in module_list.py) that no warnings will ever be shown... ;-)

(Note that they always occur in conjunction with '-D__STDC_LIMIT_MACROS'.)


-leif

> On Saturday, January 19, 2013 10:11:04 PM UTC, Volker Braun wrote:
>
> I've noticed that before. Its been with us for a while. I don't know
> where the extra -w come from, but they don't hurt.
>
>
> On Saturday, January 19, 2013 10:00:14 PM UTC, John H Palmieri wrote:
>
> gcc -fno-strict-aliasing -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall
> -Wstrict-prototypes
> -I/Users/palmieri/Desktop/Sage_stuff/sage_builds/clean/sage-5.6.rc1/local/include
> -I/Users/palmieri/Desktop/Sage_stuff/sage_builds/clean/sage-5.6.rc1/local/include/csage
> -I/Users/palmieri/Desktop/Sage_stuff/sage_builds/clean/sage-5.6.rc1/devel/sage/sage/ext
> -I/Users/palmieri/Desktop/Sage_stuff/sage_builds/clean/sage-5.6.rc1/local/include/python2.7
> -c sage/libs/linbox/linbox.cpp -o
> build/temp.macosx-10.8-x86_64-2.7/sage/libs/linbox/linbox.o
> -D__STDC_LIMIT_MACROS -w -w -w -w -w -w -w -w -w -w -w -w
>

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[Robert Bradshaw]

I'm getting

The following tests failed:


./devel/sage-0/tests/cmdline.py # File not found
Total time for all tests: 0.0 seconds
patchbot@pi:/data/sage/sage-5.6.rc1$ ./sage -t
devel/sage-0/sage/tests/cmdline.py
sage -t "devel/sage-0/sage/tests/cmdline.py"
**********************************************************************
File "/data/sage/sage-5.6.rc1/devel/sage-0/sage/tests/cmdline.py", line 347:
sage: print err
Expected:
Traceback (most recent call last):
...
RuntimeError: refusing to run doctests...
Got:
<BLANKLINE>
**********************************************************************
File "/data/sage/sage-5.6.rc1/devel/sage-0/sage/tests/cmdline.py", line 352:
sage: print err
Expected:
Traceback (most recent call last):
...
RuntimeError: refusing to run doctests...
Got:
Traceback (most recent call last):
File "/data/sage/sage-5.6.rc1/local/bin/sage-ptest", line 445, in <module>
p = multiprocessing.Pool(numthreads)
File "/data/sage/sage-5.6.rc1/local/lib/python2.7/multiprocessing/__init__.py",
line 232, in Pool
return Pool(processes, initializer, initargs, maxtasksperchild)
File "/data/sage/sage-5.6.rc1/local/lib/python2.7/multiprocessing/pool.py",
line 129, in __init__
raise ValueError("Number of processes must be at least 1")
ValueError: Number of processes must be at least 1
<BLANKLINE>
**********************************************************************
1 items had failures:
2 of 203 in __main__.example_1
***Test Failed*** 2 failures.
For whitespace errors, see the file /home/patchbot/.sage//tmp/cmdline_13352.py
[28.6 s]

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


http://patchbot.sagemath.org/log/0/debian/wheezy/sid/x86_64/3.5.0-17-generic/pi/2013-01-21%2017:16:00%20-0800?short

[Jeroen Demeyer]

Is this error new? Because it would seem strange to me that it's
something which happened in .rc1 that caused it.

I need some data about your Sage installation:
$ umask
$ id
$ ls -ld $SAGE_LOCAL
$ ls -ld $SAGE_LOCAL/bin/python*
$ ls -ld $DOT_SAGE/tmp/`hostname`/

[Justin C. Walker]

On Jan 19, 2013, at 06:20 , Jeroen Demeyer wrote:

> Dear Sage lovers,
>
> We're releasing Sage 5.6.rc1.
>
> Source archive:
>
> http://boxen.math.washington.edu/home/release/sage-5.6.rc1/sage-5.6.rc1.tar

Built w/o problems and all tests ('ptestlong') passeed on Mac OS X, both 10.6.8 (Dual 6-core Xeons) and 10.8.2 (Quad-core Core i7).

Justin

--
Justin C. Walker, Curmudgeon at Large
Institute for the Absorption of Federal Funds
-----------
I want to die, peacefully in my sleep, like my grandfather;
not screaming in terror, like his passengers.

[strogdon]

I have this one failure that I've not been able to reproduce, but it's there once; perhaps due to parallel testing? I see nothing in rc1 that could potentially cause this.

sage -t -long  -force_lib devel/sage-main/sage/schemes/plane_curves/curve.py

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

File "/storage/sage/sage-5.6.rc1/devel/sage-main/sage/schemes/plane_curves/curve.py", line 122:

    sage: C.geometric_genus()

Exception raised:

    Traceback (most recent call last):

      File "/storage/sage/sage-5.6.rc1/local/bin/ncadoctest.py", line 1231, in run_one_test

        self.run_one_example(test, example, filename, compileflags)

      File "/storage/sage/sage-5.6.rc1/local/bin/sagedoctest.py", line 38, in run_one_example

        OrigDocTestRunner.run_one_example(self, test, example, filename, compileflags)

      File "/storage/sage/sage-5.6.rc1/local/bin/ncadoctest.py", line 1172, in run_one_example

        compileflags, 1) in test.globs

      File "<doctest __main__.example_6[9]>", line 1, in <module>

        C.geometric_genus()###line 122:

    sage: C.geometric_genus()

      File "/storage/sage/sage-5.6.rc1/local/lib/python/site-packages/sage/schemes/plane_curves/curve.py", line 141, in geometric_genus

        self.__genus = self.defining_ideal().genus()

      File "/storage/sage/sage-5.6.rc1/local/lib/python/site-packages/sage/rings/polynomial/multi_polynomial_ideal.py", line 602, in __call__

        return self.f(self._instance, *args, **kwds)

      File "/storage/sage/sage-5.6.rc1/local/lib/python/site-packages/sage/rings/polynomial/multi_polynomial_ideal.py", line 1745, in genus

        self.__genus = Integer(genus(self))

      File "function.pyx", line 1252, in sage.libs.singular.function.SingularFunction.__call__ (sage/libs/singular/function.cpp:12258)

      File "function.pyx", line 1441, in sage.libs.singular.function.call_function (sage/libs/singular/function.cpp:13811)

    RuntimeError: Error in Singular function call 'genus':

     delta not found, please inform the authors

     leaving normal.lib::deltaP

     leaving normal.lib::genus

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

[Jeroen Demeyer]

On 2013-01-23 22:06, strogdon wrote:
> I have this one failure that I've not been able to reproduce, but it's
> there once; perhaps due to parallel testing? I see nothing in rc1 that
> could potentially cause this.

I have seen it also sometimes. It's one of these bugs which seem to
happen randomly sometimes. If somebody feels like further investigating
and possibly report this upstream, go ahead...

[Kannappan Sampath]

I am not being specific here, but looking at the installation process run through on my terminal, I see a whole bunch of "local variable referenced before assignment" error... Is this common and we don't fix them (asking this because, some files seem to be from old Sage...) 

Sorry for this newbie question. 

Thank you. 

[Francois Bissey]

On 20/01/13 10:50, Kannappan Sampath wrote:
> I am not being specific here, but looking at the installation process
> run through on my terminal, I see a whole bunch of "local variable
> referenced before assignment" error... Is this common and we don't fix
> them (asking this because, some files seem to be from old Sage...)
>
> Sorry for this newbie question.
>

There is a ticket somewhere about fixing them. It will come one day.
There was a change in behavior in cython sometime ago that started this.
Because there are no fatal errors it has been quite low priority.

Francois

[Dima Pasechnik]

On Sunday, 20 January 2013 06:14:10 UTC+8, Volker Braun wrote:

From setup.py:

if NO_WARN and distutils.sysconfig.get_config_var('CC').startswith("gcc"):

    extra_compile_args.append('-w')

Now "import setup" multiple times and you get -w -w -w -w ... ;-)

normally this should not happen, i.e. python modules are not imported twice. E.g.

$ cat bla

blah.py   blah.pyc  

nash:tmp dima$ cat blah.py

print "blah"

$ python

Python 2.6.1 (r261:67515, Jun 24 2010, 21:47:49) 

[GCC 4.2.1 (Apple Inc. build 5646)] on darwin

Type "help", "copyright", "credits" or "license" for more information.

>>> import blah

blah

>>> import blah

>>> import blah

>>> 

 

This could only happen if an exception is thrown during the import - does this indicate that there is a bug somewhere

in the module that gets suppressed?

Dima

[Volker Braun]

I haven't tried to trace it down, but reload(blah) would also do the trick for example.