Sage 6.8.beta7 released

[Volker Braun]

As always, you can get the latest beta version from the "develop" git branch. Alternatively, the self-contained source tarball is at http://www.sagemath.org/download-latest.html

6bc31bda Updated Sage version to 6.8.beta7

4e24d02 Trac #18837: module_list.py: remove foo_depends variables

509df17 Trac #18833: Clean up cliquer library interface

146ea48 Trac #17392: Make list of built-in normal form games

bfd679b Trac #18830: implement Lovasz theta-function for graphs

552767d Trac #18825: cython() command does not find ginac_wrap.h

54e5a89 Trac #18815: Polyhedron.to_linear_program

c649ee5 Trac #18811: Boost Clustering Coefficient

86c2ae7 Trac #17574: Empty hypergraph and __str__ function

da114f1 Trac #18820: Upgrade R to 3.2.1

47b1c3b Trac #18768: Change name of InfinityPathModel

8044966 Trac #15412: Simplify cythonization of sage/combinat.

525be4e Trac #15410: Simplify cythonization of many sage extensions.

938dae7 Trac #18159: cardinality must output Infinty or a Sage integer

73ef972 Trac #17392: Make list of built-in normal form games

1074230 Trac #18827: new style packaging for csdp

4aab354 Trac #18746: Cutwidth of a graph

ed3845f Trac #18823: make all: build Sage library only once

41276f7 Trac #18817: adding some missing links to trac in the doc

8c0effb Trac #13158: Local components bug finding minimal twist

7698e99 Trac #18809: Undo suspicious isinstance() changes from #15984

53a8e1c Trac #18662: Implement (semi-)global minimal models for elliptic curves over number fields with h>1

756eca1 Trac #18626: fix gap_packages (Guava) optional tests

1b129b4 Trac #18612: Y-axis labels on matrix_plot are reversed.

d765a12 Trac #18710: Move some make targets to build/Makefile

ea47c03 Trac #4606: elliptic curves -- implement gross-Zagier L-functions

c5e67a9 Trac #18803: Upgrade to IPython 3.2

c9adb78 Trac #18689: GAP 4.7.8

37bc05d Trac #18747: ascii and unicode arts for continued fractions

be7ed05 Trac #18592: Changing some .next() to next(...)

1cb09ca Trac #18577: Extend MathJax MAXBUFFER to allow larger equations to be displayed

c9eb473 Trac #18790: Update MPIR to 2.7.0

0045e4f Trac #18792: side effect from Pari verbose mechanism in factor()

f056068 Trac #18772: Completely remove in-place operations

a265460 Trac #18794: StandardError is not Python 3 compatible

11e6e08 Trac #18793: Make sage_setup/autogen/pari Python 3 compatible

cabec5b Trac #18670: Use abs() to test for accuracy of roots of complex-valued functions

fde55bb Trac #18167: Ref: add various missing modules to r/schemes and r/plane_curves

3c70018 Trac #18785: chang graphs

347d797 Trac #18774: Janko Groups and Livingstone graph

c0e7217 Updated Sage version to 6.8.beta6

[Daniel Krenn]

Getting an error; started in a new directory; cloned git-repo; checkout
6.8.beta7, make
This was on current Debian stable.

tail of log below. It is during the building of the documentation
(second pass).

Best,

Daniel

[reference] stats: 665 js index entries
[reference] structure: 2491 js index entries
[reference] tensor: 278 js index entries
[reference] tensor_free_modules: 889 js index entries
[reference] ... done (37981 js index entries)
[reference] Writing js search indexes... genindex py-modindex search
[reference] WARNING: html_static_path entry
'/local/data/krenn/sage/6.8.beta7/local/lib/python2.7/site-packages/sagenb-0.11.4-py2.7.egg/sagenb/data/mathjax'
does not exist
Error building the documentation.
Traceback (most recent call last):
File "/local/data/krenn/sage/6.8.beta7/src/doc/common/builder.py",
line 1626, in <module>
getattr(get_builder(name), type)()
File "/local/data/krenn/sage/6.8.beta7/src/doc/common/builder.py",
line 296, in _wrapper
getattr(get_builder(document), name)(*args, **kwds)
File "/local/data/krenn/sage/6.8.beta7/src/doc/common/builder.py",
line 516, in _wrapper
getattr(DocBuilder(self.name, lang), format)(*args, **kwds)
File "/local/data/krenn/sage/6.8.beta7/src/doc/common/builder.py",
line 110, in f
eval(compile(open(sys.argv[0]).read(), sys.argv[0], 'exec'))
File
"/local/data/krenn/sage/6.8.beta7/src/doc/common/custom-sphinx-build.py", line
219, in <module>
raise OSError(ERROR_MESSAGE)
OSError: [reference] WARNING: html_static_path entry
'/local/data/krenn/sage/6.8.beta7/local/lib/python2.7/site-packages/sagenb-0.11.4-py2.7.egg/sagenb/data/mathjax'
does not exist

make[2]: *** [doc-html] Fehler 1
make[2]: Leaving directory `/local/data/krenn/sage/6.8.beta7/build'
make[1]: *** [all] Fehler 2
make[1]: Leaving directory `/local/data/krenn/sage/6.8.beta7/build'

real 141m5.476s
user 125m53.544s
sys 6m43.069s
***************************************************************
Error building Sage.

The following package(s) may have failed to build:

The build directory may contain configuration files and other potentially
helpful information. WARNING: if you now run 'make' again, the build
directory will, by default, be deleted. Set the environment variable
SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this.

[Volker Braun]

This is now http://trac.sagemath.org/ticket/18850

[Jean-Pierre Flori]

When running on a ppc64 machine, I get:
sage -t --warn-long 97.8 src/sage/graphs/distances_all_pairs.pyx
**********************************************************************
File "src/sage/graphs/distances_all_pairs.pyx", line 1205, in sage.graphs.distances_all_pairs.diameter
Failed example:
    G.diameter(method='iFUB')
Expected:
    0
Got:
    Exception OverflowError: 'value too large to convert to uint32_t' in 'sage.graphs.distances_all_pairs.diameter_iFUB' ignored
    0
**********************************************************************
1 item had failures:
   1 of  17 in sage.graphs.distances_all_pairs.diameter
    [68 tests, 1 failure, 0.32 s]

[Nathann Cohen]

> When running on a ppc64 machine, I get:
> sage -t --warn-long 97.8 src/sage/graphs/distances_all_pairs.pyx
> **********************************************************************
> File "src/sage/graphs/distances_all_pairs.pyx", line 1205, in
> sage.graphs.distances_all_pairs.diameter
> Failed example:
> G.diameter(method='iFUB')
> Expected:
> 0
> Got:
> Exception OverflowError: 'value too large to convert to uint32_t' in
> 'sage.graphs.distances_all_pairs.diameter_iFUB' ignored
> 0
> **********************************************************************

Odd. This line computes the diameter of a 1-vertex graph O_o

Nathann

[John H Palmieri]

A doctest error:

sage -t --long --warn-long 49.8 src/sage/structure/dynamic_class.py
**********************************************************************
File "src/sage/structure/dynamic_class.py", line 354, in sage.structure.dynamic_class.dynamic_class_internal
Failed example:
    inspect.getfile(Foo2)
Expected:
    '.../sage/structure/dynamic_class.pyc'
Got:
    '/Users/palmieri/Desktop/Sage_stuff/git/sage/local/lib/python2.7/site-packages/sage/structure/dynamic_class.py'
**********************************************************************
File "src/sage/structure/dynamic_class.py", line 356, in sage.structure.dynamic_class.dynamic_class_internal
Failed example:
    inspect.getfile(Foo3)
Expected:
    '.../sage/structure/dynamic_class.pyc'
Got:
    '/Users/palmieri/Desktop/Sage_stuff/git/sage/local/lib/python2.7/site-packages/sage/structure/dynamic_class.py'

**********************************************************************
1 item had failures:

   2 of  20 in sage.structure.dynamic_class.dynamic_class_internal
    [69 tests, 2 failures, 0.33 s]

This file passes when tested on its own. This was also reported by another user at #18835, although it has nothing to do with that ticket.

  John

[Jean-Pierre Flori]

Indeed, and the issue is fixed there.
It should be in next beta.

[Dima Pasechnik]

Mirrors crap:

build failed as the network went down; restarting resulted in build completing, but it did not build a number of packages.
If I try to reinstall them, I get

IOError: [Errno 404] Not Found: '//www.mirrorservice.org/sites/www.sagemath.org//spkg/archive/list'
Error: failed to download http://www.mirrorservice.org/sites/www.sagemath.org//spkg/archive/list, aborting

e.g.:

$ sage -f hg
Attempting to download package hg
>>> Checking online list of optional packages.
>>> Checking online list of experimental packages.
>>> Checking online list of standard packages.
>>> Checking online list of huge packages.
>>> Checking online list of archive packages.

Traceback (most recent call last):

  File "/home/dima/software/sage/src/bin/sage-download-file", line 453, in <module>
    http_download(url, destination, progress=progress, ignore_errors=True)
  File "/home/dima/software/sage/src/bin/sage-download-file", line 132, in http_download
    filename, info = opener.retrieve(url, destination)
  File "/home/dima/software/sage/local/lib/python/urllib.py", line 245, in retrieve
    fp = self.open(url, data)
  File "/home/dima/software/sage/local/lib/python/urllib.py", line 213, in open
    return getattr(self, name)(url)
  File "/home/dima/software/sage/local/lib/python/urllib.py", line 364, in open_http
    return self.http_error(url, fp, errcode, errmsg, headers)
  File "/home/dima/software/sage/local/lib/python/urllib.py", line 381, in http_error
    return self.http_error_default(url, fp, errcode, errmsg, headers)
  File "/home/dima/software/sage/src/bin/sage-download-file", line 51, in http_error_default
    raise IOError(errcode, errmsg, url)
IOError: [Errno 404] Not Found: '//www.mirrorservice.org/sites/www.sagemath.org//spkg/archive/list'


Apparently this mirror is not in good shape, and no attempt is made to fix this.
Is there a way to reset the mirrors?

[Nathann Cohen]

> If I try to reinstall them, I get

> ...

> IOError: [Errno 404] Not Found:
> '//www.mirrorservice.org/sites/www.sagemath.org//spkg/archive/list'
>
>
> Apparently this mirror is not in good shape, and no attempt is made to fix
> this.
> Is there a way to reset the mirrors?

This very mirror is not at fault: during the recent host changes the
'archive' packages were removed from the mirrors. There remains one
copy of that folder at this address:
http://old.files.sagemath.org/spkg/archive/

The problem is that Sage is not aware of it, and keeps looking for
those files at the old url.

Nathann

[Volker Braun]

You might have a corrupted copy of the mirror list; There is http://trac.sagemath.org/ticket/18748 (needs review) which improves the handling of network errors, can you give it a try?

[Dima Pasechnik]

Actually, did we ever have an hg spkg?!

There was/is mercurial spkg for sure...

It looks like I have a stale list of (pseudo)packages - perhaps each call to "sage -i blah" duly puts "blah" on the list ?!


This is how the log of that ill-fated build ends:
---------------------------------------------------------------------------------------------------------

The following package(s) may have failed to build:

package: hg
log file: /home/dima/software/sage/logs/pkgs/hg.log
build directory: /home/dima/software/sage/local/var/tmp/sage/build/hg

package: pyopenssl
log file: /home/dima/software/sage/logs/pkgs/pyopenssl.log
build directory: /home/dima/software/sage/local/var/tmp/sage/build/pyopenssl

package: pyssl
log file: /home/dima/software/sage/logs/pkgs/pyssl.log
build directory: /home/dima/software/sage/local/var/tmp/sage/build/pyssl

package: ssl
log file: /home/dima/software/sage/logs/pkgs/ssl.log
build directory: /home/dima/software/sage/local/var/tmp/sage/build/ssl

The build directory may contain configuration files and other potentially
helpful information. WARNING: if you now run 'make' again, the build
directory will, by default, be deleted. Set the environment variable
SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this.

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

Dima

[Nathann Cohen]

Helloooooo !

> It looks like I have a stale list of (pseudo)packages - perhaps each call to
> "sage -i blah" duly puts "blah" on the list ?!

It seems to be something like that: the message that you see which
reports which packages may have 'failed to build' is generated by the
script build/install.

How do you think is guesses which packages failed to build? Well, it
looks for log files which contain the word "error" (line 502 of
build/install).

So if you have a file in SAGE_LOGS/ which contains the word 'error',
it will appear on that list.

And you do not want to see mine, it is incredibly long.

Nathann

[Justin C. Walker]

> On Jul 2, 2015, at 16:40, Volker Braun <vbrau...@gmail.com> wrote:
>
> As always, you can get the latest beta version from the "develop" git branch. Alternatively, the self-contained source tarball is at http://www.sagemath.org/download-latest.html

Built from tarball on OS X, 10.10.4 (Quad-core Core i7, with command line tools 6.4). Build and testing (‘ptestlong’) completed successfully!

--
Justin C. Walker, Curmudgeon-At-Large, Director
Institute for the Enhancement of the Director's Income
--------
The path of least resistance:
it's not just for electricity any more.
--------

[Dima Pasechnik]

should the script check whether these packages are real Sage packages, and dub these that are not there
"custom" packages? Otherwise it's very confusing...

So the question is where to look for these lists...

Nathann

[Vincent Knight]

Apologies if I'm missing something and this has been reported before.

`./sage -bt src/sage/game_theory` and `sage -bt --optional=all
src/sage/game_theory` both give:

```
...
Git branch: develop
Doctesting 10 files.

Traceback (most recent call last):

File "/Users/vince/sage/src/bin/sage-runtests", line 88, in <module>
err = DC.run()
File "/Users/vince/sage/local/lib/python2.7/site-packages/sage/doctest/control.py",
line 1038, in run
self.run_doctests()
File "/Users/vince/sage/local/lib/python2.7/site-packages/sage/doctest/control.py",
line 759, in run_doctests
self.dispatcher = DocTestDispatcher(self)
File "/Users/vince/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py",
line 1376, in __init__
init_sage()
File "/Users/vince/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py",
line 125, in init_sage
from sympy.printing.pretty.stringpict import stringPict
ImportError: No module named sympy.printing.pretty.stringpict
```

Mac OSX.

Apologies also if I'm missing details that could be helpful.

Vince

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--
Dr Vincent Knight
Cardiff School of Mathematics
Senghennydd Road,
Cardiff
CF24 4AG
(+44) 29 2087 5548
www.vincent-knight.com
+Vincent Knight
@drvinceknight
Skype: drvinceknight

[Vincent Knight]

On 4 July 2015 at 22:19, Vincent Knight <knig...@cf.ac.uk> wrote:
> Apologies if I'm missing something and this has been reported before.
>
> `./sage -bt src/sage/game_theory` and `sage -bt --optional=all
> src/sage/game_theory` both give:
>
> ```
> ...
> Git branch: develop
> Doctesting 10 files.
> Traceback (most recent call last):
> File "/Users/vince/sage/src/bin/sage-runtests", line 88, in <module>
> err = DC.run()
> File "/Users/vince/sage/local/lib/python2.7/site-packages/sage/doctest/control.py",
> line 1038, in run
> self.run_doctests()
> File "/Users/vince/sage/local/lib/python2.7/site-packages/sage/doctest/control.py",
> line 759, in run_doctests
> self.dispatcher = DocTestDispatcher(self)
> File "/Users/vince/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py",
> line 1376, in __init__
> init_sage()
> File "/Users/vince/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py",
> line 125, in init_sage
> from sympy.printing.pretty.stringpict import stringPict
> ImportError: No module named sympy.printing.pretty.stringpict
> ```
>
> Mac OSX.
>

This error does not reproduce on my Ubuntu box. (Tests run and pass there.)

Vince

[Volker Braun]

Looks like sympy wasn't installed correctly... can you look into the sympy logs? Maybe recompile if you don't remember how you got there?

[Vincent Knight]

On 4 Jul 2015 10:36 pm, "Volker Braun" <vbrau...@gmail.com> wrote:
>
> Looks like sympy wasn't installed correctly... can you look into the sympy logs? Maybe recompile if you don't remember how you got there?

I've turned in for the night (typing this on my tablet) but will get back to you as soon as I get a chance tomorrow.

On OSX I had time so ran:

```
make dist-clean
make
```

On Ubuntu:

```
make clean
make
```

If you could point out where the sympy logs would be I'll send them tomorrow before I recompile (or indeed throw any other instructions my way :)).

Vince

[Dima Pasechnik]

works for me (on Linux):
$ sage -bt src/sage/game_theory
python -u setup.py install
Updating Cython code....
Enabling Cython debugging support
Finished Cythonizing, time: 2.55 seconds.
Discovering Python source code....
Discovered Python source, time: 0.02 seconds.
Cleaning up stale installed files....
- cleaning /home/dima/software/sage/local/lib/python2.7/site-packages
- cleaning /home/dima/software/sage/local/lib/site-python
- cleaning /home/dima/software/sage/src/build/lib.linux-x86_64-2.7
Finished cleaning, time: 0.08 seconds.
running install
running build
running build_py
running build_ext
warning: Replacing library search directory in linker command:
  "/home/dima/software/sage.6.6/sage/local/lib" -> "/home/dima/software/sage/local/lib"

Executing 0 commands (using 1 thread)
Time to execute 0 commands: 0.11 seconds.
Total time spent compiling C/C++ extensions: 0.14 seconds.
running install_lib
running install_data
running install_egg_info
Removing /home/dima/software/sage/local/lib/python2.7/site-packages/sage-6.8.beta7-py2.7.egg-info
Writing /home/dima/software/sage/local/lib/python2.7/site-packages/sage-6.8.beta7-py2.7.egg-info
Running doctests with ID 2015-07-04-22-41-59-36f0d948.
Git branch: newdownload
Using --optional=database_gap,gap_packages,gcc,gmp,lidia,lrslib,mpir,openssl,python2,sage,scons
Doctesting 10 files.
sage -t --warn-long 73.0 src/sage/game_theory/__init__.py
    [0 tests, 0.00 s]
sage -t --warn-long 73.0 src/sage/game_theory/all.py
    [0 tests, 0.00 s]
sage -t --warn-long 73.0 src/sage/game_theory/cooperative_game.py
    [101 tests, 0.66 s]
sage -t --warn-long 73.0 src/sage/game_theory/catalog_normal_form_games.py
    [99 tests, 0.36 s]
sage -t --warn-long 73.0 src/sage/game_theory/catalog.py
    [0 tests, 0.00 s]
sage -t --warn-long 73.0 src/sage/game_theory/parser.py
    [58 tests, 0.09 s]
sage -t --warn-long 73.0 src/sage/game_theory/named_games.py
    [0 tests, 0.00 s]
sage -t --warn-long 73.0 src/sage/game_theory/normal_form_game.py
    [357 tests, 1.80 s]
sage -t --warn-long 73.0 src/sage/game_theory/gambit_docs.py
    [0 tests, 0.00 s]
sage -t --warn-long 73.0 src/sage/game_theory/matching_game.py
    [305 tests, 2.17 s]
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------

post complete log; perhaps you have dodgy packages installed?

[Dima Pasechnik]

On Saturday, 4 July 2015 22:41:35 UTC+1, Vincent Knight wrote:

On 4 Jul 2015 10:36 pm, "Volker Braun" <vbrau...@gmail.com> wrote:
>
> Looks like sympy wasn't installed correctly... can you look into the sympy logs? Maybe recompile if you don't remember how you got there?

I've turned in for the night (typing this on my tablet) but will get back to you as soon as I get a chance tomorrow.

On OSX I had time so ran:

```
make dist-clean
make
```

On Ubuntu:

```
make clean
make
```

If you could point out where the sympy logs would be I'll send them tomorrow before I recompile (or indeed throw any other instructions my way :)).

packages logs are in

$SAGE_ROOT/logs/pkgs/

Dima

[Vincent Knight]

Have just rebuilt and still have the same problem.

Here is a link to the install.log file from the original build after
running `make dist-clean` (it's 196014 lines):
https://www.dropbox.com/s/obi5rj5gmp8xoux/install.log?dl=0

No sympy logs, apologies if I'm missing something...

```
sage(develop): ls logs/pkgs/
atlas-3.10.2.log gf2x-1.1.p1.log
mpc-1.0.2.p0.log
pyparsing-2.0.1.log
backports_ssl_match_hostname-3.4.0.2.log givaro-3.7.1.log
mpfi-1.5.1.log
python2-2.7.9.log
boehm_gc-7.2d.p0.log glpk-4.55.p0.log
mpfr-3.1.2.p0.log
pyzmq-14.3.0.log
boost_cropped-1.52.0.log gsl-1.16.log
mpir-2.7.0.log
ratpoints-2.1.3.p3.log
bzip2-1.0.6.20140317.log iconv-1.14.log
ncurses-5.9.20131221.log
readline-6.3.008.log
cephes-2.8.p1.log iml-1.0.4p1.log
networkx-1.8.1.log rw-0.7.log
certifi-14.05.14.log ipython-3.2.0.log
ntl-6.2.1.p0.log
sage-6.8.beta7.log
cliquer-1.21.p2.log jinja2-2.7.3.log
numpy-1.8.1.p0.log
sagenb-0.11.4.log
config.log lcalc-1.23.p14.log
pari-2.8-1637-g489005a.p0.log
scipy-0.14.0.log
cython-0.22.p4.log libfplll-4.0.4.log
pari_galdata-20080411.log scons-1.2.0.log
dateutil-2.2.log libgap-4.7.8.log
pari_seadata_small-20090618.log
setuptools-12.4.log
docutils-0.12.log libgd-2.1.1.p0.log
patch-2.7.1.log
singular-3.1.7p1.p0.log
ecl-13.5.1.p0.log libpng-1.2.51.p0.log
pexpect-2.0.p6.log six-1.9.0.log
eclib-20150510.log linbox-1.3.2.p1.log
pillow-2.2.2.log
sphinx-1.2.2.p0.log
ecm-6.4.4.log lrcalc-1.1.7.log
pkgconf-0.9.7.log
sqlite-3.8.4.3.log
fflas_ffpack-1.6.0.p1.log m4ri-20140914.log
planarity-2.2.0.log
symmetrica-2.0.p9.log
flint-2.4.5.log m4rie-20140914.log
polybori-0.8.3.log tornado-4.1.log
freetype-2.5.2.p1.log markupsafe-0.23.log
ppl-1.1.log
zeromq-4.0.5.log
gap-4.7.8.log matplotlib-1.4.3.log
pygments-2.0.2.p0.log
zlib-1.2.8.p0.log
gcc-4.9.2.p1.log maxima-5.35.1.p2.log
pynac-0.3.7.log
zn_poly-0.9.p11.log
```

Have rebuilt, and rebuilt after running `make clean` and no
difference. Thinking of running `make dist-clean` again but holding
fire in case this situation is helpful...

V

[Volker Braun]

Its pretty clear that the build was not successful. This is http://trac.sagemath.org/ticket/18850

[reference] Writing js search indexes... genindex py-modindex search

[reference] WARNING: html_static_path entry '/Users/vince/sage/local/lib/python2.7/site-packages/sagenb-0.11.4-py2.7.egg/sagenb/data/mathjax' does not exist

Error building the documentation.

Traceback (most recent call last):

  File "/Users/vince/sage/src/doc/common/builder.py", line 1626, in <module>

    getattr(get_builder(name), type)()

  File "/Users/vince/sage/src/doc/common/builder.py", line 296, in _wrapper

    getattr(get_builder(document), name)(*args, **kwds)

  File "/Users/vince/sage/src/doc/common/builder.py", line 516, in _wrapper

    getattr(DocBuilder(self.name, lang), format)(*args, **kwds)

  File "/Users/vince/sage/src/doc/common/builder.py", line 110, in f

    eval(compile(open(sys.argv[0]).read(), sys.argv[0], 'exec'))

  File "/Users/vince/sage/src/doc/common/custom-sphinx-build.py", line 219, in <module>

    raise OSError(ERROR_MESSAGE)

OSError: [reference] WARNING: html_static_path entry '/Users/vince/sage/local/lib/python2.7/site-packages/sagenb-0.11.4-py2.7.egg/sagenb/data/mathjax' does not exist

make[1]: *** [doc-html] Error 1

[Vincent Knight]

On 5 July 2015 at 08:32, Volker Braun <vbrau...@gmail.com> wrote:
> Its pretty clear that the build was not successful. This is
> http://trac.sagemath.org/ticket/18850

Cool, I thought that ticket seemed to just indicate a problem with the
documentation build. I have much to learn as to why that's messing up
sympy for me :) Thanks and apologies for wasting people's time with a
duplication :)

[Dima Pasechnik]

On Sunday, 5 July 2015 08:11:08 UTC+1, Vincent Knight wrote:

Have just rebuilt and still have the same problem.

Here is a link to the install.log file from the original build after
running `make dist-clean` (it's 196014 lines):
https://www.dropbox.com/s/obi5rj5gmp8xoux/install.log?dl=0

No sympy logs, apologies if I'm missing something...

just do
./sage -f sympy
and report...

 
 

[Vincent Knight]

On 5 July 2015 at 09:02, Dima Pasechnik <dim...@gmail.com> wrote:
> just do
> ./sage -f sympy
> and report...

After that I ran the tests again and got:

```
ImportError: No module named mpmath.libmp
```

ran

```
./sage -f mpmath
```

Tests now run.

:)

[Volker Braun]

Thats not enough, you also need to finish "make"

[Vincent Knight]

On 5 July 2015 at 09:22, Volker Braun <vbrau...@gmail.com> wrote:
> Thats not enough, you also need to finish "make"

All seemed in order without running `make` but ran it and all seems
fine still. Thanks.

[Francois Bissey]

On power7 I get 2 doctest failures:
frb15@p2n14-c /hpc/scratch/frb15/sandbox/sage-6.8.beta7 :./sage -t --long --warn-long 95.7 src/sage/symbolic/expression.pyx
Running doctests with ID 2015-07-06-23-32-31-283f339e.
Git branch: develop
Using --optional=mpir,python2,sage,scons
Doctesting 1 file.
sage -t --long --warn-long 95.7 src/sage/symbolic/expression.pyx
**********************************************************************
File "src/sage/symbolic/expression.pyx", line 10875, in sage.symbolic.expression.Expression._plot_fast_callable
Failed example:
plot(s)
Expected:
Graphics object consisting of 1 graphics primitive
Got:
Graphics object consisting of 0 graphics primitives

**********************************************************************
1 item had failures:

1 of 10 in sage.symbolic.expression.Expression._plot_fast_callable
[2460 tests, 1 failure, 62.46 s]
----------------------------------------------------------------------
sage -t --long --warn-long 95.7 src/sage/symbolic/expression.pyx # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 63.4 seconds
cpu time: 48.1 seconds
cumulative wall time: 62.5 seconds
frb15@p2n14-c /hpc/scratch/frb15/sandbox/sage-6.8.beta7 :./sage -t --long --warn-long 95.7 src/sage/graphs/distances_all_pairs.pyx
Running doctests with ID 2015-07-06-23-34-27-43999aaf.
Git branch: develop
Using --optional=mpir,python2,sage,scons
Doctesting 1 file.
sage -t --long --warn-long 95.7 src/sage/graphs/distances_all_pairs.pyx

**********************************************************************
File "src/sage/graphs/distances_all_pairs.pyx", line 1205, in sage.graphs.distances_all_pairs.diameter
Failed example:
G.diameter(method='iFUB')
Expected:
0
Got:
Exception OverflowError: 'value too large to convert to uint32_t' in 'sage.graphs.distances_all_pairs.diameter_iFUB' ignored
0
**********************************************************************
1 item had failures:
1 of 17 in sage.graphs.distances_all_pairs.diameter

[68 tests, 1 failure, 1.66 s]
----------------------------------------------------------------------
sage -t --long --warn-long 95.7 src/sage/graphs/distances_all_pairs.pyx # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 1.8 seconds
cpu time: 0.4 seconds
cumulative wall time: 1.7 seconds


So I see it too.

François

[Jean-Pierre Flori]

 
I would say that this is a Cython bug:

 (gdb) c
Continuing.

Breakpoint 3, __pyx_f_4sage_6graphs_19distances_all_pairs_diameter_lower_bound_multi_sweep (
    __pyx_v_n=__pyx_v_n@entry=1, __pyx_v_p_vertices=__pyx_v_p_vertices@entry=0x105e79a0,
    __pyx_v_source=__pyx_v_source@entry=0)
    at /home/jpflori/sage.git/src/build/cythonized/sage/graphs/distances_all_pairs.c:11220
11220   __pyx_t_2 = __Pyx_PyInt_From_uint32_t(__pyx_v_s); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1011; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
(gdb) s
__Pyx_PyInt_From_uint32_t (value=<optimized out>)
    at /home/jpflori/sage.git/src/build/cythonized/sage/graphs/distances_all_pairs.c:18830
18830               return PyInt_FromLong((long) value);
(gdb) print sizeof(long)

At the end of the diameter_lower_bound_multi_sweep function, Cython builds a tuple with four uint32_t's.
To do so, it converts the uint32_t's to PyInt's using __Pyx_PyInt_From_uint32_t which seems to call PyInt_FromLong((long) value).
Then Cython wants to do a new uint32_t from a too large value when assigning values from the tuple.

[Jean-Pierre Flori]

Or this is a GCC bug...

[Jean-Pierre Flori]

Or the code is buggy as well :)
I guess that s and d are returned but they are uninitialized and actually contain memory addresses which are about 45 bits.

[Jean-Pierre Flori]

Le lundi 6 juillet 2015 14:56:14 UTC+2, Jean-Pierre Flori a écrit :

Or the code is buggy as well :)
I guess that s and d are returned but they are uninitialized and actually contain memory addresses which are about 45 bits.

Fix for this one at http://trac.sagemath.org/ticket/18854#

[Rob Beezer]

On SageMathCloud, built from source, passes long tests ("ptestlong") with a
single failure in

src/sage/interfaces/expect.py

which then passes when run independently.

https://cloud.sagemath.com/projects/53b77207-8614-4086-a032-432af4b4cdbd/files/sage-dev-images/

[Sébastien Labbé]

Running make ptestlong on Ubuntu 14.04 and using

--optional=arb,benzene,bliss,buckygen,cbc,cryptominisat,database_cremona_ellcurve,database_gap,database_odlyzko_zeta,database_pari,database_stein_watkins,database_symbolic_data,dot2tex,gambit,gap_packages,gcc,gdb,mcqd,modular_decomposition,mpir,nauty,plantri,python2,sage,scons,tides

I get 3 failures. The two failures in dynamic_class.py were already mentionned by John H Palmieri. For me too, when I test dynamic_class.py alone, I get All tests passed. But the one in doctest/test.py keeps being there.

----------------------------------------------------------------------
sage -t --long --warn-long 29.8 src/sage/doctest/test.py  # 1 doctest failed
sage -t --long --warn-long 29.8 src/sage/structure/dynamic_class.py  # 2 doctests failed
----------------------------------------------------------------------

Sébastien



sage -t --long --warn-long 29.8 src/sage/doctest/test.py
**********************************************************************
File "src/sage/doctest/test.py", line 330, in sage.doctest.test
Failed example:
    subprocess.call(["sage", "-t",  "--warn-long", "0", "--gdb", "1second.rst"], stdin=open(os.devnull), **kwds)  # long time, optional: gdb
Expected:
    exec gdb ...
    Running doctests...
    Doctesting 1 file.
    sage -t 1second.rst
        [2 tests, ... s]

    ----------------------------------------------------------------------
    All tests passed!
    ----------------------------------------------------------------------

    ...
    0
Got:
    exec gdb -x "$SAGE_LOCAL/bin/sage-gdb-commands" --args python "$SAGE_LOCAL/bin/sage-runtests" --serial --timeout=0 --stats_path=/home/labbe/.sage/timings2.json --optional=arb,benzene,bliss,buckygen,cbc,cryptominisat,database_cremona_ellcurve,database_gap,database_odlyzko_zeta,database_pari,database_stein_watkins,database_symbolic_data,dot2tex,gambit,gap_packages,gcc,gdb,mcqd,modular_decomposition,mpir,nauty,plantri,python2,sage,scons,tides 1second.rst
    GNU gdb (GDB) 7.8
    Copyright (C) 2014 Free Software Foundation, Inc.
    License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
    This is free software: you are free to change and redistribute it.
    There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
    and "show warranty" for details.
    This GDB was configured as "x86_64-unknown-linux-gnu".
    Type "show configuration" for configuration details.
    For bug reporting instructions, please see:
    <http://www.gnu.org/software/gdb/bugs/>.
    Find the GDB manual and other documentation resources online at:
    <http://www.gnu.org/software/gdb/documentation/>.
    For help, type "help".
    Type "apropos word" to search for commands related to "word"...
    Reading symbols from python...done.
    [Thread debugging using libthread_db enabled]
    Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
    warning: File "/home/labbe/Applications/sage-git/local/lib64/libstdc++.so.6.0.20-gdb.py" auto-loading has been declined by your `auto-load safe-path' set to "$debugdir:$datadir/auto-load".
    To enable execution of this file add
        add-auto-load-safe-path /home/labbe/Applications/sage-git/local/lib64/libstdc++.so.6.0.20-gdb.py
    line to your configuration file "/home/labbe/.gdbinit".
    To completely disable this security protection add
        set auto-load safe-path /
    line to your configuration file "/home/labbe/.gdbinit".
    For more information about this security protection see the
    "Auto-loading safe path" section in the GDB manual.  E.g., run from the shell:
        info "(gdb)Auto-loading safe path"
    Running doctests with ID 2015-07-08-18-17-37-501d940b.
    Git branch: develop
    Using --optional=arb,benzene,bliss,buckygen,cbc,cryptominisat,database_cremona_ellcurve,database_gap,database_odlyzko_zeta,database_pari,database_stein_watkins,database_symbolic_data,dot2tex,gambit,gap_packages,gcc,gdb,mcqd,modular_decomposition,mpir,nauty,plantri,python2,sage,scons,tides
    Doctesting 1 file.
    sage -t --warn-long 29.8 1second.rst
        [2 tests, 1.00 s]
    ----------------------------------------------------------------------
    All tests passed!
    ----------------------------------------------------------------------
    Total time for all tests: 1.0 seconds
        cpu time: 0.0 seconds
        cumulative wall time: 1.0 seconds
    [Inferior 1 (process 26263) exited normally]
    (gdb) quit
    0
**********************************************************************

[Sébastien Labbé]

 

But the one in doctest/test.py keeps being there.

----------------------------------------------------------------------
sage -t --long --warn-long 29.8 src/sage/doctest/test.py  # 1 doctest failed

Needs review at:

http://trac.sagemath.org/ticket/18873

[Justin C. Walker]

On Jul 2, 2015, at 16:40 , Volker Braun wrote:

> As always, you can get the latest beta version from the "develop" git
> branch. Alternatively, the self-contained source tarball is at
> http://www.sagemath.org/download-latest.html

Built from tarball on OS X, 10.6.8 (Dual 6-core Xeons) w. no problems. Testing ('ptestlong') showed 1 failure:
sage -t --long --warn-long 100.1 src/sage/interfaces/mwrank.py
Timed out
I reran the full 'ptestlong', and it completed with no problems. I think this is the lurking race condition issue that shows up randomly.

--
Justin C. Walker, Curmudgeon at Large

Director
Institute for the Enhancement of the Director's Income

-----------
Nobody knows the trouble I've been
-----------