[sage-devel] Re: Sage 4.4.2.alpha0 released

[Jaap Spies]

Minh Nguyen wrote:
> Hi folks,
>
> This release of Sage 4.4.2.alpha0 is earlier than I scheduled [1]. But
> I have found some doctest failures that could take a while to resolve.
> So getting this release out early should help with resolving them.
>

On Fedora 12, 64 bit all troubles seem far away!

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

Upgrade from sage-4.4.1

Jaap

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[Georg S. Weber]

On MacIntel OS X 10.4, building sage-4.4.2.alpha0 from scratch, the
build finishes, but I see three new issues. I'll describe them in
three different posts. (Note that with sage-4.4.1, on the same
machine, I had done a full "make testlong", which succeeded
flawlessly). The first on seems to be a trivial 32-bit vs. 64-bit
issue (probably occurs on any 32-bit machine, even without the "long"
option):

sage -t -long "devel/sage/sage/matrix/matrix1.pyx"
**********************************************************************
File "/Users/Shared/sage/test/sage-4.4.2.alpha0/devel/sage/sage/matrix/
matrix1.pyx", line 460:
sage: b.dtype
Expected:
dtype('int64')
Got:
dtype('int32')
**********************************************************************

[Georg S. Weber]

The second problem occurs in a "long" only doctest, but probably
occurs now on any machine. From what I guess skipping through the
patches newly applied to sage-4.4.2.alpha0, I'd suspect " #8479:
Wilfried Huss: numpy support for more basic functions [Reviewed
by Burcin Erocal] ", but this might be completely wrong (I didn't look
any closer):

sage -t -long "devel/sage/sage/calculus/riemann.pyx"
**********************************************************************
File "/Users/Shared/sage/test/sage-4.4.2.alpha0/devel/sage/sage/
calculus/riemann.pyx", line 110:
sage: m = Riemann_Map([f, hf], [hf, hfprime], 0.5 + 0.5*I) # long
time (8 sec)
Exception raised:
Traceback (most recent call last):
File "/Users/Shared/sage/test/sage-4.4.2.alpha0/local/bin/
ncadoctest.py", line 1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File "/Users/Shared/sage/test/sage-4.4.2.alpha0/local/bin/
sagedoctest.py", line 38, in run_one_example
OrigDocTestRunner.run_one_example(self, test, example,
filename, compileflags)
File "/Users/Shared/sage/test/sage-4.4.2.alpha0/local/bin/
ncadoctest.py", line 1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_1[7]>", line 1, in <module>
m = Riemann_Map([f, hf], [hf, hfprime], RealNumber('0.5') +
RealNumber('0.5')*I) # long time (8 sec)###line 110:
sage: m = Riemann_Map([f, hf], [hf, hfprime], 0.5 + 0.5*I) # long
time (8 sec)
File "riemann.pyx", line 176, in
sage.calculus.riemann.Riemann_Map.__init__ (sage/calculus/riemann.c:
1757)
File "expression.pyx", line 3398, in
sage.symbolic.expression.Expression.__call__ (sage/symbolic/
expression.cpp:15476)
File "/Users/Shared/sage/test/sage-4.4.2.alpha0/local/lib/python/
site-packages/sage/symbolic/callable.py", line 447, in _call_element_
raise NotImplementedError("Numpy arrays are not supported as
arguments for symbolic expressions")
NotImplementedError: Numpy arrays are not supported as arguments
for symbolic expressions
**********************************************************************
File "/Users/Shared/sage/test/sage-4.4.2.alpha0/devel/sage/sage/
calculus/riemann.pyx", line 325:
sage: m = Riemann_Map([f, hf], [hf, hfprime], 0.5 + 0.5*I) # long
time (8 sec)
Exception raised:
Traceback (most recent call last):
File "/Users/Shared/sage/test/sage-4.4.2.alpha0/local/bin/
ncadoctest.py", line 1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File "/Users/Shared/sage/test/sage-4.4.2.alpha0/local/bin/
sagedoctest.py", line 38, in run_one_example
OrigDocTestRunner.run_one_example(self, test, example,
filename, compileflags)
File "/Users/Shared/sage/test/sage-4.4.2.alpha0/local/bin/
ncadoctest.py", line 1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_5[12]>", line 1, in <module>
m = Riemann_Map([f, hf], [hf, hfprime], RealNumber('0.5') +
RealNumber('0.5')*I) # long time (8 sec)###line 325:
sage: m = Riemann_Map([f, hf], [hf, hfprime], 0.5 + 0.5*I) # long
time (8 sec)
File "riemann.pyx", line 176, in
sage.calculus.riemann.Riemann_Map.__init__ (sage/calculus/riemann.c:
1757)
File "expression.pyx", line 3398, in
sage.symbolic.expression.Expression.__call__ (sage/symbolic/
expression.cpp:15476)
File "/Users/Shared/sage/test/sage-4.4.2.alpha0/local/lib/python/
site-packages/sage/symbolic/callable.py", line 447, in _call_element_
raise NotImplementedError("Numpy arrays are not supported as
arguments for symbolic expressions")
NotImplementedError: Numpy arrays are not supported as arguments
for symbolic expressions
**********************************************************************
File "/Users/Shared/sage/test/sage-4.4.2.alpha0/devel/sage/sage/
calculus/riemann.pyx", line 330:
sage: sz1 = m.get_szego(boundary=1) # long time
Exception raised:
Traceback (most recent call last):
File "/Users/Shared/sage/test/sage-4.4.2.alpha0/local/bin/
ncadoctest.py", line 1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File "/Users/Shared/sage/test/sage-4.4.2.alpha0/local/bin/
sagedoctest.py", line 38, in run_one_example
OrigDocTestRunner.run_one_example(self, test, example,
filename, compileflags)
File "/Users/Shared/sage/test/sage-4.4.2.alpha0/local/bin/
ncadoctest.py", line 1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_5[14]>", line 1, in <module>
sz1 = m.get_szego(boundary=Integer(1)) # long time###line
330:
sage: sz1 = m.get_szego(boundary=1) # long time
File "riemann.pyx", line 348, in
sage.calculus.riemann.Riemann_Map.get_szego (sage/calculus/riemann.c:
4222)
IndexError: index out of bounds
**********************************************************************
File "/Users/Shared/sage/test/sage-4.4.2.alpha0/devel/sage/sage/
calculus/riemann.pyx", line 392:
sage: m = Riemann_Map([f, hf], [hf, hfprime], 0.5 + 0.5*I) # long
time (8 sec)
Exception raised:
Traceback (most recent call last):
File "/Users/Shared/sage/test/sage-4.4.2.alpha0/local/bin/
ncadoctest.py", line 1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File "/Users/Shared/sage/test/sage-4.4.2.alpha0/local/bin/
sagedoctest.py", line 38, in run_one_example
OrigDocTestRunner.run_one_example(self, test, example,
filename, compileflags)
File "/Users/Shared/sage/test/sage-4.4.2.alpha0/local/bin/
ncadoctest.py", line 1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_6[11]>", line 1, in <module>
m = Riemann_Map([f, hf], [hf, hfprime], RealNumber('0.5') +
RealNumber('0.5')*I) # long time (8 sec)###line 392:
sage: m = Riemann_Map([f, hf], [hf, hfprime], 0.5 + 0.5*I) # long
time (8 sec)
File "riemann.pyx", line 176, in
sage.calculus.riemann.Riemann_Map.__init__ (sage/calculus/riemann.c:
1757)
File "expression.pyx", line 3398, in
sage.symbolic.expression.Expression.__call__ (sage/symbolic/
expression.cpp:15476)
File "/Users/Shared/sage/test/sage-4.4.2.alpha0/local/lib/python/
site-packages/sage/symbolic/callable.py", line 447, in _call_element_
raise NotImplementedError("Numpy arrays are not supported as
arguments for symbolic expressions")
NotImplementedError: Numpy arrays are not supported as arguments
for symbolic expressions
**********************************************************************
File "/Users/Shared/sage/test/sage-4.4.2.alpha0/devel/sage/sage/
calculus/riemann.pyx", line 397:
sage: tp1 = m.get_theta_points(boundary=1) # long time
Exception raised:
Traceback (most recent call last):
File "/Users/Shared/sage/test/sage-4.4.2.alpha0/local/bin/
ncadoctest.py", line 1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File "/Users/Shared/sage/test/sage-4.4.2.alpha0/local/bin/
sagedoctest.py", line 38, in run_one_example
OrigDocTestRunner.run_one_example(self, test, example,
filename, compileflags)
File "/Users/Shared/sage/test/sage-4.4.2.alpha0/local/bin/
ncadoctest.py", line 1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_6[13]>", line 1, in <module>
tp1 = m.get_theta_points(boundary=Integer(1)) # long
time###line 397:
sage: tp1 = m.get_theta_points(boundary=1) # long time
File "riemann.pyx", line 407, in
sage.calculus.riemann.Riemann_Map.get_theta_points (sage/calculus/
riemann.c:4547)
IndexError: index out of bounds
**********************************************************************
3 items had failures:
1 of 15 in __main__.example_1
2 of 15 in __main__.example_5
2 of 14 in __main__.example_6
***Test Failed*** 5 failures.
For whitespace errors, see the file /Users/georgweber/.sage//
tmp/.doctest_riemann.py
[175.4 s]

----------------------------------------------------------------------
The following tests failed:


sage -t -long "devel/sage/sage/calculus/riemann.pyx"
Total time for all tests: 175.4 seconds

[Georg S. Weber]

The third issue I se with sage-4.4.2-alpha0 is the following. I did
the usual " export SAGE_BINARY_BUILD=yes " (the PIL spkg does not
build for me without this additional environment variable, something
that is "accepted") and " export MAKE='make -j2' " (my machine has a
Core2Duo CPU, so there), and then typed "make". At the end of the
install log, I then got:

Finished installing sagetex-2.2.5.spkg

real 171m37.446s
user 121m37.722s
sys 32m26.350s
To install gap, gp, singular, etc., scripts
in a standard bin directory, start sage and
type something like
sage: install_scripts('/usr/local/bin')
at the Sage command prompt.

To build the documentation, run
make doc

Sage build/upgrade complete!


Exactly, the Sage documentation is no longer built by "make"! I didn't
see a vote on this on sage-devel. If that change has been conscious
decision, I'm strongly against it. I'm OK with having e.g. build
targets "make build", building the spk and library parts only, and
having "make doc" building only the docs, but then "make" alone ought
to be equivalent to "make build && make doc", not "make build" alone.
Any comments?

I use(d) to build and test Sage in one go, typing "make && make
testlong", so the above change of behaviour resulted (of course ...)
in the following doctest failure:

sage -t -long "devel/sage/sage/misc/sagedoc.py"
**********************************************************************
File "/Users/Shared/sage/test/sage-4.4.2.alpha0/devel/sage/sage/misc/
sagedoc.py", line 891:
sage: len(search_doc('tree', interact=False).splitlines()) > 2000
Expected:
True
Got:
Warning, the following Sage documentation hasn't been built,
so documentation search results may be incomplete:
<BLANKLINE>
/Users/Shared/sage/test/sage-4.4.2.alpha0/devel/sage/doc/output/
html/en/thematic_tutorials
<BLANKLINE>
You can build this with 'sage -docbuild thematic_tutorials html'.
False
**********************************************************************
File "/Users/Shared/sage/test/sage-4.4.2.alpha0/devel/sage/sage/misc/
sagedoc.py", line 893:
sage: len(search_doc('tree', whole_word=True,
interact=False).splitlines()) < 200
Expected:
True
Got:
Warning, the following Sage documentation hasn't been built,
so documentation search results may be incomplete:
<BLANKLINE>
/Users/Shared/sage/test/sage-4.4.2.alpha0/devel/sage/doc/output/
html/en/thematic_tutorials
<BLANKLINE>
You can build this with 'sage -docbuild thematic_tutorials html'.
True
**********************************************************************
File "/Users/Shared/sage/test/sage-4.4.2.alpha0/devel/sage/sage/misc/
sagedoc.py", line 496:
sage: 'abvar/homology' in _search_src_or_doc('doc', 'homology',
'variety', interact=False)
Expected:
True
Got:
Warning, the following Sage documentation hasn't been built,
so documentation search results may be incomplete:
<BLANKLINE>
/Users/Shared/sage/test/sage-4.4.2.alpha0/devel/sage/doc/output/
html/en/thematic_tutorials
<BLANKLINE>
You can build this with 'sage -docbuild thematic_tutorials html'.
False
**********************************************************************
2 items had failures:
2 of 5 in __main__.example_14
1 of 7 in __main__.example_8
***Test Failed*** 3 failures.


After building the documentation with "make doc" (which runs through,
but shows quite some warning and error messages), the above doctest
finishes OK.


Cheers,
Georg

[John Cremona]

On 64-bit ubuntu, built from scratch, I had these (with make ptestlong):


The following tests failed:

sage -t -long devel/sage/sage/misc/sagedoc.py # 3 doctests failed
sage -t -long devel/sage/sage/libs/mwrank/all.py # 0 doctests failed
sage -t -long devel/sage/sage/calculus/riemann.pyx # 5 doctests failed

The last one was the same as reported by Georg. The middle one was
not reproducible. The first one looks like this -- does not look too
serious, but the test expected some docs to have been built which were
not.

John

sage -t -long "devel/sage/sage/misc/sagedoc.py"
**********************************************************************

File "/storage/jec/sage-4.4.2.alpha0/devel/sage/sage/misc/sagedoc.py", line 891:

sage: len(search_doc('tree', interact=False).splitlines()) > 2000
Expected:
True
Got:
Warning, the following Sage documentation hasn't been built,
so documentation search results may be incomplete:
<BLANKLINE>

/home/jec/storage/sage-4.4.2.alpha0/devel/sage/doc/output/html/en/thematic_tutorials

<BLANKLINE>
You can build this with 'sage -docbuild thematic_tutorials html'.
False
**********************************************************************

File "/storage/jec/sage-4.4.2.alpha0/devel/sage/sage/misc/sagedoc.py", line 893:

sage: len(search_doc('tree', whole_word=True,
interact=False).splitlines()) < 200
Expected:
True
Got:
Warning, the following Sage documentation hasn't been built,
so documentation search results may be incomplete:
<BLANKLINE>

/home/jec/storage/sage-4.4.2.alpha0/devel/sage/doc/output/html/en/thematic_tutorials

<BLANKLINE>
You can build this with 'sage -docbuild thematic_tutorials html'.
True
**********************************************************************

File "/storage/jec/sage-4.4.2.alpha0/devel/sage/sage/misc/sagedoc.py", line 496:

sage: 'abvar/homology' in _search_src_or_doc('doc', 'homology',
'variety', interact=False)
Expected:
True
Got:
Warning, the following Sage documentation hasn't been built,
so documentation search results may be incomplete:
<BLANKLINE>

/home/jec/storage/sage-4.4.2.alpha0/devel/sage/doc/output/html/en/thematic_tutorials

<BLANKLINE>
You can build this with 'sage -docbuild thematic_tutorials html'.
False
**********************************************************************