Update ECL to 10.4.1 and Maxima to 5.22.1 - currently the latest releases. #10187

vbraun · 2010-10-29T13:32:09Z

Note: See #10434 for a follow-up ticket.

Please update ECL and Maxima to the newest upstream release. Sage packages are here:

It's unsafe to build either ECL or Maxima in parallel, so we must not do this. Updated versions of ECL and Maxima can be found here:

http://boxen.math.washington.edu/home/kirkby/patches/ecl-10.4.1.spkg

http://www.stp.dias.ie/~vbraun/Sage/spkg/maxima-5.22.1.spkg

Note that you cannot upgrade one without the other; Both ECL and Maxima need to be upgraded simultaneously or build will fail.

Relevant tickets for ECL:

Remove extra baggage from the ECL spkg #9493: Remove extra baggage from ECL 10.2.1.p1 (again). The package has been cleaned up, but I feel removing gmp sources is too dangerous.
ECL in Sage will not build on Fedora 14, which will be released on 2nd November 2010 #10185: the old ecl-10.2.1 does not build on Fedora 14: Hopefully fixed with the updated ECL from this ticket.

Relevant tickets for maxima:

maxima package fails to install ECL library #8645: ECL library "maxima.fasb" is built at new location. The patches from this bug have been incorporated into the maxima spkg, and maxima package fails to install ECL library #8645 can be closed after this ticket.
update/upgrade maxima to latest upstream (5.21.1) #8731: update/upgrade Maxima to latest upstream (5.21.1): Latest upstream is nowadays 5.22.1.
sum(1/(1+k^2), k, -oo, oo) returns 0 #8582: sum(1/(1+k^2), k, -oo, oo) returns 0: The new Maxima seems to be able to evaluate this correctly, at leasts it returns some expression with digamma functions.

The updated Maxima code seems to be more careful about signs which leads to doctest errors. Moreover, error reporting was changed. Therefore you need to apply the following patches to the Sage library (in this order):

trac_10187_fix_easy_doctests.patch
trac_10187_general_display_prefix_workaround.patch
trac_10187_mark_some_doctests_random_until_9880_gets_merged.patch

Finally, you need to patch $SAGE_ROOT/local/bin/sage-maxima.lisp with

trac_10187_sage-maxima_lisp.patch

Upstream: Workaround found; Bug reported upstream.

CC: @williamstein @jhpalmieri @qed777 @nexttime @jaapspies @jasongrout @kcrisman @kiwifb @jpflori

Component: packages: standard

Author: Volker Braun, David Kirkby

Reviewer: Karl-Dieter Crisman, David Kirkby, Volker Braun, Leif Leonhardy

Merged: sage-4.6.1.alpha3

Issue created by migration from https://trac.sagemath.org/ticket/10187

The text was updated successfully, but these errors were encountered:

vbraun · 2010-10-29T17:20:08Z

comment:2

The doctests show one maxima regression:

sage: t = log(sqrt(2) - 1) + log(sqrt(2) + 1); t
log(sqrt(2) - 1) + log(sqrt(2) + 1)
sage: u = t.maxima_methods(); u
MaximaWrapper(log(sqrt(2) - 1) + log(sqrt(2) + 1))
sage: u.logcontract()
log((sqrt(2) - 1)*(sqrt(2) + 1))

This simplified to 0 in a previous version. But at least its not wrong ;-)

The attached patch fixes all doctests except for a timeout in maxima. That one is a different issue with maxima, which forgets to print the general-display-prefix variable for errors:

(sage subshell) volker-desktop:sage vbraun$ ./local/bin/maxima -p ./local/bin/sage-maxima.lisp 
;;; Loading #P"/home/vbraun/Sage/sage/local/lib/ecl/sb-bsd-sockets.fas"
;;; Loading #P"/home/vbraun/Sage/sage/local/lib/ecl/sockets.fas"
;;; Loading #P"/home/vbraun/Sage/sage/local/lib/ecl/defsystem.fas"
;;; Loading #P"/home/vbraun/Sage/sage/local/lib/ecl/cmp.fas"
;;; Loading #P"/home/vbraun/Sage/sage/local/lib/ecl/sysfun.lsp"
Maxima 5.22.1 http://maxima.sourceforge.net
using Lisp ECL 10.4.1
Distributed under the GNU Public License. See the file COPYING.
Dedicated to the memory of William Schelter.
The function bug_report() provides bug reporting information.
(%i1) 1;
<sage-display>(%o1)                                  1
(%i2) 1==1;
incorrect syntax: = is not a prefix operator
1==
 ^
(%i2) 1=1;
<sage-display>(%o2)                                1 = 1

sagetrac-drkirkby · 2010-10-29T17:54:28Z

comment:3

FYI, here's the failures on OpenSolaris 06/2009 with those updated versions of Maxima and ECL.

sage -t  -long -force_lib devel/sage/sage/interfaces/maxima.py
*** *** Error: TIMED OUT! PROCESS KILLED! *** ***

	 [1800.2 s]
 
----------------------------------------------------------------------

The following tests failed:

	sage -t  -long -force_lib devel/sage/sage/symbolic/integration/integral.py # 6 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/maxima_wrapper.py # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/expression.pyx # 11 doctests failed
	sage -t  -long -force_lib devel/sage/sage/misc/functional.py # 2 doctests failed
	sage -t  -long -force_lib devel/sage/sage/calculus/wester.py # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/calculus/tests.py # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/calculus/calculus.py # 5 doctests failed
	sage -t  -long -force_lib devel/sage/sage/calculus/functional.py # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/plot/plot3d/transform.pyx # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/interfaces/maxima.py # Time out
----------------------------------------------------------------------
Total time for all tests: 2628.2 seconds
make: *** [ptestlong] Error 192
drkirkby@hawk:~/sage-4.6.1.alpha0$

I've not applied any patches at this point. I'll apply patches and rerun later.

kcrisman · 2010-10-29T17:56:34Z

comment:4

Replying to @sagetrac-drkirkby:

FYI, here's the failures on OpenSolaris 06/2009 with those updated versions of Maxima and ECL.

sage -t  -long -force_lib devel/sage/sage/interfaces/maxima.py
*** *** Error: TIMED OUT! PROCESS KILLED! *** ***

	 [1800.2 s]

I'd be interested what happened if you manually removed the tests in that file which test the tab-completion for Maxima. I get a problem on Mac OS X Tiger with that file for exactly that reason. We haven't filed a ticket because nobody knows how to fix it, and tab-completion does work on that platform, just not the testing.

vbraun · 2010-10-29T18:02:07Z

comment:5

The TIMED OUT! error is the missing general-display-prefix, which causes the expect interface to wait forever for maxima to print its next prompt.

I've filed a bug upstream here: https://sourceforge.net/tracker/?func=detail&aid=3098375&group_id=4933&atid=104933

kcrisman · 2010-10-29T20:23:01Z

comment:6

Replying to @vbraun:

The TIMED OUT! error is the missing general-display-prefix, which causes the expect interface to wait forever for maxima to print its next prompt.

Okay, thanks - so that's unrelated to the Tiger timeout from earlier Maximas.

vbraun · 2010-10-29T20:50:47Z

comment:7

I've modified sage/interfaces/maxima.py to work with maxima's prompt_prefix instead. Patch is attached and fixes the remaining doctest error.

This requires that `$SAGE_LOCAL/bin/sage-maxima.lisp sets

; (setf *general-display-prefix* "<sage-display>")
(setf *prompt-prefix* "<sage-display>")

I've made a updated sage_scripts spkg here:
http://www.stp.dias.ie/~vbraun/Sage/spkg/sage_scripts-4.6.rc0.p0.spkg

To test this ticket, you need all three spkgs and both patches.

vbraun · 2010-10-29T20:50:47Z

Upstream: Workaround found; Bug reported upstream.

sagetrac-drkirkby · 2010-10-29T23:27:25Z

comment:10

One thing we don't don, which I think would be sensible, is to include the test suite for ECL. That adds 1.7 MB. From the README.ECL file:

	cd tests
	make

You will find two types of output files:

	*.out	The whole output of a test
	*.erg	The errors arising from a test

When there is no *.erg, it means that ECL passed the test.

Would it not be sensible to add these in? Then we could execute the tests with a spkg-check file, like we do other code which has self-tests.

Dave

kcrisman · 2010-10-30T00:13:59Z

comment:11

Replying to @vbraun:

I've modified sage/interfaces/maxima.py to work with maxima's prompt_prefix instead. Patch is attached and fixes the remaining doctest error.

Just a very minor note:

# we are now getting three lines of commented verbosity

but of course you changed it to get rid of the extra two lines from our constantly added packages :) so it's now five lines. Might as well change that too so future people are confused.

kcrisman · 2010-10-30T00:17:34Z

comment:12

Also, be sure to include a test that shows #8729 is fixed, as that was closed as a duplicate on the condition that #8731's doctests would show that.

sagetrac-aginiewicz · 2010-10-30T08:57:59Z

comment:13

I looked trough doctest patch and compared it with mine from #8731, I have few comments.

I think that doctest fix for sage/calculus/functional.py should be modified - it was documentation of the use of assume, but now - when maxima can calculate this integral without assumption, isn't that same as applying assumption to result? And the integral is checked in other doctest now. Maybe there is better example that still needs the assume to get result?

Also the doctest in sage/misc/functional.py was here to demonstrate numerical approximation of integral that cannot be evaluated iirc, and now when it can be evaluated, I think it should be changed to something that cannot be - like Jason did in patch in #8731.

Finally, there is typo in doctest to sage/symbolic/expression.pyx - it should say that this doctest is here to check that #7334 not #7344 is fixed (#7344 point to libjpeg issue so it cannot be it) - and it should stay in here unmodified. Also - the log thing - it's not exactly regression, it's feature. This is because of Maxima ticket 947808 - http://sourceforge.net/tracker/?func=detail&aid=947808&group_id=4933&atid=104933 - they now try to keep the expression as factored as they can without using factor. This results in observed behaviour. This doctest I think cannot be changed as it demonstrated that ticket is solved, but we should apply "x = x.simplify_rational()" after "x = x.simplify_log('one')" in definition of simplify_full - that way full simplify would result in same results as before I think, and #7334 would be still fixed. Now, this doctest shows nothing.

sagetrac-drkirkby · 2010-10-30T14:05:37Z

comment:14

There is a problem with the ECL package here. The history of all recent changes has been lost. The recent changes to the package have been:

=== ecl-10.2.1.p3 (David Kirkby, David Kirkby, 17th September 2010) ===
=== ecl-10.2.1.p2 (David Kirkby, 30th July 2010) ===
=== ecl-10.2.1.p1 (Mitesh Patel, 11th July 2010) ===
=== ecl-10.2.1.p0 (David Kirkby, 11th July 2010) ===
=== ecl-10.2.1 (William Stein, 14 February 2010) ===

but instead SPKG.txt shows

=== ecl-10.4.1.p0 (Leif Leonhardy, Volker Braun, 29th September 2010) ===
=== ecl-10.4.1 (N. Bruin, W. Stein, D. Kirkby and M. Patel 19th June 2010) ===
=== ecl-10.2.1 (William Stein, 14 February 2010) ===

This error has occurred since the package is based on one that I created several months ago, which never got merged, because their were conflicts with that and the Maxima package at the time.

The current version of ECL in Sage should have been used as a starting point - not an old one that was never merged.

I'll sort the above problem out, and add the ECL test code today.

Dave

kiwifb · 2010-10-30T22:54:43Z

comment:15

The patch fix_easy_doctest doesn't apply cleanly on either 4.6.rc0 or 4.6.1.alpha0.
Was it prepared against 4.5.3?

nexttime · 2010-10-31T02:03:04Z

comment:16

Replying to @vbraun:

I've modified sage/interfaces/maxima.py to work with maxima's prompt_prefix instead. Patch is attached and fixes the remaining doctest error.

This requires that `$SAGE_LOCAL/bin/sage-maxima.lisp sets

; (setf *general-display-prefix* "<sage-display>")
(setf *prompt-prefix* "<sage-display>")

I've made a updated sage_scripts spkg here:
http://www.stp.dias.ie/~vbraun/Sage/spkg/sage_scripts-4.6.rc0.p0.spkg

To test this ticket, you need all three spkgs and both patches.

Could you please attach a patch to the scripts repo, too (rather than a link to a complete new scripts spkg)?

Also, attaching diffs (or Mercurial patches) of the spkgs makes reviewing easier.

nexttime · 2010-10-31T02:20:38Z

comment:17

Replying to @nexttime:

Could you please attach a patch to the scripts repo, too (rather than a link to a complete new scripts spkg)?

P.S.: Of course I could do that, too, but then you wouldn't be able to update it in case you later modify the patch.

vbraun · 2010-10-31T02:45:14Z

Attachment: trac_10187_general_display_prefix_workaround.patch.gz

Updated patch

vbraun · 2010-10-31T02:51:59Z

comment:18

I've incorporated your suggestions and updated the patches. Both are (and were) against 4.6.rc0 and apply cleanly. Maybe you had the wrong order? It should be

trac_10187_fix_easy_doctests.patch
trac_10187_general_display_prefix_workaround.patch

I'll attach patches for the sage_scripts and maxima spgk for easier review. Once Dave is finished with the ecl package then this ticket is ready for review again.

kiwifb · 2010-10-31T03:47:02Z

comment:19

Wrong order indeed! I thought the two patches were orthogonal.

sagetrac-drkirkby · 2010-10-31T20:51:47Z

comment:20

I'm going to have to ask on the ECL list how to run the test suite - I can't work out where ones supposed to copy the source.

These changes are not going to make it into 4.6. The milestone is 4.6.1, and it will easily be resolved by then.

Dave

sagetrac-drkirkby · 2010-11-09T09:15:21Z

comment:21

Replying to @sagetrac-drkirkby:

I'm going to have to ask on the ECL list how to run the test suite - I can't work out where ones supposed to copy the source.

These changes are not going to make it into 4.6. The milestone is 4.6.1, and it will easily be resolved by then.

Dave

I've now got the information on the ANSI test suite from the ECL developer, though I gather the copy on the ECL site is rather out of date. Also, the ECL developer has fixed the bug that causes #9840, so I'll patch that too, so #9840 can hopefully be closed at the same time.

I'll try to get this sorted out within the next few days.

Dave

sagetrac-drkirkby · 2010-11-11T18:11:59Z

comment:22

I have put an updated ECL file at http://boxen.math.washington.edu/home/kirkby/patches/ecl-10.4.1.spkg This has only been checked on OpenSolaris - I don't have access to a Fedora 14 machine, so can't verify if it actually fixes the issues reported at #10185

I should make a few comments about this:

I have not added an spkg-check file or the Lisp tests, as I gather from the ECL developer the Lisp tests on the ECL site are outdated. Fixing this appears to be a non-trivial issue.
The repository information from the ecl-10.2.1.p3 version actually in Sage is kept, as it should be. (Volker's package was based on a 10.4.1 package I created months ago, which never got merged into Sage. So the repository information was not correct).
Despite being told the Solaris text relocation issue was resolved, it appears it is not as simple as applying a single patch as I had hoped. So link-editor thinks ECL library contains non-pic code on *all* Solaris/OpenSolaris releases - causes problems on 64-bit #9840 remains unresolved, though it should be fixed when the next stable ECL release is made.
I've cleaned the package up somewhat.
I did not remove the gmp sources, as doing so requires a new configure file to be created. Whilst I can see this is advantageous if done properly, I fear that this will be done incorrectly at some point in the future, which can result in chaos.

After

Installing the new ECL package I created, and put at http://boxen.math.washington.edu/home/kirkby/patches/ecl-10.4.1.spkg
Installing the Maxima package from http://www.stp.dias.ie/~vbraun/Sage/spkg/maxima-5.22.1.spkg
Trying to install all the patches (one failed, see below)
Rebuilding the Sage library.
Running all the doctests, which all pass.

I get one reject out of six when adding

trac_10187_general_display_prefix_workaround.patch

to sage 4.6.1.alpha0, so I think that patch needs updating. The contents of the reject are:

--- maxima.py
+++ maxima.py
@@ -728,10 +729,12 @@
         
             sage: maxima._eval_line('1+1;')
             '2'
-            sage: maxima.eval('sage0: x == x;')
+            sage: maxima._eval_line('sage0: x == x;')
             Traceback (most recent call last):
             ...
-            TypeError: error evaluating "sage0: x == x;":...
+            TypeError: Error executing code in Maxima...
+
+
         """
         if len(line) == 0:
             return ''

But as I say, all doctests passed for me, despite one patch was not fully applied!!

----------------------------------------------------------------------
All tests passed!
Total time for all tests: 1871.3 seconds

I'm leaving as needs work, as clearly the fact one patch does not apply cleanly is a problem. It also needs testing on more than one system, but I don't have access to the Fedora 14 system where this was a particular problem.

Dave

sagetrac-drkirkby · 2010-11-11T18:11:59Z

Changed author from Volker Braun to Volker Braun, David Kirkby

nexttime · 2010-12-02T17:03:26Z

comment:139

Yes, make reverted both ECL and Maxima to the previous versions.

Another ptestlong in progress...

sagetrac-drkirkby · 2010-12-02T18:52:57Z

comment:140

Am I right in assuming all these patches are against sage-4.6.1.alpha1 ?

I just built sage-4.6.1.alpha2, but some of these patches are applied, and some are not. So it looks like I'm going to have to build sage-4.6.1.alpha1. I expect it will take me a couple of hours to build it, patch it, then doctest it

Dave

nexttime · 2010-12-02T19:01:38Z

comment:141

Replying to @sagetrac-drkirkby:

Am I right in assuming all these patches are against sage-4.6.1.alpha1 ?

I just built sage-4.6.1.alpha2, but some of these patches are applied, and some are not. So it looks like I'm going to have to build sage-4.6.1.alpha1. I expect it will take me a couple of hours to build it, patch it, then doctest it

Shouldn't be necessary.

I've previously tested the spkgs and patches successfully (ptestlong) multiple times with Sage 4.6.1.alpha2 (in addition with the new MPIR and ECM, #8664 and #5847, respectively) on Ubuntu 10.04 x86_64.

On the 32-bit machine, I so far again got 47 doctest errors with the same though.

nexttime · 2010-12-02T19:27:38Z

comment:142

Hmmm, maybe a Mercurial issue?

Patches apply apparently clean on vanilla alpha2 as well (with an old Mercurial version), but I also get doctest errors on Ubuntu 9.04 x86_64.

nexttime · 2010-12-02T19:49:28Z

comment:143

Replying to @nexttime:

Hmmm, maybe a Mercurial issue?

Patches apply apparently clean on vanilla alpha2 as well (with an old Mercurial version), but I also get doctest errors on Ubuntu 9.04 x86_64.

Same with Sage's Mercurial version (1.6.x), i.e. patches apply cleanly.

Now at 199+ doctest errors on the 32-bit machine... :(

nexttime · 2010-12-02T20:00:48Z

comment:144

Ubuntu 9.04 x86_64 (gcc 4.3.3), vanilla Sage 4.6.1.alpha2 with #10187:

The following tests failed:

	sage -t  -long -force_lib devel/sage/doc/en/installation/source.rst # 1 doctests failed
	sage -t  -long -force_lib devel/sage/doc/en/a_tour_of_sage/index.rst # 3 doctests failed
	sage -t  -long -force_lib devel/sage/doc/en/constructions/polynomials.rst # 1 doctests failed
	sage -t  -long -force_lib devel/sage/doc/en/constructions/linear_algebra.rst # 5 doctests failed
	sage -t  -long -force_lib devel/sage/doc/en/constructions/calculus.rst # 31 doctests failed
	sage -t  -long -force_lib devel/sage/doc/en/constructions/interface_issues.rst # 4 doctests failed
	sage -t  -long -force_lib devel/sage/doc/en/constructions/plotting.rst # 3 doctests failed
	sage -t  -long -force_lib devel/sage/doc/en/tutorial/interfaces.rst # 18 doctests failed
	sage -t  -long -force_lib devel/sage/doc/en/tutorial/latex.rst # 3 doctests failed
	sage -t  -long -force_lib devel/sage/doc/en/tutorial/tour_algebra.rst # 21 doctests failed
	sage -t  -long -force_lib devel/sage/doc/en/bordeaux_2008/nf_introduction.rst # 8 doctests failed
	sage -t  -long -force_lib devel/sage/doc/fr/a_tour_of_sage/index.rst # 3 doctests failed
	sage -t  -long -force_lib devel/sage/doc/fr/tutorial/interfaces.rst # 18 doctests failed
	sage -t  -long -force_lib devel/sage/doc/fr/tutorial/tour_algebra.rst # 20 doctests failed
	sage -t  -long -force_lib devel/sage/sage/matrix/matrix2.pyx # 5 doctests failed
	sage -t  -long -force_lib devel/sage/sage/matrix/matrix1.pyx # 2 doctests failed
	sage -t  -long -force_lib devel/sage/sage/matrix/matrix_symbolic_dense.pyx # 40 doctests failed
	sage -t  -long -force_lib devel/sage/sage/combinat/combinat.py # 10 doctests failed
	sage -t  -long -force_lib devel/sage/sage/combinat/perfect_matching.py # 2 doctests failed
	sage -t  -long -force_lib devel/sage/sage/structure/element.pyx # 5 doctests failed
	sage -t  -long -force_lib devel/sage/sage/structure/formal_sum.py # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/expression_conversions.py # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/ring.pyx # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/function.pyx # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/random_tests.py # 2 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/maxima_wrapper.py # 8 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/pynac.pyx # 2 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/relation.py # 66 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/constants.py # 16 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/assumptions.py # 51 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/power_helper.pyx # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/function_factory.py # 4 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/constants_c.pyx # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/integration/external.py # 3 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/integration/integral.py # 64 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/expression.pyx # 247 doctests failed
	sage -t  -long -force_lib devel/sage/sage/algebras/quaternion_algebra_element.py # 4 doctests failed
	sage -t  -long -force_lib devel/sage/sage/algebras/group_algebra.py # 6 doctests failed
	sage -t  -long -force_lib devel/sage/sage/algebras/quatalg/quaternion_algebra_element.pyx # 36 doctests failed
	sage -t  -long -force_lib devel/sage/sage/algebras/quatalg/quaternion_algebra.py # 8 doctests failed
	sage -t  -long -force_lib devel/sage/sage/geometry/lattice_polytope.py # 3 doctests failed
	sage -t  -long -force_lib devel/sage/sage/interfaces/quit.py # 2 doctests failed
	sage -t  -long -force_lib devel/sage/sage/geometry/polyhedra.py # 2 doctests failed
	sage -t  -long -force_lib devel/sage/sage/interfaces/tests.py # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/interfaces/maxima.py # 224 doctests failed
	sage -t  -long -force_lib devel/sage/sage/rings/misc.py # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/rings/ring.pyx # 5 doctests failed
	sage -t  -long -force_lib devel/sage/sage/interfaces/expect.py # 26 doctests failed
	sage -t  -long -force_lib devel/sage/sage/rings/infinity.py # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/rings/fraction_field_element.pyx # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/rings/contfrac.py # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/rings/residue_field.pyx # 15 doctests failed
	sage -t  -long -force_lib devel/sage/sage/rings/integer_ring.pyx # 5 doctests failed
	sage -t  -long -force_lib devel/sage/sage/rings/number_field/number_field_element_quadratic.pyx # 2 doctests failed
	sage -t  -long -force_lib devel/sage/sage/rings/number_field/galois_group.py # 8 doctests failed
	sage -t  -long -force_lib devel/sage/sage/rings/number_field/number_field_base.pyx # 13 doctests failed
	sage -t  -long -force_lib devel/sage/sage/rings/number_field/order.py # 3 doctests failed
	sage -t  -long -force_lib devel/sage/sage/rings/number_field/number_field_element.pyx # 12 doctests failed
	sage -t  -long -force_lib devel/sage/sage/rings/number_field/number_field_rel.py # 10 doctests failed
	sage -t  -long -force_lib devel/sage/sage/rings/polynomial/polynomial_element.pyx # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/schemes/elliptic_curves/heegner.py # 2 doctests failed
	sage -t  -long -force_lib devel/sage/sage/schemes/elliptic_curves/ell_generic.py # 15 doctests failed
	sage -t  -long -force_lib devel/sage/sage/plot/arc.py # 2 doctests failed
	sage -t  -long -force_lib devel/sage/sage/plot/line.py # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/plot/plot.py # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/plot/plot3d/plot3d.py # 3 doctests failed
	sage -t  -long -force_lib devel/sage/sage/plot/plot3d/transform.pyx # 4 doctests failed
	sage -t  -long -force_lib devel/sage/sage/misc/citation.pyx # 2 doctests failed
	sage -t  -long -force_lib devel/sage/sage/misc/functional.py # 29 doctests failed
	sage -t  -long -force_lib devel/sage/sage/misc/latex.py # 3 doctests failed
	sage -t  -long -force_lib devel/sage/sage/misc/preparser.py # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/modular/modform/ambient_R.py # 5 doctests failed
	sage -t  -long -force_lib devel/sage/sage/modular/overconvergent/genus0.py # 19 doctests failed
	sage -t  -long -force_lib devel/sage/sage/functions/trig.py # 17 doctests failed
	sage -t  -long -force_lib devel/sage/sage/functions/other.py # 19 doctests failed
	sage -t  -long -force_lib devel/sage/sage/functions/piecewise.py # 65 doctests failed
	sage -t  -long -force_lib devel/sage/sage/functions/special.py # 69 doctests failed
	sage -t  -long -force_lib devel/sage/sage/functions/transcendental.py # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/functions/log.py # 8 doctests failed
	sage -t  -long -force_lib devel/sage/sage/functions/min_max.py # 2 doctests failed
	sage -t  -long -force_lib devel/sage/sage/functions/wigner.py # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/functions/hyperbolic.py # 9 doctests failed
	sage -t  -long -force_lib devel/sage/sage/functions/orthogonal_polys.py # 42 doctests failed
	sage -t  -long -force_lib devel/sage/sage/calculus/functional.py # 45 doctests failed
	sage -t  -long -force_lib devel/sage/sage/graphs/graph_generators.py # 6 doctests failed
	sage -t  -long -force_lib devel/sage/sage/calculus/calculus.py # 127 doctests failed
	sage -t  -long -force_lib devel/sage/sage/calculus/test_sympy.py # 7 doctests failed
	sage -t  -long -force_lib devel/sage/sage/calculus/functions.py # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/calculus/desolvers.py # 70 doctests failed
	sage -t  -long -force_lib devel/sage/sage/calculus/tests.py # 24 doctests failed
	sage -t  -long -force_lib devel/sage/sage/calculus/wester.py # 45 doctests failed
	sage -t  -long -force_lib devel/sage/sage/gsl/integration.pyx # 2 doctests failed
	sage -t  -long -force_lib devel/sage/sage/modules/free_module_element.pyx # 8 doctests failed
----------------------------------------------------------------------
Total time for all tests: 2000.6 seconds
make: *** [ptestlong] Error 128

Currently no idea what happens there...

nexttime · 2010-12-02T21:03:35Z

comment:145

Replying to @nexttime:

Going to retry, which again will take hours...

Now I get (Ubuntu 9.04 x86, gcc 4.3.3):

The following tests failed:

	sage -t  -long -force_lib devel/sage/doc/en/a_tour_of_sage/index.rst # 3 doctests failed
	sage -t  -long -force_lib devel/sage/doc/en/bordeaux_2008/nf_introduction.rst # 8 doctests failed
	sage -t  -long -force_lib devel/sage/doc/en/constructions/interface_issues.rst # 4 doctests failed
	sage -t  -long -force_lib devel/sage/doc/en/constructions/linear_algebra.rst # 5 doctests failed
	sage -t  -long -force_lib devel/sage/doc/en/constructions/polynomials.rst # 1 doctests failed
	sage -t  -long -force_lib devel/sage/doc/en/constructions/calculus.rst # 31 doctests failed
	sage -t  -long -force_lib devel/sage/doc/en/constructions/plotting.rst # 3 doctests failed
	sage -t  -long -force_lib devel/sage/doc/en/installation/source.rst # 1 doctests failed
	sage -t  -long -force_lib devel/sage/doc/en/tutorial/interfaces.rst # 18 doctests failed
	sage -t  -long -force_lib devel/sage/doc/en/tutorial/latex.rst # 3 doctests failed
	sage -t  -long -force_lib devel/sage/doc/en/tutorial/tour_algebra.rst # 21 doctests failed
	sage -t  -long -force_lib devel/sage/doc/fr/tutorial/interfaces.rst # 18 doctests failed
	sage -t  -long -force_lib devel/sage/doc/fr/a_tour_of_sage/index.rst # 3 doctests failed
	sage -t  -long -force_lib devel/sage/doc/fr/tutorial/tour_algebra.rst # 20 doctests failed
	sage -t  -long -force_lib devel/sage/sage/combinat/perfect_matching.py # 2 doctests failed
	sage -t  -long -force_lib devel/sage/sage/combinat/combinat.py # 10 doctests failed
	sage -t  -long -force_lib devel/sage/sage/geometry/lattice_polytope.py # 3 doctests failed
	sage -t  -long -force_lib devel/sage/sage/geometry/polyhedra.py # 2 doctests failed
	sage -t  -long -force_lib devel/sage/sage/schemes/elliptic_curves/heegner.py # 2 doctests failed
	sage -t  -long -force_lib devel/sage/sage/schemes/elliptic_curves/ell_generic.py # 15 doctests failed
	sage -t  -long -force_lib devel/sage/sage/misc/latex.py # 3 doctests failed
	sage -t  -long -force_lib devel/sage/sage/misc/preparser.py # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/misc/functional.py # 29 doctests failed
	sage -t  -long -force_lib devel/sage/sage/misc/citation.pyx # 2 doctests failed
	sage -t  -long -force_lib devel/sage/sage/graphs/graph_generators.py # 6 doctests failed
	sage -t  -long -force_lib devel/sage/sage/gsl/integration.pyx # 2 doctests failed
	sage -t  -long -force_lib devel/sage/sage/modules/free_module_element.pyx # 8 doctests failed
	sage -t  -long -force_lib devel/sage/sage/matrix/matrix1.pyx # 2 doctests failed
	sage -t  -long -force_lib devel/sage/sage/matrix/matrix2.pyx # 5 doctests failed
	sage -t  -long -force_lib devel/sage/sage/matrix/matrix_symbolic_dense.pyx # 40 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/power_helper.pyx # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/relation.py # 66 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/pynac.pyx # 2 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/function.pyx # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/function_factory.py # 4 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/ring.pyx # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/random_tests.py # 2 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/constants_c.pyx # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/maxima_wrapper.py # 8 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/expression_conversions.py # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/constants.py # 16 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/assumptions.py # 51 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/expression.pyx # 247 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/integration/integral.py # 64 doctests failed
	sage -t  -long -force_lib devel/sage/sage/symbolic/integration/external.py # 3 doctests failed
	sage -t  -long -force_lib devel/sage/sage/rings/infinity.py # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/rings/fraction_field_element.pyx # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/rings/ring.pyx # 5 doctests failed
	sage -t  -long -force_lib devel/sage/sage/rings/residue_field.pyx # 15 doctests failed
	sage -t  -long -force_lib devel/sage/sage/rings/misc.py # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/rings/contfrac.py # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/rings/integer_ring.pyx # 5 doctests failed
	sage -t  -long -force_lib devel/sage/sage/rings/polynomial/polynomial_element.pyx # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/rings/number_field/order.py # 3 doctests failed
	sage -t  -long -force_lib devel/sage/sage/rings/number_field/galois_group.py # 8 doctests failed
	sage -t  -long -force_lib devel/sage/sage/rings/number_field/number_field_element_quadratic.pyx # 2 doctests failed
	sage -t  -long -force_lib devel/sage/sage/rings/number_field/number_field_element.pyx # 12 doctests failed
	sage -t  -long -force_lib devel/sage/sage/rings/number_field/number_field_base.pyx # 13 doctests failed
	sage -t  -long -force_lib devel/sage/sage/rings/number_field/number_field_rel.py # 10 doctests failed
	sage -t  -long -force_lib devel/sage/sage/calculus/functions.py # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/calculus/calculus.py # 127 doctests failed
	sage -t  -long -force_lib devel/sage/sage/calculus/desolvers.py # 70 doctests failed
	sage -t  -long -force_lib devel/sage/sage/calculus/tests.py # 24 doctests failed
	sage -t  -long -force_lib devel/sage/sage/calculus/functional.py # 45 doctests failed
	sage -t  -long -force_lib devel/sage/sage/calculus/test_sympy.py # 7 doctests failed
	sage -t  -long -force_lib devel/sage/sage/calculus/wester.py # 45 doctests failed
	sage -t  -long -force_lib devel/sage/sage/functions/special.py # 69 doctests failed
	sage -t  -long -force_lib devel/sage/sage/functions/log.py # 8 doctests failed
	sage -t  -long -force_lib devel/sage/sage/functions/wigner.py # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/functions/min_max.py # 2 doctests failed
	sage -t  -long -force_lib devel/sage/sage/functions/hyperbolic.py # 9 doctests failed
	sage -t  -long -force_lib devel/sage/sage/functions/transcendental.py # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/functions/piecewise.py # 65 doctests failed
	sage -t  -long -force_lib devel/sage/sage/functions/orthogonal_polys.py # 42 doctests failed
	sage -t  -long -force_lib devel/sage/sage/functions/other.py # 19 doctests failed
	sage -t  -long -force_lib devel/sage/sage/functions/trig.py # 17 doctests failed
	sage -t  -long -force_lib devel/sage/sage/plot/line.py # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/plot/plot.py # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/plot/arc.py # 2 doctests failed
	sage -t  -long -force_lib devel/sage/sage/plot/plot3d/plot3d.py # 3 doctests failed
	sage -t  -long -force_lib devel/sage/sage/plot/plot3d/transform.pyx # 4 doctests failed
	sage -t  -long -force_lib devel/sage/sage/structure/element.pyx # 5 doctests failed
	sage -t  -long -force_lib devel/sage/sage/structure/formal_sum.py # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/interfaces/expect.py # 26 doctests failed
	sage -t  -long -force_lib devel/sage/sage/interfaces/tests.py # 1 doctests failed
	sage -t  -long -force_lib devel/sage/sage/interfaces/maxima.py # 224 doctests failed
	sage -t  -long -force_lib devel/sage/sage/interfaces/quit.py # 2 doctests failed
	sage -t  -long -force_lib devel/sage/sage/algebras/group_algebra.py # 6 doctests failed
	sage -t  -long -force_lib devel/sage/sage/algebras/quaternion_algebra_element.py # 4 doctests failed
	sage -t  -long -force_lib devel/sage/sage/algebras/quatalg/quaternion_algebra_element.pyx # 36 doctests failed
	sage -t  -long -force_lib devel/sage/sage/algebras/quatalg/quaternion_algebra.py # 8 doctests failed
	sage -t  -long -force_lib devel/sage/sage/modular/overconvergent/genus0.py # 19 doctests failed
	sage -t  -long -force_lib devel/sage/sage/modular/modform/ambient_R.py # 5 doctests failed
----------------------------------------------------------------------
Total time for all tests: 13357.2 seconds

which at first glance doesn't look much different; 525 doctest errors.

nexttime · 2010-12-02T21:10:16Z

comment:146

(Note that on all systems vanilla Sage 4.6.1.alpha2 passes all tests.)

vbraun · 2010-12-02T21:28:28Z

comment:147

If you would tell us what the error is then that would be much more useful than a list of failed tests. All of these work fine on Fedora 14 with sage-4.6.1.alpha2 and the new maxima/ecl. My first guess would be that you forgot to apply one of the patches (been there, done that), can you double-check?

nexttime · 2010-12-02T22:47:49Z

comment:148

Well, I didn't attach the logs since they're huge.

I've reverted all changes and started from scratch, and now all tests pass on the Ubuntu 9.04 x86_64 machine. I have absolutely no idea what went wrong in the first two attempts; in the succeeding one I used Sage's hg to apply the patches, after installing the spkgs, and afterwards ran ./sage -ba-force (rather than just ./sage -b), which IMHO shouldn't be necessary.

I did apply all patches in the right order in all cases, so something else must be wrong. Never experienced similar before...

sagetrac-drkirkby · 2010-12-02T23:10:28Z

comment:149

The patches on this ticket are not so easy to apply as usual, as part of them is already in Sage 4.6.1.alpha2. What we don't have on this ticket are changes relative to 4.6.1.alpha2.

I've built sage 4.6.1.alpha1 with the patches applied and the new .spkg files. This is on a Sun Ultra 27, 3.33 GHz Xeon processor running OpenSolaris 06/2009.

----------------------------------------------------------------------
All tests passed!
Total time for all tests: 1560.4 seconds
drkirkby@hawk:~/new/sage-4.6.1.alpha1$

I wonder if Leif's problems had anything to the patch process going wrong?

Dave

jdemeyer · 2010-12-02T23:16:12Z

comment:150

Replying to @sagetrac-drkirkby:

The patches on this ticket are not so easy to apply as usual, as part of them is already in Sage 4.6.1.alpha2.

Really? If that's true, it was unintentional. Which patches are in sage-4.6.1.alpha2?

nexttime · 2010-12-02T23:39:49Z

comment:151

Replying to @jdemeyer:

Replying to @sagetrac-drkirkby:

The patches on this ticket are not so easy to apply as usual, as part of them is already in Sage 4.6.1.alpha2.

Really? If that's true, it was unintentional. Which patches are in sage-4.6.1.alpha2?

I don't think so. I've applied all patches multiple times with -v and different Mercurial versions; no rejects, no moved hunks.

One problem I ran into seems to be that when running make with SAGE_UPGRADING=yes to (safely) install spkgs the Sage library install completely ignores the current branch, and switches back to sage-main, such that previously applied patches "vanish".

Another odd thing I discovered is that at least on Ubuntu 9.04, gcc run from Sage picks up Sage's MPFR (and GMP/MPIR).

nexttime · 2010-12-02T23:46:30Z

comment:152

Replying to @nexttime:

One problem I ran into seems to be that when running make with SAGE_UPGRADING=yes to (safely) install spkgs the Sage library install completely ignores the current branch, and switches back to sage-main, such that previously applied patches "vanish".

... which means one has to apply patches to the Sage library after all spkgs have been installed that way.

Also, there seems to be a missing dependency for libcsage, i.e. SCons doesn't always rebuild it when necessary, so one has to run ./sage -ba-force.

sagetrac-drkirkby · 2010-12-02T23:49:30Z

comment:153

Replying to @jdemeyer:

Replying to @sagetrac-drkirkby:

The patches on this ticket are not so easy to apply as usual, as part of them is already in Sage 4.6.1.alpha2.

Really? If that's true, it was unintentional. Which patches are in sage-4.6.1.alpha2?

I guess I must have been mistaken - perhaps my alpha2 was not "clean", though I thought I'd extracted a fresh tarball.

Anyway, several others have got all passes, and I got all passes if I apply this to sage-4.6.1.alpha1.

I would say I'd try again with sage-4.6.1.alpha2, but it is late here, and I'm not going to start a build now, as you wont get the results until I wake in the morning. I'm pretty convinced this is OK. To my knowledge, the only thing was some minor changes Leif wanted to the ECL package, and those have been addressed. Leif seemed happy, so I'm setting this to positive.

sagetrac-drkirkby · 2010-12-03T00:22:48Z

comment:154

Replying to @nexttime:

Another odd thing I discovered is that at least on Ubuntu 9.04, gcc run from Sage picks up Sage's MPFR (and GMP/MPIR).

I'm not surprised by that, as LD_LIBRARY_PATH gets $SAGE_LOCAL/lib prepended to it when sage is run..

When building gcc, the configure options like --with-gmp=/path/to/gmp only tell the first stage build of the compiler where to find the libraries. They do not hard-code the path of the libraries, though there are ways of doing that if you wish when building gcc. If your not careful, it is easy to build gcc where the first stage of the build works, as it finds the GMP and MPFR libraries, but the second stage fails. That's hit many people on Solaris systems, a they often will not have suitable versions of the libraries on the system.

Dave

sagetrac-drkirkby · 2010-12-03T00:34:34Z

comment:155

I'm just changing the ticket title, to be more explicit.

nexttime · 2010-12-03T01:04:18Z

comment:156

Replying to @sagetrac-drkirkby:

Replying to @nexttime:

Another odd thing I discovered is that at least on Ubuntu 9.04, gcc run from Sage picks up Sage's MPFR (and GMP/MPIR).

I'm not surprised by that, as LD_LIBRARY_PATH gets $SAGE_LOCAL/lib prepended to it when sage is run..

Yes, but I would have expected the Debian or Ubuntu developers to set the RPATH.

Not many people like setting LD_LIBRARY_PATH (which is empty outside Sage btw.).

nexttime · 2010-12-03T06:56:42Z

comment:157

Finally passed all tests (ptestlong) with Sage 4.6.1.alpha2 on

Ubuntu 9.04 x86 (gcc 4.3.3),
Ubuntu 9.04 x86_64 (gcc 4.3.3), with and without the new MPIR and GMP-ECM (Upgrade Sage's MPIR spkg to version 2.1.3 #8664 / Update GMP-ECM to 6.3 #5847),
Ubuntu 10.04 x86_64 (gcc 4.4.3) with the new MPIR and GMP-ECM.

Sorry for the noise.

jdemeyer · 2010-12-03T09:38:51Z

Merged: sage-4.6.1.alpha3

jasongrout · 2010-12-06T13:25:55Z

comment:159

I just wanted to say "Bravo!" to everyone that has diligently worked on this. Thanks for your work!

vbraun added this to the sage-4.6.1 milestone Oct 29, 2010

vbraun added c: packages: standard labels Oct 29, 2010

vbraun added the s: needs review label Oct 29, 2010

sagetrac-drkirkby mannequin added s: needs work and removed s: needs review labels Oct 30, 2010

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sagetrac-drkirkby mannequin added s: positive review and removed s: needs review labels Dec 2, 2010

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sagetrac-drkirkby mannequin changed the title ~~Update ecl and maxima~~ Update ECL to 10.4.1 and Maxima to 5.22.1 - currently the latest releases. Dec 3, 2010

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kcrisman mentioned this issue Nov 18, 2010

Discrepancy in symbol ordering in multiplication #10282

Closed

sagetrac-mvngu mannequin mentioned this issue Jun 14, 2011

add doctests from #8582 and other integration improvements from Maxima 5.22.1 #10434

Closed

Update ECL to 10.4.1 and Maxima to 5.22.1 - currently the latest releases. #10187

Update ECL to 10.4.1 and Maxima to 5.22.1 - currently the latest releases. #10187

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