Sage 9.3.rc5 released

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Volker Braun

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Apr 30, 2021, 7:13:29 PM4/30/21
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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 

c27d4d6803 (tag: 9.3.rc5, trac/develop) Updated SageMath version to 9.3.rc5
b570ac37fd Trac #31640: 2d Bezier path does not plot in 3d
bc54836830 Trac #31646: clean BezierPath constructor
bd3334c774 Trac #30518: eigenvectors over QQbar are incorrectly conjugated
de9c3d51b3 Trac #31628: fix/improve conversions to QQbar and AA
96c2708fce Trac #31641: Remove outdated MacPorts/fink ban
64b0382bba Trac #31625: Memory leak for IntegralLattice
068797f2a1 Trac #31620: Document installing sagemath kernel without copying documentation
d4650fc337 Trac #31612: Update setuptools_scm to 6.0.1
69db9b24f3 Trac #31600: threejs does not handle transparency correctly
5482111309 Trac #31541: GH Actions: Update 32-bit platforms
0e8c26ba6a Trac #29372: At the end of configure, show installation hints for non-enabled optional packages separately
a0672c621b Trac #31673: MR53: Unbreak sagelib's setup.py install
80c2258835 Trac #31645: incorrect handling of constant term when creating power series
889f3f9e16 Trac #31555: Update freetype to 2.10.4 - fixes a vulnerability
6d8b561fec Trac #25034: Special case for gen_legendre_P with n == m gives incorrect results for x in (-1,1)
990c9bc3b0 Trac #31679: Actually fix: "Do not use pynac's poly_mul_expand function until it has been debugged"
de32db6991 (tag: 9.3.rc4) Updated SageMath version to 9.3.rc4


Enrique Artal

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May 1, 2021, 10:20:01 AM5/1/21
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I have tried to compile it in Fedora 34, I know it is a very recent release and problems would be expected. The first one is that F34 uses gcc11 and it seems to be incompatible with sage, so when installing it uses gcc 9.2 package. After some problems I decided to run `make distclean` for a fresh install. I ran into some problems but 

`./configure --with-system-zeromq=no --with-system-eclib=no --with-system-flint=no --with-system-flintqs=no --with-system-ntl=no` 

finished with apparent success (in fact I did not apply the whole order once, I ran each one separately to solve compiling issues). 

The problem is that running sage I get a crash; I can attach the whole crash report but maybe the relevant line is:

ImportError: /usr/local/sage/local/lib/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /lib64/libvmaf.so.0)

I got a similar message with libzmq and this was the reason to add  --with-system-zeromq=no, but I do not guess what to do now.

Thanks for the work, Enrique

Enrique Artal

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May 1, 2021, 10:54:32 AM5/1/21
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After some extra trial make build after
./configure --with-system-zeromq=no --with-system-eclib=no --with-system-flint=no --with-system-flintqs=no --with-system-ntl=no --with-system-libgd=no --with-system-brial=no
works

Dima Pasechnik

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May 1, 2021, 2:57:38 PM5/1/21
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On Sat, 1 May 2021, 15:20 Enrique Artal, <enriqu...@gmail.com> wrote:
I have tried to compile it in Fedora 34, I know it is a very recent release and problems would be expected. The first one is that F34 uses gcc11 and it seems to be incompatible with sage, so when installing it uses gcc 9.2 package. After some problems I decided to run `make distclean` for a fresh install. I ran into some problems but 

`./configure --with-system-zeromq=no --with-system-eclib=no --with-system-flint=no --with-system-flintqs=no --with-system-ntl=no` 

finished with apparent success (in fact I did not apply the whole order once, I ran each one separately to solve compiling issues). 

The problem is that running sage I get a crash; I can attach the whole crash report but maybe the relevant line is:

ImportError: /usr/local/sage/local/lib/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /lib64/libvmaf.so.0)


this is a C++ incompatibility issue - if you insists on using gcc 9 you might have to supply all the C++ libs needed by Sage rebuilt with gcc 9.

I'd rather try gcc 11 instead.


I got a similar message with libzmq and this was the reason to add  --with-system-zeromq=no, but I do not guess what to do now.

Thanks for the work, Enrique
El sábado, 1 de mayo de 2021 a las 1:13:29 UTC+2, Volker Braun escribió:
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 

c27d4d6803 (tag: 9.3.rc5, trac/develop) Updated SageMath version to 9.3.rc5
b570ac37fd Trac #31640: 2d Bezier path does not plot in 3d
bc54836830 Trac #31646: clean BezierPath constructor
bd3334c774 Trac #30518: eigenvectors over QQbar are incorrectly conjugated
de9c3d51b3 Trac #31628: fix/improve conversions to QQbar and AA
96c2708fce Trac #31641: Remove outdated MacPorts/fink ban
64b0382bba Trac #31625: Memory leak for IntegralLattice
068797f2a1 Trac #31620: Document installing sagemath kernel without copying documentation
d4650fc337 Trac #31612: Update setuptools_scm to 6.0.1
69db9b24f3 Trac #31600: threejs does not handle transparency correctly
5482111309 Trac #31541: GH Actions: Update 32-bit platforms
0e8c26ba6a Trac #29372: At the end of configure, show installation hints for non-enabled optional packages separately
a0672c621b Trac #31673: MR53: Unbreak sagelib's setup.py install
80c2258835 Trac #31645: incorrect handling of constant term when creating power series
889f3f9e16 Trac #31555: Update freetype to 2.10.4 - fixes a vulnerability
6d8b561fec Trac #25034: Special case for gen_legendre_P with n == m gives incorrect results for x in (-1,1)
990c9bc3b0 Trac #31679: Actually fix: "Do not use pynac's poly_mul_expand function until it has been debugged"
de32db6991 (tag: 9.3.rc4) Updated SageMath version to 9.3.rc4


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Enrique Artal

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May 1, 2021, 4:39:55 PM5/1/21
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I would prefer to use gcc 11, but forcing it with configure did not work. 

François Bissey

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May 1, 2021, 4:41:40 PM5/1/21
to 'Justin C. Walker' via sage-release


> On 2/05/2021, at 06:57, Dima Pasechnik <dim...@gmail.com> wrote:
>
> I'd rather try gcc 11 instead.

If you want. We already have an issue in compiling fplll
https://github.com/fplll/fplll/issues/462
and sage itself doesn’t compile because of some issue in lcalc
as far as I can see.
https://github.com/cschwan/sage-on-gentoo/issues/634

François

Kenji Iohara

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May 1, 2021, 8:16:32 PM5/1/21
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On my Mac Book Pro with OS 11.3, I could compile it from the first built and all test passed.

> 01/05/2021 22:41、François Bissey <frp.b...@gmail.com>のメール:
> --
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Matthias Köppe

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May 1, 2021, 11:11:28 PM5/1/21
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On Saturday, May 1, 2021 at 11:57:38 AM UTC-7 Dima Pasechnik wrote:
On Sat, 1 May 2021, 15:20 Enrique Artal, <enriqu...@gmail.com> wrote:
I have tried to compile it in Fedora 34, I know it is a very recent release and problems would be expected. The first one is that F34 uses gcc11 and it seems to be incompatible with sage, so when installing it uses gcc 9.2 package. [...]
ImportError: /usr/local/sage/local/lib/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /lib64/libvmaf.so.0)
this is a C++ incompatibility issue - if you insists on using gcc 9 you might have to supply all the C++ libs needed by Sage rebuilt with gcc 9.


We should update the gcc spkg to use the latest 10.x gcc.


 

Samuel Lelièvre

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May 2, 2021, 4:37:42 AM5/2/21
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2021-05-01 à 01:13, Volker Braun:
>
> c27d4d6803 (tag: 9.3.rc5, trac/develop) Updated SageMath version to 9.3.rc5

Thanks for this new release.

On macOS 10.14.6, using many Homebrew packages,
the build from a working 9.3.rc4 succeeds. Running

make testlong

gives two failing doctests:
```
$ make testlong
...
----------------------------------------------------------------------
sage -t --long --warn-long 83.9 --random-seed=0
src/sage/tests/gap_packages.py # 1 doctest failed
sage -t --long --warn-long 83.9 --random-seed=0
src/sage/groups/abelian_gps/abelian_group_gap.py # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 16587.5 seconds
cpu time: 13377.4 seconds
cumulative wall time: 16162.1 seconds
make: *** [testlong] Error 1
$ ./sage -t --long --warn-long 83.9 --random-seed=0
src/sage/tests/gap_packages.py
Running doctests with ID 2021-05-02-10-31-33-5cd29e42.
Git branch: develop
Using --optional=build,dochtml,gap_packages,homebrew,libsemigroups,pip,sage,sage_spkg
Doctesting 1 file.
sage -t --long --warn-long 83.9 --random-seed=0 src/sage/tests/gap_packages.py
**********************************************************************
File "src/sage/tests/gap_packages.py", line 8, in sage.tests.gap_packages
Failed example:
test_packages(pkgs, only_failures=True) # optional - gap_packages
Expected:
...
Status Package GAP Output
+--------+---------+------------+
Got:
Status Package GAP Output
+--------+---------+------------+
**********************************************************************
1 item had failures:
1 of 5 in sage.tests.gap_packages
[11 tests, 1 failure, 10.67 s]
----------------------------------------------------------------------
sage -t --long --warn-long 83.9 --random-seed=0
src/sage/tests/gap_packages.py # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 10.8 seconds
cpu time: 9.2 seconds
cumulative wall time: 10.7 seconds
$ ./sage -t --long --warn-long 83.9 --random-seed=0
src/sage/groups/abelian_gps/abelian_group_gap.py
Running doctests with ID 2021-05-02-10-32-11-efc7940c.
Git branch: develop
Using --optional=build,dochtml,gap_packages,homebrew,libsemigroups,pip,sage,sage_spkg
Doctesting 1 file.
sage -t --long --warn-long 83.9 --random-seed=0
src/sage/groups/abelian_gps/abelian_group_gap.py
**********************************************************************
File "src/sage/groups/abelian_gps/abelian_group_gap.py", line 201, in
sage.groups.abelian_gps.abelian_group_gap.AbelianGroupElement_polycyclic
Failed example:
TestSuite(G.an_element()).run() # optional - gap_packages
Expected nothing
Got:
Failure in _test_pickling:
Traceback (most recent call last):
File "/opt/s/sage93k/local/lib/python3.9/site-packages/sage/misc/sage_unittest.py",
line 297, in run
test_method(tester=tester)
File "sage/structure/sage_object.pyx", line 647, in
sage.structure.sage_object.SageObject._test_pickling
(build/cythonized/sage/structure/sage_object.c:5023)
tester.assertEqual(loads(dumps(self)), self)
File "sage/misc/persist.pyx", line 935, in
sage.misc.persist.loads (build/cythonized/sage/misc/persist.c:7536)
return unpickler.load()
File "sage/structure/parent.pyx", line 898, in
sage.structure.parent.Parent.__call__
(build/cythonized/sage/structure/parent.c:9335)
return mor._call_(x)
File "sage/structure/coerce_maps.pyx", line 161, in
sage.structure.coerce_maps.DefaultConvertMap_unique._call_
(build/cythonized/sage/structure/coerce_maps.c:4622)
raise
File "sage/structure/coerce_maps.pyx", line 156, in
sage.structure.coerce_maps.DefaultConvertMap_unique._call_
(build/cythonized/sage/structure/coerce_maps.c:4514)
return C._element_constructor(x)
File "/opt/s/sage93k/local/lib/python3.9/site-packages/sage/groups/abelian_gps/abelian_group_gap.py",
line 368, in _element_constructor_
x *= gens_gap[i]**(exp[i] % orders[i])
File "sage/rings/integer.pyx", line 3413, in
sage.rings.integer.Integer.__mod__
(build/cythonized/sage/rings/integer.c:22616)
raise ZeroDivisionError("Integer modulo by zero")
ZeroDivisionError: Integer modulo by zero
------------------------------------------------------------
The following tests failed: _test_pickling
**********************************************************************
1 item had failures:
1 of 4 in sage.groups.abelian_gps.abelian_group_gap.AbelianGroupElement_polycyclic
[247 tests, 1 failure, 0.68 s]
----------------------------------------------------------------------
sage -t --long --warn-long 83.9 --random-seed=0
src/sage/groups/abelian_gps/abelian_group_gap.py # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 0.8 seconds
cpu time: 0.6 seconds
cumulative wall time: 0.7 seconds
```

Emmanuel Charpentier

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May 2, 2021, 9:03:58 AM5/2/21
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On Debian testing running on core i7 + 16 GB RAM (using gcc 10.2.1, FWIW) upgrading 9.3.rc2 (configured to use all available system packages) to 9.3.rc5 and running ptestlong results in one transient and two permanent failures (identical to those already reported for previous betas) :

File Results P/T
src/sage/tests/parigp.py Timed out T
src/sage/tests/gap_packages.py 1 doctest failed P
src/sage/groups/abelian_gps/abelian_group_gap.py 1 doctest failed P

HTH,

Emmanuel Charpentier

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May 5, 2021, 4:31:39 PM5/5/21
to sage-release

On another, long neglected, Debian testing machine, upgrading from 9.3.beta4 to 9.3.rc5 failed spectacularly, with a long list of errors pointing to various systems failing to find the 20.4 version of eclib. Rebuilding from scratch gave the same results as the previous Debian machine, modulo the parigp timeout, which doesn’t happen on this desktop machine.

HTH,

Matthias Köppe

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May 6, 2021, 1:22:35 PM5/6/21
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I have opened https://trac.sagemath.org/ticket/31786 
Meta-ticket: Support gcc 11 

This should be for Sage 9.4

Matthias Köppe

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May 6, 2021, 2:34:08 PM5/6/21
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On Friday, April 30, 2021 at 4:13:29 PM UTC-7 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 

c27d4d6803 (tag: 9.3.rc5, trac/develop) Updated SageMath version to 9.3.rc5

Thanks for preparing the new release candidate.

Following up on my previous summary of GH Actions runs for 9.3.rc2 in https://groups.google.com/g/sage-release/c/6WjKQt_e_B8/m/dpx1qILOCwAJ:

First time in a long time that the cygwin-standard build on GH Actions ran through. We have not done anything to fix https://trac.sagemath.org/ticket/31565 ("Build still non-portable despite SAGE_FAT_BINARY=yes because of numpy"), so this could either be a result of chance, or due to changes in Cygwin or changes to how GH Actions allocates machines. There are a number of doctest failures (https://github.com/sagemath/sage/runs/2485275132) that result from running the doctests without building the documentation first. Overall looking good.

The issue with fedora-34 system NTL (https://trac.sagemath.org/ticket/31624), first reported for 9.3.beta8, has become critical now that Fedora 34 has been released. I would suggest that we make an emergency fix to the ntl spkg-configure.m4 so that it rejects system NTL if we reject system gcc.


 
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