Sage 9.3.beta4 released

Volker Braun

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Dec 14, 2020, 7:22:48 PM12/14/20

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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

c4a802d2b6 (tag: 9.3.beta4) Updated SageMath version to 9.3.beta4

2fc350e432 Trac #30947: src/doc/bootstrap: Simplify by using new options of "sage -package list"

831e4e254d Trac #30628: Change font of axis labels in Three.js

92dcaf2e03 Trac #30613: Fix clipping issue for plots with small/large extents in Three.js

16741fff2c Trac #30612: Set title of HTML page with Three.js viewer

c25b0765a1 Trac #31037: Install tests in sage/tests/books

da907c1d39 Trac #31032: some raw string for pdf doc building in sage-on-gentoo

592c73ab37 Trac #31030: Adapt shuffle to deprecation in Python 3.9

f654b46a12 Trac #31026: sparse6 encoding for canonical graphs returns encoding of original graph

a01afbaefa Trac #31023: 2 internet doctests failing in findstat.py and oeis.py

1dc015c7ba Trac #31018: Prevent setting an empty CC/CXX

9076db9f98 Trac #30994: Improvements to multiple zeta values

365b32845b Trac #30987: fix lcalc on gcc-10

d297724750 Trac #30974: sage --package create PACKAGE --pypi

433b9fb730 Trac #30968: bootstrap: Simplify by using new options of "sage -package list"

eae1a0873e Trac #30962: use Parent in shuffle

e29abcfc83 Trac #30957: tox.ini, GH Actions: Add ubuntu-hirsute, linuxmint-20*, fedora-34; update debian-bullseye packages

c52506e500 Trac #30619: tox.ini: Add opensuse, add/update opensuse.txt across build/pkgs/

7503467d30 Trac #30587: Remove import of 'ppl' at startup using lazy_import with feature

0f32a15ce1 Trac #30549: Remove all the bitset access from cython files in combinatorial polyhedron

97aaf2e520 Trac #30539: More Void Linux spkg's

494c975e8d Trac #30375: Gather and clean up compiler flags

6bde0c04d5 Trac #30315: Switch jsmol to jupyter-jsmol

3f1f938f1c Trac #30154: GH Actions: cygwin: Use incremental archives for the sage-local artifact

32692c0556 Trac #30013: src/bin/sage-env: Make sure $SAGE_VENV/bin is at the beginning of the PATH

b997715b95 Trac #29852: sage: Determine SAGE_LOCAL, SAGE_ROOT via sage-config if it exists

c06aabc942 Trac #29850: Install sage-env-config as part of sage_conf

5f46b34049 Trac #29314: update GAP to version 4.11, libsemigroup to 1.0.9

3d61303663 Trac #28712: clarify acceptable input to prime_range

790c30db33 Trac #28623: Upgrade Arb to 2.18.1

77f7f815b8 Trac #31022: symmetrica: Add xz as dependency

b2c45d9162 Trac #31020: build/make/Makefile.in: Fix SAGE_CHECK logic, conditionalize sagetex dependencies on SAGE_CHECK

3dff3f40e6 Trac #31002: Specify bdist temp folder for WSL compatibility

fc7304a52d Trac #30970: Graphic function point() broken

eec48d9c5d Trac #31011: Update docs in src/sage/matrix/matrix0.pyx to use \dots instead of \hdots

9d862ed8e1 Trac #18406: Fix times in graphics doc

f252d8dd8f Trac #10653: Formatting error in doc for dynamic classes

e2d56a5a31 Trac #31014: flake8 for combinatorial Hopf algebras

1178a486f3 Trac #30988: small enhancement of MZV

462c509b37 Trac #30978: perl_cpan_polymake_prereq: Fix up install script

2f5d153968 Trac #30973: partial flake8 cleanup for misc/

dd3a160370 Trac #30967: partial flake8 cleanup for tableau

2a3296d3a7 Trac #30966: another wave of cleanup for pbori

ec88350ebe Trac #30952: conversions of posets to macaulay2

8d3a6a16fb Trac #30943: refresh fully commutative elements

c76fee190f Trac #30917: refresh the Weyl character ring

2c7e79a898 Trac #30900: Remove last traces of zope_interface

acea57e349 Trac #30890: distros info for tox

0363814f57 Trac #30822: some typos inside combinat, found by sage --tox

e6d607125e Trac #30857: additional compatibility wrappers after #24483

a4f8406bb1 Trac #30823: some typos in elliptic curves and flake8 for BSD.py

e9727bf30b Trac #31015: Cysignals testsuite fails due to FORTIFY_SOURCE

2a850d5aa1 Trac #30996: adding an option for the opposite product in free Zinbiel algebras

bb9ceadc8a Trac #30985: Update sympy to 1.7

ca088c9c93 (tag: 9.3.beta3, trac/develop) Updated SageMath version to 9.3.beta3

Thierry Dumont

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Dec 15, 2020, 3:24:51 AM12/15/20

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On Ubuntu 20-10, upgrading from 9.2 to 9.3:
-compilation ok.
-make ptestlong:

----------------------------------------------------------------------
sage -t --long --warn-long 90.3 --random-seed=0
src/sage/tests/cmdline.py # 2 doctests failed
sage -t --long --warn-long 90.3 --random-seed=0
src/sage/modules/fg_pid/fgp_module.py # 3 doctests failed
sage -t --long --warn-long 90.3 --random-seed=0
src/doc/en/constructions/algebraic_geometry.rst # 1 doctest failed
sage -t --long --warn-long 90.3 --random-seed=0
src/doc/en/developer/coding_in_other.rst # 1 doctest failed
sage -t --long --warn-long 90.3 --random-seed=0
src/sage/modules/free_module_morphism.py # 3 doctests failed
----------------------------------------------------------------------

David Coudert

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Dec 15, 2020, 4:32:02 AM12/15/20

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I’m unable to upgrade from 9.3.beta3 on fedora 32.

It fails during bootstrap. See attached file.

Thank you for your help.

David.

output.txt

David Coudert

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Dec 15, 2020, 4:42:27 AM12/15/20

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Another issue (this time on masOS 10.15.7): it seems that libsemigroups-1.0.9 is not present on mirrors.

make --no-print-directory libsemigroups-no-deps

sage-logger -p 'SAGE_CHECK=no sage-spkg   libsemigroups-1.0.9' '/Users/dcoudert/sage/logs/pkgs/libsemigroups-1.0.9.log'

[libsemigroups-1.0.9] installing. Log file: /Users/dcoudert/sage/logs/pkgs/libsemigroups-1.0.9.log

  [libsemigroups-1.0.9] error installing, exit status 1. End of log file:

  [libsemigroups-1.0.9]   [xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx]

  [libsemigroups-1.0.9]   ERROR [transfer|run:135]: [Errno 404] Not Found: '//mirrors.nju.edu.cn/sagemath/spkg/upstream/libsemigroups/libsemigroups-1.0.9.tar.gz'

  [libsemigroups-1.0.9]   http://ftp.leg.uct.ac.za/pub/packages/sage/spkg/upstream/libsemigroups/libsemigroups-1.0.9.tar.gz

  [libsemigroups-1.0.9]   [xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx]

  [libsemigroups-1.0.9]   ERROR [transfer|run:135]: [Errno 404] Not Found: '//ftp.leg.uct.ac.za/pub/packages/sage/spkg/upstream/libsemigroups/libsemigroups-1.0.9.tar.gz'

  [libsemigroups-1.0.9]   http://sagemath.c3sl.ufpr.br/spkg/upstream/libsemigroups/libsemigroups-1.0.9.tar.gz

  [libsemigroups-1.0.9]   [xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx]

  [libsemigroups-1.0.9]   ERROR [transfer|run:135]: [Errno 404] Not Found: '//sagemath.c3sl.ufpr.br/spkg/upstream/libsemigroups/libsemigroups-1.0.9.tar.gz'

  [libsemigroups-1.0.9]   http://mirrors.ustc.edu.cn/sagemath/spkg/upstream/libsemigroups/libsemigroups-1.0.9.tar.gz

  [libsemigroups-1.0.9]   [xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx]

  [libsemigroups-1.0.9]   ERROR [transfer|run:135]: [Errno 404] Not Found: '//mirrors.ustc.edu.cn/sagemath/spkg/upstream/libsemigroups/libsemigroups-1.0.9.tar.gz'

  [libsemigroups-1.0.9]   http://mirrors.tuna.tsinghua.edu.cn/sagemath/spkg/upstream/libsemigroups/libsemigroups-1.0.9.tar.gz

  [libsemigroups-1.0.9]   [xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx]

  [libsemigroups-1.0.9]   ERROR [transfer|run:135]: [Errno 404] Not Found: '//mirrors.tuna.tsinghua.edu.cn/sagemath/spkg/upstream/libsemigroups/libsemigroups-1.0.9.tar.gz'

  [libsemigroups-1.0.9]   https://mirror.csclub.uwaterloo.ca/sage/spkg/upstream/libsemigroups/libsemigroups-1.0.9.tar.gz

  [libsemigroups-1.0.9]   [xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx]

  [libsemigroups-1.0.9]   ERROR [transfer|run:135]: [Errno 404] Not Found: '//mirror.csclub.uwaterloo.ca/sage/spkg/upstream/libsemigroups/libsemigroups-1.0.9.tar.gz'

  [libsemigroups-1.0.9]   http://sagepad.org/spkg/upstream/libsemigroups/libsemigroups-1.0.9.tar.gz

  [libsemigroups-1.0.9]   [xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx]

  [libsemigroups-1.0.9]   ERROR [transfer|run:135]: [Errno 404] Not Found: '//sagepad.org/spkg/upstream/libsemigroups/libsemigroups-1.0.9.tar.gz'

  [libsemigroups-1.0.9]   ************************************************************************

  [libsemigroups-1.0.9]   Traceback (most recent call last):

  [libsemigroups-1.0.9]     File "/Users/dcoudert/sage/build/bin/../sage_bootstrap/download/cmdline.py", line 130, in run_safe

  [libsemigroups-1.0.9]       run()

  [libsemigroups-1.0.9]     File "/Users/dcoudert/sage/build/bin/../sage_bootstrap/download/cmdline.py", line 112, in run

  [libsemigroups-1.0.9]       app.download_tarball(args.url_or_tarball, args.destination, args.allow_upstream)

  [libsemigroups-1.0.9]     File "/Users/dcoudert/sage/build/bin/../sage_bootstrap/download/app.py", line 41, in download_tarball

  [libsemigroups-1.0.9]       tarball.download(allow_upstream=allow_upstream)

  [libsemigroups-1.0.9]     File "/Users/dcoudert/sage/build/bin/../sage_bootstrap/tarball.py", line 177, in download

  [libsemigroups-1.0.9]       raise FileNotMirroredError('tarball does not exist on mirror network')

  [libsemigroups-1.0.9]   FileNotMirroredError: tarball does not exist on mirror network

  [libsemigroups-1.0.9]   ************************************************************************

  [libsemigroups-1.0.9]   ************************************************************************

  [libsemigroups-1.0.9]   Error downloading libsemigroups-1.0.9.tar.gz

  [libsemigroups-1.0.9]   ************************************************************************

  [libsemigroups-1.0.9] Full log file: /Users/dcoudert/sage/logs/pkgs/libsemigroups-1.0.9.log

make[4]: *** [libsemigroups-no-deps] Error 1

make[3]: *** [/Users/dcoudert/sage/local/var/lib/sage/installed/libsemigroups-1.0.9] Error 2

make[2]: *** [all-build] Error 2

real	54m10.743s

user	49m21.128s

sys	2m23.294s

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

Error building Sage.

The following package(s) may have failed to build (not necessarily

during this run of 'make all-build'):

* package:         libsemigroups-1.0.9

  last build time: 15 déc 10:37

  log file:        /Users/dcoudert/sage/logs/pkgs/libsemigroups-1.0.9.log

It is safe to delete any log files and build directories, but they

contain information that is helpful for debugging build problems.

WARNING: If you now run 'make' again, the build directory of the

same version of the package will, by default, be deleted. Set the

environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.

make[1]: *** [all-build] Error 1

make: *** [build] Error 2

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Dima Pasechnik

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Dec 15, 2020, 5:07:15 AM12/15/20

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On Tue, Dec 15, 2020 at 9:42 AM David Coudert <david....@gmail.com> wrote:
>
> Another issue (this time on masOS 10.15.7): it seems that libsemigroups-1.0.9 is not present on mirrors.

it's probably an oversight of Volker, or just that the tarball has not
reached the mirrors yet.

You can get around by
running

./configure --enable-download-from-upstream-url
make

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Dima Pasechnik

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Dec 15, 2020, 5:14:23 AM12/15/20

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please post config.log

probably https://trac.sagemath.org/ticket/30231 didn't do the job :-(

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>
>
> Le 15 déc. 2020 à 01:22, Volker Braun <vbrau...@gmail.com> a écrit :
>

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David Coudert

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Dec 15, 2020, 5:28:07 AM12/15/20

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Here it is.

config.log

David Coudert

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Dec 15, 2020, 5:29:03 AM12/15/20

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Thanks, it works.

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Dima Pasechnik

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Dec 15, 2020, 5:40:39 AM12/15/20

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Could you replace
the line

AC_MSG_ERROR([using system pari and unable to locate pari.cfg])

with

AC_MSG_WARN([using system pari and unable to locate pari.cfg])

in

build/pkgs/gp2c/spkg-configure.m4

and try again?
(starting with ./bootstrap)

On Tue, Dec 15, 2020 at 10:28 AM David Coudert <david....@gmail.com> wrote:
>
> Here it is.

>
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Dima Pasechnik

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Dec 15, 2020, 5:44:56 AM12/15/20

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also, could you run

find /usr -name pari.cfg

and post the output here - apparently Fedora hides this file somewhere
we can't find
(and total absense of this file is a Fedora bug...)

David Coudert

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Dec 15, 2020, 6:53:34 AM12/15/20

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1) with the change in build/pkgs/gp2c/spkg-configure.m4, I can compile.

Should I open a ticket ?

2)
gelati:~> find /usr -name pari.cfg
find: '/usr/libexec/initscripts/legacy-actions/auditd': Permission denied
/usr/share/doc/pari/pari.cfg
find: '/usr/share/polkit-1/rules.d': Permission denied

I’m not root on the machine, but I can use an su account.

David.

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Dima Pasechnik

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Dec 15, 2020, 7:08:03 AM12/15/20

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On Tue, Dec 15, 2020 at 11:53 AM David Coudert <david....@gmail.com> wrote:
>
> 1) with the change in build/pkgs/gp2c/spkg-configure.m4, I can compile.
>
> Should I open a ticket ?

yes please. There should be no error there, as gp2c is optional, after all.
Also, we need to fix the code finding pari.cfg so that it does not miss
/usr/share/doc/pari/pari.cfg

>
> 2)
> gelati:~> find /usr -name pari.cfg
> find: '/usr/libexec/initscripts/legacy-actions/auditd': Permission denied
> /usr/share/doc/pari/pari.cfg
> find: '/usr/share/polkit-1/rules.d': Permission denied
>
> I’m not root on the machine, but I can use an su account.

no, no need, it has printet what we need:
/usr/share/doc/pari/pari.cfg

just fine.

Thanks
Dima

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Vincent Delecroix

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Dec 15, 2020, 7:08:51 AM12/15/20

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fpyll does not build (error in the C compilation). Log attached.

Best
Vincent

fpylll-0.5.2dev.log

config.log

config.status

Vincent Delecroix

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Dec 15, 2020, 7:23:59 AM12/15/20

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Maybe it is time to upgrade to fpylll-0.5.4 (Sage is stuck at
0.5.2dev), see ticket [#31025].

[#31025] https://trac.sagemath.org/ticket/31025

Vincent

Kenji Iohara

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Dec 15, 2020, 8:51:25 AM12/15/20

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On Mac OS 11.0.1, I couldn’t compile Sage 9.3.beta4 from the first built. Here is its log file:

config.log

Sébastien Labbé

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Dec 15, 2020, 1:45:11 PM12/15/20

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On Ubuntu 18.04, testing with various optional and external packages, I get:

Using --optional=4ti2,cbc,ccache,cryptominisat,database_jones_numfield,debian,dot2tex,e_antic,external,fricas,glucose,latte_int,libnauty,lidia,lrslib,memlimit,normaliz,notedown,pandoc_attributes,pip,pycosat,pynormaliz,rst2ipynb,sage,sage_numerical_backends_coin,sage_spkg

----------------------------------------------------------------------
sage -t --long --warn-long 72.0 --random-seed=0 src/sage/databases/findstat.py # 2 doctests failed
----------------------------------------------------------------------
External software detected for doctesting: ffmpeg,graphviz,imagemagick,internet,latex,octave,pandoc

Samething after rerunning the failed tests. It is copied below.

(Follow-up at https://trac.sagemath.org/ticket/25536)

Doctesting 1 file using 8 threads.
sage -t --long --warn-long 72.7 --random-seed=0 src/sage/databases/findstat.py
**********************************************************************
File "src/sage/databases/findstat.py", line 118, in sage.databases.findstat
Failed example:
    r = findstat(Permutations, lambda pi: pi.saliances()[0], depth=2); r # optional -- internet
Expected:
    0: St000476oMp00099oMp00127 (quality [100, 100])
    1: St001497oMp00119oMp00127 with offset 1 (quality [100, 100])
    2: St000147oMp00027oMp00127 (quality [96, 100])
    3: St000054oMp00064oMp00062 with offset 1 (quality [88, 100])
    4: St000740oMp00062 with offset 1 (quality [87, 100])
    ...
Got:
     0: St000740oMp00066 with offset 1 (quality [100, 100])
     1: St000476oMp00099oMp00127 (quality [100, 100])
     2: St001497oMp00119oMp00127 with offset 1 (quality [100, 100])
     3: St000147oMp00027oMp00127 (quality [96, 100])
     4: St000054oMp00066oMp00149 with offset 1 (quality [89, 100])
     5: St000141oMp00025oMp00127 (quality [87, 100])
     6: St001291oMp00127 with offset 1 (quality [87, 86])
     7: St000051oMp00061oMp00069 (quality [87, 86])
     8: St000316oMp00025oMp00127 (quality [87, 86])
     9: St000653oMp00129oMp00127 (quality [87, 86])
    10: St001184oMp00127oMp00064 with offset 1 (quality [87, 86])
    11: St001227oMp00028oMp00127 (quality [87, 86])
    12: St001480oMp00032oMp00127 (quality [87, 86])
    13: St000066oMp00063oMp00149 with offset 1 (quality [54, 86])
    14: St000840oMp00146oMp00127 (quality [18, 86])
    15: St000199oMp00063 with offset 1 (quality [15, 71])
    16: St000193oMp00004oMp00063 with offset 1 (quality [15, 71])
    17: St000200oMp00063oMp00062 with offset 1 (quality [15, 71])
**********************************************************************
File "src/sage/databases/findstat.py", line 129, in sage.databases.findstat
Failed example:
    r[4].info()                                                           # optional -- internet
Expected:
    after adding 1 to every value
    and applying
        Mp00062: Lehmer-code to major-code bijection: Permutations -> Permutations
    to the objects (see `.compound_map()` for details)
    <BLANKLINE>
    your input matches
        St000740: The last entry of a permutation.
    <BLANKLINE>
    among the values you sent, 87 percent are actually in the database,
    among the distinct values you sent, 100 percent are actually in the database
Got:
    after adding 1 to every value
    and applying
        Mp00149: Lehmer code rotation: Permutations -> Permutations
        Mp00066: inverse: Permutations -> Permutations
    to the objects (see `.compound_map()` for details)
    <BLANKLINE>
    your input matches
        St000054: The first entry of the permutation.
    <BLANKLINE>
    among the values you sent, 89 percent are actually in the database,
    among the distinct values you sent, 100 percent are actually in the database
**********************************************************************
1 item had failures:
   2 of 16 in sage.databases.findstat
    11 webbrowser tests not run
    0 tests not run because we ran out of time
    [392 tests, 2 failures, 41.94 s]

David Coudert

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Dec 15, 2020, 6:01:37 PM12/15/20

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And here is the file config.log after the proposed change.

Useful for the discussion on https://trac.sagemath.org/ticket/31051

config.log

Kenji Iohara

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Dec 15, 2020, 7:07:42 PM12/15/20

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I hav recompiled Sage 9.3.beta3 and beta.4 from the first built on Mac OS 11.1,

it didn’t work; it seems that it couldn’ compile Cython among all:

* package:         cython-0.29.21

  last build time: Dec 15 23:21

  log file:        /Users/iohara/Desktop/sage-9.3.beta3/logs/pkgs/cython-0.29.21.log

  build directory: /Users/iohara/Desktop/sage-9.3.beta3/local/var/tmp/sage/build/cython-0.29.21

* package:         gmpy2-2.1.0b5

  last build time: Dec 15 23:57

  log file:        /Users/iohara/Desktop/sage-9.3.beta3/logs/pkgs/gmpy2-2.1.0b5.log

  build directory: /Users/iohara/Desktop/sage-9.3.beta3/local/var/tmp/sage/build/gmpy2-2.1.0b5

* package:         markupsafe-1.1.1

  last build time: Dec 15 23:57

  log file:        /Users/iohara/Desktop/sage-9.3.beta3/logs/pkgs/markupsafe-1.1.1.log

  build directory: /Users/iohara/Desktop/sage-9.3.beta3/local/var/tmp/sage/build/markupsafe-1.1.1

* package:         fflas_ffpack-2.4.3

  last build time: Dec 16 00:14

  log file:        /Users/iohara/Desktop/sage-9.3.beta3/logs/pkgs/fflas_ffpack-2.4.3.log

  build directory: /Users/iohara/Desktop/sage-9.3.beta3/local/var/tmp/sage/build/fflas_ffpack-2.4.3

* package:         sage_conf-none

  last build time: Dec 16 00:32

  log file:        /Users/iohara/Desktop/sage-9.3.beta3/logs/pkgs/sage_conf-none.log

* package:         tornado-6.0.4

  last build time: Dec 16 00:41

  log file:        /Users/iohara/Desktop/sage-9.3.beta3/logs/pkgs/tornado-6.0.4.log

  build directory: /Users/iohara/Desktop/sage-9.3.beta3/local/var/tmp/sage/build/tornado-6.0.4

* package:         psutil-5.2.0.p2

  last build time: Dec 16 00:42

  log file:        /Users/iohara/Desktop/sage-9.3.beta3/logs/pkgs/psutil-5.2.0.p2.log

  build directory: /Users/iohara/Desktop/sage-9.3.beta3/local/var/tmp/sage/build/psutil-5.2.0.p2

* package:         pillow-7.2.0

  last build time: Dec 16 00:49

  log file:        /Users/iohara/Desktop/sage-9.3.beta3/logs/pkgs/pillow-7.2.0.log

  build directory: /Users/iohara/Desktop/sage-9.3.beta3/local/var/tmp/sage/build/pillow-7.2.0

* package:         kiwisolver-1.0.1

  last build time: Dec 16 00:49

  log file:        /Users/iohara/Desktop/sage-9.3.beta3/logs/pkgs/kiwisolver-1.0.1.log

  build directory: /Users/iohara/Desktop/sage-9.3.beta3/local/var/tmp/sage/build/kiwisolver-1.0.1

* package:         scandir-1.9.0

  last build time: Dec 16 00:49

  log file:        /Users/iohara/Desktop/sage-9.3.beta3/logs/pkgs/scandir-1.9.0.log

  build directory: /Users/iohara/Desktop/sage-9.3.beta3/local/var/tmp/sage/build/scandir-1.9.0

* package:         pyrsistent-0.16.0

  last build time: Dec 16 00:50

  log file:        /Users/iohara/Desktop/sage-9.3.beta3/logs/pkgs/pyrsistent-0.16.0.log

  build directory: /Users/iohara/Desktop/sage-9.3.beta3/local/var/tmp/sage/build/pyrsistent-0.16.0

* package:         cffi-1.14.3

  last build time: Dec 16 00:51

  log file:        /Users/iohara/Desktop/sage-9.3.beta3/logs/pkgs/cffi-1.14.3.log

  build directory: /Users/iohara/Desktop/sage-9.3.beta3/local/var/tmp/sage/build/cffi-1.14.3

15/12/2020 19:45、Sébastien Labbé <sla...@gmail.com>のメール:

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Emmanuel Charpentier

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Dec 16, 2020, 10:33:59 AM12/16/20

to sage-release

On Debian testing, it turns out that I am unable to pull the current version starting from 9.2.beta12 :

charpent@p-202-021:/usr/local/sage-9$ git status
Sur la branche develop
Votre branche est en retard sur 'origin/develop' de 2091 commits, et peut être mise à jour en avance rapide.
  (utilisez "git pull" pour mettre à jour votre branche locale)

Fichiers non suivis:
  (utilisez "git add <fichier>..." pour inclure dans ce qui sera validé)
    CRerrs.md
    CRerrs.org
    chkerrs.txt
    errs.txt
    optional_packages.txt

aucune modification ajoutée à la validation mais des fichiers non suivis sont présents (utilisez "git add" pour les suivre)
charpent@p-202-021:/usr/local/sage-9$ git pull
warning: Tirer sans spécifier comment réconcilier les branches divergentes
est découragé. Vous pouvez éliminer ce message en lançant une des
commandes suivantes avant votre prochain tirage :

  git config pull.rebase false  # fusion (stratégie par défaut)
  git config pull.rebase true   # rebasage
  git config pull.ff only       # avance rapide seulement

Vous pouvez remplacer "git config" par "git config --global" pour que
ce soit l'option par défaut pour tous les dépôts. Vous pouvez aussi
passer --rebase, --no-rebase ou --ff-only sur la ligne de commande pour
remplacer à l'invocation la valeur par défaut configurée.

error: cannot lock ref 'refs/remotes/origin/u/dimpase/WIP': 'refs/remotes/origin/u/dimpase/WIP/libgap410' existe ; impossible de créer 'refs/remotes/origin/u/dimpase/WIP'
Depuis git.sagemath.org:sage
 ! [nouvelle branche]      u/dimpase/WIP -> origin/u/dimpase/WIP  (impossible de mettre à jour la référence locale)
charpent@p-202-021:/usr/local/sage-9$ ls -a .git/refs/remotes/origin/u/dimpase/| grep WIP
charpent@p-202-021:/usr/local/sage-9$

Suggestions ?

Dima Pasechnik

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Dec 16, 2020, 10:51:32 AM12/16/20

to sage-release

Run

git gc --prune=now

and then try again.

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Emmanuel Charpentier

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Dec 17, 2020, 6:42:14 AM12/17/20

to sage-release

Nope :

charpent@p-202-021:/usr/local/sage-9$ git gc --prune=now
Énumération des objets: 901621, fait.
Décompte des objets: 100% (901621/901621), fait.
Compression par delta en utilisant jusqu'à 4 fils d'exécution
Compression des objets: 100% (143507/143507), fait.
Écriture des objets: 100% (901621/901621), fait.
Total 901621 (delta 722356), réutilisés 901608 (delta 722343), réutilisés du pack 0
charpent@p-202-021:/usr/local/sage-9$ git status
Sur la branche develop
Votre branche est en retard sur 'origin/develop' de 2091 commits, et peut être mise à jour en avance rapide.
  (utilisez "git pull" pour mettre à jour votre branche locale)

Fichiers non suivis:
  (utilisez "git add <fichier>..." pour inclure dans ce qui sera validé)
    CRerrs.md
    CRerrs.org
    chkerrs.txt
    errs.txt
    optional_packages.txt

aucune modification ajoutée à la validation mais des fichiers non suivis sont présents (utilisez "git add" pour les suivre)
charpent@p-202-021:/usr/local/sage-9$ git pull
warning: Tirer sans spécifier comment réconcilier les branches divergentes
est découragé. Vous pouvez éliminer ce message en lançant une des
commandes suivantes avant votre prochain tirage :

  git config pull.rebase false  # fusion (stratégie par défaut)
  git config pull.rebase true   # rebasage
  git config pull.ff only       # avance rapide seulement

Vous pouvez remplacer "git config" par "git config --global" pour que
ce soit l'option par défaut pour tous les dépôts. Vous pouvez aussi
passer --rebase, --no-rebase ou --ff-only sur la ligne de commande pour
remplacer à l'invocation la valeur par défaut configurée.

error: cannot lock ref 'refs/remotes/origin/u/dimpase/WIP': 'refs/remotes/origin/u/dimpase/WIP/libgap410' existe ; impossible de créer 'refs/remotes/origin/u/dimpase/WIP'
Depuis git.sagemath.org:sage
 ! [nouvelle branche]      u/dimpase/WIP -> origin/u/dimpase/WIP  (impossible de mettre à jour la référence locale)
charpent@p-202-021:/usr/local/sage-9$ git status
Sur la branche develop
Votre branche est en retard sur 'origin/develop' de 2091 commits, et peut être mise à jour en avance rapide.
  (utilisez "git pull" pour mettre à jour votre branche locale)

Fichiers non suivis:
  (utilisez "git add <fichier>..." pour inclure dans ce qui sera validé)
    CRerrs.md
    CRerrs.org
    chkerrs.txt
    errs.txt
    optional_packages.txt

aucune modification ajoutée à la validation mais des fichiers non suivis sont présents (utilisez "git add" pour les suivre)

Dima Pasechnik

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Dec 17, 2020, 6:46:05 AM12/17/20

to sage-release

once again - does your branch correspond to something remote?

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/9d7af777-7603-465f-a60a-8504e90b4c23n%40googlegroups.com.

Emmanuel Charpentier

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Dec 17, 2020, 7:41:05 AM12/17/20

to sage-release

I’m on develop…

harpent@p-202-021:/usr/local/sage-9$ git fetch
remote: Counting objects: 31, done.
remote: Compressing objects: 100% (6/6), done.
remote: Total 6 (delta 5), reused 0 (delta 0)
Dépaquetage des objets: 100% (6/6), 982 octets | 46.00 Kio/s, fait.
error: cannot lock ref 'refs/remotes/origin/u/dimpase/WIP': 'refs/remotes/origin/u/dimpase/WIP/libgap410' existe ; impossible de créer 'refs/remotes/origin/u/dimpase/WIP'
Depuis git.sagemath.org:sage
 ! [nouvelle branche]      u/dimpase/WIP -> origin/u/dimpase/WIP  (impossible de mettre à jour la référence locale)
 * [nouvelle branche]      u/mantepse/2_internet_doctests_failing_in_findstat_py -> origin/u/mantepse/2_internet_doctests_failing_in_findstat_py
charpent@p-202-021:/usr/local/sage-9$ ls .git/refs/remotes/origin/u/dimpase/
build   docs      graphs  misc     packages  singular  ticket
coding  doctests  groups  modules  python3   src       trac

I’m at loss…

Dima Pasechnik

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Dec 17, 2020, 8:13:12 AM12/17/20

to sage-release

I've removed this remote branch, so it should be OK now, one way or another.

On Thu, Dec 17, 2020 at 12:41 PM Emmanuel Charpentier

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/c796b9d5-538d-476f-9314-72511818a54cn%40googlegroups.com.

Emmanuel Charpentier

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Dec 17, 2020, 8:42:47 AM12/17/20

to sage-release

I have been able to git pull. Thanks. Now building…

Emmanuel Charpentier

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Dec 18, 2020, 11:55:29 AM12/18/20

to sage-release

On Debian testing running on core i7 + 16 GB RAM, upgrading 9.3.beta3 (configured to use all available system packages) to 9.3.beta4 leads
to :

./configure insists on installing texlive-latex-extra texlive-xetex latexmk pandoc dvipng default-jdk ffmpeg libavdevice-dev pari-gp2c, notwithstanding the fact that all of them are already installed.
ptestlong results in one transient and five permanent failures, thee of the latter already seen and reported in previous versions :

File	Results	P/T	Seen
src/sage/tests/gap_packages.py	1 doctest failed	P	N
src/sage/functions/other.py	1 doctest failed	P	Y
src/sage/misc/package.py	1 doctest failed	P	N
src/sage/schemes/elliptic_curves/ell_field.py	1 doctest failed	T	N
src/sage/misc/trace.py	1 doctest failed	P	Y
src/sage/groups/abelian_gps/abelian_group_gap.py	1 doctest failed	P	Y

The new permanent failures are as follows :

Running doctests with ID 2020-12-18-17-31-15-4e03dc22.
Git branch: develop
Using --optional=build,debian,dochtml,dot2tex,fricas,gap_jupyter,gap_packages,kenzo,libsemigroups,memlimit,pip,pysingular,sage,sage_spkg,singular_jupyter
Doctesting 1 file.
sage -t --long --warn-long 180.2 --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, 4.52 s]
----------------------------------------------------------------------
sage -t --long --warn-long 180.2 --random-seed=0 src/sage/tests/gap_packages.py  # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 4.5 seconds
    cpu time: 4.1 seconds
    cumulative wall time: 4.5 seconds

This seems cosmetic.

Running doctests with ID 2020-12-18-17-31-46-5c2d5f7b.
Git branch: develop
Using --optional=build,debian,dochtml,dot2tex,fricas,gap_jupyter,gap_packages,kenzo,libsemigroups,memlimit,pip,pysingular,sage,sage_spkg,singular_jupyter
Doctesting 1 file.
sage -t --long --warn-long 180.2 --random-seed=0 src/sage/misc/package.py
**********************************************************************
File "src/sage/misc/package.py", line 427, in sage.misc.package.standard_packages
Failed example:
    installed[0], installed[-1]  # optional - build
Expected:
    ('alabaster', 'zn_poly')
Got:
    ('alabaster', 'zipp')
**********************************************************************
1 item had failures:
   1 of   4 in sage.misc.package.standard_packages
    [49 tests, 1 failure, 4.11 s]
----------------------------------------------------------------------
sage -t --long --warn-long 180.2 --random-seed=0 src/sage/misc/package.py  # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 4.2 seconds
    cpu time: 0.3 seconds
    cumulative wall time: 4.1 seconds

This also seems cosmetic (but I may be wrong)

HTH,

Le mardi 15 décembre 2020 à 01:22:48 UTC+1, Volker Braun a écrit :

Matthias Köppe

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Dec 18, 2020, 7:19:15 PM12/18/20

to sage-release

On Friday, December 18, 2020 at 8:55:29 AM UTC-8 emanuel.c...@gmail.com wrote:

On Debian testing running on core i7 + 16 GB RAM, upgrading 9.3.beta3 (configured to use all available system packages) to 9.3.beta4 leads
to :

./configure insists on installing texlive-latex-extra texlive-xetex latexmk pandoc dvipng default-jdk ffmpeg libavdevice-dev pari-gp2c, notwithstanding the fact that all of them are already installed.

With the exception of pari-gp2c, this is https://trac.sagemath.org/ticket/30930 ("Add/update the system package information for the "_recommended" dummy package") -- whose ticket description has an explanation of what work is needed to be done.

Running doctests with ID 2020-12-18-17-31-46-5c2d5f7b.
Git branch: develop
Using --optional=build,debian,dochtml,dot2tex,fricas,gap_jupyter,gap_packages,kenzo,libsemigroups,memlimit,pip,pysingular,sage,sage_spkg,singular_jupyter
Doctesting 1 file.
sage -t --long --warn-long 180.2 --random-seed=0 src/sage/misc/package.py
**********************************************************************
File "src/sage/misc/package.py", line 427, in sage.misc.package.standard_packages
Failed example:
    installed[0], installed[-1]  # optional - build
Expected:
    ('alabaster', 'zn_poly')
Got:
    ('alabaster', 'zipp')
**********************************************************************
1 item had failures:
   1 of   4 in sage.misc.package.standard_packages
    [49 tests, 1 failure, 4.11 s]
----------------------------------------------------------------------
sage -t --long --warn-long 180.2 --random-seed=0 src/sage/misc/package.py  # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 4.2 seconds
    cpu time: 0.3 seconds
    cumulative wall time: 4.1 seconds

This also seems cosmetic

Yes, cosmetic, and fixed on the way in https://trac.sagemath.org/ticket/30940 (which needs review)

Kenji Iohara

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Dec 23, 2020, 4:40:21 AM12/23/20

to sage-r...@googlegroups.com

On mac OS 11.1, even after installing cython with Homebrew, it always claim << not installed >> when I compile sage-9.3.beta4 (this was also true for beta3 version).

(After installing cython with Homebrew, I ran

source /.../.homebrew-build-env

.) Here is the log-file for cython.

cython-0.29.21.log

Dima Pasechnik

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Dec 23, 2020, 7:07:22 AM12/23/20

to sage-release

On Wed, 23 Dec 2020, 09:40 Kenji Iohara, <simplye...@gmail.com> wrote:

On mac OS 11.1, even after installing cython with Homebrew, it always claim << not installed >> when I compile sage-9.3.beta4 (this was also true for beta3 version).

this is as expected. We are not yet supporting system-wide Python packages, this is work in progress

(After installing cython with Homebrew, I ran

source /.../.homebrew-build-env

.) Here is the log-file for cython.

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19/12/2020 1:19、Matthias Köppe <matthia...@gmail.com>のメール:

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