Sage 9.2.beta6 released

[Volker Braun]

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

ddaba54f6d (tag: 9.2.beta6, trac/develop) Updated SageMath version to 9.2.beta6

e41d396f5d Trac #30131: 2 internet doctests failing in bibd.py

fc9a0a02bd Trac #30130: get rid of comparison using _cmp_

3501a0c601 Trac #30129: Fix broken test for SAGE_ROOT from #29111

079439423e Trac #30128: Replace bashism in src/bin/sage-env

39707fa5dc Trac #30126: Categories of connected graphs and connected simplicial complexes

55047da0bd Trac #30122: Fix maxima/ecl unicode handling

1f7ed72c75 Trac #30109: Remove mentions of packages KASH and Macaulay2 from tutorials

8bac45e62f Trac #30106: sage.libs.ecl: Fix unicode handling

147309da17 Trac #30085: Implemented constructions for Kasami codes

f26319d368 Trac #29922: sage.doctest: Make imports more specific; make global environment for tests customizable

caa2305f2e Trac #29908: Test method `is_combinatorially_isomorphic`

34f7558e61 Trac #29901: .github/workflows/: Test all optional packages, add workflow for testing all experimental packages

0bc64eeb5b Trac #29899: Two bugs with dilation

7ac15bd9b6 Trac #29882: Add tutorial-like docstring material on RecursivelyEnumeratedSet

8a7d873f6f Trac #29861: Upgrade Cython to 0.29.21

6195026c92 Trac #29649: spkg-configure.m4 for zn_poly

8dd15d3424 Trac #28778: Generalize pushout of number fields with compatible embeddings

14e97a8973 Trac #30118: Handle SAGE_CHECK_PACKAGES in build/make/Makefile.in, not sage-spkg

c3a0c262d7 Trac #30147: Fix spkg-configure.m4 for sympow

acddeae308 Trac #30067: gfortran spkg-configure: Reject versions >= 10

5ffdbc5a32 Trac #29965: Make graphs doctests ready for random seeds

aa8340920c Trac #29962: Allow fuzzing of doctests

3a0ebe2271 Trac #29918: Run test suite for gale transform

0214796034 Trac #29744: diameter computation in undirected graphs using certificates

394bed7cdc Trac #29678: Fraction field of Ore polynomial ring

ef45a5f557 Trac #29446: Unify how SAGE_ROOT and SAGE_LOCAL are normalized regarding symbolic links

80a8be4739 Trac #29160: add method to find a surrounding of a polyomino with isometric copies of itself

01038ed16d Trac #21942: Cheeger constant(s) of graphs

2e3b6308f8 Trac #30088: Fix "make dist", add test run to GitHub Actions

da23ae07e7 Trac #30079: Typos in p-adic documentation

299864ec91 Trac #30115: several typos

563c8c20d2 Trac #30093: Disable test suites for curl, git, cmake

a08075649c Trac #30084: Update mcqd URL

8548d0fa5b Trac #30068: README.md: Do not recommend SAGE_CHECK=yes

cf5567c316 Trac #30065: SR.var('x', domain='real') and assume(x, 'real') are very slow

9c13a07786 Trac #29758: Allow longer text in Three.js viewer

06b06a6425 Trac #29739: add is_diagonal method to the matrix class

10f0dad9c8 Trac #29091: tox.ini: Add raspbian-buster

2d66d1ea5d Trac #30112: Coercion from ChartFunctionRing to ScalarFieldAlgebra

467fbc70a0 (tag: 9.2.beta5) Updated SageMath version to 9.2.beta5

[Samuel Lelièvre]

> Date: 2020-07-26 00:20 UTC
> From: Volker Braun
> To: sage-release
> Subject: Sage 9.2.beta6 released

>
> 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

Thanks for this new beta release!

Failed on sagelib on macOS 10.14.6 Mojave with Homebrew.

Logs for this attempt to build:

https://www.math.u-psud.fr/~lelievre/sagelogs/
slel-build-sage-9-2-b6-macos-brew-2020-07-26-fail.zip

[David Coudert]

Incremental build OK on macOS 10.14.6 Mojave with Homebrew.
may be some .configure has not been executed for you ?
David.

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[Matthias Köppe]

From your log:

[  4/517] clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I./sage/cpython -I/opt/s/sage92b6/src -I/opt/s/sage92b6/src/sage/ext -I/usr/local/Cellar/python@3.7/3.7.8_1/Frameworks/Python.framework/Versions/3.7/include/python3.7m -I/opt/s/sage92b6/local/lib/python3.7/site-packages/numpy/core/include -Ibuild/cythonized -I/usr/local/include -I/usr/local/opt/openssl@1.1/include -I/usr/local/opt/sqlite/include -I/opt/s/sage92b6/local/include -I/usr/local/Cellar/python@3.7/3.7.8_1/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c build/cythonized/sage/algebras/letterplace/letterplace_ideal.cpp -o build/temp.macosx-10.14-x86_64-3.7/build/cythonized/sage/algebras/letterplace/letterplace_ideal.o -fno-strict-aliasing -DCYTHON_CLINE_IN_TRACEBACK=1 -DSING_NDEBUG -DOM_NDEBUG -I/opt/s/sage92b6/local/include/singular -I/opt/s/sage92b6/local/include/ -std=c++11

In file included from build/cythonized/sage/algebras/letterplace/letterplace_ideal.cpp:675:

/usr/local/include/singular/Singular/libsingular.h:15:10: fatal error: 'polys/shiftop.h' file not found

#include "polys/shiftop.h"

         ^~~~~~~~~~~~~~~~~

In file included from build/cythonized/sage/algebras/letterplace/free_algebra_letterplace.cpp:675:

/usr/local/include/singular/Singular/libsingular.h:15:10: fatal error: 'polys/shiftop.h' file not found

#include "polys/shiftop.h"

         ^~~~~~~~~~~~~~~~~

In file included from build/cythonized/sage/algebras/letterplace/free_algebra_element_letterplace.cpp:675:

/usr/local/include/singular/Singular/libsingular.h:15:10: fatal error: 'polys/shiftop.h' file not found

#include "polys/shiftop.h"

         ^~~~~~~~~~~~~~~~~

build/cythonized/sage/algebras/finite_dimensional_algebras/finite_dimensional_algebra_element.c:11104:18: warning: unused function '__pyx_pw_4sage_9structure_7element_1parent' [-Wunused-function]

static PyObject *__pyx_pw_4sage_9structure_7element_1parent(PyObject *__pyx_self, PyObject *__pyx_v_x) {

                 ^

This appears to be a conflict with a version of Singular that is installed in /usr/local

[Matthias Köppe]

This will be addressed in https://trac.sagemath.org/ticket/30227

[Thierry Dumont]

On my Unbuntu 20-0:

* transition from 9.2 beta 5 to beta -: no problem
* make ptestlong : all tests passed !

t.d.

[Kenji Iohara]

On mac OS X.15.6 without gcc@9, I could ompile it.

Installing gcc@9 with Homebrew, I couldn’t compile arb….

After compilation without gcc@9,  making ptestlong, I had the next reaction:

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

sage -t --long --warn-long 125.6 --random-seed=0 src/sage/misc/sageinspect.py  # 1 doctest failed

sage -t --long --warn-long 125.6 --random-seed=0 src/sage/interfaces/interface.py  # 1 doctest failed

sage -t --long --warn-long 125.6 --random-seed=0 src/sage/repl/ipython_tests.py  # 1 doctest failed

sage -t --long --warn-long 125.6 --random-seed=0 src/sage/interfaces/r.py  # 1 doctest failed

sage -t --long --warn-long 125.6 --random-seed=0 src/doc/en/prep/Quickstarts/Statistics-and-Distributions.rst  # 1 doctest failed

sage -t --long --warn-long 125.6 --random-seed=0 src/sage/stats/r.py  # 1 doctest failed

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

Total time for all tests: 6861.9 seconds

    cpu time: 19657.6 seconds

    cumulative wall time: 26835.7 seconds

make: *** [ptestlong] Error 1

2020/07/27 7:16、Thierry Dumont <tdu...@math.univ-lyon1.fr>のメール:

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<tdumont.vcf>

[Matthias Köppe]

Fixed in #30227, please test

On Sunday, July 26, 2020 at 12:34:30 PM UTC-7, Samuel Lelievre wrote:

[Matthias Köppe]

Please post logs

On Monday, July 27, 2020 at 4:06:19 PM UTC-7, Kenji Iohara wrote:

On mac OS X.15.6 without gcc@9, I could ompile it.

Installing gcc@9 with Homebrew, I couldn’t compile arb….

After compilation without gcc@9,  making ptestlong, I had the next reaction:

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

sage -t --long --warn-long 125.6 --random-seed=0 src/sage/misc/sageinspect.py  # 1 doctest failed

sage -t --long --warn-long 125.6 --random-seed=0 src/sage/interfaces/interface.py  # 1 doctest failed

sage -t --long --warn-long 125.6 --random-seed=0 src/sage/repl/ipython_tests.py  # 1 doctest failed

sage -t --long --warn-long 125.6 --random-seed=0 src/sage/interfaces/r.py  # 1 doctest failed

sage -t --long --warn-long 125.6 --random-seed=0 src/doc/en/prep/Quickstarts/Statistics-and-Distributions.rst  # 1 doctest failed

sage -t --long --warn-long 125.6 --random-seed=0 src/sage/stats/r.py  # 1 doctest failed

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

Total time for all tests: 6861.9 seconds

    cpu time: 19657.6 seconds

    cumulative wall time: 26835.7 seconds

make: *** [ptestlong] Error 1

2020/07/27 7:16、Thierry Dumont <tdu...@math.univ-lyon1.fr>のメール:

On my Unbuntu 20-0:

* transition from 9.2 beta 5 to beta -: no problem
* make ptestlong : all tests passed !

t.d.

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[Kenji Iohara]

Here is the ptestlong.log: 

[Samuel Lelievre]

2020-07-26 20:46:10 UTC, Matthias Köppe:

>

> From your log:

>

> [  4/517] clang -Wno-unused-result [...]

> -I/opt/s/sage92b6/local/include/singular

> -I/opt/s/sage92b6/local/include/ -std=c++11

> In file included from [...]/letterplace_ideal.cpp:675:

> /usr/local/include/singular/Singular/libsingular.h:15:10:

> fatal error: 'polys/shiftop.h' file not found

> #include "polys/shiftop.h"

>         ^~~~~~~~~~~~~~~~~

> In file included from [...]/free_algebra_letterplace.cpp:675:

> /usr/local/include/singular/Singular/libsingular.h:15:10:

> fatal error: 'polys/shiftop.h' file not found

> #include "polys/shiftop.h"

>          ^~~~~~~~~~~~~~~~~

> In file included from [...]/free_algebra_element_letterplace.cpp:675:

> /usr/local/include/singular/Singular/libsingular.h:15:10:

> fatal error: 'polys/shiftop.h' file not found

> #include "polys/shiftop.h"

>          ^~~~~~~~~~~~~~~~~

> [...]/finite_dimensional_algebra_element.c:11104:18:

> warning: unused function

> '__pyx_pw_4sage_9structure_7element_1parent' [-Wunused-function]

> static PyObject

> *__pyx_pw_4sage_9structure_7element_1parent(PyObject *__pyx_self,

> PyObject *__pyx_v_x) {

>

> This appears to be a conflict with a version of Singular

> that is installed in /usr/local

2020-07-26 22:01:03 UTC, Matthias Köppe:

>

> This will be addressed in

> https://trac.sagemath.org/ticket/30227

2020-07-28 04:13:48 UTC, Matthias Köppe:

>

> Fixed in #30227, please test

Dear Matthias, thanks for investigating and for the ticket.

I uninstalled Homebrew's Singular: new failure on sagelib.

https://www.math.u-psud.fr/~lelievre/sagelogs/slel-sage-9-2-b6-mac-brew-2020-07-27-fail.zip

I then tried applying ticket 30227, new failure on sagelib.

https://www.math.u-psud.fr/~lelievre/sagelogs/

slel-sage-9-2-b6-mac-brew-2020-07-28.zip

[François Bissey]

The important bits from that last log
[198/517] creating build/temp.macosx-10.14-x86_64-3.7/build/cythonized/sage/libs/arb
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I./sage/libs/arb -I./sage/libs/flint -I./sage/libs/ntl -I./sage/cpython -I/opt/s/sage92b6/src -I/opt/s/sage92b6/src/sage/ext -I/usr/local/Cellar/python@3.7/3.7.8_1/Frameworks/Python.framework/Versions/3.7/include/python3.7m -I/opt/s/sage92b6/local/lib/python3.7/site-packages/numpy/core/include -Ibuild/cythonized -I/usr/local/include -I/usr/local/opt/openssl@1.1/include -I/usr/local/opt/sqlite/include -I/opt/s/sage92b6/local/include -I/usr/local/Cellar/python@3.7/3.7.8_1/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c build/cythonized/sage/libs/arb/arith.c -o build/temp.macosx-10.14-x86_64-3.7/build/cythonized/sage/libs/arb/arith.o -fno-strict-aliasing -DCYTHON_CLINE_IN_TRACEBACK=1 -std=c99
In file included from build/cythonized/sage/libs/arb/arith.c:656:
In file included from build/cythonized/sage/libs/arb/arb_wrap.h:14:
In file included from /opt/s/sage92b6/local/include/acb.h:22:
In file included from /opt/s/sage92b6/local/include/arf.h:27:
In file included from /opt/s/sage92b6/local/include/fmpr.h:26:
/opt/s/sage92b6/local/include/fmpz_extras.h:47:1: error: redefinition of 'fmpz_add_si'
fmpz_add_si(fmpz_t z, const fmpz_t x, slong y)
^
/usr/local/include/flint/fmpz.h:479:18: note: previous definition is here
FMPZ_INLINE void fmpz_add_si(fmpz_t f, const fmpz_t g, slong x)
^
In file included from build/cythonized/sage/libs/arb/arith.c:656:
In file included from build/cythonized/sage/libs/arb/arb_wrap.h:14:
In file included from /opt/s/sage92b6/local/include/acb.h:22:
In file included from /opt/s/sage92b6/local/include/arf.h:27:
In file included from /opt/s/sage92b6/local/include/fmpr.h:26:
/opt/s/sage92b6/local/include/fmpz_extras.h:56:1: error: redefinition of 'fmpz_sub_si'
fmpz_sub_si(fmpz_t z, const fmpz_t x, slong y)
^
/usr/local/include/flint/fmpz.h:487:18: note: previous definition is here
FMPZ_INLINE void fmpz_sub_si(fmpz_t f, const fmpz_t g, slong x)
^
2 errors generated.

I would be easier to spot if you were building sagely at j1.

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[Samuel Lelievre]

2020-07-29 08:39:13 UTC, François Bissey:

>

> The important bits from that last log

> [198/517] creating build/[...]/build/cythonized/sage/libs/arb

> [...]

> In file included from build/cythonized/sage/libs/arb/arith.c:656:

> In file included from build/cythonized/sage/libs/arb/arb_wrap.h:14:

> In file included from /opt/s/sage92b6/local/include/acb.h:22:

> In file included from /opt/s/sage92b6/local/include/arf.h:27:

> In file included from /opt/s/sage92b6/local/include/fmpr.h:26:

> /opt/s/sage92b6/local/include/fmpz_extras.h:47:1:

> error: redefinition of 'fmpz_add_si'

> fmpz_add_si(fmpz_t z, const fmpz_t x, slong y)

> /usr/local/include/flint/fmpz.h:479:18:

> note: previous definition is here

> FMPZ_INLINE void fmpz_add_si(fmpz_t f, const fmpz_t g, slong x)

> In file included from build/cythonized/sage/libs/arb/arith.c:656:

> In file included from build/cythonized/sage/libs/arb/arb_wrap.h:14:

> In file included from /opt/s/sage92b6/local/include/acb.h:22:

> In file included from /opt/s/sage92b6/local/include/arf.h:27:

> In file included from /opt/s/sage92b6/local/include/fmpr.h:26:

> /opt/s/sage92b6/local/include/fmpz_extras.h:56:1:

> error: redefinition of 'fmpz_sub_si'

> fmpz_sub_si(fmpz_t z, const fmpz_t x, slong y)

> /usr/local/include/flint/fmpz.h:487:18:

> note: previous definition is here

> FMPZ_INLINE void fmpz_sub_si(fmpz_t f, const fmpz_t g, slong x)

> 2 errors generated.

>

> I would be easier to spot if you were building sagely at j1.

Thanks for digging through and thanks for the reminder that

building with one job produces easier to analyze logs.

I built again with `-j1`, here are the logs.

https://www.math.u-psud.fr/~lelievre/sagelogs

slel-sage-9-2-b6-mac-brew-2020-07-29-fail.zip

The errors seem to involve Flint. I have Flint 2.6.1 from Homebrew.

By the way, the upgrade to Flint 2.6.1 for Sage needs review at

  upgrade to flint 2.6.1

  https://trac.sagemath.org/ticket/29719

Should I

- uninstall Homebrew's flint and try again?

- downgrade Homebrew's Flint to 2.6.0 and try again?

- wait for the upgrade to Flint 2.6.1 to get merged in Sage?

[Matthias Köppe]

On Wednesday, July 29, 2020 at 4:37:52 AM UTC-7, Samuel Lelievre wrote:

The errors seem to involve Flint. I have Flint 2.6.1 from Homebrew.

Should I

- uninstall Homebrew's flint and try again?

Yes please, so that we can get https://trac.sagemath.org/ticket/30227 done

[Samuel Lelièvre]

2020-07-29 18:13 UTC, Matthias Köppe:

New attempt: sagelib builds but dochtml fails.

- date: 2020-07-30
- version: SageMath 9.2.beta6
- existing repo with previous failures to build
- ran `make distclean`
- OS: macOS 10.14.6 Mojave
- Homebrew, removed: gap, flint
- result:
- successfully built sagelib
- failed to build dochtml
- error while building manifolds documentation
- file: `sage/manifolds/manifold.py`

Logs:
https://www.math.u-psud.fr/~lelievre/sagelogs/
slel-sage-9-2-b6-mac-brew-2020-07-30-fail.zip

Instead of uninstalling the Homebrew packages gap and flint,
could I have kept them installed and configured `make` to not
use them with this command?

$ ./configure --without-system-flint --without-system-gap

[Dima Pasechnik]

[manifolds] ImportError:
dlopen(/opt/s/sage92b6/local/lib/python3.7/site-packages/sage/libs/ecl.cpython-37m-darwin.so,
2): Symbol not found: _
ecl_process_env
[manifolds] Referenced from:
/opt/s/sage92b6/local/lib/python3.7/site-packages/sage/libs/ecl.cpython-37m-darwin.so


did you source .homebrew-build-env ?

What is the output of

otool -L /opt/s/sage92b6/local/lib/python3.7/site-packages/sage/libs/ecl.cpython-37m-darwin.so


?

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[Samuel Lelièvre]

2020-07-30 18:39 UTC, Dima Pasechnik:

>
> [manifolds] ImportError:
> dlopen(/opt/s/sage92b6/local/lib/python3.7/site-packages/sage/libs/ecl.cpython-37m-darwin.so,
> 2): Symbol not found: _
> ecl_process_env
> [manifolds] Referenced from:
> /opt/s/sage92b6/local/lib/python3.7/site-packages/sage/libs/ecl.cpython-37m-darwin.so
>

> Did you source .homebrew-build-env ?

Yes.

> What is the output of [...]?

```
$ otool -L /opt/s/sage92b6/local/lib/python3.7/site-packages/sage/libs/ecl.cpython-37m-darwin.so
/opt/s/sage92b6/local/lib/python3.7/site-packages/sage/libs/ecl.cpython-37m-darwin.so:
@rpath/libecl.20.4.dylib (compatibility version 20.4.24, current version 0.0.0)
/usr/local/opt/gmp/lib/libgmp.10.dylib (compatibility version 15.0.0,
current version 15.0.0)
/opt/s/sage92b6/local/lib/libpari-gmp.dylib (compatibility version
2.11.0, current version 2.11.2)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
version 1252.250.1)
```

[Dima Pasechnik]

Do you have another copy of libecl*.dylib or libecl*.so somewhere in
/usr/local ?

(or just ecl*.[dylib,so] - I recall at some point the naming was off)

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[Samuel Lelièvre]

2020-07-31 à 09:58 UTC, Dima Pasechnik:

>
> Do you have another copy of libecl*.dylib or libecl*.so somewhere in
> /usr/local ?
>
> (or just ecl*.[dylib,so] - I recall at some point the naming was off)

Here is what I have:
```
$ find /usr/local -iname "ecl*.so"
$ find /usr/local -iname "ecl*.dylib"
$ find /usr/local -iname "libecl*.so"
$ find /usr/local -iname "libecl*.dylib"
/usr/local/lib/libecl.20.dylib
/usr/local/lib/libecl.dylib
/usr/local/lib/libecl.20.4.dylib
/usr/local/lib/libecl.20.4.24.dylib
/usr/local/Cellar/ecl/20.4.24/lib/libecl.20.dylib
/usr/local/Cellar/ecl/20.4.24/lib/libecl.dylib
/usr/local/Cellar/ecl/20.4.24/lib/libecl.20.4.dylib
/usr/local/Cellar/ecl/20.4.24/lib/libecl.20.4.24.dylib
```

[Dima Pasechnik]

I guess all of them are actually links to
/usr/local/Cellar/ecl/20.4.24/lib/libecl.20.4.24.dylib
all of them installed by Homebrew.

anyhow, most probably the error you have is due to their presence - as they are
built with --enable-threads=yes, but Sage's is built with --enable-threads=no

> ```
>
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[Samuel Lelièvre]

2020-07-31 12:29 UTC, Dima Pasechnik:
>
> On Fri, Jul 31, 2020 at 12:43 PM Samuel Lelièvre:

> >
> > 2020-07-31 à 09:58 UTC, Dima Pasechnik:
> > >
> > > Do you have another copy of libecl*.dylib or libecl*.so somewhere in
> > > /usr/local ?
> > >
> > > (or just ecl*.[dylib,so] - I recall at some point the naming was off)
> >
> > Here is what I have:
> > ```
> > $ find /usr/local -iname "ecl*.so"
> > $ find /usr/local -iname "ecl*.dylib"
> > $ find /usr/local -iname "libecl*.so"
> > $ find /usr/local -iname "libecl*.dylib"
> > /usr/local/lib/libecl.20.dylib
> > /usr/local/lib/libecl.dylib
> > /usr/local/lib/libecl.20.4.dylib
> > /usr/local/lib/libecl.20.4.24.dylib
> > /usr/local/Cellar/ecl/20.4.24/lib/libecl.20.dylib
> > /usr/local/Cellar/ecl/20.4.24/lib/libecl.dylib
> > /usr/local/Cellar/ecl/20.4.24/lib/libecl.20.4.dylib
> > /usr/local/Cellar/ecl/20.4.24/lib/libecl.20.4.24.dylib
>
> I guess all of them are actually links to
> /usr/local/Cellar/ecl/20.4.24/lib/libecl.20.4.24.dylib
> all of them installed by Homebrew.
>
> anyhow, most probably the error you have is due to their presence - as they are
> built with --enable-threads=yes, but Sage's is built with --enable-threads=no

Thanks for the analysis. Is this something to take into account at

- spkg-configure.m4 for ecl and maxima
https://trac.sagemath.org/ticket/29617

or is it independent of spkg-configure.m4 and should configure
check the "enable-threads" status of any libecl*.[so|dylib] it finds?

Should I just uninstall Homebrew's ecl and maxima for now?

[Dima Pasechnik]

At the moment Sage should ignore all the ECL except from its own, but
it does not happen for some reason - during the building of the Cython
extension it does use the system (Homebrew) one, but then during the
Sage startup it uses Sage's own, BOOM...

Frankly I don't recall why we need single-threaded ECL.

>
> Should I just uninstall Homebrew's ecl and maxima for now?

yes, that's one way out - and rebuild Sage's ECL extension afterwards.

>
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[Samuel Lelièvre]

2020-07-31 13:01 UTC, Dima Pasechnik:
>
> On Fri, Jul 31, 2020 at 1:40 PM Samuel Lelièvre:

> >
> > 2020-07-31 12:29 UTC, Dima Pasechnik:
> > >

> > > I guess all of them are actually links to
> > > /usr/local/Cellar/ecl/20.4.24/lib/libecl.20.4.24.dylib
> > > all of them installed by Homebrew.
> > >
> > > anyhow, most probably the error you have is due to their presence - as they are
> > > built with --enable-threads=yes, but Sage's is built with --enable-threads=no
> >
> > Thanks for the analysis. Is this something to take into account at
> >
> > - spkg-configure.m4 for ecl and maxima
> > https://trac.sagemath.org/ticket/29617
> >
> > or is it independent of spkg-configure.m4 and should configure
> > check the "enable-threads" status of any libecl*.[so|dylib] it finds?
>
> At the moment Sage should ignore all the ECL except from its own, but
> it does not happen for some reason - during the building of the Cython
> extension it does use the system (Homebrew) one, but then during the
> Sage startup it uses Sage's own, BOOM...

Should I open a ticket? "Ignore system ECL until #29617 lands"?

> Frankly I don't recall why we need single-threaded ECL.

The discussion at #26579 points to #11752 as what led to disabling threads.

- Fix ecl.pyx doctests with threaded ecl
https://trac.sagemath.org/ticket/26579

- ecl.pyx should not touch SIGPWR neither SIGXCPU when initializing ecl
https://trac.sagemath.org/ticket/11752

> > Should I just uninstall Homebrew's ecl and maxima for now?
>
> yes, that's one way out - and rebuild Sage's ECL extension afterwards.

Ok thanks.

[Sébastien Labbé]

Running tests with few optional and external packages (but not internet which I think is because I was too far from the wifi), I get

Using --optional=4ti2,cbc,ccache,cryptominisat,dot2tex,e_antic,external,fricas,glucose,latte_int,lidia,lrslib,memlimit,normaliz,notedown,openssl,pandoc_attributes,pycosat,pynormaliz,python_openid,rst2ipynb,sage,sage_numerical_backends_coin,speaklater

----------------------------------------------------------------------
sage -t --long --random-seed=0 src/sage_setup/optional_extension.py  # 1 doctest failed
----------------------------------------------------------------------
External software detected for doctesting: ffmpeg,graphviz,imagemagick,latex,octave,pandoc

Failed test is copied below.

sage -t --long --random-seed=0 src/sage_setup/optional_extension.py
**********************************************************************
File "src/sage_setup/optional_extension.py", line 72, in sage_setup.optional_extension.OptionalExtension
Failed example:
    print(ext.__class__.__name__)
Expected:
    Extension
Got:
    CythonizeExtension
**********************************************************************
1 item had failures:
   1 of  10 in sage_setup.optional_extension.OptionalExtension
    0 tests not run because we ran out of time
    [12 tests, 1 failure, 0.41 s]

Do you get that failure?

[Samuel Lelièvre]

Building succeeded on Debian 10. Tests (testlong) succeeded too.

$ make testlong
All tests passed!

Then I tried

$ make testalllong

and to my surprise it built sagelib and dochtml anew.
A number of files timed out or had failing doctests,
see further email.

On macOS with Homebrew, `make` finally succeeded.
Thanks Dima, François and Matthias for all the help!
After that I ran `make testlong` and it started by
- rebuilding sagelib
- rebuilding dochtml
- rebuilding sagelib again!

```
[sagelib-9.2.beta6] installing. Log file:
/opt/s/sage92b6/logs/pkgs/sagelib-9.2.beta6.log
[sagelib-9.2.beta6] successfully installed.
[dochtml] installing. Log file: logs/dochtml.log
[dochtml] successfully installed.
[sagelib-9.2.beta6] installing. Log file:
/opt/s/sage92b6/logs/pkgs/sagelib-9.2.beta6.log
[sagelib-9.2.beta6] successfully installed.
```

Is that expected? Or something to fix?
Is there already a ticket? Should I open one?

[Dima Pasechnik]

This is probably harmless, just some "blessing" done, rather than
cythonising/compiling the
whole thing. (check the logs)

Most probably it is just unnecessary rebuilding of polybori extension,
due to its dependence on
headers in src/module_list.py:

Extension('sage.rings.polynomial.pbori',
sources = ['sage/rings/polynomial/pbori.pyx'],
depends = [SAGE_INC + "/polybori/" + hd + ".h" for hd in
["polybori", "config"]]),

If polybori comes from the system, SAGE_INC should become
/usr/include, or whatever
the appropriate header is. (Or, simpler, this "depends=" removed)
That was mentioned on e.g. #29791.

> Is there already a ticket? Should I open one?
>

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[Samuel Lelièvre]

2020-08-1 01:13 UTC, Samuel Lelièvre:

>
> Building succeeded on Debian 10. Tests (testlong) succeeded too.
>
> $ make testlong
> All tests passed!
>
> Then I tried
>
> $ make testalllong
>
> and to my surprise it built sagelib and dochtml anew.
> A number of files timed out or had failing doctests,
> see further email.

Here is the promised further email, before I forget.

```
$ make testalllong
----------------------------------------------------------------------
./sage -t --long --random-seed=0 src/sage/calculus/calculus.py # Timed out
./sage -t --long --random-seed=0 src/sage/databases/findstat.py # 17
doctests failed
./sage -t --long --random-seed=0 src/sage/databases/oeis.py # 1 doctest failed
./sage -t --long --random-seed=0 src/sage/doctest/external.py # Timed out
./sage -t --long --random-seed=0 src/sage/functions/gamma.py # Timed out
./sage -t --long --random-seed=0 src/sage/interfaces/maple.py # 15
doctests failed
./sage -t --long --random-seed=0 src/sage/interfaces/interface.py # Timed out
./sage -t --long --random-seed=0 src/sage/interfaces/mathematica.py # Timed out
./sage -t --long --random-seed=0 src/sage/interfaces/octave.py # 3
doctests failed
./sage -t --long --random-seed=0 src/sage/matrix/matrix1.pyx # Timed out
./sage -t --long --random-seed=0 src/sage/misc/remote_file.py # 1
doctest failed
./sage -t --long --random-seed=0 src/sage/misc/functional.py # Timed out
./sage -t --long --random-seed=0
src/sage/modules/free_module_element.pyx # Timed out
./sage -t --long --random-seed=0 src/sage/plot/graphics.py # 63 doctests failed
./sage -t --long --random-seed=0 src/sage/plot/plot.py # 88 doctests failed
./sage -t --long --random-seed=0 src/sage/symbolic/constants_c.pyx # Timed out
./sage -t --long --random-seed=0 src/sage/symbolic/constants.py # Timed out
./sage -t --long --random-seed=0 src/sage/symbolic/expression.pyx # Timed out
./sage -t --long --random-seed=0
src/sage/symbolic/integration/integral.py # Timed out
./sage -t --long --random-seed=0 src/sage/tests/benchmark.py # Timed out
./sage -t --long --random-seed=0
src/doc/en/constructions/interface_issues.rst # 1 doctest failed
./sage -t --long --random-seed=0
src/doc/en/constructions/linear_algebra.rst # 1 doctest failed
./sage -t --long --random-seed=0
src/doc/en/developer/coding_in_other.rst # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 33434.3 seconds
cpu time: 9398.0 seconds
cumulative wall time: 9599.4 seconds

External software detected for doctesting:

ffmpeg,graphviz,imagemagick,internet,latex,macaulay2,maple,octave,pandoc
make: *** [Makefile:181: testalllong] Error 5
```

When ran separately, they all gave
```
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------
```

[Samuel Lelièvre]

2020-08-01 01:13 UTC, Samuel Lelièvre:
>
> [...]

> On macOS with Homebrew, `make` finally succeeded.

> [...]

> After that I ran `make testlong` and it started by
> - rebuilding sagelib

> [...]

The result of `make testlong` was: All tests passed!
I then ran `make testalllong and the result was:
```
----------------------------------------------------------------------
./sage -t --long --warn-long 99.5 --random-seed=0

src/sage/misc/remote_file.py # 1 doctest failed

./sage -t --long --warn-long 99.5 --random-seed=0
src/sage/misc/latex.py # 1 doctest failed
./sage -t --long --warn-long 99.5 --random-seed=0

src/sage/databases/findstat.py # 17 doctests failed

./sage -t --long --warn-long 99.5 --random-seed=0

src/sage/databases/oeis.py # 1 doctest failed

./sage -t --long --warn-long 99.5 --random-seed=0
src/sage/plot/animate.py # Timed out
./sage -t --long --warn-long 99.5 --random-seed=0
src/sage/combinat/designs/ext_rep.py # 1 doctest failed
./sage -t --long --warn-long 99.5 --random-seed=0
src/sage/combinat/designs/design_catalog.py # 3 doctests failed
./sage -t --long --warn-long 99.5 --random-seed=0
src/sage/combinat/designs/covering_design.py # 2 doctests failed
./sage -t --long --warn-long 99.5 --random-seed=0
src/sage/tests/cmdline.py # 1 doctest failed
./sage -t --long --warn-long 99.5 --random-seed=0
src/sage/symbolic/integration/integral.py # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 45606.9 seconds
cpu time: 16345.8 seconds
cumulative wall time: 22785.9 seconds

External software detected for doctesting:

ffmpeg,imagemagick,internet,latex,pandoc
make: *** [testalllong] Error 5
```
I then ran each test by itself, getting each time: All tests passed!

[Justin C. Walker]

> On Jul 25, 2020, at 17:20 , Volker Braun <vbrau...@gmail.com> wrote:
>
> As always, you can get the latest beta version from the "develop" git branch. Alternatively, the self-contained source tarball is at http://www.sagemath.org/download-latest.html

Built from fresh clones of the 9.2.b6 branch, on three macOS systems: 10.13.6 (2019 iMac Pro, 18-core Xeon W); 10.14.6 (2017 MBP, Quad-core Core i7); and 10.15.6 (2019 MBP, 8-core Core i9).

No problems with the builds, and testing (‘ptestlong’) on each completed with no failures.

Justin


--
Justin C. Walker, Curmudgeon at Large
Director
Institute for the Enhancement of the Director's Income
--
In mathematics you don't understand
things. You just get used to them.
--John von Neumann
--