Sage 9.1.beta1 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 

dde78cbd22 (tag: 9.1.beta1, trac/develop) Updated SageMath version to 9.1.beta1

4fd5d56ece Trac #29029: some cleaning in power series pyx files

4cb8a7b996 Trac #29020: remove some deprecated stuff in modular

ed52d73c0d Trac #29014: cvxopt: use pkg-config for blas libdir in spkg-install

64438cef9b Trac #29010: Split off sage.rings.number_field.homset from sage.rings.number_field.morphism

6612330a9f Trac #29008: Move sage.rings.homset to the "new" coercion model

66cfbfcedc Trac #29001: PKG_CHECK_VAR missing on pkgconfig < 0.28

03886d35eb Trac #28995: little tweak to our lgtm config file

6d8d080aa2 Trac #28990: some fixes in sage_bootstrap and mac-app

9a911b0056 Trac #28978: Change "high mem" to "memlimit" when referring to doctesting tags

c18ebf94f0 Trac #28967: implement easy cases of inverse_mod for general commutative rings

437b96dd6a Trac #29030: Fix deprecation warnings with ipython 7

4579b22408 Trac #29027: MR40: add missing # long time tags

4200a9a134 Trac #29025: numpy: site.cfg needs a [DEFAULT] section

d5521bf8c8 Trac #29021: Bug in setting the calculus method on manifolds

5534ecd1ce Trac #29019: Make patch to pillow more robust (do not depend on "Py_MACOS_SYSROOT") and fix zlib problem on macOS

0c037c69c1 Trac #29017: Coercion map to a quotient of a polynomial ring has incorrect parent

d337302be4 Trac #29016: spkg-legacy-uninstall for R

fb6146ade2 Trac #29004: Fix broken link with hall_polynomial in HallAlgebra

89447f97ca Trac #29003: Install Sage-specific .pc files when running make, not configure

b6f7be5e5b Trac #28997: Update sage-numerical-backends-gurobi to 9.0.0

24dbe7fe89 Trac #28994: pyflakes cleanup in categories

8966c95bd5 Trac #28993: Adding keyword `prec` to the element constructor of Laurent series

e98af516aa Trac #28988: Support rpy 3.x

1f0508d28a Trac #28985: spkg-configure for gfan

1f76e74068 Trac #28973: Automorphism Fields: Notation of Inverse

6c59de24f0 Trac #28968: further improvements to GroupLibGAP

5a115e0502 Trac #28965: enhance GroupLibGAP

25b20e31be Trac #28961: Better class hierarchy for classical matrix Lie algebras

305ed5a09b Trac #28958: spkg-configure.m4 for nauty

f0b2140404 Trac #28954: polynomial degree is broken for weighted block orders

d12132f98f Trac #28611: Genus Representative

295bd69e58 Trac #28473: decomposition by clique minimal separators

d63a3bc1d3 Trac #28239: Precision of Laurent series is restricted to be positive

878ff06b8e Trac #28045: spkg-configure.m4 for libatomic

ba57ab1cca Trac #28969: fix typo in error message of IntegerMod_abstract.__abs__

34d6e53bf6 Trac #28975: return is not a function

e13339bda5 Trac #28972: some details about all(...) and return

6fa6de600d Trac #28952: Rational representative for a genus

266a6aaa9c Trac #28908: spkg-configure for cbc

f8430c4d06 Trac #28934: remove stuff about python 2.4 compatibility

582712b85d Trac #28932: fix QuadraticField constructor if embedding=False

2f6e2f2219 Trac #28931: some cleanup for contour plot

75f1dccb81 Trac #28907: remove the method MathematicaElement.N()

0e4041927e Trac #28902: Cythonize hypergeometric trace formula

b40e3a3ad7 Trac #28901: some details in matrix/

6c520b21de Trac #28772: Kneading sequences for the doubling map

0e19bcb7e6 Trac #28695: gcc: mismatch of assembler / linker during configure

495254a7fd Trac #28956: correct AC_CHECK_PROG call in spkg-configure for bzip2

85c95a6959 Trac #28955: Bug in quadratic_form_from_invariants

93ed1bbb25 Trac #28942: Maximal even overlattice

8a0e0ebfe1 Trac #28921: Mixed Forms - Zero Treatment for Scalar Multiplication

fb8d83d885 Trac #28916: MixedFormAlgebra - More Flexible Coercions

708ab81536 Trac #28886: Update FP(Y)LLL

af6498344d Trac #27086: Simplicity and simpliciality for CombinatorialPolyhedron

af2f949780 Trac #19803: difference of behavior in polyhedra with different backends

b8f53f72e8 (tag: 9.1.beta0) Updated SageMath version to 9.1.beta0

[David Coudert]

I cannot build the doc, even after a doc-clean.

cd ../.. && sage-logger -p './sage --docbuild --no-pdf-links all html ' logs/dochtml.log

[dochtml] 

[dochtml] Building reference manual, first pass.

[dochtml] 

[dochtml] [reference] Sphinx v2.3.1 en cours d'exécution

[dochtml] [reference] /Users/dcoudert/sage/local/lib/python3.7/site-packages/sphinx/util/docutils.py:285: RemovedInSphinx30Warning: function based directive support is now deprecated. Use class based directive instead.

[dochtml] [reference]   RemovedInSphinx30Warning)

[dochtml] [reference] WARNING: l'entrée html_static_path '/Users/dcoudert/sage/src/doc/common/static' n'existe pas

[dochtml] [reference] WARNING: l'entrée html_static_path 'static' n'existe pas

[dochtml] [reference] WARNING: le fichier de favicon 'favicon.ico' n'existe pas

[dochtml] [reference] construction en cours [mo]:cibles pour les fichiers po 0 qui sont périmées

[dochtml] [reference] construction [inventory]:cibles pour les fichiers sources 1 qui sont périmées

[dochtml] [reference] mise-à-jour de l'environnement :[nouvelle configuration] 1 ajouté, 0 modifié, 0 supprimé

[dochtml] [reference] lecture des sources... [100%] index

[dochtml] [reference] recherche des fichiers périmés... aucun résultat

[dochtml] [reference] environnement de sérialisation... fait

[dochtml] [reference] /Users/dcoudert/sage/src/doc/en/reference/references/index.rst:36: WARNING: La citation [AAGMRZ2019] n'est pas référencée

[dochtml] [reference] /Users/dcoudert/sage/src/doc/en/reference/references/index.rst:40: WARNING: La citation [Ab1995] n'est pas référencée

[dochtml] [reference] /Users/dcoudert/sage/src/doc/en/reference/references/index.rst:46: WARNING: La citation [AB2007] n'est pas référencée

[dochtml] [reference] /Users/dcoudert/sage/src/doc/en/reference/references/index.rst:50: WARNING: La citation [AB2008] n'est pas référencée

...

...

[dochtml] [reference] /Users/dcoudert/sage/src/doc/en/reference/references/index.rst:5429: WARNING: La citation [ZZ2005] n'est pas référencée

[dochtml] [reference] vérification de la cohérence... fait

[dochtml] [reference] document en préparation... fait

[dochtml] [reference] écriture... [100%] index

[dochtml] [reference] dumping object inventory... fait

[dochtml] [reference] build a réussi, 1284 warnings.

[dochtml] [reference] The inventory files are in local/share/doc/sage/inventory/en/reference/references.

[dochtml] Error building the documentation.

[dochtml] Traceback (most recent call last):

[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/runpy.py", line 193, in _run_module_as_main

[dochtml]     "__main__", mod_spec)

[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/runpy.py", line 85, in _run_code

[dochtml]     exec(code, run_globals)

[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__main__.py", line 2, in <module>

[dochtml]     main()

[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py", line 1720, in main

[dochtml]     builder()

[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py", line 327, in _wrapper

[dochtml]     getattr(get_builder(document), 'inventory')(*args, **kwds)

[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py", line 550, in _wrapper

[dochtml]     self._build_bibliography(lang, format, *args, **kwds)

[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py", line 527, in _build_bibliography

[dochtml]     build_many(build_ref_doc, references)

[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py", line 280, in build_many

[dochtml]     _build_many(target, args, processes=NUM_THREADS)

[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/utils.py", line 283, in build_many

[dochtml]     raise worker_exc.original_exception

[dochtml] OSError: WARNING: l'entrée html_static_path '/Users/dcoudert/sage/src/doc/common/static' n'existe pas

make[3]: *** [doc-html] Error 1

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

real 0m20.334s

user 0m10.723s

sys 0m4.168s

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

Error building Sage.

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

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

* documentation: dochtml

  log file: /Users/dcoudert/sage/logs/pkgs/../dochtml.log

The build directory may contain configuration files and other potentially

helpful information. WARNING: if you now run 'make' again, the build

directory will, by default, be deleted. Set the environment variable

SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this.

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

make: *** [all] Error 2

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[Dima Pasechnik]

On Wed, Jan 22, 2020 at 7:53 AM David Coudert <david....@gmail.com> wrote:
>
> I cannot build the doc, even after a doc-clean.
>
>
> cd ../.. && sage-logger -p './sage --docbuild --no-pdf-links all html ' logs/dochtml.log
> [dochtml]
> [dochtml] Building reference manual, first pass.
> [dochtml]
> [dochtml] [reference] Sphinx v2.3.1 en cours d'exécution

we are still on sphinx 1.8.5.
cf e.g. https://trac.sagemath.org/ticket/28856

you probably installed a new sphinx via pip or something like that, and, oops...

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/D5D0139C-7A98-4797-A7B2-AE5AEA4875DF%40gmail.com.

[David Coudert]

Le 22 janv. 2020 à 10:27, Dima Pasechnik <dim...@gmail.com> a écrit :

On Wed, Jan 22, 2020 at 7:53 AM David Coudert <david....@gmail.com> wrote:

I cannot build the doc, even after a doc-clean.


cd ../.. && sage-logger -p './sage --docbuild --no-pdf-links all html ' logs/dochtml.log
[dochtml]
[dochtml] Building reference manual, first pass.
[dochtml]
[dochtml] [reference] Sphinx v2.3.1 en cours d'exécution

we are still on sphinx 1.8.5.
cf e.g. https://trac.sagemath.org/ticket/28856

you probably installed a new sphinx via pip or something like that, and, oops…

I have not installed a new sphinx (or it’s a side effect of something else, but what ??)

D.

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[Dima Pasechnik]

On Wed, Jan 22, 2020 at 9:39 AM David Coudert <david....@gmail.com> wrote:
>
> Le 22 janv. 2020 à 10:27, Dima Pasechnik <dim...@gmail.com> a écrit :
>
> On Wed, Jan 22, 2020 at 7:53 AM David Coudert <david....@gmail.com> wrote:
>
>
> I cannot build the doc, even after a doc-clean.
>
>
> cd ../.. && sage-logger -p './sage --docbuild --no-pdf-links all html ' logs/dochtml.log
> [dochtml]
> [dochtml] Building reference manual, first pass.
> [dochtml]
> [dochtml] [reference] Sphinx v2.3.1 en cours d'exécution
>
>
> we are still on sphinx 1.8.5.
> cf e.g. https://trac.sagemath.org/ticket/28856
>
> you probably installed a new sphinx via pip or something like that, and, oops…
>
>
> I have not installed a new sphinx (or it’s a side effect of something else, but what ??)

check e.g. the following

sage: import sphinx
sage: sphinx.version_info
(1, 8, 5, 'final', 0)

if it's not 1.8.5, I'd just do

./sage -f sphinx

as to the root couse of this, I'd first look at

./sage --python -m pip list

to see the list of all pip-install packages with versions.

Or even more details:

$ ./sage --python
Python 3.7.3 (default, Jan 20 2020, 14:52:21)
[GCC 8.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>>
>>> import pkg_resources, os, time
>>> for package in pkg_resources.working_set:
... print("%s: %s" % (package,
time.ctime(os.path.getctime(package.location))))
...
zope.interface 4.6.0: Tue Jan 21 22:21:30 2020
widgetsnbextension 3.4.2: Tue Jan 21 22:21:30 2020

etc.

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/CBF8B41A-2994-4989-839F-52E050FB1C1C%40gmail.com.

[Eric Gourgoulhon]

On Ubuntu 18.04 running on a bi-Xeon E5-2623 (8 cores) + 16 GB RAM computer:

  - incremental build (with -j16) from 9.1.beta0: OK

  - all tests from ptestlong passed

Eric

[David Coudert]

sage: import sphinx

sage: sphinx.version_info

(2, 3, 1, 'final', 0)

after ./sage -f sphinx  I can compile part of the doc (I did a make doc-clean before), until the following error

[dochtml] 

[dochtml] Building en/thematic_tutorials.

[dochtml] 

[dochtml] [thematic_] building [html]: targets for 85 source files that are out of date

[dochtml] [thematic_] updating environment: 85 added, 0 changed, 0 removed

[dochtml] [thematic_] /Users/dcoudert/sage/local/lib/python3.7/site-packages/sphinx/util/nodes.py:94: FutureWarning:

[dochtml] [thematic_]    The iterable returned by Node.traverse()

[dochtml] [thematic_]    will become an iterator instead of a list in Docutils > 0.16.

[dochtml] [thematic_]   for classifier in reversed(node.parent.traverse(nodes.classifier)):

[dochtml] [thematic_] Merging environment/index files...

[dochtml] [thematic_] ... done (3 todos, 85 index, 66 citations, 0 modules)

[dochtml] [thematic_] pickling environment... fait

[dochtml] [thematic_] checking consistency... fait

[dochtml] [thematic_] preparing documents... fait

[dochtml] [thematic_] /Users/dcoudert/sage/local/lib/python3.7/site-packages/sphinx/writers/html.py:462: FutureWarning:

[dochtml] [thematic_]    The iterable returned by Node.traverse()

[dochtml] [thematic_]    will become an iterator instead of a list in Docutils > 0.16.

[dochtml] [thematic_]   target_node = image_nodes and image_nodes[0] or node.parent

[dochtml] [thematic_] /Users/dcoudert/sage/src/doc/en/thematic_tutorials/structures_in_coding_theory.rst:722: WARNING: Could not lex literal_block as "python". Highlighting skipped.

[dochtml] [thematic_] Merging js index files...

[dochtml] [thematic_] ... done (4882 js index entries)

[dochtml] [thematic_] copying extra files... fait

[dochtml] [thematic_] dumping search index in English (code: en) ... fait

[dochtml] [thematic_] dumping object inventory... fait

[dochtml] [thematic_] build réussi, 6 warnings.

[dochtml] [thematic_] The HTML pages are in local/share/doc/sage/html/en/thematic_tutorials.

[dochtml] Error building the documentation.

[dochtml] Traceback (most recent call last):

[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/runpy.py", line 193, in _run_module_as_main

[dochtml]     "__main__", mod_spec)

[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/runpy.py", line 85, in _run_code

[dochtml]     exec(code, run_globals)

[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__main__.py", line 2, in <module>

[dochtml]     main()

[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py", line 1720, in main

[dochtml]     builder()

[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py", line 336, in _wrapper

[dochtml]     build_many(build_other_doc, L)

[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py", line 280, in build_many

[dochtml]     _build_many(target, args, processes=NUM_THREADS)

[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/utils.py", line 283, in build_many

[dochtml]     raise worker_exc.original_exception

[dochtml] OSError: /Users/dcoudert/sage/src/doc/en/thematic_tutorials/structures_in_coding_theory.rst:722: WARNING: Could not lex literal_block as "python". Highlighting skipped.

[dochtml] 

[dochtml]     Note: incremental documentation builds sometimes cause spurious

[dochtml]     error messages. To be certain that these are real errors, run

[dochtml]     "make doc-clean" first and try again.

make[3]: *** [doc-html] Error 1

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

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[Steven Trogdon]

Your build may be picking up on the wrong version of pygments. Vanilla Sage uses pygments-2.3.1.p0.

./sage -f pygments

may fix the issue. On my sage-on-gentoo build, which uses a system pygments, I see the same lex literal_block as "python" Warning with pygments-2.5.2. But pygments-2.4.2 is fine.

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[Dima Pasechnik]

On Wed, Jan 22, 2020 at 6:04 PM Steven Trogdon <steven....@gmail.com> wrote:
>
> Your build may be picking up on the wrong version of pygments. Vanilla Sage uses pygments-2.3.1.p0.
>
> ./sage -f pygments
>
> may fix the issue. On my sage-on-gentoo build, which uses a system pygments, I see the same lex literal_block as "python" Warning with pygments-2.5.2. But pygments-2.4.2 is fine.

indeed, it looks plausable that more than just Sphinx got overwritten...

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[Timo Kaufmann]

For what it's worth, I'm currently working on fixing the pygments issue on nixos. The issue exists because pygments 2.5 uses `PythonLexer` as an alias for `Python3Lexer`, while previously referred to the python2 version. Packages such as ipython and sphinx use PythonLexer, leading to breakage.

I wish they just removed PythonLexer completely, that would've made debugging much easier.

[David Coudert]

Working!

Thank you.

David.

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[Timo Kaufmann]

Am Mittwoch, 22. Januar 2020 19:04:06 UTC+1 schrieb Steven Trogdon:

Your build may be picking up on the wrong version of pygments. Vanilla Sage uses pygments-2.3.1.p0.

./sage -f pygments

may fix the issue. On my sage-on-gentoo build, which uses a system pygments, I see the same lex literal_block as "python" Warning with pygments-2.5.2. But pygments-2.4.2 is fine.

I have fixed the pygments issue for nix here: https://github.com/NixOS/nixpkgs/pull/78348

Only the sphinx patch is strictly necessary to fix the docbuild. Since it doesn't look like sphinx has a python2 maintenance branch, you'll have to patch it if you want this fixed.

[François Bissey]

Is this backwards compatible with older versions of pygments?
i.e. there won’t be any issues if pygments-2.3.x is used in conjunction with patched sphinx-1.8?

François

[Harald Schilly]

Building it for CoCalc (ubuntu 18.04 docker container) it fails at SciPy. Can't find any of the required libs. There was no change in the setup, hence I wonder what's going on... I'm happy to check various env vars!

[scipy-1.2.0]     Running from scipy source directory.                                
[scipy-1.2.0]     lapack_opt_info:  
[scipy-1.2.0]     lapack_mkl_info:                                                        
[scipy-1.2.0]     Disabled lapack_mkl_info: (MKLROOT is None)
[scipy-1.2.0]     Disabled lapack_mkl_info: (MKLROOT is None)                                                              
[scipy-1.2.0]     customize UnixCCompiler    
[scipy-1.2.0]       libraries mkl_rt not found in []                                      
[scipy-1.2.0]       NOT AVAILABLE
[scipy-1.2.0]
[scipy-1.2.0]     openblas_lapack_info:
[scipy-1.2.0]     customize UnixCCompiler
[scipy-1.2.0]     Disabled openblas_lapack_info: (OPENBLAS is None)
[scipy-1.2.0]     customize UnixCCompiler
[scipy-1.2.0]       libraries openblas not found in []
[scipy-1.2.0]       NOT AVAILABLE
[scipy-1.2.0]
[scipy-1.2.0]     openblas_clapack_info:
[scipy-1.2.0]     customize UnixCCompiler
[scipy-1.2.0]     Disabled openblas_clapack_info: (OPENBLAS is None)
[scipy-1.2.0]     customize UnixCCompiler
[scipy-1.2.0]       libraries openblas,lapack not found in []
[scipy-1.2.0]       NOT AVAILABLE
[scipy-1.2.0]
[scipy-1.2.0]     atlas_3_10_threads_info:
[scipy-1.2.0]     Disabled atlas_3_10_threads_info: (PTATLAS is None)
[scipy-1.2.0]     <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
[scipy-1.2.0]       NOT AVAILABLE
[scipy-1.2.0]
[scipy-1.2.0]     atlas_3_10_info:
[scipy-1.2.0]     Disabled atlas_3_10_info: (ATLAS is None)
[scipy-1.2.0]     <class 'numpy.distutils.system_info.atlas_3_10_info'>
[scipy-1.2.0]       NOT AVAILABLE
[scipy-1.2.0]
[scipy-1.2.0]     atlas_threads_info:
[scipy-1.2.0]     Disabled atlas_threads_info: (PTATLAS is None)
[scipy-1.2.0]     <class 'numpy.distutils.system_info.atlas_threads_info'>
[scipy-1.2.0]       NOT AVAILABLE
[scipy-1.2.0]
[scipy-1.2.0]     atlas_info:
[scipy-1.2.0]     Disabled atlas_info: (ATLAS is None)
[scipy-1.2.0]     <class 'numpy.distutils.system_info.atlas_info'>
[scipy-1.2.0]       NOT AVAILABLE
[scipy-1.2.0]
[scipy-1.2.0]     accelerate_info:
[scipy-1.2.0]       NOT AVAILABLE
[scipy-1.2.0]
[scipy-1.2.0]     /ext/sage/sage-dev/local/lib/python3.7/site-packages/numpy/distutils/system_info.py:636: UserWarning:
[scipy-1.2.0]         Atlas (http://math-atlas.sourceforge.net/) libraries not found.
[scipy-1.2.0]         Directories to search for the libraries can be specified in the
[scipy-1.2.0]         numpy/distutils/site.cfg file (section [atlas]) or by setting
[scipy-1.2.0]         the ATLAS environment variable.
[scipy-1.2.0]       self.calc_info()
[scipy-1.2.0]     lapack_info:
[scipy-1.2.0]     customize UnixCCompiler
[scipy-1.2.0]       libraries openblas not found in ['/ext/sage/sage-dev/local/lib']
[scipy-1.2.0]       NOT AVAILABLE
[scipy-1.2.0]
[scipy-1.2.0]     /ext/sage/sage-dev/local/lib/python3.7/site-packages/numpy/distutils/system_info.py:636: UserWarning:
[scipy-1.2.0]         Lapack (http://www.netlib.org/lapack/) libraries not found.
[scipy-1.2.0]         Directories to search for the libraries can be specified in the
[scipy-1.2.0]         numpy/distutils/site.cfg file (section [lapack]) or by setting
[scipy-1.2.0]         the LAPACK environment variable.
[scipy-1.2.0]       self.calc_info()
[scipy-1.2.0]     lapack_src_info:
[scipy-1.2.0]       NOT AVAILABLE
[scipy-1.2.0]
[scipy-1.2.0]     /ext/sage/sage-dev/local/lib/python3.7/site-packages/numpy/distutils/system_info.py:636: UserWarning:
[scipy-1.2.0]         Lapack (http://www.netlib.org/lapack/) sources not found.
[scipy-1.2.0]         Directories to search for the sources can be specified in the
[scipy-1.2.0]         numpy/distutils/site.cfg file (section [lapack_src]) or by setting
[scipy-1.2.0]         the LAPACK_SRC environment variable.
[scipy-1.2.0]       self.calc_info()
[scipy-1.2.0]       NOT AVAILABLE

[Dima Pasechnik]

is it a rebuild after 

make distclean

?

Sage now is trying to use openblas and several packages, such as R and gsl, installed on the system

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[Timo Kaufmann]

The sphinx patch is not backwards compatible, but it can be trivially adopted to be so. The ipython patch is backwards compatible. You can use a similar try/error construct for sphinx:

https://github.com/ipython/ipython/pull/12095/commits/8805293b5e4bce9150cc2ad9c5d6d984849ae447#diff-3956ebe7dd0ddfeaf61b51b153ee71bcR48

Just be sure that you try to import `Python2Lexer` *first* (which will fail on pygments <2.5 since the name previously didn't exist). If you do it the other way around the import wouldn't fail but PythonLexer would silently refer to python3.

[Matthias Köppe]

Possibly related: https://trac.sagemath.org/ticket/29051

[Justin C. Walker]

> On Jan 21, 2020, at 15:41 , 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 w/o problems from fresh clones of the develop branch, on three macOS systems: 10.13.6 (2017 iMac Pro, 18-core Xeon W), 10.14.6 (2017 MBP, Quad-core Core i7), and 10.15.2 (2019 MBP, 8-core Core i9).

10.13.6: 1 transient failure in doctests:
sage -t --long --warn-long 75.1 src/sage/libs/gap/element.pyx
bad exit: 1

10.14.6: all tests passed!

10.15.2: all tests passed!

Justin


--
Justin C. Walker, Curmudgeon-At-Large
Institute for the Absorption of Federal Funds
--------
Men are from Earth.
Women are from Earth.
Deal with it.
--------

[Harald Schilly]

Well, I'm building from a clean git repo, i.e. that's what I do:

$ git branch
* (HEAD detached at 9.1.beta1)
 develop
 origin

$ git reset --hard
$ git clean -fdx
$ unset _JAVA_OPTIONS
$ nice make            

                       

I tried it again, same set of scipy errors.

This is from before the errors, maybe it contains some useful info. And yes, Matthias, #29051 sounds related.

[scipy-1.2.0] scipy-1.2.0                                                                                                      
[scipy-1.2.0] ====================================================                                                            
[scipy-1.2.0] Setting up build directory for scipy-1.2.0                                                                      
[scipy-1.2.0] Finished extraction                                                                                              
[scipy-1.2.0] Applying patches from ../patches...                                                                              
[scipy-1.2.0] Applying ../patches/4a8a35f2c27be9f209cfc6f347e7a57a4a62e693.patch                                              
[scipy-1.2.0] patching file scipy/io/__init__.py                                                                              
[scipy-1.2.0] patching file scipy/stats/_continuous_distns.py                                                                  
[scipy-1.2.0] patching file scipy/stats/_stats_mstats_common.py                                                                
[scipy-1.2.0] ****************************************************                                                            
[scipy-1.2.0] Host system:                                                                                                    
[scipy-1.2.0] Linux ee59ece61f58 4.15.0-1036-gcp #38-Ubuntu SMP Mon Jun 24 13:49:05 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux    
[scipy-1.2.0] ****************************************************                                                            
[scipy-1.2.0] C compiler: gcc                                                                                                  
[scipy-1.2.0] C compiler version:                                                                                              
[scipy-1.2.0] Using built-in specs.                                                                                            
[scipy-1.2.0] COLLECT_GCC=gcc                                                                                                  
[scipy-1.2.0] COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/7/lto-wrapper                                                  
[scipy-1.2.0] OFFLOAD_TARGET_NAMES=nvptx-none                                                                                  
[scipy-1.2.0] OFFLOAD_TARGET_DEFAULT=1                                                                                        
[scipy-1.2.0] Target: x86_64-linux-gnu                                                                                        
[scipy-1.2.0] Configured with: ../src/configure -v --with-pkgversion='Ubuntu 7.4.0-1ubuntu1~18.04.1' --with-bugurl=file:///usr/
share/doc/gcc-7/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++ --prefix=/usr --with-gcc-major-version-
only --program-suffix=-7 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --wi
thout-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-lib
stdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --
enable-libmpx --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib --enable-objc-gc=auto --enable-
multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=g
eneric --enable-offload-targets=nvptx-none --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_
64-linux-gnu --target=x86_64-linux-gnu                                                                                        
[scipy-1.2.0] Thread model: posix                                                                                              
[scipy-1.2.0] gcc version 7.4.0 (Ubuntu 7.4.0-1ubuntu1~18.04.1)                                                                

  

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[Emmanuel Charpentier]

On Debian testing running on core i7 + 16 GB RAM, after upgrading a Python 3-based 9.1.beta0 to 9.1.bet1, ptestalllong gets 5 transient
and 3 permanent failures:

File	Result	P/T
src/sage/plot/animate.py	7 doctests failed	T
src/sage/databases/oeis.py	1 doctest failed	T
src/sage/tests/gap_packages.py	1 doctest failed	P
src/sage/misc/latex.py	1 doctest failed	T
src/sage/numerical/backends/glpk_backend.pyx	1 doctest failed	P
src/sage/repl/load.py	1 doctest failed	T
src/sage/libs/glpk/error.pyx	1 doctest failed	P
src/sage/databases/findstat.py	8 doctests failed	T

All of these failures have already been reported multiple times.

External software detected for doctesting: ffmpeg,graphviz,imagemagick,internet,latex,mathematica,pandoc

HTH,

[Jaap Spies]

On Raspberry Pi 4 4GB on Raspbian Buster build failed with fplll:

libtool: link: g++ -std=gnu++11 -std=c++11 -fPIC -I/home/pi/sagemath/sage-9.1.be

ta1/local/include/ -O3 -Wl,-rpath -Wl,/home/pi/sagemath/sage-9.1.beta1/local/lib

 -o .libs/fplll main.o  -L/home/pi/sagemath/sage-9.1.beta1/local/lib -L/lib ./.l

ibs/libfplll.so -lmpfr -lgmp -pthread -Wl,-rpath -Wl,/home/pi/sagemath/sage-9.1.

beta1/local/lib

/usr/bin/ld: ./.libs/libfplll.so: undefined reference to `__atomic_store_8'

/usr/bin/ld: ./.libs/libfplll.so: undefined reference to `__atomic_load_8'

collect2: error: ld returned 1 exit status

make[7]: *** [Makefile:1165: fplll] Error 1

make[7]: Leaving directory '/home/pi/sagemath/sage-9.1.beta1/local/var/tmp/sage/

build/fplll-5.3.2/src/fplll'

make[6]: *** [Makefile:739: all] Error 2

make[6]: Leaving directory '/home/pi/sagemath/sage-9.1.beta1/local/var/tmp/sage/

:

log attached

[Dima Pasechnik]

On Sun, Jan 26, 2020 at 11:08 AM Jaap Spies <jaap...@gmail.com> wrote:
>
> On Raspberry Pi 4 4GB on Raspbian Buster build failed with fplll:
>
> libtool: link: g++ -std=gnu++11 -std=c++11 -fPIC -I/home/pi/sagemath/sage-9.1.be
> ta1/local/include/ -O3 -Wl,-rpath -Wl,/home/pi/sagemath/sage-9.1.beta1/local/lib
> -o .libs/fplll main.o -L/home/pi/sagemath/sage-9.1.beta1/local/lib -L/lib ./.l
> ibs/libfplll.so -lmpfr -lgmp -pthread -Wl,-rpath -Wl,/home/pi/sagemath/sage-9.1.
> beta1/local/lib
> /usr/bin/ld: ./.libs/libfplll.so: undefined reference to `__atomic_store_8'
> /usr/bin/ld: ./.libs/libfplll.so: undefined reference to `__atomic_load_8'
> collect2: error: ld returned 1 exit status
> make[7]: *** [Makefile:1165: fplll] Error 1
> make[7]: Leaving directory '/home/pi/sagemath/sage-9.1.beta1/local/var/tmp/sage/
> build/fplll-5.3.2/src/fplll'
> make[6]: *** [Makefile:739: all] Error 2
> make[6]: Leaving directory '/home/pi/sagemath/sage-9.1.beta1/local/var/tmp/sage/
> :
> log attached

Thanks, this might be due to an ARM-specific problem with fplll, I cc
to the fplll author.
Not sure whether they do any tests on ARM.

Dima

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[Martin R. Albrecht]

Hi all,

Sorry, I have no idea about this. But indeed, we never test on ARM. Feel free to open an issue on FPLLL’s issue tracker but I’m not sure there’s much we can do without a machine to test things on.

Cheers,
Martin

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[Jaap Spies]

Why does it work on beta0 en not with beta1? Any recent changes? I see 5.2.1 _>  5.3.2

Testing that Sage starts...

[2020-01-26 17:38:30] SageMath version 9.1.beta0, Release Date: 2020-01-10

Yes, Sage starts.

make[3]: Leaving directory '/home/pi/sagemath/sage-9.1.beta0/build/make'

make[2]: Leaving directory '/home/pi/sagemath/sage-9.1.beta0/build/make'

real 325m50.869s

user 1043m32.225s

sys 77m48.384s

Sage build/upgrade complete!

make[1]: Leaving directory '/home/pi/sagemath/sage-9.1.beta0'

pi@rasp4g:~/sagemath/sage-9.1.beta0 $ 

On Sunday, January 26, 2020 at 12:19:44 PM UTC+1, Dima Pasechnik wrote:

On Sun, Jan 26, 2020 at 11:08 AM Jaap Spies <jaap...@gmail.com> wrote:
>
> On Raspberry Pi 4 4GB on Raspbian Buster build failed with fplll:
>
> libtool: link: g++ -std=gnu++11 -std=c++11 -fPIC -I/home/pi/sagemath/sage-9.1.be
> ta1/local/include/ -O3 -Wl,-rpath -Wl,/home/pi/sagemath/sage-9.1.beta1/local/lib
>  -o .libs/fplll main.o  -L/home/pi/sagemath/sage-9.1.beta1/local/lib -L/lib ./.l
> ibs/libfplll.so -lmpfr -lgmp -pthread -Wl,-rpath -Wl,/home/pi/sagemath/sage-9.1.
> beta1/local/lib
> /usr/bin/ld: ./.libs/libfplll.so: undefined reference to `__atomic_store_8'
> /usr/bin/ld: ./.libs/libfplll.so: undefined reference to `__atomic_load_8'
> collect2: error: ld returned 1 exit status
> make[7]: *** [Makefile:1165: fplll] Error 1
> make[7]: Leaving directory '/home/pi/sagemath/sage-9.1.beta1/local/var/tmp/sage/
> build/fplll-5.3.2/src/fplll'
> make[6]: *** [Makefile:739: all] Error 2
> make[6]: Leaving directory '/home/pi/sagemath/sage-9.1.beta1/local/var/tmp/sage/
> :
> log attached

Thanks, this might be due to an ARM-specific  problem with fplll, I cc
to the fplll author.
Not sure whether they do any tests on ARM.

Dima

[snipped]

[Jaap Spies]

Hi Martin,

I'm kind of back to Sage. It's the Raspberry Pi! The actual machine I tested sage on, is a Raspberry Pi B4 with 4GB RAM and with the root / partition mounted on a WD sdd of 500 GB. Affordable, I think.

Cheers,

Jaap

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[Martin R. Albrecht]

We got some new multicore code in 5.3.x, that seems to trigger it.

[Samuel Lelievre]

2020-01-26 18:37:59 UTC, Martin Albrecht:

>
> Sorry, I have no idea about this. But indeed, we never test on ARM.
> Feel free to open an issue on FPLLL’s issue tracker but I’m not sure
> there’s much we can do without a machine to test things on.

I opened this issue:

  https://github.com/fplll/fplll/issues/432

It might be possible to use GitHub actions to test on ARM.