Sage 9.4.beta2 released

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Volker Braun

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Jun 19, 2021, 5:01:48 PM6/19/21
to sage-release
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 

46c5c53b4d (tag: 9.4.beta2, trac/develop) Updated SageMath version to 9.4.beta2
8b70b5bba7 Trac #31928: Failure when testing sage_conf version
826fe92cb6 Trac #31833: remove deprecated stuff in function factory
3ee4a426bc Trac #31829: fix doc detail in set partition
f13536ab0a Trac #31821: Run tests on combinatorial polyhedron
4a7ed9696c Trac #31816: Get rid of sage-pip-uninstall
c429cf8325 Trac #31815: python3: Upgrade to 3.9.5
7776cd1541 Trac #31810: Speedup number field element __getitem__ and for Gaussians
e7c96bf5f3 Trac #31809: WeilPolynomials segfault with squarefree=True
fb8d32171b Trac #31795: faster conversion between power series and polynomials
dc95374a4c Trac #31794: refine relint configuration and make it pass on combinat
a47ce39285 Trac #31793: some details in partitions
26f0031e04 Trac #31789: remove deprecated stuff in words
33227c71b7 Trac #31784: Mixed form name bug for pullback bundle
edf5ff8e48 Trac #31780: remove deprecation in free_module
066dee45e5 Trac #31779: more bijections for parallelogram polyominoes
19d4c34a4c Trac #31767: Enhanced checks for sign() with qqbar elements with addition and subtraction
b1f2788e4c Trac #31760: Speedup WordMorphism.growing_letters
448488c701 Trac #31759: Fix bug in WordMorphism.periodic_point
15a4387f3d Trac #31753: Bug in charpoly over discrete valuation rings
ce8c7303db Trac #31752: error when creating random polynomials
45adbc1ff2 Trac #31734: Add linestyle option to polygon2d
ce7572e422 Trac #31725: Implement meet, join, etc. methods for posets
afae1ae23b Trac #31721: Endow parents with __pow__
d1bfa2e4c5 Trac #31717: Empty families should be false
516f170369 Trac #31716: more scalar conversions
151e01da9f Trac #31710: taking the roots of CBF['x'](0) crashes Sage
3a08098e77 Trac #31708: Let gf2e and gfpn matrices stack on top of a vector
85cd76954b Trac #31705: sage.geometry.polyhedron: More lazy imports
7d21b32efe Trac #31704: Remove Python 2 compatibility from manifolds
30cb045f66 Trac #31700: eigenvalue defined in sage/matrix/matrix_symbolic_dense.pyx is incorrectly called in sage/modules/free_module_morphism.py
89289d09dd Trac #31699: setuptools/pip/pkgconfig/packaging/importlib-metadata upgrade for Sage 9.4
c6b6feb82c Trac #31669: Category of chain complexes: (co)homology functor
984feea49e Trac #31593: configure: Paths within $SAGE_LOCAL ($prefix) for sage_conf
0871b12176 Trac #31591: Expose MemoryAllocator as python package
57cd97207f Trac #31589: Normaliz 3.8.10, PyNormaliz 2.14
4363ed9915 Trac #31008: Upgrade NumPy to 1.20.3, SciPy 1.6.3, networkx 2.5.1
b14e8d1c93 Trac #29985: Make schemes doctests ready for random seeds
3814878a31 Trac #29984: Make symbolic doctests ready for random seeds
0664307a7e Trac #29983: Make finance doctests ready for random seeds
5f4b614072 Trac #29981: Make documentation doctests ready for random seeds
cf864e5968 Trac #29970: Make arith doctests ready for random seeds
f7292698d8 Trac #31893: Fix timeout in sageinspect.py tests
eb0eeb3621 Trac #31921: Knotinfo db interface looks for the wrong python module
667c748d07 Trac #31913: Relaxed padics segfault on 32-bit: libflint.so (_fmpz_clear_mpz)
2e7386bf9b Trac #28647: conversion of Symbolic Ring to FriCAS Expression Integer
d1c618875a Trac #27365: integration over polyhedron with induced measure
571bc46d13 Trac #11323: Fix ComplexNumber.__pow__  to allow float^complex
732c966cee Trac #31869: Fix segfault when multiplying x * ((3*i + 4)*x - 5)
20614c6ac7 Trac #31629: Fix a regression in show(obj) for string obj
4b103a8d37 Trac #31534: tox.ini: In -maximal environments, use IGNORE_MISSING_SYSTEM_PACKAGES=yes for all non-current distributions
3861157d5a Trac #31832: Update fplll 5.4.1, fpylll to 0.5.6 - adds support for gcc 11
30ee8d6505 (tag: 9.4.beta1) Updated SageMath version to 9.4.beta1

David Coudert

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Jun 20, 2021, 3:34:51 AM6/20/21
to sage-r...@googlegroups.com
Thank you for this new beta.

I have a build error on a Intel MacBook Air with macOS 10.15.7, after make distclean, .bootstrap, source .homebrew-build-env, 
./configure and finally make.
I have installed numpy 1.20.3  with homebrew, but it is re-installed by sage and the new installation is not correct

Any help is more than welcome.
David.

cd '/Users/dcoudert/sage/build/pkgs/sagelib' && . '/Users/dcoudert/sage/src/bin/sage-src-env-config' && . '/Users/dcoudert/sage/src/bin/sage-env-config' && . '/Users/dcoudert/sage/src/bin/sage-env' && . '/Users/dcoudert/sage/build/bin/sage-build-env-config' && . '/Users/dcoudert/sage/build/bin/sage-build-env' && SAGE_SPKG_WHEELS=/Users/dcoudert/sage/local/var/lib/sage/wheels SAGE_INST_LOCAL=/Users/dcoudert/sage/local sage-logger -p '/Users/dcoudert/sage/build/pkgs/sagelib/spkg-install' '/Users/dcoudert/sage/logs/pkgs/sagelib-9.4.beta2.log'
[sagelib-9.4.beta2] Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/c++/4.2.1
[sagelib-9.4.beta2] Discovering Python/Cython source code....
[sagelib-9.4.beta2] distributions = ['']
[sagelib-9.4.beta2] Discovered Python/Cython sources, time: 5.91 seconds.
[sagelib-9.4.beta2] running build
[sagelib-9.4.beta2] Generating auto-generated sources
[sagelib-9.4.beta2] Building interpreters for fast_callable
[sagelib-9.4.beta2] running build_cython
[sagelib-9.4.beta2] Enabling Cython debugging support
[sagelib-9.4.beta2] ************************************************************************
[sagelib-9.4.beta2] Traceback (most recent call last):
[sagelib-9.4.beta2]   File "/Users/dcoudert/sage/build/pkgs/sagelib/src/setup.py", line 96, in <module>
[sagelib-9.4.beta2]     code = setup(
[sagelib-9.4.beta2]   File "/Users/dcoudert/sage/local/lib/python3.9/site-packages/setuptools/__init__.py", line 153, in setup
[sagelib-9.4.beta2]     return distutils.core.setup(**attrs)
[sagelib-9.4.beta2]   File "/Users/dcoudert/sage/local/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 148, in setup
[sagelib-9.4.beta2]     dist.run_commands()
[sagelib-9.4.beta2]   File "/Users/dcoudert/sage/local/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 967, in run_commands
[sagelib-9.4.beta2]     self.run_command(cmd)
[sagelib-9.4.beta2]   File "/Users/dcoudert/sage/local/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 986, in run_command
[sagelib-9.4.beta2]     cmd_obj.run()
[sagelib-9.4.beta2]   File "/Users/dcoudert/sage/build/pkgs/sagelib/src/sage_setup/command/sage_build.py", line 37, in run
[sagelib-9.4.beta2]     build.run(self)
[sagelib-9.4.beta2]   File "/Users/dcoudert/sage/local/lib/python3.9/site-packages/setuptools/_distutils/command/build.py", line 135, in run
[sagelib-9.4.beta2]     self.run_command(cmd_name)
[sagelib-9.4.beta2]   File "/Users/dcoudert/sage/local/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 313, in run_command
[sagelib-9.4.beta2]     self.distribution.run_command(command)
[sagelib-9.4.beta2]   File "/Users/dcoudert/sage/local/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 986, in run_command
[sagelib-9.4.beta2]     cmd_obj.run()
[sagelib-9.4.beta2]   File "/Users/dcoudert/sage/build/pkgs/sagelib/src/sage_setup/command/sage_build_cython.py", line 211, in run
[sagelib-9.4.beta2]     self.sage_include_dirs = sage_include_directories(use_sources=True)
[sagelib-9.4.beta2]   File "/Users/dcoudert/sage/build/pkgs/sagelib/src/sage/env.py", line 376, in sage_include_directories
[sagelib-9.4.beta2]     import numpy
[sagelib-9.4.beta2]   File "/Users/dcoudert/sage/local/lib/python3.9/site-packages/numpy/__init__.py", line 145, in <module>
[sagelib-9.4.beta2]     from . import core
[sagelib-9.4.beta2]   File "/Users/dcoudert/sage/local/lib/python3.9/site-packages/numpy/core/__init__.py", line 22, in <module>
[sagelib-9.4.beta2]     from . import multiarray
[sagelib-9.4.beta2]   File "/Users/dcoudert/sage/local/lib/python3.9/site-packages/numpy/core/multiarray.py", line 12, in <module>
[sagelib-9.4.beta2]     from . import overrides
[sagelib-9.4.beta2]   File "/Users/dcoudert/sage/local/lib/python3.9/site-packages/numpy/core/overrides.py", line 7, in <module>
[sagelib-9.4.beta2]     from numpy.core._multiarray_umath import (
[sagelib-9.4.beta2] RuntimeError: NumPy was built with baseline optimizations: 
[sagelib-9.4.beta2] (SSE SSE2 SSE3 SSSE3 SSE41 POPCNT SSE42 AVX F16C FMA3 AVX2 AVX512F AVX512CD AVX512_SKX AVX512_CLX AVX512_CNL AVX512_ICL) but your machine doesn't support:
[sagelib-9.4.beta2] (AVX512F).
[sagelib-9.4.beta2] ************************************************************************
[sagelib-9.4.beta2] Error building the Sage library
[sagelib-9.4.beta2] ************************************************************************
[sagelib-9.4.beta2] Please email sage-devel (http://groups.google.com/group/sage-devel)
[sagelib-9.4.beta2] explaining the problem and including the relevant part of the log file
[sagelib-9.4.beta2]   /Users/dcoudert/sage/logs/pkgs/sagelib-9.4.beta2.log
[sagelib-9.4.beta2] Describe your computer, operating system, etc.
[sagelib-9.4.beta2] ************************************************************************
[sagelib-9.4.beta2] 
[sagelib-9.4.beta2] real 0m8.595s
[sagelib-9.4.beta2] user 0m1.665s
[sagelib-9.4.beta2] sys 0m1.330s
make[4]: *** [sagelib-SAGE_VENV-no-deps] Error 1
make[3]: *** [/Users/dcoudert/sage/local/var/lib/sage/installed/sagelib-9.4.beta2] Error 2
make[2]: *** [all-build] Error 2

real 0m9.441s
user 0m2.046s
sys 0m1.507s
***************************************************************
Error building Sage.

The following package(s) may have failed to build (not necessarily
during this run of 'make all-build'):

* package:         sagelib-9.4.beta2
  last build time: 20 jui 09:28
  log file:        /Users/dcoudert/sage/logs/pkgs/sagelib-9.4.beta2.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





install.log

Dima Pasechnik

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Jun 20, 2021, 5:03:33 AM6/20/21
to sage-release
On Sun, Jun 20, 2021 at 8:34 AM David Coudert <david....@gmail.com> wrote:
>
> Thank you for this new beta.
>
> I have a build error on a Intel MacBook Air with macOS 10.15.7, after make distclean, .bootstrap, source .homebrew-build-env,
> ./configure and finally make.
> I have installed numpy 1.20.3 with homebrew, but it is re-installed by sage and the new installation is not correct

we wish one could just install system numpy and use it, but we are not
there yet.

What you describe can be attributed to updating the tools (or OS) in
the middle of the build.
Can you

make numpy-clean
make numpy
make build

again ?
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>
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Dima Pasechnik

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Jun 20, 2021, 5:04:10 AM6/20/21
to sage-release
maybe also

make sagelib-clean

before

make build

David Coudert

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Jun 20, 2021, 5:45:09 AM6/20/21
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Not working (I also did sagelib-clean)  :(


sapristi:sage dcoudert$ make build -j1
/Library/Developer/CommandLineTools/usr/bin/make build/make/Makefile --stop
make[1]: `build/make/Makefile' is up to date.
build/bin/sage-logger \
"cd build/make && ./install 'base-toolchain'" logs/install.log
*** ALL ENVIRONMENT VARIABLES BEFORE BUILD: ***
ACLOCAL_PATH=/usr/local/opt/gettext/share/aclocal:/usr/local/opt/gettext/share/aclocal:/usr/local/opt/gettext/share/aclocal:/usr/local/opt/gettext/share/aclocal:/usr/local/opt/gettext/share/aclocal:
CPATH=/usr/local/opt/ntl/include:/usr/local/opt/bzip2/include:/usr/local/opt/readline/include:/usr/local/include:/usr/local/opt/ntl/include:/usr/local/opt/bzip2/include:/usr/local/opt/readline/include:/usr/local/include:/usr/local/opt/ntl/include:/usr/local/opt/bzip2/include:/usr/local/opt/readline/include:/usr/local/include:/usr/local/opt/ntl/include:/usr/local/opt/bzip2/include:/usr/local/opt/readline/include:/usr/local/include:/usr/local/opt/ntl/include:/usr/local/opt/bzip2/include:/usr/local/opt/readline/include:/usr/local/include
CPLEX_HOME=/Applications/CPLEX_Studio1210
DOT_SAGE=/Users/dcoudert/.sage
GRB_LICENSE_FILE=/Users/dcoudert/gurobi.lic
GUROBI_HOME=/Library/gurobi811/mac64
HOME=/Users/dcoudert
LANG=fr_FR.UTF-8
LIBRARY_PATH=/usr/local/opt/ntl/lib:/usr/local/opt/bzip2/lib:/usr/local/opt/readline/lib:/usr/local/lib:/usr/local/opt/ntl/lib:/usr/local/opt/bzip2/lib:/usr/local/opt/readline/lib:/usr/local/lib:/usr/local/opt/ntl/lib:/usr/local/opt/bzip2/lib:/usr/local/opt/readline/lib:/usr/local/lib:/usr/local/opt/ntl/lib:/usr/local/opt/bzip2/lib:/usr/local/opt/readline/lib:/usr/local/lib:/usr/local/opt/ntl/lib:/usr/local/opt/bzip2/lib:/usr/local/opt/readline/lib:/usr/local/lib
LOGNAME=dcoudert
LaunchInstanceID=3C3EC403-D547-4498-AA74-D137AE14FF3D
MAKE=make
MAKEFLAGS= V=1
MAKELEVEL=1
MFLAGS=
PATH=/Users/dcoudert/sage/build/bin:/Users/dcoudert/sage/src/bin:/Users/dcoudert/sage/local/bin:/usr/local/opt/texinfo/bin:/usr/local/opt/bzip2/bin:/usr/local/opt/gettext/bin:/usr/local/opt/texinfo/bin:/usr/local/opt/bzip2/bin:/usr/local/opt/gettext/bin:/usr/local/opt/texinfo/bin:/usr/local/opt/bzip2/bin:/usr/local/opt/gettext/bin:/usr/local/opt/texinfo/bin:/usr/local/opt/bzip2/bin:/usr/local/opt/gettext/bin:/usr/local/opt/texinfo/bin:/usr/local/opt/bzip2/bin:/usr/local/opt/gettext/bin:/Users/dcoudert/git-trac-command/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/Library/Apple/usr/bin
PKG_CONFIG_PATH=/usr/local/opt/zlib/lib/pkgconfig:/usr/local/opt/sqlite/lib/pkgconfig:/usr/local/opt/readline/lib/pkgconfig:/usr/local/opt/openssl/lib/pkgconfig:/usr/local/opt/openblas/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/local/opt/zlib/lib/pkgconfig:/usr/local/opt/sqlite/lib/pkgconfig:/usr/local/opt/readline/lib/pkgconfig:/usr/local/opt/openssl/lib/pkgconfig:/usr/local/opt/openblas/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/local/opt/zlib/lib/pkgconfig:/usr/local/opt/sqlite/lib/pkgconfig:/usr/local/opt/readline/lib/pkgconfig:/usr/local/opt/openssl/lib/pkgconfig:/usr/local/opt/openblas/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/local/opt/zlib/lib/pkgconfig:/usr/local/opt/sqlite/lib/pkgconfig:/usr/local/opt/readline/lib/pkgconfig:/usr/local/opt/openssl/lib/pkgconfig:/usr/local/opt/openblas/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/local/opt/zlib/lib/pkgconfig:/usr/local/opt/sqlite/lib/pkgconfig:/usr/local/opt/readline/lib/pkgconfig:/usr/local/opt/openssl/lib/pkgconfig:/usr/local/opt/openblas/lib/pkgconfig:/usr/local/lib/pkgconfig:
PWD=/Users/dcoudert/sage/build/make
PYTHONPATH=/Users/dcoudert/sage/local
SAGE_ENV_CONFIG_SOURCED=1
SAGE_LOCAL=/Users/dcoudert/sage/local
SAGE_LOGFILE=logs/install.log
SAGE_LOGS=/Users/dcoudert/sage/logs/pkgs
SAGE_NUM_THREADS=1
SAGE_NUM_THREADS_PARALLEL=8
SAGE_ORIG_PATH=/usr/local/opt/texinfo/bin:/usr/local/opt/bzip2/bin:/usr/local/opt/gettext/bin:/usr/local/opt/texinfo/bin:/usr/local/opt/bzip2/bin:/usr/local/opt/gettext/bin:/usr/local/opt/texinfo/bin:/usr/local/opt/bzip2/bin:/usr/local/opt/gettext/bin:/usr/local/opt/texinfo/bin:/usr/local/opt/bzip2/bin:/usr/local/opt/gettext/bin:/usr/local/opt/texinfo/bin:/usr/local/opt/bzip2/bin:/usr/local/opt/gettext/bin:/Users/dcoudert/git-trac-command/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/Library/Apple/usr/bin
SAGE_ORIG_PATH_SET=True
SAGE_PKGCONFIG=/Users/dcoudert/sage/local/lib/pkgconfig
SAGE_ROOT=/Users/dcoudert/sage
SAGE_SHARE=/Users/dcoudert/sage/local/share
SAGE_SRC=/Users/dcoudert/sage/src
SECURITYSESSIONID=186a6
SHELL=/bin/bash
SHLVL=4
SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.UrmclevFdH/Listeners
TERM=xterm-256color
TERM_PROGRAM=Apple_Terminal
TERM_PROGRAM_VERSION=433
TERM_SESSION_ID=9FFFB793-84B5-46BB-9E04-4B267CFDEF14
TMPDIR=/var/folders/5q/t180zjs936d_lt3p1cz3mql4000_hf/T/
USER=dcoudert
XPC_FLAGS=0x0
XPC_SERVICE_NAME=0
_=/usr/bin/env
__CF_USER_TEXT_ENCODING=0x2A0E:0x0:0x1
***********************************************
make --no-print-directory toolchain
make[2]: Nothing to be done for `toolchain'.

real 0m0.104s
user 0m0.077s
sys 0m0.015s
Sage build/upgrade complete!
/Library/Developer/CommandLineTools/usr/bin/make all-build
/Library/Developer/CommandLineTools/usr/bin/make build/make/Makefile --stop
make[2]: `build/make/Makefile' is up to date.
build/bin/sage-logger \
"cd build/make && ./install 'all-build'" logs/install.log
*** ALL ENVIRONMENT VARIABLES BEFORE BUILD: ***
ACLOCAL_PATH=/usr/local/opt/gettext/share/aclocal:/usr/local/opt/gettext/share/aclocal:/usr/local/opt/gettext/share/aclocal:/usr/local/opt/gettext/share/aclocal:/usr/local/opt/gettext/share/aclocal:
CPATH=/usr/local/opt/ntl/include:/usr/local/opt/bzip2/include:/usr/local/opt/readline/include:/usr/local/include:/usr/local/opt/ntl/include:/usr/local/opt/bzip2/include:/usr/local/opt/readline/include:/usr/local/include:/usr/local/opt/ntl/include:/usr/local/opt/bzip2/include:/usr/local/opt/readline/include:/usr/local/include:/usr/local/opt/ntl/include:/usr/local/opt/bzip2/include:/usr/local/opt/readline/include:/usr/local/include:/usr/local/opt/ntl/include:/usr/local/opt/bzip2/include:/usr/local/opt/readline/include:/usr/local/include
CPLEX_HOME=/Applications/CPLEX_Studio1210
DOT_SAGE=/Users/dcoudert/.sage
GRB_LICENSE_FILE=/Users/dcoudert/gurobi.lic
GUROBI_HOME=/Library/gurobi811/mac64
HOME=/Users/dcoudert
LANG=fr_FR.UTF-8
LIBRARY_PATH=/usr/local/opt/ntl/lib:/usr/local/opt/bzip2/lib:/usr/local/opt/readline/lib:/usr/local/lib:/usr/local/opt/ntl/lib:/usr/local/opt/bzip2/lib:/usr/local/opt/readline/lib:/usr/local/lib:/usr/local/opt/ntl/lib:/usr/local/opt/bzip2/lib:/usr/local/opt/readline/lib:/usr/local/lib:/usr/local/opt/ntl/lib:/usr/local/opt/bzip2/lib:/usr/local/opt/readline/lib:/usr/local/lib:/usr/local/opt/ntl/lib:/usr/local/opt/bzip2/lib:/usr/local/opt/readline/lib:/usr/local/lib
LOGNAME=dcoudert
LaunchInstanceID=3C3EC403-D547-4498-AA74-D137AE14FF3D
MAKE=make
MAKEFLAGS= V=1
MAKELEVEL=2
MFLAGS=
PATH=/Users/dcoudert/sage/build/bin:/Users/dcoudert/sage/src/bin:/Users/dcoudert/sage/local/bin:/usr/local/opt/texinfo/bin:/usr/local/opt/bzip2/bin:/usr/local/opt/gettext/bin:/usr/local/opt/texinfo/bin:/usr/local/opt/bzip2/bin:/usr/local/opt/gettext/bin:/usr/local/opt/texinfo/bin:/usr/local/opt/bzip2/bin:/usr/local/opt/gettext/bin:/usr/local/opt/texinfo/bin:/usr/local/opt/bzip2/bin:/usr/local/opt/gettext/bin:/usr/local/opt/texinfo/bin:/usr/local/opt/bzip2/bin:/usr/local/opt/gettext/bin:/Users/dcoudert/git-trac-command/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/Library/Apple/usr/bin
PKG_CONFIG_PATH=/usr/local/opt/zlib/lib/pkgconfig:/usr/local/opt/sqlite/lib/pkgconfig:/usr/local/opt/readline/lib/pkgconfig:/usr/local/opt/openssl/lib/pkgconfig:/usr/local/opt/openblas/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/local/opt/zlib/lib/pkgconfig:/usr/local/opt/sqlite/lib/pkgconfig:/usr/local/opt/readline/lib/pkgconfig:/usr/local/opt/openssl/lib/pkgconfig:/usr/local/opt/openblas/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/local/opt/zlib/lib/pkgconfig:/usr/local/opt/sqlite/lib/pkgconfig:/usr/local/opt/readline/lib/pkgconfig:/usr/local/opt/openssl/lib/pkgconfig:/usr/local/opt/openblas/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/local/opt/zlib/lib/pkgconfig:/usr/local/opt/sqlite/lib/pkgconfig:/usr/local/opt/readline/lib/pkgconfig:/usr/local/opt/openssl/lib/pkgconfig:/usr/local/opt/openblas/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/local/opt/zlib/lib/pkgconfig:/usr/local/opt/sqlite/lib/pkgconfig:/usr/local/opt/readline/lib/pkgconfig:/usr/local/opt/openssl/lib/pkgconfig:/usr/local/opt/openblas/lib/pkgconfig:/usr/local/lib/pkgconfig:
PWD=/Users/dcoudert/sage/build/make
PYTHONPATH=/Users/dcoudert/sage/local
SAGE_ENV_CONFIG_SOURCED=1
SAGE_LOCAL=/Users/dcoudert/sage/local
SAGE_LOGFILE=logs/install.log
SAGE_LOGS=/Users/dcoudert/sage/logs/pkgs
SAGE_NUM_THREADS=1
SAGE_NUM_THREADS_PARALLEL=8
SAGE_ORIG_PATH=/usr/local/opt/texinfo/bin:/usr/local/opt/bzip2/bin:/usr/local/opt/gettext/bin:/usr/local/opt/texinfo/bin:/usr/local/opt/bzip2/bin:/usr/local/opt/gettext/bin:/usr/local/opt/texinfo/bin:/usr/local/opt/bzip2/bin:/usr/local/opt/gettext/bin:/usr/local/opt/texinfo/bin:/usr/local/opt/bzip2/bin:/usr/local/opt/gettext/bin:/usr/local/opt/texinfo/bin:/usr/local/opt/bzip2/bin:/usr/local/opt/gettext/bin:/Users/dcoudert/git-trac-command/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/Library/Apple/usr/bin
SAGE_ORIG_PATH_SET=True
SAGE_PKGCONFIG=/Users/dcoudert/sage/local/lib/pkgconfig
SAGE_ROOT=/Users/dcoudert/sage
SAGE_SHARE=/Users/dcoudert/sage/local/share
SAGE_SRC=/Users/dcoudert/sage/src
SECURITYSESSIONID=186a6
SHELL=/bin/bash
SHLVL=4
SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.UrmclevFdH/Listeners
TERM=xterm-256color
TERM_PROGRAM=Apple_Terminal
TERM_PROGRAM_VERSION=433
TERM_SESSION_ID=9FFFB793-84B5-46BB-9E04-4B267CFDEF14
TMPDIR=/var/folders/5q/t180zjs936d_lt3p1cz3mql4000_hf/T/
USER=dcoudert
XPC_FLAGS=0x0
XPC_SERVICE_NAME=0
_=/usr/bin/env
__CF_USER_TEXT_ENCODING=0x2A0E:0x0:0x1
***********************************************
make --no-print-directory /Users/dcoudert/sage/local/var/lib/sage/installed/.dummy
make[3]: `/Users/dcoudert/sage/local/var/lib/sage/installed/.dummy' is up to date.
make --no-print-directory /Users/dcoudert/sage/local/var/lib/sage/installed/.dummy
make[3]: `/Users/dcoudert/sage/local/var/lib/sage/installed/.dummy' is up to date.
make --no-print-directory /Users/dcoudert/sage/local/var/lib/sage/installed/.dummy
make[3]: `/Users/dcoudert/sage/local/var/lib/sage/installed/.dummy' is up to date.
make --no-print-directory /Users/dcoudert/sage/local/var/lib/sage/installed/.dummy
make[3]: `/Users/dcoudert/sage/local/var/lib/sage/installed/.dummy' is up to date.
make --no-print-directory all-sage
make --no-print-directory sagelib-SAGE_VENV-no-deps
cd '/Users/dcoudert/sage/build/pkgs/sagelib' && . '/Users/dcoudert/sage/src/bin/sage-src-env-config' && . '/Users/dcoudert/sage/src/bin/sage-env-config' && . '/Users/dcoudert/sage/src/bin/sage-env' && . '/Users/dcoudert/sage/build/bin/sage-build-env-config' && . '/Users/dcoudert/sage/build/bin/sage-build-env' && SAGE_SPKG_WHEELS=/Users/dcoudert/sage/local/var/lib/sage/wheels SAGE_INST_LOCAL=/Users/dcoudert/sage/local sage-logger -p '/Users/dcoudert/sage/build/pkgs/sagelib/spkg-install' '/Users/dcoudert/sage/logs/pkgs/sagelib-9.4.beta2.log'
[sagelib-9.4.beta2] Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/c++/4.2.1
[sagelib-9.4.beta2] Discovering Python/Cython source code....
[sagelib-9.4.beta2] distributions = ['']
[sagelib-9.4.beta2] Discovered Python/Cython sources, time: 3.49 seconds.
[sagelib-9.4.beta2] running build
[sagelib-9.4.beta2] Generating auto-generated sources
[sagelib-9.4.beta2] Building interpreters for fast_callable
[sagelib-9.4.beta2] -> First build of interpreters
[sagelib-9.4.beta2] real 0m6.860s
[sagelib-9.4.beta2] user 0m2.224s
[sagelib-9.4.beta2] sys 0m1.317s
make[4]: *** [sagelib-SAGE_VENV-no-deps] Error 1
make[3]: *** [/Users/dcoudert/sage/local/var/lib/sage/installed/sagelib-9.4.beta2] Error 2
make[2]: *** [all-build] Error 2

real 0m8.657s
user 0m2.685s
sys 0m1.501s
***************************************************************
Error building Sage.

The following package(s) may have failed to build (not necessarily
during this run of 'make all-build'):

* package:         sagelib-9.4.beta2
  last build time: 20 jui 11:43
  log file:        /Users/dcoudert/sage/logs/pkgs/sagelib-9.4.beta2.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

Dima Pasechnik

unread,
Jun 20, 2021, 6:49:50 AM6/20/21
to sage-release
this seems to be a numpy bug,
or perhaps we use different compiler configurations to build numpy and
to build sagelib --- this would be a Sage bug, perhaps - but on the
other hand the compiler/CPU characteristics
seem to be taken from numpy in

[sagelib-9.4.beta2] from . import overrides
[sagelib-9.4.beta2] File
"/Users/dcoudert/sage/local/lib/python3.9/site-packages/numpy/core/overrides.py",
line 7, in <module>
[sagelib-9.4.beta2] from numpy.core._multiarray_umath import (
[sagelib-9.4.beta2] RuntimeError: NumPy was built with baseline optimizations:
[sagelib-9.4.beta2] (SSE SSE2 SSE3 SSSE3 SSE41 POPCNT SSE42 AVX F16C
FMA3 AVX2 AVX512F AVX512CD AVX512_SKX AVX512_CLX AVX512_CNL
AVX512_ICL) but your machine doesn't support:
[sagelib-9.4.beta2] (AVX512F).

But numpy config is such a black box....

Dima
> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/743D2339-7ED7-4540-AF62-F7AE9866EF28%40gmail.com.

Matthias Köppe

unread,
Jun 20, 2021, 11:46:33 AM6/20/21
to sage-release

David Coudert

unread,
Jun 20, 2021, 12:57:44 PM6/20/21
to sage-r...@googlegroups.com
So I think I have to wait (and try to go back to previous beta).
Thanks,
David.

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Dima Pasechnik

unread,
Jun 21, 2021, 8:38:03 AM6/21/21
to sage-release

Please see https://trac.sagemath.org/ticket/32021 for this issue.
Did you build/install numpy in an unusual way?

Kenji Iohara

unread,
Jun 21, 2021, 8:52:07 AM6/21/21
to sage-r...@googlegroups.com
Hello,

 Thanks for this new version. On my mac book pro OS 11.3, 
 after reinstalling the packages recommended when we execute ./configure, it compiled from the first built.
 But when I tried, brew install ... and brew upgrade as was also indicated after brew instal ...; for some packages,; 
 I couldn't compile it. 

Kenji
 

2021年6月21日(月) 14:38 Dima Pasechnik <dim...@gmail.com>:

David Coudert

unread,
Jun 21, 2021, 8:56:34 AM6/21/21
to sage-r...@googlegroups.com
After distclean, I just did
./boostrap
source .homebrew-build-env
./configure
make build

I have also install lumpy with homebrew but it is apparently not taken into account.

So I think I did nothing unusual.

David.

Justin C. Walker

unread,
Jun 22, 2021, 3:52:52 PM6/22/21
to sage-r...@googlegroups.com


> On Jun 19, 2021, at 14:01 , 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 a fresh clone of the develop tree on macOS 10.13.6 (2017 iMac Pro, 18-core Xeon W). Testing (‘ptestlong’) had one failure:

sage -t --long --warn-long 70.4 --random-seed=0 src/sage/graphs/bipartite_graph.py # 1 doctest failed

The failure was intermittent: in a loop, the failure occurred about 5% of the time.

Justin

--
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Institute for the Absorption of Federal Funds
-----------
If it weren't for carbon-14, I wouldn't date at all.
-----------


Samuel Lelièvre

unread,
Jun 28, 2021, 5:50:49 AM6/28/21
to sage-release
2021-06-22 19:52 UTC, 'Justin C. Walker' via sage-release:
>
> Built from a fresh clone of the develop tree on macOS 10.13.6
> (2017 iMac Pro, 18-core Xeon W).
> Testing (‘ptestlong’) had one failure:
>
> sage -t --long --warn-long 70.4 --random-seed=0 src/sage/graphs/bipartite_graph.py # 1 doctest failed
>
> The failure was intermittent: in a loop, the failure occurred about 5% of the time.

On macOS 10.14.6, I also get this failure intermittently (also in Sage
9.4.beta3).
```
$ ./sage -t --long --random-seed=0 src/sage/graphs/bipartite_graph.py
Running doctests with ID 2021-06-28-11-23-02-ee62df2f.
Git branch: develop
Using --optional=build,dochtml,homebrew,pip,sage,sage_spkg
Doctesting 1 file.
sage -t --long --warn-long 71.8 --random-seed=0
src/sage/graphs/bipartite_graph.py
**********************************************************************
File "src/sage/graphs/bipartite_graph.py", line 329, in
sage.graphs.bipartite_graph.BipartiteGraph.__init__
Failed example:
print(round(get_memory_usage() - start_mem))
Expected:
0.0
Got:
1.0
**********************************************************************
1 item had failures:
1 of 14 in sage.graphs.bipartite_graph.BipartiteGraph.__init__
[320 tests, 1 failure, 2.13 s]
----------------------------------------------------------------------
sage -t --long --warn-long 71.8 --random-seed=0
src/sage/graphs/bipartite_graph.py # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 2.2 seconds
cpu time: 2.1 seconds
cumulative wall time: 2.1 seconds
Pytest is not installed, skip checking tests that rely on it.
```

Related tickets:

- Memory leak in bipartite_graph
https://trac.sagemath.org/ticket/31313

- Add gc.collect() to the memleak test from #31313
https://trac.sagemath.org/ticket/31671

Might be worth a new ticket.

Justin C. Walker

unread,
Jun 29, 2021, 12:02:05 AM6/29/21
to 'jonatha...@googlemail.com' via sage-release


> On Jun 19, 2021, at 14:01 , 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 a fresh clone of the develop tree on macOS 10.15.7 (2019 MBP, 8-core Core i9).

No problems in the build, and all tests (‘ptestlong’) passed!

Justin

--
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Only outlaws will have LuteFisk
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