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
5ec24db181 (tag: 9.2.beta12, trac/develop) Updated SageMath version to 9.2.beta12
ubuntu-bionic-standard (https://github.com/sagemath/sage/runs/1078907737):[dochtml] UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 2661: ordinal not in range(128)[dochtml] Full log file: logs/dochtml.logMakefile:1874: recipe for target 'doc-html' failed
On Debian testing running on core i5 + 8 GB RAM, upgrading 9.2.beta11
to 9.2.beta12
after make python3-clean
using all system packages and running ptestlong
gives 7 permanent failures :
File | Result | P/T |
---|---|---|
src/sage/schemes/hyperelliptic_curves/monsky_washnitzer.py | Killed due to abort | P |
src/sage/rings/complex_arb.pyx | 6 doctests failed | P |
src/sage/modules/fg_pid/fgp_module.py | 3 doctests failed | P |
src/doc/en/constructions/algebraic_geometry.rst | 1 doctest failed | P |
src/sage/rings/real_arb.pyx | 2 doctests failed | P |
src/sage/modules/free_module_morphism.py | 3 doctests failed | P |
src/doc/en/developer/coding_in_other.rst | 1 doctest failed | P |
These failures have been reported already for 2.9.beta11
on the same machine, except for the failure observed for coding_in_other.rst
, which was transient in 2.9.beta11
and is now permanent.
Of note :
./configure
failed to recognize the system’s Python packages ; notwithstanding this failure,$SAGE_LOCAL/bin/python3.8
is a symlink to /usr/bin/python3.8
sage -standard | grep python
reports python3
as(not_installed)
gap-packages
still no longer installs (complains about multiply-defined symbols).HTH,
Again, the doctests gets interrupted with an error OSError: [Errno 24] Too many open files. Is it related to Python 3.8?
On Sunday, September 6, 2020 at 4:25:39 PM UTC-7, Volker Braun wrote:As always, you can get the latest beta version from the "develop" git branch. Alternatively, the self-contained source tarball is at http://www.sagemath.org/download-latest.html
5ec24db181 (tag: 9.2.beta12, trac/develop) Updated SageMath version to 9.2.beta12
Tests have started at https://github.com/sagemath/sage/actions .
On Sunday, September 6, 2020 at 4:25:39 PM UTC-7, Volker Braun wrote:As always, you can get the latest beta version from the "develop" git branch. Alternatively, the self-contained source tarball is at http://www.sagemath.org/download-latest.html5ec24db181 (tag: 9.2.beta12, trac/develop) Updated SageMath version to 9.2.beta12
Tests have started at https://github.com/sagemath/sage/actions
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On Sunday, September 6, 2020 at 4:25:39 PM UTC-7, Volker Braun wrote:As always, you can get the latest beta version from the "develop" git branch. Alternatively, the self-contained source tarball is at http://www.sagemath.org/download-latest.html5ec24db181 (tag: 9.2.beta12, trac/develop) Updated SageMath version to 9.2.beta12
Tests have started at https://github.com/sagemath/sage/actions
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Le 9 sept. 2020 à 12:04, Dima Pasechnik <dim...@gmail.com> a écrit :On Wed, Sep 9, 2020 at 10:49 AM David Coudert <david....@gmail.com> wrote:
If I understand well, I’m facing the case (not completely sure):
homebrew-macos-python3_xcode-gcc_spkg-{minimal,standard}: Various build errors (ignore for Sage 9.2)
no, this is for macOS 11, still in beta, and not going to be supported in 9.2Is your xcode up to date?
That is: macOS 10.15.6 with clang version 11.0.3 (clang-1103.0.32.62) and all recommended packages installed with homebrew, and unable to compile beta12.
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If I understand well, I’m facing the case (not completely sure):homebrew-macos-python3_xcode-gcc_spkg-{minimal,standard}: Various build errors (ignore for Sage 9.2)That is: macOS 10.15.6 with clang version 11.0.3 (clang-1103.0.32.62) and all recommended packages installed with homebrew, and unable to compile beta12.
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The traces of fortran 9 (and actually gcc 9) are due to .homebrew-build-env. which contains:for l in "gcc@9/lib/gcc/9"; do
if [ -d "$HOMEBREW/opt/$l" ]; then
LIBRARY_PATH="$HOMEBREW/opt/$l:$LIBRARY_PATH"
fi
done
Le 9 sept. 2020 à 17:01, Dima Pasechnik <dim...@gmail.com> a écrit :
ok, you have a non-standard arb in your Homebrew install.you need to reinstall it, or perhaps better just remove it.you also have traces of gfortran 9 in LIBRARY_PATH - investigate and clean...
I can try to install ntl and flint, but then I have to remove dependencies as well, right ?sapristi:sage dcoudert$ brew uninstall ntl flintError: Refusing to uninstall /usr/local/Cellar/flint/2.6.3because it is required by arb, which is currently installed.You can override this and force removal with:brew uninstall --ignore-dependencies ntl flintLe mercredi 9 septembre 2020 à 16:53:47 UTC+2, matthia...@gmail.com a écrit :On Wednesday, September 9, 2020 at 2:49:19 AM UTC-7, david....@gmail.com wrote:If I understand well, I’m facing the case (not completely sure):homebrew-macos-python3_xcode-gcc_spkg-{minimal,standard}: Various build errors (ignore for Sage 9.2)That is: macOS 10.15.6 with clang version 11.0.3 (clang-1103.0.32.62) and all recommended packages installed with homebrew, and unable to compile beta12.Actually your configuration is "homebrew-macos-standard" with probably some extra homebrew packages installed.(The configuration factor "gcc_spkg" refers to using gcc 9.2 from our SPKG instead of Xcode "gcc" (clang).)My guess is that if you uninstall homebrew's ntl and flint packages and build from scratch (distclean), the build would go through.https://trac.sagemath.org/ticket/27764 and tickets referenced within address the NTL / thread-local storage issues.--
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by the way, I am not able to pick up Homebrew's python3.8 in the presence of python3.7, unless I modify python3's spkg-configure.m4 to exclude python3.7 and python3 from the list of Pythons it checks for.
conda-forge-macos-standard (https://github.com/sagemath/sage/runs/1078909711):
[sagelib-9.2.beta12] /Users/runner/work/sage/sage/.tox/local-conda-forge-macos-standard/local/include/linbox/algorithms/det-rational.h:96:39: error: no viable overloaded '='
[sagelib-9.2.beta12] void detMul (const Integer& m) {mul = m;} [...]
I have created https://trac.sagemath.org/ticket/30535 for this
here it is. The account shell is zsh, but this most probably does not matter.
On Wed, Sep 9, 2020 at 6:31 PM Matthias Köppe <matthia...@gmail.com> wrote:
>
> On Wednesday, September 9, 2020 at 10:11:14 AM UTC-7, Dima Pasechnik wrote:
>>
>> by the way, I am not able to pick up Homebrew's python3.8 in the presence of python3.7, unless I modify python3's spkg-configure.m4 to exclude python3.7 and python3 from the list of Pythons it checks for.
>>>
>>>
>
> config.log?
>
>
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Very strange, can you run it with ./configure CONFIG_SHELL="bash -x" and post the output?
for as_dir in $PATH
/usr/local/opt/gettext/bin:/usr/local/opt/gettext/bin:/usr/local/opt/python@3.7/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/Apple/usr/bin
for each $as_dir it loops over the list of Pythons we provide,
and the first match happens to be Python3.7, not Python3.8.
Indeed, to verify this,
Checking whether SageMath should install SPKG python3...
checking whether any of sqlite libpng bzip2 xz libffi is installed as or will be installed as SPKG... no
checking for python3 >= 3.6, < 3.9 with modules sqlite3, ctypes, math, hashlib, crypt, readline, socket, zlib, distutils.core...
ac_path_PYTHON3= /usr/local/opt/gettext/bin/python3.8
ac_path_PYTHON3= /usr/local/opt/gettext/bin/python3.7
ac_path_PYTHON3= /usr/local/opt/gettext/bin/python3.6
ac_path_PYTHON3= /usr/local/opt/gettext/bin/python3
ac_path_PYTHON3= /usr/local/opt/gettext/bin/python3.8
ac_path_PYTHON3= /usr/local/opt/gettext/bin/python3.7
ac_path_PYTHON3= /usr/local/opt/gettext/bin/python3.6
ac_path_PYTHON3= /usr/local/opt/gettext/bin/python3
ac_path_PYTHON3= /usr/local/opt/python@3.7/bin/python3.8
ac_path_PYTHON3= /usr/local/opt/python@3.7/bin/python3.7
checking ... whether /usr/local/opt/python@3.7/bin/python3.7 is good... yes
checking for python3 >= 3.6, < 3.9 with modules sqlite3, ctypes, math, hashlib, crypt, readline, socket, zlib, distutils.core... /usr/local/opt/python@3.7/bin/python3.7
Indeed, intuitively, one would think that the outer loop should be over the programs in the list,
not the entries in the PATH, but, alas, it seems that all the autoconf macros dealing with finding
executables loop over the PATH entries first.
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The autoconf macro in question is looping over the entries in the PATH (and this is documented behaviour)So the outer loop isfor as_dir in $PATH
now, the PATH is a bit funny in my case:/usr/local/opt/gettext/bin:/usr/local/opt/gettext/bin:/usr/local/opt/python@3.7/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/Apple/usr/bin
for each $as_dir it loops over the list of Pythons we provide,
and the first match happens to be Python3.7, not Python3.8.
% cat ~/.zshrc
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except that on macOS+Homebrew the latter wants the PATH like this:% cat ~/.zshrc
export PATH="/usr/local/opt/python@3.7/bin:$PATH"I am not sure whether putting /usr/local/bin first won't break Homebrew.
On Ubuntu 18.04, it picks up the python3.6 available on the machine:
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On Ubuntu 18.04, it picks up the python3.6 available on the machine:## -------------------------------------------------------- ##
## Checking whether SageMath should install SPKG python3... ##
## -------------------------------------------------------- ##
configure:29604: checking whether any of sqlite libpng bzip2 xz libffi is installed as or will be installed as SPKG
configure:29613: result: no
configure:29623: checking for python3 >= 3.6, < 3.9 with modules sqlite3, ctypes, math, hashlib, crypt, readline, socket, zlib, distutils.core
configure:29629: result:
configure:29644: checking ... whether /usr/bin/python3.6 is good
[dochtml] File "/home/slabbe/GitBox/sage/local/lib/python3.6/site-packages/sage_setup/docbuild/utils.py", line 289, in build_many[dochtml] raise worker_exc.original_exception
[dochtml] UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 2661: ordinal not in range(128)
On a MacBook Air (early 2014) with
macOS 10.14.6 Mojave, with Homebrew
(but having removed Homebrew packages
gcc@9, python@3.7, arb, flint, gap, singular),
`make` succeeds but `make testlong` fails
unexpectedly still referring to python@3.7.
9.2.beta11 has introduced crashes of the doctests in `src/sage/interfaces/singular.py` that were reproducible on about 20% of the test runs and have been observed by several other people as well. I have tracked that issue down to the Pexpect upgrade in #29240 via bisection. With 9.2.beta12 on the other hand, I cannot reproduce the problem anymore, possibly because of the Python upgrade. There are still reports about this with 9.2.beta12 though, so maybe this helps analyze the problem.
With a clean build on Ubuntu 20.04, ptestlong passes, but Jupyter does not start anymore due to an SSL problem, Which packages need to be installed for this and why was this not a problem previously? OpenSSL is installed on the system:
$ openssl versionOpenSSL 1.1.1f 31 Mar 2020
> Am 11.09.2020 um 20:17 schrieb Matthias Köppe <matthia...@gmail.com>:
>
> Is "libssl-dev" installed? (see build/pkgs/openssl/distros/debian.txt)
I think it might be better to stop the build earlier (and maybe ask for confirmation) before proceeding to build Python, to avoid building Python and all its dependencies a second time after installing OpenSSL. That is, unless there is a reason to build Sage without OpenSSL.
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Probably you want to configure with CC=clang CXX=clang++
On Thursday, September 10, 2020 at 6:52:09 AM UTC-7, Sébastien Labbé wrote:On Ubuntu 18.04, it picks up the python3.6 available on the machine:## -------------------------------------------------------- ##
## Checking whether SageMath should install SPKG python3... ##
## -------------------------------------------------------- ##
configure:29604: checking whether any of sqlite libpng bzip2 xz libffi is installed as or will be installed as SPKG
configure:29613: result: no
configure:29623: checking for python3 >= 3.6, < 3.9 with modules sqlite3, ctypes, math, hashlib, crypt, readline, socket, zlib, distutils.core
configure:29629: result:
configure:29644: checking ... whether /usr/bin/python3.6 is goodCould you clarify if you expected it to use a different version of python?
Very similar (but not identical !) results on a slightly different machine :
On Debian testing running on core i7 + 16 GB RAM, upgrading 9.2.beta11
to 9.10.beta12
and running ptestlong
gets 7 permanent and 1 transient failures :
File | Result | P/T |
---|---|---|
src/sage/schemes/hyperelliptic_curves/monsky_washnitzer.py | Killed due to abort | P |
src/sage/tests/parigp.py | Timed out | T |
src/sage/rings/complex_arb.pyx | 6 doctests failed | P |
src/sage/modules/fg_pid/fgp_module.py | 3 doctests failed | P |
src/doc/en/constructions/algebraic_geometry.rst | 1 doctest failed | P |
src/doc/en/developer/coding_in_other.rst | 1 doctest failed | P |
src/sage/rings/real_arb.pyx | 2 doctests failed | P |
src/sage/modules/free_module_morphism.py | 3 doctests failed | P |
HTH,
On Debian testing running on core i5 + 8 GB RAM, upgrading
9.2.beta11
to9.2.beta12
aftermake python3-clean
using all system packages and runningptestlong
gives 7 permanent failures :
File Result P/T src/sage/schemes/hyperelliptic_curves/monsky_washnitzer.py Killed due to abort P src/sage/rings/complex_arb.pyx 6 doctests failed P src/sage/modules/fg_pid/fgp_module.py 3 doctests failed P src/doc/en/constructions/algebraic_geometry.rst 1 doctest failed P src/sage/rings/real_arb.pyx 2 doctests failed P src/sage/modules/free_module_morphism.py 3 doctests failed P src/doc/en/developer/coding_in_other.rst 1 doctest failed P These failures have been reported already for
2.9.beta11
on the same machine, except for the failure observed forcoding_in_other.rst
, which was transient in2.9.beta11
and is now permanent.Of note :
./configure
failed to recognize the system’s Python packages ; notwithstanding this failure,
$SAGE_LOCAL/bin/python3.8
is a symlink to/usr/bin/python3.8
sage -standard | grep python
reportspython3
as(not_installed)
gap-packages
still no longer installs (complains about multiply-defined symbols).HTH,
Le lundi 7 septembre 2020 01:25:39 UTC+2, Volker Braun a écrit :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
Again, if there is anything that should be merged in this beta cycle then a positively-reviewed patch has to materialize real soon ;-)5ec24db181 (tag: 9.2.beta12, trac/develop) Updated SageMath version to 9.2.beta125efa8df9cd Trac #30454: some details in doc of number fieldsd1a1a28695 Trac #30443: Simplify setting and getting "edges" of edges, ridges, incidences in `CombinatorialPolyhedron`f8c4e4b530 Trac #30409: Optional ideal parameter for normalize_coordinates603aa8806e Trac #28722: update constants for S-unit solver21f7af35b4 Trac #14735: Bug with Python int division in wigner.py7d9921cca9 Trac #30490: Reduce doctesting time for polyhedra11c8e5b6ff Trac #30487: GH Actions: Test also with Xcode 12 beta80c4c5e916 Trac #30479: deprecate random_DAG505f3f4065 Trac #30470: Make spanning_trees an iterator80d9314aef Trac #30455: pep8 cleanup of the file e_one_stard6b5a59b02 Trac #30452: "sage -startuptime" should accept file names too9e5a3ba06e Trac #30449: Fix docbuild warning in combinat plus improve formatting875d7180ca Trac #30442: Implement general table art for tableau-like objectse8696d8001 Trac #30440: Pyramid for combinatorial polyhedrondfa0d227a5 Trac #30410: Command "sage -tox"b8421f50e2 Trac #30401: Unions of subsets of a fixed open set X are not known to be subsets of Xe0b21bfd1d Trac #30395: enhance fricas lists50d0934dff Trac #30382: More voidlinux.txt1185b94e8d Trac #30212: Fix tkz-graph and tkz-berge links: altermundus.com is gone4974b90112 Trac #28982: Use CombinatorialPolyhedron to obtain faces lattice of polyhedradcf19afbfc Trac #27952: upgrade Normaliz to 3.8.8, PyNormaliz to 2.12, add script package libnautya5f5293ca6 Trac #30496: fix conversion of GAP univariate rat functions, which are polynomial with valuation>0596988abf2 Trac #30489: Two fixes for test suite for products of polyhedrab9c5e0bdbd Trac #30488: ci-cygwin: Remove sage_brialb0465d76c9 Trac #30317: Update pip to 20.2.2, setuptools to 49.6.0d96db5467d Trac #27754: Upgrade: Python 3.8.5c353bce995 (tag: 9.2.beta11) Updated SageMath version to 9.2.beta11
Recommendations of packages to install can still be improved,see the dedicated ticket:but we need to balance the maintenance effort with the gains.
In this case, what you can conclude is:- satisfactory versions of these packages (or possibly packagesthat depend on them) for that OS were not found- on some version of that OS, satisfactory versions of thesepackages exist that would avoid having to build themand what we should do about it is probably adapt the wordingto better convey that. For instance:hint: installing the following system packages, if not alreadypresent, is recommended and may avoid building some SPKGs fromsource (though some may have to be built anyway):
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[...] what we should do about it is probably adapt the wording
to better convey that. For instance:hint: installing the following system packages, if not alreadypresent, is recommended and may avoid building some SPKGs fromsource (though some may have to be built anyway):[...]
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This is now:- Sage Trac ticket 30624Improve configure's recommendation messageI don't have time to work on it now.