Sage 10.5.beta8 released
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Volker Braun
Oct 26, 2024, 4:45:46 PM10/26/24
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As always, you can get the latest beta version from the "develop" git branch. Alternatively, the self-contained source tarball is at http://www.sagemath.org/download-latest.html
1b3f398d2a8 (tag: 10.5.beta8, github/develop) Updated SageMath version to 10.5.beta8
9a5d35a91d4 gh-38855: Fixes for Xcode 16 and gcc/gfortran, boost_cropped
ce4a78dcb41 gh-38851: src/sage/graphs/generic_graph.py: work around doctest hang
5b5b42f8fc2 gh-38845: Fix docstring format for `EllipticCurve_with_prime_order`
9d43795c1cd gh-38841: Fix `transformation` parameter for LLL on matrices over QQ
8a5615f1752 gh-38837: Fix bug in covering map of simplicial set with degenerate faces.
a90e4a3d0af gh-38833: Respect sparse=True in vector constructor when passed ndarray
2304cfd66fb gh-38826: src/sage/env.py: canonicalize paths in a test
3232e30e4d9 gh-38825: Fix two tests that fail on a heavily-loaded machine
2af76132c15 gh-38822: Upgrade database_knotinfo to version 2024.10.1
1b5ea274e48 gh-38819: fixing some typos
e028eccc206 gh-38816: fix all pep E302 in manifolds and geometry
96ea212c409 gh-38812: Make codecov/patch informational (not fail)
28aa6c31adb gh-38808: faster comparison of elliptic-curve morphisms
3e3fd150028 gh-38805: use specialized 2-dimensional .log() method in .matrix_on_subgroup()
d69ef019ae8 gh-38804: GAP 4.13.1
05c92eb4b5a gh-38798: adding method tikz to class Graph
bd5df794cb9 gh-38797: make sure .division_points() returns the correct result for m=-1
e70d9fea9d2 gh-38770: Add "needs" tags for giac and libgiac
2be2d84239a gh-38740: fixing some suggestions by ruff
9ea031057b5 gh-38734: GH Actions: Build sagemath-tdlib wheel
5c90b600f44 gh-38680: Improve counting of local solutions for QuadraticForm at p=2
5c25c12c6d4 gh-38487: convenience methods for field embeddings
67e62345024 gh-38259: Fixed and improvements in `is_LLL_reduced` and `approximate_closest_vector`
61e1f4aa637 gh-36524: Compile everything with meson
7e4f7bdc0be gh-36226: Use CPU time for --warn-long
7726cd9e1d0 (tag: 10.5.beta7) Updated SageMath version to 10.5.beta7
9a5d35a91d4 gh-38855: Fixes for Xcode 16 and gcc/gfortran, boost_cropped
ce4a78dcb41 gh-38851: src/sage/graphs/generic_graph.py: work around doctest hang
5b5b42f8fc2 gh-38845: Fix docstring format for `EllipticCurve_with_prime_order`
9d43795c1cd gh-38841: Fix `transformation` parameter for LLL on matrices over QQ
8a5615f1752 gh-38837: Fix bug in covering map of simplicial set with degenerate faces.
a90e4a3d0af gh-38833: Respect sparse=True in vector constructor when passed ndarray
2304cfd66fb gh-38826: src/sage/env.py: canonicalize paths in a test
3232e30e4d9 gh-38825: Fix two tests that fail on a heavily-loaded machine
2af76132c15 gh-38822: Upgrade database_knotinfo to version 2024.10.1
1b5ea274e48 gh-38819: fixing some typos
e028eccc206 gh-38816: fix all pep E302 in manifolds and geometry
96ea212c409 gh-38812: Make codecov/patch informational (not fail)
28aa6c31adb gh-38808: faster comparison of elliptic-curve morphisms
3e3fd150028 gh-38805: use specialized 2-dimensional .log() method in .matrix_on_subgroup()
d69ef019ae8 gh-38804: GAP 4.13.1
05c92eb4b5a gh-38798: adding method tikz to class Graph
bd5df794cb9 gh-38797: make sure .division_points() returns the correct result for m=-1
e70d9fea9d2 gh-38770: Add "needs" tags for giac and libgiac
2be2d84239a gh-38740: fixing some suggestions by ruff
9ea031057b5 gh-38734: GH Actions: Build sagemath-tdlib wheel
5c90b600f44 gh-38680: Improve counting of local solutions for QuadraticForm at p=2
5c25c12c6d4 gh-38487: convenience methods for field embeddings
67e62345024 gh-38259: Fixed and improvements in `is_LLL_reduced` and `approximate_closest_vector`
61e1f4aa637 gh-36524: Compile everything with meson
7e4f7bdc0be gh-36226: Use CPU time for --warn-long
7726cd9e1d0 (tag: 10.5.beta7) Updated SageMath version to 10.5.beta7
Marc Culler
Oct 27, 2024, 6:44:53 PM10/27/24
to sage-release
I am seeing a build failure for gap_packages-4.13.1 on macOS 15 with M1 CPU. A header file seems to be missing:
[spkg-install] In file included from src/bipart.cpp:38:
[spkg-install] libsemigroups/include/libsemigroups/report.hpp:42:10: fatal error: 'textflowcpp/TextFlow.hpp' file not found
[spkg-install] #include "textflowcpp/TextFlow.hpp"
[spkg-install] ^~~~~~~~~~~~~~~~~~~~~~~~~~
[spkg-install] 1 error generated.
[spkg-install] make[5]: *** [gen/src/bipart.o] Error 1
[spkg-install] libsemigroups/include/libsemigroups/report.hpp:42:10: fatal error: 'textflowcpp/TextFlow.hpp' file not found
[spkg-install] #include "textflowcpp/TextFlow.hpp"
[spkg-install] ^~~~~~~~~~~~~~~~~~~~~~~~~~
[spkg-install] 1 error generated.
[spkg-install] make[5]: *** [gen/src/bipart.o] Error 1
(I don;t seem to have the option of attaching files on this list, so the full log file is not attached.)
- Marc
Dima Pasechnik
Oct 27, 2024, 7:26:18 PM10/27/24
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libsemigroups is a separate spkg, it is (or it should be) a pre-req for gap_packages
Marc Culler
Oct 27, 2024, 9:50:13 PM10/27/24
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I know that libsemigroups is a separate spkg. That is not the issue. In fact the missing header file exists in the Sage tree, both in the local/include directory and in the gap_packages build directory (which is still there because the build failed).
% find . -name TextFlow.hpp
./local/include/libsemigroups/textflowcpp/TextFlow.hpp
./local/var/tmp/sage/build/gap_packages-4.13.1/src/pkg/semigroups/libsemigroups/extern/textflowcpp/TextFlow.hpp
./local/include/libsemigroups/textflowcpp/TextFlow.hpp
./local/var/tmp/sage/build/gap_packages-4.13.1/src/pkg/semigroups/libsemigroups/extern/textflowcpp/TextFlow.hpp
The problem is that the build script for the new gap_packages spkg is not setting the options needed to make the compiler look in either of those places. I would assume that a -I option is missing somewhere. Perhaps a patch is needed to add that option in the appropriate place.
Here is the compiler command that generates the error, copied from the log file:
[spkg-install] g++ -std=gnu++11 -std=gnu++11 -pthread -O2 -mmacosx-version-min=11.0 -stdlib=libc++ -fno-common -MQ gen/src/bipart.o -MMD -MP -MF gen/src/bipart.d -I./bin/include -I./bin/include/libsemigroups -std=gnu++14 -O3 -Igapbind14/include/ -Ilibsemigroups/extern/fmt-8.0.1/include -Ilibsemigroups/include -DFMT_HEADER_ONLY -DNDEBUG -O2 -mmacosx-version-min=11.0 -stdlib=libc++ -o gen/src/bipart.o -I/private/var/tmp/sage-10.5-current/local/include/gap -I/private/var/tmp/sage-10.5-current/local/include -DUSE_GASMAN=1 -c src/bipart.cpp
It seems to be looking in libsemigroups/include but it should also be looking in libsemigroups/include/extern.
- Marc
On Sun, Oct 27, 2024 at 6:26 PM Dima Pasechnik <dim...@gmail.com> wrote:
Dima Pasechnik
Oct 28, 2024, 4:25:27 AM10/28/24
to sage-r...@googlegroups.com
I think it is probably a Sage's spkgs' dependincies bug. (you need pkg-config for the packages involved).
In more detail,
GAP package semigroups's sources carry a vendored version of libsemigroups, but it should not be used. Instead its ./configure should find the external (to it) libsemigroups installation, and use it.
The build script of gap_packages does deal with -I options for particular packages, it assumes that this is taken care of by the aforementioned ./configure - which in this case should figure out that the correct -I by calling
pkg-config --cflags libsemigroups
Can you check if it works? (invoke ./sage --buildsh
and in this shell execute the call above)
In fact, pkg-config should be a dependency of libsemigroups (pkgconf should be in build/pkgs/libsemigroups/dependencies), and of gap_packages (pkgconf should be in build/pkgs/gap_packages/dependencies).
But it is not -- so this is a Sage bug, potentially being the reason behind your problem.
In more detail,
GAP package semigroups's sources carry a vendored version of libsemigroups, but it should not be used. Instead its ./configure should find the external (to it) libsemigroups installation, and use it.
The build script of gap_packages does deal with -I options for particular packages, it assumes that this is taken care of by the aforementioned ./configure - which in this case should figure out that the correct -I by calling
pkg-config --cflags libsemigroups
Can you check if it works? (invoke ./sage --buildsh
and in this shell execute the call above)
In fact, pkg-config should be a dependency of libsemigroups (pkgconf should be in build/pkgs/libsemigroups/dependencies), and of gap_packages (pkgconf should be in build/pkgs/gap_packages/dependencies).
But it is not -- so this is a Sage bug, potentially being the reason behind your problem.
Emmanuel Charpentier
Oct 28, 2024, 5:57:11 AM10/28/24
to sage-release
FWIW, upgrading from 10.5.beta7 to 10.5.beta8 on Ubuntu 24.4 running under WSL/Windows11 on core i7 + 32 GB RAM, I just stumbled on the very same error.
Emmanuel Charpentier
Oct 28, 2024, 6:07:17 AM10/28/24
to sage-release
No such luck (see previous post for config) :
Le lundi 28 octobre 2024 à 09:25:27 UTC+1, Dima Pasechnik a écrit :
I think it is probably a Sage's spkgs' dependincies bug. (you need pkg-config for the packages involved).
In more detail,
GAP package semigroups's sources carry a vendored version of libsemigroups, but it should not be used. Instead its ./configure should find the external (to it) libsemigroups installation, and use it.
The build script of gap_packages does deal with -I options for particular packages, it assumes that this is taken care of by the aforementioned ./configure - which in this case should figure out that the correct -I by calling
pkg-config --cflags libsemigroups
Can you check if it works? (invoke ./sage --buildsh
and in this shell execute the call above)
charpent@SAP5342949:/usr/local/sage-10$ ./sage --buildsh
Starting subshell with Sage environment variables set. Don't forget
to exit when you are done. Beware:
* Do not do anything with other copies of Sage on your system.
* Do not use this for installing Sage packages using "sage -i" or for
running "make" at Sage's root directory. These should be done
outside the Sage shell.
Bypassing shell configuration files...
Note: SAGE_ROOT=/usr/local/sage-10
(sage-buildsh) charpent@SAP5342949:sage-10$ pkg-config --cflags libsemigroup
Package libsemigroup was not found in the pkg-config search path.
Perhaps you should add the directory containing `libsemigroup.pc'
to the PKG_CONFIG_PATH environment variable
Package 'libsemigroup', required by 'virtual:world', not found
However (in another window) :
charpent@SAP5342949:/usr/local/sage-10$ ./sage -optional | grep -v ot_instal /usr/local/sage-10/src/sage/misc/package.py:118: UserWarning: failed to fetch the version of pkg='auditwheel_or_delocate' at https://pypi.org/pypi/auditwheel_or_delocate/json warnings.warn("failed to fetch the version of pkg={!r} at {}".format(pkg, url)) /usr/local/sage-10/src/sage/misc/package.py:118: UserWarning: failed to fetch the version of pkg='ore_algebra' at https://pypi.org/pypi/ore_algebra/json warnings.warn("failed to fetch the version of pkg={!r} at {}".format(pkg, url)) [package]...............................[latest version] ([version]) build...................................? (1.2.1) cypari2.................................? (2.2.0) dot2tex.................................2.11.3.p0 (2.11.3.p0) fricas..................................1.3.11 (1.3.11) gap_jupyter.............................0.9 (0.9) hatch_fancy_pypi_readme.................? (24.1.0) hatch_vcs...............................? (0.4.0) jmol....................................14.29.52 (14.29.52) jupyter_jsmol...........................2022.1.0 (2022.1.0) jupyter_kernel_gap......................? (0.9) jupyter_kernel_singular.................? (0.9.7) libsemigroups...........................2.3.2 (2.3.2) msolve..................................0.6.5 (0.6.5) pysingular..............................0.9.7 (0.9.7) python3_venv............................? (3.12--usr-bin-python3) python_dateutil.........................? (2.9.0.post0) sagemath................................? (0.0.0) sagemath_standard.......................? (10.5b8) singular_jupyter........................0.9.7 (0.9.7)Stuck…
Emmanuel Charpentier
Oct 28, 2024, 6:11:06 AM10/28/24
to sage-release
And, BTW :
(sage-buildsh) charpent@SAP5342949:sage-10$ ls $PKG_CONFIG_PATH Singular.pc cblas.pc fflas-ffpack.pc gsl.pc libpolys.pc msolve.pc bdw-gc.pc eclib.pc fplll.pc lapack.pc libsemigroups.pc omalloc.pc blas.pc factory.pc givaro.pc libgap.pc linbox.pc singular_resources.pcHTH,
Dima Pasechnik
Oct 28, 2024, 9:33:39 AM10/28/24
to sage-r...@googlegroups.com, Michael Orlitzky
The upgrade to GAP 4.13.1 simply missed the necessary libsemigroups bump.
- they should be done in lockstep.
What happens, I think, is that GAP semigroup package tries instead to
build its own libsemigroup, but it does not work.
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- they should be done in lockstep.
What happens, I think, is that GAP semigroup package tries instead to
build its own libsemigroup, but it does not work.
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Emmanuel Charpentier
Oct 28, 2024, 10:04:39 AM10/28/24
to sage-release
Any suggestion on the ways to solve the present problem ? The only one I can think of would be to revert to 10.5.beta7 (by detaching head), `make build` then `make`.
Advice ?
Dima Pasechnik
Oct 28, 2024, 10:30:51 AM10/28/24
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Doing an upgrade of libsemigroups should be next to trivial.
Let me try.
Let me try.
Emmanuel Charpentier
Oct 28, 2024, 10:33:56 AM10/28/24
to sage-release
Re-reading my messages, I noticed that I mistyped pkg-config --cflags libsemigroup (which gives the error I reported) for pkg-config --cflags libsemigroups (which works silently). But even after running the correct pkg-config command, gap_packages-4.13.1 still fails to build, with a different error message :
[spkg-install] g++ -std=gnu++11 -pthread -g -O2 -fPIC -MQ gen/src/cong.o -MMD -MP -MF gen/src/cong.d -std=gnu++14 -O3 -mavx -flax-vector-conversions -Igapbind14/include/ -DHPCOMBI_CONSTEXPR_FUN_ARGS -DFMT_HEADER_ONLY -DNDEBUG -g -O2 -o gen/src/cong.o -I/usr/local/sage-10/local/include/gap -I/usr/local/sage-10/local/include -DUSE_GASMAN=1 -c src/cong.cpp [spkg-install] In file included from /usr/local/sage-10/local/include/libsemigroups/knuth-bendix.hpp:34, [spkg-install] from /usr/local/sage-10/local/include/libsemigroups/cong.hpp:30, [spkg-install] from src/to_cpp.hpp:54, [spkg-install] from src/cong.cpp:29: [spkg-install] /usr/local/sage-10/local/include/libsemigroups/digraph.hpp:58:10: fatal error: Eigen/Core: No such file or directory [spkg-install] 58 | #include <Eigen/Core> [spkg-install] | ^~~~~~~~~~~~ [spkg-install] compilation terminated. [spkg-install] make[5]: *** [Makefile.gappkg:130: gen/src/cong.o] Error 1 [spkg-install] ************************************************************************************************************************ [spkg-install] Error building gap_packages-4.13.1 [spkg-install] ************************************************************************************************************************ ************************************************************************ Error installing package gap_packages-4.13.1 ************************************************************************ Please email sage-devel (http://groups.google.com/group/sage-devel) explaining the problem and including the log files /usr/local/sage-10/logs/pkgs/gap_packages-4.13.1.log and /usr/local/sage-10/config.logLogs follow.
Dima Pasechnik
Oct 28, 2024, 10:36:32 AM10/28/24
to sage-r...@googlegroups.com
On Mon, Oct 28, 2024 at 2:33 PM Emmanuel Charpentier
<emanuel.c...@gmail.com> wrote:
>
> Re-reading my messages, I noticed that I mistyped pkg-config --cflags libsemigroup (which gives the error I reported) for pkg-config --cflags libsemigroups (which works silently). But even after running the correct pkg-config command, gap_packages-4.13.1 still fails to build, with a different error message :
>
> [spkg-install] g++ -std=gnu++11 -pthread -g -O2 -fPIC -MQ gen/src/cong.o -MMD -MP -MF gen/src/cong.d -std=gnu++14 -O3 -mavx -flax-vector-conversions -Igapbind14/include/ -DHPCOMBI_CONSTEXPR_FUN_ARGS -DFMT_HEADER_ONLY -DNDEBUG -g -O2 -o gen/src/cong.o -I/usr/local/sage-10/local/include/gap -I/usr/local/sage-10/local/include -DUSE_GASMAN=1 -c src/cong.cpp [spkg-install] In file included from /usr/local/sage-10/local/include/libsemigroups/knuth-bendix.hpp:34, [spkg-install] from /usr/local/sage-10/local/include/libsemigroups/cong.hpp:30, [spkg-install] from src/to_cpp.hpp:54, [spkg-install] from src/cong.cpp:29: [spkg-install] /usr/local/sage-10/local/include/libsemigroups/digraph.hpp:58:10: fatal error: Eigen/Core: No such file or directory [spkg-install] 58 | #include <Eigen/Core> [spkg-install] | ^~~~~~~~~~~~ [spkg-install] compilation terminated. [spkg-install] make[5]: *** [Makefile.gappkg:130: gen/src/cong.o] Error 1 [spkg-install] ************************************************************************************************************************ [spkg-install] Error building gap_packages-4.13.1 [spkg-install] ************************************************************************************************************************ ************************************************************************ Error installing package gap_packages-4.13.1 ************************************************************************ Please email sage-devel (http://groups.google.com/group/sage-devel) explaining the problem and including the log files /usr/local/sage-10/logs/pkgs/gap_packages-4.13.1.log and /usr/local/sage-10/config.log
>
> Logs follow.
Just give me few hours to fix this, I am pretty sure that a proper
<emanuel.c...@gmail.com> wrote:
>
> Re-reading my messages, I noticed that I mistyped pkg-config --cflags libsemigroup (which gives the error I reported) for pkg-config --cflags libsemigroups (which works silently). But even after running the correct pkg-config command, gap_packages-4.13.1 still fails to build, with a different error message :
>
> [spkg-install] g++ -std=gnu++11 -pthread -g -O2 -fPIC -MQ gen/src/cong.o -MMD -MP -MF gen/src/cong.d -std=gnu++14 -O3 -mavx -flax-vector-conversions -Igapbind14/include/ -DHPCOMBI_CONSTEXPR_FUN_ARGS -DFMT_HEADER_ONLY -DNDEBUG -g -O2 -o gen/src/cong.o -I/usr/local/sage-10/local/include/gap -I/usr/local/sage-10/local/include -DUSE_GASMAN=1 -c src/cong.cpp [spkg-install] In file included from /usr/local/sage-10/local/include/libsemigroups/knuth-bendix.hpp:34, [spkg-install] from /usr/local/sage-10/local/include/libsemigroups/cong.hpp:30, [spkg-install] from src/to_cpp.hpp:54, [spkg-install] from src/cong.cpp:29: [spkg-install] /usr/local/sage-10/local/include/libsemigroups/digraph.hpp:58:10: fatal error: Eigen/Core: No such file or directory [spkg-install] 58 | #include <Eigen/Core> [spkg-install] | ^~~~~~~~~~~~ [spkg-install] compilation terminated. [spkg-install] make[5]: *** [Makefile.gappkg:130: gen/src/cong.o] Error 1 [spkg-install] ************************************************************************************************************************ [spkg-install] Error building gap_packages-4.13.1 [spkg-install] ************************************************************************************************************************ ************************************************************************ Error installing package gap_packages-4.13.1 ************************************************************************ Please email sage-devel (http://groups.google.com/group/sage-devel) explaining the problem and including the log files /usr/local/sage-10/logs/pkgs/gap_packages-4.13.1.log and /usr/local/sage-10/config.log
>
> Logs follow.
upgrade of libsemigroups will be the fix.
Dima Pasechnik
Oct 28, 2024, 11:58:55 AM10/28/24
to sage-r...@googlegroups.com
The libsemigroup issue is fixed by https://github.com/sagemath/sage/pull/38875
(the version bump was forgotten, basically)
Please test and review
On Mon, Oct 28, 2024 at 2:41 PM Emmanuel Charpentier
<emanuel.c...@gmail.com> wrote:
>
> The promised logs.
>
> HTH,
(the version bump was forgotten, basically)
Please test and review
On Mon, Oct 28, 2024 at 2:41 PM Emmanuel Charpentier
<emanuel.c...@gmail.com> wrote:
>
> The promised logs.
>
> HTH,
>
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Emmanuel Charpentier
Oct 28, 2024, 12:48:45 PM10/28/24
to sage-release
Le lundi 28 octobre 2024 à 16:58:55 UTC+1, Dima Pasechnik a écrit :
The libsemigroup issue is fixed by https://github.com/sagemath/sage/pull/38875
(the version bump was forgotten, basically)
Please test and review
Nope, make -j8 build failed. Logs follow
Emmanuel Charpentier
Oct 28, 2024, 12:59:18 PM10/28/24
to sage-release
The relevant error is different :
```
[gap_packages-4.13.1] [spkg-install] g++ -std=gnu++11 -pthread -g -O2 -fPIC -MQ gen/src/cong.o -MMD -MP -MF gen/src/cong.d -std=gnu++14 -O3 -mavx -flax-vector-conversions -Igapbind14/include/ -DHPCOMBI_CONSTEXPR_FUN_ARGS -DFMT_HEADER_ONLY -DNDEBUG -g -O2 -o gen/src/cong.o -I/usr/local/sage-10/local/include/gap -I/usr/local/sage-10/local/include -DUSE_GASMAN=1 -c src/cong.cpp
[gap_packages-4.13.1] [spkg-install] In file included from /usr/local/sage-10/local/include/libsemigroups/knuth-bendix.hpp:34,
[gap_packages-4.13.1] [spkg-install] from /usr/local/sage-10/local/include/libsemigroups/cong.hpp:30,
[gap_packages-4.13.1] [spkg-install] from src/to_cpp.hpp:54,
[gap_packages-4.13.1] [spkg-install] from src/cong.cpp:29:
[gap_packages-4.13.1] [spkg-install] /usr/local/sage-10/local/include/libsemigroups/digraph.hpp:58:10: fatal error: Eigen/Core: No such file or directory
[gap_packages-4.13.1] [spkg-install] 58 | #include <Eigen/Core>
[gap_packages-4.13.1] [spkg-install] | ^~~~~~~~~~~~
[gap_packages-4.13.1] [spkg-install] compilation terminated.
[gap_packages-4.13.1] [spkg-install] make[5]: *** [Makefile.gappkg:130: gen/src/cong.o] Error 1
[gap_packages-4.13.1] [spkg-install] In file included from /usr/local/sage-10/local/include/libsemigroups/knuth-bendix.hpp:34,
[gap_packages-4.13.1] [spkg-install] from /usr/local/sage-10/local/include/libsemigroups/cong.hpp:30,
[gap_packages-4.13.1] [spkg-install] from src/to_cpp.hpp:54,
[gap_packages-4.13.1] [spkg-install] from src/cong.cpp:29:
[gap_packages-4.13.1] [spkg-install] /usr/local/sage-10/local/include/libsemigroups/digraph.hpp:58:10: fatal error: Eigen/Core: No such file or directory
[gap_packages-4.13.1] [spkg-install] 58 | #include <Eigen/Core>
[gap_packages-4.13.1] [spkg-install] | ^~~~~~~~~~~~
[gap_packages-4.13.1] [spkg-install] compilation terminated.
[gap_packages-4.13.1] [spkg-install] make[5]: *** [Makefile.gappkg:130: gen/src/cong.o] Error 1
```
HTH,
Marc Culler
Oct 28, 2024, 1:15:37 PM10/28/24
to sage-release
I agree that this in not fixed, in spite of my positive review of the PR.
I did not get that error, but I see by looking at the timestamps that my sage/local/include/libsemigroups/Eigen directory was left over from the install of the previous version.
Michael Orlitzky points out that the libsemigroups package is configured with --disable-eigen. But apparently that option does not work correctly.
- Marc
Emmanuel Charpentier
Oct 29, 2024, 4:59:35 AM10/29/24
to sage-release
The updated PR (re-fetched at Tue Oct 29 09:22:19 CET 2024) does not solve the problem. Without make dist-clean, I get the same problem as before :
[gap_packages-4.13.1] [spkg-install] g++ -std=gnu++11 -pthread -g -O2 -fPIC -MQ gen/src/cong.o -MMD -MP -MF gen/src/cong.d -std=gnu++14 -O3 -mavx -flax-vector-conversions -Igapbind14/include/ -DHPCOMBI_CONSTEXPR_FUN_ARGS -DFMT_HEADER_ONLY -DNDEBUG -g -O2 -o gen/src/cong.o -I/usr/local/sage-10/local/include/gap -I/usr/local/sage-10/local/include -DUSE_GASMAN=1 -c src/cong.cpp
[gap_packages-4.13.1] [spkg-install] In file included from /usr/local/sage-10/local/include/libsemigroups/knuth-bendix.hpp:34,
[gap_packages-4.13.1] [spkg-install] from /usr/local/sage-10/local/include/libsemigroups/cong.hpp:30,
[gap_packages-4.13.1] [spkg-install] from src/to_cpp.hpp:54,
[gap_packages-4.13.1] [spkg-install] from src/cong.cpp:29:
[gap_packages-4.13.1] [spkg-install] /usr/local/sage-10/local/include/libsemigroups/digraph.hpp:58:10: fatal error: Eigen/Core: No such file or directory
[gap_packages-4.13.1] [spkg-install] 58 | #include <Eigen/Core>
[gap_packages-4.13.1] [spkg-install] | ^~~~~~~~~~~~
[gap_packages-4.13.1] [spkg-install] compilation terminated.
HTH,
Dima Pasechnik
Oct 29, 2024, 5:36:17 AM10/29/24
to sage-r...@googlegroups.com
On Tue, Oct 29, 2024 at 8:59 AM Emmanuel Charpentier
<emanuel.c...@gmail.com> wrote:
>
> The updated PR (re-fetched at Tue Oct 29 09:22:19 CET 2024) does not solve the problem. Without make dist-clean, I get the same problem as before :
It certainly does the job after `make distclean`, and we have hard
<emanuel.c...@gmail.com> wrote:
>
> The updated PR (re-fetched at Tue Oct 29 09:22:19 CET 2024) does not solve the problem. Without make dist-clean, I get the same problem as before :
time figuring out how exactly the old state
(the presence of traces of Eigen headers somewhere deep in the guts of
the build system) is cached.
I'd actually propose to add Eigen as an optional package, but
meanwhile we need a PR to unblock the built
of gap_packages.
Emmanuel Charpentier
Oct 29, 2024, 9:35:28 AM10/29/24
to sage-release
Le mardi 29 octobre 2024 à 10:36:17 UTC+1, Dima Pasechnik a écrit :
On Tue, Oct 29, 2024 at 8:59 AM Emmanuel Charpentier
<emanuel.c...@gmail.com> wrote:
>
> The updated PR (re-fetched at Tue Oct 29 09:22:19 CET 2024) does not solve the problem. Without make dist-clean, I get the same problem as before :
It certainly does the job after `make distclean`,
Nope.
After make distclean, ./bootstrap,,configure $(./config.status --config, make -j8 build still triggers the same problem :
[gap_packages-4.13.1] [spkg-install] g++ -std=gnu++11 -pthread -g -O2 -fPIC -MQ gen/src/bipart.o -MMD -MP -MF gen/src/bipart.d -I./bin/include -I./bin/include/libsemigroups -std=gnu++14 -O3 -mavx -flax-vector-conversions -Igapbind14/include/ -DHPCOMBI_CONSTEXPR_FUN_ARGS -Ilibsemigroups/extern/HPCombi/include -Ilibsemigroups/extern/HPCombi/include/fallback -Ilibsemigroups/extern/fmt-8.0.1/include -Ilibsemigroups/include -DFMT_HEADER_ONLY -DNDEBUG -g -O2 -o gen/src/bipart.o -I/usr/local/sage-10/local/include/gap -I/usr/local/sage-10/local/include -DUSE_GASMAN=1 -c src/bipart.cpp [gap_packages-4.13.1] [spkg-install] In file included from src/bipart.cpp:38: [gap_packages-4.13.1] [spkg-install] libsemigroups/include/libsemigroups/report.hpp:42:10: fatal error: textflowcpp/TextFlow.hpp: No such file or directory [gap_packages-4.13.1] [spkg-install] 42 | #include "textflowcpp/TextFlow.hpp" [gap_packages-4.13.1] [spkg-install] | ^~~~~~~~~~~~~~~~~~~~~~~~~~ [gap_packages-4.13.1] [spkg-install] compilation terminated.Marc Culler
Oct 29, 2024, 12:17:06 PM10/29/24
to sage-release
While there are certainly build environments that do work to build gap_packages, it is clearly not robust. I think it would be a mistake to ignore this, because it is guaranteed to produce lots of support emails.
The issue here is with the file TextFlow.hpp. When libsemigroups is installed, that file ends up with the following path
$SAGE_LOCAL/include/libsemigroups/textflowcpp/TextFlow.hpp
I also see the file in
$SAGE_LOCAL/lib/gap/pkg/semigroups/libsemigroups/extern/textflowcpp/TextFlow.hpp
I think the first one is the sensible one to use. We can count on libsemigroups being installed before gap_packages because gap_packages lists it as a dependency.
If you look at the g++ command which is failing, it specifies the directories to be searched for headers with:
-I./bin/include
-I./bin/include/libsemigroups
-Igapbind14/include/
-Ilibsemigroups/extern/HPCombi/include
-Ilibsemigroups/extern/HPCombi/include/fallback
-Ilibsemigroups/extern/fmt-8.0.1/include
-Ilibsemigroups/include
-I/usr/local/sage-10/local/include/gap
-I/usr/local/sage-10/local/include
-I./bin/include/libsemigroups
-Igapbind14/include/
-Ilibsemigroups/extern/HPCombi/include
-Ilibsemigroups/extern/HPCombi/include/fallback
-Ilibsemigroups/extern/fmt-8.0.1/include
-Ilibsemigroups/include
-I/usr/local/sage-10/local/include/gap
-I/usr/local/sage-10/local/include
That list does not include $SAGE_LOCAL/include/libsemigroups/textflowcpp
(I am guessing that in this case $SAGE_LOCAL == /usr/local/sage-10)
I think it might fix this problem to add the following line at the top of build/pkgs/gap_packages/spkg-install.in:
export CFLAGS="${CFLAGS} -I${SAGE_LOCAL}/include/libsemigroups/textflowcpp"
Emmanuel, would you try that?
(Of course it might only reveal that there is another -I option needed, but that would be progress.)
- Marc
Marc Culler
Oct 29, 2024, 12:19:20 PM10/29/24
to sage-release
I meant:
I am guessing that in this case $SAGE_LOCAL == /usr/local/sage-10/local)
Dima Pasechnik
Oct 29, 2024, 12:59:25 PM10/29/24
to sage-r...@googlegroups.com
semigroups.
With external libsemigroups it should have none of -Ilibsemigroups/extern/* - as this is a vendored copy of libsemigroups, which has nothing to do with the already installed libsemigroups.
I'll look into it later today.
>> I think it might fix this problem to add the following line at the top of
>> build/pkgs/gap_packages/spkg-install.in:
>>
>> export CFLAGS="${CFLAGS} -I${SAGE_LOCAL}/include/libsemigroups/textflowcpp"
>>
>> Emmanuel, would you try that?
>>
>> (Of course it might only reveal that there is another -I option needed,
>> but that would be progress.)
>>
>> - Marc
>>
>>
>>
>>
>>
>> On Tuesday, October 29, 2024 at 8:35:28 AM UTC-5 emanuel.c...@gmail.com
>> wrote:
>>
>>> Le mardi 29 octobre 2024 à 10:36:17 UTC+1, Dima Pasechnik a écrit :
>>>
>>> On Tue, Oct 29, 2024 at 8:59 AM Emmanuel Charpentier
>>> <emanuel.c...@gmail.com> wrote:
>>> >
>>> > The updated PR (re-fetched at Tue Oct 29 09:22:19 CET 2024) does not
>>> solve the problem. Without make dist-clean, I get the same problem as
>>> before :
>>>
>>> It certainly does the job after `make distclean`,
>>>
>>> Nope.
>>>
Emmanuel Charpentier
Oct 30, 2024, 8:10:22 AM10/30/24
to sage-release
I tried to clean things as much as possible :
- restart WSL by closing all Ubuntu Windows, then wsl shutdown in Powershell.
- make disclean
- ./bootstrap
At this point, I checked that $(SAGE_ROOT)/local/include/libsemigroups didn’t exist.
- ./configure $(./config.status --config)
IIRC, at this point, $(SAGE_ROOT)/local.include stil didn’t exit, but I can”‘t check it (console buffer too small…).
- time make -j8 build fails after 72 minutes (plus small change). End of the output :
and, of course :
charpent@SAP5342949:/usr/local/sage-10$ ls local/include/libsemigroups/ Eigen digraph-helper.hpp kambites.hpp sims1.tpp HPCombi digraph-with-sources.hpp kbe.hpp siso.hpp action.hpp digraph-with-sources.tpp knuth-bendix.hpp stephen.hpp adapters.hpp digraph.hpp konieczny.hpp stl.hpp backward-cpp exception.hpp libsemigroups.hpp string-view.hpp bipart.hpp fastest-bmat.hpp make-froidure-pin.hpp string.hpp bitset.hpp felsch-digraph.hpp make-present.hpp suffix-tree.hpp bmat.hpp felsch-digraph.tpp matrix.hpp tce.hpp bmat8.hpp felsch-tree.hpp node-manager.hpp textflowcpp bruidhinn-traits.hpp forest.hpp obvinf.hpp timer.hpp config.hpp fpsemi-examples.hpp order.hpp todd-coxeter-digraph.hpp cong-intf.hpp fpsemi-intf.hpp pbr.hpp todd-coxeter-digraph.tpp cong-pair-impl.hpp fpsemi.hpp pool.hpp todd-coxeter.hpp cong-pair.hpp freeband.hpp present.hpp transf.hpp cong-wrap.hpp froidure-pin-base.hpp present.tpp types.hpp cong.hpp froidure-pin-impl.hpp race.hpp uf.hpp constants.hpp froidure-pin.hpp report.hpp ukkonen.hpp containers.hpp function-ref.hpp runner.hpp ukkonen.tpp coset.hpp hpcombi.hpp schreier-sims-helper.hpp wilo.hpp debug.hpp int-range.hpp schreier-sims.hpp wislo.hpp deprecated.hpp iterator.hpp sims1.hpp word.hppGrrrr… Something I do not understand :
charpent@SAP5342949:/usr/local/sage-10$ ls -l /usr/local/sage-10/local/bin/g* -rwxr-xr-x 1 charpent charpent 10843 Oct 30 09:30 /usr/local/sage-10/local/bin/gac -rwxr-xr-x 1 charpent charpent 18184 Oct 30 09:30 /usr/local/sage-10/local/bin/gap -rwxr-xr-x 1 charpent charpent 1558 Oct 30 09:22 /usr/local/sage-10/local/bin/givaro-config charpent@SAP5342949:/usr/local/sage-10$ which giac /usr/bin/giacAny ideas ?
Dima Pasechnik
Oct 30, 2024, 8:16:07 AM10/30/24
to sage-r...@googlegroups.com
can you try
git clean -fdx
instead of
make distclean
This will remove absolutely everything not in the git tree from
/usr/local/sage-10
On Wed, Oct 30, 2024 at 12:10 PM Emmanuel Charpentier
> To view this discussion visit https://groups.google.com/d/msgid/sage-release/e9241966-97d0-4b5b-a0c5-178440119732n%40googlegroups.com.
git clean -fdx
instead of
make distclean
This will remove absolutely everything not in the git tree from
/usr/local/sage-10
On Wed, Oct 30, 2024 at 12:10 PM Emmanuel Charpentier
Emmanuel Charpentier
Oct 30, 2024, 1:11:14 PM10/30/24
to sage-release
Different error this time : fails at 43 minutes on Pythran installation :
[pytz_deprecation_shim-0.1.0.post0] Finished installing pytz_deprecation_shim-0.1.0.post0 make --no-print-directory pythran-SAGE_VENV-no-deps [pythran-0.15.0] Attempting to download package pythran-0.15.0.tar.gz from mirrors [pythran-0.15.0] https://github.com/sagemath/sage/releases/download/10.5/pythran-0.15.0.tar.gz [pythran-0.15.0] [xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx] [pythran-0.15.0] ERROR [transfer|run:135]: [Errno socket error] [Errno 404] Not Found: '//github.com/sagemath/sage/releases/download/10.5/pythran-0.15.0.tar.gz' [pythran-0.15.0] https://github.com/sagemath/sage/releases/download/10.4/pythran-0.15.0.tar.gz [pythran-0.15.0] [......................................................................] [pythran-0.15.0] Setting up build directory /usr/local/sage-10/local/var/lib/sage/venv-python3.12/var/tmp/sage/build/pythran-0.15.0 [pythran-0.15.0] No patch files found in ../patches [pythran-0.15.0] Host system: Linux SAP5342949 5.15.153.1-microsoft-standard-WSL2 #1 SMP Fri Mar 29 23:14:13 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux [pythran-0.15.0] C compiler: gcc, Using built-in specs., COLLECT_GCC=gcc, COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-linux-gnu/13/lto-wrapper, OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa, OFFLOAD_TARGET_DEFAULT=1, Target: x86_64-linux-gnu, Configured with: ../src/configure -v --with-pkgversion='Ubuntu 13.2.0-23ubuntu4' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-13-uJ7kn6/gcc-13-13.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-13-uJ7kn6/gcc-13-13.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu, Thread model: posix, Supported LTO compression algorithms: zlib zstd, gcc version 13.2.0 (Ubuntu 13.2.0-23ubuntu4) [pythran-0.15.0] No stamp file for package 'pythran' in /usr/local/sage-10/local/var/lib/sage/venv-python3.12/var/lib/sage/installed [pythran-0.15.0] No spkg-legacy-uninstall script; nothing to do [pythran-0.15.0] [spkg-install] Installing pythran-0.15.0 [pythran-0.15.0] [spkg-install] * Creating isolated environment: venv+pip... [pythran-0.15.0] [spkg-install] * Installing packages in isolated environment: [pythran-0.15.0] [spkg-install] - setuptools [pythran-0.15.0] [spkg-install] * Getting build dependencies for wheel... [pythran-0.15.0] [spkg-install] running egg_info [pythran-0.15.0] [spkg-install] writing pythran.egg-info/PKG-INFO [pythran-0.15.0] [spkg-install] writing dependency_links to pythran.egg-info/dependency_links.txt [pythran-0.15.0] [spkg-install] writing entry points to pythran.egg-info/entry_points.txt [pythran-0.15.0] [spkg-install] writing requirements to pythran.egg-info/requires.txt [pythran-0.15.0] [spkg-install] writing top-level names to pythran.egg-info/top_level.txt [pythran-0.15.0] [spkg-install] reading manifest file 'pythran.egg-info/SOURCES.txt' [pythran-0.15.0] [spkg-install] reading manifest template 'MANIFEST.in' [pythran-0.15.0] [spkg-install] adding license file 'LICENSE' [pythran-0.15.0] [spkg-install] adding license file 'AUTHORS' [pythran-0.15.0] [spkg-install] writing manifest file 'pythran.egg-info/SOURCES.txt' [pythran-0.15.0] [spkg-install] * Building wheel... [pythran-0.15.0] [spkg-install] running bdist_wheel [pythran-0.15.0] [spkg-install] running build [pythran-0.15.0] [spkg-install] running build_py [pythran-0.15.0] [spkg-install] creating build [pythran-0.15.0] [spkg-install] creating build/lib [pythran-0.15.0] [spkg-install] creating build/lib/pythran [pythran-0.15.0] [spkg-install] copying pythran/run.py -> build/lib/pythran [pythran-0.15.0] [spkg-install] copying pythran/tables.py -> build/lib/pythran [pythran-0.15.0] [spkg-install] copying pythran/version.py -> build/lib/pythran [pythran-0.15.0] [spkg-install] copying pythran/syntax.py -> build/lib/pythran [pythran-0.15.0] [spkg-install] copying pythran/intrinsic.py -> build/lib/pythran [pythran-0.15.0] [spkg-install] copying pythran/utils.py -> build/lib/pythran [pythran-0.15.0] [spkg-install] copying pythran/magic.py -> build/lib/pythran [pythran-0.15.0] [spkg-install] copying pythran/__init__.py -> build/lib/pythran [pythran-0.15.0] [spkg-install] copying pythran/openmp.py -> build/lib/pythran [pythran-0.15.0] [spkg-install] copying pythran/spec.py -> build/lib/pythran [pythran-0.15.0] [spkg-install] copying pythran/toolchain.py -> build/lib/pythran [pythran-0.15.0] [spkg-install] copying pythran/metadata.py -> build/lib/pythran [pythran-0.15.0] [spkg-install] copying pythran/dist.py -> build/lib/pythran [pythran-0.15.0] [spkg-install] copying pythran/graph.py -> build/lib/pythran [pythran-0.15.0] [spkg-install] copying pythran/frontend.py -> build/lib/pythran [pythran-0.15.0] [spkg-install] copying pythran/passmanager.py -> build/lib/pythran [pythran-0.15.0] [spkg-install] copying pythran/interval.py -> build/lib/pythran [pythran-0.15.0] [spkg-install] copying pythran/backend.py -> build/lib/pythran [pythran-0.15.0] [spkg-install] copying pythran/conversion.py -> build/lib/pythran [pythran-0.15.0] [spkg-install] copying pythran/cxxtypes.py -> build/lib/pythran [pythran-0.15.0] [spkg-install] copying pythran/unparse.py -> build/lib/pythran [pythran-0.15.0] [spkg-install] copying pythran/typing.py -> build/lib/pythran [pythran-0.15.0] [spkg-install] copying pythran/middlend.py -> build/lib/pythran [pythran-0.15.0] [spkg-install] copying pythran/errors.py -> build/lib/pythran [pythran-0.15.0] [spkg-install] copying pythran/cxxgen.py -> build/lib/pythran [pythran-0.15.0] [spkg-install] copying pythran/log.py -> build/lib/pythran [pythran-0.15.0] [spkg-install] copying pythran/config.py -> build/lib/pythran [pythran-0.15.0] [spkg-install] creating build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/optimizable_comprehension.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/aliases.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/ancestors.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/use_def_chain.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/global_declarations.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/cfg.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/imported_ids.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/__init__.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/intrinsics.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/literals.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/extended_syntax_check.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/is_assigned.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/ordered_global_declarations.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/yield_points.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/potential_iterator.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/inlinable.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/globals_analysis.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/fixed_size_list.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/parallel_maps.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/node_count.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/range_values.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/argument_effects.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/pure_expressions.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/static_expressions.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/use_omp.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/global_effects.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/ast_matcher.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/local_declarations.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/has_return.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/identifiers.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/dependencies.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/constant_expressions.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/lazyness_analysis.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/immediates.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/argument_read_once.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/scope.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/pure_functions.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] copying pythran/analyses/locals_analysis.py -> build/lib/pythran/analyses [pythran-0.15.0] [spkg-install] creating build/lib/pythran/transformations [pythran-0.15.0] [spkg-install] copying pythran/transformations/expand_globals.py -> build/lib/pythran/transformations [pythran-0.15.0] [spkg-install] copying pythran/transformations/remove_comprehension.py -> build/lib/pythran/transformations [pythran-0.15.0] [spkg-install] copying pythran/transformations/normalize_tuples.py -> build/lib/pythran/transformations [pythran-0.15.0] [spkg-install] copying pythran/transformations/normalize_exception.py -> build/lib/pythran/transformations [pythran-0.15.0] [spkg-install] copying pythran/transformations/__init__.py -> build/lib/pythran/transformations [pythran-0.15.0] [spkg-install] copying pythran/transformations/normalize_compare.py -> build/lib/pythran/transformations [pythran-0.15.0] [spkg-install] copying pythran/transformations/remove_nested_functions.py -> build/lib/pythran/transformations [pythran-0.15.0] [spkg-install] copying pythran/transformations/normalize_typeis.py -> build/lib/pythran/transformations [pythran-0.15.0] [spkg-install] copying pythran/transformations/normalize_return.py -> build/lib/pythran/transformations [pythran-0.15.0] [spkg-install] copying pythran/transformations/normalize_static_if.py -> build/lib/pythran/transformations [pythran-0.15.0] [spkg-install] copying pythran/transformations/expand_import_all.py -> build/lib/pythran/transformations [pythran-0.15.0] [spkg-install] copying pythran/transformations/remove_fstrings.py -> build/lib/pythran/transformations [pythran-0.15.0] [spkg-install] copying pythran/transformations/remove_named_arguments.py -> build/lib/pythran/transformations [pythran-0.15.0] [spkg-install] copying pythran/transformations/extract_doc_strings.py -> build/lib/pythran/transformations [pythran-0.15.0] [spkg-install] copying pythran/transformations/normalize_method_calls.py -> build/lib/pythran/transformations [pythran-0.15.0] [spkg-install] copying pythran/transformations/remove_lambdas.py -> build/lib/pythran/transformations [pythran-0.15.0] [spkg-install] copying pythran/transformations/expand_builtins.py -> build/lib/pythran/transformations [pythran-0.15.0] [spkg-install] copying pythran/transformations/normalize_is_none.py -> build/lib/pythran/transformations [pythran-0.15.0] [spkg-install] copying pythran/transformations/normalize_ifelse.py -> build/lib/pythran/transformations [pythran-0.15.0] [spkg-install] copying pythran/transformations/expand_imports.py -> build/lib/pythran/transformations [pythran-0.15.0] [spkg-install] copying pythran/transformations/unshadow_parameters.py -> build/lib/pythran/transformations [pythran-0.15.0] [spkg-install] copying pythran/transformations/false_polymorphism.py -> build/lib/pythran/transformations [pythran-0.15.0] [spkg-install] copying pythran/transformations/handle_import.py -> build/lib/pythran/transformations [pythran-0.15.0] [spkg-install] creating build/lib/pythran/optimizations [pythran-0.15.0] [spkg-install] copying pythran/optimizations/simplify_except.py -> build/lib/pythran/optimizations [pythran-0.15.0] [spkg-install] copying pythran/optimizations/list_to_tuple.py -> build/lib/pythran/optimizations [pythran-0.15.0] [spkg-install] copying pythran/optimizations/__init__.py -> build/lib/pythran/optimizations [pythran-0.15.0] [spkg-install] copying pythran/optimizations/forward_substitution.py -> build/lib/pythran/optimizations [pythran-0.15.0] [spkg-install] copying pythran/optimizations/loop_full_unrolling.py -> build/lib/pythran/optimizations [pythran-0.15.0] [spkg-install] copying pythran/optimizations/copyto.py -> build/lib/pythran/optimizations [pythran-0.15.0] [spkg-install] copying pythran/optimizations/comprehension_patterns.py -> build/lib/pythran/optimizations [pythran-0.15.0] [spkg-install] copying pythran/optimizations/square.py -> build/lib/pythran/optimizations [pythran-0.15.0] [spkg-install] copying pythran/optimizations/inline_builtins.py -> build/lib/pythran/optimizations [pythran-0.15.0] [spkg-install] copying pythran/optimizations/iter_transformation.py -> build/lib/pythran/optimizations [pythran-0.15.0] [spkg-install] copying pythran/optimizations/range_based_simplify.py -> build/lib/pythran/optimizations [pythran-0.15.0] [spkg-install] copying pythran/optimizations/list_comp_to_genexp.py -> build/lib/pythran/optimizations [pythran-0.15.0] [spkg-install] copying pythran/optimizations/dead_code_elimination.py -> build/lib/pythran/optimizations [pythran-0.15.0] [spkg-install] copying pythran/optimizations/modindex.py -> build/lib/pythran/optimizations [pythran-0.15.0] [spkg-install] copying pythran/optimizations/inlining.py -> build/lib/pythran/optimizations [pythran-0.15.0] [spkg-install] copying pythran/optimizations/range_loop_unfolding.py -> build/lib/pythran/optimizations [pythran-0.15.0] [spkg-install] copying pythran/optimizations/pattern_transform.py -> build/lib/pythran/optimizations [pythran-0.15.0] [spkg-install] copying pythran/optimizations/constant_folding.py -> build/lib/pythran/optimizations [pythran-0.15.0] [spkg-install] copying pythran/optimizations/tuple_to_shape.py -> build/lib/pythran/optimizations [pythran-0.15.0] [spkg-install] copying pythran/optimizations/remove_dead_functions.py -> build/lib/pythran/optimizations [pythran-0.15.0] [spkg-install] creating build/lib/omp [pythran-0.15.0] [spkg-install] copying omp/__init__.py -> build/lib/omp [pythran-0.15.0] [spkg-install] creating build/lib/pythran/types [pythran-0.15.0] [spkg-install] copying pythran/types/tog.py -> build/lib/pythran/types [pythran-0.15.0] [spkg-install] copying pythran/types/__init__.py -> build/lib/pythran/types [pythran-0.15.0] [spkg-install] copying pythran/types/types.py -> build/lib/pythran/types [pythran-0.15.0] [spkg-install] copying pythran/types/signature.py -> build/lib/pythran/types [pythran-0.15.0] [spkg-install] copying pythran/types/type_dependencies.py -> build/lib/pythran/types [pythran-0.15.0] [spkg-install] copying pythran/types/conversion.py -> build/lib/pythran/types [pythran-0.15.0] [spkg-install] copying pythran/types/reorder.py -> build/lib/pythran/types [pythran-0.15.0] [spkg-install] running egg_info [pythran-0.15.0] [spkg-install] writing pythran.egg-info/PKG-INFO [pythran-0.15.0] [spkg-install] writing dependency_links to pythran.egg-info/dependency_links.txt [pythran-0.15.0] [spkg-install] writing entry points to pythran.egg-info/entry_points.txt [pythran-0.15.0] [spkg-install] writing requirements to pythran.egg-info/requires.txt [pythran-0.15.0] [spkg-install] writing top-level names to pythran.egg-info/top_level.txt [pythran-0.15.0] [spkg-install] reading manifest file 'pythran.egg-info/SOURCES.txt' [pythran-0.15.0] [spkg-install] reading manifest template 'MANIFEST.in' [pythran-0.15.0] [spkg-install] adding license file 'LICENSE' [pythran-0.15.0] [spkg-install] adding license file 'AUTHORS' [pythran-0.15.0] [spkg-install] writing manifest file 'pythran.egg-info/SOURCES.txt' [pythran-0.15.0] [spkg-install] /tmp/build-env-ejvolwqg/lib/python3.12/site-packages/setuptools/command/build_py.py:218: _Warning: Package 'pythran.boost' is absent from the `packages` configuration. [pythran-0.15.0] [spkg-install] !! [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] ******************************************************************************** [pythran-0.15.0] [spkg-install] ############################ [pythran-0.15.0] [spkg-install] # Package would be ignored # [pythran-0.15.0] [spkg-install] ############################ [pythran-0.15.0] [spkg-install] Python recognizes 'pythran.boost' as an importable package[^1], [pythran-0.15.0] [spkg-install] but it is absent from setuptools' `packages` configuration. [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] This leads to an ambiguous overall configuration. If you want to distribute this [pythran-0.15.0] [spkg-install] package, please make sure that 'pythran.boost' is explicitly added [pythran-0.15.0] [spkg-install] to the `packages` configuration field. [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] Alternatively, you can also rely on setuptools' discovery methods [pythran-0.15.0] [spkg-install] (for example by using `find_namespace_packages(...)`/`find_namespace:` [pythran-0.15.0] [spkg-install] instead of `find_packages(...)`/`find:`). [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] You can read more about "package discovery" on setuptools documentation page: [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] If you don't want 'pythran.boost' to be distributed and are [pythran-0.15.0] [spkg-install] already explicitly excluding 'pythran.boost' via [pythran-0.15.0] [spkg-install] `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, [pythran-0.15.0] [spkg-install] you can try to use `exclude_package_data`, or `include-package-data=False` in [pythran-0.15.0] [spkg-install] combination with a more fine grained `package-data` configuration. [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] You can read more about "package data files" on setuptools documentation page: [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] [^1]: For Python, any directory (with suitable naming) can be imported, [pythran-0.15.0] [spkg-install] even if it does not contain any `.py` files. [pythran-0.15.0] [spkg-install] On the other hand, currently there is no concept of package data [pythran-0.15.0] [spkg-install] directory, all directories are treated like packages. [pythran-0.15.0] [spkg-install] ******************************************************************************** [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] !! [pythran-0.15.0] [spkg-install] check.warn(importable) [pythran-0.15.0] [spkg-install] /tmp/build-env-ejvolwqg/lib/python3.12/site-packages/setuptools/command/build_py.py:218: _Warning: Package 'pythran.boost.atomic' is absent from the `packages` configuration. [pythran-0.15.0] [spkg-install] !!followed by a lot of copies of the last error message.
I sent the relevant logs about 3 hours ago, but they failed to appear on the list.
HTH,
Emmanuel Charpentier
Oct 30, 2024, 1:23:30 PM10/30/24
to sage-release
Google Drive hyperlink to the logs.
Emmanuel Charpentier
Nov 2, 2024, 3:14:01 PM11/2/24
to sage-release
New data point : Trying to rebuild in a new tree 10.5.beta7 fails at pythran (again).
Setup :
./bootstrap ./configure --enable-dot2text --enable-fricas --enable-msolve --with-system-fricas=yes --enable-gap_jupyter --enable-gap_packages --enable-singular_jupyter --without-system-brial make -j8 download # Downloads about 15 GB in about 1h35. make -j8 buildThe latter fails in about 35 minutes. Start of the error message :
[pythran-0.15.0] [spkg-install] writing manifest file 'pythran.egg-info/SOURCES.txt' [pythran-0.15.0] [spkg-install] /tmp/build-env-r7bzv9fy/lib/python3.12/site-packages/setuptools/command/build_py.py:218: _Warning: Package 'pythran.boost' is absent from the `packages` configuration. [pythran-0.15.0] [spkg-install] !! [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] ******************************************************************************** [pythran-0.15.0] [spkg-install] ############################ [pythran-0.15.0] [spkg-install] # Package would be ignored # [pythran-0.15.0] [spkg-install] ############################ [pythran-0.15.0] [spkg-install] Python recognizes 'pythran.boost' as an importable package[^1], [pythran-0.15.0] [spkg-install] but it is absent from setuptools' `packages` configuration. [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] This leads to an ambiguous overall configuration. If you want to distribute this [pythran-0.15.0] [spkg-install] package, please make sure that 'pythran.boost' is explicitly added [pythran-0.15.0] [spkg-install] to the `packages` configuration field. [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] Alternatively, you can also rely on setuptools' discovery methods [pythran-0.15.0] [spkg-install] (for example by using `find_namespace_packages(...)`/`find_namespace:` [pythran-0.15.0] [spkg-install] instead of `find_packages(...)`/`find:`). [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] You can read more about "package discovery" on setuptools documentation page: [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] If you don't want 'pythran.boost' to be distributed and are [pythran-0.15.0] [spkg-install] already explicitly excluding 'pythran.boost' via [pythran-0.15.0] [spkg-install] `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, [pythran-0.15.0] [spkg-install] you can try to use `exclude_package_data`, or `include-package-data=False` in [pythran-0.15.0] [spkg-install] combination with a more fine grained `package-data` configuration. [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] You can read more about "package data files" on setuptools documentation page: [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] [^1]: For Python, any directory (with suitable naming) can be imported, [pythran-0.15.0] [spkg-install] even if it does not contain any `.py` files. [pythran-0.15.0] [spkg-install] On the other hand, currently there is no concept of package data [pythran-0.15.0] [spkg-install] directory, all directories are treated like packages. [pythran-0.15.0] [spkg-install] ******************************************************************************** [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] !! [pythran-0.15.0] [spkg-install] check.warn(importable) [pythran-0.15.0] [spkg-install] /tmp/build-env-r7bzv9fy/lib/python3.12/site-packages/setuptools/command/build_py.py:218: _Warning: Package 'pythran.boost.atomic' is absent from the `packages` configuration. [pythran-0.15.0] [spkg-install] !! [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] ******************************************************************************** [pythran-0.15.0] [spkg-install] ############################ [pythran-0.15.0] [spkg-install] # Package would be ignored # [pythran-0.15.0] [spkg-install] ############################ [pythran-0.15.0] [spkg-install] Python recognizes 'pythran.boost.atomic' as an importable package[^1], [pythran-0.15.0] [spkg-install] but it is absent from setuptools' `packages` configuration. [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] This leads to an ambiguous overall configuration. If you want to distribute this [pythran-0.15.0] [spkg-install] package, please make sure that 'pythran.boost.atomic' is explicitly added [pythran-0.15.0] [spkg-install] to the `packages` configuration field. [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] Alternatively, you can also rely on setuptools' discovery methods [pythran-0.15.0] [spkg-install] (for example by using `find_namespace_packages(...)`/`find_namespace:` [pythran-0.15.0] [spkg-install] instead of `find_packages(...)`/`find:`). [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] You can read more about "package discovery" on setuptools documentation page: [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] If you don't want 'pythran.boost.atomic' to be distributed and are [pythran-0.15.0] [spkg-install] already explicitly excluding 'pythran.boost.atomic' via [pythran-0.15.0] [spkg-install] `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, [pythran-0.15.0] [spkg-install] you can try to use `exclude_package_data`, or `include-package-data=False` in [pythran-0.15.0] [spkg-install] combination with a more fine grained `package-data` configuration. [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] You can read more about "package data files" on setuptools documentation page: [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] [^1]: For Python, any directory (with suitable naming) can be imported, [pythran-0.15.0] [spkg-install] even if it does not contain any `.py` files. [pythran-0.15.0] [spkg-install] On the other hand, currently there is no concept of package data [pythran-0.15.0] [spkg-install] directory, all directories are treated like packages. [pythran-0.15.0] [spkg-install] ******************************************************************************** [pythran-0.15.0] [spkg-install] [pythran-0.15.0] [spkg-install] !! [pythran-0.15.0] [spkg-install] check.warn(importable)followed by many similar error messages relative to boostcomponents, “absent from thepackagesconfiguration.“.
HTH,
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