Sage 10.7.beta2 released

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Volker Braun

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Apr 29, 2025, 6:56:13 PMApr 29
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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


7888c42db95 (github/develop, tag: 10.7.beta2) Updated SageMath version to 10.7.beta2
14e996467f7 gh-39995: typing annotations for is_something in knots,quadratic_forms,quivers
8156226328c gh-39994: typing annotation for is_something in modules/
a5b97563a64 gh-39989: Refactor imports in PoorManMap and Sequence classes
edf324ef728 gh-39987: add some typing annotations in modular folder
0ab46d1c7a8 gh-39982: Implement conversion of log(2) to Giac
4c7c421f230 gh-39976: fix e_antic patch header
a8606913389 gh-39972: some fixes for ruff C4
a48c9c3f811 gh-39971: micro details in pyx files in matroids
9e061a17cfb gh-39970: convert between two implementations of fin-dim algebras
65a11d4c4c3 gh-39969: Replace conda with mamba for consistency
f7131a813a0 gh-39968: fix again the pycodestyle linter
9da003611db gh-39965: Modified iterator & counter type from int to Py_ssize_t throughout Matrix class
f0e41038c05 gh-39963: Add offset argument to diagonal method
eb80cc0859c gh-39962: Docs: Migrate developer walkthrough to Meson
b800a70d0dc gh-39958: some care for unused variables in rings/polynomial/ pyx files
c1a1bc7229d gh-39954: Meson: automatically install into venv if activated
b932b401188 gh-39946: add parameter immutable to methods in `src/sage/graphs/graph_decompositions/graph_products.pyx`
93bfdb80798 gh-39942: Fix various issues with CI
bc6bd4e0efd gh-39939: Add sphinx-copybutton to dependency of sage-docbuild
3678dc6ec12 gh-39936: update givaro to 4.2.1
82553b199ce gh-39935: improve graph backends to fix bug in `lex_BFS`
0795808f6d2 gh-39925: add parameter immutable to methods in `src/sage/graphs/line_graph.pyx`
0cdea6fb801 gh-39884: Make generic polynomial multiplication interruptible
06d1fde3dbd gh-39856: Improve NotImplementedError for sqrt(Mod(a,n), all=True)
ac81b0b8759 gh-39852: Handle empty matrices over univariate polynomials
3e469e136e3 gh-39792: Add Simplified Chinese translation of a_tour_of_sage and tutorial
d0ed6df699a gh-39783: Add LINS to gap_packages
b36120dd9e2 gh-39716: Added code to calculate crt for non-coprime moduli in Integer
3dd3925708a gh-39661: Changed gens to tuple in ModularFormsSpace.
c5972879f7d gh-39660: Changed gens to tuple in AbstractLinearCodeNoMetric, mwrank_EllipticCurve, and FiniteSubgroup.
09dd1efec2c gh-39636: cython-lint for calculus/ folder
e7eabc46c40 gh-39480: Added enhancement for power series that allows access to the coefficients of specific terms
d76572e8b07 gh-39436: Refactor O() and fix O() for lazy power series ring
c3a4aa64425 gh-39279: Show signature for binding=False cython functions
e0cf1e41d41 (tag: 10.7.beta1) Updated SageMath version to 10.7.beta1

David Coudert

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Apr 30, 2025, 10:38:23 AMApr 30
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Thank you for this new beta. Unfortunately, I’m unable to compile on macOS.

On macOS 15.4.1, after brew upgrade
With a fresh clone and a fresh shell

./bootstrap
source .homebrew-build-env 
./configure
make build
….
….

[gfan-0.6.2.p1] [spkg-install] g++ -std=gnu++11 -g -O2 -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/linalgfloat.cpp -o src/linalgfloat.o

[gfan-0.6.2.p1] [spkg-install] g++ -std=gnu++11 -g -O2 -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/primarydecomposition.cpp -o src/primarydecomposition.o

[gfan-0.6.2.p1] [spkg-install] g++ -std=gnu++11 -g -O2 -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/tropicaldeterminant.cpp -o src/tropicaldeterminant.o

[gfan-0.6.2.p1] [spkg-install] g++ -std=gnu++11 -g -O2 -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/determinantpoly.cpp -o src/determinantpoly.o

[gfan-0.6.2.p1] [spkg-install] g++ -std=gnu++11 -g -O2 -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/traverser_sphere.cpp -o src/traverser_sphere.o

[gfan-0.6.2.p1] [spkg-install] g++ -std=gnu++11 -g -O2 -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/gfanlib_zcone.cpp -o src/gfanlib_zcone.o

[gfan-0.6.2.p1] [spkg-install] In file included from src/gfanlib_zcone.cpp:8:

[gfan-0.6.2.p1] [spkg-install] In file included from src/gfanlib_zcone.h:11:

[gfan-0.6.2.p1] [spkg-install] src/gfanlib_matrix.h:123:18: error: no member named 'vectormultiply' in 'Matrix<typ>'

[gfan-0.6.2.p1] [spkg-install]   123 |         ret[i]=a.vectormultiply(b.column(i));

[gfan-0.6.2.p1] [spkg-install]       |                ~ ^

[gfan-0.6.2.p1] [spkg-install] 1 error generated.

[gfan-0.6.2.p1] [spkg-install] make[5]: *** [src/gfanlib_zcone.o] Error 1

[gfan-0.6.2.p1] [spkg-install] ********************************************************************************

[gfan-0.6.2.p1] [spkg-install] Error building gfan-0.6.2.p1

[gfan-0.6.2.p1] [spkg-install] ********************************************************************************

[gfan-0.6.2.p1] ************************************************************************

[gfan-0.6.2.p1] Error installing package gfan-0.6.2.p1

[gfan-0.6.2.p1] ************************************************************************

[gfan-0.6.2.p1] Please email sage-devel (http://groups.google.com/group/sage-devel)

[gfan-0.6.2.p1] explaining the problem and including the log files

[gfan-0.6.2.p1]   /Users/dcoudert/sage/logs/pkgs/gfan-0.6.2.p1.log

[gfan-0.6.2.p1] and

[gfan-0.6.2.p1]   /Users/dcoudert/sage/config.log

[gfan-0.6.2.p1] Describe your computer, operating system, etc.

[gfan-0.6.2.p1] If you want to try to fix the problem yourself, *don't* just cd to

[gfan-0.6.2.p1] /Users/dcoudert/sage/local/var/tmp/sage/build/gfan-0.6.2.p1 and type 'make' or whatever is appropriate.

[gfan-0.6.2.p1] Instead, the following commands setup all environment variables

[gfan-0.6.2.p1] correctly and load a subshell for you to debug the error:

[gfan-0.6.2.p1]   (cd '/Users/dcoudert/sage/local/var/tmp/sage/build/gfan-0.6.2.p1' && '/Users/dcoudert/sage/sage' --buildsh)

[gfan-0.6.2.p1] When you are done debugging, you can type "exit" to leave the subshell.

[gfan-0.6.2.p1] ************************************************************************

[gfan-0.6.2.p1] real 1m4.630s user 1m0.048s sys 0m53.683s

make[4]: *** [gfan-SAGE_LOCAL-no-deps] Error 1

make[3]: *** [/Users/dcoudert/sage/local/var/lib/sage/installed/gfan-0.6.2.p1] Error 2

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

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

Error building Sage.


Let me know which log files is needed to better understand.

Best,
David.


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David Coudert

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Apr 30, 2025, 11:47:03 AMApr 30
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May be it’s time to upgrade fan to version 0.7 (august 2024). Our current version is from 2017.
https://users-math.au.dk/jensen/software/gfan/gfan.html

It seems that the failing instruction has been removed. But I don’t understand why it was working well with previous versions of sagemath...

David.

Dima Pasechnik

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Apr 30, 2025, 11:53:49 AMApr 30
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The problem is probably due to clang 17.0.0 appearing in the recent XCode, causing, as usual in Apple's case with major compiler updates,
a massive breakage of C++ code.
By the way, you can get a working gfan on macOS from Homebrew, by using Macayley2 tab:
https://github.com/Macaulay2/homebrew-tap
E.g. to install gfan from there, do
brew install Macaulay2/tap/gfan

(you can also enable the whole tap globally by doing "brew tap Macaulay2/tap", then "brew install gfan" will do)

Dima






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David Coudert

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Apr 30, 2025, 2:35:11 PMApr 30
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Thank you Dima, this solves the issue with gfan.

Unfortunately, I also have issues with singular (although I have a brew version) and linbox.


[spkg-install] libtool: compile:  g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I./include -I./include -I. -DFACTORY_BUILDING_DLL -I/Users/dcoudert/sage/local/var/tmp/sage/build/singular-4.4.0/src -I/Users/dcoudert/sage/local/var/tmp/sage/build/singular-4.4.0/src -DSING_NDEBUG -DOM_NDEBUG -g -O2 -pipe -fno-common -g0 -O3 -Wno-unused-function -Wno-trigraphs -Wno-unused-parameter -Wunknown-pragmas -Wno-unused-variable -fomit-frame-pointer -fwrapv -fvisibility=default -finline-functions -fno-exceptions -fno-threadsafe-statics -funroll-loops -fno-rtti -Qunused-arguments -c facIrredTest.cc  -fno-common -DPIC -o .libs/facIrredTest.o

[spkg-install] /bin/bash ./libtool  --tag=CXX   --mode=compile g++ -std=gnu++11 -DHAVE_CONFIG_H -I.  -I./include -I./include -I. -DFACTORY_BUILDING_DLL -I/Users/dcoudert/sage/local/var/tmp/sage/build/singular-4.4.0/src -I/Users/dcoudert/sage/local/var/tmp/sage/build/singular-4.4.0/src      -DSING_NDEBUG -DOM_NDEBUG   -g -O2 -pipe -fno-common -g0 -O3 -Wno-unused-function -Wno-trigraphs -Wno-unused-parameter -Wunknown-pragmas -Wno-unused-variable -fomit-frame-pointer -fwrapv -fvisibility=default -finline-functions -fno-exceptions -fno-threadsafe-statics -funroll-loops -fno-rtti -Qunused-arguments -c -o facMul.lo facMul.cc

[spkg-install] libtool: compile:  g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I./include -I./include -I. -DFACTORY_BUILDING_DLL -I/Users/dcoudert/sage/local/var/tmp/sage/build/singular-4.4.0/src -I/Users/dcoudert/sage/local/var/tmp/sage/build/singular-4.4.0/src -DSING_NDEBUG -DOM_NDEBUG -g -O2 -pipe -fno-common -g0 -O3 -Wno-unused-function -Wno-trigraphs -Wno-unused-parameter -Wunknown-pragmas -Wno-unused-variable -fomit-frame-pointer -fwrapv -fvisibility=default -finline-functions -fno-exceptions -fno-threadsafe-statics -funroll-loops -fno-rtti -Qunused-arguments -c facMul.cc  -fno-common -DPIC -o .libs/facMul.o

[spkg-install] facMul.cc:1258:3: error: use of undeclared identifier 'flint_mpn_zero'

[spkg-install]  1258 |   flint_mpn_zero (result->coeffs, d*(degAy+1));

[spkg-install]       |   ^

[spkg-install] facMul.cc:1267:5: error: use of undeclared identifier 'flint_mpn_copyi'

[spkg-install]  1267 |     flint_mpn_copyi (result->coeffs+k, buf->coeffs, nmod_poly_length(buf));

[spkg-install]       |     ^

[spkg-install] 2 errors generated.

[spkg-install] make[9]: *** [facMul.lo] Error 1

[spkg-install] make[8]: *** [all-recursive] Error 1

[spkg-install] make[7]: *** [all] Error 2

[spkg-install] make[6]: *** [all-recursive] Error 1

[spkg-install] make[5]: *** [all] Error 2

[spkg-install] ********************************************************************************

[spkg-install] Error building singular-4.4.0

[spkg-install] ********************************************************************************

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

Error installing package singular-4.4.0

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

Please email sage-devel (http://groups.google.com/group/sage-devel)

explaining the problem and including the log files

  /Users/dcoudert/sage/logs/pkgs/singular-4.4.0.log




[spkg-install] In file included from ../../linbox/matrix/dense-matrix.h:85:

[spkg-install] In file included from ../../linbox/matrix/densematrix/blas-matrix.h:42:

[spkg-install] In file included from ../../linbox/vector/blas-vector.h:47:

[spkg-install] ../../linbox/vector/blas-subvector.h:121:20: error: no member named 'data' in 'BlasSubvector<_Vector>'

[spkg-install]   121 |             _ptr(V.data()+beg), _size(dim), _inc(inc), _field(&V.field()) {}

[spkg-install]       |                  ~ ^

[spkg-install] In file included from diophantine-solver.C:26:

[spkg-install] In file included from ../../linbox/algorithms/diophantine-solver.h:29:

[spkg-install] In file included from ../../linbox/algorithms/rational-solver.h:41:

[spkg-install] In file included from ../../linbox/solutions/methods.h:26:

[spkg-install] In file included from ../../linbox/matrix/dense-matrix.h:85:

[spkg-install] In file included from ../../linbox/matrix/densematrix/blas-matrix.h:43:

[spkg-install] In file included from ../../linbox/vector/stream.h:872:

[spkg-install] In file included from ../../linbox/vector/stream-gf2.h:77:

[spkg-install] ../../linbox/field/gf2.h:984:29: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]

[spkg-install]   984 |                 return r ^= a & static_cast<bool>(x);

[spkg-install]       |                             ^~~~~~~~~~~~~~~~~~~~~~~~

[spkg-install]       |                               &&

[spkg-install] ../../linbox/field/gf2.h:984:29: note: cast one or both operands to int to silence this warning

[spkg-install] ../../linbox/field/gf2.h:995:33: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]

[spkg-install]   995 |                 return r = r ^ (a & static_cast<bool>(x));

[spkg-install]       |                                ~^~~~~~~~~~~~~~~~~~~~~~~~~

[spkg-install]       |                                   &&

[spkg-install] ../../linbox/field/gf2.h:995:33: note: cast one or both operands to int to silence this warning

[spkg-install] In file included from diophantine-solver.C:26:

[spkg-install] In file included from ../../linbox/algorithms/diophantine-solver.h:29:

[spkg-install] In file included from ../../linbox/algorithms/rational-solver.h:41:

[spkg-install] In file included from ../../linbox/solutions/methods.h:26:

[spkg-install] In file included from ../../linbox/matrix/dense-matrix.h:85:

[spkg-install] In file included from ../../linbox/matrix/densematrix/blas-matrix.h:50:

[spkg-install] In file included from ../../linbox/matrix/densematrix/blas-submatrix.h:36:

[spkg-install] In file included from /Users/dcoudert/sage/local/include/fflas-ffpack/fflas-ffpack.h:35:

[spkg-install] In file included from /Users/dcoudert/sage/local/include/fflas-ffpack/ffpack/ffpack.h:1983:

[spkg-install] /Users/dcoudert/sage/local/include/fflas-ffpack/ffpack/ffpack_charpoly.inl:193:20: warning: variable 'nbfac' set but not used [-Wunused-but-set-variable]

[spkg-install]   193 |             size_t nbfac = 0;

[spkg-install]       |                    ^

[spkg-install] In file included from diophantine-solver.C:26:

[spkg-install] In file included from ../../linbox/algorithms/diophantine-solver.h:29:

[spkg-install] In file included from ../../linbox/algorithms/rational-solver.h:41:

[spkg-install] In file included from ../../linbox/solutions/methods.h:26:

[spkg-install] In file included from ../../linbox/matrix/dense-matrix.h:85:

[spkg-install] In file included from ../../linbox/matrix/densematrix/blas-matrix.h:50:

[spkg-install] In file included from ../../linbox/matrix/densematrix/blas-submatrix.h:36:

[spkg-install] In file included from /Users/dcoudert/sage/local/include/fflas-ffpack/fflas-ffpack.h:35:

[spkg-install] In file included from /Users/dcoudert/sage/local/include/fflas-ffpack/ffpack/ffpack.h:1987:

[spkg-install] /Users/dcoudert/sage/local/include/fflas-ffpack/ffpack/ffpack_permutation.inl:60:16: warning: variable 'nonpivrowstomove' set but not used [-Wunused-but-set-variable]

[spkg-install]    60 |         size_t nonpivrowstomove = 0;

[spkg-install]       |                ^

[spkg-install] In file included from diophantine-solver.C:26:

[spkg-install] In file included from ../../linbox/algorithms/diophantine-solver.h:29:

[spkg-install] In file included from ../../linbox/algorithms/rational-solver.h:44:

[spkg-install] In file included from ../../linbox/blackbox/lambda-sparse.h:29:

[spkg-install] In file included from ../../linbox/matrix/sparse-matrix.h:82:

[spkg-install] In file included from ../../linbox/matrix/sparsematrix/sparse-map-map-matrix.h:207:

[spkg-install] ../../linbox/matrix/sparsematrix/sparse-map-map-matrix.inl:414:6: warning: variable 'count' set but not used [-Wunused-but-set-variable]

[spkg-install]   414 |         int count=0;

[spkg-install]       |             ^

[spkg-install] In file included from diophantine-solver.C:26:

[spkg-install] In file included from ../../linbox/algorithms/diophantine-solver.h:29:

[spkg-install] In file included from ../../linbox/algorithms/rational-solver.h:583:

[spkg-install] In file included from ../../linbox/algorithms/./dixon-solver/dixon-solver-dense.h:363:

[spkg-install] In file included from ../../linbox/algorithms/./dixon-solver/./dixon-solver-dense.inl:26:

[spkg-install] In file included from ../../linbox/algorithms/lifting-container.h:45:

[spkg-install] In file included from ../../linbox/algorithms/block-massey-domain.h:42:

[spkg-install] In file included from ../../linbox/algorithms/polynomial-matrix/order-basis.h:41:

[spkg-install] In file included from ../../linbox/algorithms/polynomial-matrix/polynomial-matrix-domain.h:34:

[spkg-install] ../../linbox/algorithms/polynomial-matrix/matpoly-mult-fft.h:330:16: warning: variable 'nbp' set but not used [-Wunused-but-set-variable]

[spkg-install]   330 |         size_t nbp=0;

[spkg-install]       |                ^

[spkg-install] In file included from diophantine-solver.C:26:

[spkg-install] In file included from ../../linbox/algorithms/diophantine-solver.h:29:

[spkg-install] In file included from ../../linbox/algorithms/rational-solver.h:583:

[spkg-install] In file included from ../../linbox/algorithms/./dixon-solver/dixon-solver-dense.h:363:

[spkg-install] In file included from ../../linbox/algorithms/./dixon-solver/./dixon-solver-dense.inl:26:

[spkg-install] In file included from ../../linbox/algorithms/lifting-container.h:45:

[spkg-install] In file included from ../../linbox/algorithms/block-massey-domain.h:42:

[spkg-install] In file included from ../../linbox/algorithms/polynomial-matrix/order-basis.h:41:

[spkg-install] In file included from ../../linbox/algorithms/polynomial-matrix/polynomial-matrix-domain.h:34:

[spkg-install] In file included from ../../linbox/algorithms/polynomial-matrix/matpoly-mult-fft.h:373:

[spkg-install] ../../linbox/algorithms/polynomial-matrix/matpoly-mult-fft-wordsize.inl:61:20: warning: variable 'lpts' set but not used [-Wunused-but-set-variable]

[spkg-install]    61 |             size_t lpts = 0;

[spkg-install]       |                    ^

[spkg-install] In file included from diophantine-solver.C:26:

[spkg-install] In file included from ../../linbox/algorithms/diophantine-solver.h:29:

[spkg-install] In file included from ../../linbox/algorithms/rational-solver.h:583:

[spkg-install] In file included from ../../linbox/algorithms/./dixon-solver/dixon-solver-dense.h:363:

[spkg-install] In file included from ../../linbox/algorithms/./dixon-solver/./dixon-solver-dense.inl:28:

[spkg-install] ../../linbox/algorithms/rational-reconstruction.h:339:8: warning: variable 'counter' set but not used [-Wunused-but-set-variable]

[spkg-install]   339 |                         int counter=0;

[spkg-install]       |                             ^

[spkg-install] ../../linbox/algorithms/rational-reconstruction.h:924:29: warning: variable 'counter' set but not used [-Wunused-but-set-variable]

[spkg-install]   924 |                         int counter=0;

[spkg-install]       |                             ^

[spkg-install] 10 warnings and 1 error generated.

[spkg-install] make[9]: *** [diophantine-solver.lo] Error 1

[spkg-install] make[8]: *** [all-recursive] Error 1

[spkg-install] make[7]: *** [all-recursive] Error 1

[spkg-install] make[6]: *** [all-recursive] Error 1

[spkg-install] make[5]: *** [all] Error 2

[spkg-install] ********************************************************************************

[spkg-install] Error building linbox-1.7.0+sage-2024-05-18

[spkg-install] ********************************************************************************

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

Error installing package linbox-1.7.0+sage-2024-05-18

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

Please email sage-devel (http://groups.google.com/group/sage-devel)

explaining the problem and including the log files






Dima Pasechnik

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Apr 30, 2025, 3:05:33 PMApr 30
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The issue with Singular is that it's refused by ./configure for some reason on your config.log can reveal to us.
Perhaps you've got to uninstall its built from source dependencies, and let them come from Homebrew instead.

David Coudert

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Apr 30, 2025, 4:18:42 PMApr 30
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My config log is attached.

Not sure how to do what you propose...

config.log

Dima Pasechnik

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May 1, 2025, 1:14:28 AMMay 1
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Oh, sorry, I forgot that the current Homebrew singular is not good enough, as it's not built with flint.
We should make our own Homebrew tap with singular built with flint, or, better, try to get singular with flint dependency into core Homebrew.
(actually, Homebrew's flint should be good enough to be used with the updated Singular)

Dima


On Wed, Apr 30, 2025 at 3:18 PM David Coudert <david....@gmail.com> wrote:
My config log is attached.

Not sure how to do what you propose...

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David Coudert

unread,
May 1, 2025, 5:03:39 AMMay 1
to sage-r...@googlegroups.com
Using https://github.com/sagemath/sage/pull/40033 and --with-system-flint=no  fix the issue with flint and singular.

However, the compilation of linbox is failing

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/solutions/methods.h:26:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/matrix/dense-matrix.h:85:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/matrix/densematrix/blas-matrix.h:42:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/vector/blas-vector.h:47:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] ../../linbox/vector/blas-subvector.h:121:20: error: no member named 'data' in 'BlasSubvector<_Vector>'

[linbox-1.7.0+sage-2024-05-18] [spkg-install]   121 |             _ptr(V.data()+beg), _size(dim), _inc(inc), _field(&V.field()) {}

[linbox-1.7.0+sage-2024-05-18] [spkg-install]       |                  ~ ^

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from diophantine-solver.C:26:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/diophantine-solver.h:29:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/rational-solver.h:41:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/solutions/methods.h:26:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/matrix/dense-matrix.h:85:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/matrix/densematrix/blas-matrix.h:43:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/vector/stream.h:872:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/vector/stream-gf2.h:77:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] ../../linbox/field/gf2.h:984:29: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]

[linbox-1.7.0+sage-2024-05-18] [spkg-install]   984 |                 return r ^= a & static_cast<bool>(x);

[linbox-1.7.0+sage-2024-05-18] [spkg-install]       |                             ^~~~~~~~~~~~~~~~~~~~~~~~

[linbox-1.7.0+sage-2024-05-18] [spkg-install]       |                               &&

[linbox-1.7.0+sage-2024-05-18] [spkg-install] ../../linbox/field/gf2.h:984:29: note: cast one or both operands to int to silence this warning

[linbox-1.7.0+sage-2024-05-18] [spkg-install] ../../linbox/field/gf2.h:995:33: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]

[linbox-1.7.0+sage-2024-05-18] [spkg-install]   995 |                 return r = r ^ (a & static_cast<bool>(x));

[linbox-1.7.0+sage-2024-05-18] [spkg-install]       |                                ~^~~~~~~~~~~~~~~~~~~~~~~~~

[linbox-1.7.0+sage-2024-05-18] [spkg-install]       |                                   &&

[linbox-1.7.0+sage-2024-05-18] [spkg-install] ../../linbox/field/gf2.h:995:33: note: cast one or both operands to int to silence this warning

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from diophantine-solver.C:26:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/diophantine-solver.h:29:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/rational-solver.h:41:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/solutions/methods.h:26:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/matrix/dense-matrix.h:85:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/matrix/densematrix/blas-matrix.h:50:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/matrix/densematrix/blas-submatrix.h:36:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from /Users/dcoudert/sage/local/include/fflas-ffpack/fflas-ffpack.h:35:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from /Users/dcoudert/sage/local/include/fflas-ffpack/ffpack/ffpack.h:1983:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] /Users/dcoudert/sage/local/include/fflas-ffpack/ffpack/ffpack_charpoly.inl:193:20: warning: variable 'nbfac' set but not used [-Wunused-but-set-variable]

[linbox-1.7.0+sage-2024-05-18] [spkg-install]   193 |             size_t nbfac = 0;

[linbox-1.7.0+sage-2024-05-18] [spkg-install]       |                    ^

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from diophantine-solver.C:26:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/diophantine-solver.h:29:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/rational-solver.h:41:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/solutions/methods.h:26:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/matrix/dense-matrix.h:85:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/matrix/densematrix/blas-matrix.h:50:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/matrix/densematrix/blas-submatrix.h:36:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from /Users/dcoudert/sage/local/include/fflas-ffpack/fflas-ffpack.h:35:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from /Users/dcoudert/sage/local/include/fflas-ffpack/ffpack/ffpack.h:1987:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] /Users/dcoudert/sage/local/include/fflas-ffpack/ffpack/ffpack_permutation.inl:60:16: warning: variable 'nonpivrowstomove' set but not used [-Wunused-but-set-variable]

[linbox-1.7.0+sage-2024-05-18] [spkg-install]    60 |         size_t nonpivrowstomove = 0;

[linbox-1.7.0+sage-2024-05-18] [spkg-install]       |                ^

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from diophantine-solver.C:26:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/diophantine-solver.h:29:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/rational-solver.h:44:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/blackbox/lambda-sparse.h:29:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/matrix/sparse-matrix.h:82:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/matrix/sparsematrix/sparse-map-map-matrix.h:207:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] ../../linbox/matrix/sparsematrix/sparse-map-map-matrix.inl:414:6: warning: variable 'count' set but not used [-Wunused-but-set-variable]

[linbox-1.7.0+sage-2024-05-18] [spkg-install]   414 |         int count=0;

[linbox-1.7.0+sage-2024-05-18] [spkg-install]       |             ^

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from diophantine-solver.C:26:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/diophantine-solver.h:29:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/rational-solver.h:583:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/./dixon-solver/dixon-solver-dense.h:363:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/./dixon-solver/./dixon-solver-dense.inl:26:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/lifting-container.h:45:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/block-massey-domain.h:42:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/polynomial-matrix/order-basis.h:41:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/polynomial-matrix/polynomial-matrix-domain.h:34:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] ../../linbox/algorithms/polynomial-matrix/matpoly-mult-fft.h:330:16: warning: variable 'nbp' set but not used [-Wunused-but-set-variable]

[linbox-1.7.0+sage-2024-05-18] [spkg-install]   330 |         size_t nbp=0;

[linbox-1.7.0+sage-2024-05-18] [spkg-install]       |                ^

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from diophantine-solver.C:26:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/diophantine-solver.h:29:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/rational-solver.h:583:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/./dixon-solver/dixon-solver-dense.h:363:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/./dixon-solver/./dixon-solver-dense.inl:26:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/lifting-container.h:45:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/block-massey-domain.h:42:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/polynomial-matrix/order-basis.h:41:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/polynomial-matrix/polynomial-matrix-domain.h:34:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/polynomial-matrix/matpoly-mult-fft.h:373:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] ../../linbox/algorithms/polynomial-matrix/matpoly-mult-fft-wordsize.inl:61:20: warning: variable 'lpts' set but not used [-Wunused-but-set-variable]

[linbox-1.7.0+sage-2024-05-18] [spkg-install]    61 |             size_t lpts = 0;

[linbox-1.7.0+sage-2024-05-18] [spkg-install]       |                    ^

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from diophantine-solver.C:26:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/diophantine-solver.h:29:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/rational-solver.h:583:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/./dixon-solver/dixon-solver-dense.h:363:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] In file included from ../../linbox/algorithms/./dixon-solver/./dixon-solver-dense.inl:28:

[linbox-1.7.0+sage-2024-05-18] [spkg-install] ../../linbox/algorithms/rational-reconstruction.h:339:8: warning: variable 'counter' set but not used [-Wunused-but-set-variable]

[linbox-1.7.0+sage-2024-05-18] [spkg-install]   339 |                         int counter=0;

[linbox-1.7.0+sage-2024-05-18] [spkg-install]       |                             ^

[linbox-1.7.0+sage-2024-05-18] [spkg-install] ../../linbox/algorithms/rational-reconstruction.h:924:29: warning: variable 'counter' set but not used [-Wunused-but-set-variable]

[linbox-1.7.0+sage-2024-05-18] [spkg-install]   924 |                         int counter=0;

[linbox-1.7.0+sage-2024-05-18] [spkg-install]       |                             ^

[linbox-1.7.0+sage-2024-05-18] [spkg-install] 10 warnings and 1 error generated.

[linbox-1.7.0+sage-2024-05-18] [spkg-install] make[9]: *** [diophantine-solver.lo] Error 1

[linbox-1.7.0+sage-2024-05-18] [spkg-install] make[8]: *** [all-recursive] Error 1

[linbox-1.7.0+sage-2024-05-18] [spkg-install] make[7]: *** [all-recursive] Error 1

[linbox-1.7.0+sage-2024-05-18] [spkg-install] make[6]: *** [all-recursive] Error 1

[linbox-1.7.0+sage-2024-05-18] [spkg-install] make[5]: *** [all] Error 2

[linbox-1.7.0+sage-2024-05-18] [spkg-install] ********************************************************************************

[linbox-1.7.0+sage-2024-05-18] [spkg-install] Error building linbox-1.7.0+sage-2024-05-18

[linbox-1.7.0+sage-2024-05-18] [spkg-install] ********************************************************************************

[linbox-1.7.0+sage-2024-05-18] ************************************************************************

[linbox-1.7.0+sage-2024-05-18] Error installing package linbox-1.7.0+sage-2024-05-18






David Coudert

unread,
May 1, 2025, 12:06:53 PMMay 1
to sage-r...@googlegroups.com
Using https://github.com/sagemath/sage/pull/40033 and --with-system-flint=no  fix the issue with flint and singular.

Using in addition https://github.com/sagemath/sage/pull/39985, I can also compile linbox.

But now it’s failing to compile ipykernel.


[ipykernel-6.27.1] Using cached file /Users/dcoudert/sage/upstream/ipykernel-6.27.1.tar.gz

[ipykernel-6.27.1] Setting up build directory /Users/dcoudert/sage/local/var/lib/sage/venv-python3.12/var/tmp/sage/build/ipykernel-6.27.1

[ipykernel-6.27.1] No patch files found in ../patches

[ipykernel-6.27.1] Host system: Darwin MAC-04017247 24.4.0 Darwin Kernel Version 24.4.0: Fri Apr 11 18:33:47 PDT 2025; root:xnu-11417.101.15~117/RELEASE_ARM64_T6000 arm64

[ipykernel-6.27.1] C compiler: gcc, Apple clang version 17.0.0 (clang-1700.0.13.3), Target: arm64-apple-darwin24.4.0, Thread model: posix, InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

[ipykernel-6.27.1] No stamp file for package 'ipykernel' in /Users/dcoudert/sage/local/var/lib/sage/venv-python3.12/var/lib/sage/installed

[ipykernel-6.27.1] No spkg-legacy-uninstall script; nothing to do

[ipykernel-6.27.1] [spkg-install] Installing ipykernel-6.27.1

[ipykernel-6.27.1] [spkg-install] * Creating isolated environment: venv+pip...

[ipykernel-6.27.1] [spkg-install] * Installing packages in isolated environment:

[ipykernel-6.27.1] [spkg-install]   - hatchling>=1.4

[ipykernel-6.27.1] [spkg-install]   - jupyter_client>=6

[ipykernel-6.27.1] [spkg-install] > /Users/dcoudert/sage/local/var/lib/sage/venv-python3.12/bin/python3 -m pip

[ipykernel-6.27.1] [spkg-install]   --python /private/var/folders/hw/w6ldqpgn52vdvv03cgbkkr3h3lhtdp/T/build-

[ipykernel-6.27.1] [spkg-install]   env-6_cu53wi/bin/python install --use-pep517 --no-warn-script-location --no-

[ipykernel-6.27.1] [spkg-install]   compile -r /var/folders/hw/w6ldqpgn52vdvv03cgbkkr3h3lhtdp/T/build-

[ipykernel-6.27.1] [spkg-install]   reqs-9x5l7vuh.txt

[ipykernel-6.27.1] [spkg-install] < Looking in links: /Users/dcoudert/sage/local/var/lib/sage/venv-

[ipykernel-6.27.1] [spkg-install]   python3.12/var/lib/sage/wheels

[ipykernel-6.27.1] [spkg-install] < Processing /Users/dcoudert/sage/local/var/lib/sage/venv-

[ipykernel-6.27.1] [spkg-install]   python3.12/var/lib/sage/wheels/jupyter_client-8.3.1-py3-none-any.whl (from

[ipykernel-6.27.1] [spkg-install]   -r /var/folders/hw/w6ldqpgn52vdvv03cgbkkr3h3lhtdp/T/build-reqs-9x5l7vuh.txt

[ipykernel-6.27.1] [spkg-install]   (line 1))

[ipykernel-6.27.1] [spkg-install] < Processing /Users/dcoudert/sage/local/var/lib/sage/venv-

[ipykernel-6.27.1] [spkg-install]   python3.12/var/lib/sage/wheels/hatchling-1.25.0-py3-none-any.whl (from -r

[ipykernel-6.27.1] [spkg-install]   /var/folders/hw/w6ldqpgn52vdvv03cgbkkr3h3lhtdp/T/build-reqs-9x5l7vuh.txt

[ipykernel-6.27.1] [spkg-install]   (line 2))

[ipykernel-6.27.1] [spkg-install] < INFO: pip is looking at multiple versions of jupyter-client to determine

[ipykernel-6.27.1] [spkg-install]   which version is compatible with other requirements. This could take a

[ipykernel-6.27.1] [spkg-install]   while.

[ipykernel-6.27.1] [spkg-install] < ERROR: Could not find a version that satisfies the requirement jupyter-

[ipykernel-6.27.1] [spkg-install]   core!=5.0.*,>=4.12 (from jupyter-client) (from versions: none)

[ipykernel-6.27.1] [spkg-install] < ERROR: No matching distribution found for jupyter-core!=5.0.*,>=4.12

[ipykernel-6.27.1] [spkg-install] 

[ipykernel-6.27.1] [spkg-install] Traceback (most recent call last):

[ipykernel-6.27.1] [spkg-install]   File "/Users/dcoudert/sage/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/build/__main__.py", line 178, in _handle_build_error

[ipykernel-6.27.1] [spkg-install]     yield

[ipykernel-6.27.1] [spkg-install]   File "/Users/dcoudert/sage/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/build/__main__.py", line 429, in main

[ipykernel-6.27.1] [spkg-install]     built = build_call(

[ipykernel-6.27.1] [spkg-install]             ^^^^^^^^^^^

[ipykernel-6.27.1] [spkg-install]   File "/Users/dcoudert/sage/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/build/__main__.py", line 238, in build_package

[ipykernel-6.27.1] [spkg-install]     out = _build(isolation, srcdir, outdir, distribution, config_settings, skip_dependency_check, installer)

[ipykernel-6.27.1] [spkg-install]           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

[ipykernel-6.27.1] [spkg-install]   File "/Users/dcoudert/sage/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/build/__main__.py", line 170, in _build

[ipykernel-6.27.1] [spkg-install]     return _build_in_isolated_env(srcdir, outdir, distribution, config_settings, installer)

[ipykernel-6.27.1] [spkg-install]            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

[ipykernel-6.27.1] [spkg-install]   File "/Users/dcoudert/sage/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/build/__main__.py", line 135, in _build_in_isolated_env

[ipykernel-6.27.1] [spkg-install]     env.install(builder.build_system_requires)

[ipykernel-6.27.1] [spkg-install]   File "/Users/dcoudert/sage/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/build/env.py", line 136, in install

[ipykernel-6.27.1] [spkg-install]     self._env_backend.install_requirements(requirements)

[ipykernel-6.27.1] [spkg-install]   File "/Users/dcoudert/sage/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/build/env.py", line 265, in install_requirements

[ipykernel-6.27.1] [spkg-install]     run_subprocess(cmd)

[ipykernel-6.27.1] [spkg-install]   File "/Users/dcoudert/sage/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/build/_ctx.py", line 71, in run_subprocess

[ipykernel-6.27.1] [spkg-install]     subprocess.run(cmd, capture_output=True, check=True, env=env)

[ipykernel-6.27.1] [spkg-install]   File "/opt/homebrew/Cellar/pyt...@3.12/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/subprocess.py", line 571, in run

[ipykernel-6.27.1] [spkg-install]     raise CalledProcessError(retcode, process.args,

[ipykernel-6.27.1] [spkg-install] subprocess.CalledProcessError: Command '['/Users/dcoudert/sage/local/var/lib/sage/venv-python3.12/bin/python3', '-m', 'pip', '--python', '/private/var/folders/hw/w6ldqpgn52vdvv03cgbkkr3h3lhtdp/T/build-env-6_cu53wi/bin/python', 'install', '--use-pep517', '--no-warn-script-location', '--no-compile', '-r', '/var/folders/hw/w6ldqpgn52vdvv03cgbkkr3h3lhtdp/T/build-reqs-9x5l7vuh.txt']' returned non-zero exit status 1.

[ipykernel-6.27.1] [spkg-install] 

[ipykernel-6.27.1] [spkg-install] ERROR Command '['/Users/dcoudert/sage/local/var/lib/sage/venv-python3.12/bin/python3', '-m', 'pip', '--python', '/private/var/folders/hw/w6ldqpgn52vdvv03cgbkkr3h3lhtdp/T/build-env-6_cu53wi/bin/python', 'install', '--use-pep517', '--no-warn-script-location', '--no-compile', '-r', '/var/folders/hw/w6ldqpgn52vdvv03cgbkkr3h3lhtdp/T/build-reqs-9x5l7vuh.txt']' returned non-zero exit status 1.

[ipykernel-6.27.1] [spkg-install] Warning: building with "python3 -m build --wheel --outdir=dist   ." failed.

[ipykernel-6.27.1] [spkg-install] Retrying with "python3 -m build --wheel --outdir=dist --no-isolation --skip-dependency-check  .".

[ipykernel-6.27.1] [spkg-install] * Building wheel...

[ipykernel-6.27.1] [spkg-install] Traceback (most recent call last):

[ipykernel-6.27.1] [spkg-install]   File "/Users/dcoudert/sage/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/pyproject_hooks/_in_process/_in_process.py", line 373, in <module>

[ipykernel-6.27.1] [spkg-install]     main()

[ipykernel-6.27.1] [spkg-install]   File "/Users/dcoudert/sage/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/pyproject_hooks/_in_process/_in_process.py", line 357, in main

[ipykernel-6.27.1] [spkg-install]     json_out["return_val"] = hook(**hook_input["kwargs"])

[ipykernel-6.27.1] [spkg-install]                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

[ipykernel-6.27.1] [spkg-install]   File "/Users/dcoudert/sage/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/pyproject_hooks/_in_process/_in_process.py", line 271, in build_wheel

[ipykernel-6.27.1] [spkg-install]     return _build_backend().build_wheel(

[ipykernel-6.27.1] [spkg-install]            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

[ipykernel-6.27.1] [spkg-install]   File "/Users/dcoudert/sage/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/hatchling/build.py", line 58, in build_wheel

[ipykernel-6.27.1] [spkg-install]     return os.path.basename(next(builder.build(directory=wheel_directory, versions=['standard'])))

[ipykernel-6.27.1] [spkg-install]                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

[ipykernel-6.27.1] [spkg-install]   File "/Users/dcoudert/sage/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/hatchling/builders/plugin/interface.py", line 147, in build

[ipykernel-6.27.1] [spkg-install]     build_hook.initialize(version, build_data)

[ipykernel-6.27.1] [spkg-install]   File "/Users/dcoudert/sage/local/var/lib/sage/venv-python3.12/var/tmp/sage/build/ipykernel-6.27.1/src/hatch_build.py", line 17, in initialize

[ipykernel-6.27.1] [spkg-install]     from ipykernel.kernelspec import make_ipkernel_cmd, write_kernel_spec

[ipykernel-6.27.1] [spkg-install]   File "/Users/dcoudert/sage/local/var/lib/sage/venv-python3.12/var/tmp/sage/build/ipykernel-6.27.1/src/ipykernel/__init__.py", line 7, in <module>

[ipykernel-6.27.1] [spkg-install]     from .connect import *

[ipykernel-6.27.1] [spkg-install]   File "/Users/dcoudert/sage/local/var/lib/sage/venv-python3.12/var/tmp/sage/build/ipykernel-6.27.1/src/ipykernel/connect.py", line 12, in <module>

[ipykernel-6.27.1] [spkg-install]     import jupyter_client

[ipykernel-6.27.1] [spkg-install]   File "/Users/dcoudert/sage/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/jupyter_client/__init__.py", line 3, in <module>

[ipykernel-6.27.1] [spkg-install]     from .asynchronous import AsyncKernelClient

[ipykernel-6.27.1] [spkg-install]   File "/Users/dcoudert/sage/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/jupyter_client/asynchronous/__init__.py", line 1, in <module>

[ipykernel-6.27.1] [spkg-install]     from .client import AsyncKernelClient  # noqa

[ipykernel-6.27.1] [spkg-install]     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

[ipykernel-6.27.1] [spkg-install]   File "/Users/dcoudert/sage/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/jupyter_client/asynchronous/client.py", line 8, in <module>

[ipykernel-6.27.1] [spkg-install]     from ..channels import AsyncZMQSocketChannel, HBChannel

[ipykernel-6.27.1] [spkg-install]   File "/Users/dcoudert/sage/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/jupyter_client/channels.py", line 12, in <module>

[ipykernel-6.27.1] [spkg-install]     from jupyter_core.utils import ensure_async

[ipykernel-6.27.1] [spkg-install] ModuleNotFoundError: No module named 'jupyter_core'

[ipykernel-6.27.1] [spkg-install] 

[ipykernel-6.27.1] [spkg-install] ERROR Backend subprocess exited when trying to invoke build_wheel

[ipykernel-6.27.1] [spkg-install] ********************************************************************************

[ipykernel-6.27.1] [spkg-install] Error building a wheel for ipykernel-6.27.1

[ipykernel-6.27.1] [spkg-install] ********************************************************************************

[ipykernel-6.27.1] ************************************************************************

[ipykernel-6.27.1] Error installing package ipykernel-6.27.1

[ipykernel-6.27.1] ************************************************************************

[ipykernel-6.27.1] Please email sage-devel (http://groups.google.com/group/sage-devel)

[ipykernel-6.27.1] explaining the problem and including the log files

[ipykernel-6.27.1]   /Users/dcoudert/sage/logs/pkgs/ipykernel-6.27.1.log

[ipykernel-6.27.1] and

[ipykernel-6.27.1]   /Users/dcoudert/sage/config.log

[ipykernel-6.27.1] Describe your computer, operating system, etc.

[ipykernel-6.27.1] If you want to try to fix the problem yourself, *don't* just cd to

[ipykernel-6.27.1] /Users/dcoudert/sage/local/var/lib/sage/venv-python3.12/var/tmp/sage/build/ipykernel-6.27.1 and type 'make' or whatever is appropriate.

[ipykernel-6.27.1] Instead, the following commands setup all environment variables

[ipykernel-6.27.1] correctly and load a subshell for you to debug the error:

[ipykernel-6.27.1]   (cd '/Users/dcoudert/sage/local/var/lib/sage/venv-python3.12/var/tmp/sage/build/ipykernel-6.27.1' && '/Users/dcoudert/sage/sage' --buildsh)

[ipykernel-6.27.1] When you are done debugging, you can type "exit" to leave the subshell.

[ipykernel-6.27.1] ************************************************************************

[ipykernel-6.27.1] real 0m19.726s user 0m0.914s sys 0m0.488s

make[4]: *** [ipykernel-SAGE_VENV-no-deps] Error 1

make[3]: *** [/Users/dcoudert/sage/local/var/lib/sage/venv-python3.12/var/lib/sage/installed/ipykernel-6.27.1] Error 2

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

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

Dima Pasechnik

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May 1, 2025, 12:49:19 PMMay 1
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here, "ModuleNotFoundError: No module named 'jupyter_core'" seems to indicate that the error was earlier.

By the way, please review https://github.com/sagemath/sage/pull/39985 

David Coudert

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May 1, 2025, 1:25:17 PMMay 1
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Le 1 mai 2025 à 18:49, Dima Pasechnik <dim...@gmail.com> a écrit :

here, "ModuleNotFoundError: No module named 'jupyter_core'" seems to indicate that the error was earlier.

In config.log, it is written

real_configure:70441: will use system package and not install SPKG jupyter_core


Note that there is no homebrew recipe in  build/pkgs/jupyter_core/distros/ 

I will try adding —with-system-jupyter_core=no


By the way, please review https://github.com/sagemath/sage/pull/39985 

Done.


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Dima Pasechnik

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May 1, 2025, 2:38:52 PMMay 1
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On Thu, May 1, 2025 at 12:25 PM David Coudert <david....@gmail.com> wrote:


Le 1 mai 2025 à 18:49, Dima Pasechnik <dim...@gmail.com> a écrit :

here, "ModuleNotFoundError: No module named 'jupyter_core'" seems to indicate that the error was earlier.

In config.log, it is written

real_configure:70441: will use system package and not install SPKG jupyter_core


our  jupyter_core and ipykernel are much older than upstream.

I am not going to work on updating Sage's jupyter/ipython/notebook/sphinx, because it's much easier to just pip install these,
and it's a lot of makework.
All this stuff should be just purged from sage-distro, as I argued for years.

If anyone wants to pick up the torch, welcome.

Yes, —with-system-jupyter_core=no hopefully works.


David Coudert

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May 2, 2025, 3:29:14 AMMay 2
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and
./configure --enable-system-site-packages --with-system-flint=no --with-system-jupyter_core=no
Its finally working ! 
Thank you Dima.

John H Palmieri

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May 8, 2025, 2:31:21 PMMay 8
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On OS X 15.4.1, latest Xcode, lots of homebrew packages: I cannot build gap. (This has been true for a while, not new to this beta release.) The tail end of the log file:

[spkg-install] /usr/bin/install -c -d -m 0755 /Users/jpalmier/Sage/TESTING/sage-10.7.beta2/local/var/tmp/sage/build/gap-4.14.0/inst/Users/jpalmier/Sage/TESTING/sage-10.7.beta2/local/lib
[spkg-install] /usr/bin/install -c -m 0644 libgap.9.dylib /Users/jpalmier/Sage/TESTING/sage-10.7.beta2/local/var/tmp/sage/build/gap-4.14.0/inst/Users/jpalmier/Sage/TESTING/sage-10.7.beta2/local/lib
[spkg-install] ln -sf libgap.9.dylib /Users/jpalmier/Sage/TESTING/sage-10.7.beta2/local/var/tmp/sage/build/gap-4.14.0/inst/Users/jpalmier/Sage/TESTING/sage-10.7.beta2/local/lib/libgap.dylib
[spkg-install] /usr/bin/install -c -d -m 0755 /Users/jpalmier/Sage/TESTING/sage-10.7.beta2/local/var/tmp/sage/build/gap-4.14.0/inst/Users/jpalmier/Sage/TESTING/sage-10.7.beta2/local/lib/pkgconfig
[spkg-install] /usr/bin/install -c -m 0644 libgap.pc /Users/jpalmier/Sage/TESTING/sage-10.7.beta2/local/var/tmp/sage/build/gap-4.14.0/inst/Users/jpalmier/Sage/TESTING/sage-10.7.beta2/local/lib/pkgconfig
[spkg-install] gcc         -pthread -lpthread -L/Users/jpalmier/Sage/TESTING/sage-10.7.beta2/local/lib -L/Users/jpalmier/Sage/TESTING/sage-10.7.beta2/local/lib  build/obj/build/main.c.o  -lgmp -lz -lreadline     -L/Users/jpalmier/Sage/TESTING/sage-10.7.beta2/local/var/tmp/sage/build/gap-4.14.0/src -lgap -o build/gap-install
[spkg-install] error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: changing install names or rpaths can't be redone for: build/gap-install (for architecture arm64) because larger updated load commands do not fit (the program must be relinked, and you may need to use -headerpad or -headerpad_max_install_names)
[spkg-install] make[5]: *** [build/gap-install] Error 1

Suggestions?

(By the way, I interact with Google groups using my browser, not via email. How do I attach files? There used to be a button for this, but I don't see it any more.)

Dima Pasechnik

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May 8, 2025, 2:47:59 PMMay 8
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Hi John,
please post the complete logs/pkgs/gap...log. From what you posted it's not even clear what gcc stands for here.
Dima

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John H Palmieri

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May 8, 2025, 5:11:04 PMMay 8
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As I said before, I don't know how to attach files here. Here are links to the files:

John H Palmieri

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May 10, 2025, 1:04:05 PMMay 10
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Same problem on another similarly configured machine.

Dima Pasechnik

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May 10, 2025, 8:07:38 PMMay 10
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perhaps it's a proper GAP problem?

can you build GAP standalone?


To view this discussion visit https://groups.google.com/d/msgid/sage-release/72b30850-1e88-4871-a64e-e3d7bf7668c0n%40googlegroups.com.

John H Palmieri

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May 12, 2025, 12:31:59 PMMay 12
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On Saturday, May 10, 2025 at 5:07:38 PM UTC-7 Dima Pasechnik wrote:

perhaps it's a proper GAP problem?

can you build GAP standalone?


It looks like it. If I unpack the tarball that Sage downloaded, and I type `./configure; make`, then I get a functional `gap` executable.

John H Palmieri

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May 12, 2025, 12:32:31 PMMay 12
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On Monday, May 12, 2025 at 9:31:59 AM UTC-7 John H Palmieri wrote:
On Saturday, May 10, 2025 at 5:07:38 PM UTC-7 Dima Pasechnik wrote:

perhaps it's a proper GAP problem?

can you build GAP standalone?


It looks like it. If I unpack the tarball that Sage downloaded, and I type `./configure; make`, then I get a functional `gap` executable.

(The gap tarball, that is.)

John H Palmieri

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May 13, 2025, 5:36:49 PMMay 13
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This is a very awkward workaround: 

$ ./configure
$ make gap # THIS FAILS
$ ./sage --buildsh
% cd SAGE_ROOT/local/var/tmp/sage/build/gap-4.14.0/src
% make install
% exit # (to exit the buildsh shell)
$ make gap # THIS NOW SUCCEEDS

Somehow the presence of the file local/lib/libgap.9.dylib (and libgap.dylib, a symlink pointing to it) lets the build complete, I have no idea why.

Dima Pasechnik

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May 13, 2025, 8:13:59 PMMay 13
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Hi John,
Can you try adding `-Wl,-headerpad_max_install_names` (or, perhaps, `-Wl,-headerpad`) to LDFLAGS for GAP?
Dima


To view this discussion visit https://groups.google.com/d/msgid/sage-release/b0f285e8-ed03-4d5c-bf21-a7f77db9b002n%40googlegroups.com.

John H Palmieri

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May 14, 2025, 12:39:51 PMMay 14
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Thanks, Dima, adding `-Wl,-headerpad_max_install_names` works. (Adding `-Wl,-headerpad` did not, by the way.)

Dima Pasechnik

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May 14, 2025, 4:44:44 PMMay 14
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This ought to be reported upstream - I don't think it's something specific in Sage we do that causes this issue. Rather, it's a deficiency in GAP's "make install", which is not very well tested, as it doesn't have too many "consumers".

At least make it a Sage issue, on which we can CC GAP people.

Dima 

John H Palmieri

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May 14, 2025, 7:35:06 PMMay 14
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