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.
On Wed, Apr 30, 2025 at 1:35 PM David Coudert <[email protected]> wrote: > 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 > > > > > > Le 30 avr. 2025 à 17:53, Dima Pasechnik <[email protected]> a écrit : > > 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 > > > > > > > > On Wed, Apr 30, 2025 at 10:47 AM David Coudert <[email protected]> > wrote: > >> 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. >> >> Le 30 avr. 2025 à 16:38, David Coudert <[email protected]> a écrit >> : >> >> 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. >> >> >> Le 30 avr. 2025 à 00:56, Volker Braun <[email protected]> a écrit : >> >> As always, you can get the latest beta version from the "develop" git >> branch. Alternatively, the self-contained source tarball is at >> http://www.sagemath.org/download-latest.html >> >> >> 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 >> >> -- >> You received this message because you are subscribed to the Google Groups >> "sage-release" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> To view this discussion visit >> https://groups.google.com/d/msgid/sage-release/6bab54a4-23a4-41e0-abb9-5ccd903afe79n%40googlegroups.com >> <https://groups.google.com/d/msgid/sage-release/6bab54a4-23a4-41e0-abb9-5ccd903afe79n%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> >> >> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "sage-release" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> To view this discussion visit >> https://groups.google.com/d/msgid/sage-release/5763CF9F-C9DE-42FA-897B-A45B69BB801B%40gmail.com >> <https://groups.google.com/d/msgid/sage-release/5763CF9F-C9DE-42FA-897B-A45B69BB801B%40gmail.com?utm_medium=email&utm_source=footer> >> . >> > > -- > You received this message because you are subscribed to the Google 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