Re: [sage-devel] attempting Sage build on M1
On Tue, Jun 1, 2021 at 7:15 PM kcrisman wrote: > > >> apparently _imaging.cpython-39-darwin.so does not link to the right >> libraries. >> What's the output of >> >> otool -L >> /Users/karl.crisman/Downloads/BrewSage/sage-9.4.beta0/local/lib/python3.9/site-packages/PIL/_imaging.cpython-39-darwin.so > > > /Users/karl.crisman/Downloads/BrewSage/sage-9.4.beta0/local/lib/python3.9/site-packages/PIL/_imaging.cpython-39-darwin.so: > /opt/homebrew/opt/zlib/lib/libz.1.dylib (compatibility version 1.0.0, current > version 1.2.11) > /opt/homebrew/opt/libtiff/lib/libtiff.5.dylib (compatibility version 13.0.0, > current version 13.0.0) > /opt/homebrew/opt/libxcb/lib/libxcb.1.dylib (compatibility version 3.0.0, > current version 3.0.0) > /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version > 1292.100.5) OK, so it doesn't link to a JPEG library for some reason - but needs a symbol from there. On an inter macOS I see /usr/local/opt/openjpeg/lib/libopenjp2.7.dylib among the libraries Please post logs/pkgs/pillow-8.1.2.log > > >> >> >> >> >> >> > However, I did see some of this type as well in the sage/numerical tests: >> > >> > ImportError: >> > dlopen(/Users/karl.crisman/Downloads/BrewSage/sage-9.4.beta0/local/lib/python3.9/site-packages/cvxopt/cholmod.cpython-39-darwin.so, >> > 2): Symbol not found: _cholmod_l_allocate_dense >> > Referenced from: >> > /Users/karl.crisman/Downloads/BrewSage/sage-9.4.beta0/local/lib/python3.9/site-packages/cvxopt/cholmod.cpython-39-darwin.so >> > Expected in: flat namespace >> > in >> > /Users/karl.crisman/Downloads/BrewSage/sage-9.4.beta0/local/lib/python3.9/site-packages/cvxopt/cholmod.cpython-39-darwin.so >> >> same as for PIL, the output >> >> otool -L >> /Users/karl.crisman/Downloads/BrewSage/sage-9.4.beta0/local/lib/python3.9/site-packages/cvxopt/cholmod.cpython-39-darwin.so >> >> > > /Users/karl.crisman/Downloads/BrewSage/sage-9.4.beta0/local/lib/python3.9/site-packages/cvxopt/cholmod.cpython-39-darwin.so: > /opt/homebrew/opt/openblas/lib/libopenblas.0.dylib (compatibility version > 0.0.0, current version 0.0.0) > /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version > 1292.100.5) > so it does not link any suitesparse libraries, a bug. Pldease post logs/pkgs/cvxopt-1.2.6.log > -- > You received this message because you are subscribed to the Google Groups > "sage-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-devel+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/8b014e63-24c1-45f5-8b71-b9570eb12758n%40googlegroups.com. -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/CAAWYfq3zv0f-EOO%2BpeFOqPsR8iR-tuD5JiZ5CXEvwCz_W7W9hg%40mail.gmail.com.
Re: [sage-devel] attempting Sage build on M1
> apparently _imaging.cpython-39-darwin.so does not link to the right > libraries. > What's the output of > > otool -L > /Users/karl.crisman/Downloads/BrewSage/sage-9.4.beta0/local/lib/python3.9/site-packages/PIL/_ > imaging.cpython-39-darwin.so > /Users/karl.crisman/Downloads/BrewSage/sage-9.4.beta0/local/lib/python3.9/site-packages/PIL/_imaging.cpython-39-darwin.so: /opt/homebrew/opt/zlib/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /opt/homebrew/opt/libtiff/lib/libtiff.5.dylib (compatibility version 13.0.0, current version 13.0.0) /opt/homebrew/opt/libxcb/lib/libxcb.1.dylib (compatibility version 3.0.0, current version 3.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) > > > > > > However, I did see some of this type as well in the sage/numerical > tests: > > > > ImportError: > dlopen(/Users/karl.crisman/Downloads/BrewSage/sage-9.4.beta0/local/lib/python3.9/site-packages/cvxopt/ > cholmod.cpython-39-darwin.so, 2): Symbol not found: > _cholmod_l_allocate_dense > > Referenced from: > /Users/karl.crisman/Downloads/BrewSage/sage-9.4.beta0/local/lib/python3.9/site-packages/cvxopt/ > cholmod.cpython-39-darwin.so > > Expected in: flat namespace > > in > /Users/karl.crisman/Downloads/BrewSage/sage-9.4.beta0/local/lib/python3.9/site-packages/cvxopt/ > cholmod.cpython-39-darwin.so > > same as for PIL, the output > > otool -L > /Users/karl.crisman/Downloads/BrewSage/sage-9.4.beta0/local/lib/python3.9/site-packages/cvxopt/ > cholmod.cpython-39-darwin.so > > > /Users/karl.crisman/Downloads/BrewSage/sage-9.4.beta0/local/lib/python3.9/site-packages/cvxopt/cholmod.cpython-39-darwin.so: /opt/homebrew/opt/openblas/lib/libopenblas.0.dylib (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/8b014e63-24c1-45f5-8b71-b9570eb12758n%40googlegroups.com.
Re: [sage-devel] attempting Sage build on M1
On Tue, Jun 1, 2021 at 4:23 PM Dima Pasechnik wrote:
>
> On Mon, May 31, 2021 at 9:24 PM kcrisman wrote:
> >
> > Not as bad as you might think on the test failures. make ptest gives the
> > following - many or even most of which seem to be plotting errors exactly
> > like this one (and even "plot(x)" does not work from the CLI, same error):
> >
> > ImportError:
> > dlopen(/Users/karl.crisman/Downloads/BrewSage/sage-9.4.beta0/local/lib/python3.9/site-packages/PIL/_imaging.cpython-39-darwin.so,
> > 2): Symbol not found: _opj_create_compress
> > Referenced from:
> > /Users/karl.crisman/Downloads/BrewSage/sage-9.4.beta0/local/lib/python3.9/site-packages/PIL/_imaging.cpython-39-darwin.so
> > Expected in: flat namespace
> >
> apparently _imaging.cpython-39-darwin.so does not link to the right libraries.
> What's the output of
>
> otool -L
> /Users/karl.crisman/Downloads/BrewSage/sage-9.4.beta0/local/lib/python3.9/site-packages/PIL/_imaging.cpython-39-darwin.so
>
> ?
>
> PIL comes from pillow package, which has its own build system...
>
>
>
>
>
> > However, I did see some of this type as well in the sage/numerical tests:
> >
> > ImportError:
> > dlopen(/Users/karl.crisman/Downloads/BrewSage/sage-9.4.beta0/local/lib/python3.9/site-packages/cvxopt/cholmod.cpython-39-darwin.so,
> > 2): Symbol not found: _cholmod_l_allocate_dense
> > Referenced from:
> > /Users/karl.crisman/Downloads/BrewSage/sage-9.4.beta0/local/lib/python3.9/site-packages/cvxopt/cholmod.cpython-39-darwin.so
> > Expected in: flat namespace
> > in
> > /Users/karl.crisman/Downloads/BrewSage/sage-9.4.beta0/local/lib/python3.9/site-packages/cvxopt/cholmod.cpython-39-darwin.so
>
> same as for PIL, the output
>
> otool -L
> /Users/karl.crisman/Downloads/BrewSage/sage-9.4.beta0/local/lib/python3.9/site-packages/cvxopt/cholmod.cpython-39-darwin.so
>
> please. (As well, cvxopt does its own config...)
see, in https://github.com/cvxopt/cvxopt/blob/master/setup.py there is
if sys.platform.startswith("darwin"):
# macOS
SUITESPARSE_LIB_DIR = '/usr/local/lib'
SUITESPARSE_INC_DIR = '/usr/local/include'
# Guess SUITESPARSE_LIB_DIR and SUITESPARSE_INC_DIR
which is wrong for M1 Homebrew...
>
>
> >
> > I didn't see any others in a first read through, though it's a very long
> > log file of course (attached). Thanks for any thoughts - honestly, this is
> > a lot closer to being ready to roll than I had dared anticipate.
> >
> > --
> >
> > sage -t --random-seed=0 src/sage/plot/plot3d/base.pyx # Timed out
> >
> > sage -t --random-seed=0 src/sage/symbolic/expression.pyx # 7 doctests
> > failed
> >
> > sage -t --random-seed=0
> > src/sage/tests/books/computational-mathematics-with-sagemath/integration_doctest.py
> > # 1 doctest failed
> >
> > sage -t --random-seed=0 src/sage/plot/plot3d/plot3d.py # Timed out
> >
> > sage -t --random-seed=0 src/sage/plot/plot3d/shapes2.py # Timed out
> >
> > sage -t --random-seed=0 src/sage/plot/plot3d/parametric_plot3d.py # Timed
> > out
> >
> > sage -t --random-seed=0 src/sage/plot/plot3d/implicit_plot3d.py # Timed out
> >
> > sage -t --random-seed=0 src/sage/plot/plot3d/platonic.py # 1 doctest failed
> >
> > sage -t --random-seed=0 src/sage/geometry/polyhedron/base.py # 6 doctests
> > failed
> >
> > sage -t --random-seed=0 src/sage/plot/plot3d/list_plot3d.py # 14 doctests
> > failed
> >
> > sage -t --random-seed=0
> > src/doc/en/thematic_tutorials/vector_calculus/vector_calc_cartesian.rst #
> > 1 doctest failed
> >
> > sage -t --random-seed=0
> > src/doc/en/thematic_tutorials/vector_calculus/vector_calc_change.rst # 1
> > doctest failed
> >
> > sage -t --random-seed=0
> > src/sage/schemes/elliptic_curves/ell_rational_field.py # 1 doctest failed
> >
> > sage -t --random-seed=0
> > src/sage/manifolds/differentiable/integrated_curve.py # 4 doctests failed
> >
> > sage -t --random-seed=0 src/sage/plot/graphics.py # 76 doctests failed
> >
> > sage -t --random-seed=0
> > src/sage/combinat/root_system/root_lattice_realizations.py # 7 doctests
> > failed
> >
> > sage -t --random-seed=0 src/sage/combinat/root_system/plot.py # 9 doctests
> > failed
> >
> > sage -t --random-seed=0 src/sage/plot/plot3d/parametric_surface.pyx # 3
> > doctests failed
> >
> > sage -t --random-seed=0 src/sage/calculus/functional.py # 1 doctest failed
> >
> > sage -t --random-seed=0 src/sage/geometry/hyperplane_arrangement/plot.py #
> > 4 doctests failed
> >
> > sage -t --random-seed=0 src/sage/plot/plot.py # 61 doctests failed
> >
> > sage -t --random-seed=0 src/sage/manifolds/differentiable/vectorfield.py #
> > 1 doctest failed
> >
> > sage -t --random-seed=0
> > src/doc/en/thematic_tutorials/vector_calculus/vector_calc_plane.rst # 1
> > doctest failed
> >
> > sage -t --random-seed=0 src/sage/schemes/curves/projective_curve.py # 1
> > doctest failed
> >
> > sage -t --random-seed=0
Re: [sage-devel] attempting Sage build on M1
On Mon, May 31, 2021 at 9:24 PM kcrisman wrote: > > Not as bad as you might think on the test failures. make ptest gives the > following - many or even most of which seem to be plotting errors exactly > like this one (and even "plot(x)" does not work from the CLI, same error): > > ImportError: > dlopen(/Users/karl.crisman/Downloads/BrewSage/sage-9.4.beta0/local/lib/python3.9/site-packages/PIL/_imaging.cpython-39-darwin.so, > 2): Symbol not found: _opj_create_compress > Referenced from: > /Users/karl.crisman/Downloads/BrewSage/sage-9.4.beta0/local/lib/python3.9/site-packages/PIL/_imaging.cpython-39-darwin.so > Expected in: flat namespace > apparently _imaging.cpython-39-darwin.so does not link to the right libraries. What's the output of otool -L /Users/karl.crisman/Downloads/BrewSage/sage-9.4.beta0/local/lib/python3.9/site-packages/PIL/_imaging.cpython-39-darwin.so ? PIL comes from pillow package, which has its own build system... > However, I did see some of this type as well in the sage/numerical tests: > > ImportError: > dlopen(/Users/karl.crisman/Downloads/BrewSage/sage-9.4.beta0/local/lib/python3.9/site-packages/cvxopt/cholmod.cpython-39-darwin.so, > 2): Symbol not found: _cholmod_l_allocate_dense > Referenced from: > /Users/karl.crisman/Downloads/BrewSage/sage-9.4.beta0/local/lib/python3.9/site-packages/cvxopt/cholmod.cpython-39-darwin.so > Expected in: flat namespace > in > /Users/karl.crisman/Downloads/BrewSage/sage-9.4.beta0/local/lib/python3.9/site-packages/cvxopt/cholmod.cpython-39-darwin.so same as for PIL, the output otool -L /Users/karl.crisman/Downloads/BrewSage/sage-9.4.beta0/local/lib/python3.9/site-packages/cvxopt/cholmod.cpython-39-darwin.so please. (As well, cvxopt does its own config...) > > I didn't see any others in a first read through, though it's a very long log > file of course (attached). Thanks for any thoughts - honestly, this is a lot > closer to being ready to roll than I had dared anticipate. > > -- > > sage -t --random-seed=0 src/sage/plot/plot3d/base.pyx # Timed out > > sage -t --random-seed=0 src/sage/symbolic/expression.pyx # 7 doctests failed > > sage -t --random-seed=0 > src/sage/tests/books/computational-mathematics-with-sagemath/integration_doctest.py > # 1 doctest failed > > sage -t --random-seed=0 src/sage/plot/plot3d/plot3d.py # Timed out > > sage -t --random-seed=0 src/sage/plot/plot3d/shapes2.py # Timed out > > sage -t --random-seed=0 src/sage/plot/plot3d/parametric_plot3d.py # Timed out > > sage -t --random-seed=0 src/sage/plot/plot3d/implicit_plot3d.py # Timed out > > sage -t --random-seed=0 src/sage/plot/plot3d/platonic.py # 1 doctest failed > > sage -t --random-seed=0 src/sage/geometry/polyhedron/base.py # 6 doctests > failed > > sage -t --random-seed=0 src/sage/plot/plot3d/list_plot3d.py # 14 doctests > failed > > sage -t --random-seed=0 > src/doc/en/thematic_tutorials/vector_calculus/vector_calc_cartesian.rst # 1 > doctest failed > > sage -t --random-seed=0 > src/doc/en/thematic_tutorials/vector_calculus/vector_calc_change.rst # 1 > doctest failed > > sage -t --random-seed=0 > src/sage/schemes/elliptic_curves/ell_rational_field.py # 1 doctest failed > > sage -t --random-seed=0 src/sage/manifolds/differentiable/integrated_curve.py > # 4 doctests failed > > sage -t --random-seed=0 src/sage/plot/graphics.py # 76 doctests failed > > sage -t --random-seed=0 > src/sage/combinat/root_system/root_lattice_realizations.py # 7 doctests > failed > > sage -t --random-seed=0 src/sage/combinat/root_system/plot.py # 9 doctests > failed > > sage -t --random-seed=0 src/sage/plot/plot3d/parametric_surface.pyx # 3 > doctests failed > > sage -t --random-seed=0 src/sage/calculus/functional.py # 1 doctest failed > > sage -t --random-seed=0 src/sage/geometry/hyperplane_arrangement/plot.py # 4 > doctests failed > > sage -t --random-seed=0 src/sage/plot/plot.py # 61 doctests failed > > sage -t --random-seed=0 src/sage/manifolds/differentiable/vectorfield.py # 1 > doctest failed > > sage -t --random-seed=0 > src/doc/en/thematic_tutorials/vector_calculus/vector_calc_plane.rst # 1 > doctest failed > > sage -t --random-seed=0 src/sage/schemes/curves/projective_curve.py # 1 > doctest failed > > sage -t --random-seed=0 src/sage/plot/contour_plot.py # 3 doctests failed > > sage -t --random-seed=0 src/sage/schemes/riemann_surfaces/riemann_surface.py > # 1 doctest failed > > sage -t --random-seed=0 src/sage/misc/sagedoc.py # 4 doctests failed > > sage -t --random-seed=0 src/sage/schemes/curves/affine_curve.py # 1 doctest > failed > > sage -t --random-seed=0 src/sage/schemes/elliptic_curves/heegner.py # 1 > doctest failed > > sage -t --random-seed=0 src/sage/manifolds/chart.py # 2 doctests failed > > sage -t --random-seed=0 src/sage/geometry/polyhedron/plot.py # 2 doctests > failed > > sage -t
