configure: Accept gcc/gfortran 10.x

[mkoeppe]

As all build errors of standard packages with gcc/gfortran 10 have been fixed, we change the gcc and gfortran configure scripts to again accept these versions.

This ticket does not change the version of the gcc spkg.

Previous tickets:

• gf2x: #29390 gf2x build fails on fedora-32-minimal
• SciPy: Upgrade to SciPy 1.2.3 (last release supporting py2 - #29443) does not fix it
• #29766: Upgrade NumPy?, scipy, networkx, add pybind11 package (dup: #29425)
• sympow: see #3360
• palp: #29859
• gcc: #29674: fedora-32: Building gcc (9.2.0) spkg fails with gcc 10
• #30067 gfortran spkg-configure: Reject versions >= 10

Related discussions:

• ​https://groups.google.com/d/msg/sage-devel/JFZ6a5KGEJk/8DCWFD8dAwAJ
• ​https://groups.google.com/d/msg/sage-release/7-z1I5bUB4w/-K5Weg0IAwAJ

[fbissey]

Any more details on palp?

[fbissey]

Also, if we are targeting 9.2 we can move to higher scipy.

[mkoeppe]

Replying to fbissey:

Any more details on palp?

For example here: ​https://github.com/mkoeppe/sage/runs/618646432?check_suite_focus=true

[mkoeppe]

Replying to fbissey:

Also, if we are targeting 9.2 we can move to higher scipy.

As far as I can see there is no release yet with the fix

[mkoeppe]

Question is whether we want to fix this for 9.1 already.

[mkoeppe]

Presumably Fedora 32 has patched packages.

[dimpase]

Replying to mkoeppe:

Replying to fbissey:

Any more details on palp?

For example here: ​https://github.com/mkoeppe/sage/runs/618646432?check_suite_focus=true

2020-04-26T04:55:26.7728042Z   [palp-2.1.p2]   MoriCone.c: In function 'Triang2dSFan':
2020-04-26T04:55:26.7728579Z   [palp-2.1.p2]   MoriCone.c:489:48: warning: 'Z[0]' may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-04-26T04:55:26.7729093Z   [palp-2.1.p2]     489 | #define BZangle(a,b) (ConeAngle(B.x[Z[a]],B.x[Z[b]])) // Gale-points
2020-04-26T04:55:26.7729654Z   [palp-2.1.p2]         |                                                ^
2020-04-26T04:55:26.7730199Z   [palp-2.1.p2]   gcc -O3 -W -Wall  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE   -c -o SingularInput.o SingularInput.c
2020-04-26T04:55:26.7730774Z   [palp-2.1.p2]   gcc -O3 -W -Wall  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o poly.x poly.o Coord.o Rat.o Vertex.o Polynf.o LG.o
2020-04-26T04:55:26.7731343Z   [palp-2.1.p2]   gcc -O3 -W -Wall  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o class.x class.o Coord.o Rat.o Vertex.o Polynf.o Subpoly.o Subadd.o Subdb.o
2020-04-26T04:55:26.7731892Z   [palp-2.1.p2]   gcc -O3 -W -Wall  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o cws.x cws.o Coord.o Rat.o Vertex.o Polynf.o LG.o
2020-04-26T04:55:26.7732465Z   [palp-2.1.p2]   gcc -O3 -W -Wall  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o nef.x nef.o Coord.o Rat.o Vertex.o Polynf.o E_Poly.o Nefpart.o LG.o
2020-04-26T04:55:26.7733264Z   [palp-2.1.p2]   gcc -O3 -W -Wall  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o mori.x mori.o Coord.o Rat.o Vertex.o Polynf.o MoriCone.o SingularInput.o LG.o
2020-04-26T04:55:26.7733900Z   [palp-2.1.p2]   /usr/bin/ld: MoriCone.o:(.bss+0x0): multiple definition of `nr_SR_elements'; mori.o:(.bss+0x10): first defined here
2020-04-26T04:55:26.7734659Z   [palp-2.1.p2]   /usr/bin/ld: SingularInput.o:(.bss+0x0): multiple definition of `nr_SR_elements'; mori.o:(.bss+0x10): first defined here
2020-04-26T04:55:26.7735158Z   [palp-2.1.p2]   /usr/bin/ld: SingularInput.o: in function `HyperSurfSingular':
2020-04-26T04:55:26.7735673Z   [palp-2.1.p2]   SingularInput.c:(.text+0x1e1): warning: the use of `tmpnam' is dangerous, better use `mkstemp'
2020-04-26T04:55:26.7736112Z   [palp-2.1.p2]   collect2: error: ld returned 1 exit status
2020-04-26T04:55:26.7736565Z   [palp-2.1.p2]   make[4]: *** [Makefile:50: mori] Error 1
2020-04-26T04:55:26.7737028Z   [palp-2.1.p2]   make[4]: Target 'all' not remade because of errors.
2020-04-26T04:55:26.7737532Z   [palp-2.1.p2]   make[4]: Leaving directory '/sage/local/var/tmp/sage/build/palp-2.1.p2/src'
2020-04-26T04:55:26.7738036Z   [palp-2.1.p2]   ********************************************************************************
2020-04-26T04:55:26.7738482Z   [palp-2.1.p2]   Error building palp-2.1.p2

• before the logs exprire...

[enriqueartal]

Besides the packages cited in the description (cannot say about gf2x) gap_packages does not build, due to cohomolo package.

[gh-timokau]

Palp 2.11 mentions gcc 10 compatibility:

palp-2.11.tar.gz: Small change in Mori.h for compatibility with gcc_10 and other minor patches (thanks to J. Puydt) [May 18, 2020].

-- ​http://hep.itp.tuwien.ac.at/~kreuzer/CY/CYpalp.html

[gh-timokau]

Unfortunately I'm not sure if the upstream source tarball for palp 2.11 is finalized though. Since I've packaged it 3 days ago (​https://github.com/NixOS/nixpkgs/pull/87944) the tarball silently changed.

[fbissey]

Replying to gh-timokau:

Unfortunately I'm not sure if the upstream source tarball for palp 2.11 is finalized though. Since I've packaged it 3 days ago (​https://github.com/NixOS/nixpkgs/pull/87944) the tarball silently changed.

I just adopted the patch already shipped in fedora until a new release.

• sympow is fixed by upgrading to the new fork.
• scipy can be fixed by adding some fortran flags until they fix the code, -std=legacy I think. I otherwise built sage-on-gentoo successfully with gcc-10 but I am not sure I have scanned absolutely all the packages.

[gh-timokau]

For what it's worth, upstream confirmed that palp 2.11 is stable and no further changes are expected.

[mkoeppe]

I have opened #29859 for palp

[dimpase]

Homebrew is pushing to use gcc10, their current gcc+gfortran is gcc10, and their current openblas, scipy are all gcc10-dependent.

[mkoeppe]

Last 10 new commits:

​e592bdc	Merge branch 't/29425/trac/local_conda_forge_macos_standard__build_error_with_numpy' into t/29766/packages/networkx24
​11bf67f	Merge branch 't/29813/add_pytest_as_a_type_optional__source_pip_package' into t/29766/packages/networkx24
​db0fa41	build/pkgs/scipy: Add patch for scipy pr 11320
​2efe841	Merge tag '9.2.beta3' into t/29766/packages/networkx24
​634ce73	build/pkgs: Update numpy to 1.19, scipy to 1.5.1
​a2e1978	build/pkgs/scipy/patches/pr-11320.patch: Remove
​0879c3b	build/pkgs/{numpy,scipy}/checksums.ini: Set upstream_url to pypi.io
​8a70ebe	right place for warnings.filterwarnings() for networkx & scipy
​e9dc48d	Merge branch 'u/dimpase/packages/networkx24' of git://trac.sagemath.org/sage into t/29456/meta_ticket__support_gcc_10__needed_for_fedora_32_build__released_end_of_april_2020_
​5f3b27c	build/pkgs/gcc/spkg-configure.m4: Do not reject gcc (gnu) >= 10

[mkoeppe]

Tests run at ​https://github.com/mkoeppe/sage/actions/runs/164860999

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​bfb2fb4	tox.ini: Add environment local-homebrew-usrlocal
​aded967	Merge commit '8195cb821e01e0cb627240d7135d5634c265cab0' of git://trac.sagemath.org/sage into t/29929/tox_ini__add_a_macos_environment_without_homebrew__conda
​07d657d	Merge tag '9.2.beta4' into t/29929/tox_ini__add_a_macos_environment_without_homebrew__conda
​bd15fb9	build/bin/write-dockerfile.sh, tox.ini: Do not run testsuites that need pip (ssl)
​87db1a5	Merge branch 't/29929/tox_ini__add_a_macos_environment_without_homebrew__conda' into t/29456/meta_ticket__support_gcc_10__needed_for_fedora_32_build__released_end_of_april_2020_

[mkoeppe]

Again testing with CI fixes from #29929 at ​https://github.com/mkoeppe/sage/actions/runs/165937251

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​25393b0	Handle SAGE_CHECK_PACKAGES in build/make/Makefile.in, not sage-spkg
​5aca238	Merge branch 't/30118/handle_sage_check_packages_in_build_make_makefile_in__not_sage_spkg' into t/29929/tox_ini__add_a_macos_environment_without_homebrew__conda
​7feee5c	Merge branch 't/29929/tox_ini__add_a_macos_environment_without_homebrew__conda' into t/29456/meta_ticket__support_gcc_10__needed_for_fedora_32_build__released_end_of_april_2020_

[mkoeppe]

New tests (using #30118) at ​https://github.com/mkoeppe/sage/actions/runs/166179877

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​b25b74a	Merge tag '9.2.beta5' into t/29456/meta_ticket__support_gcc_10__needed_for_fedora_32_build__released_end_of_april_2020_
​0356be9	Merge branch 't/29929/tox_ini__add_a_macos_environment_without_homebrew__conda' into t/29766/packages/networkx24
​abb8c7e	Merge branch 't/29766/packages/networkx24' into t/29456/meta_ticket__support_gcc_10__needed_for_fedora_32_build__released_end_of_april_2020_
​6954deb	build/pkgs/networkx/dependencies: Conditionalize on SAGE_CHECK_networkx
​e5bf863	Merge branch 't/29766/packages/networkx24' into t/29456/meta_ticket__support_gcc_10__needed_for_fedora_32_build__released_end_of_april_2020_

[mkoeppe]

Test with updated #29766 at ​https://github.com/mkoeppe/sage/actions/runs/167913617

[enriqueartal]

Tested successfully, up to the download of numpy and scipy.

[mkoeppe]

Tests running at ​https://github.com/mkoeppe/sage/actions/runs/168165380

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​d39817f	build/pkgs/numpy: Downgrade to 1.18.5 to fix build error on debian-jessie
​879375b	Merge branch 't/29766/packages/networkx24' into t/29456/meta_ticket__support_gcc_10__needed_for_fedora_32_build__released_end_of_april_2020_
​a17c655	m4/sage_spkg_collect.m4: Do not include script packages in SAGE_SDIST_PACKAGES
​827923a	bootstrap: Accept 2020s in config.guess version check
​c30ac54	tox.ini: Add local-nobootstrap
​de6464d	.github/workflows/tox.yml: Add jobs "dist", "local-macos-nohomebrew
​775b7f7	Trac #30088: add a few explanatory comments to m4/sage_spkg_collect.m4.
​160862f	m4/sage_spkg_collect.m4: Mention sagelib in the comment
​d1a2cbf	Merge branch 't/30088/fix__make_sdist___add_test_run_to_github_actions' into t/29929/tox_ini__add_a_macos_environment_without_homebrew__conda
​7cf9a5c	Merge branch 't/29929/tox_ini__add_a_macos_environment_without_homebrew__conda' into t/29456/meta_ticket__support_gcc_10__needed_for_fedora_32_build__released_end_of_april_2020_

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​fcddf69	Revert "build/pkgs/numpy: Downgrade to 1.18.5 to fix build error on debian-jessie"
​3558737	build/pkgs/numpy/patches/16871.patch: New
​4e6d8a3	Merge branch 't/29766/packages/networkx24' into t/29456/meta_ticket__support_gcc_10__needed_for_fedora_32_build__released_end_of_april_2020_

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​ba0ccb6	Experimental: Use numpy PR 16871
​c24d109	build/pkgs/cython: Updatt to 0.29.21
​79bf297	Merge branch 't/29861/upgrade_cython_to_0_29_20' into t/29456/meta_ticket__support_gcc_10__needed_for_fedora_32_build__released_end_of_april_2020_
​2035df2	Fixup: Experimental: Use numpy PR 16871

[git]

Branch pushed to git repo; I updated commit sha1. This was a forced push. Last 10 new commits:

​56fe1c2	Merge branch 't/3360/sympow-2.23.2' into t/29456/meta_ticket__support_gcc_10__needed_for_fedora_32_build__released_end_of_april_2020_
​1bf6249	Update numpy to 1.19.1, add patches
​061e975	Merge branch 'u/mkoeppe/upgrade_cython_to_0_29_20' of git://trac.sagemath.org/sage into t/29766/packages/networkx24
​fc7592c	Merge branch 't/29929/tox_ini__add_a_macos_environment_without_homebrew__conda' into t/29766/packages/networkx24
​7fe5985	right place for warnings.filterwarnings() for networkx & scipy
​5fa0bba	build/pkgs/scipy: Update to 1.5.2
​3890e1a	build/make/Makefile.in: Improve handling of SAGE_CHECK_PACKAGES
​5d4b013	build/make/Makefile.in: Handle the case in which SAGE_CHECK_PACKAGES is set using a command argument
​fb9806a	Merge branch 't/29766/packages/networkx24' into t/29456/meta_ticket__support_gcc_10__needed_for_fedora_32_build__released_end_of_april_2020_
​95e8a22	build/pkgs/{gcc,gfortran}/spkg-configure.m4: Accept gcc 10.x

[mkoeppe]

Re-enabled gcc 10. Tests run at ​https://github.com/mkoeppe/sage/actions/runs/199625493

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​c898920

build/pkgs/gcc/spkg-configure.m4: Fixup

[enriqueartal]

I have just built it successfully. It failed the installation of gap_packages because of package cohomolo but it also fails to compile in gap itself.

[mkoeppe]

Thanks for testing!

If there's no ticket for gap_packages yet, could you open one please?

[dimpase]

Replying to mkoeppe:

Thanks for testing!

If there's no ticket for gap_packages yet, could you open one please?

I just opened ​https://github.com/gap-packages/cohomolo/issues/24 (verified that it's a problem with gcc-10 on Gentoo)

[mkoeppe]

Thanks.

[charpent]

Replying to vbraun:

FWIW, worked for me for the upgrade to 9.2.beta9...

[dimpase]

this seems not to be in beta9, right? should it be in beta10?