I've rebased <https://github.com/sagemath/sage/pull/40397> over the latest beta, maybe it helps. If no, and if upgrading xcode followed by upgrading homebrew didn't work, I would have tried to build scipy separately, just to see if it works. Perhaps upgrading scipy might help (either to 1.15.3, or to the latest, 1.16.1)
On August 1, 2025 1:21:41 PM PDT, Aaron Lauve <la...@math.luc.edu> wrote: >Dima, >I think the answer to your question is "essentially, yes"... > >lauve@edinburgh pkgs % brew doctor > >*Please note that these warnings are just used to help the Homebrew >maintainers* > >*with debugging if you file an issue. If everything you use Homebrew for is* > >*working fine: please don't worry or file an issue; just ignore this. >Thanks!* > > >Warning: Some installed kegs have no formulae! > >This means they were either deleted or installed manually. > >You should find replacements for the following formulae: > > arb > > >Warning: Some installed formulae are deprecated or disabled. > >You should find replacements for the following formulae: > > icu4c@76 > > six > >lauve@edinburgh pkgs % brew info gcc > >==> *gcc*: stable 15.1.0, HEAD > >GNU compiler collection > >https://gcc.gnu.org/ > >Installed > >/opt/homebrew/Cellar/gcc/15.1.0 (1,957 files, 492.3MB) * > > Poured from bottle using the formulae.brew.sh API on 2025-06-24 at >09:16:18 > >From: https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/g/gcc.rb > >License: GPL-3.0-or-later WITH GCC-exception-3.1 > >==> *Dependencies* > >Build: *make **✘* > >Required: *gmp **✔*, *isl **✔*, *libmpc **✔*, *mpfr **✔*, *zstd **✔* > >==> *Options* > >--HEAD > >Install HEAD version > >==> *Analytics* > >install: 81,926 (30 days), 289,275 (90 days), 1,317,053 (365 days) > >install-on-request: 45,610 (30 days), 163,188 (90 days), 680,062 (365 days) > >build-error: 3,245 (30 days) > >lauve@edinburgh pkgs % which gfortran > >/opt/homebrew/bin/gfortran > > > > >On Friday, August 1, 2025 at 3:08:38 PM UTC-5 dim...@gmail.com wrote: > >> It's rather obscure, to me at least, bug. >> Your gfortran is rejected by the scipy build script. Does "brew doctor" >> report that everything is OK with your Homebrew install? >> >> >> >> On August 1, 2025 11:58:50 AM PDT, Aaron Lauve <la...@math.luc.edu> wrote: >> >>> Thanks, Dima, >>> >>> requested config log attached. >>> I cannot find the meson log file in the location requested: >>> >>> lauve@edinburgh src % pwd >>> >>> >>> /Applications/sage/local/var/lib/sage/venv-python3.13/var/tmp/sage/build/scipy-1.15.2/src >>> >>> >>> lauve@edinburgh src % ls -al >>> >>> total 288 >>> >>> drwxr-xr-x 22 lauve admin 704 Jul 31 09:21 . >>> >>> drwxr-xr-x 24 lauve admin 768 Aug 1 13:41 .. >>> >>> drwxr-xr-x 4 lauve admin 128 Jul 31 09:21 .devcontainer >>> >>> drwxr-xr-x 6 lauve admin 192 Jul 31 09:21 benchmarks >>> >>> -rw-r--r-- 1 lauve admin 1277 Jul 31 09:21 CITATION.bib >>> >>> -rw-r--r-- 1 lauve admin 1112 Jul 31 09:21 CONTRIBUTING.rst >>> >>> -rw-r--r-- 1 lauve admin 59699 Jul 31 09:21 dev.py >>> >>> drwxr-xr-x 2 lauve admin 64 Jul 31 09:21 dist >>> >>> drwxr-xr-x 6 lauve admin 192 Jul 31 09:21 doc >>> >>> -rw-r--r-- 1 lauve admin 1536 Jul 31 09:21 LICENSE.txt >>> >>> -rw-r--r-- 1 lauve admin 12881 Jul 31 09:21 LICENSES_bundled.txt >>> >>> -rw-r--r-- 1 lauve admin 6168 Jul 31 09:21 meson.build >>> >>> -rw-r--r-- 1 lauve admin 759 Jul 31 09:21 meson.options >>> >>> -rw-r--r-- 1 lauve admin 13973 Jul 31 09:21 mypy.ini >>> >>> -rw-r--r-- 1 lauve admin 8511 Jul 31 09:21 PKG-INFO >>> >>> -rw-r--r-- 1 lauve admin 6263 Jul 31 09:21 pyproject.toml >>> >>> -rw-r--r-- 1 lauve admin 1270 Jul 31 09:21 pytest.ini >>> >>> -rw-r--r-- 1 lauve admin 3576 Jul 31 09:21 README.rst >>> >>> drwxr-xr-x 9 lauve admin 288 Jul 31 09:21 requirements >>> >>> drwxr-xr-x 30 lauve admin 960 Jul 31 09:21 scipy >>> >>> drwxr-xr-x 3 lauve admin 96 Jul 31 09:21 subprojects >>> >>> drwxr-xr-x 24 lauve admin 768 Jul 31 09:21 tools >>> >>> >>> I'm attaching *some* meson log file, found in the usual sage/logs/pkgs/ >>> directory >>> >>> >>> On Friday, August 1, 2025 at 12:58:53 PM UTC-5 dim...@gmail.com wrote: >>> >>>> from your log: >>>> >>>> ./meson.build:80:0: ERROR: Compiler gfortran cannot compile programs. >>>> [scipy-1.15.2] [spkg-install] >>>> [scipy-1.15.2] [spkg-install] A full log can be found at >>>> /Applications/sage/local/var/lib/sage/venv-python3.13/var/tmp/sage/build/scipy-1.15.2/src/.mesonpy-7kk9_dof/meson-logs/meson-log.txt >>>> >>>> Can you post the latter file, and the top level >>>> config.log ? >>>> >>>> >>>> On July 31, 2025 7:57:24 AM PDT, Aaron Lauve <la...@math.luc.edu> wrote: >>>> >>>>> https://github.com/sagemath/sage/pull/40397 >>>>> >>>>> (abbreviated) error logs attached. >>>>> >>>>> >>>>> >>>>> On Thursday, July 10, 2025 at 12:56:42 PM UTC-5 dim...@gmail.com wrote: >>>>> >>>>> On Thu, Jul 10, 2025 at 12:05 PM Lauve, Aaron <ala...@luc.edu> wrote: >>>>> > >>>>> > Thanks, Dima. >>>>> > >>>>> > >>>>> > >>>>> > “Yes” to using gfortran provided by homebrew (at least I presume) >>>>> > >>>>> > Here’s what brew has to say about that: >>>>> > >>>>> > >>>>> > >>>>> > lauve@edinburgh sage % brew info gfortran >>>>> > >>>>> > ==> gcc: stable 15.1.0, HEAD >>>>> > >>>>> > GNU compiler collection >>>>> > >>>>> > https://gcc.gnu.org/ >>>>> > >>>>> > Installed >>>>> > >>>>> > /opt/homebrew/Cellar/gcc/15.1.0 (1,957 files, 492.3MB) * >>>>> > >>>>> > Poured from bottle using the formulae.brew.sh API on 2025-06-24 at >>>>> 09:16:18 >>>>> > >>>>> > From: >>>>> https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/g/gcc.rb >>>>> > >>>>> > License: GPL-3.0-or-later WITH GCC-exception-3.1 >>>>> > >>>>> > ==> Dependencies >>>>> > >>>>> > Build: make ✘ >>>>> > >>>>> > Required: gmp ✔, isl ✔, libmpc ✔, mpfr ✔, zstd ✔ >>>>> > >>>>> > ==> Options >>>>> > >>>>> > --HEAD >>>>> > >>>>> > Install HEAD version >>>>> > >>>>> > >>>>> > >>>>> > I notice that ‘gcc’ mentioned above is 15.1.0 while the relevant line >>>>> in the config file is 14.2.0. >>>>> 14.2.0 is Sage's version of gfortran, but there are lines >>>>> >>>>> real_configure:11002: checking for gfortran >>>>> real_configure:11023: found /opt/homebrew/bin/gfortran >>>>> real_configure:11035: result: gfortran >>>>> real_configure:11061: checking for Fortran compiler version >>>>> real_configure:11070: gfortran --version >&5 >>>>> GNU Fortran (Homebrew GCC 15.1.0) 15.1.0 >>>>> [...] >>>>> real_configure:18788: will use system package and not install SPKG >>>>> gfortran >>>>> >>>>> which really say what it is, and what's going to be used. >>>>> >>>>> > >>>>> > Attaching the toplevel config.log file. >>>>> >>>>> right, I knew about this, I mentioned to Homebrew people that it's a >>>>> bug: >>>>> https://github.com/Homebrew/homebrew-core/issues/209091 >>>>> but they decided not to do anything about it. >>>>> >>>>> The problem is that `openblas.pc` supplied by them does not work with >>>>> Apple's "gcc", i.e. clang. >>>>> It only works with "real" gcc, which we'd rather avoid using in order >>>>> not to create even more mess than what's our >>>>> current build system already is. >>>>> A quick an dirty fix is to replace their `openblas.pc` with the >>>>> corrected one, where openmp is not mentioned >>>>> at all - in the same vein as done in >>>>> https://github.com/sagemath/sage/pull/40397 >>>>> (I'll post such a file somewhere) >>>>> >>>>> As OpenBLAS people were more keen to listen at >>>>> https://github.com/Homebrew/homebrew-core/issues/209091 they >>>>> https://github.com/OpenMathLib/OpenBLAS/pull/5180 >>>>> and so it won't be hard to create a custom Homebrew tap with the >>>>> alternative, working with clang, configuration. >>>>> Although I think Accelerate is not the better path to go forward. >>>>> >>>>> >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > Also, maybe “yes” to being an Apple Accelerate Guinea pig. Let’s see >>>>> what transpires… >>>>> >>>>> Thanks! I've just made a draft PR from the branch I mentioned >>>>> https://github.com/sagemath/sage/pull/40397 >>>>> >>>>> Would most appreciate feedback from you and any other volunteers. >>>>> >>>>> Cheers, >>>>> Dima >>>>> >>>>> >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > -- >>>>> > >>>>> > Aaron Lauve (he/him/his) >>>>> > >>>>> > Drop in for a visit >>>>> > >>>>> > 773.508.3727 | BVM 501 | ala...@luc.edu >>>>> > >>>>> > ~~~~~~~~~~ >>>>> > >>>>> > Associate Professor and Graduate Program Director for Mathematics >>>>> > >>>>> > Department of Mathematics & Statistics >>>>> > >>>>> > Loyola University Chicago >>>>> > >>>>> > >>>>> > >>>>> > From: Dima Pasechnik <dim...@gmail.com> >>>>> > Date: Thursday, July 10, 2025 at 11:54 AM >>>>> > To: sage-...@googlegroups.com <sage-...@googlegroups.com>, Lauve, >>>>> Aaron <ala...@luc.edu> >>>>> > Subject: Re: [sage-devel] Re: openblas fail on build from source >>>>> > >>>>> > [You don't often get email from dim...@gmail.com. Learn why this is >>>>> important at https://aka.ms/LearnAboutSenderIdentification ] >>>>> > >>>>> > Hi Aaron, >>>>> > thanks for the report. >>>>> > The email interface to google groups allows bigger attachments, by >>>>> the way. >>>>> > (you can also email these logs directly to me) >>>>> > >>>>> > There could be several reasons for all this, but first of all, it's >>>>> > good to understand why the Homebrew's openblas is not accepted. >>>>> > Can you send us the top-level config.log ? >>>>> > >>>>> > As far as building from source is concerned, I assume you use >>>>> gfortran >>>>> > from Homebrew, right? >>>>> > It could be that 1.3.28 is too old for your OS/hardware, and we need >>>>> > to bump our package version. >>>>> > >>>>> > Last but not the least, I'm at the moment working on allowing the >>>>> user >>>>> > to rather use the Apple Accelerate framework instead of openblas, see >>>>> > >>>>> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fdimpase%2Fsage%2Ftree%2Faccel_wip&data=05%7C02%7Calauve%40luc.edu%7C66bdbab0def2439a0b0b08ddbfd27cfa%7C021f4fe32b9c48248378bbcf9ec5accb%7C0%7C0%7C638877632994015794%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=hfdKe%2FfqH%2BrfN%2Fbi7gZXn1xaFoZm%2FcshCLKopIqAegQ%3D&reserved=0 >>>>> >>>>> > If you're interested in testing the latter, I can provide more >>>>> instructions. >>>>> > >>>>> > Best >>>>> > Dima >>>>> > >>>>> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpasechnik.info%2Fdima%2F&data=05%7C02%7Calauve%40luc.edu%7C66bdbab0def2439a0b0b08ddbfd27cfa%7C021f4fe32b9c48248378bbcf9ec5accb%7C0%7C0%7C638877632994054935%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=ppL6jxXxs2%2F2Ppv5K95jvyzWJxiSZ9UdjWAPHC%2BnC04%3D&reserved=0 >>>>> >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > On Thu, Jul 10, 2025 at 11:16 AM Aaron Lauve <la...@math.luc.edu> >>>>> wrote: >>>>> > > >>>>> > > oops. forgot to attach the log. and then GoogleGroups complained it >>>>> was too long. >>>>> > > I'm attaching 'head -n1000' and 'tail -n1000' instead of the full >>>>> log. Hope that's helpful. >>>>> > > >>>>> > > -- >>>>> > > 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+...@googlegroups.com. >>>>> > > To view this discussion visit >>>>> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgroups.google.com%2Fd%2Fmsgid%2Fsage-devel%2Ff5c7a22b-2dee-425d-bd0b-e540cffbce5fn%2540googlegroups.com&data=05%7C02%7Calauve%40luc.edu%7C66bdbab0def2439a0b0b08ddbfd27cfa%7C021f4fe32b9c48248378bbcf9ec5accb%7C0%7C0%7C638877632994081750%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=Iwm2GGTj%2FyADuVPv8aPns0uF5bnTXdHMF6kttW1lpok%3D&reserved=0. >>>>> >>>>> >>>>> >>>>> > >-- >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 visit >https://groups.google.com/d/msgid/sage-devel/dddf2add-333d-476d-a823-fd97b3addc39n%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 visit https://groups.google.com/d/msgid/sage-devel/6AFA443E-3239-4441-A371-0AE58F10A315%40gmail.com.
