Success!
pulled latest version, upgraded brew and command-line tools.
also (maybe all of the above wasn't necessary) I read the instructions
in #40397 and ran
"export
PKG_CONFIG_PATH=`pwd`/build/platform/macos/pkgconfig:$PKG_CONFIG_PATH"
which I didn't do the first time.
Thanks again, Dima, et al.,
Aaron
On Saturday, August 2, 2025 at 12:42:56 AM UTC-5 dim...@gmail.com wrote:
> 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.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
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