It's from homebrew's gcc. I did `brew reinstall gcc` followed by `make distclean && ./configure && make meson_python && make` and it still fails at scipy, same error. I removed the cached download file for homebrew's gcc and tried again, same result. I have not yet tried Sage's gcc.
On Thursday, September 21, 2023 at 11:18:15 PM UTC-7 Dima Pasechnik wrote: > Where is gfortran coming from here? > Do you build it with Sage, or use an external one? > > If the external one, e.g. from Homebrew, you most probably need to > update/reinstall. > Ditto in Sage > > > On Fri, 22 Sept 2023, 00:52 John H Palmieri, <jhpalm...@gmail.com> wrote: > >> A new problem, after upgrading to OS X 13.6 and the newest version of the >> command-line tools: scipy fails to build again, this time with the error: >> >> ../../meson.build:82:0: ERROR: Unable to detect linker for compiler >> `gfortran -Wl,--version >> -L/Users/palmieri/Desktop/Sage/TESTING/sage-10.2.beta3/local/lib >> -Wl,-rpath,/Users/palmieri/Desktop/Sage/TESTING/sage-10.2.beta3/local/lib >> -L/Users/palmieri/Desktop/Sage/TESTING/sage-10.2.beta3/local/lib >> -Wl,-rpath,/Users/palmieri/Desktop/Sage/TESTING/sage-10.2.beta3/local/lib` >> stdout: >> stderr: collect2 version 13.2.0 >> /usr/bin/ld -syslibroot >> /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/ -dynamic -arch arm64 >> -platform_version macos 13.0.0 0.0 -o a.out >> -L/Users/palmieri/Desktop/Sage/TESTING/sage-10.2.beta3/local/lib >> -L/Users/palmieri/Desktop/Sage/TESTING/sage-10.2.beta3/local/lib >> -L/opt/homebrew/Cellar/gcc/13.2.0/bin/../lib/gcc/current/gcc/aarch64-apple-darwin22/13 >> >> -L/opt/homebrew/Cellar/gcc/13.2.0/bin/../lib/gcc/current/gcc >> -L/Users/palmieri/Desktop/Sage/TESTING/sage-10.2.beta3/local/lib >> -L/Users/palmieri/Desktop/Sage/TESTING/sage-10.2.beta3/local/lib >> -L/opt/homebrew/opt/primesieve/lib -L/opt/homebrew/opt/bdw-gc/lib >> -L/opt/homebrew/opt/libpng/lib -L/opt/homebrew/opt/ntl/lib >> -L/opt/homebrew/opt/bzip2/lib -L/opt/homebrew/opt/readline/lib >> -L/opt/homebrew/lib >> -L/opt/homebrew/Cellar/gcc/13.2.0/bin/../lib/gcc/current/gcc/aarch64-apple-darwin22/13/../../.. >> >> --version -rpath >> /Users/palmieri/Desktop/Sage/TESTING/sage-10.2.beta3/local/lib -rpath >> /Users/palmieri/Desktop/Sage/TESTING/sage-10.2.beta3/local/lib -lemutls_w >> -lgcc -lSystem -lgcc -no_compact_unwind -rpath @loader_path -rpath >> /opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc/aarch64-apple-darwin22/13 >> >> -rpath /opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc -rpath >> /Users/palmieri/Desktop/Sage/TESTING/sage-10.2.beta3/local/lib -rpath >> /Users/palmieri/Desktop/Sage/TESTING/sage-10.2.beta3/local/lib -rpath >> /opt/homebrew/Cellar/primesieve/11.1/lib -rpath >> /opt/homebrew/Cellar/bdw-gc/8.2.4/lib -rpath >> /opt/homebrew/Cellar/libpng/1.6.40/lib -rpath >> /opt/homebrew/Cellar/ntl/11.5.1/lib -rpath >> /opt/homebrew/Cellar/bzip2/1.0.8/lib -rpath >> /opt/homebrew/Cellar/readline/8.2.1/lib -rpath /opt/homebrew/lib -rpath >> /opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current >> ld: unknown options: --version >> collect2: error: ld returned 1 exit status >> >> Suggestions? >> >> On Sunday, September 17, 2023 at 11:25:02 AM UTC-7 John H Palmieri wrote: >> >>> Similar problem for me on OS X. I don't understand something: the >>> dependencies for scipy include meson_python, but that package is not >>> installed before scipy attempts to build, and fails. Running "make >>> meson_python" and then "make scipy" succeeds, as does "make". >>> >>> >>> >>> On Saturday, September 16, 2023 at 2:59:58 PM UTC-7 Kwankyu Lee wrote: >>> >>>> Succeeded after sage -pip install meson-python. >>>> >>>> On Sunday, September 17, 2023 at 6:52:59 AM UTC+9 Kwankyu Lee wrote: >>>> >>>>> Incremental build failed >>>>> >>>>> [scipy-1.11.2] >>>>> [......................................................................] >>>>> [scipy-1.11.2] scipy-1.11.2 >>>>> [scipy-1.11.2] ==================================================== >>>>> [sagelib-10.2.beta3] Removing file or directory >>>>> /Users/kwankyu/GitHub/sage-dev/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/sagemath-standard.egg-link >>>>> [sagelib-10.2.beta3] Removing pth entries from >>>>> /Users/kwankyu/GitHub/sage-dev/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/easy-install.pth: >>>>> [sagelib-10.2.beta3] Removing entry: >>>>> /Users/kwankyu/GitHub/sage-dev/src >>>>> [sagelib-10.2.beta3] Successfully uninstalled >>>>> sagemath-standard-10.2b3 >>>>> [sagelib-10.2.beta3] Running setup.py develop for sagemath-standard >>>>> [sagelib-10.2.beta3] Running command python setup.py develop >>>>> [scipy-1.11.2] Setting up build directory for scipy-1.11.2 >>>>> [scipy-1.11.2] Finished extraction >>>>> [scipy-1.11.2] Applying patches from ../patches... >>>>> [scipy-1.11.2] Applying ../patches/numpy-include.patch >>>>> [scipy-1.11.2] patching file scipy/spatial/setup.py >>>>> [scipy-1.11.2] Hunk #1 succeeded at 39 (offset -1 lines). >>>>> [scipy-1.11.2] Applying ../patches/tests_no_internet_dependency.patch >>>>> [scipy-1.11.2] patching file scipy/datasets/meson.build >>>>> [scipy-1.11.2] **************************************************** >>>>> [scipy-1.11.2] Host system: >>>>> [scipy-1.11.2] Darwin Helios.local 22.6.0 Darwin Kernel Version >>>>> 22.6.0: Wed Jul 5 22:21:56 PDT 2023; >>>>> root:xnu-8796.141.3~6/RELEASE_X86_64 >>>>> x86_64 >>>>> [scipy-1.11.2] **************************************************** >>>>> [scipy-1.11.2] C compiler: gcc >>>>> [scipy-1.11.2] C compiler version: >>>>> [scipy-1.11.2] Apple clang version 14.0.3 (clang-1403.0.22.14.1) >>>>> [scipy-1.11.2] Target: x86_64-apple-darwin22.6.0 >>>>> [scipy-1.11.2] Thread model: posix >>>>> [scipy-1.11.2] InstalledDir: >>>>> /Library/Developer/CommandLineTools/usr/bin >>>>> [scipy-1.11.2] **************************************************** >>>>> [scipy-1.11.2] Package 'scipy' is currently not installed >>>>> [scipy-1.11.2] No legacy uninstaller found for 'scipy'; nothing to do >>>>> [scipy-1.11.2] Installing scipy-1.11.2 >>>>> [scipy-1.11.2] DEPRECATION: --no-binary currently disables reading >>>>> from the cache of locally built wheels. In the future --no-binary will >>>>> not >>>>> influence the wheel cache. pip 23.1 will enforce this behaviour change. A >>>>> possible replacement is to use the --no-cache-dir option. You can use the >>>>> flag --use-feature=no-binary-enable-wheel-cache to test the upcoming >>>>> behaviour. Discussion can be found at >>>>> https://github.com/pypa/pip/issues/11453 >>>>> [scipy-1.11.2] Processing >>>>> /Users/kwankyu/GitHub/sage-dev/local/var/lib/sage/venv-python3.10/var/tmp/sage/build/scipy-1.11.2/src >>>>> [scipy-1.11.2] Preparing metadata (pyproject.toml): started >>>>> [scipy-1.11.2] Running command Preparing metadata (pyproject.toml) >>>>> [scipy-1.11.2] Preparing metadata (pyproject.toml): finished with >>>>> status 'done' >>>>> [scipy-1.11.2] ERROR: Exception: >>>>> [scipy-1.11.2] Traceback (most recent call last): >>>>> [scipy-1.11.2] File >>>>> "/Users/kwankyu/GitHub/sage-dev/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/pip/_internal/cli/base_command.py", >>>>> >>>>> line 160, in exc_logging_wrapper >>>>> [scipy-1.11.2] status = run_func(*args) >>>>> [scipy-1.11.2] File >>>>> "/Users/kwankyu/GitHub/sage-dev/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/pip/_internal/cli/req_command.py", >>>>> >>>>> line 247, in wrapper >>>>> [scipy-1.11.2] return func(self, options, args) >>>>> [scipy-1.11.2] File >>>>> "/Users/kwankyu/GitHub/sage-dev/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/pip/_internal/commands/wheel.py", >>>>> >>>>> line 170, in run >>>>> [scipy-1.11.2] requirement_set = resolver.resolve(reqs, >>>>> check_supported_wheels=True) >>>>> [scipy-1.11.2] File >>>>> "/Users/kwankyu/GitHub/sage-dev/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/resolver.py", >>>>> >>>>> line 73, in resolve >>>>> [scipy-1.11.2] collected = >>>>> self.factory.collect_root_requirements(root_reqs) >>>>> [scipy-1.11.2] File >>>>> "/Users/kwankyu/GitHub/sage-dev/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/factory.py", >>>>> >>>>> line 491, in collect_root_requirements >>>>> [scipy-1.11.2] req = self._make_requirement_from_install_req( >>>>> [scipy-1.11.2] File >>>>> "/Users/kwankyu/GitHub/sage-dev/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/factory.py", >>>>> >>>>> line 453, in _make_requirement_from_install_req >>>>> [scipy-1.11.2] cand = self._make_candidate_from_link( >>>>> [scipy-1.11.2] File >>>>> "/Users/kwankyu/GitHub/sage-dev/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/factory.py", >>>>> >>>>> line 206, in _make_candidate_from_link >>>>> [scipy-1.11.2] self._link_candidate_cache[link] = LinkCandidate( >>>>> [scipy-1.11.2] File >>>>> "/Users/kwankyu/GitHub/sage-dev/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/candidates.py", >>>>> >>>>> line 297, in __init__ >>>>> [scipy-1.11.2] super().__init__( >>>>> [scipy-1.11.2] File >>>>> "/Users/kwankyu/GitHub/sage-dev/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/candidates.py", >>>>> >>>>> line 162, in __init__ >>>>> [scipy-1.11.2] self.dist = self._prepare() >>>>> [scipy-1.11.2] File >>>>> "/Users/kwankyu/GitHub/sage-dev/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/candidates.py", >>>>> >>>>> line 231, in _prepare >>>>> [scipy-1.11.2] dist = self._prepare_distribution() >>>>> [scipy-1.11.2] File >>>>> "/Users/kwankyu/GitHub/sage-dev/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/candidates.py", >>>>> >>>>> line 308, in _prepare_distribution >>>>> [scipy-1.11.2] return >>>>> preparer.prepare_linked_requirement(self._ireq, parallel_builds=True) >>>>> [scipy-1.11.2] File >>>>> "/Users/kwankyu/GitHub/sage-dev/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/pip/_internal/operations/prepare.py", >>>>> >>>>> line 491, in prepare_linked_requirement >>>>> [scipy-1.11.2] return self._prepare_linked_requirement(req, >>>>> parallel_builds) >>>>> [scipy-1.11.2] File >>>>> "/Users/kwankyu/GitHub/sage-dev/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/pip/_internal/operations/prepare.py", >>>>> >>>>> line 577, in _prepare_linked_requirement >>>>> [scipy-1.11.2] dist = _get_prepared_distribution( >>>>> [scipy-1.11.2] File >>>>> "/Users/kwankyu/GitHub/sage-dev/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/pip/_internal/operations/prepare.py", >>>>> >>>>> line 69, in _get_prepared_distribution >>>>> [scipy-1.11.2] abstract_dist.prepare_distribution_metadata( >>>>> [scipy-1.11.2] File >>>>> "/Users/kwankyu/GitHub/sage-dev/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/pip/_internal/distributions/sdist.py", >>>>> >>>>> line 61, in prepare_distribution_metadata >>>>> [scipy-1.11.2] self.req.prepare_metadata() >>>>> [scipy-1.11.2] File >>>>> "/Users/kwankyu/GitHub/sage-dev/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/pip/_internal/req/req_install.py", >>>>> >>>>> line 535, in prepare_metadata >>>>> [scipy-1.11.2] self.metadata_directory = generate_metadata( >>>>> [scipy-1.11.2] File >>>>> "/Users/kwankyu/GitHub/sage-dev/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/pip/_internal/operations/build/metadata.py", >>>>> >>>>> line 35, in generate_metadata >>>>> [scipy-1.11.2] distinfo_dir = >>>>> backend.prepare_metadata_for_build_wheel(metadata_dir) >>>>> [scipy-1.11.2] File >>>>> "/Users/kwankyu/GitHub/sage-dev/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/pip/_internal/utils/misc.py", >>>>> >>>>> line 706, in prepare_metadata_for_build_wheel >>>>> [scipy-1.11.2] return super().prepare_metadata_for_build_wheel( >>>>> [scipy-1.11.2] File >>>>> "/Users/kwankyu/GitHub/sage-dev/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/pip/_vendor/pep517/wrappers.py", >>>>> >>>>> line 189, in prepare_metadata_for_build_wheel >>>>> [scipy-1.11.2] return >>>>> self._call_hook('prepare_metadata_for_build_wheel', { >>>>> [scipy-1.11.2] File >>>>> "/Users/kwankyu/GitHub/sage-dev/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/pip/_vendor/pep517/wrappers.py", >>>>> >>>>> line 319, in _call_hook >>>>> [scipy-1.11.2] raise BackendUnavailable(data.get('traceback', '')) >>>>> [scipy-1.11.2] pip._vendor.pep517.wrappers.BackendUnavailable: >>>>> Traceback (most recent call last): >>>>> [scipy-1.11.2] File >>>>> "/Users/kwankyu/GitHub/sage-dev/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", >>>>> >>>>> line 77, in _build_backend >>>>> [scipy-1.11.2] obj = import_module(mod_path) >>>>> [scipy-1.11.2] File >>>>> "/usr/local/Cellar/pyt...@3.10/3.10.9/Frameworks/Python.framework/Versions/3.10/lib/python3.10/importlib/__init__.py", >>>>> >>>>> line 126, in import_module >>>>> [scipy-1.11.2] return _bootstrap._gcd_import(name[level:], >>>>> package, level) >>>>> [scipy-1.11.2] File "<frozen importlib._bootstrap>", line 1050, in >>>>> _gcd_import >>>>> [scipy-1.11.2] File "<frozen importlib._bootstrap>", line 1027, in >>>>> _find_and_load >>>>> [scipy-1.11.2] File "<frozen importlib._bootstrap>", line 1004, in >>>>> _find_and_load_unlocked >>>>> [scipy-1.11.2] ModuleNotFoundError: No module named 'mesonpy' >>>>> [scipy-1.11.2] >>>>> [scipy-1.11.2] >>>>> ******************************************************************************** >>>>> [scipy-1.11.2] Error building a wheel for scipy-1.11.2 >>>>> [scipy-1.11.2] >>>>> ******************************************************************************** >>>>> [scipy-1.11.2] >>>>> [scipy-1.11.2] real 0m0.924s >>>>> [scipy-1.11.2] user 0m0.663s >>>>> [scipy-1.11.2] sys 0m0.184s >>>>> [scipy-1.11.2] >>>>> ************************************************************************ >>>>> [scipy-1.11.2] Error installing package scipy-1.11.2 >>>>> >>>>> On Sunday, September 17, 2023 at 12:31:53 AM UTC+9 Volker Braun wrote: >>>>> >>>>>> 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 >>>>>> >>>>>> >>>>>> 80f6d772a15 (tag: 10.2.beta3, github/develop) Updated SageMath >>>>>> version to 10.2.beta3 >>>>>> f32860b2015 gh-36263: Fix setuptools version bounds in generated >>>>>> `pyproject.toml` files >>>>>> c95bd1440b4 gh-36260: `MPowerSeries`: Don't go through symbolics to >>>>>> compute exp(0), log(1) >>>>>> cac16e2fa5d gh-36256: Support more system-site packages >>>>>> 238b1dc6eef gh-36255: numpy-1.25 compatibility >>>>>> 486d3b99e87 gh-36250: various details in sets/disjoint_set >>>>>> 357b34b55f7 gh-36249: E228 and E225 in groups,interfaces,modules,plot >>>>>> adc3df9e5c0 gh-36248: some care for unused variables in matrix/ >>>>>> 413b5d679c5 gh-36247: fix E228 and E225 in categories/ >>>>>> 96d249a37d9 gh-36243: ⬆️ Bump actions/checkout from 3 to 4 >>>>>> 4bb48bddfa4 gh-36241: ⬆️ Bump myrotvorets/set-commit-status-action >>>>>> from 1.1.7 to 2.0.0 >>>>>> 191d1f97ba6 gh-36240: Fix Python package metadata generated by >>>>>> `bootstrap` >>>>>> 905d3c2d486 gh-36238: `sage -t`: Distinguish .pxd from .pyx in >>>>>> doctest basenames >>>>>> b6b50a80e96 gh-36235: support for ecl 23.9.9 >>>>>> 683b05bb5a2 gh-36232: Make `min_spanning_tree` robust to incomparable >>>>>> vertex labels >>>>>> 8d09d156fcf gh-36231: fix typo in documentation >>>>>> 33182d9feaa gh-36225: improve the use of graphs in >>>>>> `sage/combinat/posets/*` >>>>>> 33d6cc5a001 gh-36224: Add cycle_type() and fix to_cycle() to >>>>>> SignedPermutation. >>>>>> 3e6db2405df gh-36221: get rid of xrange again >>>>>> 029450c8712 gh-36219: configure.ac: disable webencodings,tinycss2 >>>>>> with --disable-notebook >>>>>> 3ea961767e8 gh-36218: src/bin/sage-env: set >>>>>> PYDEVD_DISABLE_FILE_VALIDATION=1 >>>>>> f95e442cb4b gh-36213: Fix sync labels issues for step 2 going live >>>>>> e74579d32b9 gh-36212: singular: added missing #endif >>>>>> 322ad22e8c8 gh-36210: configure.ac: disable mathjax with >>>>>> --disable-doc >>>>>> 6fe3561bbbb gh-36209: build/pkgs/ipython/dependencies: drop jinja2 >>>>>> 78efe5546db gh-36206: Remove some obsolete "six" dependencies >>>>>> 1a1df6f6fbe gh-36186: Drop obsolete html5lib package >>>>>> 5b2f125a842 gh-36176: build/pkgs/tox: Update, require tox >= 4.2.7, >>>>>> update dependencies >>>>>> 9dd8a772e53 gh-36168: `sage.groups`: Modularization fixes, `# needs`, >>>>>> doctest cosmetics >>>>>> 4f4fbc29184 gh-36165: Fix reduction of cusps for Gamma(N) >>>>>> 45537351d7e gh-36122: Added hash function to elements of the >>>>>> fundamental group of an extended affine Weyl group >>>>>> 5b9137c7204 gh-35970: src/sage/combinat/affine_permutation.py: Fix >>>>>> docstring markup >>>>>> bbe57a4d34d gh-35964: Matroids: Don't forget to check rank in >>>>>> `equals`, `is_isomorphism` >>>>>> 23b1a0af6f0 gh-35875: Implementing moment angle complexes >>>>>> 3a3126ffc0e gh-35767: add .basis_matrix() wrapper to quaternion orders >>>>>> d412568dff7 gh-35485: New comparison mode to lazy series and better >>>>>> undefined check >>>>>> 21a624a7b45 gh-35362: Implement infinite sums and products for lazy >>>>>> series >>>>>> 8c040276465 gh-35038: Implement Milnor fiber and Coxeter complexes >>>>>> 41031292ff1 (tag: 10.2.beta2) Updated SageMath version to 10.2.beta2 >>>>>> >>>>> -- >> > 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 sage-release...@googlegroups.com. >> > To view this discussion on the web visit >> https://groups.google.com/d/msgid/sage-release/8ea52d9b-96c1-4792-af11-6589218cf564n%40googlegroups.com >> >> <https://groups.google.com/d/msgid/sage-release/8ea52d9b-96c1-4792-af11-6589218cf564n%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > -- You received this message because you are subscribed to the Google Groups "sage-release" group. 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