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. 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