Can you build scipy from source using their instructions?

On Sat, 23 Sept 2023, 06:25 John H Palmieri, <[email protected]> wrote:

> 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, <[email protected]> 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/[email protected]/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
>>>>>>>
>>>>>> --
>>>
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