2025-09-08T10:26:09,455 Created temporary directory: /tmp/pip-build-tracker-gttgwpjt
2025-09-08T10:26:09,455 Initialized build tracking at /tmp/pip-build-tracker-gttgwpjt
2025-09-08T10:26:09,455 Created build tracker: /tmp/pip-build-tracker-gttgwpjt
2025-09-08T10:26:09,456 Entered build tracker: /tmp/pip-build-tracker-gttgwpjt
2025-09-08T10:26:09,456 Created temporary directory: /tmp/pip-wheel-vb8cf02e
2025-09-08T10:26:09,459 Created temporary directory: /tmp/pip-ephem-wheel-cache-nyra0fe9
2025-09-08T10:26:09,513 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-09-08T10:26:09,516 2 location(s) to search for versions of pymcell:
2025-09-08T10:26:09,516 * https://pypi.org/simple/pymcell/
2025-09-08T10:26:09,516 * https://www.piwheels.org/simple/pymcell/
2025-09-08T10:26:09,516 Fetching project page and analyzing links: https://pypi.org/simple/pymcell/
2025-09-08T10:26:09,516 Getting page https://pypi.org/simple/pymcell/
2025-09-08T10:26:09,517 Found index url https://pypi.org/simple/
2025-09-08T10:26:09,589 Fetched page https://pypi.org/simple/pymcell/ as application/vnd.pypi.simple.v1+json
2025-09-08T10:26:09,589   Found link https://files.pythonhosted.org/packages/d2/c8/171b381142a8c44139007524e4e1df60ffccb7baa1112f736787276d3f69/pymcell-0.1.tar.gz (from https://pypi.org/simple/pymcell/), version: 0.1
2025-09-08T10:26:09,590   Found link https://files.pythonhosted.org/packages/15/c4/2c54dd1441778cf446f9357aea6fd378e3d8fd46628aa9245d965afcb409/pymcell-0.2.tar.gz (from https://pypi.org/simple/pymcell/), version: 0.2
2025-09-08T10:26:09,590 Fetching project page and analyzing links: https://www.piwheels.org/simple/pymcell/
2025-09-08T10:26:09,590 Getting page https://www.piwheels.org/simple/pymcell/
2025-09-08T10:26:09,591 Found index url https://www.piwheels.org/simple/
2025-09-08T10:26:09,687 Fetched page https://www.piwheels.org/simple/pymcell/ as text/html
2025-09-08T10:26:09,689   Skipping link: No binaries permitted for pymcell: https://archive1.piwheels.org/simple/pymcell/pymcell-0.2-cp311-cp311-linux_armv6l.whl#sha256=ad8c7517ed0c37c4aca8cdf336c9281ea0a5b22d0060f11c67958d2c38a2cc61 (from https://www.piwheels.org/simple/pymcell/)
2025-09-08T10:26:09,689   Skipping link: No binaries permitted for pymcell: https://archive1.piwheels.org/simple/pymcell/pymcell-0.2-cp311-cp311-linux_armv7l.whl#sha256=ad8c7517ed0c37c4aca8cdf336c9281ea0a5b22d0060f11c67958d2c38a2cc61 (from https://www.piwheels.org/simple/pymcell/)
2025-09-08T10:26:09,689   Skipping link: No binaries permitted for pymcell: https://archive1.piwheels.org/simple/pymcell/pymcell-0.2-cp39-cp39-linux_armv6l.whl#sha256=e96b2042c3c8dfb8c8b35e822be8717206520d3bed5f2d01e4afecf00ce9e3cf (from https://www.piwheels.org/simple/pymcell/)
2025-09-08T10:26:09,690   Skipping link: No binaries permitted for pymcell: https://archive1.piwheels.org/simple/pymcell/pymcell-0.2-cp39-cp39-linux_armv7l.whl#sha256=e96b2042c3c8dfb8c8b35e822be8717206520d3bed5f2d01e4afecf00ce9e3cf (from https://www.piwheels.org/simple/pymcell/)
2025-09-08T10:26:09,690   Skipping link: No binaries permitted for pymcell: https://archive1.piwheels.org/simple/pymcell/pymcell-0.1-cp311-cp311-linux_armv6l.whl#sha256=43c1131338d4734b273ab6d278df180046cfdf826948a2676b653df095a93347 (from https://www.piwheels.org/simple/pymcell/)
2025-09-08T10:26:09,690   Skipping link: No binaries permitted for pymcell: https://archive1.piwheels.org/simple/pymcell/pymcell-0.1-cp311-cp311-linux_armv7l.whl#sha256=43c1131338d4734b273ab6d278df180046cfdf826948a2676b653df095a93347 (from https://www.piwheels.org/simple/pymcell/)
2025-09-08T10:26:09,690   Skipping link: No binaries permitted for pymcell: https://archive1.piwheels.org/simple/pymcell/pymcell-0.1-cp39-cp39-linux_armv6l.whl#sha256=93642a08f3b2b702c68d3e07632f2804cb9c62976cca999019bee9575489e7d0 (from https://www.piwheels.org/simple/pymcell/)
2025-09-08T10:26:09,690   Skipping link: No binaries permitted for pymcell: https://archive1.piwheels.org/simple/pymcell/pymcell-0.1-cp39-cp39-linux_armv7l.whl#sha256=93642a08f3b2b702c68d3e07632f2804cb9c62976cca999019bee9575489e7d0 (from https://www.piwheels.org/simple/pymcell/)
2025-09-08T10:26:09,690 Skipping link: not a file: https://www.piwheels.org/simple/pymcell/
2025-09-08T10:26:09,691 Skipping link: not a file: https://pypi.org/simple/pymcell/
2025-09-08T10:26:09,714 Given no hashes to check 1 links for project 'pymcell': discarding no candidates
2025-09-08T10:26:09,715 Collecting pymcell==0.2
2025-09-08T10:26:09,716   Created temporary directory: /tmp/pip-unpack-09cscn22
2025-09-08T10:26:09,858   Downloading pymcell-0.2.tar.gz (657 kB)
2025-09-08T10:26:10,067   Added pymcell==0.2 from https://files.pythonhosted.org/packages/15/c4/2c54dd1441778cf446f9357aea6fd378e3d8fd46628aa9245d965afcb409/pymcell-0.2.tar.gz to build tracker '/tmp/pip-build-tracker-gttgwpjt'
2025-09-08T10:26:10,068   Running setup.py (path:/tmp/pip-wheel-vb8cf02e/pymcell_49a8a47b5a0d426a8ff5f3b5437a2ae8/setup.py) egg_info for package pymcell
2025-09-08T10:26:10,068   Created temporary directory: /tmp/pip-pip-egg-info-_7hcbd82
2025-09-08T10:26:10,068   Preparing metadata (setup.py): started
2025-09-08T10:26:10,069   Running command python setup.py egg_info
2025-09-08T10:26:11,063   /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'description-file' in 'metadata' (setup.cfg), please use the underscore name 'description_file' instead.
2025-09-08T10:26:11,063   !!

2025-09-08T10:26:11,063           ********************************************************************************
2025-09-08T10:26:11,063           Usage of dash-separated 'description-file' will not be supported in future
2025-09-08T10:26:11,063           versions. Please use the underscore name 'description_file' instead.
2025-09-08T10:26:11,063           (Affected: pymcell).

2025-09-08T10:26:11,063           By 2026-Mar-03, you need to update your project and remove deprecated calls
2025-09-08T10:26:11,064           or your builds will no longer be supported.

2025-09-08T10:26:11,064           See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
2025-09-08T10:26:11,064           ********************************************************************************

2025-09-08T10:26:11,064   !!
2025-09-08T10:26:11,064     opt = self._enforce_underscore(opt, section)
2025-09-08T10:26:11,558   Preparing metadata (setup.py): finished with status 'done'
2025-09-08T10:26:11,563   Source in /tmp/pip-wheel-vb8cf02e/pymcell_49a8a47b5a0d426a8ff5f3b5437a2ae8 has version 0.2, which satisfies requirement pymcell==0.2 from https://files.pythonhosted.org/packages/15/c4/2c54dd1441778cf446f9357aea6fd378e3d8fd46628aa9245d965afcb409/pymcell-0.2.tar.gz
2025-09-08T10:26:11,563   Removed pymcell==0.2 from https://files.pythonhosted.org/packages/15/c4/2c54dd1441778cf446f9357aea6fd378e3d8fd46628aa9245d965afcb409/pymcell-0.2.tar.gz from build tracker '/tmp/pip-build-tracker-gttgwpjt'
2025-09-08T10:26:11,566 Created temporary directory: /tmp/pip-unpack-uthcjj1r
2025-09-08T10:26:11,566 Created temporary directory: /tmp/pip-unpack-4kmd40t9
2025-09-08T10:26:11,566 Building wheels for collected packages: pymcell
2025-09-08T10:26:11,567   Created temporary directory: /tmp/pip-wheel-8lh5xi7d
2025-09-08T10:26:11,568   DEPRECATION: Building 'pymcell' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'pymcell'. Discussion can be found at https://github.com/pypa/pip/issues/6334
2025-09-08T10:26:11,569   Building wheel for pymcell (setup.py): started
2025-09-08T10:26:11,569   Destination directory: /tmp/pip-wheel-8lh5xi7d
2025-09-08T10:26:11,569   Running command python setup.py bdist_wheel
2025-09-08T10:26:12,556   /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'description-file' in 'metadata' (setup.cfg), please use the underscore name 'description_file' instead.
2025-09-08T10:26:12,557   !!

2025-09-08T10:26:12,557           ********************************************************************************
2025-09-08T10:26:12,557           Usage of dash-separated 'description-file' will not be supported in future
2025-09-08T10:26:12,557           versions. Please use the underscore name 'description_file' instead.
2025-09-08T10:26:12,557           (Affected: pymcell).

2025-09-08T10:26:12,557           By 2026-Mar-03, you need to update your project and remove deprecated calls
2025-09-08T10:26:12,557           or your builds will no longer be supported.

2025-09-08T10:26:12,558           See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
2025-09-08T10:26:12,558           ********************************************************************************

2025-09-08T10:26:12,558   !!
2025-09-08T10:26:12,558     opt = self._enforce_underscore(opt, section)
2025-09-08T10:26:13,221   Deprecated command line option: -py3. Ignored, this option is no longer supported.
2025-09-08T10:26:30,526   dyngeom_lex.c: In function ‘yy_get_next_buffer’:
2025-09-08T10:26:30,526   dyngeom_lex.c:1395:47: warning: comparison of integer expressions of different signedness: ‘int’ and ‘yy_size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2025-09-08T10:26:36,584   ./src/init.c: In function ‘output_relreg_eval_tree’:
2025-09-08T10:26:36,588   ./src/init.c:3669:5: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
2025-09-08T10:26:36,588    3669 |     strncpy(prefixA, prefix, l);
2025-09-08T10:26:36,588         |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
2025-09-08T10:26:36,591   ./src/init.c:3661:14: note: length computed here
2025-09-08T10:26:36,592    3661 |   size_t l = strlen(prefix);
2025-09-08T10:26:36,592         |              ^~~~~~~~~~~~~~
2025-09-08T10:26:36,595   ./src/init.c:3670:5: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
2025-09-08T10:26:36,595    3670 |     strncpy(prefixB, prefix, l);
2025-09-08T10:26:36,595         |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
2025-09-08T10:26:36,598   ./src/init.c:3661:14: note: length computed here
2025-09-08T10:26:36,599    3661 |   size_t l = strlen(prefix);
2025-09-08T10:26:36,599         |              ^~~~~~~~~~~~~~
2025-09-08T10:26:54,039   ./src/pymcell_wrap.c: In function ‘_wrap_mcell_argparse’:
2025-09-08T10:26:54,043   ./src/pymcell_wrap.c:4519:19: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2025-09-08T10:26:54,043    4519 |           arg2[i] = PyUnicode_AsUTF8(PyList_GetItem(swig_obj[1],i));
2025-09-08T10:26:54,043         |                   ^
2025-09-08T10:26:54,410   ./src/pymcell_wrap.c: In function ‘_wrap_mcell_modify_multiple_rate_constants’:
2025-09-08T10:26:54,418   ./src/pymcell_wrap.c:8674:19: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2025-09-08T10:26:54,418    8674 |           arg2[i] = PyUnicode_AsUTF8(PyList_GetItem(swig_obj[1],i));
2025-09-08T10:26:54,418         |                   ^
2025-09-08T10:27:17,808   ./src/react_output.c: In function ‘oexpr_title’:
2025-09-08T10:27:17,809   ./src/react_output.c:1157:46: warning: bitwise comparison always evaluates to false [-Wtautological-compare]
2025-09-08T10:27:17,810    1157 |     if ((root->expr_flags & OEXPR_TYPE_MASK) == OEXPR_LEFT_INT)
2025-09-08T10:27:17,810         |                                              ^~
2025-09-08T10:27:18,939   ./src/react_trig.c: In function ‘trigger_trimolecular’:
2025-09-08T10:27:18,939   ./src/react_trig.c:439:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
2025-09-08T10:27:18,939     439 |             ((geomB + geomC) * (geomB - geomC))) {
2025-09-08T10:27:18,939         |             ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2025-09-08T10:27:22,594   ./src/util.c: In function ‘poisson_dist’:
2025-09-08T10:27:22,594   ./src/util.c:1101:1: warning: control reaches end of non-void function [-Wreturn-type]
2025-09-08T10:27:22,594    1101 | }
2025-09-08T10:27:22,594         | ^
2025-09-08T10:27:29,476   ./src/wall_util.c: In function ‘release_onto_regions’:
2025-09-08T10:27:29,478   ./src/wall_util.c:2032:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
2025-09-08T10:27:29,478    2032 |       if (grid_index >= w->grid->n_tiles)
2025-09-08T10:27:29,478         |       ^~
2025-09-08T10:27:29,480   ./src/wall_util.c:2035:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
2025-09-08T10:27:29,480    2035 |         struct surface_molecule_list *sm_list = w->grid->sm_list[grid_index];
2025-09-08T10:27:29,480         |         ^~~~~~
2025-09-08T10:27:33,175   /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2025-09-08T10:27:33,175   !!

2025-09-08T10:27:33,175           ********************************************************************************
2025-09-08T10:27:33,175           Please avoid running ``setup.py`` directly.
2025-09-08T10:27:33,176           Instead, use pypa/build, pypa/installer or other
2025-09-08T10:27:33,176           standards-based tools.

2025-09-08T10:27:33,176           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-09-08T10:27:33,176           or your builds will no longer be supported.

2025-09-08T10:27:33,176           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2025-09-08T10:27:33,176           ********************************************************************************

2025-09-08T10:27:33,176   !!
2025-09-08T10:27:33,176     self.initialize_options()
2025-09-08T10:27:34,485   Building wheel for pymcell (setup.py): finished with status 'done'
2025-09-08T10:27:34,499   Created wheel for pymcell: filename=pymcell-0.2-cp313-cp313-linux_armv7l.whl size=1295629 sha256=c1ea6607226596f62de4ea77f354e201ac50cd37c42db4a0d627bbb27d41128c
2025-09-08T10:27:34,500   Stored in directory: /tmp/pip-ephem-wheel-cache-nyra0fe9/wheels/e5/fb/10/1a46b80158d13f41e30c8ebc7e2ad906e91374f4e3fce988e1
2025-09-08T10:27:34,507 Successfully built pymcell
2025-09-08T10:27:34,511 Removed build tracker: '/tmp/pip-build-tracker-gttgwpjt'