2026-05-17T16:27:20,779 Created temporary directory: /tmp/pip-ephem-wheel-cache-_8j4qnq_
2026-05-17T16:27:20,781 Created temporary directory: /tmp/pip-build-tracker-lcmg8u5m
2026-05-17T16:27:20,781 Initialized build tracking at /tmp/pip-build-tracker-lcmg8u5m
2026-05-17T16:27:20,782 Created build tracker: /tmp/pip-build-tracker-lcmg8u5m
2026-05-17T16:27:20,782 Entered build tracker: /tmp/pip-build-tracker-lcmg8u5m
2026-05-17T16:27:20,783 Created temporary directory: /tmp/pip-wheel-efb39i9f
2026-05-17T16:27:20,786 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
2026-05-17T16:27:20,788 Created temporary directory: /tmp/pip-ephem-wheel-cache-04mv3_b2
2026-05-17T16:27:20,811 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-05-17T16:27:20,814 2 location(s) to search for versions of td2:
2026-05-17T16:27:20,814 * https://pypi.org/simple/td2/
2026-05-17T16:27:20,814 * https://www.piwheels.org/simple/td2/
2026-05-17T16:27:20,815 Fetching project page and analyzing links: https://pypi.org/simple/td2/
2026-05-17T16:27:20,816 Getting page https://pypi.org/simple/td2/
2026-05-17T16:27:20,817 Found index url https://pypi.org/simple
2026-05-17T16:27:21,047 Fetched page https://pypi.org/simple/td2/ as application/vnd.pypi.simple.v1+json
2026-05-17T16:27:21,052   Skipping link: No binaries permitted for td2: https://files.pythonhosted.org/packages/43/52/258b0d913bfa795951cd68eb8f202e56bb686e2ac215bd537f5e5d8523a9/TD2-0.1.0-py3-none-any.whl (from https://pypi.org/simple/td2/) (requires-python:>=3.8)
2026-05-17T16:27:21,053   Found link https://files.pythonhosted.org/packages/ad/37/151603746c26b5ef38676339bbf67afdb530888937fbb8e1e775f27208ac/td2-0.1.0.tar.gz (from https://pypi.org/simple/td2/) (requires-python:>=3.8), version: 0.1.0
2026-05-17T16:27:21,054   Skipping link: No binaries permitted for td2: https://files.pythonhosted.org/packages/f6/f9/c52c232ea9f0677a8dcc8372c808f2db059730d017e5081a1c0ce151398c/TD2-1.0.0-py3-none-any.whl (from https://pypi.org/simple/td2/) (requires-python:<3.13,>=3.9)
2026-05-17T16:27:21,055   Found link https://files.pythonhosted.org/packages/42/df/2123f303f9668376b0783d67b0dc1d77ab320fcd7cd6499b54d2bbdf24ee/td2-1.0.0.tar.gz (from https://pypi.org/simple/td2/) (requires-python:<3.13,>=3.9), version: 1.0.0
2026-05-17T16:27:21,056   Skipping link: No binaries permitted for td2: https://files.pythonhosted.org/packages/ff/a4/ab6be14acf5c1f585afc4881d8fc05f1aa2ba8985326d9af761acf9feaa4/td2-1.0.1-py3-none-any.whl (from https://pypi.org/simple/td2/) (requires-python:<3.13,>=3.9)
2026-05-17T16:27:21,057   Found link https://files.pythonhosted.org/packages/27/76/0de889e7ac948b0a6c8de999fac74484afebb986c22a31f1541ed61cf3a9/td2-1.0.1.tar.gz (from https://pypi.org/simple/td2/) (requires-python:<3.13,>=3.9), version: 1.0.1
2026-05-17T16:27:21,058   Skipping link: No binaries permitted for td2: https://files.pythonhosted.org/packages/0b/85/7fa6d4c7d930f86d60ad89ece226cabe83198b2f640b4936c9b826934d8e/TD2-1.0.2-py3-none-any.whl (from https://pypi.org/simple/td2/) (requires-python:<3.13,>=3.9)
2026-05-17T16:27:21,058   Skipping link: No binaries permitted for td2: https://files.pythonhosted.org/packages/59/7f/c557088b575b11b930a810c4b08d7947c231bfbd6083e23691ab6d4f35d7/td2-1.0.2-py3-none-any.whl (from https://pypi.org/simple/td2/) (requires-python:<3.13,>=3.9)
2026-05-17T16:27:21,059   Found link https://files.pythonhosted.org/packages/03/86/7cacd5aebbaf6de14d05cd2c46ab4d8214bd5674713e018237f19510054f/td2-1.0.2.tar.gz (from https://pypi.org/simple/td2/) (requires-python:<3.13,>=3.9), version: 1.0.2
2026-05-17T16:27:21,060   Skipping link: No binaries permitted for td2: https://files.pythonhosted.org/packages/9c/12/08401c017e913b8fd32b212039af4a257aad486f53600624d391560eb554/TD2-1.0.3-py3-none-any.whl (from https://pypi.org/simple/td2/) (requires-python:<3.13,>=3.9)
2026-05-17T16:27:21,061   Found link https://files.pythonhosted.org/packages/f1/d4/7572f90f0da85e70bd129c15ed61ae301c5897b5e65d3156c602cf62fa1a/td2-1.0.3.tar.gz (from https://pypi.org/simple/td2/) (requires-python:<3.13,>=3.9), version: 1.0.3
2026-05-17T16:27:21,062   Skipping link: No binaries permitted for td2: https://files.pythonhosted.org/packages/c3/e0/adcb22d02f8881bdfce4a3c89003203115487946a2015cb5350d7c8884f3/TD2-1.0.5-py3-none-any.whl (from https://pypi.org/simple/td2/) (requires-python:<3.13,>=3.9)
2026-05-17T16:27:21,063   Found link https://files.pythonhosted.org/packages/d6/33/ef87f351e48b90f3fe892c982e721592fdbbf7b40d9bf34faf0a3a13198b/td2-1.0.5.tar.gz (from https://pypi.org/simple/td2/) (requires-python:<3.13,>=3.9), version: 1.0.5
2026-05-17T16:27:21,064   Skipping link: No binaries permitted for td2: https://files.pythonhosted.org/packages/ab/bc/6cb935774ae1b624faff92638a3422f0f12aeaf5f61ff820adbbd36464fc/td2-1.0.6-py3-none-any.whl (from https://pypi.org/simple/td2/) (requires-python:<3.13,>=3.9)
2026-05-17T16:27:21,065   Found link https://files.pythonhosted.org/packages/ef/4f/51dd7d1bd195d6e58d3efca71051ccd24219e3ad7c50098ecd63d9d83970/td2-1.0.6.tar.gz (from https://pypi.org/simple/td2/) (requires-python:<3.13,>=3.9), version: 1.0.6
2026-05-17T16:27:21,065   Skipping link: No binaries permitted for td2: https://files.pythonhosted.org/packages/91/09/e6b5b77a22ae4b1ba61570290521443af62c352ebf233e3cf759c273a28f/td2-1.0.7-py3-none-any.whl (from https://pypi.org/simple/td2/) (requires-python:<3.13,>=3.9)
2026-05-17T16:27:21,066   Found link https://files.pythonhosted.org/packages/4f/2d/a780cc5ead61cf0815ca9d553533cea7e9a78e439432b19c5b98700a70c6/td2-1.0.7.tar.gz (from https://pypi.org/simple/td2/) (requires-python:<3.13,>=3.9), version: 1.0.7
2026-05-17T16:27:21,067   Skipping link: No binaries permitted for td2: https://files.pythonhosted.org/packages/a0/2b/389c465b2ef974a0026df17383e31ef987e7afe13905fed462c90eb3bacd/td2-1.0.8-py3-none-any.whl (from https://pypi.org/simple/td2/) (requires-python:<3.13,>=3.9)
2026-05-17T16:27:21,068   Found link https://files.pythonhosted.org/packages/1c/54/4993afb799b2da259e1a5c7a9030dc6851f18b17e955728d7b31ce0a872c/td2-1.0.8.tar.gz (from https://pypi.org/simple/td2/) (requires-python:<3.13,>=3.9), version: 1.0.8
2026-05-17T16:27:21,069   Skipping link: No binaries permitted for td2: https://files.pythonhosted.org/packages/44/99/7c5d2e82dac052f9932891c5a1706be45b2cff49493cb31751f623975ff5/td2-1.1.0-py3-none-any.whl (from https://pypi.org/simple/td2/) (requires-python:<3.14,>=3.9)
2026-05-17T16:27:21,070   Found link https://files.pythonhosted.org/packages/ce/65/86d4061f1e3e9e5a1bc07d59aca4c886d0430cc75d2b4e506c2f4906660c/td2-1.1.0.tar.gz (from https://pypi.org/simple/td2/) (requires-python:<3.14,>=3.9), version: 1.1.0
2026-05-17T16:27:21,071 Fetching project page and analyzing links: https://www.piwheels.org/simple/td2/
2026-05-17T16:27:21,072 Getting page https://www.piwheels.org/simple/td2/
2026-05-17T16:27:21,073 Found index url https://www.piwheels.org/simple
2026-05-17T16:27:21,252 Fetched page https://www.piwheels.org/simple/td2/ as text/html
2026-05-17T16:27:21,256   Skipping link: No binaries permitted for td2: https://archive1.piwheels.org/simple/td2/td2-1.0.8-py3-none-any.whl#sha256=944490d97bf8993312b1bf67261afdcb5d0d3cfa6dd20e6b7742099438a69562 (from https://www.piwheels.org/simple/td2/) (requires-python:>=3.9, <3.13)
2026-05-17T16:27:21,256   Skipping link: No binaries permitted for td2: https://archive1.piwheels.org/simple/td2/td2-1.0.7-py3-none-any.whl#sha256=3c6f782386166cea654790740affad1c75ed2897d476e6b5057d41cc1ee40544 (from https://www.piwheels.org/simple/td2/) (requires-python:>=3.9, <3.13)
2026-05-17T16:27:21,257   Skipping link: No binaries permitted for td2: https://archive1.piwheels.org/simple/td2/td2-1.0.6-py3-none-any.whl#sha256=036476c742d1f379694335713c2332f65ac1a3aff11da540ca2963a72e530f18 (from https://www.piwheels.org/simple/td2/) (requires-python:>=3.9, <3.13)
2026-05-17T16:27:21,258   Skipping link: No binaries permitted for td2: https://archive1.piwheels.org/simple/td2/td2-1.0.5-py3-none-any.whl#sha256=09e084f02acf615c53f50a29b00bf08971b806a3ab1eb60d1019227f7e92eb7c (from https://www.piwheels.org/simple/td2/) (requires-python:>=3.9, <3.13)
2026-05-17T16:27:21,258   Skipping link: No binaries permitted for td2: https://archive1.piwheels.org/simple/td2/td2-1.0.3-py3-none-any.whl#sha256=7f47b70ec5e865a83e73c173f75fff821f550fe092c77b1898bc9bc12e23872d (from https://www.piwheels.org/simple/td2/) (requires-python:>=3.9, <3.13)
2026-05-17T16:27:21,259   Skipping link: No binaries permitted for td2: https://archive1.piwheels.org/simple/td2/td2-1.0.2-py3-none-any.whl#sha256=94ae7a7132596b9a383262b643caa9c9353ca36fce313b3cd7ad471f5aae0607 (from https://www.piwheels.org/simple/td2/) (requires-python:>=3.9, <3.13)
2026-05-17T16:27:21,259   Skipping link: No binaries permitted for td2: https://archive1.piwheels.org/simple/td2/td2-1.0.1-py3-none-any.whl#sha256=8c2dbb85f1878bd9ee408cf25a898ede78c5fd23f195feebb2dfe45f6c4d2f71 (from https://www.piwheels.org/simple/td2/) (requires-python:>=3.9, <3.13)
2026-05-17T16:27:21,260   Skipping link: No binaries permitted for td2: https://archive1.piwheels.org/simple/td2/TD2-1.0.0-py3-none-any.whl#sha256=43bbd429280f386d4b2ece6c595361d46faf2e27fdad8718c138f6c6939b666a (from https://www.piwheels.org/simple/td2/) (requires-python:>=3.9, <3.13)
2026-05-17T16:27:21,261   Skipping link: No binaries permitted for td2: https://archive1.piwheels.org/simple/td2/TD2-0.1.0-py3-none-any.whl#sha256=4507f8bdeadbc4ccf6326f26068254f66be05e8371ee1f05b27e0f616670f199 (from https://www.piwheels.org/simple/td2/) (requires-python:>=3.8)
2026-05-17T16:27:21,261 Skipping link: not a file: https://www.piwheels.org/simple/td2/
2026-05-17T16:27:21,262 Skipping link: not a file: https://pypi.org/simple/td2/
2026-05-17T16:27:21,282 Given no hashes to check 1 links for project 'td2': discarding no candidates
2026-05-17T16:27:21,300 Collecting td2==1.1.0
2026-05-17T16:27:21,302   Created temporary directory: /tmp/pip-unpack-0sxnfmkv
2026-05-17T16:27:21,465   Downloading td2-1.1.0.tar.gz (46 kB)
2026-05-17T16:27:21,616   Added td2==1.1.0 from https://files.pythonhosted.org/packages/ce/65/86d4061f1e3e9e5a1bc07d59aca4c886d0430cc75d2b4e506c2f4906660c/td2-1.1.0.tar.gz to build tracker '/tmp/pip-build-tracker-lcmg8u5m'
2026-05-17T16:27:21,618   Running setup.py (path:/tmp/pip-wheel-efb39i9f/td2_5f1bb02790c54aba910c871c1f41ee1e/setup.py) egg_info for package td2
2026-05-17T16:27:21,619   Created temporary directory: /tmp/pip-pip-egg-info-pp68ubxy
2026-05-17T16:27:21,620   Preparing metadata (setup.py): started
2026-05-17T16:27:21,621   Running command python setup.py egg_info
2026-05-17T16:27:22,491   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-05-17T16:27:22,491   !!

2026-05-17T16:27:22,492           ********************************************************************************
2026-05-17T16:27:22,493           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-05-17T16:27:22,494           License :: OSI Approved :: MIT License

2026-05-17T16:27:22,495           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-05-17T16:27:22,496           ********************************************************************************

2026-05-17T16:27:22,497   !!
2026-05-17T16:27:22,497     self._finalize_license_expression()
2026-05-17T16:27:22,519   running egg_info
2026-05-17T16:27:22,545   creating /tmp/pip-pip-egg-info-pp68ubxy/TD2.egg-info
2026-05-17T16:27:22,546   writing /tmp/pip-pip-egg-info-pp68ubxy/TD2.egg-info/PKG-INFO
2026-05-17T16:27:22,550   writing dependency_links to /tmp/pip-pip-egg-info-pp68ubxy/TD2.egg-info/dependency_links.txt
2026-05-17T16:27:22,552   writing entry points to /tmp/pip-pip-egg-info-pp68ubxy/TD2.egg-info/entry_points.txt
2026-05-17T16:27:22,554   writing requirements to /tmp/pip-pip-egg-info-pp68ubxy/TD2.egg-info/requires.txt
2026-05-17T16:27:22,555   writing top-level names to /tmp/pip-pip-egg-info-pp68ubxy/TD2.egg-info/top_level.txt
2026-05-17T16:27:22,557   writing manifest file '/tmp/pip-pip-egg-info-pp68ubxy/TD2.egg-info/SOURCES.txt'
2026-05-17T16:27:22,657   reading manifest file '/tmp/pip-pip-egg-info-pp68ubxy/TD2.egg-info/SOURCES.txt'
2026-05-17T16:27:22,659   reading manifest template 'MANIFEST.in'
2026-05-17T16:27:22,660   warning: no files found matching 'tables/table_*.json'
2026-05-17T16:27:22,660   adding license file 'LICENSE.txt'
2026-05-17T16:27:22,664   writing manifest file '/tmp/pip-pip-egg-info-pp68ubxy/TD2.egg-info/SOURCES.txt'
2026-05-17T16:27:22,772   Preparing metadata (setup.py): finished with status 'done'
2026-05-17T16:27:22,776   Source in /tmp/pip-wheel-efb39i9f/td2_5f1bb02790c54aba910c871c1f41ee1e has version 1.1.0, which satisfies requirement td2==1.1.0 from https://files.pythonhosted.org/packages/ce/65/86d4061f1e3e9e5a1bc07d59aca4c886d0430cc75d2b4e506c2f4906660c/td2-1.1.0.tar.gz
2026-05-17T16:27:22,777   Removed td2==1.1.0 from https://files.pythonhosted.org/packages/ce/65/86d4061f1e3e9e5a1bc07d59aca4c886d0430cc75d2b4e506c2f4906660c/td2-1.1.0.tar.gz from build tracker '/tmp/pip-build-tracker-lcmg8u5m'
2026-05-17T16:27:22,783 Created temporary directory: /tmp/pip-unpack-lexb2g67
2026-05-17T16:27:22,783 Building wheels for collected packages: td2
2026-05-17T16:27:22,788   Created temporary directory: /tmp/pip-wheel-e01wlgro
2026-05-17T16:27:22,788   Building wheel for td2 (setup.py): started
2026-05-17T16:27:22,789   Destination directory: /tmp/pip-wheel-e01wlgro
2026-05-17T16:27:22,790   Running command python setup.py bdist_wheel
2026-05-17T16:27:23,633   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-05-17T16:27:23,633   !!

2026-05-17T16:27:23,635           ********************************************************************************
2026-05-17T16:27:23,635           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-05-17T16:27:23,636           License :: OSI Approved :: MIT License

2026-05-17T16:27:23,637           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-05-17T16:27:23,638           ********************************************************************************

2026-05-17T16:27:23,639   !!
2026-05-17T16:27:23,640     self._finalize_license_expression()
2026-05-17T16:27:23,641   running bdist_wheel
2026-05-17T16:27:23,772   running build
2026-05-17T16:27:23,773   running build_py
2026-05-17T16:27:23,803   creating build/lib/api
2026-05-17T16:27:23,805   copying api/__init__.py -> build/lib/api
2026-05-17T16:27:23,807   creating build/lib/TD2
2026-05-17T16:27:23,808   copying TD2/help.py -> build/lib/TD2
2026-05-17T16:27:23,811   copying TD2/Predict.py -> build/lib/TD2
2026-05-17T16:27:23,813   copying TD2/translator.py -> build/lib/TD2
2026-05-17T16:27:23,816   copying TD2/LongOrfs.py -> build/lib/TD2
2026-05-17T16:27:23,819   copying TD2/__init__.py -> build/lib/TD2
2026-05-17T16:27:23,821   copying TD2/get_tables.py -> build/lib/TD2
2026-05-17T16:27:23,824   creating build/lib/tests
2026-05-17T16:27:23,825   copying tests/visualize_benchmark.py -> build/lib/tests
2026-05-17T16:27:23,827   copying tests/test_gff.py -> build/lib/tests
2026-05-17T16:27:23,829   copying tests/test_version.py -> build/lib/tests
2026-05-17T16:27:23,831   copying tests/compare_peps.py -> build/lib/tests
2026-05-17T16:27:23,833   copying tests/test_predict_math.py -> build/lib/tests
2026-05-17T16:27:23,836   copying tests/test_translate.py -> build/lib/tests
2026-05-17T16:27:23,838   copying tests/visualize_mane_composition.py -> build/lib/tests
2026-05-17T16:27:23,840   copying tests/test_end_to_end_mane.py -> build/lib/tests
2026-05-17T16:27:23,842   copying tests/test_find_orfs.py -> build/lib/tests
2026-05-17T16:27:23,844   copying tests/longorfs_low_memory.py -> build/lib/tests
2026-05-17T16:27:23,847   copying tests/ambiguous_codon_test.py -> build/lib/tests
2026-05-17T16:27:23,849   copying tests/visualize_chess.py -> build/lib/tests
2026-05-17T16:27:23,851   copying tests/partition_mane.py -> build/lib/tests
2026-05-17T16:27:23,853   copying tests/test_transcriptome_regression.py -> build/lib/tests
2026-05-17T16:27:23,856   copying tests/__init__.py -> build/lib/tests
2026-05-17T16:27:23,857   copying tests/test_find_orfs_real.py -> build/lib/tests
2026-05-17T16:27:23,859   copying tests/test_reverse_complement.py -> build/lib/tests
2026-05-17T16:27:23,862   creating build/lib/TD2/tables
2026-05-17T16:27:23,863   copying TD2/tables/__init__.py -> build/lib/TD2/tables
2026-05-17T16:27:23,865   creating build/lib/tests/data
2026-05-17T16:27:23,866   copying tests/data/__init__.py -> build/lib/tests/data
2026-05-17T16:27:23,868   running egg_info
2026-05-17T16:27:23,897   writing TD2.egg-info/PKG-INFO
2026-05-17T16:27:23,902   writing dependency_links to TD2.egg-info/dependency_links.txt
2026-05-17T16:27:23,903   writing entry points to TD2.egg-info/entry_points.txt
2026-05-17T16:27:23,905   writing requirements to TD2.egg-info/requires.txt
2026-05-17T16:27:23,906   writing top-level names to TD2.egg-info/top_level.txt
2026-05-17T16:27:23,951   reading manifest file 'TD2.egg-info/SOURCES.txt'
2026-05-17T16:27:23,955   reading manifest template 'MANIFEST.in'
2026-05-17T16:27:23,956   warning: no files found matching 'tables/table_*.json'
2026-05-17T16:27:23,957   adding license file 'LICENSE.txt'
2026-05-17T16:27:23,961   writing manifest file 'TD2.egg-info/SOURCES.txt'
2026-05-17T16:27:23,975   copying TD2/tables/table_1.json -> build/lib/TD2/tables
2026-05-17T16:27:23,977   copying TD2/tables/table_2.json -> build/lib/TD2/tables
2026-05-17T16:27:23,980   copying TD2/tables/table_3.json -> build/lib/TD2/tables
2026-05-17T16:27:23,982   copying TD2/tables/table_4.json -> build/lib/TD2/tables
2026-05-17T16:27:23,984   copying TD2/tables/table_5.json -> build/lib/TD2/tables
2026-05-17T16:27:23,986   copying TD2/tables/table_6.json -> build/lib/TD2/tables
2026-05-17T16:27:23,989   copying TD2/tables/table_9.json -> build/lib/TD2/tables
2026-05-17T16:27:23,991   copying TD2/tables/table_10.json -> build/lib/TD2/tables
2026-05-17T16:27:23,993   copying TD2/tables/table_11.json -> build/lib/TD2/tables
2026-05-17T16:27:23,995   copying TD2/tables/table_12.json -> build/lib/TD2/tables
2026-05-17T16:27:23,997   copying TD2/tables/table_13.json -> build/lib/TD2/tables
2026-05-17T16:27:23,999   copying TD2/tables/table_14.json -> build/lib/TD2/tables
2026-05-17T16:27:24,002   copying TD2/tables/table_15.json -> build/lib/TD2/tables
2026-05-17T16:27:24,004   copying TD2/tables/table_16.json -> build/lib/TD2/tables
2026-05-17T16:27:24,006   copying TD2/tables/table_21.json -> build/lib/TD2/tables
2026-05-17T16:27:24,008   copying TD2/tables/table_22.json -> build/lib/TD2/tables
2026-05-17T16:27:24,010   copying TD2/tables/table_23.json -> build/lib/TD2/tables
2026-05-17T16:27:24,012   copying TD2/tables/table_24.json -> build/lib/TD2/tables
2026-05-17T16:27:24,015   copying TD2/tables/table_25.json -> build/lib/TD2/tables
2026-05-17T16:27:24,017   copying TD2/tables/table_26.json -> build/lib/TD2/tables
2026-05-17T16:27:24,019   copying TD2/tables/table_27.json -> build/lib/TD2/tables
2026-05-17T16:27:24,021   copying TD2/tables/table_28.json -> build/lib/TD2/tables
2026-05-17T16:27:24,023   copying TD2/tables/table_29.json -> build/lib/TD2/tables
2026-05-17T16:27:24,026   copying TD2/tables/table_30.json -> build/lib/TD2/tables
2026-05-17T16:27:24,028   copying TD2/tables/table_31.json -> build/lib/TD2/tables
2026-05-17T16:27:24,030   copying TD2/tables/table_33.json -> build/lib/TD2/tables
2026-05-17T16:27:24,071   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2026-05-17T16:27:24,072   !!

2026-05-17T16:27:24,073           ********************************************************************************
2026-05-17T16:27:24,074           Please avoid running ``setup.py`` directly.
2026-05-17T16:27:24,075           Instead, use pypa/build, pypa/installer or other
2026-05-17T16:27:24,075           standards-based tools.

2026-05-17T16:27:24,076           This deprecation is overdue, please update your project and remove deprecated
2026-05-17T16:27:24,076           calls to avoid build errors in the future.

2026-05-17T16:27:24,077           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2026-05-17T16:27:24,078           ********************************************************************************

2026-05-17T16:27:24,079   !!
2026-05-17T16:27:24,079     self.initialize_options()
2026-05-17T16:27:24,102   installing to build/bdist.linux-armv7l/wheel
2026-05-17T16:27:24,103   running install
2026-05-17T16:27:24,126   running install_lib
2026-05-17T16:27:24,155   creating build/bdist.linux-armv7l/wheel
2026-05-17T16:27:24,157   creating build/bdist.linux-armv7l/wheel/api
2026-05-17T16:27:24,158   copying build/lib/api/__init__.py -> build/bdist.linux-armv7l/wheel/./api
2026-05-17T16:27:24,161   creating build/bdist.linux-armv7l/wheel/TD2
2026-05-17T16:27:24,162   copying build/lib/TD2/help.py -> build/bdist.linux-armv7l/wheel/./TD2
2026-05-17T16:27:24,164   creating build/bdist.linux-armv7l/wheel/TD2/tables
2026-05-17T16:27:24,166   copying build/lib/TD2/tables/table_2.json -> build/bdist.linux-armv7l/wheel/./TD2/tables
2026-05-17T16:27:24,168   copying build/lib/TD2/tables/table_23.json -> build/bdist.linux-armv7l/wheel/./TD2/tables
2026-05-17T16:27:24,170   copying build/lib/TD2/tables/table_11.json -> build/bdist.linux-armv7l/wheel/./TD2/tables
2026-05-17T16:27:24,172   copying build/lib/TD2/tables/table_21.json -> build/bdist.linux-armv7l/wheel/./TD2/tables
2026-05-17T16:27:24,174   copying build/lib/TD2/tables/table_28.json -> build/bdist.linux-armv7l/wheel/./TD2/tables
2026-05-17T16:27:24,176   copying build/lib/TD2/tables/table_10.json -> build/bdist.linux-armv7l/wheel/./TD2/tables
2026-05-17T16:27:24,178   copying build/lib/TD2/tables/table_22.json -> build/bdist.linux-armv7l/wheel/./TD2/tables
2026-05-17T16:27:24,180   copying build/lib/TD2/tables/table_24.json -> build/bdist.linux-armv7l/wheel/./TD2/tables
2026-05-17T16:27:24,182   copying build/lib/TD2/tables/table_16.json -> build/bdist.linux-armv7l/wheel/./TD2/tables
2026-05-17T16:27:24,184   copying build/lib/TD2/tables/table_12.json -> build/bdist.linux-armv7l/wheel/./TD2/tables
2026-05-17T16:27:24,186   copying build/lib/TD2/tables/table_5.json -> build/bdist.linux-armv7l/wheel/./TD2/tables
2026-05-17T16:27:24,188   copying build/lib/TD2/tables/table_4.json -> build/bdist.linux-armv7l/wheel/./TD2/tables
2026-05-17T16:27:24,190   copying build/lib/TD2/tables/table_27.json -> build/bdist.linux-armv7l/wheel/./TD2/tables
2026-05-17T16:27:24,192   copying build/lib/TD2/tables/table_26.json -> build/bdist.linux-armv7l/wheel/./TD2/tables
2026-05-17T16:27:24,194   copying build/lib/TD2/tables/table_13.json -> build/bdist.linux-armv7l/wheel/./TD2/tables
2026-05-17T16:27:24,196   copying build/lib/TD2/tables/table_14.json -> build/bdist.linux-armv7l/wheel/./TD2/tables
2026-05-17T16:27:24,198   copying build/lib/TD2/tables/__init__.py -> build/bdist.linux-armv7l/wheel/./TD2/tables
2026-05-17T16:27:24,200   copying build/lib/TD2/tables/table_15.json -> build/bdist.linux-armv7l/wheel/./TD2/tables
2026-05-17T16:27:24,202   copying build/lib/TD2/tables/table_31.json -> build/bdist.linux-armv7l/wheel/./TD2/tables
2026-05-17T16:27:24,204   copying build/lib/TD2/tables/table_25.json -> build/bdist.linux-armv7l/wheel/./TD2/tables
2026-05-17T16:27:24,206   copying build/lib/TD2/tables/table_29.json -> build/bdist.linux-armv7l/wheel/./TD2/tables
2026-05-17T16:27:24,208   copying build/lib/TD2/tables/table_33.json -> build/bdist.linux-armv7l/wheel/./TD2/tables
2026-05-17T16:27:24,210   copying build/lib/TD2/tables/table_9.json -> build/bdist.linux-armv7l/wheel/./TD2/tables
2026-05-17T16:27:24,212   copying build/lib/TD2/tables/table_1.json -> build/bdist.linux-armv7l/wheel/./TD2/tables
2026-05-17T16:27:24,214   copying build/lib/TD2/tables/table_3.json -> build/bdist.linux-armv7l/wheel/./TD2/tables
2026-05-17T16:27:24,216   copying build/lib/TD2/tables/table_6.json -> build/bdist.linux-armv7l/wheel/./TD2/tables
2026-05-17T16:27:24,218   copying build/lib/TD2/tables/table_30.json -> build/bdist.linux-armv7l/wheel/./TD2/tables
2026-05-17T16:27:24,220   copying build/lib/TD2/Predict.py -> build/bdist.linux-armv7l/wheel/./TD2
2026-05-17T16:27:24,223   copying build/lib/TD2/translator.py -> build/bdist.linux-armv7l/wheel/./TD2
2026-05-17T16:27:24,225   copying build/lib/TD2/LongOrfs.py -> build/bdist.linux-armv7l/wheel/./TD2
2026-05-17T16:27:24,228   copying build/lib/TD2/__init__.py -> build/bdist.linux-armv7l/wheel/./TD2
2026-05-17T16:27:24,230   copying build/lib/TD2/get_tables.py -> build/bdist.linux-armv7l/wheel/./TD2
2026-05-17T16:27:24,233   creating build/bdist.linux-armv7l/wheel/tests
2026-05-17T16:27:24,234   copying build/lib/tests/visualize_benchmark.py -> build/bdist.linux-armv7l/wheel/./tests
2026-05-17T16:27:24,237   copying build/lib/tests/test_gff.py -> build/bdist.linux-armv7l/wheel/./tests
2026-05-17T16:27:24,239   copying build/lib/tests/test_version.py -> build/bdist.linux-armv7l/wheel/./tests
2026-05-17T16:27:24,241   copying build/lib/tests/compare_peps.py -> build/bdist.linux-armv7l/wheel/./tests
2026-05-17T16:27:24,243   copying build/lib/tests/test_predict_math.py -> build/bdist.linux-armv7l/wheel/./tests
2026-05-17T16:27:24,245   copying build/lib/tests/test_translate.py -> build/bdist.linux-armv7l/wheel/./tests
2026-05-17T16:27:24,247   copying build/lib/tests/visualize_mane_composition.py -> build/bdist.linux-armv7l/wheel/./tests
2026-05-17T16:27:24,249   copying build/lib/tests/test_end_to_end_mane.py -> build/bdist.linux-armv7l/wheel/./tests
2026-05-17T16:27:24,251   copying build/lib/tests/test_find_orfs.py -> build/bdist.linux-armv7l/wheel/./tests
2026-05-17T16:27:24,253   copying build/lib/tests/longorfs_low_memory.py -> build/bdist.linux-armv7l/wheel/./tests
2026-05-17T16:27:24,256   copying build/lib/tests/ambiguous_codon_test.py -> build/bdist.linux-armv7l/wheel/./tests
2026-05-17T16:27:24,259   copying build/lib/tests/visualize_chess.py -> build/bdist.linux-armv7l/wheel/./tests
2026-05-17T16:27:24,261   copying build/lib/tests/partition_mane.py -> build/bdist.linux-armv7l/wheel/./tests
2026-05-17T16:27:24,263   copying build/lib/tests/test_transcriptome_regression.py -> build/bdist.linux-armv7l/wheel/./tests
2026-05-17T16:27:24,265   copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests
2026-05-17T16:27:24,267   copying build/lib/tests/test_find_orfs_real.py -> build/bdist.linux-armv7l/wheel/./tests
2026-05-17T16:27:24,269   copying build/lib/tests/test_reverse_complement.py -> build/bdist.linux-armv7l/wheel/./tests
2026-05-17T16:27:24,272   creating build/bdist.linux-armv7l/wheel/tests/data
2026-05-17T16:27:24,273   copying build/lib/tests/data/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/data
2026-05-17T16:27:24,275   running install_egg_info
2026-05-17T16:27:24,310   Copying TD2.egg-info to build/bdist.linux-armv7l/wheel/./TD2-1.1.0-py3.11.egg-info
2026-05-17T16:27:24,323   running install_scripts
2026-05-17T16:27:24,337   creating build/bdist.linux-armv7l/wheel/td2-1.1.0.dist-info/WHEEL
2026-05-17T16:27:24,339   creating '/tmp/pip-wheel-e01wlgro/td2-1.1.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2026-05-17T16:27:24,343   adding 'TD2/LongOrfs.py'
2026-05-17T16:27:24,347   adding 'TD2/Predict.py'
2026-05-17T16:27:24,348   adding 'TD2/__init__.py'
2026-05-17T16:27:24,350   adding 'TD2/get_tables.py'
2026-05-17T16:27:24,352   adding 'TD2/help.py'
2026-05-17T16:27:24,354   adding 'TD2/translator.py'
2026-05-17T16:27:24,356   adding 'TD2/tables/__init__.py'
2026-05-17T16:27:24,358   adding 'TD2/tables/table_1.json'
2026-05-17T16:27:24,359   adding 'TD2/tables/table_10.json'
2026-05-17T16:27:24,360   adding 'TD2/tables/table_11.json'
2026-05-17T16:27:24,362   adding 'TD2/tables/table_12.json'
2026-05-17T16:27:24,363   adding 'TD2/tables/table_13.json'
2026-05-17T16:27:24,365   adding 'TD2/tables/table_14.json'
2026-05-17T16:27:24,366   adding 'TD2/tables/table_15.json'
2026-05-17T16:27:24,367   adding 'TD2/tables/table_16.json'
2026-05-17T16:27:24,369   adding 'TD2/tables/table_2.json'
2026-05-17T16:27:24,370   adding 'TD2/tables/table_21.json'
2026-05-17T16:27:24,372   adding 'TD2/tables/table_22.json'
2026-05-17T16:27:24,373   adding 'TD2/tables/table_23.json'
2026-05-17T16:27:24,375   adding 'TD2/tables/table_24.json'
2026-05-17T16:27:24,376   adding 'TD2/tables/table_25.json'
2026-05-17T16:27:24,377   adding 'TD2/tables/table_26.json'
2026-05-17T16:27:24,379   adding 'TD2/tables/table_27.json'
2026-05-17T16:27:24,380   adding 'TD2/tables/table_28.json'
2026-05-17T16:27:24,382   adding 'TD2/tables/table_29.json'
2026-05-17T16:27:24,383   adding 'TD2/tables/table_3.json'
2026-05-17T16:27:24,384   adding 'TD2/tables/table_30.json'
2026-05-17T16:27:24,386   adding 'TD2/tables/table_31.json'
2026-05-17T16:27:24,387   adding 'TD2/tables/table_33.json'
2026-05-17T16:27:24,389   adding 'TD2/tables/table_4.json'
2026-05-17T16:27:24,390   adding 'TD2/tables/table_5.json'
2026-05-17T16:27:24,392   adding 'TD2/tables/table_6.json'
2026-05-17T16:27:24,393   adding 'TD2/tables/table_9.json'
2026-05-17T16:27:24,395   adding 'api/__init__.py'
2026-05-17T16:27:24,397   adding 'td2-1.1.0.dist-info/licenses/LICENSE.txt'
2026-05-17T16:27:24,399   adding 'tests/__init__.py'
2026-05-17T16:27:24,400   adding 'tests/ambiguous_codon_test.py'
2026-05-17T16:27:24,402   adding 'tests/compare_peps.py'
2026-05-17T16:27:24,404   adding 'tests/longorfs_low_memory.py'
2026-05-17T16:27:24,406   adding 'tests/partition_mane.py'
2026-05-17T16:27:24,407   adding 'tests/test_end_to_end_mane.py'
2026-05-17T16:27:24,409   adding 'tests/test_find_orfs.py'
2026-05-17T16:27:24,411   adding 'tests/test_find_orfs_real.py'
2026-05-17T16:27:24,412   adding 'tests/test_gff.py'
2026-05-17T16:27:24,414   adding 'tests/test_predict_math.py'
2026-05-17T16:27:24,415   adding 'tests/test_reverse_complement.py'
2026-05-17T16:27:24,416   adding 'tests/test_transcriptome_regression.py'
2026-05-17T16:27:24,418   adding 'tests/test_translate.py'
2026-05-17T16:27:24,419   adding 'tests/test_version.py'
2026-05-17T16:27:24,421   adding 'tests/visualize_benchmark.py'
2026-05-17T16:27:24,422   adding 'tests/visualize_chess.py'
2026-05-17T16:27:24,424   adding 'tests/visualize_mane_composition.py'
2026-05-17T16:27:24,425   adding 'tests/data/__init__.py'
2026-05-17T16:27:24,426   adding 'td2-1.1.0.dist-info/METADATA'
2026-05-17T16:27:24,427   adding 'td2-1.1.0.dist-info/WHEEL'
2026-05-17T16:27:24,428   adding 'td2-1.1.0.dist-info/entry_points.txt'
2026-05-17T16:27:24,429   adding 'td2-1.1.0.dist-info/top_level.txt'
2026-05-17T16:27:24,431   adding 'td2-1.1.0.dist-info/RECORD'
2026-05-17T16:27:24,433   removing build/bdist.linux-armv7l/wheel
2026-05-17T16:27:24,556   Building wheel for td2 (setup.py): finished with status 'done'
2026-05-17T16:27:24,559   Created wheel for td2: filename=td2-1.1.0-py3-none-any.whl size=65376 sha256=a0bce00bd703c218dc33b9c335891df86466080d29fff9cbbe3ec221dd90978b
2026-05-17T16:27:24,561   Stored in directory: /tmp/pip-ephem-wheel-cache-04mv3_b2/wheels/71/4d/38/626cc85bc388a9a821d392c321e3a5f6f0772279be92a9b453
2026-05-17T16:27:24,573 Successfully built td2
2026-05-17T16:27:24,578 Removed build tracker: '/tmp/pip-build-tracker-lcmg8u5m'