2026-06-25T23:09:10,345 Created temporary directory: /tmp/pip-ephem-wheel-cache-63uww1f2
2026-06-25T23:09:10,347 Created temporary directory: /tmp/pip-build-tracker-kl97pgol
2026-06-25T23:09:10,348 Initialized build tracking at /tmp/pip-build-tracker-kl97pgol
2026-06-25T23:09:10,348 Created build tracker: /tmp/pip-build-tracker-kl97pgol
2026-06-25T23:09:10,349 Entered build tracker: /tmp/pip-build-tracker-kl97pgol
2026-06-25T23:09:10,349 Created temporary directory: /tmp/pip-wheel-2l6b_0bf
2026-06-25T23:09:10,352 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
2026-06-25T23:09:10,355 Created temporary directory: /tmp/pip-ephem-wheel-cache-d77wsp7q
2026-06-25T23:09:10,376 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-06-25T23:09:10,380 2 location(s) to search for versions of oncoref:
2026-06-25T23:09:10,380 * https://pypi.org/simple/oncoref/
2026-06-25T23:09:10,380 * https://www.piwheels.org/simple/oncoref/
2026-06-25T23:09:10,381 Fetching project page and analyzing links: https://pypi.org/simple/oncoref/
2026-06-25T23:09:10,381 Getting page https://pypi.org/simple/oncoref/
2026-06-25T23:09:10,383 Found index url https://pypi.org/simple
2026-06-25T23:09:10,532 Fetched page https://pypi.org/simple/oncoref/ as application/vnd.pypi.simple.v1+json
2026-06-25T23:09:10,537   Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/28/98/3c08853ca8c6e4f7ea1625192d883f4890b4482814b60c92972610af6a91/oncoref-1.6.0-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-25T23:09:10,539   Found link https://files.pythonhosted.org/packages/d3/fa/b1f2479c8c9b44597623ab898f37be9f1c317250cac13115edb09adf0bd0/oncoref-1.6.0.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.6.0
2026-06-25T23:09:10,539   Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/00/bc/d076f0b5f3ab5d26840cd8eee073af59210bb90aba8a7826d64980c08e70/oncoref-1.7.0-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-25T23:09:10,540   Found link https://files.pythonhosted.org/packages/6b/4f/2b9be7b2858be7ca1c850ea67261cfe41c9595b7d57ed818b20af88c815c/oncoref-1.7.0.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.7.0
2026-06-25T23:09:10,541   Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/3d/cf/214dbe1e3f3ca56d6354d7f2f87283085238025685b7287be5a3020db87c/oncoref-1.8.0-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-25T23:09:10,542   Found link https://files.pythonhosted.org/packages/10/a1/9b3e573b2e9ce5903eef398c68d06cd3d1425a88c87c3f5d8dbe79cbfb3c/oncoref-1.8.0.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.8.0
2026-06-25T23:09:10,543   Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/56/b4/103c9511736de31d6182b47aaf4f03da47c52933be96ea7a060ad7478ae3/oncoref-1.8.1-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-25T23:09:10,544   Found link https://files.pythonhosted.org/packages/21/3e/8080dbac7eaa58029775dd4937cb7dc70d1e65b52e358ccb75b5dd8ed63e/oncoref-1.8.1.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.8.1
2026-06-25T23:09:10,544   Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/02/4f/03495de60734a5fb8a50476fd036af4b0262949e609827f759349cc1ff6b/oncoref-1.8.2-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-25T23:09:10,545   Found link https://files.pythonhosted.org/packages/e6/18/5ee9311af10f46d71490d6563884c80cb170f106e31164d3a2cf7e47d1e8/oncoref-1.8.2.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.8.2
2026-06-25T23:09:10,546   Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/9b/4f/60a3e4e56d57a916f462597f08c5c4915e19cb97fc1cd0b85c110e41659e/oncoref-1.8.3-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-25T23:09:10,547   Found link https://files.pythonhosted.org/packages/e7/7d/22a2797b33413bfe0f46708f396b9b1f9ad9dbc253d94fcbeb6ccf9ad5ff/oncoref-1.8.3.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.8.3
2026-06-25T23:09:10,548   Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/ca/bb/0981e424fd20641c70c1607dc7e707ff53036f90e7482b18ef4f2b100bba/oncoref-1.8.4-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-25T23:09:10,549   Found link https://files.pythonhosted.org/packages/da/8f/e45e879798fcad2b21996a64d69c0034e947ca8c07b2668b484580bcccd2/oncoref-1.8.4.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.8.4
2026-06-25T23:09:10,549   Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/b8/72/7cb35a084c989d648fc0ef20be3c0b9d888092e0e13aabc75710797dfbbd/oncoref-1.8.5-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-25T23:09:10,550   Found link https://files.pythonhosted.org/packages/0a/e2/de65c5e1582fe009b3f640e94e6ecd5cf2f139d490750374cdad3af0e14c/oncoref-1.8.5.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.8.5
2026-06-25T23:09:10,551   Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/71/92/3cd4d589831ccb90b12732347718e54d84097a6c780ced1810f52e3b302a/oncoref-1.8.6-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-25T23:09:10,551   Found link https://files.pythonhosted.org/packages/fe/29/0640ff92bcb51841b69a4d04ccf94a5173a18ee10c54786b959026ca4362/oncoref-1.8.6.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.8.6
2026-06-25T23:09:10,552   Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/f2/29/f869b37c956b8836b9c9b45e89ab7dad98a93270e6bd395b45a7ca5657ad/oncoref-1.8.7-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-25T23:09:10,553   Found link https://files.pythonhosted.org/packages/62/2d/434129dfb4157eb2bf8c4f89ff3f5c74e65b2a62e619fcd1154388d70aa4/oncoref-1.8.7.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.8.7
2026-06-25T23:09:10,554   Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/06/89/59174cc23b5ca908c5eed6c89f147d28265749466c702e7c45a91004c4d2/oncoref-1.8.8-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-25T23:09:10,554   Found link https://files.pythonhosted.org/packages/f4/fd/e8f16e540188ecdfa8d331e209374ed0c47ef44e27eae34fc4a262b6e49a/oncoref-1.8.8.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.8.8
2026-06-25T23:09:10,555   Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/21/11/175fa74783a3e4662792af69e82e51a7a991e710858efaeb92a8695d8fda/oncoref-1.8.9-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-25T23:09:10,556   Found link https://files.pythonhosted.org/packages/9f/cb/7d81ce8e2dab2710860db8ae18d8f1c3a34052d74f01459afa76de5af686/oncoref-1.8.9.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.8.9
2026-06-25T23:09:10,557   Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/f8/12/a1f0c9d212afc8cd24b0451f400a187bdd47f18e3cad7f29f2777550ae1a/oncoref-1.8.10-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-25T23:09:10,558   Found link https://files.pythonhosted.org/packages/77/61/378430e4677aa8b166ce384cbe1d113e10edaa5f59609a77f4c766be2571/oncoref-1.8.10.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.8.10
2026-06-25T23:09:10,559 Fetching project page and analyzing links: https://www.piwheels.org/simple/oncoref/
2026-06-25T23:09:10,559 Getting page https://www.piwheels.org/simple/oncoref/
2026-06-25T23:09:10,560 Found index url https://www.piwheels.org/simple
2026-06-25T23:09:16,732 Fetched page https://www.piwheels.org/simple/oncoref/ as text/html
2026-06-25T23:09:16,736   Skipping link: No binaries permitted for oncoref: https://www.piwheels.org/simple/oncoref/oncoref-1.8.9-py3-none-any.whl#sha256=2415de57054126a885d64b626bbb12657ce55d0791a686b7aba85fd8b784d399 (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-25T23:09:16,737   Skipping link: No binaries permitted for oncoref: https://www.piwheels.org/simple/oncoref/oncoref-1.8.8-py3-none-any.whl#sha256=f1b7351039ce534abc9d36a03b53fd9479b1629b4a6fd8698bc500162f1cd362 (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-25T23:09:16,738   Skipping link: No binaries permitted for oncoref: https://www.piwheels.org/simple/oncoref/oncoref-1.8.7-py3-none-any.whl#sha256=84f80af8afa25d02579e67983b74fd2e515df1ce6d0cb602ecb6808e994f8f63 (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-25T23:09:16,738   Skipping link: No binaries permitted for oncoref: https://www.piwheels.org/simple/oncoref/oncoref-1.8.6-py3-none-any.whl#sha256=460f281fc846e410a5992e3a87193febdfac8bf81f3e5497a5e5d72ae58176bf (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-25T23:09:16,739   Skipping link: No binaries permitted for oncoref: https://www.piwheels.org/simple/oncoref/oncoref-1.8.5-py3-none-any.whl#sha256=cfedb20aa2c2593dfb010bc01a13d5b6c732ec5cf013fd70b65c71d1adb71f7e (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-25T23:09:16,739   Skipping link: No binaries permitted for oncoref: https://www.piwheels.org/simple/oncoref/oncoref-1.8.4-py3-none-any.whl#sha256=d649c7a749c099fe67033ecbdbafe4bf8bcd93bd71d9830ce2a6127a1c093cad (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-25T23:09:16,740   Skipping link: No binaries permitted for oncoref: https://www.piwheels.org/simple/oncoref/oncoref-1.8.3-py3-none-any.whl#sha256=bf75676ac99a0d1c144249b8cf320ac292b65716c9ffdc50ad27b55db1153821 (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-25T23:09:16,741   Skipping link: No binaries permitted for oncoref: https://archive1.piwheels.org/simple/oncoref/oncoref-1.8.2-py3-none-any.whl#sha256=9f47ca1a637e6255fbf29fd252834c85e5d19238a980add71843cd860b39777e (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-25T23:09:16,741   Skipping link: No binaries permitted for oncoref: https://archive1.piwheels.org/simple/oncoref/oncoref-1.8.1-py3-none-any.whl#sha256=12f0eb28c115080796010095a4032b844d9ea4383bc0ea2e2b75a3e5f21c9392 (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-25T23:09:16,742   Skipping link: No binaries permitted for oncoref: https://archive1.piwheels.org/simple/oncoref/oncoref-1.8.0-py3-none-any.whl#sha256=6f9be6d1511d7e84166b02f2cd219b977025db68916073cb4bd1ebdfc8919914 (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-25T23:09:16,742   Skipping link: No binaries permitted for oncoref: https://archive1.piwheels.org/simple/oncoref/oncoref-1.7.0-py3-none-any.whl#sha256=249750fecb30a99d715c221ca1ca76a4ff790891f0051782cd528395d14db6ed (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-25T23:09:16,743   Skipping link: No binaries permitted for oncoref: https://archive1.piwheels.org/simple/oncoref/oncoref-1.6.0-py3-none-any.whl#sha256=e8383754a89924adfeb524e978f9d8e304fe5f179989515ee7ee4ae3eaa3d997 (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-25T23:09:16,744 Skipping link: not a file: https://www.piwheels.org/simple/oncoref/
2026-06-25T23:09:16,744 Skipping link: not a file: https://pypi.org/simple/oncoref/
2026-06-25T23:09:16,766 Given no hashes to check 1 links for project 'oncoref': discarding no candidates
2026-06-25T23:09:16,786 Collecting oncoref==1.8.10
2026-06-25T23:09:16,788   Created temporary directory: /tmp/pip-unpack-x2zd7ise
2026-06-25T23:09:17,056   Downloading oncoref-1.8.10.tar.gz (1.7 MB)
2026-06-25T23:09:17,763   Added oncoref==1.8.10 from https://files.pythonhosted.org/packages/77/61/378430e4677aa8b166ce384cbe1d113e10edaa5f59609a77f4c766be2571/oncoref-1.8.10.tar.gz to build tracker '/tmp/pip-build-tracker-kl97pgol'
2026-06-25T23:09:17,770   Created temporary directory: /tmp/pip-build-env-2m6zaowq
2026-06-25T23:09:17,775   Installing build dependencies: started
2026-06-25T23:09:17,776   Running command pip subprocess to install build dependencies
2026-06-25T23:09:18,911   Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11)
2026-06-25T23:09:19,329   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
2026-06-25T23:09:19,353   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-06-25T23:09:23,618   Collecting setuptools>=61.0
2026-06-25T23:09:23,618     Obtaining dependency information for setuptools>=61.0 from https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl.metadata
2026-06-25T23:09:24,819     Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl.metadata (6.5 kB)
2026-06-25T23:09:25,884   Collecting wheel
2026-06-25T23:09:25,885     Obtaining dependency information for wheel from https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata
2026-06-25T23:09:27,712     Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB)
2026-06-25T23:09:28,744   Collecting packaging>=24.0
2026-06-25T23:09:28,746     Obtaining dependency information for packaging>=24.0 from https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata
2026-06-25T23:09:30,808     Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata (3.5 kB)
2026-06-25T23:09:32,815   Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB)
2026-06-25T23:09:32,868   Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB)
2026-06-25T23:09:32,956   WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))': /simple/setuptools/setuptools-82.0.1-py3-none-any.whl
2026-06-25T23:09:33,511   Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB)
2026-06-25T23:09:35,148   Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB)
2026-06-25T23:09:35,193   Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB)
2026-06-25T23:09:36,327   Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB)
2026-06-25T23:09:39,072   Installing collected packages: setuptools, packaging, wheel
2026-06-25T23:09:42,608     Creating /tmp/pip-build-env-2m6zaowq/overlay/local/bin
2026-06-25T23:09:42,610     changing mode of /tmp/pip-build-env-2m6zaowq/overlay/local/bin/wheel to 755
2026-06-25T23:09:42,632   Successfully installed packaging-26.2 setuptools-82.0.1 wheel-0.47.0
2026-06-25T23:09:42,919   Installing build dependencies: finished with status 'done'
2026-06-25T23:09:42,925   Getting requirements to build wheel: started
2026-06-25T23:09:42,927   Running command Getting requirements to build wheel
2026-06-25T23:09:43,637   running egg_info
2026-06-25T23:09:43,643   writing oncoref.egg-info/PKG-INFO
2026-06-25T23:09:43,649   writing dependency_links to oncoref.egg-info/dependency_links.txt
2026-06-25T23:09:43,651   writing entry points to oncoref.egg-info/entry_points.txt
2026-06-25T23:09:43,654   writing requirements to oncoref.egg-info/requires.txt
2026-06-25T23:09:43,656   writing top-level names to oncoref.egg-info/top_level.txt
2026-06-25T23:09:43,691   reading manifest file 'oncoref.egg-info/SOURCES.txt'
2026-06-25T23:09:43,701   reading manifest template 'MANIFEST.in'
2026-06-25T23:09:43,703   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression'
2026-06-25T23:09:43,704   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles'
2026-06-25T23:09:43,706   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives'
2026-06-25T23:09:43,707   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5'
2026-06-25T23:09:43,708   warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv'
2026-06-25T23:09:43,709   warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv'
2026-06-25T23:09:43,710   adding license file 'LICENSE'
2026-06-25T23:09:43,718   writing manifest file 'oncoref.egg-info/SOURCES.txt'
2026-06-25T23:09:43,817   Getting requirements to build wheel: finished with status 'done'
2026-06-25T23:09:43,820   Created temporary directory: /tmp/pip-modern-metadata-p32xhw86
2026-06-25T23:09:43,823   Preparing metadata (pyproject.toml): started
2026-06-25T23:09:43,824   Running command Preparing metadata (pyproject.toml)
2026-06-25T23:09:44,464   running dist_info
2026-06-25T23:09:44,474   creating /tmp/pip-modern-metadata-p32xhw86/oncoref.egg-info
2026-06-25T23:09:44,475   writing /tmp/pip-modern-metadata-p32xhw86/oncoref.egg-info/PKG-INFO
2026-06-25T23:09:44,481   writing dependency_links to /tmp/pip-modern-metadata-p32xhw86/oncoref.egg-info/dependency_links.txt
2026-06-25T23:09:44,483   writing entry points to /tmp/pip-modern-metadata-p32xhw86/oncoref.egg-info/entry_points.txt
2026-06-25T23:09:44,485   writing requirements to /tmp/pip-modern-metadata-p32xhw86/oncoref.egg-info/requires.txt
2026-06-25T23:09:44,486   writing top-level names to /tmp/pip-modern-metadata-p32xhw86/oncoref.egg-info/top_level.txt
2026-06-25T23:09:44,488   writing manifest file '/tmp/pip-modern-metadata-p32xhw86/oncoref.egg-info/SOURCES.txt'
2026-06-25T23:09:44,520   reading manifest file '/tmp/pip-modern-metadata-p32xhw86/oncoref.egg-info/SOURCES.txt'
2026-06-25T23:09:44,522   reading manifest template 'MANIFEST.in'
2026-06-25T23:09:44,523   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression'
2026-06-25T23:09:44,525   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles'
2026-06-25T23:09:44,526   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives'
2026-06-25T23:09:44,527   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5'
2026-06-25T23:09:44,528   warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv'
2026-06-25T23:09:44,529   warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv'
2026-06-25T23:09:44,529   adding license file 'LICENSE'
2026-06-25T23:09:44,536   writing manifest file '/tmp/pip-modern-metadata-p32xhw86/oncoref.egg-info/SOURCES.txt'
2026-06-25T23:09:44,537   creating '/tmp/pip-modern-metadata-p32xhw86/oncoref-1.8.10.dist-info'
2026-06-25T23:09:44,663   Preparing metadata (pyproject.toml): finished with status 'done'
2026-06-25T23:09:44,667   Source in /tmp/pip-wheel-2l6b_0bf/oncoref_e4d33e0eb21f4e58915432cbb8efdb30 has version 1.8.10, which satisfies requirement oncoref==1.8.10 from https://files.pythonhosted.org/packages/77/61/378430e4677aa8b166ce384cbe1d113e10edaa5f59609a77f4c766be2571/oncoref-1.8.10.tar.gz
2026-06-25T23:09:44,668   Removed oncoref==1.8.10 from https://files.pythonhosted.org/packages/77/61/378430e4677aa8b166ce384cbe1d113e10edaa5f59609a77f4c766be2571/oncoref-1.8.10.tar.gz from build tracker '/tmp/pip-build-tracker-kl97pgol'
2026-06-25T23:09:44,675 Created temporary directory: /tmp/pip-unpack-fouhuihq
2026-06-25T23:09:44,675 Building wheels for collected packages: oncoref
2026-06-25T23:09:44,680   Created temporary directory: /tmp/pip-wheel-e4qa67zy
2026-06-25T23:09:44,681   Destination directory: /tmp/pip-wheel-e4qa67zy
2026-06-25T23:09:44,683   Building wheel for oncoref (pyproject.toml): started
2026-06-25T23:09:44,684   Running command Building wheel for oncoref (pyproject.toml)
2026-06-25T23:09:45,326   running bdist_wheel
2026-06-25T23:09:45,344   running build
2026-06-25T23:09:45,344   running build_py
2026-06-25T23:09:45,351   creating build/lib/oncoref
2026-06-25T23:09:45,353   copying oncoref/ici_response.py -> build/lib/oncoref
2026-06-25T23:09:45,355   copying oncoref/coverage.py -> build/lib/oncoref
2026-06-25T23:09:45,358   copying oncoref/normalization.py -> build/lib/oncoref
2026-06-25T23:09:45,361   copying oncoref/gene_families.py -> build/lib/oncoref
2026-06-25T23:09:45,364   copying oncoref/tmb.py -> build/lib/oncoref
2026-06-25T23:09:45,366   copying oncoref/reference_data.py -> build/lib/oncoref
2026-06-25T23:09:45,368   copying oncoref/apd1.py -> build/lib/oncoref
2026-06-25T23:09:45,370   copying oncoref/cta.py -> build/lib/oncoref
2026-06-25T23:09:45,373   copying oncoref/__init__.py -> build/lib/oncoref
2026-06-25T23:09:45,375   copying oncoref/cta_curation_plots.py -> build/lib/oncoref
2026-06-25T23:09:45,377   copying oncoref/cta_peptides.py -> build/lib/oncoref
2026-06-25T23:09:45,379   copying oncoref/load_dataset.py -> build/lib/oncoref
2026-06-25T23:09:45,381   copying oncoref/fusions.py -> build/lib/oncoref
2026-06-25T23:09:45,383   copying oncoref/antigen_coverage.py -> build/lib/oncoref
2026-06-25T23:09:45,385   copying oncoref/samples.py -> build/lib/oncoref
2026-06-25T23:09:45,387   copying oncoref/cli.py -> build/lib/oncoref
2026-06-25T23:09:45,390   copying oncoref/cta_regen.py -> build/lib/oncoref
2026-06-25T23:09:45,393   copying oncoref/proteoforms.py -> build/lib/oncoref
2026-06-25T23:09:45,395   copying oncoref/ici.py -> build/lib/oncoref
2026-06-25T23:09:45,397   copying oncoref/cta_tissues.py -> build/lib/oncoref
2026-06-25T23:09:45,400   copying oncoref/cancer_ontology.py -> build/lib/oncoref
2026-06-25T23:09:45,401   copying oncoref/data_manifest.py -> build/lib/oncoref
2026-06-25T23:09:45,404   copying oncoref/catalog.py -> build/lib/oncoref
2026-06-25T23:09:45,406   copying oncoref/version.py -> build/lib/oncoref
2026-06-25T23:09:45,408   copying oncoref/data_bundle.py -> build/lib/oncoref
2026-06-25T23:09:45,410   copying oncoref/response_signatures.py -> build/lib/oncoref
2026-06-25T23:09:45,412   copying oncoref/hpa.py -> build/lib/oncoref
2026-06-25T23:09:45,414   copying oncoref/source_matrices.py -> build/lib/oncoref
2026-06-25T23:09:45,417   copying oncoref/expression_engine.py -> build/lib/oncoref
2026-06-25T23:09:45,419   copying oncoref/gene_qc.py -> build/lib/oncoref
2026-06-25T23:09:45,421   copying oncoref/gene_ids.py -> build/lib/oncoref
2026-06-25T23:09:45,423   copying oncoref/expression.py -> build/lib/oncoref
2026-06-25T23:09:45,427   copying oncoref/cancer_types.py -> build/lib/oncoref
2026-06-25T23:09:45,430   copying oncoref/cancer_genes.py -> build/lib/oncoref
2026-06-25T23:09:45,432   copying oncoref/expression_registry.py -> build/lib/oncoref
2026-06-25T23:09:45,435   copying oncoref/plots.py -> build/lib/oncoref
2026-06-25T23:09:45,438   copying oncoref/peptides.py -> build/lib/oncoref
2026-06-25T23:09:45,440   copying oncoref/incidence.py -> build/lib/oncoref
2026-06-25T23:09:45,442   copying oncoref/cta_coverage.py -> build/lib/oncoref
2026-06-25T23:09:45,444   copying oncoref/cohorts.py -> build/lib/oncoref
2026-06-25T23:09:45,445   copying oncoref/expression_builders.py -> build/lib/oncoref
2026-06-25T23:09:45,448   copying oncoref/genome.py -> build/lib/oncoref
2026-06-25T23:09:45,462   creating build/lib/oncoref/data
2026-06-25T23:09:45,463   copying oncoref/data/cancer-viral-antigens.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,466   copying oncoref/data/cancer-incidence-mortality.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,468   copying oncoref/data/cancer-code-burden-map.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,470   copying oncoref/data/proteoform-groups.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,472   copying oncoref/data/cancer-driver-genes.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,476   copying oncoref/data/tissue-burden-map.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,478   copying oncoref/data/family-burden-map.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,480   copying oncoref/data/cohort-registry.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,482   copying oncoref/data/mitochondrial-genes.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,484   copying oncoref/data/cancer-normal-tissue-map.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,486   copying oncoref/data/censored-gene-reference-tpm.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,489   copying oncoref/data/cancer-key-genes.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,494   copying oncoref/data/cancer-response-signatures.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,496   copying oncoref/data/disease-state-rules.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,498   copying oncoref/data/cancer-apd1-response.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,501   copying oncoref/data/cta-candidate-references.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,503   copying oncoref/data/proteoform-groups-genome.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,506   copying oncoref/data/source-matrices.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,508   copying oncoref/data/cancer-type-registry.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,511   copying oncoref/data/cancer-frameshift-burden.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,513   copying oncoref/data/numt-pseudogenes.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,515   copying oncoref/data/degenerate-subtype-pairs.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,518   copying oncoref/data/ribosomal-protein-genes.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,520   copying oncoref/data/cta-ihc-unreliable.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,522   copying oncoref/data/cancer-ici-response-estimates.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,528   copying oncoref/data/housekeeping-genes.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,530   copying oncoref/data/cancer-subtype-groupings.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,532   copying oncoref/data/narrative-gene-sets.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,534   copying oncoref/data/rrna-and-pseudogenes.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,537   copying oncoref/data/small-noncoding-rnas.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,541   copying oncoref/data/fusion-expression-effects.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,544   copying oncoref/data/fusion-surrogate-expression.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,546   copying oncoref/data/clean-tpm-censored-genes.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,550   copying oncoref/data/cancer-driver-variants.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,554   copying oncoref/data/cancer-tmb.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,557   copying oncoref/data/hemoglobin-genes.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,559   copying oncoref/data/ribosomal-protein-pseudogenes.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,562   copying oncoref/data/cancer-fusions.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,565   copying oncoref/data/cancer-cohort-aggregates.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,568   copying oncoref/data/rare-cancer-fusion-rules.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,571   copying oncoref/data/ensembl-id-aliases.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,581   copying oncoref/data/proteoform-collapse-overrides.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,584   copying oncoref/data/cancer-expression-source-candidates.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,587   copying oncoref/data/cancer-lineage-groups.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,589   copying oncoref/data/cdna-identical-gene-groups.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,592   copying oncoref/data/cancer-type-genes.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,595   copying oncoref/data/cancer-ici-response.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,599   copying oncoref/data/clean-tpm-biological-housekeeping-genes.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,601   copying oncoref/data/cancer-lineage-group-overrides.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,604   copying oncoref/data/histone-genes.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,607   copying oncoref/data/extra-tx-mappings.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,610   copying oncoref/data/nuclear-retained-lncrnas.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,612   copying oncoref/data/cancer-testis-antigens.csv -> build/lib/oncoref/data
2026-06-25T23:09:45,618   copying oncoref/data/cancer-reference-expression-samples.csv.gz -> build/lib/oncoref/data
2026-06-25T23:09:45,626   copying oncoref/data/canonical-gene-space.csv.gz -> build/lib/oncoref/data
2026-06-25T23:09:45,639   copying oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/lib/oncoref/data
2026-06-25T23:09:45,649   copying oncoref/data/expression_sources.yaml -> build/lib/oncoref/data
2026-06-25T23:09:45,663   installing to build/bdist.linux-armv7l/wheel
2026-06-25T23:09:45,663   running install
2026-06-25T23:09:45,687   running install_lib
2026-06-25T23:09:45,692   creating build/bdist.linux-armv7l/wheel
2026-06-25T23:09:45,694   creating build/bdist.linux-armv7l/wheel/oncoref
2026-06-25T23:09:45,696   copying build/lib/oncoref/ici_response.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,698   copying build/lib/oncoref/coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,700   copying build/lib/oncoref/normalization.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,703   copying build/lib/oncoref/gene_families.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,706   copying build/lib/oncoref/tmb.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,708   copying build/lib/oncoref/reference_data.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,710   copying build/lib/oncoref/apd1.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,712   copying build/lib/oncoref/cta.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,714   copying build/lib/oncoref/__init__.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,717   copying build/lib/oncoref/cta_curation_plots.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,719   copying build/lib/oncoref/cta_peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,721   copying build/lib/oncoref/load_dataset.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,723   copying build/lib/oncoref/fusions.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,726   copying build/lib/oncoref/antigen_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,728   copying build/lib/oncoref/samples.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,730   copying build/lib/oncoref/cli.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,732   copying build/lib/oncoref/cta_regen.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,735   copying build/lib/oncoref/proteoforms.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,738   copying build/lib/oncoref/ici.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,740   copying build/lib/oncoref/cta_tissues.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,742   copying build/lib/oncoref/cancer_ontology.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,744   copying build/lib/oncoref/data_manifest.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,746   copying build/lib/oncoref/catalog.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,748   copying build/lib/oncoref/version.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,750   copying build/lib/oncoref/data_bundle.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,752   copying build/lib/oncoref/response_signatures.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,754   copying build/lib/oncoref/hpa.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,756   copying build/lib/oncoref/source_matrices.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,759   copying build/lib/oncoref/expression_engine.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,761   copying build/lib/oncoref/gene_qc.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,763   copying build/lib/oncoref/gene_ids.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,766   creating build/bdist.linux-armv7l/wheel/oncoref/data
2026-06-25T23:09:45,767   copying build/lib/oncoref/data/cancer-viral-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,769   copying build/lib/oncoref/data/cancer-incidence-mortality.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,771   copying build/lib/oncoref/data/cancer-code-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,773   copying build/lib/oncoref/data/proteoform-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,775   copying build/lib/oncoref/data/cancer-driver-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,778   copying build/lib/oncoref/data/tissue-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,780   copying build/lib/oncoref/data/family-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,782   copying build/lib/oncoref/data/cohort-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,784   copying build/lib/oncoref/data/mitochondrial-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,785   copying build/lib/oncoref/data/cancer-normal-tissue-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,788   copying build/lib/oncoref/data/censored-gene-reference-tpm.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,790   copying build/lib/oncoref/data/cancer-key-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,795   copying build/lib/oncoref/data/cancer-response-signatures.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,796   copying build/lib/oncoref/data/disease-state-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,798   copying build/lib/oncoref/data/cancer-apd1-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,801   copying build/lib/oncoref/data/cta-candidate-references.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,803   copying build/lib/oncoref/data/proteoform-groups-genome.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,806   copying build/lib/oncoref/data/source-matrices.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,809   copying build/lib/oncoref/data/cancer-type-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,812   copying build/lib/oncoref/data/cancer-frameshift-burden.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,814   copying build/lib/oncoref/data/cancer-reference-expression-samples.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,822   copying build/lib/oncoref/data/numt-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,826   copying build/lib/oncoref/data/degenerate-subtype-pairs.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,828   copying build/lib/oncoref/data/ribosomal-protein-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,830   copying build/lib/oncoref/data/cta-ihc-unreliable.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,833   copying build/lib/oncoref/data/expression_sources.yaml -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,836   copying build/lib/oncoref/data/cancer-ici-response-estimates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,843   copying build/lib/oncoref/data/housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,845   copying build/lib/oncoref/data/cancer-subtype-groupings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,847   copying build/lib/oncoref/data/narrative-gene-sets.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,849   copying build/lib/oncoref/data/rrna-and-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,852   copying build/lib/oncoref/data/small-noncoding-rnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,858   copying build/lib/oncoref/data/fusion-expression-effects.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,860   copying build/lib/oncoref/data/fusion-surrogate-expression.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,863   copying build/lib/oncoref/data/clean-tpm-censored-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,868   copying build/lib/oncoref/data/cancer-driver-variants.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,871   copying build/lib/oncoref/data/cancer-tmb.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,874   copying build/lib/oncoref/data/hemoglobin-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,876   copying build/lib/oncoref/data/ribosomal-protein-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,880   copying build/lib/oncoref/data/cancer-fusions.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,883   copying build/lib/oncoref/data/cancer-cohort-aggregates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,886   copying build/lib/oncoref/data/rare-cancer-fusion-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,888   copying build/lib/oncoref/data/ensembl-id-aliases.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,899   copying build/lib/oncoref/data/proteoform-collapse-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,901   copying build/lib/oncoref/data/cancer-expression-source-candidates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,904   copying build/lib/oncoref/data/cancer-lineage-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,906   copying build/lib/oncoref/data/cdna-identical-gene-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,909   copying build/lib/oncoref/data/cancer-type-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,912   copying build/lib/oncoref/data/cancer-ici-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,915   copying build/lib/oncoref/data/clean-tpm-biological-housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,918   copying build/lib/oncoref/data/canonical-gene-space.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,931   copying build/lib/oncoref/data/cancer-lineage-group-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,933   copying build/lib/oncoref/data/histone-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,935   copying build/lib/oncoref/data/extra-tx-mappings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,938   copying build/lib/oncoref/data/nuclear-retained-lncrnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,940   copying build/lib/oncoref/data/cancer-testis-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,946   copying build/lib/oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-25T23:09:45,958   copying build/lib/oncoref/expression.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,962   copying build/lib/oncoref/cancer_types.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,966   copying build/lib/oncoref/cancer_genes.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,969   copying build/lib/oncoref/expression_registry.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,971   copying build/lib/oncoref/plots.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,975   copying build/lib/oncoref/peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,978   copying build/lib/oncoref/incidence.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,980   copying build/lib/oncoref/cta_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,982   copying build/lib/oncoref/cohorts.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,985   copying build/lib/oncoref/expression_builders.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,988   copying build/lib/oncoref/genome.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-25T23:09:45,990   running install_egg_info
2026-06-25T23:09:46,003   running egg_info
2026-06-25T23:09:46,008   writing oncoref.egg-info/PKG-INFO
2026-06-25T23:09:46,013   writing dependency_links to oncoref.egg-info/dependency_links.txt
2026-06-25T23:09:46,015   writing entry points to oncoref.egg-info/entry_points.txt
2026-06-25T23:09:46,017   writing requirements to oncoref.egg-info/requires.txt
2026-06-25T23:09:46,018   writing top-level names to oncoref.egg-info/top_level.txt
2026-06-25T23:09:46,037   reading manifest file 'oncoref.egg-info/SOURCES.txt'
2026-06-25T23:09:46,045   reading manifest template 'MANIFEST.in'
2026-06-25T23:09:46,047   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression'
2026-06-25T23:09:46,048   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles'
2026-06-25T23:09:46,050   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives'
2026-06-25T23:09:46,051   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5'
2026-06-25T23:09:46,052   warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv'
2026-06-25T23:09:46,053   warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv'
2026-06-25T23:09:46,053   adding license file 'LICENSE'
2026-06-25T23:09:46,061   writing manifest file 'oncoref.egg-info/SOURCES.txt'
2026-06-25T23:09:46,063   Copying oncoref.egg-info to build/bdist.linux-armv7l/wheel/./oncoref-1.8.10-py3.11.egg-info
2026-06-25T23:09:46,076   running install_scripts
2026-06-25T23:09:46,088   creating build/bdist.linux-armv7l/wheel/oncoref-1.8.10.dist-info/WHEEL
2026-06-25T23:09:46,091   creating '/tmp/pip-wheel-e4qa67zy/.tmp-4uvuexrc/oncoref-1.8.10-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2026-06-25T23:09:46,095   adding 'oncoref/__init__.py'
2026-06-25T23:09:46,097   adding 'oncoref/antigen_coverage.py'
2026-06-25T23:09:46,098   adding 'oncoref/apd1.py'
2026-06-25T23:09:46,100   adding 'oncoref/cancer_genes.py'
2026-06-25T23:09:46,101   adding 'oncoref/cancer_ontology.py'
2026-06-25T23:09:46,108   adding 'oncoref/cancer_types.py'
2026-06-25T23:09:46,111   adding 'oncoref/catalog.py'
2026-06-25T23:09:46,114   adding 'oncoref/cli.py'
2026-06-25T23:09:46,115   adding 'oncoref/cohorts.py'
2026-06-25T23:09:46,119   adding 'oncoref/coverage.py'
2026-06-25T23:09:46,122   adding 'oncoref/cta.py'
2026-06-25T23:09:46,123   adding 'oncoref/cta_coverage.py'
2026-06-25T23:09:46,125   adding 'oncoref/cta_curation_plots.py'
2026-06-25T23:09:46,127   adding 'oncoref/cta_peptides.py'
2026-06-25T23:09:46,130   adding 'oncoref/cta_regen.py'
2026-06-25T23:09:46,131   adding 'oncoref/cta_tissues.py'
2026-06-25T23:09:46,134   adding 'oncoref/data_bundle.py'
2026-06-25T23:09:46,136   adding 'oncoref/data_manifest.py'
2026-06-25T23:09:46,144   adding 'oncoref/expression.py'
2026-06-25T23:09:46,147   adding 'oncoref/expression_builders.py'
2026-06-25T23:09:46,149   adding 'oncoref/expression_engine.py'
2026-06-25T23:09:46,150   adding 'oncoref/expression_registry.py'
2026-06-25T23:09:46,152   adding 'oncoref/fusions.py'
2026-06-25T23:09:46,154   adding 'oncoref/gene_families.py'
2026-06-25T23:09:46,156   adding 'oncoref/gene_ids.py'
2026-06-25T23:09:46,158   adding 'oncoref/gene_qc.py'
2026-06-25T23:09:46,160   adding 'oncoref/genome.py'
2026-06-25T23:09:46,162   adding 'oncoref/hpa.py'
2026-06-25T23:09:46,166   adding 'oncoref/ici.py'
2026-06-25T23:09:46,168   adding 'oncoref/ici_response.py'
2026-06-25T23:09:46,170   adding 'oncoref/incidence.py'
2026-06-25T23:09:46,171   adding 'oncoref/load_dataset.py'
2026-06-25T23:09:46,175   adding 'oncoref/normalization.py'
2026-06-25T23:09:46,178   adding 'oncoref/peptides.py'
2026-06-25T23:09:46,185   adding 'oncoref/plots.py'
2026-06-25T23:09:46,188   adding 'oncoref/proteoforms.py'
2026-06-25T23:09:46,190   adding 'oncoref/reference_data.py'
2026-06-25T23:09:46,191   adding 'oncoref/response_signatures.py'
2026-06-25T23:09:46,193   adding 'oncoref/samples.py'
2026-06-25T23:09:46,194   adding 'oncoref/source_matrices.py'
2026-06-25T23:09:46,196   adding 'oncoref/tmb.py'
2026-06-25T23:09:46,197   adding 'oncoref/version.py'
2026-06-25T23:09:46,201   adding 'oncoref/data/cancer-apd1-response.csv'
2026-06-25T23:09:46,202   adding 'oncoref/data/cancer-code-burden-map.csv'
2026-06-25T23:09:46,204   adding 'oncoref/data/cancer-cohort-aggregates.csv'
2026-06-25T23:09:46,209   adding 'oncoref/data/cancer-driver-genes.csv'
2026-06-25T23:09:46,211   adding 'oncoref/data/cancer-driver-variants.csv'
2026-06-25T23:09:46,214   adding 'oncoref/data/cancer-expression-source-candidates.csv'
2026-06-25T23:09:46,215   adding 'oncoref/data/cancer-frameshift-burden.csv'
2026-06-25T23:09:46,218   adding 'oncoref/data/cancer-fusions.csv'
2026-06-25T23:09:46,236   adding 'oncoref/data/cancer-ici-response-estimates.csv'
2026-06-25T23:09:46,240   adding 'oncoref/data/cancer-ici-response.csv'
2026-06-25T23:09:46,242   adding 'oncoref/data/cancer-incidence-mortality.csv'
2026-06-25T23:09:46,256   adding 'oncoref/data/cancer-key-genes.csv'
2026-06-25T23:09:46,258   adding 'oncoref/data/cancer-lineage-group-overrides.csv'
2026-06-25T23:09:46,259   adding 'oncoref/data/cancer-lineage-groups.csv'
2026-06-25T23:09:46,261   adding 'oncoref/data/cancer-normal-tissue-map.csv'
2026-06-25T23:09:46,290   adding 'oncoref/data/cancer-reference-expression-samples.csv.gz'
2026-06-25T23:09:46,293   adding 'oncoref/data/cancer-response-signatures.csv'
2026-06-25T23:09:46,294   adding 'oncoref/data/cancer-subtype-groupings.csv'
2026-06-25T23:09:46,305   adding 'oncoref/data/cancer-testis-antigens.csv'
2026-06-25T23:09:46,308   adding 'oncoref/data/cancer-tmb.csv'
2026-06-25T23:09:46,311   adding 'oncoref/data/cancer-type-genes.csv'
2026-06-25T23:09:46,314   adding 'oncoref/data/cancer-type-registry.csv'
2026-06-25T23:09:46,316   adding 'oncoref/data/cancer-viral-antigens.csv'
2026-06-25T23:09:46,368   adding 'oncoref/data/canonical-gene-space.csv.gz'
2026-06-25T23:09:46,373   adding 'oncoref/data/cdna-identical-gene-groups.csv'
2026-06-25T23:09:46,377   adding 'oncoref/data/censored-gene-reference-tpm.csv'
2026-06-25T23:09:46,379   adding 'oncoref/data/clean-tpm-biological-housekeeping-genes.csv'
2026-06-25T23:09:46,389   adding 'oncoref/data/clean-tpm-censored-genes.csv'
2026-06-25T23:09:46,391   adding 'oncoref/data/cohort-registry.csv'
2026-06-25T23:09:46,393   adding 'oncoref/data/cta-candidate-references.csv'
2026-06-25T23:09:46,394   adding 'oncoref/data/cta-ihc-unreliable.csv'
2026-06-25T23:09:46,395   adding 'oncoref/data/degenerate-subtype-pairs.csv'
2026-06-25T23:09:46,397   adding 'oncoref/data/disease-state-rules.csv'
2026-06-25T23:09:46,423   adding 'oncoref/data/ensembl-id-aliases.csv'
2026-06-25T23:09:46,430   adding 'oncoref/data/expression_sources.yaml'
2026-06-25T23:09:46,431   adding 'oncoref/data/extra-tx-mappings.csv'
2026-06-25T23:09:46,433   adding 'oncoref/data/family-burden-map.csv'
2026-06-25T23:09:46,434   adding 'oncoref/data/fusion-expression-effects.csv'
2026-06-25T23:09:46,435   adding 'oncoref/data/fusion-surrogate-expression.csv'
2026-06-25T23:09:46,437   adding 'oncoref/data/hemoglobin-genes.csv'
2026-06-25T23:09:46,438   adding 'oncoref/data/histone-genes.csv'
2026-06-25T23:09:46,439   adding 'oncoref/data/housekeeping-genes.csv'
2026-06-25T23:09:46,441   adding 'oncoref/data/mitochondrial-genes.csv'
2026-06-25T23:09:46,442   adding 'oncoref/data/narrative-gene-sets.csv'
2026-06-25T23:09:46,482   adding 'oncoref/data/ncbi-symbol-synonyms.csv.gz'
2026-06-25T23:09:46,486   adding 'oncoref/data/nuclear-retained-lncrnas.csv'
2026-06-25T23:09:46,488   adding 'oncoref/data/numt-pseudogenes.csv'
2026-06-25T23:09:46,489   adding 'oncoref/data/proteoform-collapse-overrides.csv'
2026-06-25T23:09:46,492   adding 'oncoref/data/proteoform-groups-genome.csv'
2026-06-25T23:09:46,493   adding 'oncoref/data/proteoform-groups.csv'
2026-06-25T23:09:46,495   adding 'oncoref/data/rare-cancer-fusion-rules.csv'
2026-06-25T23:09:46,497   adding 'oncoref/data/ribosomal-protein-genes.csv'
2026-06-25T23:09:46,503   adding 'oncoref/data/ribosomal-protein-pseudogenes.csv'
2026-06-25T23:09:46,506   adding 'oncoref/data/rrna-and-pseudogenes.csv'
2026-06-25T23:09:46,524   adding 'oncoref/data/small-noncoding-rnas.csv'
2026-06-25T23:09:46,526   adding 'oncoref/data/source-matrices.csv'
2026-06-25T23:09:46,528   adding 'oncoref/data/tissue-burden-map.csv'
2026-06-25T23:09:46,531   adding 'oncoref-1.8.10.dist-info/licenses/LICENSE'
2026-06-25T23:09:46,533   adding 'oncoref-1.8.10.dist-info/METADATA'
2026-06-25T23:09:46,534   adding 'oncoref-1.8.10.dist-info/WHEEL'
2026-06-25T23:09:46,535   adding 'oncoref-1.8.10.dist-info/entry_points.txt'
2026-06-25T23:09:46,537   adding 'oncoref-1.8.10.dist-info/top_level.txt'
2026-06-25T23:09:46,538   adding 'oncoref-1.8.10.dist-info/RECORD'
2026-06-25T23:09:46,561   removing build/bdist.linux-armv7l/wheel
2026-06-25T23:09:46,685   Building wheel for oncoref (pyproject.toml): finished with status 'done'
2026-06-25T23:09:46,724   Created wheel for oncoref: filename=oncoref-1.8.10-py3-none-any.whl size=1662236 sha256=3e789fd35641073e8afc8885dcef12d74a2323c2e0c8dad7b5e369392675e83a
2026-06-25T23:09:46,725   Stored in directory: /tmp/pip-ephem-wheel-cache-d77wsp7q/wheels/c3/81/13/abff38e68b4686aff86b5c09b4b499cfdbff6c21ff3b14b956
2026-06-25T23:09:46,740 Successfully built oncoref
2026-06-25T23:09:46,781 Removed build tracker: '/tmp/pip-build-tracker-kl97pgol'