2026-06-24T02:36:51,725 Created temporary directory: /tmp/pip-ephem-wheel-cache-lf5bhafv
2026-06-24T02:36:51,727 Created temporary directory: /tmp/pip-build-tracker-irfi93_d
2026-06-24T02:36:51,727 Initialized build tracking at /tmp/pip-build-tracker-irfi93_d
2026-06-24T02:36:51,728 Created build tracker: /tmp/pip-build-tracker-irfi93_d
2026-06-24T02:36:51,728 Entered build tracker: /tmp/pip-build-tracker-irfi93_d
2026-06-24T02:36:51,729 Created temporary directory: /tmp/pip-wheel-2eii2cfo
2026-06-24T02:36:51,732 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
2026-06-24T02:36:51,734 Created temporary directory: /tmp/pip-ephem-wheel-cache-nw8yvb7s
2026-06-24T02:36:51,756 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-06-24T02:36:51,759 2 location(s) to search for versions of oncoref:
2026-06-24T02:36:51,759 * https://pypi.org/simple/oncoref/
2026-06-24T02:36:51,759 * https://www.piwheels.org/simple/oncoref/
2026-06-24T02:36:51,760 Fetching project page and analyzing links: https://pypi.org/simple/oncoref/
2026-06-24T02:36:51,761 Getting page https://pypi.org/simple/oncoref/
2026-06-24T02:36:51,762 Found index url https://pypi.org/simple
2026-06-24T02:36:52,087 Fetched page https://pypi.org/simple/oncoref/ as application/vnd.pypi.simple.v1+json
2026-06-24T02:36:52,091   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)
2026-06-24T02:36:52,093   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
2026-06-24T02:36:52,093   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)
2026-06-24T02:36:52,094   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
2026-06-24T02:36:52,095   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)
2026-06-24T02:36:52,096   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
2026-06-24T02:36:52,097   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)
2026-06-24T02:36:52,098   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
2026-06-24T02:36:52,098   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)
2026-06-24T02:36:52,099   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
2026-06-24T02:36:52,100   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)
2026-06-24T02:36:52,101   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
2026-06-24T02:36:52,102   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)
2026-06-24T02:36:52,102   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
2026-06-24T02:36:52,103   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)
2026-06-24T02:36:52,104   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
2026-06-24T02:36:52,104   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)
2026-06-24T02:36:52,105   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
2026-06-24T02:36:52,106 Fetching project page and analyzing links: https://www.piwheels.org/simple/oncoref/
2026-06-24T02:36:52,107 Getting page https://www.piwheels.org/simple/oncoref/
2026-06-24T02:36:52,108 Found index url https://www.piwheels.org/simple
2026-06-24T02:36:52,417 Fetched page https://www.piwheels.org/simple/oncoref/ as text/html
2026-06-24T02:36:52,420   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)
2026-06-24T02:36:52,421   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)
2026-06-24T02:36:52,422   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)
2026-06-24T02:36:52,422   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)
2026-06-24T02:36:52,423   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)
2026-06-24T02:36:52,423   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)
2026-06-24T02:36:52,424   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)
2026-06-24T02:36:52,424   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)
2026-06-24T02:36:52,425 Skipping link: not a file: https://www.piwheels.org/simple/oncoref/
2026-06-24T02:36:52,425 Skipping link: not a file: https://pypi.org/simple/oncoref/
2026-06-24T02:36:52,446 Given no hashes to check 1 links for project 'oncoref': discarding no candidates
2026-06-24T02:36:52,464 Collecting oncoref==1.8.6
2026-06-24T02:36:52,467   Created temporary directory: /tmp/pip-unpack-ejj8uvw7
2026-06-24T02:36:52,796   Downloading oncoref-1.8.6.tar.gz (1.7 MB)
2026-06-24T02:36:53,516   Added oncoref==1.8.6 from https://files.pythonhosted.org/packages/fe/29/0640ff92bcb51841b69a4d04ccf94a5173a18ee10c54786b959026ca4362/oncoref-1.8.6.tar.gz to build tracker '/tmp/pip-build-tracker-irfi93_d'
2026-06-24T02:36:53,526   Created temporary directory: /tmp/pip-build-env-tnl5076g
2026-06-24T02:36:53,531   Installing build dependencies: started
2026-06-24T02:36:53,533   Running command pip subprocess to install build dependencies
2026-06-24T02:36:54,687   Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11)
2026-06-24T02:36:55,104   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
2026-06-24T02:36:55,127   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-06-24T02:36:57,139   Collecting setuptools>=61.0
2026-06-24T02:36:57,141     Obtaining dependency information for setuptools>=61.0 from https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl.metadata
2026-06-24T02:36:57,156     Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl.metadata (6.5 kB)
2026-06-24T02:36:57,391   Collecting wheel
2026-06-24T02:36:57,392     Obtaining dependency information for wheel from https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata
2026-06-24T02:36:57,406     Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB)
2026-06-24T02:36:57,591   Collecting packaging>=24.0
2026-06-24T02:36:57,592     Obtaining dependency information for packaging>=24.0 from https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata
2026-06-24T02:36:57,606     Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata (3.5 kB)
2026-06-24T02:36:57,798   Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB)
2026-06-24T02:36:57,819   Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB)
2026-06-24T02:36:57,917   Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB)
2026-06-24T02:36:57,949   Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB)
2026-06-24T02:36:57,974   Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB)
2026-06-24T02:36:58,070   Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB)
2026-06-24T02:37:00,820   Installing collected packages: setuptools, packaging, wheel
2026-06-24T02:37:04,234     Creating /tmp/pip-build-env-tnl5076g/overlay/local/bin
2026-06-24T02:37:04,237     changing mode of /tmp/pip-build-env-tnl5076g/overlay/local/bin/wheel to 755
2026-06-24T02:37:04,259   Successfully installed packaging-26.2 setuptools-82.0.1 wheel-0.47.0
2026-06-24T02:37:04,548   Installing build dependencies: finished with status 'done'
2026-06-24T02:37:04,555   Getting requirements to build wheel: started
2026-06-24T02:37:04,556   Running command Getting requirements to build wheel
2026-06-24T02:37:05,276   running egg_info
2026-06-24T02:37:05,282   writing oncoref.egg-info/PKG-INFO
2026-06-24T02:37:05,288   writing dependency_links to oncoref.egg-info/dependency_links.txt
2026-06-24T02:37:05,290   writing entry points to oncoref.egg-info/entry_points.txt
2026-06-24T02:37:05,293   writing requirements to oncoref.egg-info/requires.txt
2026-06-24T02:37:05,295   writing top-level names to oncoref.egg-info/top_level.txt
2026-06-24T02:37:05,329   reading manifest file 'oncoref.egg-info/SOURCES.txt'
2026-06-24T02:37:05,338   reading manifest template 'MANIFEST.in'
2026-06-24T02:37:05,341   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression'
2026-06-24T02:37:05,342   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles'
2026-06-24T02:37:05,344   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives'
2026-06-24T02:37:05,345   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5'
2026-06-24T02:37:05,346   warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv'
2026-06-24T02:37:05,348   warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv'
2026-06-24T02:37:05,348   adding license file 'LICENSE'
2026-06-24T02:37:05,357   writing manifest file 'oncoref.egg-info/SOURCES.txt'
2026-06-24T02:37:05,456   Getting requirements to build wheel: finished with status 'done'
2026-06-24T02:37:05,460   Created temporary directory: /tmp/pip-modern-metadata-y0d0udb6
2026-06-24T02:37:05,463   Preparing metadata (pyproject.toml): started
2026-06-24T02:37:05,464   Running command Preparing metadata (pyproject.toml)
2026-06-24T02:37:06,149   running dist_info
2026-06-24T02:37:06,159   creating /tmp/pip-modern-metadata-y0d0udb6/oncoref.egg-info
2026-06-24T02:37:06,160   writing /tmp/pip-modern-metadata-y0d0udb6/oncoref.egg-info/PKG-INFO
2026-06-24T02:37:06,166   writing dependency_links to /tmp/pip-modern-metadata-y0d0udb6/oncoref.egg-info/dependency_links.txt
2026-06-24T02:37:06,168   writing entry points to /tmp/pip-modern-metadata-y0d0udb6/oncoref.egg-info/entry_points.txt
2026-06-24T02:37:06,170   writing requirements to /tmp/pip-modern-metadata-y0d0udb6/oncoref.egg-info/requires.txt
2026-06-24T02:37:06,172   writing top-level names to /tmp/pip-modern-metadata-y0d0udb6/oncoref.egg-info/top_level.txt
2026-06-24T02:37:06,173   writing manifest file '/tmp/pip-modern-metadata-y0d0udb6/oncoref.egg-info/SOURCES.txt'
2026-06-24T02:37:06,205   reading manifest file '/tmp/pip-modern-metadata-y0d0udb6/oncoref.egg-info/SOURCES.txt'
2026-06-24T02:37:06,207   reading manifest template 'MANIFEST.in'
2026-06-24T02:37:06,209   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression'
2026-06-24T02:37:06,209   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles'
2026-06-24T02:37:06,210   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives'
2026-06-24T02:37:06,211   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5'
2026-06-24T02:37:06,212   warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv'
2026-06-24T02:37:06,213   warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv'
2026-06-24T02:37:06,213   adding license file 'LICENSE'
2026-06-24T02:37:06,220   writing manifest file '/tmp/pip-modern-metadata-y0d0udb6/oncoref.egg-info/SOURCES.txt'
2026-06-24T02:37:06,221   creating '/tmp/pip-modern-metadata-y0d0udb6/oncoref-1.8.6.dist-info'
2026-06-24T02:37:06,348   Preparing metadata (pyproject.toml): finished with status 'done'
2026-06-24T02:37:06,353   Source in /tmp/pip-wheel-2eii2cfo/oncoref_e028dd029fbb426483a526f60fe8eab3 has version 1.8.6, which satisfies requirement oncoref==1.8.6 from https://files.pythonhosted.org/packages/fe/29/0640ff92bcb51841b69a4d04ccf94a5173a18ee10c54786b959026ca4362/oncoref-1.8.6.tar.gz
2026-06-24T02:37:06,354   Removed oncoref==1.8.6 from https://files.pythonhosted.org/packages/fe/29/0640ff92bcb51841b69a4d04ccf94a5173a18ee10c54786b959026ca4362/oncoref-1.8.6.tar.gz from build tracker '/tmp/pip-build-tracker-irfi93_d'
2026-06-24T02:37:06,360 Created temporary directory: /tmp/pip-unpack-44fv8zvt
2026-06-24T02:37:06,361 Building wheels for collected packages: oncoref
2026-06-24T02:37:06,365   Created temporary directory: /tmp/pip-wheel-qvdcy5wq
2026-06-24T02:37:06,366   Destination directory: /tmp/pip-wheel-qvdcy5wq
2026-06-24T02:37:06,368   Building wheel for oncoref (pyproject.toml): started
2026-06-24T02:37:06,369   Running command Building wheel for oncoref (pyproject.toml)
2026-06-24T02:37:07,000   running bdist_wheel
2026-06-24T02:37:07,017   running build
2026-06-24T02:37:07,018   running build_py
2026-06-24T02:37:07,025   creating build/lib/oncoref
2026-06-24T02:37:07,027   copying oncoref/load_dataset.py -> build/lib/oncoref
2026-06-24T02:37:07,029   copying oncoref/catalog.py -> build/lib/oncoref
2026-06-24T02:37:07,032   copying oncoref/ici.py -> build/lib/oncoref
2026-06-24T02:37:07,034   copying oncoref/gene_ids.py -> build/lib/oncoref
2026-06-24T02:37:07,036   copying oncoref/apd1.py -> build/lib/oncoref
2026-06-24T02:37:07,038   copying oncoref/cancer_types.py -> build/lib/oncoref
2026-06-24T02:37:07,041   copying oncoref/expression_engine.py -> build/lib/oncoref
2026-06-24T02:37:07,043   copying oncoref/cta_curation_plots.py -> build/lib/oncoref
2026-06-24T02:37:07,045   copying oncoref/reference_data.py -> build/lib/oncoref
2026-06-24T02:37:07,048   copying oncoref/version.py -> build/lib/oncoref
2026-06-24T02:37:07,049   copying oncoref/expression_builders.py -> build/lib/oncoref
2026-06-24T02:37:07,052   copying oncoref/plots.py -> build/lib/oncoref
2026-06-24T02:37:07,055   copying oncoref/ici_response.py -> build/lib/oncoref
2026-06-24T02:37:07,057   copying oncoref/cta_regen.py -> build/lib/oncoref
2026-06-24T02:37:07,059   copying oncoref/data_manifest.py -> build/lib/oncoref
2026-06-24T02:37:07,062   copying oncoref/cancer_genes.py -> build/lib/oncoref
2026-06-24T02:37:07,064   copying oncoref/cli.py -> build/lib/oncoref
2026-06-24T02:37:07,067   copying oncoref/cta.py -> build/lib/oncoref
2026-06-24T02:37:07,069   copying oncoref/cta_coverage.py -> build/lib/oncoref
2026-06-24T02:37:07,071   copying oncoref/gene_families.py -> build/lib/oncoref
2026-06-24T02:37:07,073   copying oncoref/proteoforms.py -> build/lib/oncoref
2026-06-24T02:37:07,076   copying oncoref/data_bundle.py -> build/lib/oncoref
2026-06-24T02:37:07,079   copying oncoref/response_signatures.py -> build/lib/oncoref
2026-06-24T02:37:07,080   copying oncoref/expression_registry.py -> build/lib/oncoref
2026-06-24T02:37:07,083   copying oncoref/normalization.py -> build/lib/oncoref
2026-06-24T02:37:07,086   copying oncoref/incidence.py -> build/lib/oncoref
2026-06-24T02:37:07,088   copying oncoref/__init__.py -> build/lib/oncoref
2026-06-24T02:37:07,090   copying oncoref/cancer_ontology.py -> build/lib/oncoref
2026-06-24T02:37:07,092   copying oncoref/peptides.py -> build/lib/oncoref
2026-06-24T02:37:07,094   copying oncoref/antigen_coverage.py -> build/lib/oncoref
2026-06-24T02:37:07,096   copying oncoref/tmb.py -> build/lib/oncoref
2026-06-24T02:37:07,098   copying oncoref/source_matrices.py -> build/lib/oncoref
2026-06-24T02:37:07,100   copying oncoref/genome.py -> build/lib/oncoref
2026-06-24T02:37:07,103   copying oncoref/gene_qc.py -> build/lib/oncoref
2026-06-24T02:37:07,105   copying oncoref/hpa.py -> build/lib/oncoref
2026-06-24T02:37:07,107   copying oncoref/cta_peptides.py -> build/lib/oncoref
2026-06-24T02:37:07,109   copying oncoref/coverage.py -> build/lib/oncoref
2026-06-24T02:37:07,111   copying oncoref/expression.py -> build/lib/oncoref
2026-06-24T02:37:07,114   copying oncoref/fusions.py -> build/lib/oncoref
2026-06-24T02:37:07,116   copying oncoref/samples.py -> build/lib/oncoref
2026-06-24T02:37:07,118   copying oncoref/cta_tissues.py -> build/lib/oncoref
2026-06-24T02:37:07,120   copying oncoref/cohorts.py -> build/lib/oncoref
2026-06-24T02:37:07,134   creating build/lib/oncoref/data
2026-06-24T02:37:07,135   copying oncoref/data/cohort-registry.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,138   copying oncoref/data/cancer-incidence-mortality.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,141   copying oncoref/data/histone-genes.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,143   copying oncoref/data/cta-candidate-references.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,145   copying oncoref/data/cancer-driver-genes.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,149   copying oncoref/data/cancer-lineage-groups.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,151   copying oncoref/data/cancer-cohort-aggregates.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,153   copying oncoref/data/cancer-subtype-groupings.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,155   copying oncoref/data/small-noncoding-rnas.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,160   copying oncoref/data/clean-tpm-biological-housekeeping-genes.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,163   copying oncoref/data/numt-pseudogenes.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,166   copying oncoref/data/cancer-response-signatures.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,168   copying oncoref/data/hemoglobin-genes.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,170   copying oncoref/data/narrative-gene-sets.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,172   copying oncoref/data/cancer-fusions.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,175   copying oncoref/data/proteoform-groups.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,177   copying oncoref/data/cancer-type-registry.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,180   copying oncoref/data/cancer-testis-antigens.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,185   copying oncoref/data/extra-tx-mappings.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,187   copying oncoref/data/mitochondrial-genes.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,189   copying oncoref/data/rare-cancer-fusion-rules.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,192   copying oncoref/data/cancer-viral-antigens.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,194   copying oncoref/data/fusion-surrogate-expression.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,196   copying oncoref/data/cancer-type-genes.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,199   copying oncoref/data/nuclear-retained-lncrnas.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,201   copying oncoref/data/degenerate-subtype-pairs.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,204   copying oncoref/data/cancer-frameshift-burden.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,206   copying oncoref/data/family-burden-map.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,208   copying oncoref/data/censored-gene-reference-tpm.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,211   copying oncoref/data/rrna-and-pseudogenes.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,214   copying oncoref/data/ensembl-id-aliases.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,224   copying oncoref/data/cancer-apd1-response.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,227   copying oncoref/data/cancer-expression-source-candidates.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,230   copying oncoref/data/cancer-ici-response-estimates.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,236   copying oncoref/data/cancer-key-genes.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,241   copying oncoref/data/ribosomal-protein-genes.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,244   copying oncoref/data/tissue-burden-map.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,246   copying oncoref/data/cancer-lineage-group-overrides.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,249   copying oncoref/data/clean-tpm-censored-genes.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,253   copying oncoref/data/cancer-code-burden-map.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,255   copying oncoref/data/cancer-ici-response.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,258   copying oncoref/data/housekeeping-genes.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,260   copying oncoref/data/cta-ihc-unreliable.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,262   copying oncoref/data/disease-state-rules.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,264   copying oncoref/data/proteoform-groups-genome.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,267   copying oncoref/data/ribosomal-protein-pseudogenes.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,271   copying oncoref/data/cancer-tmb.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,273   copying oncoref/data/cdna-identical-gene-groups.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,276   copying oncoref/data/cancer-driver-variants.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,279   copying oncoref/data/fusion-expression-effects.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,281   copying oncoref/data/source-matrices.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,284   copying oncoref/data/proteoform-collapse-overrides.csv -> build/lib/oncoref/data
2026-06-24T02:37:07,286   copying oncoref/data/cancer-reference-expression-samples.csv.gz -> build/lib/oncoref/data
2026-06-24T02:37:07,292   copying oncoref/data/canonical-gene-space.csv.gz -> build/lib/oncoref/data
2026-06-24T02:37:07,302   copying oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/lib/oncoref/data
2026-06-24T02:37:07,310   copying oncoref/data/expression_sources.yaml -> build/lib/oncoref/data
2026-06-24T02:37:07,325   installing to build/bdist.linux-armv7l/wheel
2026-06-24T02:37:07,325   running install
2026-06-24T02:37:07,349   running install_lib
2026-06-24T02:37:07,355   creating build/bdist.linux-armv7l/wheel
2026-06-24T02:37:07,358   creating build/bdist.linux-armv7l/wheel/oncoref
2026-06-24T02:37:07,359   copying build/lib/oncoref/load_dataset.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,362   copying build/lib/oncoref/catalog.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,365   copying build/lib/oncoref/ici.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,368   copying build/lib/oncoref/gene_ids.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,370   copying build/lib/oncoref/apd1.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,373   copying build/lib/oncoref/cancer_types.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,376   copying build/lib/oncoref/expression_engine.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,378   copying build/lib/oncoref/cta_curation_plots.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,381   copying build/lib/oncoref/reference_data.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,383   copying build/lib/oncoref/version.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,385   copying build/lib/oncoref/expression_builders.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,388   copying build/lib/oncoref/plots.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,392   copying build/lib/oncoref/ici_response.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,394   copying build/lib/oncoref/cta_regen.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,396   copying build/lib/oncoref/data_manifest.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,399   copying build/lib/oncoref/cancer_genes.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,402   copying build/lib/oncoref/cli.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,405   copying build/lib/oncoref/cta.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,407   copying build/lib/oncoref/cta_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,409   copying build/lib/oncoref/gene_families.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,412   copying build/lib/oncoref/proteoforms.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,415   copying build/lib/oncoref/data_bundle.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,417   copying build/lib/oncoref/response_signatures.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,419   copying build/lib/oncoref/expression_registry.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,422   copying build/lib/oncoref/normalization.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,424   copying build/lib/oncoref/incidence.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,427   copying build/lib/oncoref/__init__.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,429   copying build/lib/oncoref/cancer_ontology.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,432   copying build/lib/oncoref/peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,434   copying build/lib/oncoref/antigen_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,436   copying build/lib/oncoref/tmb.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,440   creating build/bdist.linux-armv7l/wheel/oncoref/data
2026-06-24T02:37:07,441   copying build/lib/oncoref/data/cohort-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,444   copying build/lib/oncoref/data/cancer-incidence-mortality.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,446   copying build/lib/oncoref/data/histone-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,448   copying build/lib/oncoref/data/cta-candidate-references.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,450   copying build/lib/oncoref/data/cancer-driver-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,454   copying build/lib/oncoref/data/cancer-reference-expression-samples.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,462   copying build/lib/oncoref/data/cancer-lineage-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,464   copying build/lib/oncoref/data/canonical-gene-space.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,477   copying build/lib/oncoref/data/cancer-cohort-aggregates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,480   copying build/lib/oncoref/data/cancer-subtype-groupings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,482   copying build/lib/oncoref/data/small-noncoding-rnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,488   copying build/lib/oncoref/data/clean-tpm-biological-housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,490   copying build/lib/oncoref/data/numt-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,493   copying build/lib/oncoref/data/cancer-response-signatures.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,495   copying build/lib/oncoref/data/hemoglobin-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,498   copying build/lib/oncoref/data/narrative-gene-sets.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,500   copying build/lib/oncoref/data/cancer-fusions.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,503   copying build/lib/oncoref/data/proteoform-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,505   copying build/lib/oncoref/data/cancer-type-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,508   copying build/lib/oncoref/data/cancer-testis-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,514   copying build/lib/oncoref/data/extra-tx-mappings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,516   copying build/lib/oncoref/data/mitochondrial-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,518   copying build/lib/oncoref/data/rare-cancer-fusion-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,521   copying build/lib/oncoref/data/cancer-viral-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,523   copying build/lib/oncoref/data/fusion-surrogate-expression.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,525   copying build/lib/oncoref/data/cancer-type-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,528   copying build/lib/oncoref/data/nuclear-retained-lncrnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,530   copying build/lib/oncoref/data/degenerate-subtype-pairs.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,532   copying build/lib/oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,544   copying build/lib/oncoref/data/cancer-frameshift-burden.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,546   copying build/lib/oncoref/data/family-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,548   copying build/lib/oncoref/data/censored-gene-reference-tpm.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,551   copying build/lib/oncoref/data/rrna-and-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,553   copying build/lib/oncoref/data/ensembl-id-aliases.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,560   copying build/lib/oncoref/data/cancer-apd1-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,563   copying build/lib/oncoref/data/cancer-expression-source-candidates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,565   copying build/lib/oncoref/data/cancer-ici-response-estimates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,571   copying build/lib/oncoref/data/cancer-key-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,575   copying build/lib/oncoref/data/ribosomal-protein-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,577   copying build/lib/oncoref/data/tissue-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,579   copying build/lib/oncoref/data/cancer-lineage-group-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,580   copying build/lib/oncoref/data/clean-tpm-censored-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,584   copying build/lib/oncoref/data/cancer-code-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,586   copying build/lib/oncoref/data/cancer-ici-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,588   copying build/lib/oncoref/data/housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,590   copying build/lib/oncoref/data/cta-ihc-unreliable.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,592   copying build/lib/oncoref/data/disease-state-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,594   copying build/lib/oncoref/data/proteoform-groups-genome.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,596   copying build/lib/oncoref/data/ribosomal-protein-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,599   copying build/lib/oncoref/data/expression_sources.yaml -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,602   copying build/lib/oncoref/data/cancer-tmb.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,604   copying build/lib/oncoref/data/cdna-identical-gene-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,607   copying build/lib/oncoref/data/cancer-driver-variants.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,610   copying build/lib/oncoref/data/fusion-expression-effects.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,611   copying build/lib/oncoref/data/source-matrices.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,613   copying build/lib/oncoref/data/proteoform-collapse-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T02:37:07,615   copying build/lib/oncoref/source_matrices.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,617   copying build/lib/oncoref/genome.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,619   copying build/lib/oncoref/gene_qc.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,621   copying build/lib/oncoref/hpa.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,623   copying build/lib/oncoref/cta_peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,625   copying build/lib/oncoref/coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,628   copying build/lib/oncoref/expression.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,631   copying build/lib/oncoref/fusions.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,634   copying build/lib/oncoref/samples.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,636   copying build/lib/oncoref/cta_tissues.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,638   copying build/lib/oncoref/cohorts.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T02:37:07,639   running install_egg_info
2026-06-24T02:37:07,648   running egg_info
2026-06-24T02:37:07,654   writing oncoref.egg-info/PKG-INFO
2026-06-24T02:37:07,659   writing dependency_links to oncoref.egg-info/dependency_links.txt
2026-06-24T02:37:07,660   writing entry points to oncoref.egg-info/entry_points.txt
2026-06-24T02:37:07,662   writing requirements to oncoref.egg-info/requires.txt
2026-06-24T02:37:07,663   writing top-level names to oncoref.egg-info/top_level.txt
2026-06-24T02:37:07,682   reading manifest file 'oncoref.egg-info/SOURCES.txt'
2026-06-24T02:37:07,691   reading manifest template 'MANIFEST.in'
2026-06-24T02:37:07,693   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression'
2026-06-24T02:37:07,694   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles'
2026-06-24T02:37:07,695   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives'
2026-06-24T02:37:07,697   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5'
2026-06-24T02:37:07,698   warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv'
2026-06-24T02:37:07,699   warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv'
2026-06-24T02:37:07,699   adding license file 'LICENSE'
2026-06-24T02:37:07,708   writing manifest file 'oncoref.egg-info/SOURCES.txt'
2026-06-24T02:37:07,709   Copying oncoref.egg-info to build/bdist.linux-armv7l/wheel/./oncoref-1.8.6-py3.11.egg-info
2026-06-24T02:37:07,721   running install_scripts
2026-06-24T02:37:07,733   creating build/bdist.linux-armv7l/wheel/oncoref-1.8.6.dist-info/WHEEL
2026-06-24T02:37:07,736   creating '/tmp/pip-wheel-qvdcy5wq/.tmp-lnuq4b3a/oncoref-1.8.6-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2026-06-24T02:37:07,740   adding 'oncoref/__init__.py'
2026-06-24T02:37:07,741   adding 'oncoref/antigen_coverage.py'
2026-06-24T02:37:07,743   adding 'oncoref/apd1.py'
2026-06-24T02:37:07,744   adding 'oncoref/cancer_genes.py'
2026-06-24T02:37:07,746   adding 'oncoref/cancer_ontology.py'
2026-06-24T02:37:07,751   adding 'oncoref/cancer_types.py'
2026-06-24T02:37:07,753   adding 'oncoref/catalog.py'
2026-06-24T02:37:07,756   adding 'oncoref/cli.py'
2026-06-24T02:37:07,758   adding 'oncoref/cohorts.py'
2026-06-24T02:37:07,761   adding 'oncoref/coverage.py'
2026-06-24T02:37:07,764   adding 'oncoref/cta.py'
2026-06-24T02:37:07,766   adding 'oncoref/cta_coverage.py'
2026-06-24T02:37:07,767   adding 'oncoref/cta_curation_plots.py'
2026-06-24T02:37:07,769   adding 'oncoref/cta_peptides.py'
2026-06-24T02:37:07,771   adding 'oncoref/cta_regen.py'
2026-06-24T02:37:07,773   adding 'oncoref/cta_tissues.py'
2026-06-24T02:37:07,776   adding 'oncoref/data_bundle.py'
2026-06-24T02:37:07,778   adding 'oncoref/data_manifest.py'
2026-06-24T02:37:07,787   adding 'oncoref/expression.py'
2026-06-24T02:37:07,789   adding 'oncoref/expression_builders.py'
2026-06-24T02:37:07,791   adding 'oncoref/expression_engine.py'
2026-06-24T02:37:07,793   adding 'oncoref/expression_registry.py'
2026-06-24T02:37:07,795   adding 'oncoref/fusions.py'
2026-06-24T02:37:07,797   adding 'oncoref/gene_families.py'
2026-06-24T02:37:07,799   adding 'oncoref/gene_ids.py'
2026-06-24T02:37:07,800   adding 'oncoref/gene_qc.py'
2026-06-24T02:37:07,803   adding 'oncoref/genome.py'
2026-06-24T02:37:07,804   adding 'oncoref/hpa.py'
2026-06-24T02:37:07,807   adding 'oncoref/ici.py'
2026-06-24T02:37:07,809   adding 'oncoref/ici_response.py'
2026-06-24T02:37:07,811   adding 'oncoref/incidence.py'
2026-06-24T02:37:07,813   adding 'oncoref/load_dataset.py'
2026-06-24T02:37:07,816   adding 'oncoref/normalization.py'
2026-06-24T02:37:07,818   adding 'oncoref/peptides.py'
2026-06-24T02:37:07,825   adding 'oncoref/plots.py'
2026-06-24T02:37:07,828   adding 'oncoref/proteoforms.py'
2026-06-24T02:37:07,830   adding 'oncoref/reference_data.py'
2026-06-24T02:37:07,832   adding 'oncoref/response_signatures.py'
2026-06-24T02:37:07,833   adding 'oncoref/samples.py'
2026-06-24T02:37:07,835   adding 'oncoref/source_matrices.py'
2026-06-24T02:37:07,836   adding 'oncoref/tmb.py'
2026-06-24T02:37:07,838   adding 'oncoref/version.py'
2026-06-24T02:37:07,841   adding 'oncoref/data/cancer-apd1-response.csv'
2026-06-24T02:37:07,843   adding 'oncoref/data/cancer-code-burden-map.csv'
2026-06-24T02:37:07,844   adding 'oncoref/data/cancer-cohort-aggregates.csv'
2026-06-24T02:37:07,849   adding 'oncoref/data/cancer-driver-genes.csv'
2026-06-24T02:37:07,852   adding 'oncoref/data/cancer-driver-variants.csv'
2026-06-24T02:37:07,854   adding 'oncoref/data/cancer-expression-source-candidates.csv'
2026-06-24T02:37:07,856   adding 'oncoref/data/cancer-frameshift-burden.csv'
2026-06-24T02:37:07,858   adding 'oncoref/data/cancer-fusions.csv'
2026-06-24T02:37:07,876   adding 'oncoref/data/cancer-ici-response-estimates.csv'
2026-06-24T02:37:07,880   adding 'oncoref/data/cancer-ici-response.csv'
2026-06-24T02:37:07,882   adding 'oncoref/data/cancer-incidence-mortality.csv'
2026-06-24T02:37:07,896   adding 'oncoref/data/cancer-key-genes.csv'
2026-06-24T02:37:07,899   adding 'oncoref/data/cancer-lineage-group-overrides.csv'
2026-06-24T02:37:07,900   adding 'oncoref/data/cancer-lineage-groups.csv'
2026-06-24T02:37:07,929   adding 'oncoref/data/cancer-reference-expression-samples.csv.gz'
2026-06-24T02:37:07,932   adding 'oncoref/data/cancer-response-signatures.csv'
2026-06-24T02:37:07,933   adding 'oncoref/data/cancer-subtype-groupings.csv'
2026-06-24T02:37:07,945   adding 'oncoref/data/cancer-testis-antigens.csv'
2026-06-24T02:37:07,948   adding 'oncoref/data/cancer-tmb.csv'
2026-06-24T02:37:07,950   adding 'oncoref/data/cancer-type-genes.csv'
2026-06-24T02:37:07,954   adding 'oncoref/data/cancer-type-registry.csv'
2026-06-24T02:37:07,956   adding 'oncoref/data/cancer-viral-antigens.csv'
2026-06-24T02:37:08,008   adding 'oncoref/data/canonical-gene-space.csv.gz'
2026-06-24T02:37:08,015   adding 'oncoref/data/cdna-identical-gene-groups.csv'
2026-06-24T02:37:08,019   adding 'oncoref/data/censored-gene-reference-tpm.csv'
2026-06-24T02:37:08,020   adding 'oncoref/data/clean-tpm-biological-housekeeping-genes.csv'
2026-06-24T02:37:08,031   adding 'oncoref/data/clean-tpm-censored-genes.csv'
2026-06-24T02:37:08,033   adding 'oncoref/data/cohort-registry.csv'
2026-06-24T02:37:08,035   adding 'oncoref/data/cta-candidate-references.csv'
2026-06-24T02:37:08,036   adding 'oncoref/data/cta-ihc-unreliable.csv'
2026-06-24T02:37:08,038   adding 'oncoref/data/degenerate-subtype-pairs.csv'
2026-06-24T02:37:08,039   adding 'oncoref/data/disease-state-rules.csv'
2026-06-24T02:37:08,066   adding 'oncoref/data/ensembl-id-aliases.csv'
2026-06-24T02:37:08,073   adding 'oncoref/data/expression_sources.yaml'
2026-06-24T02:37:08,075   adding 'oncoref/data/extra-tx-mappings.csv'
2026-06-24T02:37:08,076   adding 'oncoref/data/family-burden-map.csv'
2026-06-24T02:37:08,078   adding 'oncoref/data/fusion-expression-effects.csv'
2026-06-24T02:37:08,079   adding 'oncoref/data/fusion-surrogate-expression.csv'
2026-06-24T02:37:08,081   adding 'oncoref/data/hemoglobin-genes.csv'
2026-06-24T02:37:08,082   adding 'oncoref/data/histone-genes.csv'
2026-06-24T02:37:08,083   adding 'oncoref/data/housekeeping-genes.csv'
2026-06-24T02:37:08,085   adding 'oncoref/data/mitochondrial-genes.csv'
2026-06-24T02:37:08,086   adding 'oncoref/data/narrative-gene-sets.csv'
2026-06-24T02:37:08,126   adding 'oncoref/data/ncbi-symbol-synonyms.csv.gz'
2026-06-24T02:37:08,130   adding 'oncoref/data/nuclear-retained-lncrnas.csv'
2026-06-24T02:37:08,132   adding 'oncoref/data/numt-pseudogenes.csv'
2026-06-24T02:37:08,134   adding 'oncoref/data/proteoform-collapse-overrides.csv'
2026-06-24T02:37:08,137   adding 'oncoref/data/proteoform-groups-genome.csv'
2026-06-24T02:37:08,138   adding 'oncoref/data/proteoform-groups.csv'
2026-06-24T02:37:08,140   adding 'oncoref/data/rare-cancer-fusion-rules.csv'
2026-06-24T02:37:08,141   adding 'oncoref/data/ribosomal-protein-genes.csv'
2026-06-24T02:37:08,148   adding 'oncoref/data/ribosomal-protein-pseudogenes.csv'
2026-06-24T02:37:08,150   adding 'oncoref/data/rrna-and-pseudogenes.csv'
2026-06-24T02:37:08,169   adding 'oncoref/data/small-noncoding-rnas.csv'
2026-06-24T02:37:08,172   adding 'oncoref/data/source-matrices.csv'
2026-06-24T02:37:08,173   adding 'oncoref/data/tissue-burden-map.csv'
2026-06-24T02:37:08,177   adding 'oncoref-1.8.6.dist-info/licenses/LICENSE'
2026-06-24T02:37:08,179   adding 'oncoref-1.8.6.dist-info/METADATA'
2026-06-24T02:37:08,180   adding 'oncoref-1.8.6.dist-info/WHEEL'
2026-06-24T02:37:08,181   adding 'oncoref-1.8.6.dist-info/entry_points.txt'
2026-06-24T02:37:08,182   adding 'oncoref-1.8.6.dist-info/top_level.txt'
2026-06-24T02:37:08,184   adding 'oncoref-1.8.6.dist-info/RECORD'
2026-06-24T02:37:08,204   removing build/bdist.linux-armv7l/wheel
2026-06-24T02:37:08,327   Building wheel for oncoref (pyproject.toml): finished with status 'done'
2026-06-24T02:37:08,366   Created wheel for oncoref: filename=oncoref-1.8.6-py3-none-any.whl size=1649813 sha256=460f281fc846e410a5992e3a87193febdfac8bf81f3e5497a5e5d72ae58176bf
2026-06-24T02:37:08,368   Stored in directory: /tmp/pip-ephem-wheel-cache-nw8yvb7s/wheels/21/15/c3/15690fa65bd69fbfa15baef62d2100da84a3dc532bfd6a18e1
2026-06-24T02:37:08,382 Successfully built oncoref
2026-06-24T02:37:08,424 Removed build tracker: '/tmp/pip-build-tracker-irfi93_d'