2026-06-23T20:45:17,983 Created temporary directory: /tmp/pip-ephem-wheel-cache-93rskjuv
2026-06-23T20:45:17,985 Created temporary directory: /tmp/pip-build-tracker-jvo_4eek
2026-06-23T20:45:17,985 Initialized build tracking at /tmp/pip-build-tracker-jvo_4eek
2026-06-23T20:45:17,986 Created build tracker: /tmp/pip-build-tracker-jvo_4eek
2026-06-23T20:45:17,986 Entered build tracker: /tmp/pip-build-tracker-jvo_4eek
2026-06-23T20:45:17,987 Created temporary directory: /tmp/pip-wheel-dsqkny0q
2026-06-23T20:45:17,990 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
2026-06-23T20:45:17,992 Created temporary directory: /tmp/pip-ephem-wheel-cache-byv8qeoc
2026-06-23T20:45:18,014 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-06-23T20:45:18,017 2 location(s) to search for versions of oncoref:
2026-06-23T20:45:18,017 * https://pypi.org/simple/oncoref/
2026-06-23T20:45:18,017 * https://www.piwheels.org/simple/oncoref/
2026-06-23T20:45:18,018 Fetching project page and analyzing links: https://pypi.org/simple/oncoref/
2026-06-23T20:45:18,019 Getting page https://pypi.org/simple/oncoref/
2026-06-23T20:45:18,020 Found index url https://pypi.org/simple
2026-06-23T20:45:18,272 Fetched page https://pypi.org/simple/oncoref/ as application/vnd.pypi.simple.v1+json
2026-06-23T20:45:18,276   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)
2026-06-23T20:45:18,277   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
2026-06-23T20:45:18,278   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)
2026-06-23T20:45:18,279   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
2026-06-23T20:45:18,280   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)
2026-06-23T20:45:18,281   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
2026-06-23T20:45:18,282   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)
2026-06-23T20:45:18,283   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
2026-06-23T20:45:18,283   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)
2026-06-23T20:45:18,284   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
2026-06-23T20:45:18,285   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)
2026-06-23T20:45:18,286   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
2026-06-23T20:45:18,287   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)
2026-06-23T20:45:18,287   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
2026-06-23T20:45:18,288   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)
2026-06-23T20:45:18,289   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
2026-06-23T20:45:18,290 Fetching project page and analyzing links: https://www.piwheels.org/simple/oncoref/
2026-06-23T20:45:18,290 Getting page https://www.piwheels.org/simple/oncoref/
2026-06-23T20:45:18,292 Found index url https://www.piwheels.org/simple
2026-06-23T20:45:18,605 Fetched page https://www.piwheels.org/simple/oncoref/ as text/html
2026-06-23T20:45:18,608   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)
2026-06-23T20:45:18,609   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)
2026-06-23T20:45:18,610   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)
2026-06-23T20:45:18,610   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)
2026-06-23T20:45:18,611   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)
2026-06-23T20:45:18,612   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)
2026-06-23T20:45:18,612   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)
2026-06-23T20:45:18,613 Skipping link: not a file: https://www.piwheels.org/simple/oncoref/
2026-06-23T20:45:18,614 Skipping link: not a file: https://pypi.org/simple/oncoref/
2026-06-23T20:45:18,634 Given no hashes to check 1 links for project 'oncoref': discarding no candidates
2026-06-23T20:45:18,653 Collecting oncoref==1.8.5
2026-06-23T20:45:18,656   Created temporary directory: /tmp/pip-unpack-ll1511ax
2026-06-23T20:45:18,995   Downloading oncoref-1.8.5.tar.gz (1.7 MB)
2026-06-23T20:45:19,686   Added oncoref==1.8.5 from https://files.pythonhosted.org/packages/0a/e2/de65c5e1582fe009b3f640e94e6ecd5cf2f139d490750374cdad3af0e14c/oncoref-1.8.5.tar.gz to build tracker '/tmp/pip-build-tracker-jvo_4eek'
2026-06-23T20:45:19,693   Created temporary directory: /tmp/pip-build-env-w_qzqczq
2026-06-23T20:45:19,698   Installing build dependencies: started
2026-06-23T20:45:19,699   Running command pip subprocess to install build dependencies
2026-06-23T20:45:20,854   Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11)
2026-06-23T20:45:21,267   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
2026-06-23T20:45:21,289   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-06-23T20:45:23,290   Collecting setuptools>=61.0
2026-06-23T20:45:23,291     Obtaining dependency information for setuptools>=61.0 from https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl.metadata
2026-06-23T20:45:23,307     Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl.metadata (6.5 kB)
2026-06-23T20:45:23,546   Collecting wheel
2026-06-23T20:45:23,547     Obtaining dependency information for wheel from https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata
2026-06-23T20:45:23,561     Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB)
2026-06-23T20:45:23,744   Collecting packaging>=24.0
2026-06-23T20:45:23,745     Obtaining dependency information for packaging>=24.0 from https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata
2026-06-23T20:45:23,759     Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata (3.5 kB)
2026-06-23T20:45:23,950   Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB)
2026-06-23T20:45:23,969   Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB)
2026-06-23T20:45:24,060   Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB)
2026-06-23T20:45:24,099   Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB)
2026-06-23T20:45:24,125   Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB)
2026-06-23T20:45:24,220   Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB)
2026-06-23T20:45:27,000   Installing collected packages: setuptools, packaging, wheel
2026-06-23T20:45:30,426     Creating /tmp/pip-build-env-w_qzqczq/overlay/local/bin
2026-06-23T20:45:30,429     changing mode of /tmp/pip-build-env-w_qzqczq/overlay/local/bin/wheel to 755
2026-06-23T20:45:30,453   Successfully installed packaging-26.2 setuptools-82.0.1 wheel-0.47.0
2026-06-23T20:45:30,740   Installing build dependencies: finished with status 'done'
2026-06-23T20:45:30,746   Getting requirements to build wheel: started
2026-06-23T20:45:30,748   Running command Getting requirements to build wheel
2026-06-23T20:45:31,471   running egg_info
2026-06-23T20:45:31,477   writing oncoref.egg-info/PKG-INFO
2026-06-23T20:45:31,483   writing dependency_links to oncoref.egg-info/dependency_links.txt
2026-06-23T20:45:31,485   writing entry points to oncoref.egg-info/entry_points.txt
2026-06-23T20:45:31,487   writing requirements to oncoref.egg-info/requires.txt
2026-06-23T20:45:31,489   writing top-level names to oncoref.egg-info/top_level.txt
2026-06-23T20:45:31,523   reading manifest file 'oncoref.egg-info/SOURCES.txt'
2026-06-23T20:45:31,532   reading manifest template 'MANIFEST.in'
2026-06-23T20:45:31,533   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression'
2026-06-23T20:45:31,534   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles'
2026-06-23T20:45:31,535   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives'
2026-06-23T20:45:31,537   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5'
2026-06-23T20:45:31,538   warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv'
2026-06-23T20:45:31,539   warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv'
2026-06-23T20:45:31,539   adding license file 'LICENSE'
2026-06-23T20:45:31,547   writing manifest file 'oncoref.egg-info/SOURCES.txt'
2026-06-23T20:45:31,645   Getting requirements to build wheel: finished with status 'done'
2026-06-23T20:45:31,648   Created temporary directory: /tmp/pip-modern-metadata-ukcdvq6x
2026-06-23T20:45:31,650   Preparing metadata (pyproject.toml): started
2026-06-23T20:45:31,651   Running command Preparing metadata (pyproject.toml)
2026-06-23T20:45:32,296   running dist_info
2026-06-23T20:45:32,306   creating /tmp/pip-modern-metadata-ukcdvq6x/oncoref.egg-info
2026-06-23T20:45:32,307   writing /tmp/pip-modern-metadata-ukcdvq6x/oncoref.egg-info/PKG-INFO
2026-06-23T20:45:32,313   writing dependency_links to /tmp/pip-modern-metadata-ukcdvq6x/oncoref.egg-info/dependency_links.txt
2026-06-23T20:45:32,315   writing entry points to /tmp/pip-modern-metadata-ukcdvq6x/oncoref.egg-info/entry_points.txt
2026-06-23T20:45:32,317   writing requirements to /tmp/pip-modern-metadata-ukcdvq6x/oncoref.egg-info/requires.txt
2026-06-23T20:45:32,318   writing top-level names to /tmp/pip-modern-metadata-ukcdvq6x/oncoref.egg-info/top_level.txt
2026-06-23T20:45:32,320   writing manifest file '/tmp/pip-modern-metadata-ukcdvq6x/oncoref.egg-info/SOURCES.txt'
2026-06-23T20:45:32,351   reading manifest file '/tmp/pip-modern-metadata-ukcdvq6x/oncoref.egg-info/SOURCES.txt'
2026-06-23T20:45:32,353   reading manifest template 'MANIFEST.in'
2026-06-23T20:45:32,355   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression'
2026-06-23T20:45:32,356   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles'
2026-06-23T20:45:32,357   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives'
2026-06-23T20:45:32,358   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5'
2026-06-23T20:45:32,359   warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv'
2026-06-23T20:45:32,360   warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv'
2026-06-23T20:45:32,361   adding license file 'LICENSE'
2026-06-23T20:45:32,367   writing manifest file '/tmp/pip-modern-metadata-ukcdvq6x/oncoref.egg-info/SOURCES.txt'
2026-06-23T20:45:32,369   creating '/tmp/pip-modern-metadata-ukcdvq6x/oncoref-1.8.5.dist-info'
2026-06-23T20:45:32,494   Preparing metadata (pyproject.toml): finished with status 'done'
2026-06-23T20:45:32,499   Source in /tmp/pip-wheel-dsqkny0q/oncoref_06d49204d5e74ca9a01f167b984b4107 has version 1.8.5, which satisfies requirement oncoref==1.8.5 from https://files.pythonhosted.org/packages/0a/e2/de65c5e1582fe009b3f640e94e6ecd5cf2f139d490750374cdad3af0e14c/oncoref-1.8.5.tar.gz
2026-06-23T20:45:32,500   Removed oncoref==1.8.5 from https://files.pythonhosted.org/packages/0a/e2/de65c5e1582fe009b3f640e94e6ecd5cf2f139d490750374cdad3af0e14c/oncoref-1.8.5.tar.gz from build tracker '/tmp/pip-build-tracker-jvo_4eek'
2026-06-23T20:45:32,506 Created temporary directory: /tmp/pip-unpack-jdnmj77v
2026-06-23T20:45:32,507 Building wheels for collected packages: oncoref
2026-06-23T20:45:32,511   Created temporary directory: /tmp/pip-wheel-t6_nacu8
2026-06-23T20:45:32,511   Destination directory: /tmp/pip-wheel-t6_nacu8
2026-06-23T20:45:32,513   Building wheel for oncoref (pyproject.toml): started
2026-06-23T20:45:32,514   Running command Building wheel for oncoref (pyproject.toml)
2026-06-23T20:45:33,140   running bdist_wheel
2026-06-23T20:45:33,157   running build
2026-06-23T20:45:33,158   running build_py
2026-06-23T20:45:33,165   creating build/lib/oncoref
2026-06-23T20:45:33,167   copying oncoref/load_dataset.py -> build/lib/oncoref
2026-06-23T20:45:33,169   copying oncoref/catalog.py -> build/lib/oncoref
2026-06-23T20:45:33,171   copying oncoref/ici.py -> build/lib/oncoref
2026-06-23T20:45:33,174   copying oncoref/gene_ids.py -> build/lib/oncoref
2026-06-23T20:45:33,177   copying oncoref/apd1.py -> build/lib/oncoref
2026-06-23T20:45:33,178   copying oncoref/cancer_types.py -> build/lib/oncoref
2026-06-23T20:45:33,181   copying oncoref/expression_engine.py -> build/lib/oncoref
2026-06-23T20:45:33,184   copying oncoref/cta_curation_plots.py -> build/lib/oncoref
2026-06-23T20:45:33,186   copying oncoref/reference_data.py -> build/lib/oncoref
2026-06-23T20:45:33,188   copying oncoref/version.py -> build/lib/oncoref
2026-06-23T20:45:33,190   copying oncoref/expression_builders.py -> build/lib/oncoref
2026-06-23T20:45:33,192   copying oncoref/plots.py -> build/lib/oncoref
2026-06-23T20:45:33,196   copying oncoref/ici_response.py -> build/lib/oncoref
2026-06-23T20:45:33,197   copying oncoref/cta_regen.py -> build/lib/oncoref
2026-06-23T20:45:33,200   copying oncoref/data_manifest.py -> build/lib/oncoref
2026-06-23T20:45:33,203   copying oncoref/cancer_genes.py -> build/lib/oncoref
2026-06-23T20:45:33,205   copying oncoref/cli.py -> build/lib/oncoref
2026-06-23T20:45:33,208   copying oncoref/cta.py -> build/lib/oncoref
2026-06-23T20:45:33,214   copying oncoref/cta_coverage.py -> build/lib/oncoref
2026-06-23T20:45:33,218   copying oncoref/gene_families.py -> build/lib/oncoref
2026-06-23T20:45:33,224   copying oncoref/proteoforms.py -> build/lib/oncoref
2026-06-23T20:45:33,227   copying oncoref/data_bundle.py -> build/lib/oncoref
2026-06-23T20:45:33,229   copying oncoref/response_signatures.py -> build/lib/oncoref
2026-06-23T20:45:33,231   copying oncoref/expression_registry.py -> build/lib/oncoref
2026-06-23T20:45:33,234   copying oncoref/normalization.py -> build/lib/oncoref
2026-06-23T20:45:33,237   copying oncoref/incidence.py -> build/lib/oncoref
2026-06-23T20:45:33,239   copying oncoref/__init__.py -> build/lib/oncoref
2026-06-23T20:45:33,242   copying oncoref/cancer_ontology.py -> build/lib/oncoref
2026-06-23T20:45:33,245   copying oncoref/peptides.py -> build/lib/oncoref
2026-06-23T20:45:33,247   copying oncoref/antigen_coverage.py -> build/lib/oncoref
2026-06-23T20:45:33,249   copying oncoref/tmb.py -> build/lib/oncoref
2026-06-23T20:45:33,252   copying oncoref/source_matrices.py -> build/lib/oncoref
2026-06-23T20:45:33,255   copying oncoref/genome.py -> build/lib/oncoref
2026-06-23T20:45:33,257   copying oncoref/gene_qc.py -> build/lib/oncoref
2026-06-23T20:45:33,260   copying oncoref/hpa.py -> build/lib/oncoref
2026-06-23T20:45:33,262   copying oncoref/cta_peptides.py -> build/lib/oncoref
2026-06-23T20:45:33,265   copying oncoref/coverage.py -> build/lib/oncoref
2026-06-23T20:45:33,268   copying oncoref/expression.py -> build/lib/oncoref
2026-06-23T20:45:33,272   copying oncoref/fusions.py -> build/lib/oncoref
2026-06-23T20:45:33,275   copying oncoref/samples.py -> build/lib/oncoref
2026-06-23T20:45:33,277   copying oncoref/cta_tissues.py -> build/lib/oncoref
2026-06-23T20:45:33,280   copying oncoref/cohorts.py -> build/lib/oncoref
2026-06-23T20:45:33,293   creating build/lib/oncoref/data
2026-06-23T20:45:33,295   copying oncoref/data/cohort-registry.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,299   copying oncoref/data/cancer-incidence-mortality.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,302   copying oncoref/data/histone-genes.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,304   copying oncoref/data/cta-candidate-references.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,307   copying oncoref/data/cancer-driver-genes.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,311   copying oncoref/data/cancer-lineage-groups.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,313   copying oncoref/data/cancer-cohort-aggregates.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,316   copying oncoref/data/cancer-subtype-groupings.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,318   copying oncoref/data/small-noncoding-rnas.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,323   copying oncoref/data/numt-pseudogenes.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,326   copying oncoref/data/cancer-response-signatures.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,328   copying oncoref/data/hemoglobin-genes.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,330   copying oncoref/data/narrative-gene-sets.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,332   copying oncoref/data/cancer-fusions.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,335   copying oncoref/data/proteoform-groups.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,337   copying oncoref/data/cancer-type-registry.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,340   copying oncoref/data/cancer-testis-antigens.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,345   copying oncoref/data/extra-tx-mappings.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,347   copying oncoref/data/mitochondrial-genes.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,350   copying oncoref/data/rare-cancer-fusion-rules.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,352   copying oncoref/data/cancer-viral-antigens.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,354   copying oncoref/data/fusion-surrogate-expression.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,357   copying oncoref/data/cancer-type-genes.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,359   copying oncoref/data/nuclear-retained-lncrnas.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,361   copying oncoref/data/degenerate-subtype-pairs.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,363   copying oncoref/data/cancer-frameshift-burden.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,365   copying oncoref/data/family-burden-map.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,368   copying oncoref/data/censored-gene-reference-tpm.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,370   copying oncoref/data/rrna-and-pseudogenes.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,373   copying oncoref/data/ensembl-id-aliases.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,381   copying oncoref/data/cancer-apd1-response.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,384   copying oncoref/data/cancer-expression-source-candidates.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,387   copying oncoref/data/cancer-ici-response-estimates.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,394   copying oncoref/data/cancer-key-genes.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,400   copying oncoref/data/ribosomal-protein-genes.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,402   copying oncoref/data/tissue-burden-map.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,404   copying oncoref/data/cancer-lineage-group-overrides.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,407   copying oncoref/data/clean-tpm-censored-genes.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,412   copying oncoref/data/cancer-code-burden-map.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,414   copying oncoref/data/cancer-ici-response.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,417   copying oncoref/data/housekeeping-genes.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,419   copying oncoref/data/cta-ihc-unreliable.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,421   copying oncoref/data/disease-state-rules.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,423   copying oncoref/data/proteoform-groups-genome.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,426   copying oncoref/data/ribosomal-protein-pseudogenes.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,429   copying oncoref/data/cancer-tmb.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,432   copying oncoref/data/cdna-identical-gene-groups.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,434   copying oncoref/data/cancer-driver-variants.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,437   copying oncoref/data/fusion-expression-effects.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,439   copying oncoref/data/source-matrices.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,441   copying oncoref/data/proteoform-collapse-overrides.csv -> build/lib/oncoref/data
2026-06-23T20:45:33,443   copying oncoref/data/cancer-reference-expression-samples.csv.gz -> build/lib/oncoref/data
2026-06-23T20:45:33,450   copying oncoref/data/canonical-gene-space.csv.gz -> build/lib/oncoref/data
2026-06-23T20:45:33,459   copying oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/lib/oncoref/data
2026-06-23T20:45:33,468   copying oncoref/data/expression_sources.yaml -> build/lib/oncoref/data
2026-06-23T20:45:33,482   installing to build/bdist.linux-armv7l/wheel
2026-06-23T20:45:33,483   running install
2026-06-23T20:45:33,506   running install_lib
2026-06-23T20:45:33,511   creating build/bdist.linux-armv7l/wheel
2026-06-23T20:45:33,514   creating build/bdist.linux-armv7l/wheel/oncoref
2026-06-23T20:45:33,515   copying build/lib/oncoref/load_dataset.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,517   copying build/lib/oncoref/catalog.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,519   copying build/lib/oncoref/ici.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,522   copying build/lib/oncoref/gene_ids.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,524   copying build/lib/oncoref/apd1.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,526   copying build/lib/oncoref/cancer_types.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,529   copying build/lib/oncoref/expression_engine.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,531   copying build/lib/oncoref/cta_curation_plots.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,534   copying build/lib/oncoref/reference_data.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,536   copying build/lib/oncoref/version.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,538   copying build/lib/oncoref/expression_builders.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,540   copying build/lib/oncoref/plots.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,544   copying build/lib/oncoref/ici_response.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,546   copying build/lib/oncoref/cta_regen.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,548   copying build/lib/oncoref/data_manifest.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,551   copying build/lib/oncoref/cancer_genes.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,553   copying build/lib/oncoref/cli.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,555   copying build/lib/oncoref/cta.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,558   copying build/lib/oncoref/cta_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,560   copying build/lib/oncoref/gene_families.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,562   copying build/lib/oncoref/proteoforms.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,565   copying build/lib/oncoref/data_bundle.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,567   copying build/lib/oncoref/response_signatures.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,569   copying build/lib/oncoref/expression_registry.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,571   copying build/lib/oncoref/normalization.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,573   copying build/lib/oncoref/incidence.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,575   copying build/lib/oncoref/__init__.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,577   copying build/lib/oncoref/cancer_ontology.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,579   copying build/lib/oncoref/peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,581   copying build/lib/oncoref/antigen_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,582   copying build/lib/oncoref/tmb.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,586   creating build/bdist.linux-armv7l/wheel/oncoref/data
2026-06-23T20:45:33,587   copying build/lib/oncoref/data/cohort-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,589   copying build/lib/oncoref/data/cancer-incidence-mortality.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,591   copying build/lib/oncoref/data/histone-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,593   copying build/lib/oncoref/data/cta-candidate-references.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,595   copying build/lib/oncoref/data/cancer-driver-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,598   copying build/lib/oncoref/data/cancer-reference-expression-samples.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,604   copying build/lib/oncoref/data/cancer-lineage-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,606   copying build/lib/oncoref/data/canonical-gene-space.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,615   copying build/lib/oncoref/data/cancer-cohort-aggregates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,617   copying build/lib/oncoref/data/cancer-subtype-groupings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,619   copying build/lib/oncoref/data/small-noncoding-rnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,623   copying build/lib/oncoref/data/numt-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,626   copying build/lib/oncoref/data/cancer-response-signatures.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,628   copying build/lib/oncoref/data/hemoglobin-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,629   copying build/lib/oncoref/data/narrative-gene-sets.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,631   copying build/lib/oncoref/data/cancer-fusions.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,634   copying build/lib/oncoref/data/proteoform-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,636   copying build/lib/oncoref/data/cancer-type-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,638   copying build/lib/oncoref/data/cancer-testis-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,643   copying build/lib/oncoref/data/extra-tx-mappings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,645   copying build/lib/oncoref/data/mitochondrial-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,647   copying build/lib/oncoref/data/rare-cancer-fusion-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,649   copying build/lib/oncoref/data/cancer-viral-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,651   copying build/lib/oncoref/data/fusion-surrogate-expression.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,653   copying build/lib/oncoref/data/cancer-type-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,656   copying build/lib/oncoref/data/nuclear-retained-lncrnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,657   copying build/lib/oncoref/data/degenerate-subtype-pairs.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,659   copying build/lib/oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,667   copying build/lib/oncoref/data/cancer-frameshift-burden.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,669   copying build/lib/oncoref/data/family-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,671   copying build/lib/oncoref/data/censored-gene-reference-tpm.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,673   copying build/lib/oncoref/data/rrna-and-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,675   copying build/lib/oncoref/data/ensembl-id-aliases.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,683   copying build/lib/oncoref/data/cancer-apd1-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,685   copying build/lib/oncoref/data/cancer-expression-source-candidates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,688   copying build/lib/oncoref/data/cancer-ici-response-estimates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,693   copying build/lib/oncoref/data/cancer-key-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,697   copying build/lib/oncoref/data/ribosomal-protein-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,699   copying build/lib/oncoref/data/tissue-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,701   copying build/lib/oncoref/data/cancer-lineage-group-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,702   copying build/lib/oncoref/data/clean-tpm-censored-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,706   copying build/lib/oncoref/data/cancer-code-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,708   copying build/lib/oncoref/data/cancer-ici-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,710   copying build/lib/oncoref/data/housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,712   copying build/lib/oncoref/data/cta-ihc-unreliable.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,714   copying build/lib/oncoref/data/disease-state-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,716   copying build/lib/oncoref/data/proteoform-groups-genome.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,719   copying build/lib/oncoref/data/ribosomal-protein-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,722   copying build/lib/oncoref/data/expression_sources.yaml -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,724   copying build/lib/oncoref/data/cancer-tmb.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,727   copying build/lib/oncoref/data/cdna-identical-gene-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,729   copying build/lib/oncoref/data/cancer-driver-variants.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,732   copying build/lib/oncoref/data/fusion-expression-effects.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,734   copying build/lib/oncoref/data/source-matrices.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,735   copying build/lib/oncoref/data/proteoform-collapse-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T20:45:33,737   copying build/lib/oncoref/source_matrices.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,739   copying build/lib/oncoref/genome.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,741   copying build/lib/oncoref/gene_qc.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,743   copying build/lib/oncoref/hpa.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,745   copying build/lib/oncoref/cta_peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,747   copying build/lib/oncoref/coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,749   copying build/lib/oncoref/expression.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,752   copying build/lib/oncoref/fusions.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,754   copying build/lib/oncoref/samples.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,756   copying build/lib/oncoref/cta_tissues.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,758   copying build/lib/oncoref/cohorts.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T20:45:33,759   running install_egg_info
2026-06-23T20:45:33,768   running egg_info
2026-06-23T20:45:33,773   writing oncoref.egg-info/PKG-INFO
2026-06-23T20:45:33,778   writing dependency_links to oncoref.egg-info/dependency_links.txt
2026-06-23T20:45:33,780   writing entry points to oncoref.egg-info/entry_points.txt
2026-06-23T20:45:33,782   writing requirements to oncoref.egg-info/requires.txt
2026-06-23T20:45:33,783   writing top-level names to oncoref.egg-info/top_level.txt
2026-06-23T20:45:33,802   reading manifest file 'oncoref.egg-info/SOURCES.txt'
2026-06-23T20:45:33,811   reading manifest template 'MANIFEST.in'
2026-06-23T20:45:33,813   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression'
2026-06-23T20:45:33,814   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles'
2026-06-23T20:45:33,815   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives'
2026-06-23T20:45:33,817   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5'
2026-06-23T20:45:33,818   warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv'
2026-06-23T20:45:33,819   warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv'
2026-06-23T20:45:33,819   adding license file 'LICENSE'
2026-06-23T20:45:33,827   writing manifest file 'oncoref.egg-info/SOURCES.txt'
2026-06-23T20:45:33,829   Copying oncoref.egg-info to build/bdist.linux-armv7l/wheel/./oncoref-1.8.5-py3.11.egg-info
2026-06-23T20:45:33,841   running install_scripts
2026-06-23T20:45:33,852   creating build/bdist.linux-armv7l/wheel/oncoref-1.8.5.dist-info/WHEEL
2026-06-23T20:45:33,855   creating '/tmp/pip-wheel-t6_nacu8/.tmp-3azkk033/oncoref-1.8.5-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2026-06-23T20:45:33,859   adding 'oncoref/__init__.py'
2026-06-23T20:45:33,860   adding 'oncoref/antigen_coverage.py'
2026-06-23T20:45:33,862   adding 'oncoref/apd1.py'
2026-06-23T20:45:33,864   adding 'oncoref/cancer_genes.py'
2026-06-23T20:45:33,865   adding 'oncoref/cancer_ontology.py'
2026-06-23T20:45:33,870   adding 'oncoref/cancer_types.py'
2026-06-23T20:45:33,873   adding 'oncoref/catalog.py'
2026-06-23T20:45:33,876   adding 'oncoref/cli.py'
2026-06-23T20:45:33,878   adding 'oncoref/cohorts.py'
2026-06-23T20:45:33,881   adding 'oncoref/coverage.py'
2026-06-23T20:45:33,884   adding 'oncoref/cta.py'
2026-06-23T20:45:33,885   adding 'oncoref/cta_coverage.py'
2026-06-23T20:45:33,887   adding 'oncoref/cta_curation_plots.py'
2026-06-23T20:45:33,889   adding 'oncoref/cta_peptides.py'
2026-06-23T20:45:33,891   adding 'oncoref/cta_regen.py'
2026-06-23T20:45:33,893   adding 'oncoref/cta_tissues.py'
2026-06-23T20:45:33,895   adding 'oncoref/data_bundle.py'
2026-06-23T20:45:33,898   adding 'oncoref/data_manifest.py'
2026-06-23T20:45:33,906   adding 'oncoref/expression.py'
2026-06-23T20:45:33,909   adding 'oncoref/expression_builders.py'
2026-06-23T20:45:33,911   adding 'oncoref/expression_engine.py'
2026-06-23T20:45:33,912   adding 'oncoref/expression_registry.py'
2026-06-23T20:45:33,914   adding 'oncoref/fusions.py'
2026-06-23T20:45:33,916   adding 'oncoref/gene_families.py'
2026-06-23T20:45:33,917   adding 'oncoref/gene_ids.py'
2026-06-23T20:45:33,919   adding 'oncoref/gene_qc.py'
2026-06-23T20:45:33,921   adding 'oncoref/genome.py'
2026-06-23T20:45:33,923   adding 'oncoref/hpa.py'
2026-06-23T20:45:33,926   adding 'oncoref/ici.py'
2026-06-23T20:45:33,927   adding 'oncoref/ici_response.py'
2026-06-23T20:45:33,929   adding 'oncoref/incidence.py'
2026-06-23T20:45:33,931   adding 'oncoref/load_dataset.py'
2026-06-23T20:45:33,935   adding 'oncoref/normalization.py'
2026-06-23T20:45:33,937   adding 'oncoref/peptides.py'
2026-06-23T20:45:33,943   adding 'oncoref/plots.py'
2026-06-23T20:45:33,946   adding 'oncoref/proteoforms.py'
2026-06-23T20:45:33,948   adding 'oncoref/reference_data.py'
2026-06-23T20:45:33,950   adding 'oncoref/response_signatures.py'
2026-06-23T20:45:33,951   adding 'oncoref/samples.py'
2026-06-23T20:45:33,953   adding 'oncoref/source_matrices.py'
2026-06-23T20:45:33,954   adding 'oncoref/tmb.py'
2026-06-23T20:45:33,955   adding 'oncoref/version.py'
2026-06-23T20:45:33,959   adding 'oncoref/data/cancer-apd1-response.csv'
2026-06-23T20:45:33,960   adding 'oncoref/data/cancer-code-burden-map.csv'
2026-06-23T20:45:33,962   adding 'oncoref/data/cancer-cohort-aggregates.csv'
2026-06-23T20:45:33,967   adding 'oncoref/data/cancer-driver-genes.csv'
2026-06-23T20:45:33,969   adding 'oncoref/data/cancer-driver-variants.csv'
2026-06-23T20:45:33,972   adding 'oncoref/data/cancer-expression-source-candidates.csv'
2026-06-23T20:45:33,973   adding 'oncoref/data/cancer-frameshift-burden.csv'
2026-06-23T20:45:33,976   adding 'oncoref/data/cancer-fusions.csv'
2026-06-23T20:45:33,994   adding 'oncoref/data/cancer-ici-response-estimates.csv'
2026-06-23T20:45:33,998   adding 'oncoref/data/cancer-ici-response.csv'
2026-06-23T20:45:34,000   adding 'oncoref/data/cancer-incidence-mortality.csv'
2026-06-23T20:45:34,014   adding 'oncoref/data/cancer-key-genes.csv'
2026-06-23T20:45:34,017   adding 'oncoref/data/cancer-lineage-group-overrides.csv'
2026-06-23T20:45:34,018   adding 'oncoref/data/cancer-lineage-groups.csv'
2026-06-23T20:45:34,046   adding 'oncoref/data/cancer-reference-expression-samples.csv.gz'
2026-06-23T20:45:34,050   adding 'oncoref/data/cancer-response-signatures.csv'
2026-06-23T20:45:34,051   adding 'oncoref/data/cancer-subtype-groupings.csv'
2026-06-23T20:45:34,063   adding 'oncoref/data/cancer-testis-antigens.csv'
2026-06-23T20:45:34,066   adding 'oncoref/data/cancer-tmb.csv'
2026-06-23T20:45:34,068   adding 'oncoref/data/cancer-type-genes.csv'
2026-06-23T20:45:34,072   adding 'oncoref/data/cancer-type-registry.csv'
2026-06-23T20:45:34,073   adding 'oncoref/data/cancer-viral-antigens.csv'
2026-06-23T20:45:34,126   adding 'oncoref/data/canonical-gene-space.csv.gz'
2026-06-23T20:45:34,132   adding 'oncoref/data/cdna-identical-gene-groups.csv'
2026-06-23T20:45:34,136   adding 'oncoref/data/censored-gene-reference-tpm.csv'
2026-06-23T20:45:34,147   adding 'oncoref/data/clean-tpm-censored-genes.csv'
2026-06-23T20:45:34,149   adding 'oncoref/data/cohort-registry.csv'
2026-06-23T20:45:34,150   adding 'oncoref/data/cta-candidate-references.csv'
2026-06-23T20:45:34,152   adding 'oncoref/data/cta-ihc-unreliable.csv'
2026-06-23T20:45:34,153   adding 'oncoref/data/degenerate-subtype-pairs.csv'
2026-06-23T20:45:34,154   adding 'oncoref/data/disease-state-rules.csv'
2026-06-23T20:45:34,181   adding 'oncoref/data/ensembl-id-aliases.csv'
2026-06-23T20:45:34,188   adding 'oncoref/data/expression_sources.yaml'
2026-06-23T20:45:34,189   adding 'oncoref/data/extra-tx-mappings.csv'
2026-06-23T20:45:34,190   adding 'oncoref/data/family-burden-map.csv'
2026-06-23T20:45:34,192   adding 'oncoref/data/fusion-expression-effects.csv'
2026-06-23T20:45:34,193   adding 'oncoref/data/fusion-surrogate-expression.csv'
2026-06-23T20:45:34,194   adding 'oncoref/data/hemoglobin-genes.csv'
2026-06-23T20:45:34,196   adding 'oncoref/data/histone-genes.csv'
2026-06-23T20:45:34,197   adding 'oncoref/data/housekeeping-genes.csv'
2026-06-23T20:45:34,198   adding 'oncoref/data/mitochondrial-genes.csv'
2026-06-23T20:45:34,200   adding 'oncoref/data/narrative-gene-sets.csv'
2026-06-23T20:45:34,240   adding 'oncoref/data/ncbi-symbol-synonyms.csv.gz'
2026-06-23T20:45:34,244   adding 'oncoref/data/nuclear-retained-lncrnas.csv'
2026-06-23T20:45:34,246   adding 'oncoref/data/numt-pseudogenes.csv'
2026-06-23T20:45:34,247   adding 'oncoref/data/proteoform-collapse-overrides.csv'
2026-06-23T20:45:34,250   adding 'oncoref/data/proteoform-groups-genome.csv'
2026-06-23T20:45:34,251   adding 'oncoref/data/proteoform-groups.csv'
2026-06-23T20:45:34,253   adding 'oncoref/data/rare-cancer-fusion-rules.csv'
2026-06-23T20:45:34,254   adding 'oncoref/data/ribosomal-protein-genes.csv'
2026-06-23T20:45:34,260   adding 'oncoref/data/ribosomal-protein-pseudogenes.csv'
2026-06-23T20:45:34,263   adding 'oncoref/data/rrna-and-pseudogenes.csv'
2026-06-23T20:45:34,281   adding 'oncoref/data/small-noncoding-rnas.csv'
2026-06-23T20:45:34,284   adding 'oncoref/data/source-matrices.csv'
2026-06-23T20:45:34,285   adding 'oncoref/data/tissue-burden-map.csv'
2026-06-23T20:45:34,289   adding 'oncoref-1.8.5.dist-info/licenses/LICENSE'
2026-06-23T20:45:34,290   adding 'oncoref-1.8.5.dist-info/METADATA'
2026-06-23T20:45:34,292   adding 'oncoref-1.8.5.dist-info/WHEEL'
2026-06-23T20:45:34,293   adding 'oncoref-1.8.5.dist-info/entry_points.txt'
2026-06-23T20:45:34,293   adding 'oncoref-1.8.5.dist-info/top_level.txt'
2026-06-23T20:45:34,295   adding 'oncoref-1.8.5.dist-info/RECORD'
2026-06-23T20:45:34,316   removing build/bdist.linux-armv7l/wheel
2026-06-23T20:45:34,435   Building wheel for oncoref (pyproject.toml): finished with status 'done'
2026-06-23T20:45:34,473   Created wheel for oncoref: filename=oncoref-1.8.5-py3-none-any.whl size=1647077 sha256=cfedb20aa2c2593dfb010bc01a13d5b6c732ec5cf013fd70b65c71d1adb71f7e
2026-06-23T20:45:34,475   Stored in directory: /tmp/pip-ephem-wheel-cache-byv8qeoc/wheels/e8/65/5f/a5630ea7d1fe6752713e52a6dcc0bbe5cd60b6eb267c7e3622
2026-06-23T20:45:34,490 Successfully built oncoref
2026-06-23T20:45:34,548 Removed build tracker: '/tmp/pip-build-tracker-jvo_4eek'