2026-06-22T16:21:06,859 Created temporary directory: /tmp/pip-ephem-wheel-cache-m_r0khzo
2026-06-22T16:21:06,861 Created temporary directory: /tmp/pip-build-tracker-r4o6vuug
2026-06-22T16:21:06,862 Initialized build tracking at /tmp/pip-build-tracker-r4o6vuug
2026-06-22T16:21:06,862 Created build tracker: /tmp/pip-build-tracker-r4o6vuug
2026-06-22T16:21:06,863 Entered build tracker: /tmp/pip-build-tracker-r4o6vuug
2026-06-22T16:21:06,864 Created temporary directory: /tmp/pip-wheel-rb7t3zav
2026-06-22T16:21:06,867 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
2026-06-22T16:21:06,869 Created temporary directory: /tmp/pip-ephem-wheel-cache-h19sepdw
2026-06-22T16:21:06,891 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-06-22T16:21:06,895 2 location(s) to search for versions of oncoref:
2026-06-22T16:21:06,895 * https://pypi.org/simple/oncoref/
2026-06-22T16:21:06,895 * https://www.piwheels.org/simple/oncoref/
2026-06-22T16:21:06,896 Fetching project page and analyzing links: https://pypi.org/simple/oncoref/
2026-06-22T16:21:06,897 Getting page https://pypi.org/simple/oncoref/
2026-06-22T16:21:06,898 Found index url https://pypi.org/simple
2026-06-22T16:21:07,228 Fetched page https://pypi.org/simple/oncoref/ as application/vnd.pypi.simple.v1+json
2026-06-22T16:21:07,231   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)
2026-06-22T16:21:07,232   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
2026-06-22T16:21:07,233   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)
2026-06-22T16:21:07,234   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
2026-06-22T16:21:07,235   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)
2026-06-22T16:21:07,236   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
2026-06-22T16:21:07,236   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)
2026-06-22T16:21:07,237   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
2026-06-22T16:21:07,238   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)
2026-06-22T16:21:07,239   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
2026-06-22T16:21:07,240   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)
2026-06-22T16:21:07,241   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
2026-06-22T16:21:07,242 Fetching project page and analyzing links: https://www.piwheels.org/simple/oncoref/
2026-06-22T16:21:07,243 Getting page https://www.piwheels.org/simple/oncoref/
2026-06-22T16:21:07,244 Found index url https://www.piwheels.org/simple
2026-06-22T16:21:07,542 Fetched page https://www.piwheels.org/simple/oncoref/ as text/html
2026-06-22T16:21:07,544   Skipping link: No binaries permitted for oncoref: https://www.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)
2026-06-22T16:21:07,545   Skipping link: No binaries permitted for oncoref: https://www.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)
2026-06-22T16:21:07,545   Skipping link: No binaries permitted for oncoref: https://www.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)
2026-06-22T16:21:07,546   Skipping link: No binaries permitted for oncoref: https://www.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)
2026-06-22T16:21:07,547   Skipping link: No binaries permitted for oncoref: https://www.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)
2026-06-22T16:21:07,547 Skipping link: not a file: https://www.piwheels.org/simple/oncoref/
2026-06-22T16:21:07,548 Skipping link: not a file: https://pypi.org/simple/oncoref/
2026-06-22T16:21:07,567 Given no hashes to check 1 links for project 'oncoref': discarding no candidates
2026-06-22T16:21:07,584 Collecting oncoref==1.8.3
2026-06-22T16:21:07,587   Created temporary directory: /tmp/pip-unpack-_d4nb5vk
2026-06-22T16:21:07,918   Downloading oncoref-1.8.3.tar.gz (1.7 MB)
2026-06-22T16:21:08,648   Added oncoref==1.8.3 from https://files.pythonhosted.org/packages/e7/7d/22a2797b33413bfe0f46708f396b9b1f9ad9dbc253d94fcbeb6ccf9ad5ff/oncoref-1.8.3.tar.gz to build tracker '/tmp/pip-build-tracker-r4o6vuug'
2026-06-22T16:21:08,656   Created temporary directory: /tmp/pip-build-env-cgu89uzm
2026-06-22T16:21:08,661   Installing build dependencies: started
2026-06-22T16:21:08,662   Running command pip subprocess to install build dependencies
2026-06-22T16:21:09,955   Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11)
2026-06-22T16:21:10,495   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
2026-06-22T16:21:10,522   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-06-22T16:21:12,586   Collecting setuptools>=61.0
2026-06-22T16:21:12,588     Obtaining dependency information for setuptools>=61.0 from https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl.metadata
2026-06-22T16:21:12,616     Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl.metadata (6.5 kB)
2026-06-22T16:21:12,855   Collecting wheel
2026-06-22T16:21:12,857     Obtaining dependency information for wheel from https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata
2026-06-22T16:21:12,872     Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB)
2026-06-22T16:21:13,061   Collecting packaging>=24.0
2026-06-22T16:21:13,063     Obtaining dependency information for packaging>=24.0 from https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata
2026-06-22T16:21:13,078     Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata (3.5 kB)
2026-06-22T16:21:13,288   Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB)
2026-06-22T16:21:13,308   Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB)
2026-06-22T16:21:13,403   Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB)
2026-06-22T16:21:13,435   Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB)
2026-06-22T16:21:13,458   Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB)
2026-06-22T16:21:13,549   Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB)
2026-06-22T16:21:16,354   Installing collected packages: setuptools, packaging, wheel
2026-06-22T16:21:19,929     Creating /tmp/pip-build-env-cgu89uzm/overlay/local/bin
2026-06-22T16:21:19,931     changing mode of /tmp/pip-build-env-cgu89uzm/overlay/local/bin/wheel to 755
2026-06-22T16:21:19,953   Successfully installed packaging-26.2 setuptools-82.0.1 wheel-0.47.0
2026-06-22T16:21:20,242   Installing build dependencies: finished with status 'done'
2026-06-22T16:21:20,249   Getting requirements to build wheel: started
2026-06-22T16:21:20,251   Running command Getting requirements to build wheel
2026-06-22T16:21:20,960   running egg_info
2026-06-22T16:21:20,966   writing oncoref.egg-info/PKG-INFO
2026-06-22T16:21:20,972   writing dependency_links to oncoref.egg-info/dependency_links.txt
2026-06-22T16:21:20,974   writing entry points to oncoref.egg-info/entry_points.txt
2026-06-22T16:21:20,977   writing requirements to oncoref.egg-info/requires.txt
2026-06-22T16:21:20,979   writing top-level names to oncoref.egg-info/top_level.txt
2026-06-22T16:21:21,013   reading manifest file 'oncoref.egg-info/SOURCES.txt'
2026-06-22T16:21:21,023   reading manifest template 'MANIFEST.in'
2026-06-22T16:21:21,025   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression'
2026-06-22T16:21:21,026   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles'
2026-06-22T16:21:21,028   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives'
2026-06-22T16:21:21,029   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5'
2026-06-22T16:21:21,031   warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv'
2026-06-22T16:21:21,032   warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv'
2026-06-22T16:21:21,033   adding license file 'LICENSE'
2026-06-22T16:21:21,041   writing manifest file 'oncoref.egg-info/SOURCES.txt'
2026-06-22T16:21:21,139   Getting requirements to build wheel: finished with status 'done'
2026-06-22T16:21:21,143   Created temporary directory: /tmp/pip-modern-metadata-95bftdz3
2026-06-22T16:21:21,145   Preparing metadata (pyproject.toml): started
2026-06-22T16:21:21,147   Running command Preparing metadata (pyproject.toml)
2026-06-22T16:21:21,808   running dist_info
2026-06-22T16:21:21,818   creating /tmp/pip-modern-metadata-95bftdz3/oncoref.egg-info
2026-06-22T16:21:21,819   writing /tmp/pip-modern-metadata-95bftdz3/oncoref.egg-info/PKG-INFO
2026-06-22T16:21:21,825   writing dependency_links to /tmp/pip-modern-metadata-95bftdz3/oncoref.egg-info/dependency_links.txt
2026-06-22T16:21:21,827   writing entry points to /tmp/pip-modern-metadata-95bftdz3/oncoref.egg-info/entry_points.txt
2026-06-22T16:21:21,830   writing requirements to /tmp/pip-modern-metadata-95bftdz3/oncoref.egg-info/requires.txt
2026-06-22T16:21:21,831   writing top-level names to /tmp/pip-modern-metadata-95bftdz3/oncoref.egg-info/top_level.txt
2026-06-22T16:21:21,832   writing manifest file '/tmp/pip-modern-metadata-95bftdz3/oncoref.egg-info/SOURCES.txt'
2026-06-22T16:21:21,864   reading manifest file '/tmp/pip-modern-metadata-95bftdz3/oncoref.egg-info/SOURCES.txt'
2026-06-22T16:21:21,866   reading manifest template 'MANIFEST.in'
2026-06-22T16:21:21,867   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression'
2026-06-22T16:21:21,868   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles'
2026-06-22T16:21:21,869   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives'
2026-06-22T16:21:21,870   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5'
2026-06-22T16:21:21,871   warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv'
2026-06-22T16:21:21,872   warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv'
2026-06-22T16:21:21,873   adding license file 'LICENSE'
2026-06-22T16:21:21,879   writing manifest file '/tmp/pip-modern-metadata-95bftdz3/oncoref.egg-info/SOURCES.txt'
2026-06-22T16:21:21,880   creating '/tmp/pip-modern-metadata-95bftdz3/oncoref-1.8.3.dist-info'
2026-06-22T16:21:22,008   Preparing metadata (pyproject.toml): finished with status 'done'
2026-06-22T16:21:22,012   Source in /tmp/pip-wheel-rb7t3zav/oncoref_8e49adc6f0c44341b1b156dd3c415e5c has version 1.8.3, which satisfies requirement oncoref==1.8.3 from https://files.pythonhosted.org/packages/e7/7d/22a2797b33413bfe0f46708f396b9b1f9ad9dbc253d94fcbeb6ccf9ad5ff/oncoref-1.8.3.tar.gz
2026-06-22T16:21:22,013   Removed oncoref==1.8.3 from https://files.pythonhosted.org/packages/e7/7d/22a2797b33413bfe0f46708f396b9b1f9ad9dbc253d94fcbeb6ccf9ad5ff/oncoref-1.8.3.tar.gz from build tracker '/tmp/pip-build-tracker-r4o6vuug'
2026-06-22T16:21:22,019 Created temporary directory: /tmp/pip-unpack-72s0h_6x
2026-06-22T16:21:22,020 Building wheels for collected packages: oncoref
2026-06-22T16:21:22,024   Created temporary directory: /tmp/pip-wheel-2j1x157k
2026-06-22T16:21:22,025   Destination directory: /tmp/pip-wheel-2j1x157k
2026-06-22T16:21:22,027   Building wheel for oncoref (pyproject.toml): started
2026-06-22T16:21:22,028   Running command Building wheel for oncoref (pyproject.toml)
2026-06-22T16:21:22,650   running bdist_wheel
2026-06-22T16:21:22,670   running build
2026-06-22T16:21:22,671   running build_py
2026-06-22T16:21:22,678   creating build/lib/oncoref
2026-06-22T16:21:22,680   copying oncoref/tmb.py -> build/lib/oncoref
2026-06-22T16:21:22,683   copying oncoref/peptides.py -> build/lib/oncoref
2026-06-22T16:21:22,685   copying oncoref/coverage.py -> build/lib/oncoref
2026-06-22T16:21:22,688   copying oncoref/gene_ids.py -> build/lib/oncoref
2026-06-22T16:21:22,690   copying oncoref/hpa.py -> build/lib/oncoref
2026-06-22T16:21:22,693   copying oncoref/cta_regen.py -> build/lib/oncoref
2026-06-22T16:21:22,696   copying oncoref/cta.py -> build/lib/oncoref
2026-06-22T16:21:22,699   copying oncoref/cancer_types.py -> build/lib/oncoref
2026-06-22T16:21:22,702   copying oncoref/data_bundle.py -> build/lib/oncoref
2026-06-22T16:21:22,705   copying oncoref/gene_qc.py -> build/lib/oncoref
2026-06-22T16:21:22,708   copying oncoref/plots.py -> build/lib/oncoref
2026-06-22T16:21:22,713   copying oncoref/proteoforms.py -> build/lib/oncoref
2026-06-22T16:21:22,716   copying oncoref/response_signatures.py -> build/lib/oncoref
2026-06-22T16:21:22,718   copying oncoref/gene_families.py -> build/lib/oncoref
2026-06-22T16:21:22,721   copying oncoref/ici.py -> build/lib/oncoref
2026-06-22T16:21:22,724   copying oncoref/fusions.py -> build/lib/oncoref
2026-06-22T16:21:22,726   copying oncoref/expression_registry.py -> build/lib/oncoref
2026-06-22T16:21:22,729   copying oncoref/cta_tissues.py -> build/lib/oncoref
2026-06-22T16:21:22,731   copying oncoref/genome.py -> build/lib/oncoref
2026-06-22T16:21:22,733   copying oncoref/reference_data.py -> build/lib/oncoref
2026-06-22T16:21:22,736   copying oncoref/apd1.py -> build/lib/oncoref
2026-06-22T16:21:22,738   copying oncoref/expression.py -> build/lib/oncoref
2026-06-22T16:21:22,742   copying oncoref/expression_engine.py -> build/lib/oncoref
2026-06-22T16:21:22,744   copying oncoref/cli.py -> build/lib/oncoref
2026-06-22T16:21:22,747   copying oncoref/cancer_genes.py -> build/lib/oncoref
2026-06-22T16:21:22,750   copying oncoref/expression_builders.py -> build/lib/oncoref
2026-06-22T16:21:22,752   copying oncoref/__init__.py -> build/lib/oncoref
2026-06-22T16:21:22,756   copying oncoref/cta_curation_plots.py -> build/lib/oncoref
2026-06-22T16:21:22,758   copying oncoref/source_matrices.py -> build/lib/oncoref
2026-06-22T16:21:22,762   copying oncoref/normalization.py -> build/lib/oncoref
2026-06-22T16:21:22,765   copying oncoref/load_dataset.py -> build/lib/oncoref
2026-06-22T16:21:22,768   copying oncoref/version.py -> build/lib/oncoref
2026-06-22T16:21:22,770   copying oncoref/catalog.py -> build/lib/oncoref
2026-06-22T16:21:22,773   copying oncoref/incidence.py -> build/lib/oncoref
2026-06-22T16:21:22,775   copying oncoref/data_manifest.py -> build/lib/oncoref
2026-06-22T16:21:22,778   copying oncoref/samples.py -> build/lib/oncoref
2026-06-22T16:21:22,793   creating build/lib/oncoref/data
2026-06-22T16:21:22,794   copying oncoref/data/cancer-driver-genes.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,800   copying oncoref/data/cancer-code-burden-map.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,802   copying oncoref/data/family-burden-map.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,804   copying oncoref/data/source-matrices.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,807   copying oncoref/data/proteoform-collapse-overrides.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,809   copying oncoref/data/proteoform-groups.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,812   copying oncoref/data/ribosomal-protein-pseudogenes.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,815   copying oncoref/data/rare-cancer-fusion-rules.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,818   copying oncoref/data/cancer-lineage-group-overrides.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,821   copying oncoref/data/cta-candidate-references.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,825   copying oncoref/data/cancer-testis-antigens.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,831   copying oncoref/data/cancer-ici-response.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,834   copying oncoref/data/cancer-subtype-groupings.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,837   copying oncoref/data/cohort-registry.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,841   copying oncoref/data/histone-genes.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,844   copying oncoref/data/cancer-apd1-response.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,848   copying oncoref/data/ribosomal-protein-genes.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,850   copying oncoref/data/cancer-incidence-mortality.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,854   copying oncoref/data/clean-tpm-censored-genes.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,860   copying oncoref/data/cta-ihc-unreliable.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,863   copying oncoref/data/cancer-fusions.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,867   copying oncoref/data/narrative-gene-sets.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,870   copying oncoref/data/cancer-driver-variants.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,874   copying oncoref/data/tissue-burden-map.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,877   copying oncoref/data/degenerate-subtype-pairs.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,880   copying oncoref/data/cancer-type-genes.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,884   copying oncoref/data/ensembl-id-aliases.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,898   copying oncoref/data/cancer-key-genes.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,905   copying oncoref/data/cancer-viral-antigens.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,908   copying oncoref/data/cancer-cohort-aggregates.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,910   copying oncoref/data/hemoglobin-genes.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,912   copying oncoref/data/extra-tx-mappings.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,916   copying oncoref/data/proteoform-groups-genome.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,919   copying oncoref/data/cancer-lineage-groups.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,922   copying oncoref/data/censored-gene-reference-tpm.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,926   copying oncoref/data/numt-pseudogenes.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,929   copying oncoref/data/fusion-expression-effects.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,932   copying oncoref/data/cancer-ici-response-estimates.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,941   copying oncoref/data/cancer-type-registry.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,946   copying oncoref/data/mitochondrial-genes.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,948   copying oncoref/data/housekeeping-genes.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,951   copying oncoref/data/disease-state-rules.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,953   copying oncoref/data/rrna-and-pseudogenes.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,956   copying oncoref/data/cancer-response-signatures.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,959   copying oncoref/data/small-noncoding-rnas.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,969   copying oncoref/data/cancer-frameshift-burden.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,974   copying oncoref/data/nuclear-retained-lncrnas.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,978   copying oncoref/data/cdna-identical-gene-groups.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,982   copying oncoref/data/cancer-expression-source-candidates.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,986   copying oncoref/data/fusion-surrogate-expression.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,989   copying oncoref/data/cancer-tmb.csv -> build/lib/oncoref/data
2026-06-22T16:21:22,993   copying oncoref/data/canonical-gene-space.csv.gz -> build/lib/oncoref/data
2026-06-22T16:21:23,015   copying oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/lib/oncoref/data
2026-06-22T16:21:23,031   copying oncoref/data/cancer-reference-expression-samples.csv.gz -> build/lib/oncoref/data
2026-06-22T16:21:23,039   copying oncoref/data/expression_sources.yaml -> build/lib/oncoref/data
2026-06-22T16:21:23,053   installing to build/bdist.linux-armv7l/wheel
2026-06-22T16:21:23,054   running install
2026-06-22T16:21:23,076   running install_lib
2026-06-22T16:21:23,081   creating build/bdist.linux-armv7l/wheel
2026-06-22T16:21:23,084   creating build/bdist.linux-armv7l/wheel/oncoref
2026-06-22T16:21:23,086   copying build/lib/oncoref/tmb.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,088   copying build/lib/oncoref/peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,090   copying build/lib/oncoref/coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,093   copying build/lib/oncoref/gene_ids.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,096   copying build/lib/oncoref/hpa.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,098   copying build/lib/oncoref/cta_regen.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,101   copying build/lib/oncoref/cta.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,103   copying build/lib/oncoref/cancer_types.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,106   copying build/lib/oncoref/data_bundle.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,108   copying build/lib/oncoref/gene_qc.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,111   copying build/lib/oncoref/plots.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,114   copying build/lib/oncoref/proteoforms.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,116   copying build/lib/oncoref/response_signatures.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,118   copying build/lib/oncoref/gene_families.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,121   copying build/lib/oncoref/ici.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,123   copying build/lib/oncoref/fusions.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,125   copying build/lib/oncoref/expression_registry.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,128   copying build/lib/oncoref/cta_tissues.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,131   copying build/lib/oncoref/genome.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,133   copying build/lib/oncoref/reference_data.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,136   copying build/lib/oncoref/apd1.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,138   copying build/lib/oncoref/expression.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,141   copying build/lib/oncoref/expression_engine.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,145   creating build/bdist.linux-armv7l/wheel/oncoref/data
2026-06-22T16:21:23,146   copying build/lib/oncoref/data/cancer-driver-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,149   copying build/lib/oncoref/data/cancer-code-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,151   copying build/lib/oncoref/data/family-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,154   copying build/lib/oncoref/data/source-matrices.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,156   copying build/lib/oncoref/data/proteoform-collapse-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,158   copying build/lib/oncoref/data/proteoform-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,160   copying build/lib/oncoref/data/ribosomal-protein-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,164   copying build/lib/oncoref/data/canonical-gene-space.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,174   copying build/lib/oncoref/data/rare-cancer-fusion-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,177   copying build/lib/oncoref/data/cancer-lineage-group-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,179   copying build/lib/oncoref/data/cta-candidate-references.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,182   copying build/lib/oncoref/data/cancer-testis-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,187   copying build/lib/oncoref/data/expression_sources.yaml -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,190   copying build/lib/oncoref/data/cancer-ici-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,194   copying build/lib/oncoref/data/cancer-subtype-groupings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,196   copying build/lib/oncoref/data/cohort-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,199   copying build/lib/oncoref/data/histone-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,201   copying build/lib/oncoref/data/cancer-apd1-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,204   copying build/lib/oncoref/data/ribosomal-protein-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,206   copying build/lib/oncoref/data/cancer-incidence-mortality.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,209   copying build/lib/oncoref/data/clean-tpm-censored-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,214   copying build/lib/oncoref/data/cta-ihc-unreliable.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,216   copying build/lib/oncoref/data/cancer-fusions.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,220   copying build/lib/oncoref/data/narrative-gene-sets.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,222   copying build/lib/oncoref/data/cancer-driver-variants.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,225   copying build/lib/oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,234   copying build/lib/oncoref/data/tissue-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,236   copying build/lib/oncoref/data/degenerate-subtype-pairs.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,238   copying build/lib/oncoref/data/cancer-type-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,242   copying build/lib/oncoref/data/ensembl-id-aliases.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,251   copying build/lib/oncoref/data/cancer-key-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,256   copying build/lib/oncoref/data/cancer-viral-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,259   copying build/lib/oncoref/data/cancer-cohort-aggregates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,261   copying build/lib/oncoref/data/hemoglobin-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,263   copying build/lib/oncoref/data/extra-tx-mappings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,265   copying build/lib/oncoref/data/proteoform-groups-genome.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,267   copying build/lib/oncoref/data/cancer-lineage-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,270   copying build/lib/oncoref/data/censored-gene-reference-tpm.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,272   copying build/lib/oncoref/data/numt-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,274   copying build/lib/oncoref/data/fusion-expression-effects.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,276   copying build/lib/oncoref/data/cancer-ici-response-estimates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,284   copying build/lib/oncoref/data/cancer-type-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,287   copying build/lib/oncoref/data/mitochondrial-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,289   copying build/lib/oncoref/data/housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,291   copying build/lib/oncoref/data/disease-state-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,293   copying build/lib/oncoref/data/rrna-and-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,296   copying build/lib/oncoref/data/cancer-response-signatures.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,298   copying build/lib/oncoref/data/small-noncoding-rnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,303   copying build/lib/oncoref/data/cancer-frameshift-burden.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,305   copying build/lib/oncoref/data/nuclear-retained-lncrnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,306   copying build/lib/oncoref/data/cdna-identical-gene-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,309   copying build/lib/oncoref/data/cancer-expression-source-candidates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,311   copying build/lib/oncoref/data/fusion-surrogate-expression.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,313   copying build/lib/oncoref/data/cancer-reference-expression-samples.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,319   copying build/lib/oncoref/data/cancer-tmb.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-22T16:21:23,322   copying build/lib/oncoref/cli.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,324   copying build/lib/oncoref/cancer_genes.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,326   copying build/lib/oncoref/expression_builders.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,329   copying build/lib/oncoref/__init__.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,331   copying build/lib/oncoref/cta_curation_plots.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,333   copying build/lib/oncoref/source_matrices.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,336   copying build/lib/oncoref/normalization.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,339   copying build/lib/oncoref/load_dataset.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,341   copying build/lib/oncoref/version.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,343   copying build/lib/oncoref/catalog.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,345   copying build/lib/oncoref/incidence.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,348   copying build/lib/oncoref/data_manifest.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,350   copying build/lib/oncoref/samples.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-22T16:21:23,352   running install_egg_info
2026-06-22T16:21:23,361   running egg_info
2026-06-22T16:21:23,366   writing oncoref.egg-info/PKG-INFO
2026-06-22T16:21:23,372   writing dependency_links to oncoref.egg-info/dependency_links.txt
2026-06-22T16:21:23,373   writing entry points to oncoref.egg-info/entry_points.txt
2026-06-22T16:21:23,376   writing requirements to oncoref.egg-info/requires.txt
2026-06-22T16:21:23,377   writing top-level names to oncoref.egg-info/top_level.txt
2026-06-22T16:21:23,396   reading manifest file 'oncoref.egg-info/SOURCES.txt'
2026-06-22T16:21:23,404   reading manifest template 'MANIFEST.in'
2026-06-22T16:21:23,406   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression'
2026-06-22T16:21:23,407   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles'
2026-06-22T16:21:23,408   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives'
2026-06-22T16:21:23,410   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5'
2026-06-22T16:21:23,411   warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv'
2026-06-22T16:21:23,412   warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv'
2026-06-22T16:21:23,412   adding license file 'LICENSE'
2026-06-22T16:21:23,420   writing manifest file 'oncoref.egg-info/SOURCES.txt'
2026-06-22T16:21:23,422   Copying oncoref.egg-info to build/bdist.linux-armv7l/wheel/./oncoref-1.8.3-py3.11.egg-info
2026-06-22T16:21:23,433   running install_scripts
2026-06-22T16:21:23,446   creating build/bdist.linux-armv7l/wheel/oncoref-1.8.3.dist-info/WHEEL
2026-06-22T16:21:23,449   creating '/tmp/pip-wheel-2j1x157k/.tmp-0dxa5swz/oncoref-1.8.3-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2026-06-22T16:21:23,453   adding 'oncoref/__init__.py'
2026-06-22T16:21:23,454   adding 'oncoref/apd1.py'
2026-06-22T16:21:23,456   adding 'oncoref/cancer_genes.py'
2026-06-22T16:21:23,461   adding 'oncoref/cancer_types.py'
2026-06-22T16:21:23,463   adding 'oncoref/catalog.py'
2026-06-22T16:21:23,466   adding 'oncoref/cli.py'
2026-06-22T16:21:23,470   adding 'oncoref/coverage.py'
2026-06-22T16:21:23,472   adding 'oncoref/cta.py'
2026-06-22T16:21:23,474   adding 'oncoref/cta_curation_plots.py'
2026-06-22T16:21:23,477   adding 'oncoref/cta_regen.py'
2026-06-22T16:21:23,479   adding 'oncoref/cta_tissues.py'
2026-06-22T16:21:23,481   adding 'oncoref/data_bundle.py'
2026-06-22T16:21:23,484   adding 'oncoref/data_manifest.py'
2026-06-22T16:21:23,492   adding 'oncoref/expression.py'
2026-06-22T16:21:23,495   adding 'oncoref/expression_builders.py'
2026-06-22T16:21:23,497   adding 'oncoref/expression_engine.py'
2026-06-22T16:21:23,498   adding 'oncoref/expression_registry.py'
2026-06-22T16:21:23,500   adding 'oncoref/fusions.py'
2026-06-22T16:21:23,502   adding 'oncoref/gene_families.py'
2026-06-22T16:21:23,504   adding 'oncoref/gene_ids.py'
2026-06-22T16:21:23,506   adding 'oncoref/gene_qc.py'
2026-06-22T16:21:23,508   adding 'oncoref/genome.py'
2026-06-22T16:21:23,510   adding 'oncoref/hpa.py'
2026-06-22T16:21:23,513   adding 'oncoref/ici.py'
2026-06-22T16:21:23,515   adding 'oncoref/incidence.py'
2026-06-22T16:21:23,517   adding 'oncoref/load_dataset.py'
2026-06-22T16:21:23,521   adding 'oncoref/normalization.py'
2026-06-22T16:21:23,523   adding 'oncoref/peptides.py'
2026-06-22T16:21:23,530   adding 'oncoref/plots.py'
2026-06-22T16:21:23,533   adding 'oncoref/proteoforms.py'
2026-06-22T16:21:23,535   adding 'oncoref/reference_data.py'
2026-06-22T16:21:23,537   adding 'oncoref/response_signatures.py'
2026-06-22T16:21:23,538   adding 'oncoref/samples.py'
2026-06-22T16:21:23,540   adding 'oncoref/source_matrices.py'
2026-06-22T16:21:23,541   adding 'oncoref/tmb.py'
2026-06-22T16:21:23,543   adding 'oncoref/version.py'
2026-06-22T16:21:23,547   adding 'oncoref/data/cancer-apd1-response.csv'
2026-06-22T16:21:23,548   adding 'oncoref/data/cancer-code-burden-map.csv'
2026-06-22T16:21:23,549   adding 'oncoref/data/cancer-cohort-aggregates.csv'
2026-06-22T16:21:23,554   adding 'oncoref/data/cancer-driver-genes.csv'
2026-06-22T16:21:23,557   adding 'oncoref/data/cancer-driver-variants.csv'
2026-06-22T16:21:23,559   adding 'oncoref/data/cancer-expression-source-candidates.csv'
2026-06-22T16:21:23,561   adding 'oncoref/data/cancer-frameshift-burden.csv'
2026-06-22T16:21:23,564   adding 'oncoref/data/cancer-fusions.csv'
2026-06-22T16:21:23,581   adding 'oncoref/data/cancer-ici-response-estimates.csv'
2026-06-22T16:21:23,586   adding 'oncoref/data/cancer-ici-response.csv'
2026-06-22T16:21:23,587   adding 'oncoref/data/cancer-incidence-mortality.csv'
2026-06-22T16:21:23,602   adding 'oncoref/data/cancer-key-genes.csv'
2026-06-22T16:21:23,604   adding 'oncoref/data/cancer-lineage-group-overrides.csv'
2026-06-22T16:21:23,605   adding 'oncoref/data/cancer-lineage-groups.csv'
2026-06-22T16:21:23,634   adding 'oncoref/data/cancer-reference-expression-samples.csv.gz'
2026-06-22T16:21:23,638   adding 'oncoref/data/cancer-response-signatures.csv'
2026-06-22T16:21:23,639   adding 'oncoref/data/cancer-subtype-groupings.csv'
2026-06-22T16:21:23,650   adding 'oncoref/data/cancer-testis-antigens.csv'
2026-06-22T16:21:23,653   adding 'oncoref/data/cancer-tmb.csv'
2026-06-22T16:21:23,656   adding 'oncoref/data/cancer-type-genes.csv'
2026-06-22T16:21:23,660   adding 'oncoref/data/cancer-type-registry.csv'
2026-06-22T16:21:23,661   adding 'oncoref/data/cancer-viral-antigens.csv'
2026-06-22T16:21:23,714   adding 'oncoref/data/canonical-gene-space.csv.gz'
2026-06-22T16:21:23,720   adding 'oncoref/data/cdna-identical-gene-groups.csv'
2026-06-22T16:21:23,724   adding 'oncoref/data/censored-gene-reference-tpm.csv'
2026-06-22T16:21:23,734   adding 'oncoref/data/clean-tpm-censored-genes.csv'
2026-06-22T16:21:23,737   adding 'oncoref/data/cohort-registry.csv'
2026-06-22T16:21:23,738   adding 'oncoref/data/cta-candidate-references.csv'
2026-06-22T16:21:23,740   adding 'oncoref/data/cta-ihc-unreliable.csv'
2026-06-22T16:21:23,741   adding 'oncoref/data/degenerate-subtype-pairs.csv'
2026-06-22T16:21:23,748   adding 'oncoref/data/disease-state-rules.csv'
2026-06-22T16:21:23,775   adding 'oncoref/data/ensembl-id-aliases.csv'
2026-06-22T16:21:23,782   adding 'oncoref/data/expression_sources.yaml'
2026-06-22T16:21:23,784   adding 'oncoref/data/extra-tx-mappings.csv'
2026-06-22T16:21:23,785   adding 'oncoref/data/family-burden-map.csv'
2026-06-22T16:21:23,786   adding 'oncoref/data/fusion-expression-effects.csv'
2026-06-22T16:21:23,788   adding 'oncoref/data/fusion-surrogate-expression.csv'
2026-06-22T16:21:23,789   adding 'oncoref/data/hemoglobin-genes.csv'
2026-06-22T16:21:23,790   adding 'oncoref/data/histone-genes.csv'
2026-06-22T16:21:23,792   adding 'oncoref/data/housekeeping-genes.csv'
2026-06-22T16:21:23,793   adding 'oncoref/data/mitochondrial-genes.csv'
2026-06-22T16:21:23,794   adding 'oncoref/data/narrative-gene-sets.csv'
2026-06-22T16:21:23,834   adding 'oncoref/data/ncbi-symbol-synonyms.csv.gz'
2026-06-22T16:21:23,838   adding 'oncoref/data/nuclear-retained-lncrnas.csv'
2026-06-22T16:21:23,841   adding 'oncoref/data/numt-pseudogenes.csv'
2026-06-22T16:21:23,842   adding 'oncoref/data/proteoform-collapse-overrides.csv'
2026-06-22T16:21:23,845   adding 'oncoref/data/proteoform-groups-genome.csv'
2026-06-22T16:21:23,846   adding 'oncoref/data/proteoform-groups.csv'
2026-06-22T16:21:23,848   adding 'oncoref/data/rare-cancer-fusion-rules.csv'
2026-06-22T16:21:23,849   adding 'oncoref/data/ribosomal-protein-genes.csv'
2026-06-22T16:21:23,856   adding 'oncoref/data/ribosomal-protein-pseudogenes.csv'
2026-06-22T16:21:23,858   adding 'oncoref/data/rrna-and-pseudogenes.csv'
2026-06-22T16:21:23,877   adding 'oncoref/data/small-noncoding-rnas.csv'
2026-06-22T16:21:23,880   adding 'oncoref/data/source-matrices.csv'
2026-06-22T16:21:23,881   adding 'oncoref/data/tissue-burden-map.csv'
2026-06-22T16:21:23,885   adding 'oncoref-1.8.3.dist-info/licenses/LICENSE'
2026-06-22T16:21:23,886   adding 'oncoref-1.8.3.dist-info/METADATA'
2026-06-22T16:21:23,888   adding 'oncoref-1.8.3.dist-info/WHEEL'
2026-06-22T16:21:23,889   adding 'oncoref-1.8.3.dist-info/entry_points.txt'
2026-06-22T16:21:23,889   adding 'oncoref-1.8.3.dist-info/top_level.txt'
2026-06-22T16:21:23,891   adding 'oncoref-1.8.3.dist-info/RECORD'
2026-06-22T16:21:23,910   removing build/bdist.linux-armv7l/wheel
2026-06-22T16:21:24,030   Building wheel for oncoref (pyproject.toml): finished with status 'done'
2026-06-22T16:21:24,075   Created wheel for oncoref: filename=oncoref-1.8.3-py3-none-any.whl size=1639990 sha256=bf75676ac99a0d1c144249b8cf320ac292b65716c9ffdc50ad27b55db1153821
2026-06-22T16:21:24,076   Stored in directory: /tmp/pip-ephem-wheel-cache-h19sepdw/wheels/de/8b/5c/916e153ef2867bf1125f4ec8ef538234dc9425af16132bea42
2026-06-22T16:21:24,091 Successfully built oncoref
2026-06-22T16:21:24,141 Removed build tracker: '/tmp/pip-build-tracker-r4o6vuug'