2026-08-31T14:26:10,963 Created temporary directory: /tmp/pip-ephem-wheel-cache-t4svc_5z 2026-08-31T14:26:10,965 Created temporary directory: /tmp/pip-build-tracker-js2ask4c 2026-08-31T14:26:10,966 Initialized build tracking at /tmp/pip-build-tracker-js2ask4c 2026-08-31T14:26:10,966 Created build tracker: /tmp/pip-build-tracker-js2ask4c 2026-08-31T14:26:10,967 Entered build tracker: /tmp/pip-build-tracker-js2ask4c 2026-08-31T14:26:10,968 Created temporary directory: /tmp/pip-wheel-c083qqlm 2026-08-31T14:26:10,971 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 2026-08-31T14:26:10,973 Created temporary directory: /tmp/pip-ephem-wheel-cache-su86s1nh 2026-08-31T14:26:10,995 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-08-31T14:26:10,999 2 location(s) to search for versions of oncoref: 2026-08-31T14:26:10,999 * https://pypi.org/simple/oncoref/ 2026-08-31T14:26:10,999 * https://www.piwheels.org/simple/oncoref/ 2026-08-31T14:26:11,000 Fetching project page and analyzing links: https://pypi.org/simple/oncoref/ 2026-08-31T14:26:11,000 Getting page https://pypi.org/simple/oncoref/ 2026-08-31T14:26:11,002 Found index url https://pypi.org/simple 2026-08-31T14:26:11,281 Fetched page https://pypi.org/simple/oncoref/ as application/vnd.pypi.simple.v1+json 2026-08-31T14:26:11,347 Skipping link: No binaries permitted for oncoref: 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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) 2026-08-31T14:26:11,352 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 2026-08-31T14:26:11,353 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) 2026-08-31T14:26:11,354 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: 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(requires-python:>=3.9) 2026-08-31T14:26:11,364 Found link https://files.pythonhosted.org/packages/62/2d/434129dfb4157eb2bf8c4f89ff3f5c74e65b2a62e619fcd1154388d70aa4/oncoref-1.8.7.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.8.7 2026-08-31T14:26:11,365 Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/06/89/59174cc23b5ca908c5eed6c89f147d28265749466c702e7c45a91004c4d2/oncoref-1.8.8-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9) 2026-08-31T14:26:11,366 Found link https://files.pythonhosted.org/packages/f4/fd/e8f16e540188ecdfa8d331e209374ed0c47ef44e27eae34fc4a262b6e49a/oncoref-1.8.8.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.8.8 2026-08-31T14:26:11,366 Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/21/11/175fa74783a3e4662792af69e82e51a7a991e710858efaeb92a8695d8fda/oncoref-1.8.9-py3-none-any.whl 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Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/5e/38/d4f824676b3d280e159182422711e46a9be12a1078869b3b3da846a959d6/oncoref-1.8.13-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9) 2026-08-31T14:26:11,374 Found link https://files.pythonhosted.org/packages/53/53/a8ca36b70ca14b5654f882f5a6fec1709a385bc2cc18d4bde37a2f32d454/oncoref-1.8.13.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.8.13 2026-08-31T14:26:11,375 Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/2f/c1/703bd890ae830651eae083a090278ba8254ac89bae1c0bfefed061c3e2eb/oncoref-1.8.14-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9) 2026-08-31T14:26:11,376 Found link https://files.pythonhosted.org/packages/72/05/f82628c00d880f035d82572d1160a43c00ca2e7c45b010b4a9f300a5a863/oncoref-1.8.14.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.8.14 2026-08-31T14:26:11,376 Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/ac/42/91b2b04455fb29d40afb47dc7ee2eae30218a24c4d540d95191d31f6f98e/oncoref-1.8.15-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9) 2026-08-31T14:26:11,377 Found link https://files.pythonhosted.org/packages/26/8a/9cb4754077d37b89ed3ee3781cffdb03040d90286aaaedacba8cb238d7c3/oncoref-1.8.15.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.8.15 2026-08-31T14:26:11,378 Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/53/3f/1af50bb6d208ada32a29b7e3ed29169932b97542b48e765c1d96130b7f3d/oncoref-1.8.16-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9) 2026-08-31T14:26:11,379 Found link 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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) 2026-08-31T14:26:12,017 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) 2026-08-31T14:26:12,017 Skipping link: not a file: https://www.piwheels.org/simple/oncoref/ 2026-08-31T14:26:12,018 Skipping link: not a file: https://pypi.org/simple/oncoref/ 2026-08-31T14:26:12,059 Given no hashes to check 1 links for project 'oncoref': discarding no candidates 2026-08-31T14:26:12,078 Collecting oncoref==1.8.188 2026-08-31T14:26:12,080 Created temporary directory: /tmp/pip-unpack-pf_t9olf 2026-08-31T14:26:12,248 Downloading oncoref-1.8.188.tar.gz (13.8 MB) 2026-08-31T14:26:14,416 Added oncoref==1.8.188 from https://files.pythonhosted.org/packages/42/35/8047adcbcc126f834db7931e1516a9851f33503d41ed54e08b0635d2b72b/oncoref-1.8.188.tar.gz to build tracker '/tmp/pip-build-tracker-js2ask4c' 2026-08-31T14:26:14,423 Created temporary directory: /tmp/pip-build-env-xw5hdmwm 2026-08-31T14:26:14,427 Installing build dependencies: started 2026-08-31T14:26:14,429 Running command pip subprocess to install build dependencies 2026-08-31T14:26:15,596 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-08-31T14:26:16,018 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 2026-08-31T14:26:16,040 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-08-31T14:26:17,882 Collecting setuptools>=77.0.0 2026-08-31T14:26:17,883 Obtaining dependency information for setuptools>=77.0.0 from https://www.piwheels.org/simple/setuptools/setuptools-84.0.0-py3-none-any.whl.metadata 2026-08-31T14:26:17,897 Using cached https://www.piwheels.org/simple/setuptools/setuptools-84.0.0-py3-none-any.whl.metadata (6.6 kB) 2026-08-31T14:26:18,144 Collecting wheel 2026-08-31T14:26:18,145 Obtaining dependency information for wheel from https://www.piwheels.org/simple/wheel/wheel-0.48.0-py3-none-any.whl.metadata 2026-08-31T14:26:18,164 Using cached https://www.piwheels.org/simple/wheel/wheel-0.48.0-py3-none-any.whl.metadata (2.3 kB) 2026-08-31T14:26:18,358 Collecting packaging>=24.0 2026-08-31T14:26:18,359 Obtaining dependency information for packaging>=24.0 from https://www.piwheels.org/simple/packaging/packaging-26.3-py3-none-any.whl.metadata 2026-08-31T14:26:18,373 Using cached https://www.piwheels.org/simple/packaging/packaging-26.3-py3-none-any.whl.metadata (3.6 kB) 2026-08-31T14:26:18,575 Using cached https://www.piwheels.org/simple/wheel/wheel-0.48.0-py3-none-any.whl (33 kB) 2026-08-31T14:26:18,597 Using cached https://www.piwheels.org/simple/packaging/packaging-26.3-py3-none-any.whl (129 kB) 2026-08-31T14:26:18,670 Using cached https://www.piwheels.org/simple/setuptools/setuptools-84.0.0-py3-none-any.whl (818 kB) 2026-08-31T14:26:18,750 Using cached https://www.piwheels.org/simple/wheel/wheel-0.48.0-py3-none-any.whl (33 kB) 2026-08-31T14:26:18,778 Using cached https://www.piwheels.org/simple/packaging/packaging-26.3-py3-none-any.whl (129 kB) 2026-08-31T14:26:18,865 Using cached https://www.piwheels.org/simple/setuptools/setuptools-84.0.0-py3-none-any.whl (818 kB) 2026-08-31T14:26:21,646 Installing collected packages: setuptools, packaging, wheel 2026-08-31T14:26:24,606 Creating /tmp/pip-build-env-xw5hdmwm/overlay/local/bin 2026-08-31T14:26:24,609 changing mode of /tmp/pip-build-env-xw5hdmwm/overlay/local/bin/wheel to 755 2026-08-31T14:26:24,630 Successfully installed packaging-26.3 setuptools-84.0.0 wheel-0.48.0 2026-08-31T14:26:24,916 Installing build dependencies: finished with status 'done' 2026-08-31T14:26:24,923 Getting requirements to build wheel: started 2026-08-31T14:26:24,924 Running command Getting requirements to build wheel 2026-08-31T14:26:25,636 running egg_info 2026-08-31T14:26:25,642 writing oncoref.egg-info/PKG-INFO 2026-08-31T14:26:25,648 writing dependency_links to oncoref.egg-info/dependency_links.txt 2026-08-31T14:26:25,650 writing entry points to oncoref.egg-info/entry_points.txt 2026-08-31T14:26:25,652 writing requirements to oncoref.egg-info/requires.txt 2026-08-31T14:26:25,654 writing top-level names to oncoref.egg-info/top_level.txt 2026-08-31T14:26:25,695 reading manifest file 'oncoref.egg-info/SOURCES.txt' 2026-08-31T14:26:25,709 reading manifest template 'MANIFEST.in' 2026-08-31T14:26:25,729 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-08-31T14:26:25,730 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-08-31T14:26:25,732 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-08-31T14:26:25,734 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-08-31T14:26:25,735 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-08-31T14:26:25,736 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-08-31T14:26:25,737 adding license file 'LICENSE' 2026-08-31T14:26:25,749 writing manifest file 'oncoref.egg-info/SOURCES.txt' 2026-08-31T14:26:25,848 Getting requirements to build wheel: finished with status 'done' 2026-08-31T14:26:25,852 Created temporary directory: /tmp/pip-modern-metadata-lzr8ti4s 2026-08-31T14:26:25,854 Preparing metadata (pyproject.toml): started 2026-08-31T14:26:25,855 Running command Preparing metadata (pyproject.toml) 2026-08-31T14:26:26,543 running dist_info 2026-08-31T14:26:26,553 creating /tmp/pip-modern-metadata-lzr8ti4s/oncoref.egg-info 2026-08-31T14:26:26,554 writing /tmp/pip-modern-metadata-lzr8ti4s/oncoref.egg-info/PKG-INFO 2026-08-31T14:26:26,560 writing dependency_links to /tmp/pip-modern-metadata-lzr8ti4s/oncoref.egg-info/dependency_links.txt 2026-08-31T14:26:26,562 writing entry points to /tmp/pip-modern-metadata-lzr8ti4s/oncoref.egg-info/entry_points.txt 2026-08-31T14:26:26,564 writing requirements to /tmp/pip-modern-metadata-lzr8ti4s/oncoref.egg-info/requires.txt 2026-08-31T14:26:26,565 writing top-level names to /tmp/pip-modern-metadata-lzr8ti4s/oncoref.egg-info/top_level.txt 2026-08-31T14:26:26,567 writing manifest file '/tmp/pip-modern-metadata-lzr8ti4s/oncoref.egg-info/SOURCES.txt' 2026-08-31T14:26:26,604 reading manifest file '/tmp/pip-modern-metadata-lzr8ti4s/oncoref.egg-info/SOURCES.txt' 2026-08-31T14:26:26,606 reading manifest template 'MANIFEST.in' 2026-08-31T14:26:26,624 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-08-31T14:26:26,625 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-08-31T14:26:26,626 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-08-31T14:26:26,628 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-08-31T14:26:26,629 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-08-31T14:26:26,630 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-08-31T14:26:26,630 adding license file 'LICENSE' 2026-08-31T14:26:26,639 writing manifest file '/tmp/pip-modern-metadata-lzr8ti4s/oncoref.egg-info/SOURCES.txt' 2026-08-31T14:26:26,641 creating '/tmp/pip-modern-metadata-lzr8ti4s/oncoref-1.8.188.dist-info' 2026-08-31T14:26:26,770 Preparing metadata (pyproject.toml): finished with status 'done' 2026-08-31T14:26:26,775 Source in /tmp/pip-wheel-c083qqlm/oncoref_10c59f7932b044beb878db4e81443d8a has version 1.8.188, which satisfies requirement oncoref==1.8.188 from https://files.pythonhosted.org/packages/42/35/8047adcbcc126f834db7931e1516a9851f33503d41ed54e08b0635d2b72b/oncoref-1.8.188.tar.gz 2026-08-31T14:26:26,776 Removed oncoref==1.8.188 from https://files.pythonhosted.org/packages/42/35/8047adcbcc126f834db7931e1516a9851f33503d41ed54e08b0635d2b72b/oncoref-1.8.188.tar.gz from build tracker '/tmp/pip-build-tracker-js2ask4c' 2026-08-31T14:26:26,783 Created temporary directory: /tmp/pip-unpack-nc2cp0u9 2026-08-31T14:26:26,783 Building wheels for collected packages: oncoref 2026-08-31T14:26:26,788 Created temporary directory: /tmp/pip-wheel-2t0py3jk 2026-08-31T14:26:26,788 Destination directory: /tmp/pip-wheel-2t0py3jk 2026-08-31T14:26:26,791 Building wheel for oncoref (pyproject.toml): started 2026-08-31T14:26:26,792 Running command Building wheel for oncoref (pyproject.toml) 2026-08-31T14:26:27,423 running bdist_wheel 2026-08-31T14:26:27,441 running build 2026-08-31T14:26:27,441 running build_py 2026-08-31T14:26:27,448 creating build/lib/oncoref 2026-08-31T14:26:27,451 copying oncoref/cancer_types.py -> build/lib/oncoref 2026-08-31T14:26:27,455 copying oncoref/ici.py -> build/lib/oncoref 2026-08-31T14:26:27,458 copying oncoref/response_signatures.py -> build/lib/oncoref 2026-08-31T14:26:27,460 copying oncoref/data_manifest.py -> build/lib/oncoref 2026-08-31T14:26:27,463 copying oncoref/apd1.py -> build/lib/oncoref 2026-08-31T14:26:27,465 copying oncoref/__init__.py -> build/lib/oncoref 2026-08-31T14:26:27,468 copying oncoref/_reference_sources.py -> build/lib/oncoref 2026-08-31T14:26:27,470 copying oncoref/samples.py -> build/lib/oncoref 2026-08-31T14:26:27,472 copying oncoref/fusions.py -> build/lib/oncoref 2026-08-31T14:26:27,474 copying oncoref/proteoforms.py -> build/lib/oncoref 2026-08-31T14:26:27,477 copying oncoref/reference_data.py -> build/lib/oncoref 2026-08-31T14:26:27,480 copying oncoref/expression_registry.py -> build/lib/oncoref 2026-08-31T14:26:27,482 copying oncoref/cta_curation_plots.py -> build/lib/oncoref 2026-08-31T14:26:27,485 copying oncoref/drivers.py -> build/lib/oncoref 2026-08-31T14:26:27,487 copying oncoref/rna_protein.py -> build/lib/oncoref 2026-08-31T14:26:27,490 copying oncoref/expression_engine.py -> build/lib/oncoref 2026-08-31T14:26:27,493 copying oncoref/cancer_genes.py -> build/lib/oncoref 2026-08-31T14:26:27,495 copying oncoref/version.py -> build/lib/oncoref 2026-08-31T14:26:27,497 copying oncoref/peptides.py -> build/lib/oncoref 2026-08-31T14:26:27,499 copying oncoref/gene_families.py -> build/lib/oncoref 2026-08-31T14:26:27,501 copying oncoref/gene_qc.py -> build/lib/oncoref 2026-08-31T14:26:27,504 copying oncoref/cta_peptides.py -> build/lib/oncoref 2026-08-31T14:26:27,506 copying oncoref/tmb.py -> build/lib/oncoref 2026-08-31T14:26:27,508 copying oncoref/genome.py -> build/lib/oncoref 2026-08-31T14:26:27,510 copying oncoref/normalization.py -> build/lib/oncoref 2026-08-31T14:26:27,513 copying oncoref/cta_coverage.py -> build/lib/oncoref 2026-08-31T14:26:27,515 copying oncoref/expression_builders.py -> build/lib/oncoref 2026-08-31T14:26:27,522 copying oncoref/source_matrices.py -> build/lib/oncoref 2026-08-31T14:26:27,525 copying oncoref/cta.py -> build/lib/oncoref 2026-08-31T14:26:27,528 copying oncoref/plots.py -> build/lib/oncoref 2026-08-31T14:26:27,531 copying oncoref/representative_partitions.py -> build/lib/oncoref 2026-08-31T14:26:27,534 copying oncoref/coverage.py -> build/lib/oncoref 2026-08-31T14:26:27,537 copying oncoref/cohorts.py -> build/lib/oncoref 2026-08-31T14:26:27,538 copying oncoref/antigen_coverage.py -> build/lib/oncoref 2026-08-31T14:26:27,540 copying oncoref/expression.py -> build/lib/oncoref 2026-08-31T14:26:27,547 copying oncoref/ici_response.py -> build/lib/oncoref 2026-08-31T14:26:27,549 copying oncoref/catalog.py -> build/lib/oncoref 2026-08-31T14:26:27,552 copying oncoref/therapy_evidence.py -> build/lib/oncoref 2026-08-31T14:26:27,554 copying oncoref/cta_tissues.py -> build/lib/oncoref 2026-08-31T14:26:27,556 copying oncoref/cta_regen.py -> build/lib/oncoref 2026-08-31T14:26:27,559 copying oncoref/tumor_references.py -> build/lib/oncoref 2026-08-31T14:26:27,561 copying oncoref/hpa.py -> build/lib/oncoref 2026-08-31T14:26:27,564 copying oncoref/cli.py -> build/lib/oncoref 2026-08-31T14:26:27,567 copying oncoref/gene_ids.py -> build/lib/oncoref 2026-08-31T14:26:27,570 copying oncoref/expression_source_adapters.py -> build/lib/oncoref 2026-08-31T14:26:27,574 copying oncoref/data_bundle.py -> build/lib/oncoref 2026-08-31T14:26:27,577 copying oncoref/incidence.py -> build/lib/oncoref 2026-08-31T14:26:27,580 copying oncoref/cancer_ontology.py -> build/lib/oncoref 2026-08-31T14:26:27,582 copying oncoref/load_dataset.py -> build/lib/oncoref 2026-08-31T14:26:27,600 creating build/lib/oncoref/data 2026-08-31T14:26:27,601 copying oncoref/data/cancer-frameshift-burden.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,603 copying oncoref/data/source-matrices.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,606 copying oncoref/data/cancer-tmb.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,609 copying oncoref/data/representative-source-adjudications.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,611 copying oncoref/data/cancer-apd1-response.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,615 copying oncoref/data/cancer-type-genes.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,618 copying oncoref/data/cancer-code-burden-map.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,620 copying oncoref/data/cancer-key-gene-citation-audit.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,625 copying oncoref/data/cta-ihc-unreliable.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,627 copying oncoref/data/fusion-expression-effects.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,630 copying oncoref/data/family-burden-map.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,632 copying oncoref/data/extra-tx-mappings.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,635 copying oncoref/data/rare-cancer-fusion-rules.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,638 copying oncoref/data/cancer-response-signatures.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,640 copying oncoref/data/histone-genes.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,643 copying oncoref/data/cancer-incidence-mortality.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,645 copying oncoref/data/cancer-reference-sample-molecular-provenance.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,649 copying oncoref/data/cancer-key-genes.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,657 copying oncoref/data/rna-protein-hpa-prior-sources.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,659 copying oncoref/data/mitochondrial-genes.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,661 copying oncoref/data/cancer-fusions.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,664 copying oncoref/data/tissue-burden-map.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,666 copying oncoref/data/ribosomal-protein-pseudogenes.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,669 copying oncoref/data/cancer-driver-variants.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,672 copying oncoref/data/cancer-who-soft-tissue-bone-audit.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,675 copying oncoref/data/cancer-ici-response-estimates.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,683 copying oncoref/data/cancer-cohort-aggregates.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,685 copying oncoref/data/cancer-subtype-groupings.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,687 copying oncoref/data/cancer-type-registry.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,691 copying oncoref/data/housekeeping-genes.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,693 copying oncoref/data/nuclear-retained-lncrnas.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,695 copying oncoref/data/cancer-entity-driver-spectrum.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,697 copying oncoref/data/small-noncoding-rnas.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,703 copying oncoref/data/ribosomal-protein-genes.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,705 copying oncoref/data/numt-pseudogenes.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,708 copying oncoref/data/cancer-reference-expression-availability.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,712 copying oncoref/data/cdna-identical-gene-groups.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,715 copying oncoref/data/censored-gene-reference-tpm.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,719 copying oncoref/data/cta-clinical-targets.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,721 copying oncoref/data/expression-artifact-gene-universe-deltas.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,728 copying oncoref/data/cta-specificity-audit.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,731 copying oncoref/data/rrna-and-pseudogenes.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,733 copying oncoref/data/cancer-viral-antigens.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,736 copying oncoref/data/proteoform-groups.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,738 copying oncoref/data/cancer-mismatch-repair-statuses.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,740 copying oncoref/data/cancer-lineage-groups.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,742 copying oncoref/data/clean-tpm-censored-genes.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,764 copying oncoref/data/therapy-benefit-toxicity-evidence.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,766 copying oncoref/data/proteoform-groups-genome.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,769 copying oncoref/data/cancer-lineage-group-overrides.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,771 copying oncoref/data/cancer-ici-response.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,774 copying oncoref/data/cancer-testis-antigens.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,780 copying oncoref/data/gse294016-sample-diagnoses.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,782 copying oncoref/data/ensembl-id-aliases.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,792 copying oncoref/data/hpa-safety-tissue-map.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,794 copying oncoref/data/cta-candidate-references.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,797 copying oncoref/data/cancer-fusion-citation-audit.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,799 copying oncoref/data/hemoglobin-genes.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,801 copying oncoref/data/cohort-registry.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,804 copying oncoref/data/cancer-driver-genes.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,807 copying oncoref/data/cancer-normal-tissue-map.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,810 copying oncoref/data/narrative-gene-sets.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,812 copying oncoref/data/cancer-ici-source-locator-audit.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,817 copying oncoref/data/cancer-expression-source-candidates.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,821 copying oncoref/data/disease-state-rules.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,823 copying oncoref/data/rna-protein-calibration-sources.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,825 copying oncoref/data/proteoform-collapse-overrides.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,827 copying oncoref/data/clean-tpm-biological-housekeeping-genes.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,830 copying oncoref/data/degenerate-subtype-pairs.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,832 copying oncoref/data/fusion-surrogate-expression.csv -> build/lib/oncoref/data 2026-08-31T14:26:27,834 copying oncoref/data/cancer-reference-expression-samples.csv.gz -> build/lib/oncoref/data 2026-08-31T14:26:27,843 copying oncoref/data/ncbi-entrez-gene-mappings.csv.gz -> build/lib/oncoref/data 2026-08-31T14:26:27,866 copying oncoref/data/rna-protein-calibration-samples.csv.gz -> build/lib/oncoref/data 2026-08-31T14:26:27,868 copying oncoref/data/rna-protein-hpa-priors.csv.gz -> build/lib/oncoref/data 2026-08-31T14:26:27,880 copying oncoref/data/rna-protein-calibrations.csv.gz -> build/lib/oncoref/data 2026-08-31T14:26:28,028 copying oncoref/data/canonical-gene-space.csv.gz -> build/lib/oncoref/data 2026-08-31T14:26:28,037 copying oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/lib/oncoref/data 2026-08-31T14:26:28,046 copying oncoref/data/expression_sources.yaml -> build/lib/oncoref/data 2026-08-31T14:26:28,062 installing to build/bdist.linux-armv7l/wheel 2026-08-31T14:26:28,063 running install 2026-08-31T14:26:28,085 running install_lib 2026-08-31T14:26:28,092 creating build/bdist.linux-armv7l/wheel 2026-08-31T14:26:28,095 creating build/bdist.linux-armv7l/wheel/oncoref 2026-08-31T14:26:28,097 copying build/lib/oncoref/cancer_types.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,101 copying build/lib/oncoref/ici.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,104 copying build/lib/oncoref/response_signatures.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,105 copying build/lib/oncoref/data_manifest.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,108 copying build/lib/oncoref/apd1.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,110 copying build/lib/oncoref/__init__.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,113 copying build/lib/oncoref/_reference_sources.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,115 copying build/lib/oncoref/samples.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,117 copying build/lib/oncoref/fusions.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,119 copying build/lib/oncoref/proteoforms.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,122 copying build/lib/oncoref/reference_data.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,124 copying build/lib/oncoref/expression_registry.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,127 copying build/lib/oncoref/cta_curation_plots.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,129 copying build/lib/oncoref/drivers.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,131 copying build/lib/oncoref/rna_protein.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,134 copying build/lib/oncoref/expression_engine.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,136 copying build/lib/oncoref/cancer_genes.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,138 copying build/lib/oncoref/version.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,140 copying build/lib/oncoref/peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,143 copying build/lib/oncoref/gene_families.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,145 copying build/lib/oncoref/gene_qc.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,147 copying build/lib/oncoref/cta_peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,149 copying build/lib/oncoref/tmb.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,151 copying build/lib/oncoref/genome.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,154 copying build/lib/oncoref/normalization.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,156 copying build/lib/oncoref/cta_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,159 copying build/lib/oncoref/expression_builders.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,164 copying build/lib/oncoref/source_matrices.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,166 copying build/lib/oncoref/cta.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,169 copying build/lib/oncoref/plots.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,172 copying build/lib/oncoref/representative_partitions.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,174 copying build/lib/oncoref/coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,177 copying build/lib/oncoref/cohorts.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,179 copying build/lib/oncoref/antigen_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,181 copying build/lib/oncoref/expression.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,188 creating build/bdist.linux-armv7l/wheel/oncoref/data 2026-08-31T14:26:28,189 copying build/lib/oncoref/data/cancer-frameshift-burden.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,191 copying build/lib/oncoref/data/source-matrices.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,194 copying build/lib/oncoref/data/cancer-tmb.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,196 copying build/lib/oncoref/data/representative-source-adjudications.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,198 copying build/lib/oncoref/data/cancer-apd1-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,201 copying build/lib/oncoref/data/cancer-type-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,204 copying build/lib/oncoref/data/cancer-reference-expression-samples.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,210 copying build/lib/oncoref/data/cancer-code-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,212 copying build/lib/oncoref/data/cancer-key-gene-citation-audit.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,216 copying build/lib/oncoref/data/cta-ihc-unreliable.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,218 copying build/lib/oncoref/data/fusion-expression-effects.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,220 copying build/lib/oncoref/data/family-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,221 copying build/lib/oncoref/data/extra-tx-mappings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,223 copying build/lib/oncoref/data/rare-cancer-fusion-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,225 copying build/lib/oncoref/data/ncbi-entrez-gene-mappings.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,242 copying build/lib/oncoref/data/cancer-response-signatures.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,243 copying build/lib/oncoref/data/histone-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,245 copying build/lib/oncoref/data/cancer-incidence-mortality.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,248 copying build/lib/oncoref/data/cancer-reference-sample-molecular-provenance.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,251 copying build/lib/oncoref/data/cancer-key-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,255 copying build/lib/oncoref/data/rna-protein-hpa-prior-sources.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,257 copying build/lib/oncoref/data/mitochondrial-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,258 copying build/lib/oncoref/data/cancer-fusions.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,261 copying build/lib/oncoref/data/tissue-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,262 copying build/lib/oncoref/data/ribosomal-protein-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,265 copying build/lib/oncoref/data/cancer-driver-variants.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,268 copying build/lib/oncoref/data/cancer-who-soft-tissue-bone-audit.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,271 copying build/lib/oncoref/data/cancer-ici-response-estimates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,279 copying build/lib/oncoref/data/cancer-cohort-aggregates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,281 copying build/lib/oncoref/data/cancer-subtype-groupings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,283 copying build/lib/oncoref/data/rna-protein-calibration-samples.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,286 copying build/lib/oncoref/data/cancer-type-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,290 copying build/lib/oncoref/data/housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,292 copying build/lib/oncoref/data/nuclear-retained-lncrnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,294 copying build/lib/oncoref/data/cancer-entity-driver-spectrum.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,297 copying build/lib/oncoref/data/small-noncoding-rnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,303 copying build/lib/oncoref/data/ribosomal-protein-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,305 copying build/lib/oncoref/data/numt-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,308 copying build/lib/oncoref/data/cancer-reference-expression-availability.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,313 copying build/lib/oncoref/data/cdna-identical-gene-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,316 copying build/lib/oncoref/data/censored-gene-reference-tpm.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,321 copying build/lib/oncoref/data/cta-clinical-targets.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,324 copying build/lib/oncoref/data/expression-artifact-gene-universe-deltas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,336 copying build/lib/oncoref/data/cta-specificity-audit.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,338 copying build/lib/oncoref/data/rrna-and-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,341 copying build/lib/oncoref/data/cancer-viral-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,343 copying build/lib/oncoref/data/proteoform-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,345 copying build/lib/oncoref/data/cancer-mismatch-repair-statuses.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,347 copying build/lib/oncoref/data/rna-protein-hpa-priors.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,362 copying build/lib/oncoref/data/cancer-lineage-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,363 copying build/lib/oncoref/data/rna-protein-calibrations.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,533 copying build/lib/oncoref/data/canonical-gene-space.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,547 copying build/lib/oncoref/data/clean-tpm-censored-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,566 copying build/lib/oncoref/data/therapy-benefit-toxicity-evidence.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,569 copying build/lib/oncoref/data/proteoform-groups-genome.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,572 copying build/lib/oncoref/data/cancer-lineage-group-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,574 copying build/lib/oncoref/data/cancer-ici-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,577 copying build/lib/oncoref/data/cancer-testis-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,584 copying build/lib/oncoref/data/gse294016-sample-diagnoses.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,586 copying build/lib/oncoref/data/ensembl-id-aliases.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,600 copying build/lib/oncoref/data/hpa-safety-tissue-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,602 copying build/lib/oncoref/data/cta-candidate-references.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,604 copying build/lib/oncoref/data/cancer-fusion-citation-audit.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,608 copying build/lib/oncoref/data/hemoglobin-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,610 copying build/lib/oncoref/data/cohort-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,613 copying build/lib/oncoref/data/cancer-driver-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,617 copying build/lib/oncoref/data/cancer-normal-tissue-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,620 copying build/lib/oncoref/data/narrative-gene-sets.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,622 copying build/lib/oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,637 copying build/lib/oncoref/data/expression_sources.yaml -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,642 copying build/lib/oncoref/data/cancer-ici-source-locator-audit.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,650 copying build/lib/oncoref/data/cancer-expression-source-candidates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,654 copying build/lib/oncoref/data/disease-state-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,656 copying build/lib/oncoref/data/rna-protein-calibration-sources.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,659 copying build/lib/oncoref/data/proteoform-collapse-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,661 copying build/lib/oncoref/data/clean-tpm-biological-housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,664 copying build/lib/oncoref/data/degenerate-subtype-pairs.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,666 copying build/lib/oncoref/data/fusion-surrogate-expression.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-08-31T14:26:28,669 copying build/lib/oncoref/ici_response.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,672 copying build/lib/oncoref/catalog.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,675 copying build/lib/oncoref/therapy_evidence.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,677 copying build/lib/oncoref/cta_tissues.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,680 copying build/lib/oncoref/cta_regen.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,683 copying build/lib/oncoref/tumor_references.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,686 copying build/lib/oncoref/hpa.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,689 copying build/lib/oncoref/cli.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,691 copying build/lib/oncoref/gene_ids.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,694 copying build/lib/oncoref/expression_source_adapters.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,698 copying build/lib/oncoref/data_bundle.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,701 copying build/lib/oncoref/incidence.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,703 copying build/lib/oncoref/cancer_ontology.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,705 copying build/lib/oncoref/load_dataset.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-08-31T14:26:28,707 running install_egg_info 2026-08-31T14:26:28,716 running egg_info 2026-08-31T14:26:28,721 writing oncoref.egg-info/PKG-INFO 2026-08-31T14:26:28,726 writing dependency_links to oncoref.egg-info/dependency_links.txt 2026-08-31T14:26:28,727 writing entry points to oncoref.egg-info/entry_points.txt 2026-08-31T14:26:28,729 writing requirements to oncoref.egg-info/requires.txt 2026-08-31T14:26:28,730 writing top-level names to oncoref.egg-info/top_level.txt 2026-08-31T14:26:28,752 reading manifest file 'oncoref.egg-info/SOURCES.txt' 2026-08-31T14:26:28,766 reading manifest template 'MANIFEST.in' 2026-08-31T14:26:28,785 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-08-31T14:26:28,787 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-08-31T14:26:28,788 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-08-31T14:26:28,790 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-08-31T14:26:28,791 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-08-31T14:26:28,792 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-08-31T14:26:28,793 adding license file 'LICENSE' 2026-08-31T14:26:28,805 writing manifest file 'oncoref.egg-info/SOURCES.txt' 2026-08-31T14:26:28,807 Copying oncoref.egg-info to build/bdist.linux-armv7l/wheel/./oncoref-1.8.188-py3.11.egg-info 2026-08-31T14:26:28,820 running install_scripts 2026-08-31T14:26:28,833 creating build/bdist.linux-armv7l/wheel/oncoref-1.8.188.dist-info/WHEEL 2026-08-31T14:26:28,836 creating '/tmp/pip-wheel-2t0py3jk/.tmp-vcv2xps8/oncoref-1.8.188-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-08-31T14:26:28,840 adding 'oncoref/__init__.py' 2026-08-31T14:26:28,842 adding 'oncoref/_reference_sources.py' 2026-08-31T14:26:28,843 adding 'oncoref/antigen_coverage.py' 2026-08-31T14:26:28,845 adding 'oncoref/apd1.py' 2026-08-31T14:26:28,847 adding 'oncoref/cancer_genes.py' 2026-08-31T14:26:28,848 adding 'oncoref/cancer_ontology.py' 2026-08-31T14:26:28,861 adding 'oncoref/cancer_types.py' 2026-08-31T14:26:28,864 adding 'oncoref/catalog.py' 2026-08-31T14:26:28,867 adding 'oncoref/cli.py' 2026-08-31T14:26:28,868 adding 'oncoref/cohorts.py' 2026-08-31T14:26:28,873 adding 'oncoref/coverage.py' 2026-08-31T14:26:28,876 adding 'oncoref/cta.py' 2026-08-31T14:26:28,878 adding 'oncoref/cta_coverage.py' 2026-08-31T14:26:28,880 adding 'oncoref/cta_curation_plots.py' 2026-08-31T14:26:28,881 adding 'oncoref/cta_peptides.py' 2026-08-31T14:26:28,884 adding 'oncoref/cta_regen.py' 2026-08-31T14:26:28,886 adding 'oncoref/cta_tissues.py' 2026-08-31T14:26:28,892 adding 'oncoref/data_bundle.py' 2026-08-31T14:26:28,895 adding 'oncoref/data_manifest.py' 2026-08-31T14:26:28,897 adding 'oncoref/drivers.py' 2026-08-31T14:26:28,927 adding 'oncoref/expression.py' 2026-08-31T14:26:28,953 adding 'oncoref/expression_builders.py' 2026-08-31T14:26:28,958 adding 'oncoref/expression_engine.py' 2026-08-31T14:26:28,961 adding 'oncoref/expression_registry.py' 2026-08-31T14:26:28,974 adding 'oncoref/expression_source_adapters.py' 2026-08-31T14:26:28,977 adding 'oncoref/fusions.py' 2026-08-31T14:26:28,979 adding 'oncoref/gene_families.py' 2026-08-31T14:26:28,982 adding 'oncoref/gene_ids.py' 2026-08-31T14:26:28,985 adding 'oncoref/gene_qc.py' 2026-08-31T14:26:28,987 adding 'oncoref/genome.py' 2026-08-31T14:26:28,989 adding 'oncoref/hpa.py' 2026-08-31T14:26:28,994 adding 'oncoref/ici.py' 2026-08-31T14:26:28,995 adding 'oncoref/ici_response.py' 2026-08-31T14:26:28,997 adding 'oncoref/incidence.py' 2026-08-31T14:26:28,999 adding 'oncoref/load_dataset.py' 2026-08-31T14:26:29,004 adding 'oncoref/normalization.py' 2026-08-31T14:26:29,007 adding 'oncoref/peptides.py' 2026-08-31T14:26:29,014 adding 'oncoref/plots.py' 2026-08-31T14:26:29,017 adding 'oncoref/proteoforms.py' 2026-08-31T14:26:29,019 adding 'oncoref/reference_data.py' 2026-08-31T14:26:29,021 adding 'oncoref/representative_partitions.py' 2026-08-31T14:26:29,022 adding 'oncoref/response_signatures.py' 2026-08-31T14:26:29,025 adding 'oncoref/rna_protein.py' 2026-08-31T14:26:29,027 adding 'oncoref/samples.py' 2026-08-31T14:26:29,029 adding 'oncoref/source_matrices.py' 2026-08-31T14:26:29,031 adding 'oncoref/therapy_evidence.py' 2026-08-31T14:26:29,033 adding 'oncoref/tmb.py' 2026-08-31T14:26:29,036 adding 'oncoref/tumor_references.py' 2026-08-31T14:26:29,037 adding 'oncoref/version.py' 2026-08-31T14:26:29,042 adding 'oncoref/data/cancer-apd1-response.csv' 2026-08-31T14:26:29,043 adding 'oncoref/data/cancer-code-burden-map.csv' 2026-08-31T14:26:29,044 adding 'oncoref/data/cancer-cohort-aggregates.csv' 2026-08-31T14:26:29,049 adding 'oncoref/data/cancer-driver-genes.csv' 2026-08-31T14:26:29,052 adding 'oncoref/data/cancer-driver-variants.csv' 2026-08-31T14:26:29,053 adding 'oncoref/data/cancer-entity-driver-spectrum.csv' 2026-08-31T14:26:29,057 adding 'oncoref/data/cancer-expression-source-candidates.csv' 2026-08-31T14:26:29,059 adding 'oncoref/data/cancer-frameshift-burden.csv' 2026-08-31T14:26:29,062 adding 'oncoref/data/cancer-fusion-citation-audit.csv' 2026-08-31T14:26:29,066 adding 'oncoref/data/cancer-fusions.csv' 2026-08-31T14:26:29,090 adding 'oncoref/data/cancer-ici-response-estimates.csv' 2026-08-31T14:26:29,096 adding 'oncoref/data/cancer-ici-response.csv' 2026-08-31T14:26:29,103 adding 'oncoref/data/cancer-ici-source-locator-audit.csv' 2026-08-31T14:26:29,105 adding 'oncoref/data/cancer-incidence-mortality.csv' 2026-08-31T14:26:29,121 adding 'oncoref/data/cancer-key-gene-citation-audit.csv' 2026-08-31T14:26:29,134 adding 'oncoref/data/cancer-key-genes.csv' 2026-08-31T14:26:29,136 adding 'oncoref/data/cancer-lineage-group-overrides.csv' 2026-08-31T14:26:29,137 adding 'oncoref/data/cancer-lineage-groups.csv' 2026-08-31T14:26:29,139 adding 'oncoref/data/cancer-mismatch-repair-statuses.csv' 2026-08-31T14:26:29,140 adding 'oncoref/data/cancer-normal-tissue-map.csv' 2026-08-31T14:26:29,148 adding 'oncoref/data/cancer-reference-expression-availability.csv' 2026-08-31T14:26:29,178 adding 'oncoref/data/cancer-reference-expression-samples.csv.gz' 2026-08-31T14:26:29,184 adding 'oncoref/data/cancer-reference-sample-molecular-provenance.csv' 2026-08-31T14:26:29,186 adding 'oncoref/data/cancer-response-signatures.csv' 2026-08-31T14:26:29,187 adding 'oncoref/data/cancer-subtype-groupings.csv' 2026-08-31T14:26:29,198 adding 'oncoref/data/cancer-testis-antigens.csv' 2026-08-31T14:26:29,201 adding 'oncoref/data/cancer-tmb.csv' 2026-08-31T14:26:29,204 adding 'oncoref/data/cancer-type-genes.csv' 2026-08-31T14:26:29,210 adding 'oncoref/data/cancer-type-registry.csv' 2026-08-31T14:26:29,211 adding 'oncoref/data/cancer-viral-antigens.csv' 2026-08-31T14:26:29,214 adding 'oncoref/data/cancer-who-soft-tissue-bone-audit.csv' 2026-08-31T14:26:29,266 adding 'oncoref/data/canonical-gene-space.csv.gz' 2026-08-31T14:26:29,271 adding 'oncoref/data/cdna-identical-gene-groups.csv' 2026-08-31T14:26:29,281 adding 'oncoref/data/censored-gene-reference-tpm.csv' 2026-08-31T14:26:29,283 adding 'oncoref/data/clean-tpm-biological-housekeeping-genes.csv' 2026-08-31T14:26:29,318 adding 'oncoref/data/clean-tpm-censored-genes.csv' 2026-08-31T14:26:29,326 adding 'oncoref/data/cohort-registry.csv' 2026-08-31T14:26:29,328 adding 'oncoref/data/cta-candidate-references.csv' 2026-08-31T14:26:29,329 adding 'oncoref/data/cta-clinical-targets.csv' 2026-08-31T14:26:29,330 adding 'oncoref/data/cta-ihc-unreliable.csv' 2026-08-31T14:26:29,331 adding 'oncoref/data/cta-specificity-audit.csv' 2026-08-31T14:26:29,333 adding 'oncoref/data/degenerate-subtype-pairs.csv' 2026-08-31T14:26:29,334 adding 'oncoref/data/disease-state-rules.csv' 2026-08-31T14:26:29,361 adding 'oncoref/data/ensembl-id-aliases.csv' 2026-08-31T14:26:29,375 adding 'oncoref/data/expression-artifact-gene-universe-deltas.csv' 2026-08-31T14:26:29,386 adding 'oncoref/data/expression_sources.yaml' 2026-08-31T14:26:29,389 adding 'oncoref/data/extra-tx-mappings.csv' 2026-08-31T14:26:29,390 adding 'oncoref/data/family-burden-map.csv' 2026-08-31T14:26:29,391 adding 'oncoref/data/fusion-expression-effects.csv' 2026-08-31T14:26:29,393 adding 'oncoref/data/fusion-surrogate-expression.csv' 2026-08-31T14:26:29,394 adding 'oncoref/data/gse294016-sample-diagnoses.csv' 2026-08-31T14:26:29,395 adding 'oncoref/data/hemoglobin-genes.csv' 2026-08-31T14:26:29,397 adding 'oncoref/data/histone-genes.csv' 2026-08-31T14:26:29,398 adding 'oncoref/data/housekeeping-genes.csv' 2026-08-31T14:26:29,400 adding 'oncoref/data/hpa-safety-tissue-map.csv' 2026-08-31T14:26:29,401 adding 'oncoref/data/mitochondrial-genes.csv' 2026-08-31T14:26:29,402 adding 'oncoref/data/narrative-gene-sets.csv' 2026-08-31T14:26:29,504 adding 'oncoref/data/ncbi-entrez-gene-mappings.csv.gz' 2026-08-31T14:26:29,549 adding 'oncoref/data/ncbi-symbol-synonyms.csv.gz' 2026-08-31T14:26:29,553 adding 'oncoref/data/nuclear-retained-lncrnas.csv' 2026-08-31T14:26:29,555 adding 'oncoref/data/numt-pseudogenes.csv' 2026-08-31T14:26:29,556 adding 'oncoref/data/proteoform-collapse-overrides.csv' 2026-08-31T14:26:29,559 adding 'oncoref/data/proteoform-groups-genome.csv' 2026-08-31T14:26:29,560 adding 'oncoref/data/proteoform-groups.csv' 2026-08-31T14:26:29,562 adding 'oncoref/data/rare-cancer-fusion-rules.csv' 2026-08-31T14:26:29,564 adding 'oncoref/data/representative-source-adjudications.csv' 2026-08-31T14:26:29,565 adding 'oncoref/data/ribosomal-protein-genes.csv' 2026-08-31T14:26:29,571 adding 'oncoref/data/ribosomal-protein-pseudogenes.csv' 2026-08-31T14:26:29,573 adding 'oncoref/data/rna-protein-calibration-samples.csv.gz' 2026-08-31T14:26:29,575 adding 'oncoref/data/rna-protein-calibration-sources.csv' 2026-08-31T14:26:30,736 adding 'oncoref/data/rna-protein-calibrations.csv.gz' 2026-08-31T14:26:30,799 adding 'oncoref/data/rna-protein-hpa-prior-sources.csv' 2026-08-31T14:26:30,888 adding 'oncoref/data/rna-protein-hpa-priors.csv.gz' 2026-08-31T14:26:30,895 adding 'oncoref/data/rrna-and-pseudogenes.csv' 2026-08-31T14:26:30,914 adding 'oncoref/data/small-noncoding-rnas.csv' 2026-08-31T14:26:30,917 adding 'oncoref/data/source-matrices.csv' 2026-08-31T14:26:30,918 adding 'oncoref/data/therapy-benefit-toxicity-evidence.csv' 2026-08-31T14:26:30,919 adding 'oncoref/data/tissue-burden-map.csv' 2026-08-31T14:26:30,923 adding 'oncoref-1.8.188.dist-info/licenses/LICENSE' 2026-08-31T14:26:30,925 adding 'oncoref-1.8.188.dist-info/METADATA' 2026-08-31T14:26:30,926 adding 'oncoref-1.8.188.dist-info/WHEEL' 2026-08-31T14:26:30,927 adding 'oncoref-1.8.188.dist-info/entry_points.txt' 2026-08-31T14:26:30,928 adding 'oncoref-1.8.188.dist-info/top_level.txt' 2026-08-31T14:26:30,930 adding 'oncoref-1.8.188.dist-info/RECORD' 2026-08-31T14:26:31,082 removing build/bdist.linux-armv7l/wheel 2026-08-31T14:26:31,219 Building wheel for oncoref (pyproject.toml): finished with status 'done' 2026-08-31T14:26:31,498 Created wheel for oncoref: filename=oncoref-1.8.188-py3-none-any.whl size=13566142 sha256=99ef9065dfe370636c0c27dab179b3409e54c6bf17c3e63f4def7a090830c902 2026-08-31T14:26:31,499 Stored in directory: /tmp/pip-ephem-wheel-cache-su86s1nh/wheels/93/95/3a/4c5d7cf8e784e1cbfe700d30e6119853eb6cf685b14754ace4 2026-08-31T14:26:31,520 Successfully built oncoref 2026-08-31T14:26:31,829 Removed build tracker: '/tmp/pip-build-tracker-js2ask4c'