2026-07-31T13:56:33,588 Created temporary directory: /tmp/pip-ephem-wheel-cache-6y6z4004 2026-07-31T13:56:33,590 Created temporary directory: /tmp/pip-build-tracker-ua06aj92 2026-07-31T13:56:33,591 Initialized build tracking at /tmp/pip-build-tracker-ua06aj92 2026-07-31T13:56:33,591 Created build tracker: /tmp/pip-build-tracker-ua06aj92 2026-07-31T13:56:33,591 Entered build tracker: /tmp/pip-build-tracker-ua06aj92 2026-07-31T13:56:33,592 Created temporary directory: /tmp/pip-wheel-oa1rxrr9 2026-07-31T13:56:33,595 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 2026-07-31T13:56:33,598 Created temporary directory: /tmp/pip-ephem-wheel-cache-3l67p0vd 2026-07-31T13:56:33,622 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-07-31T13:56:33,625 2 location(s) to search for versions of oncoref: 2026-07-31T13:56:33,625 * https://pypi.org/simple/oncoref/ 2026-07-31T13:56:33,625 * https://www.piwheels.org/simple/oncoref/ 2026-07-31T13:56:33,626 Fetching project page and analyzing links: https://pypi.org/simple/oncoref/ 2026-07-31T13:56:33,627 Getting page https://pypi.org/simple/oncoref/ 2026-07-31T13:56:33,628 Found index url https://pypi.org/simple 2026-07-31T13:56:33,825 Fetched page https://pypi.org/simple/oncoref/ as application/vnd.pypi.simple.v1+json 2026-07-31T13:56:33,881 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) 2026-07-31T13:56:33,886 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 2026-07-31T13:56:33,887 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) 2026-07-31T13:56:33,888 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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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) 2026-07-31T13:56:33,907 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 2026-07-31T13:56:33,907 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) 2026-07-31T13:56:33,908 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 2026-07-31T13:56:33,909 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) 2026-07-31T13:56:33,910 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 2026-07-31T13:56:33,911 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) 2026-07-31T13:56:33,912 Found link 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2026-07-31T13:56:34,525 Given no hashes to check 1 links for project 'oncoref': discarding no candidates 2026-07-31T13:56:34,543 Collecting oncoref==1.8.163 2026-07-31T13:56:34,545 Created temporary directory: /tmp/pip-unpack-7q3xns1u 2026-07-31T13:56:34,694 Downloading oncoref-1.8.163.tar.gz (3.0 MB) 2026-07-31T13:56:35,549 Added oncoref==1.8.163 from https://files.pythonhosted.org/packages/f4/93/deaaf0d9f5aa07aaca5ecca095632bcd7f1051b5629c98f84880903c1fe3/oncoref-1.8.163.tar.gz to build tracker '/tmp/pip-build-tracker-ua06aj92' 2026-07-31T13:56:35,556 Created temporary directory: /tmp/pip-build-env-q7ra9dvh 2026-07-31T13:56:35,560 Installing build dependencies: started 2026-07-31T13:56:35,561 Running command pip subprocess to install build dependencies 2026-07-31T13:56:36,692 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-07-31T13:56:37,347 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 2026-07-31T13:56:37,370 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-07-31T13:56:39,407 Collecting setuptools>=77.0.0 2026-07-31T13:56:39,408 Obtaining dependency information for setuptools>=77.0.0 from https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl.metadata 2026-07-31T13:56:39,429 Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl.metadata (6.6 kB) 2026-07-31T13:56:39,666 Collecting wheel 2026-07-31T13:56:39,667 Obtaining dependency information for wheel from https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata 2026-07-31T13:56:39,681 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB) 2026-07-31T13:56:39,866 Collecting packaging>=24.0 2026-07-31T13:56:39,868 Obtaining dependency information for packaging>=24.0 from https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata 2026-07-31T13:56:39,885 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata (3.5 kB) 2026-07-31T13:56:40,076 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB) 2026-07-31T13:56:40,097 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB) 2026-07-31T13:56:40,174 Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl (1.0 MB) 2026-07-31T13:56:40,207 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB) 2026-07-31T13:56:40,234 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB) 2026-07-31T13:56:40,324 Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl (1.0 MB) 2026-07-31T13:56:43,077 Installing collected packages: setuptools, packaging, wheel 2026-07-31T13:56:46,528 Creating /tmp/pip-build-env-q7ra9dvh/overlay/local/bin 2026-07-31T13:56:46,530 changing mode of /tmp/pip-build-env-q7ra9dvh/overlay/local/bin/wheel to 755 2026-07-31T13:56:46,551 Successfully installed packaging-26.2 setuptools-83.0.0 wheel-0.47.0 2026-07-31T13:56:46,845 Installing build dependencies: finished with status 'done' 2026-07-31T13:56:46,852 Getting requirements to build wheel: started 2026-07-31T13:56:46,853 Running command Getting requirements to build wheel 2026-07-31T13:56:47,545 running egg_info 2026-07-31T13:56:47,551 writing oncoref.egg-info/PKG-INFO 2026-07-31T13:56:47,557 writing dependency_links to oncoref.egg-info/dependency_links.txt 2026-07-31T13:56:47,559 writing entry points to oncoref.egg-info/entry_points.txt 2026-07-31T13:56:47,562 writing requirements to oncoref.egg-info/requires.txt 2026-07-31T13:56:47,563 writing top-level names to oncoref.egg-info/top_level.txt 2026-07-31T13:56:47,601 reading manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-31T13:56:47,612 reading manifest template 'MANIFEST.in' 2026-07-31T13:56:47,625 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-07-31T13:56:47,627 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-07-31T13:56:47,628 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-07-31T13:56:47,630 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-07-31T13:56:47,631 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-07-31T13:56:47,632 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-07-31T13:56:47,633 adding license file 'LICENSE' 2026-07-31T13:56:47,643 writing manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-31T13:56:47,745 Getting requirements to build wheel: finished with status 'done' 2026-07-31T13:56:47,749 Created temporary directory: /tmp/pip-modern-metadata-lcguyyag 2026-07-31T13:56:47,751 Preparing metadata (pyproject.toml): started 2026-07-31T13:56:47,753 Running command Preparing metadata (pyproject.toml) 2026-07-31T13:56:48,395 running dist_info 2026-07-31T13:56:48,405 creating /tmp/pip-modern-metadata-lcguyyag/oncoref.egg-info 2026-07-31T13:56:48,406 writing /tmp/pip-modern-metadata-lcguyyag/oncoref.egg-info/PKG-INFO 2026-07-31T13:56:48,412 writing dependency_links to /tmp/pip-modern-metadata-lcguyyag/oncoref.egg-info/dependency_links.txt 2026-07-31T13:56:48,414 writing entry points to /tmp/pip-modern-metadata-lcguyyag/oncoref.egg-info/entry_points.txt 2026-07-31T13:56:48,416 writing requirements to /tmp/pip-modern-metadata-lcguyyag/oncoref.egg-info/requires.txt 2026-07-31T13:56:48,417 writing top-level names to /tmp/pip-modern-metadata-lcguyyag/oncoref.egg-info/top_level.txt 2026-07-31T13:56:48,419 writing manifest file '/tmp/pip-modern-metadata-lcguyyag/oncoref.egg-info/SOURCES.txt' 2026-07-31T13:56:48,453 reading manifest file '/tmp/pip-modern-metadata-lcguyyag/oncoref.egg-info/SOURCES.txt' 2026-07-31T13:56:48,454 reading manifest template 'MANIFEST.in' 2026-07-31T13:56:48,467 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-07-31T13:56:48,468 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-07-31T13:56:48,469 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-07-31T13:56:48,470 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-07-31T13:56:48,471 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-07-31T13:56:48,472 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-07-31T13:56:48,473 adding license file 'LICENSE' 2026-07-31T13:56:48,480 writing manifest file '/tmp/pip-modern-metadata-lcguyyag/oncoref.egg-info/SOURCES.txt' 2026-07-31T13:56:48,482 creating '/tmp/pip-modern-metadata-lcguyyag/oncoref-1.8.163.dist-info' 2026-07-31T13:56:48,609 Preparing metadata (pyproject.toml): finished with status 'done' 2026-07-31T13:56:48,614 Source in /tmp/pip-wheel-oa1rxrr9/oncoref_d0d8c917fe1a4dbcac29e5903f8e2be6 has version 1.8.163, which satisfies requirement oncoref==1.8.163 from https://files.pythonhosted.org/packages/f4/93/deaaf0d9f5aa07aaca5ecca095632bcd7f1051b5629c98f84880903c1fe3/oncoref-1.8.163.tar.gz 2026-07-31T13:56:48,615 Removed oncoref==1.8.163 from https://files.pythonhosted.org/packages/f4/93/deaaf0d9f5aa07aaca5ecca095632bcd7f1051b5629c98f84880903c1fe3/oncoref-1.8.163.tar.gz from build tracker '/tmp/pip-build-tracker-ua06aj92' 2026-07-31T13:56:48,621 Created temporary directory: /tmp/pip-unpack-vx1cv_gd 2026-07-31T13:56:48,622 Building wheels for collected packages: oncoref 2026-07-31T13:56:48,626 Created temporary directory: /tmp/pip-wheel-l9m67pk_ 2026-07-31T13:56:48,627 Destination directory: /tmp/pip-wheel-l9m67pk_ 2026-07-31T13:56:48,629 Building wheel for oncoref (pyproject.toml): started 2026-07-31T13:56:48,630 Running command Building wheel for oncoref (pyproject.toml) 2026-07-31T13:56:49,254 running bdist_wheel 2026-07-31T13:56:49,271 running build 2026-07-31T13:56:49,272 running build_py 2026-07-31T13:56:49,279 creating build/lib/oncoref 2026-07-31T13:56:49,282 copying oncoref/apd1.py -> build/lib/oncoref 2026-07-31T13:56:49,285 copying oncoref/hpa.py -> build/lib/oncoref 2026-07-31T13:56:49,287 copying oncoref/representative_partitions.py -> build/lib/oncoref 2026-07-31T13:56:49,289 copying oncoref/ici_response.py -> build/lib/oncoref 2026-07-31T13:56:49,292 copying oncoref/__init__.py -> build/lib/oncoref 2026-07-31T13:56:49,294 copying oncoref/cancer_types.py -> build/lib/oncoref 2026-07-31T13:56:49,298 copying oncoref/proteoforms.py -> build/lib/oncoref 2026-07-31T13:56:49,301 copying oncoref/load_dataset.py -> build/lib/oncoref 2026-07-31T13:56:49,303 copying oncoref/gene_ids.py -> build/lib/oncoref 2026-07-31T13:56:49,305 copying oncoref/antigen_coverage.py -> build/lib/oncoref 2026-07-31T13:56:49,307 copying oncoref/cohorts.py -> build/lib/oncoref 2026-07-31T13:56:49,309 copying oncoref/data_manifest.py -> build/lib/oncoref 2026-07-31T13:56:49,312 copying oncoref/cta_tissues.py -> build/lib/oncoref 2026-07-31T13:56:49,314 copying oncoref/expression_registry.py -> build/lib/oncoref 2026-07-31T13:56:49,316 copying oncoref/catalog.py -> build/lib/oncoref 2026-07-31T13:56:49,319 copying oncoref/version.py -> build/lib/oncoref 2026-07-31T13:56:49,320 copying oncoref/cancer_ontology.py -> build/lib/oncoref 2026-07-31T13:56:49,323 copying oncoref/response_signatures.py -> build/lib/oncoref 2026-07-31T13:56:49,324 copying oncoref/fusions.py -> build/lib/oncoref 2026-07-31T13:56:49,327 copying oncoref/peptides.py -> build/lib/oncoref 2026-07-31T13:56:49,329 copying oncoref/samples.py -> build/lib/oncoref 2026-07-31T13:56:49,331 copying oncoref/cta.py -> build/lib/oncoref 2026-07-31T13:56:49,334 copying oncoref/data_bundle.py -> build/lib/oncoref 2026-07-31T13:56:49,337 copying oncoref/cli.py -> build/lib/oncoref 2026-07-31T13:56:49,340 copying oncoref/plots.py -> build/lib/oncoref 2026-07-31T13:56:49,343 copying oncoref/cta_regen.py -> build/lib/oncoref 2026-07-31T13:56:49,345 copying oncoref/cta_curation_plots.py -> build/lib/oncoref 2026-07-31T13:56:49,348 copying oncoref/coverage.py -> build/lib/oncoref 2026-07-31T13:56:49,350 copying oncoref/cancer_genes.py -> build/lib/oncoref 2026-07-31T13:56:49,353 copying oncoref/expression.py -> build/lib/oncoref 2026-07-31T13:56:49,358 copying oncoref/cta_peptides.py -> build/lib/oncoref 2026-07-31T13:56:49,360 copying oncoref/cta_coverage.py -> build/lib/oncoref 2026-07-31T13:56:49,362 copying oncoref/normalization.py -> build/lib/oncoref 2026-07-31T13:56:49,364 copying oncoref/_reference_sources.py -> build/lib/oncoref 2026-07-31T13:56:49,366 copying oncoref/gene_families.py -> build/lib/oncoref 2026-07-31T13:56:49,369 copying oncoref/expression_engine.py -> build/lib/oncoref 2026-07-31T13:56:49,371 copying oncoref/expression_source_adapters.py -> build/lib/oncoref 2026-07-31T13:56:49,374 copying oncoref/source_matrices.py -> build/lib/oncoref 2026-07-31T13:56:49,377 copying oncoref/tmb.py -> build/lib/oncoref 2026-07-31T13:56:49,379 copying oncoref/incidence.py -> build/lib/oncoref 2026-07-31T13:56:49,382 copying oncoref/gene_qc.py -> build/lib/oncoref 2026-07-31T13:56:49,384 copying oncoref/genome.py -> build/lib/oncoref 2026-07-31T13:56:49,387 copying oncoref/reference_data.py -> build/lib/oncoref 2026-07-31T13:56:49,389 copying oncoref/expression_builders.py -> build/lib/oncoref 2026-07-31T13:56:49,394 copying oncoref/ici.py -> build/lib/oncoref 2026-07-31T13:56:49,410 creating build/lib/oncoref/data 2026-07-31T13:56:49,411 copying oncoref/data/cta-candidate-references.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,414 copying oncoref/data/proteoform-collapse-overrides.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,416 copying oncoref/data/source-matrices.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,419 copying oncoref/data/cancer-frameshift-burden.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,421 copying oncoref/data/cohort-registry.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,424 copying oncoref/data/cancer-lineage-group-overrides.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,426 copying oncoref/data/cdna-identical-gene-groups.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,429 copying oncoref/data/clean-tpm-censored-genes.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,434 copying oncoref/data/cancer-ici-response.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,437 copying oncoref/data/fusion-expression-effects.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,439 copying oncoref/data/cancer-ici-response-estimates.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,447 copying oncoref/data/cancer-type-genes.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,449 copying oncoref/data/cta-ihc-unreliable.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,452 copying oncoref/data/cancer-key-gene-citation-audit.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,457 copying oncoref/data/fusion-surrogate-expression.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,460 copying oncoref/data/proteoform-groups.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,463 copying oncoref/data/tissue-burden-map.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,465 copying oncoref/data/cancer-fusions.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,468 copying oncoref/data/cancer-reference-expression-availability.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,473 copying oncoref/data/ribosomal-protein-pseudogenes.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,477 copying oncoref/data/gse294016-sample-diagnoses.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,479 copying oncoref/data/disease-state-rules.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,481 copying oncoref/data/cta-specificity-audit.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,483 copying oncoref/data/cancer-incidence-mortality.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,486 copying oncoref/data/numt-pseudogenes.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,489 copying oncoref/data/cancer-driver-genes.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,493 copying oncoref/data/cancer-type-registry.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,497 copying oncoref/data/cancer-code-burden-map.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,499 copying oncoref/data/degenerate-subtype-pairs.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,501 copying oncoref/data/histone-genes.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,503 copying oncoref/data/cancer-normal-tissue-map.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,506 copying oncoref/data/cancer-testis-antigens.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,512 copying oncoref/data/cta-clinical-targets.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,514 copying oncoref/data/cancer-subtype-groupings.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,516 copying oncoref/data/small-noncoding-rnas.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,522 copying oncoref/data/narrative-gene-sets.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,524 copying oncoref/data/representative-source-adjudications.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,526 copying oncoref/data/cancer-apd1-response.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,529 copying oncoref/data/cancer-viral-antigens.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,532 copying oncoref/data/nuclear-retained-lncrnas.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,534 copying oncoref/data/housekeeping-genes.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,536 copying oncoref/data/extra-tx-mappings.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,539 copying oncoref/data/cancer-tmb.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,542 copying oncoref/data/ensembl-id-aliases.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,553 copying oncoref/data/ribosomal-protein-genes.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,555 copying oncoref/data/family-burden-map.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,557 copying oncoref/data/clean-tpm-biological-housekeeping-genes.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,560 copying oncoref/data/cancer-key-genes.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,565 copying oncoref/data/cancer-cohort-aggregates.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,567 copying oncoref/data/cancer-expression-source-candidates.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,570 copying oncoref/data/cancer-lineage-groups.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,573 copying oncoref/data/rare-cancer-fusion-rules.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,575 copying oncoref/data/expression-artifact-gene-universe-deltas.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,583 copying oncoref/data/censored-gene-reference-tpm.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,586 copying oncoref/data/cancer-driver-variants.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,589 copying oncoref/data/mitochondrial-genes.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,591 copying oncoref/data/hemoglobin-genes.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,593 copying oncoref/data/cancer-fusion-citation-audit.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,596 copying oncoref/data/cancer-who-soft-tissue-bone-audit.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,599 copying oncoref/data/proteoform-groups-genome.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,602 copying oncoref/data/rrna-and-pseudogenes.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,605 copying oncoref/data/cancer-mismatch-repair-statuses.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,607 copying oncoref/data/cancer-response-signatures.csv -> build/lib/oncoref/data 2026-07-31T13:56:49,610 copying oncoref/data/cancer-reference-expression-samples.csv.gz -> build/lib/oncoref/data 2026-07-31T13:56:49,617 copying oncoref/data/canonical-gene-space.csv.gz -> build/lib/oncoref/data 2026-07-31T13:56:49,628 copying oncoref/data/ncbi-entrez-gene-mappings.csv.gz -> build/lib/oncoref/data 2026-07-31T13:56:49,643 copying oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/lib/oncoref/data 2026-07-31T13:56:49,650 copying oncoref/data/expression_sources.yaml -> build/lib/oncoref/data 2026-07-31T13:56:49,665 installing to build/bdist.linux-armv7l/wheel 2026-07-31T13:56:49,666 running install 2026-07-31T13:56:49,689 running install_lib 2026-07-31T13:56:49,695 creating build/bdist.linux-armv7l/wheel 2026-07-31T13:56:49,697 creating build/bdist.linux-armv7l/wheel/oncoref 2026-07-31T13:56:49,698 copying build/lib/oncoref/apd1.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:49,701 copying build/lib/oncoref/hpa.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:49,703 copying build/lib/oncoref/representative_partitions.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:49,705 copying build/lib/oncoref/ici_response.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:49,707 copying build/lib/oncoref/__init__.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:49,710 copying build/lib/oncoref/cancer_types.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:49,714 copying build/lib/oncoref/proteoforms.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:49,717 copying build/lib/oncoref/load_dataset.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:49,719 copying build/lib/oncoref/gene_ids.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:49,722 copying build/lib/oncoref/antigen_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:49,724 copying build/lib/oncoref/cohorts.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:49,726 copying build/lib/oncoref/data_manifest.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:49,728 copying build/lib/oncoref/cta_tissues.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:49,730 copying build/lib/oncoref/expression_registry.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:49,733 copying build/lib/oncoref/catalog.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:49,735 copying build/lib/oncoref/version.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:49,738 copying build/lib/oncoref/cancer_ontology.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:49,740 copying build/lib/oncoref/response_signatures.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:49,742 copying build/lib/oncoref/fusions.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:49,745 copying build/lib/oncoref/peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:49,748 copying build/lib/oncoref/samples.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:49,752 creating build/bdist.linux-armv7l/wheel/oncoref/data 2026-07-31T13:56:49,754 copying build/lib/oncoref/data/cta-candidate-references.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,757 copying build/lib/oncoref/data/proteoform-collapse-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,759 copying build/lib/oncoref/data/source-matrices.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,762 copying build/lib/oncoref/data/cancer-frameshift-burden.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,764 copying build/lib/oncoref/data/cohort-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,767 copying build/lib/oncoref/data/cancer-lineage-group-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,770 copying build/lib/oncoref/data/cdna-identical-gene-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,773 copying build/lib/oncoref/data/clean-tpm-censored-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,780 copying build/lib/oncoref/data/cancer-ici-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,783 copying build/lib/oncoref/data/cancer-reference-expression-samples.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,796 copying build/lib/oncoref/data/fusion-expression-effects.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,798 copying build/lib/oncoref/data/expression_sources.yaml -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,804 copying build/lib/oncoref/data/canonical-gene-space.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,822 copying build/lib/oncoref/data/cancer-ici-response-estimates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,832 copying build/lib/oncoref/data/cancer-type-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,835 copying build/lib/oncoref/data/cta-ihc-unreliable.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,837 copying build/lib/oncoref/data/cancer-key-gene-citation-audit.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,843 copying build/lib/oncoref/data/fusion-surrogate-expression.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,846 copying build/lib/oncoref/data/proteoform-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,848 copying build/lib/oncoref/data/tissue-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,850 copying build/lib/oncoref/data/cancer-fusions.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,852 copying build/lib/oncoref/data/cancer-reference-expression-availability.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,857 copying build/lib/oncoref/data/ribosomal-protein-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,859 copying build/lib/oncoref/data/gse294016-sample-diagnoses.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,861 copying build/lib/oncoref/data/disease-state-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,863 copying build/lib/oncoref/data/cta-specificity-audit.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,866 copying build/lib/oncoref/data/cancer-incidence-mortality.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,868 copying build/lib/oncoref/data/numt-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,870 copying build/lib/oncoref/data/cancer-driver-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,873 copying build/lib/oncoref/data/cancer-type-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,877 copying build/lib/oncoref/data/cancer-code-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,878 copying build/lib/oncoref/data/degenerate-subtype-pairs.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,880 copying build/lib/oncoref/data/histone-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,882 copying build/lib/oncoref/data/cancer-normal-tissue-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,884 copying build/lib/oncoref/data/cancer-testis-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,889 copying build/lib/oncoref/data/cta-clinical-targets.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,891 copying build/lib/oncoref/data/cancer-subtype-groupings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,893 copying build/lib/oncoref/data/ncbi-entrez-gene-mappings.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,908 copying build/lib/oncoref/data/small-noncoding-rnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,913 copying build/lib/oncoref/data/narrative-gene-sets.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,914 copying build/lib/oncoref/data/representative-source-adjudications.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,916 copying build/lib/oncoref/data/cancer-apd1-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,919 copying build/lib/oncoref/data/cancer-viral-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,921 copying build/lib/oncoref/data/nuclear-retained-lncrnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,923 copying build/lib/oncoref/data/housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,924 copying build/lib/oncoref/data/extra-tx-mappings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,927 copying build/lib/oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,935 copying build/lib/oncoref/data/cancer-tmb.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,938 copying build/lib/oncoref/data/ensembl-id-aliases.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,947 copying build/lib/oncoref/data/ribosomal-protein-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,949 copying build/lib/oncoref/data/family-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,951 copying build/lib/oncoref/data/clean-tpm-biological-housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,953 copying build/lib/oncoref/data/cancer-key-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,959 copying build/lib/oncoref/data/cancer-cohort-aggregates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,961 copying build/lib/oncoref/data/cancer-expression-source-candidates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,964 copying build/lib/oncoref/data/cancer-lineage-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,966 copying build/lib/oncoref/data/rare-cancer-fusion-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,969 copying build/lib/oncoref/data/expression-artifact-gene-universe-deltas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,977 copying build/lib/oncoref/data/censored-gene-reference-tpm.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,981 copying build/lib/oncoref/data/cancer-driver-variants.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,984 copying build/lib/oncoref/data/mitochondrial-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,986 copying build/lib/oncoref/data/hemoglobin-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,988 copying build/lib/oncoref/data/cancer-fusion-citation-audit.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,991 copying build/lib/oncoref/data/cancer-who-soft-tissue-bone-audit.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,994 copying build/lib/oncoref/data/proteoform-groups-genome.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:49,997 copying build/lib/oncoref/data/rrna-and-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:50,000 copying build/lib/oncoref/data/cancer-mismatch-repair-statuses.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:50,003 copying build/lib/oncoref/data/cancer-response-signatures.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T13:56:50,005 copying build/lib/oncoref/cta.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:50,009 copying build/lib/oncoref/data_bundle.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:50,012 copying build/lib/oncoref/cli.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:50,015 copying build/lib/oncoref/plots.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:50,018 copying build/lib/oncoref/cta_regen.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:50,022 copying build/lib/oncoref/cta_curation_plots.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:50,024 copying build/lib/oncoref/coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:50,028 copying build/lib/oncoref/cancer_genes.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:50,031 copying build/lib/oncoref/expression.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:50,038 copying build/lib/oncoref/cta_peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:50,040 copying build/lib/oncoref/cta_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:50,043 copying build/lib/oncoref/normalization.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:50,046 copying build/lib/oncoref/_reference_sources.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:50,049 copying build/lib/oncoref/gene_families.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:50,052 copying build/lib/oncoref/expression_engine.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:50,055 copying build/lib/oncoref/expression_source_adapters.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:50,059 copying build/lib/oncoref/source_matrices.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:50,062 copying build/lib/oncoref/tmb.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:50,065 copying build/lib/oncoref/incidence.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:50,067 copying build/lib/oncoref/gene_qc.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:50,070 copying build/lib/oncoref/genome.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:50,073 copying build/lib/oncoref/reference_data.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:50,076 copying build/lib/oncoref/expression_builders.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:50,082 copying build/lib/oncoref/ici.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T13:56:50,085 running install_egg_info 2026-07-31T13:56:50,094 running egg_info 2026-07-31T13:56:50,100 writing oncoref.egg-info/PKG-INFO 2026-07-31T13:56:50,106 writing dependency_links to oncoref.egg-info/dependency_links.txt 2026-07-31T13:56:50,108 writing entry points to oncoref.egg-info/entry_points.txt 2026-07-31T13:56:50,111 writing requirements to oncoref.egg-info/requires.txt 2026-07-31T13:56:50,112 writing top-level names to oncoref.egg-info/top_level.txt 2026-07-31T13:56:50,133 reading manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-31T13:56:50,145 reading manifest template 'MANIFEST.in' 2026-07-31T13:56:50,159 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-07-31T13:56:50,161 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-07-31T13:56:50,163 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-07-31T13:56:50,165 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-07-31T13:56:50,167 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-07-31T13:56:50,168 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-07-31T13:56:50,169 adding license file 'LICENSE' 2026-07-31T13:56:50,180 writing manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-31T13:56:50,182 Copying oncoref.egg-info to build/bdist.linux-armv7l/wheel/./oncoref-1.8.163-py3.11.egg-info 2026-07-31T13:56:50,195 running install_scripts 2026-07-31T13:56:50,208 creating build/bdist.linux-armv7l/wheel/oncoref-1.8.163.dist-info/WHEEL 2026-07-31T13:56:50,211 creating '/tmp/pip-wheel-l9m67pk_/.tmp-45p8_hzg/oncoref-1.8.163-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-07-31T13:56:50,216 adding 'oncoref/__init__.py' 2026-07-31T13:56:50,218 adding 'oncoref/_reference_sources.py' 2026-07-31T13:56:50,220 adding 'oncoref/antigen_coverage.py' 2026-07-31T13:56:50,222 adding 'oncoref/apd1.py' 2026-07-31T13:56:50,224 adding 'oncoref/cancer_genes.py' 2026-07-31T13:56:50,226 adding 'oncoref/cancer_ontology.py' 2026-07-31T13:56:50,239 adding 'oncoref/cancer_types.py' 2026-07-31T13:56:50,242 adding 'oncoref/catalog.py' 2026-07-31T13:56:50,246 adding 'oncoref/cli.py' 2026-07-31T13:56:50,248 adding 'oncoref/cohorts.py' 2026-07-31T13:56:50,252 adding 'oncoref/coverage.py' 2026-07-31T13:56:50,256 adding 'oncoref/cta.py' 2026-07-31T13:56:50,258 adding 'oncoref/cta_coverage.py' 2026-07-31T13:56:50,261 adding 'oncoref/cta_curation_plots.py' 2026-07-31T13:56:50,262 adding 'oncoref/cta_peptides.py' 2026-07-31T13:56:50,266 adding 'oncoref/cta_regen.py' 2026-07-31T13:56:50,268 adding 'oncoref/cta_tissues.py' 2026-07-31T13:56:50,273 adding 'oncoref/data_bundle.py' 2026-07-31T13:56:50,276 adding 'oncoref/data_manifest.py' 2026-07-31T13:56:50,303 adding 'oncoref/expression.py' 2026-07-31T13:56:50,330 adding 'oncoref/expression_builders.py' 2026-07-31T13:56:50,335 adding 'oncoref/expression_engine.py' 2026-07-31T13:56:50,337 adding 'oncoref/expression_registry.py' 2026-07-31T13:56:50,344 adding 'oncoref/expression_source_adapters.py' 2026-07-31T13:56:50,346 adding 'oncoref/fusions.py' 2026-07-31T13:56:50,349 adding 'oncoref/gene_families.py' 2026-07-31T13:56:50,353 adding 'oncoref/gene_ids.py' 2026-07-31T13:56:50,355 adding 'oncoref/gene_qc.py' 2026-07-31T13:56:50,358 adding 'oncoref/genome.py' 2026-07-31T13:56:50,360 adding 'oncoref/hpa.py' 2026-07-31T13:56:50,365 adding 'oncoref/ici.py' 2026-07-31T13:56:50,367 adding 'oncoref/ici_response.py' 2026-07-31T13:56:50,369 adding 'oncoref/incidence.py' 2026-07-31T13:56:50,372 adding 'oncoref/load_dataset.py' 2026-07-31T13:56:50,377 adding 'oncoref/normalization.py' 2026-07-31T13:56:50,380 adding 'oncoref/peptides.py' 2026-07-31T13:56:50,387 adding 'oncoref/plots.py' 2026-07-31T13:56:50,391 adding 'oncoref/proteoforms.py' 2026-07-31T13:56:50,393 adding 'oncoref/reference_data.py' 2026-07-31T13:56:50,396 adding 'oncoref/representative_partitions.py' 2026-07-31T13:56:50,398 adding 'oncoref/response_signatures.py' 2026-07-31T13:56:50,400 adding 'oncoref/samples.py' 2026-07-31T13:56:50,403 adding 'oncoref/source_matrices.py' 2026-07-31T13:56:50,405 adding 'oncoref/tmb.py' 2026-07-31T13:56:50,407 adding 'oncoref/version.py' 2026-07-31T13:56:50,412 adding 'oncoref/data/cancer-apd1-response.csv' 2026-07-31T13:56:50,414 adding 'oncoref/data/cancer-code-burden-map.csv' 2026-07-31T13:56:50,415 adding 'oncoref/data/cancer-cohort-aggregates.csv' 2026-07-31T13:56:50,421 adding 'oncoref/data/cancer-driver-genes.csv' 2026-07-31T13:56:50,424 adding 'oncoref/data/cancer-driver-variants.csv' 2026-07-31T13:56:50,427 adding 'oncoref/data/cancer-expression-source-candidates.csv' 2026-07-31T13:56:50,429 adding 'oncoref/data/cancer-frameshift-burden.csv' 2026-07-31T13:56:50,433 adding 'oncoref/data/cancer-fusion-citation-audit.csv' 2026-07-31T13:56:50,437 adding 'oncoref/data/cancer-fusions.csv' 2026-07-31T13:56:50,457 adding 'oncoref/data/cancer-ici-response-estimates.csv' 2026-07-31T13:56:50,462 adding 'oncoref/data/cancer-ici-response.csv' 2026-07-31T13:56:50,464 adding 'oncoref/data/cancer-incidence-mortality.csv' 2026-07-31T13:56:50,480 adding 'oncoref/data/cancer-key-gene-citation-audit.csv' 2026-07-31T13:56:50,495 adding 'oncoref/data/cancer-key-genes.csv' 2026-07-31T13:56:50,497 adding 'oncoref/data/cancer-lineage-group-overrides.csv' 2026-07-31T13:56:50,499 adding 'oncoref/data/cancer-lineage-groups.csv' 2026-07-31T13:56:50,501 adding 'oncoref/data/cancer-mismatch-repair-statuses.csv' 2026-07-31T13:56:50,503 adding 'oncoref/data/cancer-normal-tissue-map.csv' 2026-07-31T13:56:50,510 adding 'oncoref/data/cancer-reference-expression-availability.csv' 2026-07-31T13:56:50,540 adding 'oncoref/data/cancer-reference-expression-samples.csv.gz' 2026-07-31T13:56:50,544 adding 'oncoref/data/cancer-response-signatures.csv' 2026-07-31T13:56:50,545 adding 'oncoref/data/cancer-subtype-groupings.csv' 2026-07-31T13:56:50,558 adding 'oncoref/data/cancer-testis-antigens.csv' 2026-07-31T13:56:50,561 adding 'oncoref/data/cancer-tmb.csv' 2026-07-31T13:56:50,564 adding 'oncoref/data/cancer-type-genes.csv' 2026-07-31T13:56:50,570 adding 'oncoref/data/cancer-type-registry.csv' 2026-07-31T13:56:50,572 adding 'oncoref/data/cancer-viral-antigens.csv' 2026-07-31T13:56:50,575 adding 'oncoref/data/cancer-who-soft-tissue-bone-audit.csv' 2026-07-31T13:56:50,628 adding 'oncoref/data/canonical-gene-space.csv.gz' 2026-07-31T13:56:50,634 adding 'oncoref/data/cdna-identical-gene-groups.csv' 2026-07-31T13:56:50,638 adding 'oncoref/data/censored-gene-reference-tpm.csv' 2026-07-31T13:56:50,640 adding 'oncoref/data/clean-tpm-biological-housekeeping-genes.csv' 2026-07-31T13:56:50,651 adding 'oncoref/data/clean-tpm-censored-genes.csv' 2026-07-31T13:56:50,655 adding 'oncoref/data/cohort-registry.csv' 2026-07-31T13:56:50,657 adding 'oncoref/data/cta-candidate-references.csv' 2026-07-31T13:56:50,658 adding 'oncoref/data/cta-clinical-targets.csv' 2026-07-31T13:56:50,660 adding 'oncoref/data/cta-ihc-unreliable.csv' 2026-07-31T13:56:50,662 adding 'oncoref/data/cta-specificity-audit.csv' 2026-07-31T13:56:50,664 adding 'oncoref/data/degenerate-subtype-pairs.csv' 2026-07-31T13:56:50,666 adding 'oncoref/data/disease-state-rules.csv' 2026-07-31T13:56:50,693 adding 'oncoref/data/ensembl-id-aliases.csv' 2026-07-31T13:56:50,708 adding 'oncoref/data/expression-artifact-gene-universe-deltas.csv' 2026-07-31T13:56:50,718 adding 'oncoref/data/expression_sources.yaml' 2026-07-31T13:56:50,721 adding 'oncoref/data/extra-tx-mappings.csv' 2026-07-31T13:56:50,723 adding 'oncoref/data/family-burden-map.csv' 2026-07-31T13:56:50,725 adding 'oncoref/data/fusion-expression-effects.csv' 2026-07-31T13:56:50,727 adding 'oncoref/data/fusion-surrogate-expression.csv' 2026-07-31T13:56:50,729 adding 'oncoref/data/gse294016-sample-diagnoses.csv' 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'oncoref/data/representative-source-adjudications.csv' 2026-07-31T13:56:50,903 adding 'oncoref/data/ribosomal-protein-genes.csv' 2026-07-31T13:56:50,910 adding 'oncoref/data/ribosomal-protein-pseudogenes.csv' 2026-07-31T13:56:50,913 adding 'oncoref/data/rrna-and-pseudogenes.csv' 2026-07-31T13:56:50,932 adding 'oncoref/data/small-noncoding-rnas.csv' 2026-07-31T13:56:50,935 adding 'oncoref/data/source-matrices.csv' 2026-07-31T13:56:50,937 adding 'oncoref/data/tissue-burden-map.csv' 2026-07-31T13:56:50,940 adding 'oncoref-1.8.163.dist-info/licenses/LICENSE' 2026-07-31T13:56:50,942 adding 'oncoref-1.8.163.dist-info/METADATA' 2026-07-31T13:56:50,944 adding 'oncoref-1.8.163.dist-info/WHEEL' 2026-07-31T13:56:50,945 adding 'oncoref-1.8.163.dist-info/entry_points.txt' 2026-07-31T13:56:50,946 adding 'oncoref-1.8.163.dist-info/top_level.txt' 2026-07-31T13:56:50,949 adding 'oncoref-1.8.163.dist-info/RECORD' 2026-07-31T13:56:50,983 removing build/bdist.linux-armv7l/wheel 2026-07-31T13:56:51,110 Building wheel for oncoref (pyproject.toml): finished with status 'done' 2026-07-31T13:56:51,171 Created wheel for oncoref: filename=oncoref-1.8.163-py3-none-any.whl size=2829348 sha256=ae4c895e05df28362c195d5dd97899270cf2ca3d45b60875b8019cb542284e03 2026-07-31T13:56:51,172 Stored in directory: /tmp/pip-ephem-wheel-cache-3l67p0vd/wheels/31/66/27/f56463d6973c7ea420860864c335a7e55665e2ee36548ab2de 2026-07-31T13:56:51,189 Successfully built oncoref 2026-07-31T13:56:51,259 Removed build tracker: '/tmp/pip-build-tracker-ua06aj92'