2026-10-19T05:07:08,414 Created temporary directory: /tmp/pip-ephem-wheel-cache-8v4hyvwq 2026-10-19T05:07:08,416 Created temporary directory: /tmp/pip-build-tracker-nw0xh8a2 2026-10-19T05:07:08,417 Initialized build tracking at /tmp/pip-build-tracker-nw0xh8a2 2026-10-19T05:07:08,417 Created build tracker: /tmp/pip-build-tracker-nw0xh8a2 2026-10-19T05:07:08,418 Entered build tracker: /tmp/pip-build-tracker-nw0xh8a2 2026-10-19T05:07:08,419 Created temporary directory: /tmp/pip-wheel-aa97zv7f 2026-10-19T05:07:08,422 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 2026-10-19T05:07:08,424 Created temporary directory: /tmp/pip-ephem-wheel-cache-odttlzy5 2026-10-19T05:07:08,445 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-10-19T05:07:08,449 2 location(s) to search for versions of oncoref: 2026-10-19T05:07:08,449 * https://pypi.org/simple/oncoref/ 2026-10-19T05:07:08,449 * https://www.piwheels.org/simple/oncoref/ 2026-10-19T05:07:08,450 Fetching project page and analyzing links: https://pypi.org/simple/oncoref/ 2026-10-19T05:07:08,450 Getting page https://pypi.org/simple/oncoref/ 2026-10-19T05:07:08,452 Found index url https://pypi.org/simple 2026-10-19T05:07:08,659 Fetched page https://pypi.org/simple/oncoref/ as application/vnd.pypi.simple.v1+json 2026-10-19T05:07:08,734 Skipping link: No binaries permitted for oncoref: 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https://archive1.piwheels.org/simple/oncoref/oncoref-1.8.14-py3-none-any.whl#sha256=ac41cf84ca97c695a15f40326738750e2762e39f366bf99300777803874b26da (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-10-19T05:07:09,452 Skipping link: No binaries permitted for oncoref: https://archive1.piwheels.org/simple/oncoref/oncoref-1.8.13-py3-none-any.whl#sha256=91c3e1fa8448033a913075559a2ee2b76fcbad64e20aeb7696484a9a5619dbef (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-10-19T05:07:09,453 Skipping link: No binaries permitted for oncoref: https://archive1.piwheels.org/simple/oncoref/oncoref-1.8.12-py3-none-any.whl#sha256=2a0e59477b8939fc63d4a78f31b0b793fb2f49ea2aab861d853fa8479ccf9608 (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-10-19T05:07:09,453 Skipping link: No binaries permitted for oncoref: https://archive1.piwheels.org/simple/oncoref/oncoref-1.8.11-py3-none-any.whl#sha256=602ac0deb73739e65dfb65105b23357a94a67eb9e1faac0880bff5203ed4a818 (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-10-19T05:07:09,454 Skipping link: No binaries permitted for oncoref: https://archive1.piwheels.org/simple/oncoref/oncoref-1.8.10-py3-none-any.whl#sha256=3e789fd35641073e8afc8885dcef12d74a2323c2e0c8dad7b5e369392675e83a (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-10-19T05:07:09,455 Skipping link: No binaries permitted for oncoref: https://archive1.piwheels.org/simple/oncoref/oncoref-1.8.9-py3-none-any.whl#sha256=2415de57054126a885d64b626bbb12657ce55d0791a686b7aba85fd8b784d399 (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-10-19T05:07:09,455 Skipping link: No binaries permitted for oncoref: https://archive1.piwheels.org/simple/oncoref/oncoref-1.8.8-py3-none-any.whl#sha256=f1b7351039ce534abc9d36a03b53fd9479b1629b4a6fd8698bc500162f1cd362 (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-10-19T05:07:09,456 Skipping link: No binaries permitted for oncoref: https://archive1.piwheels.org/simple/oncoref/oncoref-1.8.7-py3-none-any.whl#sha256=84f80af8afa25d02579e67983b74fd2e515df1ce6d0cb602ecb6808e994f8f63 (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-10-19T05:07:09,456 Skipping link: No binaries permitted for oncoref: https://archive1.piwheels.org/simple/oncoref/oncoref-1.8.6-py3-none-any.whl#sha256=460f281fc846e410a5992e3a87193febdfac8bf81f3e5497a5e5d72ae58176bf (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-10-19T05:07:09,457 Skipping link: No binaries permitted for oncoref: https://archive1.piwheels.org/simple/oncoref/oncoref-1.8.5-py3-none-any.whl#sha256=cfedb20aa2c2593dfb010bc01a13d5b6c732ec5cf013fd70b65c71d1adb71f7e (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-10-19T05:07:09,457 Skipping link: No binaries permitted for oncoref: https://archive1.piwheels.org/simple/oncoref/oncoref-1.8.4-py3-none-any.whl#sha256=d649c7a749c099fe67033ecbdbafe4bf8bcd93bd71d9830ce2a6127a1c093cad (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-10-19T05:07:09,458 Skipping link: No binaries permitted for oncoref: https://archive1.piwheels.org/simple/oncoref/oncoref-1.8.3-py3-none-any.whl#sha256=bf75676ac99a0d1c144249b8cf320ac292b65716c9ffdc50ad27b55db1153821 (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-10-19T05:07:09,458 Skipping link: No binaries permitted for oncoref: https://archive1.piwheels.org/simple/oncoref/oncoref-1.8.2-py3-none-any.whl#sha256=9f47ca1a637e6255fbf29fd252834c85e5d19238a980add71843cd860b39777e (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-10-19T05:07:09,459 Skipping link: No binaries permitted for oncoref: https://archive1.piwheels.org/simple/oncoref/oncoref-1.8.1-py3-none-any.whl#sha256=12f0eb28c115080796010095a4032b844d9ea4383bc0ea2e2b75a3e5f21c9392 (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-10-19T05:07:09,460 Skipping link: No binaries permitted for oncoref: https://archive1.piwheels.org/simple/oncoref/oncoref-1.8.0-py3-none-any.whl#sha256=6f9be6d1511d7e84166b02f2cd219b977025db68916073cb4bd1ebdfc8919914 (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-10-19T05:07:09,460 Skipping link: No binaries permitted for oncoref: https://archive1.piwheels.org/simple/oncoref/oncoref-1.7.0-py3-none-any.whl#sha256=249750fecb30a99d715c221ca1ca76a4ff790891f0051782cd528395d14db6ed (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-10-19T05:07:09,461 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) 2026-10-19T05:07:09,462 Skipping link: not a file: https://www.piwheels.org/simple/oncoref/ 2026-10-19T05:07:09,462 Skipping link: not a file: https://pypi.org/simple/oncoref/ 2026-10-19T05:07:09,507 Given no hashes to check 1 links for project 'oncoref': discarding no candidates 2026-10-19T05:07:09,526 Collecting oncoref==1.9.14 2026-10-19T05:07:09,528 Created temporary directory: /tmp/pip-unpack-2xo3c8tr 2026-10-19T05:07:09,685 Downloading oncoref-1.9.14.tar.gz (14.7 MB) 2026-10-19T05:07:12,402 Added oncoref==1.9.14 from https://files.pythonhosted.org/packages/00/bd/44f4cba3ef5c6a22b93d1a5b8d4e2907159fab1a5c63c06b5105850617e0/oncoref-1.9.14.tar.gz to build tracker '/tmp/pip-build-tracker-nw0xh8a2' 2026-10-19T05:07:12,410 Created temporary directory: /tmp/pip-build-env-u0i2uzt1 2026-10-19T05:07:12,414 Installing build dependencies: started 2026-10-19T05:07:12,415 Running command pip subprocess to install build dependencies 2026-10-19T05:07:13,538 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-10-19T05:07:13,988 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 2026-10-19T05:07:14,011 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-10-19T05:07:15,775 Collecting setuptools>=77.0.0 2026-10-19T05:07:15,776 Obtaining dependency information for setuptools>=77.0.0 from https://www.piwheels.org/simple/setuptools/setuptools-84.0.0-py3-none-any.whl.metadata 2026-10-19T05:07:15,790 Using cached https://www.piwheels.org/simple/setuptools/setuptools-84.0.0-py3-none-any.whl.metadata (6.6 kB) 2026-10-19T05:07:16,023 Collecting wheel 2026-10-19T05:07:16,024 Obtaining dependency information for wheel from https://www.piwheels.org/simple/wheel/wheel-0.48.0-py3-none-any.whl.metadata 2026-10-19T05:07:16,038 Using cached https://www.piwheels.org/simple/wheel/wheel-0.48.0-py3-none-any.whl.metadata (2.3 kB) 2026-10-19T05:07:16,221 Collecting packaging>=24.0 2026-10-19T05:07:16,222 Obtaining dependency information for packaging>=24.0 from https://www.piwheels.org/simple/packaging/packaging-26.3-py3-none-any.whl.metadata 2026-10-19T05:07:16,233 Using cached https://www.piwheels.org/simple/packaging/packaging-26.3-py3-none-any.whl.metadata (3.6 kB) 2026-10-19T05:07:16,422 Using cached https://www.piwheels.org/simple/wheel/wheel-0.48.0-py3-none-any.whl (33 kB) 2026-10-19T05:07:16,448 Using cached https://www.piwheels.org/simple/packaging/packaging-26.3-py3-none-any.whl (129 kB) 2026-10-19T05:07:16,514 Using cached https://www.piwheels.org/simple/setuptools/setuptools-84.0.0-py3-none-any.whl (818 kB) 2026-10-19T05:07:16,544 Using cached https://www.piwheels.org/simple/wheel/wheel-0.48.0-py3-none-any.whl (33 kB) 2026-10-19T05:07:16,572 Using cached https://www.piwheels.org/simple/packaging/packaging-26.3-py3-none-any.whl (129 kB) 2026-10-19T05:07:16,652 Using cached https://www.piwheels.org/simple/setuptools/setuptools-84.0.0-py3-none-any.whl (818 kB) 2026-10-19T05:07:19,387 Installing collected packages: setuptools, packaging, wheel 2026-10-19T05:07:22,080 Creating /tmp/pip-build-env-u0i2uzt1/overlay/local/bin 2026-10-19T05:07:22,082 changing mode of /tmp/pip-build-env-u0i2uzt1/overlay/local/bin/wheel to 755 2026-10-19T05:07:22,103 Successfully installed packaging-26.3 setuptools-84.0.0 wheel-0.48.0 2026-10-19T05:07:22,386 Installing build dependencies: finished with status 'done' 2026-10-19T05:07:22,392 Getting requirements to build wheel: started 2026-10-19T05:07:22,393 Running command Getting requirements to build wheel 2026-10-19T05:07:23,094 running egg_info 2026-10-19T05:07:23,100 writing oncoref.egg-info/PKG-INFO 2026-10-19T05:07:23,107 writing dependency_links to oncoref.egg-info/dependency_links.txt 2026-10-19T05:07:23,109 writing entry points to oncoref.egg-info/entry_points.txt 2026-10-19T05:07:23,113 writing requirements to oncoref.egg-info/requires.txt 2026-10-19T05:07:23,114 writing top-level names to oncoref.egg-info/top_level.txt 2026-10-19T05:07:23,161 reading manifest file 'oncoref.egg-info/SOURCES.txt' 2026-10-19T05:07:23,181 reading manifest template 'MANIFEST.in' 2026-10-19T05:07:23,209 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-10-19T05:07:23,211 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-10-19T05:07:23,213 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-10-19T05:07:23,215 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-10-19T05:07:23,216 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-10-19T05:07:23,218 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-10-19T05:07:23,218 adding license file 'LICENSE' 2026-10-19T05:07:23,236 writing manifest file 'oncoref.egg-info/SOURCES.txt' 2026-10-19T05:07:23,335 Getting requirements to build wheel: finished with status 'done' 2026-10-19T05:07:23,338 Created temporary directory: /tmp/pip-modern-metadata-9j7yuyd3 2026-10-19T05:07:23,340 Preparing metadata (pyproject.toml): started 2026-10-19T05:07:23,341 Running command Preparing metadata (pyproject.toml) 2026-10-19T05:07:24,019 running dist_info 2026-10-19T05:07:24,029 creating /tmp/pip-modern-metadata-9j7yuyd3/oncoref.egg-info 2026-10-19T05:07:24,030 writing /tmp/pip-modern-metadata-9j7yuyd3/oncoref.egg-info/PKG-INFO 2026-10-19T05:07:24,037 writing dependency_links to /tmp/pip-modern-metadata-9j7yuyd3/oncoref.egg-info/dependency_links.txt 2026-10-19T05:07:24,038 writing entry points to /tmp/pip-modern-metadata-9j7yuyd3/oncoref.egg-info/entry_points.txt 2026-10-19T05:07:24,042 writing requirements to /tmp/pip-modern-metadata-9j7yuyd3/oncoref.egg-info/requires.txt 2026-10-19T05:07:24,043 writing top-level names to /tmp/pip-modern-metadata-9j7yuyd3/oncoref.egg-info/top_level.txt 2026-10-19T05:07:24,044 writing manifest file '/tmp/pip-modern-metadata-9j7yuyd3/oncoref.egg-info/SOURCES.txt' 2026-10-19T05:07:24,089 reading manifest file '/tmp/pip-modern-metadata-9j7yuyd3/oncoref.egg-info/SOURCES.txt' 2026-10-19T05:07:24,091 reading manifest template 'MANIFEST.in' 2026-10-19T05:07:24,118 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-10-19T05:07:24,119 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-10-19T05:07:24,121 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-10-19T05:07:24,122 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-10-19T05:07:24,123 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-10-19T05:07:24,125 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-10-19T05:07:24,125 adding license file 'LICENSE' 2026-10-19T05:07:24,138 writing manifest file '/tmp/pip-modern-metadata-9j7yuyd3/oncoref.egg-info/SOURCES.txt' 2026-10-19T05:07:24,140 creating '/tmp/pip-modern-metadata-9j7yuyd3/oncoref-1.9.14.dist-info' 2026-10-19T05:07:24,267 Preparing metadata (pyproject.toml): finished with status 'done' 2026-10-19T05:07:24,272 Source in /tmp/pip-wheel-aa97zv7f/oncoref_9b981964db9a4471b8853612bebbcc60 has version 1.9.14, which satisfies requirement oncoref==1.9.14 from https://files.pythonhosted.org/packages/00/bd/44f4cba3ef5c6a22b93d1a5b8d4e2907159fab1a5c63c06b5105850617e0/oncoref-1.9.14.tar.gz 2026-10-19T05:07:24,273 Removed oncoref==1.9.14 from https://files.pythonhosted.org/packages/00/bd/44f4cba3ef5c6a22b93d1a5b8d4e2907159fab1a5c63c06b5105850617e0/oncoref-1.9.14.tar.gz from build tracker '/tmp/pip-build-tracker-nw0xh8a2' 2026-10-19T05:07:24,281 Created temporary directory: /tmp/pip-unpack-lk7zf_or 2026-10-19T05:07:24,282 Building wheels for collected packages: oncoref 2026-10-19T05:07:24,286 Created temporary directory: /tmp/pip-wheel-ma07yk96 2026-10-19T05:07:24,287 Destination directory: /tmp/pip-wheel-ma07yk96 2026-10-19T05:07:24,289 Building wheel for oncoref (pyproject.toml): started 2026-10-19T05:07:24,290 Running command Building wheel for oncoref (pyproject.toml) 2026-10-19T05:07:24,917 running bdist_wheel 2026-10-19T05:07:24,934 running build 2026-10-19T05:07:24,935 running build_py 2026-10-19T05:07:24,943 creating build/lib/oncoref 2026-10-19T05:07:24,945 copying oncoref/cancer_ontology.py -> build/lib/oncoref 2026-10-19T05:07:24,947 copying oncoref/expression_registry.py -> build/lib/oncoref 2026-10-19T05:07:24,950 copying oncoref/human_protein_atlas.py -> build/lib/oncoref 2026-10-19T05:07:24,953 copying oncoref/cta_sources.py -> build/lib/oncoref 2026-10-19T05:07:24,955 copying oncoref/bgee_srp009687.py -> build/lib/oncoref 2026-10-19T05:07:24,957 copying oncoref/fusions.py -> build/lib/oncoref 2026-10-19T05:07:24,959 copying oncoref/gene_ids.py -> build/lib/oncoref 2026-10-19T05:07:24,961 copying oncoref/genome.py -> build/lib/oncoref 2026-10-19T05:07:24,964 copying oncoref/proteoforms.py -> build/lib/oncoref 2026-10-19T05:07:24,966 copying oncoref/bgee_srp181218.py -> build/lib/oncoref 2026-10-19T05:07:24,968 copying oncoref/incidence.py -> build/lib/oncoref 2026-10-19T05:07:24,970 copying oncoref/species_antigens.py -> build/lib/oncoref 2026-10-19T05:07:24,973 copying oncoref/response_signatures.py -> build/lib/oncoref 2026-10-19T05:07:24,974 copying oncoref/cta_gate_audit.py -> build/lib/oncoref 2026-10-19T05:07:24,976 copying oncoref/cta_evidence_adapters.py -> build/lib/oncoref 2026-10-19T05:07:24,978 copying oncoref/expression_builders.py -> build/lib/oncoref 2026-10-19T05:07:24,983 copying oncoref/cta_tissues.py -> build/lib/oncoref 2026-10-19T05:07:24,985 copying oncoref/expression.py -> build/lib/oncoref 2026-10-19T05:07:24,992 copying oncoref/ici_response.py -> build/lib/oncoref 2026-10-19T05:07:24,995 copying oncoref/mouse.py -> build/lib/oncoref 2026-10-19T05:07:24,996 copying oncoref/hpa.py -> build/lib/oncoref 2026-10-19T05:07:24,999 copying oncoref/catalog.py -> build/lib/oncoref 2026-10-19T05:07:25,001 copying oncoref/_reference_sources.py -> build/lib/oncoref 2026-10-19T05:07:25,003 copying oncoref/cta_evidence_model.py -> build/lib/oncoref 2026-10-19T05:07:25,006 copying oncoref/gse304066.py -> build/lib/oncoref 2026-10-19T05:07:25,008 copying oncoref/cta_regen.py -> build/lib/oncoref 2026-10-19T05:07:25,011 copying oncoref/pfizer_canine_protein.py -> build/lib/oncoref 2026-10-19T05:07:25,013 copying oncoref/source_matrices.py -> build/lib/oncoref 2026-10-19T05:07:25,016 copying oncoref/expression_source_adapters.py -> build/lib/oncoref 2026-10-19T05:07:25,020 copying oncoref/figure_output.py -> build/lib/oncoref 2026-10-19T05:07:25,022 copying oncoref/gene_identity.py -> build/lib/oncoref 2026-10-19T05:07:25,025 copying oncoref/cta_landscape.py -> build/lib/oncoref 2026-10-19T05:07:25,028 copying oncoref/cta_coverage.py -> build/lib/oncoref 2026-10-19T05:07:25,030 copying oncoref/__init__.py -> build/lib/oncoref 2026-10-19T05:07:25,034 copying oncoref/figure_style.py -> build/lib/oncoref 2026-10-19T05:07:25,037 copying oncoref/cta.py -> build/lib/oncoref 2026-10-19T05:07:25,042 copying oncoref/version.py -> build/lib/oncoref 2026-10-19T05:07:25,045 copying oncoref/sequence_groups.py -> build/lib/oncoref 2026-10-19T05:07:25,048 copying oncoref/therapy_evidence.py -> build/lib/oncoref 2026-10-19T05:07:25,050 copying oncoref/coverage.py -> build/lib/oncoref 2026-10-19T05:07:25,055 copying oncoref/gene_families.py -> build/lib/oncoref 2026-10-19T05:07:25,058 copying oncoref/reference_identity.py -> build/lib/oncoref 2026-10-19T05:07:25,060 copying oncoref/plots.py -> build/lib/oncoref 2026-10-19T05:07:25,066 copying oncoref/cancer_genes.py -> build/lib/oncoref 2026-10-19T05:07:25,072 copying oncoref/peptides.py -> build/lib/oncoref 2026-10-19T05:07:25,075 copying oncoref/data_bundle.py -> build/lib/oncoref 2026-10-19T05:07:25,080 copying oncoref/doga.py -> build/lib/oncoref 2026-10-19T05:07:25,083 copying oncoref/reference_data.py -> build/lib/oncoref 2026-10-19T05:07:25,087 copying oncoref/cancer_types.py -> build/lib/oncoref 2026-10-19T05:07:25,095 copying oncoref/cta_review.py -> build/lib/oncoref 2026-10-19T05:07:25,098 copying oncoref/ici.py -> build/lib/oncoref 2026-10-19T05:07:25,101 copying oncoref/gene_qc.py -> build/lib/oncoref 2026-10-19T05:07:25,104 copying oncoref/_table_io.py -> build/lib/oncoref 2026-10-19T05:07:25,105 copying oncoref/species.py -> build/lib/oncoref 2026-10-19T05:07:25,107 copying oncoref/data_manifest.py -> build/lib/oncoref 2026-10-19T05:07:25,110 copying oncoref/normalization.py -> build/lib/oncoref 2026-10-19T05:07:25,114 copying oncoref/apd1.py -> build/lib/oncoref 2026-10-19T05:07:25,116 copying oncoref/cta_evidence_schema.py -> build/lib/oncoref 2026-10-19T05:07:25,118 copying oncoref/rna_protein.py -> build/lib/oncoref 2026-10-19T05:07:25,122 copying oncoref/pfizer_canine_rna.py -> build/lib/oncoref 2026-10-19T05:07:25,124 copying oncoref/barkbase.py -> build/lib/oncoref 2026-10-19T05:07:25,125 copying oncoref/expression_contract.py -> build/lib/oncoref 2026-10-19T05:07:25,128 copying oncoref/samples.py -> build/lib/oncoref 2026-10-19T05:07:25,130 copying oncoref/species_assets.py -> build/lib/oncoref 2026-10-19T05:07:25,133 copying oncoref/canine.py -> build/lib/oncoref 2026-10-19T05:07:25,134 copying oncoref/representative_partitions.py -> build/lib/oncoref 2026-10-19T05:07:25,137 copying oncoref/_downloads.py -> build/lib/oncoref 2026-10-19T05:07:25,139 copying oncoref/cli.py -> build/lib/oncoref 2026-10-19T05:07:25,142 copying oncoref/human.py -> build/lib/oncoref 2026-10-19T05:07:25,143 copying oncoref/load_dataset.py -> build/lib/oncoref 2026-10-19T05:07:25,146 copying oncoref/expression_provenance_plots.py -> build/lib/oncoref 2026-10-19T05:07:25,150 copying oncoref/cta_peptides.py -> build/lib/oncoref 2026-10-19T05:07:25,153 copying oncoref/cta_provenance.py -> build/lib/oncoref 2026-10-19T05:07:25,156 copying oncoref/drivers.py -> build/lib/oncoref 2026-10-19T05:07:25,160 copying oncoref/legacy.py -> build/lib/oncoref 2026-10-19T05:07:25,163 copying oncoref/hpa_cancer.py -> build/lib/oncoref 2026-10-19T05:07:25,166 copying oncoref/expression_engine.py -> build/lib/oncoref 2026-10-19T05:07:25,170 copying oncoref/cohorts.py -> build/lib/oncoref 2026-10-19T05:07:25,173 copying oncoref/species_expression.py -> build/lib/oncoref 2026-10-19T05:07:25,178 copying oncoref/cta_curation_plots.py -> build/lib/oncoref 2026-10-19T05:07:25,183 copying oncoref/_evidence_resolution.py -> build/lib/oncoref 2026-10-19T05:07:25,187 copying oncoref/human_cta_snapshot.py -> build/lib/oncoref 2026-10-19T05:07:25,191 copying oncoref/tmb.py -> build/lib/oncoref 2026-10-19T05:07:25,196 copying oncoref/tumor_references.py -> build/lib/oncoref 2026-10-19T05:07:25,200 copying oncoref/antigen_coverage.py -> build/lib/oncoref 2026-10-19T05:07:25,236 creating build/lib/oncoref/data 2026-10-19T05:07:25,238 copying oncoref/data/histone-genes.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,242 copying oncoref/data/hpa-cancer-rna-cohorts.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,245 copying oncoref/data/cta-ihc-unreliable.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,248 copying oncoref/data/driver-gene-evidence.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,255 copying oncoref/data/cancer-tmb.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,259 copying oncoref/data/tissue-burden-map.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,261 copying oncoref/data/ribosomal-protein-genes.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,264 copying oncoref/data/cancer-subtype-groupings.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,266 copying oncoref/data/numt-pseudogenes.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,269 copying oncoref/data/cancer-expression-source-candidates.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,272 copying oncoref/data/cancer-code-burden-map.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,274 copying oncoref/data/censored-gene-reference-tpm.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,278 copying oncoref/data/proteoform-groups.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,281 copying oncoref/data/cancer-driver-variants.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,284 copying oncoref/data/rna-protein-calibration-sources.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,287 copying oncoref/data/clean-tpm-biological-housekeeping-genes.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,290 copying oncoref/data/source-matrices.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,293 copying oncoref/data/narrative-gene-sets.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,296 copying oncoref/data/cancer-reference-sample-molecular-provenance.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,301 copying oncoref/data/ensembl-id-aliases.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,312 copying oncoref/data/cta-specificity-audit.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,315 copying oncoref/data/cta-gene-publication-evidence.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,318 copying oncoref/data/cancer-type-genes.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,320 copying oncoref/data/cta-clinical-targets.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,323 copying oncoref/data/cancer-testis-antigens-extended.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,348 copying oncoref/data/cancer-key-gene-citation-audit.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,353 copying oncoref/data/cancer-reference-expression-availability.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,357 copying oncoref/data/hpa-safety-tissue-map.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,360 copying oncoref/data/representative-source-adjudications.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,362 copying oncoref/data/degenerate-subtype-pairs.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,364 copying oncoref/data/ribosomal-protein-pseudogenes.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,367 copying oncoref/data/cdna-identical-gene-groups.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,370 copying oncoref/data/cancer-cohort-aggregates.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,372 copying oncoref/data/disease-state-rules.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,374 copying oncoref/data/cancer-who-soft-tissue-bone-audit.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,377 copying oncoref/data/rna-protein-hpa-prior-sources.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,379 copying oncoref/data/extra-tx-mappings.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,382 copying oncoref/data/legacy-dataset-dispositions.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,384 copying oncoref/data/cancer-fusion-citation-audit.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,387 copying oncoref/data/cta-publication-sources.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,390 copying oncoref/data/housekeeping-genes.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,392 copying oncoref/data/cta-candidate-references.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,394 copying oncoref/data/cancer-type-registry.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,397 copying oncoref/data/cancer-viral-antigens.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,399 copying oncoref/data/hpa-cancer-crosswalk.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,402 copying oncoref/data/family-burden-map.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,404 copying oncoref/data/cancer-lineage-groups.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,406 copying oncoref/data/cancer-lineage-group-overrides.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,408 copying oncoref/data/cancer-ici-response.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,411 copying oncoref/data/cancer-normal-tissue-map.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,415 copying oncoref/data/mitochondrial-genes.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,420 copying oncoref/data/cancer-apd1-response.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,423 copying oncoref/data/expression-artifact-gene-universe-deltas.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,438 copying oncoref/data/therapy-benefit-toxicity-evidence.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,443 copying oncoref/data/cancer-testis-antigens.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,474 copying oncoref/data/fusion-surrogate-expression.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,478 copying oncoref/data/cancer-fusions.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,483 copying oncoref/data/cta-reviewed-evidence.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,486 copying oncoref/data/cancer-driver-genes.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,492 copying oncoref/data/nuclear-retained-lncrnas.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,494 copying oncoref/data/proteoform-groups-genome.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,497 copying oncoref/data/cta-warning-reviews.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,499 copying oncoref/data/hemoglobin-genes.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,501 copying oncoref/data/rare-cancer-fusion-rules.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,504 copying oncoref/data/cancer-entity-driver-spectrum.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,506 copying oncoref/data/cancer-ici-source-locator-audit.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,513 copying oncoref/data/cancer-incidence-mortality.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,517 copying oncoref/data/proteoform-collapse-overrides.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,520 copying oncoref/data/cancer-ici-response-estimates.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,535 copying oncoref/data/gse294016-sample-diagnoses.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,537 copying oncoref/data/rrna-and-pseudogenes.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,540 copying oncoref/data/cta-publication-membership.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,584 copying oncoref/data/cohort-registry.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,587 copying oncoref/data/cancer-response-signatures.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,589 copying oncoref/data/fusion-expression-effects.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,591 copying oncoref/data/clean-tpm-censored-genes.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,609 copying oncoref/data/driver-variant-evidence.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,616 copying oncoref/data/cancer-frameshift-burden.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,618 copying oncoref/data/small-noncoding-rnas.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,623 copying oncoref/data/cancer-mismatch-repair-statuses.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,626 copying oncoref/data/cancer-key-genes.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,636 copying oncoref/data/cancer-tmb-source-audit.csv -> build/lib/oncoref/data 2026-10-19T05:07:25,649 copying oncoref/data/canonical-gene-space.csv.gz -> build/lib/oncoref/data 2026-10-19T05:07:25,670 copying oncoref/data/ncbi-entrez-gene-mappings.csv.gz -> build/lib/oncoref/data 2026-10-19T05:07:25,712 copying oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/lib/oncoref/data 2026-10-19T05:07:25,724 copying oncoref/data/cancer-reference-expression-samples.csv.gz -> build/lib/oncoref/data 2026-10-19T05:07:25,732 copying oncoref/data/rna-protein-calibration-samples.csv.gz -> build/lib/oncoref/data 2026-10-19T05:07:25,735 copying oncoref/data/rna-protein-hpa-priors.csv.gz -> build/lib/oncoref/data 2026-10-19T05:07:25,753 copying oncoref/data/rna-protein-calibrations.csv.gz -> build/lib/oncoref/data 2026-10-19T05:07:25,985 copying oncoref/data/expression_sources.yaml -> build/lib/oncoref/data 2026-10-19T05:07:25,994 creating build/lib/oncoref/data/species/dog 2026-10-19T05:07:25,998 copying oncoref/data/species/dog/expression_sources.yaml -> build/lib/oncoref/data/species/dog 2026-10-19T05:07:26,004 copying oncoref/data/species/dog/bgee-srp181218-samples.json -> build/lib/oncoref/data/species/dog 2026-10-19T05:07:26,011 copying oncoref/data/species/dog/pfizer-dog-protein-samples.json -> build/lib/oncoref/data/species/dog 2026-10-19T05:07:26,016 copying oncoref/data/species/dog/cta-evidence.json -> build/lib/oncoref/data/species/dog 2026-10-19T05:07:26,028 copying oncoref/data/species/dog/assets.json -> build/lib/oncoref/data/species/dog 2026-10-19T05:07:26,037 copying oncoref/data/species/dog/bgee-srp009687-samples.json -> build/lib/oncoref/data/species/dog 2026-10-19T05:07:26,045 copying oncoref/data/species/dog/barkbase-samples.json -> build/lib/oncoref/data/species/dog 2026-10-19T05:07:26,066 copying oncoref/data/species/dog/lineage_overlaps.json -> build/lib/oncoref/data/species/dog 2026-10-19T05:07:26,070 copying oncoref/data/hpa-cancer-sources.json -> build/lib/oncoref/data 2026-10-19T05:07:26,094 installing to build/bdist.linux-armv7l/wheel 2026-10-19T05:07:26,095 running install 2026-10-19T05:07:26,132 running install_lib 2026-10-19T05:07:26,140 creating build/bdist.linux-armv7l/wheel 2026-10-19T05:07:26,144 creating build/bdist.linux-armv7l/wheel/oncoref 2026-10-19T05:07:26,145 copying build/lib/oncoref/cancer_ontology.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,148 copying build/lib/oncoref/expression_registry.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,151 copying build/lib/oncoref/human_protein_atlas.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,153 copying build/lib/oncoref/cta_sources.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,155 copying build/lib/oncoref/bgee_srp009687.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,157 copying build/lib/oncoref/fusions.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,160 copying build/lib/oncoref/gene_ids.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,162 copying build/lib/oncoref/genome.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,165 copying build/lib/oncoref/proteoforms.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,167 copying build/lib/oncoref/bgee_srp181218.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,169 copying build/lib/oncoref/incidence.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,172 copying build/lib/oncoref/species_antigens.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,175 copying build/lib/oncoref/response_signatures.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,177 copying build/lib/oncoref/cta_gate_audit.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,179 copying build/lib/oncoref/cta_evidence_adapters.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,180 copying build/lib/oncoref/expression_builders.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,195 copying build/lib/oncoref/cta_tissues.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,207 copying build/lib/oncoref/expression.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,224 copying build/lib/oncoref/ici_response.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,227 copying build/lib/oncoref/mouse.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,229 copying build/lib/oncoref/hpa.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,232 copying build/lib/oncoref/catalog.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,235 copying build/lib/oncoref/_reference_sources.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,237 copying build/lib/oncoref/cta_evidence_model.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,239 copying build/lib/oncoref/gse304066.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,241 copying build/lib/oncoref/cta_regen.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,244 copying build/lib/oncoref/pfizer_canine_protein.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,246 copying build/lib/oncoref/source_matrices.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,249 copying build/lib/oncoref/expression_source_adapters.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,259 copying build/lib/oncoref/figure_output.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,264 copying build/lib/oncoref/gene_identity.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,267 copying build/lib/oncoref/cta_landscape.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,271 copying build/lib/oncoref/cta_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,275 copying build/lib/oncoref/__init__.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,280 copying build/lib/oncoref/figure_style.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,285 copying build/lib/oncoref/cta.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,293 creating build/bdist.linux-armv7l/wheel/oncoref/data 2026-10-19T05:07:26,294 copying build/lib/oncoref/data/histone-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,297 copying build/lib/oncoref/data/hpa-cancer-sources.json -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,300 copying build/lib/oncoref/data/hpa-cancer-rna-cohorts.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,302 copying build/lib/oncoref/data/cta-ihc-unreliable.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,304 copying build/lib/oncoref/data/driver-gene-evidence.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,318 copying build/lib/oncoref/data/cancer-tmb.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,328 copying build/lib/oncoref/data/tissue-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,335 copying build/lib/oncoref/data/ribosomal-protein-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,341 copying build/lib/oncoref/data/cancer-subtype-groupings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,343 copying build/lib/oncoref/data/numt-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,345 copying build/lib/oncoref/data/cancer-expression-source-candidates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,348 copying build/lib/oncoref/data/cancer-code-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,350 copying build/lib/oncoref/data/censored-gene-reference-tpm.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,354 copying build/lib/oncoref/data/proteoform-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,356 copying build/lib/oncoref/data/cancer-driver-variants.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,360 copying build/lib/oncoref/data/canonical-gene-space.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,375 copying build/lib/oncoref/data/rna-protein-calibration-sources.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,378 creating build/bdist.linux-armv7l/wheel/oncoref/data/species 2026-10-19T05:07:26,380 creating build/bdist.linux-armv7l/wheel/oncoref/data/species/dog 2026-10-19T05:07:26,381 copying build/lib/oncoref/data/species/dog/bgee-srp181218-samples.json -> build/bdist.linux-armv7l/wheel/./oncoref/data/species/dog 2026-10-19T05:07:26,391 copying build/lib/oncoref/data/species/dog/expression_sources.yaml -> build/bdist.linux-armv7l/wheel/./oncoref/data/species/dog 2026-10-19T05:07:26,393 copying build/lib/oncoref/data/species/dog/pfizer-dog-protein-samples.json -> build/bdist.linux-armv7l/wheel/./oncoref/data/species/dog 2026-10-19T05:07:26,397 copying build/lib/oncoref/data/species/dog/cta-evidence.json -> build/bdist.linux-armv7l/wheel/./oncoref/data/species/dog 2026-10-19T05:07:26,404 copying build/lib/oncoref/data/species/dog/assets.json -> build/bdist.linux-armv7l/wheel/./oncoref/data/species/dog 2026-10-19T05:07:26,406 copying build/lib/oncoref/data/species/dog/bgee-srp009687-samples.json -> build/bdist.linux-armv7l/wheel/./oncoref/data/species/dog 2026-10-19T05:07:26,409 copying build/lib/oncoref/data/species/dog/barkbase-samples.json -> build/bdist.linux-armv7l/wheel/./oncoref/data/species/dog 2026-10-19T05:07:26,414 copying build/lib/oncoref/data/species/dog/lineage_overlaps.json -> build/bdist.linux-armv7l/wheel/./oncoref/data/species/dog 2026-10-19T05:07:26,416 copying build/lib/oncoref/data/clean-tpm-biological-housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,418 copying build/lib/oncoref/data/source-matrices.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,420 copying build/lib/oncoref/data/narrative-gene-sets.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,422 copying build/lib/oncoref/data/cancer-reference-sample-molecular-provenance.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,426 copying build/lib/oncoref/data/ensembl-id-aliases.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,438 copying build/lib/oncoref/data/expression_sources.yaml -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,442 copying build/lib/oncoref/data/cta-specificity-audit.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,445 copying build/lib/oncoref/data/cta-gene-publication-evidence.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,447 copying build/lib/oncoref/data/cancer-type-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,450 copying build/lib/oncoref/data/cta-clinical-targets.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,452 copying build/lib/oncoref/data/cancer-testis-antigens-extended.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,489 copying build/lib/oncoref/data/cancer-key-gene-citation-audit.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,500 copying build/lib/oncoref/data/cancer-reference-expression-availability.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,512 copying build/lib/oncoref/data/hpa-safety-tissue-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,515 copying build/lib/oncoref/data/representative-source-adjudications.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,517 copying build/lib/oncoref/data/degenerate-subtype-pairs.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,519 copying build/lib/oncoref/data/ribosomal-protein-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,522 copying build/lib/oncoref/data/cdna-identical-gene-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,525 copying build/lib/oncoref/data/cancer-cohort-aggregates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,527 copying build/lib/oncoref/data/disease-state-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,529 copying build/lib/oncoref/data/ncbi-entrez-gene-mappings.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,544 copying build/lib/oncoref/data/cancer-who-soft-tissue-bone-audit.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,547 copying build/lib/oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,554 copying build/lib/oncoref/data/rna-protein-hpa-prior-sources.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,556 copying build/lib/oncoref/data/extra-tx-mappings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,558 copying build/lib/oncoref/data/legacy-dataset-dispositions.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,560 copying build/lib/oncoref/data/cancer-fusion-citation-audit.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,563 copying build/lib/oncoref/data/cta-publication-sources.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,565 copying build/lib/oncoref/data/housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,567 copying build/lib/oncoref/data/cta-candidate-references.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,569 copying build/lib/oncoref/data/cancer-reference-expression-samples.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,575 copying build/lib/oncoref/data/cancer-type-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,579 copying build/lib/oncoref/data/cancer-viral-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,581 copying build/lib/oncoref/data/hpa-cancer-crosswalk.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,583 copying build/lib/oncoref/data/family-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,585 copying build/lib/oncoref/data/cancer-lineage-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,587 copying build/lib/oncoref/data/cancer-lineage-group-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,589 copying build/lib/oncoref/data/cancer-ici-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,591 copying build/lib/oncoref/data/cancer-normal-tissue-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,593 copying build/lib/oncoref/data/mitochondrial-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,595 copying build/lib/oncoref/data/cancer-apd1-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,597 copying build/lib/oncoref/data/expression-artifact-gene-universe-deltas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,604 copying build/lib/oncoref/data/therapy-benefit-toxicity-evidence.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,606 copying build/lib/oncoref/data/cancer-testis-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,625 copying build/lib/oncoref/data/fusion-surrogate-expression.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,627 copying build/lib/oncoref/data/cancer-fusions.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,630 copying build/lib/oncoref/data/rna-protein-calibration-samples.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,632 copying build/lib/oncoref/data/cta-reviewed-evidence.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,635 copying build/lib/oncoref/data/cancer-driver-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,638 copying build/lib/oncoref/data/nuclear-retained-lncrnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,639 copying build/lib/oncoref/data/proteoform-groups-genome.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,642 copying build/lib/oncoref/data/cta-warning-reviews.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,644 copying build/lib/oncoref/data/hemoglobin-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,646 copying build/lib/oncoref/data/rare-cancer-fusion-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,648 copying build/lib/oncoref/data/cancer-entity-driver-spectrum.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,650 copying build/lib/oncoref/data/cancer-ici-source-locator-audit.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,655 copying build/lib/oncoref/data/cancer-incidence-mortality.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,657 copying build/lib/oncoref/data/proteoform-collapse-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,659 copying build/lib/oncoref/data/cancer-ici-response-estimates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,667 copying build/lib/oncoref/data/gse294016-sample-diagnoses.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,669 copying build/lib/oncoref/data/rrna-and-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,672 copying build/lib/oncoref/data/cta-publication-membership.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,726 copying build/lib/oncoref/data/cohort-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,729 copying build/lib/oncoref/data/cancer-response-signatures.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,731 copying build/lib/oncoref/data/fusion-expression-effects.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,733 copying build/lib/oncoref/data/clean-tpm-censored-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,748 copying build/lib/oncoref/data/driver-variant-evidence.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,753 copying build/lib/oncoref/data/rna-protein-hpa-priors.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,766 copying build/lib/oncoref/data/cancer-frameshift-burden.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,768 copying build/lib/oncoref/data/small-noncoding-rnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,773 copying build/lib/oncoref/data/rna-protein-calibrations.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,958 copying build/lib/oncoref/data/cancer-mismatch-repair-statuses.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,960 copying build/lib/oncoref/data/cancer-key-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,964 copying build/lib/oncoref/data/cancer-tmb-source-audit.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-10-19T05:07:26,967 copying build/lib/oncoref/version.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,970 copying build/lib/oncoref/sequence_groups.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,972 copying build/lib/oncoref/therapy_evidence.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,975 copying build/lib/oncoref/coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,977 copying build/lib/oncoref/gene_families.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,980 copying build/lib/oncoref/reference_identity.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,982 copying build/lib/oncoref/plots.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,985 copying build/lib/oncoref/cancer_genes.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,988 copying build/lib/oncoref/peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,990 copying build/lib/oncoref/data_bundle.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,994 copying build/lib/oncoref/doga.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,996 copying build/lib/oncoref/reference_data.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:26,998 copying build/lib/oncoref/cancer_types.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,002 copying build/lib/oncoref/cta_review.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,005 copying build/lib/oncoref/ici.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,009 copying build/lib/oncoref/gene_qc.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,011 copying build/lib/oncoref/_table_io.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,013 copying build/lib/oncoref/species.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,016 copying build/lib/oncoref/data_manifest.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,019 copying build/lib/oncoref/normalization.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,022 copying build/lib/oncoref/apd1.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,024 copying build/lib/oncoref/cta_evidence_schema.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,027 copying build/lib/oncoref/rna_protein.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,030 copying build/lib/oncoref/pfizer_canine_rna.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,032 copying build/lib/oncoref/barkbase.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,034 copying build/lib/oncoref/expression_contract.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,037 copying build/lib/oncoref/samples.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,039 copying build/lib/oncoref/species_assets.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,042 copying build/lib/oncoref/canine.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,044 copying build/lib/oncoref/representative_partitions.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,047 copying build/lib/oncoref/_downloads.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,049 copying build/lib/oncoref/cli.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,052 copying build/lib/oncoref/human.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,054 copying build/lib/oncoref/load_dataset.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,057 copying build/lib/oncoref/expression_provenance_plots.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,059 copying build/lib/oncoref/cta_peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,062 copying build/lib/oncoref/cta_provenance.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,065 copying build/lib/oncoref/drivers.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,068 copying build/lib/oncoref/legacy.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,070 copying build/lib/oncoref/hpa_cancer.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,073 copying build/lib/oncoref/expression_engine.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,076 copying build/lib/oncoref/cohorts.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,079 copying build/lib/oncoref/species_expression.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,081 copying build/lib/oncoref/cta_curation_plots.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,085 copying build/lib/oncoref/_evidence_resolution.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,088 copying build/lib/oncoref/human_cta_snapshot.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,090 copying build/lib/oncoref/tmb.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,093 copying build/lib/oncoref/tumor_references.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,096 copying build/lib/oncoref/antigen_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-10-19T05:07:27,098 running install_egg_info 2026-10-19T05:07:27,108 running egg_info 2026-10-19T05:07:27,114 writing oncoref.egg-info/PKG-INFO 2026-10-19T05:07:27,120 writing dependency_links to oncoref.egg-info/dependency_links.txt 2026-10-19T05:07:27,122 writing entry points to oncoref.egg-info/entry_points.txt 2026-10-19T05:07:27,126 writing requirements to oncoref.egg-info/requires.txt 2026-10-19T05:07:27,127 writing top-level names to oncoref.egg-info/top_level.txt 2026-10-19T05:07:27,158 reading manifest file 'oncoref.egg-info/SOURCES.txt' 2026-10-19T05:07:27,178 reading manifest template 'MANIFEST.in' 2026-10-19T05:07:27,221 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-10-19T05:07:27,223 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-10-19T05:07:27,226 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-10-19T05:07:27,228 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-10-19T05:07:27,230 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-10-19T05:07:27,233 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-10-19T05:07:27,233 adding license file 'LICENSE' 2026-10-19T05:07:27,251 writing manifest file 'oncoref.egg-info/SOURCES.txt' 2026-10-19T05:07:27,253 Copying oncoref.egg-info to build/bdist.linux-armv7l/wheel/./oncoref-1.9.14-py3.11.egg-info 2026-10-19T05:07:27,266 running install_scripts 2026-10-19T05:07:27,281 creating build/bdist.linux-armv7l/wheel/oncoref-1.9.14.dist-info/WHEEL 2026-10-19T05:07:27,284 creating '/tmp/pip-wheel-ma07yk96/.tmp-4ue1t90p/oncoref-1.9.14-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-10-19T05:07:27,290 adding 'oncoref/__init__.py' 2026-10-19T05:07:27,292 adding 'oncoref/_downloads.py' 2026-10-19T05:07:27,294 adding 'oncoref/_evidence_resolution.py' 2026-10-19T05:07:27,296 adding 'oncoref/_reference_sources.py' 2026-10-19T05:07:27,298 adding 'oncoref/_table_io.py' 2026-10-19T05:07:27,300 adding 'oncoref/antigen_coverage.py' 2026-10-19T05:07:27,302 adding 'oncoref/apd1.py' 2026-10-19T05:07:27,304 adding 'oncoref/barkbase.py' 2026-10-19T05:07:27,305 adding 'oncoref/bgee_srp009687.py' 2026-10-19T05:07:27,307 adding 'oncoref/bgee_srp181218.py' 2026-10-19T05:07:27,308 adding 'oncoref/cancer_genes.py' 2026-10-19T05:07:27,310 adding 'oncoref/cancer_ontology.py' 2026-10-19T05:07:27,322 adding 'oncoref/cancer_types.py' 2026-10-19T05:07:27,324 adding 'oncoref/canine.py' 2026-10-19T05:07:27,326 adding 'oncoref/catalog.py' 2026-10-19T05:07:27,331 adding 'oncoref/cli.py' 2026-10-19T05:07:27,332 adding 'oncoref/cohorts.py' 2026-10-19T05:07:27,337 adding 'oncoref/coverage.py' 2026-10-19T05:07:27,341 adding 'oncoref/cta.py' 2026-10-19T05:07:27,343 adding 'oncoref/cta_coverage.py' 2026-10-19T05:07:27,347 adding 'oncoref/cta_curation_plots.py' 2026-10-19T05:07:27,349 adding 'oncoref/cta_evidence_adapters.py' 2026-10-19T05:07:27,351 adding 'oncoref/cta_evidence_model.py' 2026-10-19T05:07:27,353 adding 'oncoref/cta_evidence_schema.py' 2026-10-19T05:07:27,354 adding 'oncoref/cta_gate_audit.py' 2026-10-19T05:07:27,357 adding 'oncoref/cta_landscape.py' 2026-10-19T05:07:27,359 adding 'oncoref/cta_peptides.py' 2026-10-19T05:07:27,361 adding 'oncoref/cta_provenance.py' 2026-10-19T05:07:27,365 adding 'oncoref/cta_regen.py' 2026-10-19T05:07:27,370 adding 'oncoref/cta_review.py' 2026-10-19T05:07:27,373 adding 'oncoref/cta_sources.py' 2026-10-19T05:07:27,375 adding 'oncoref/cta_tissues.py' 2026-10-19T05:07:27,382 adding 'oncoref/data_bundle.py' 2026-10-19T05:07:27,385 adding 'oncoref/data_manifest.py' 2026-10-19T05:07:27,386 adding 'oncoref/doga.py' 2026-10-19T05:07:27,389 adding 'oncoref/drivers.py' 2026-10-19T05:07:27,420 adding 'oncoref/expression.py' 2026-10-19T05:07:27,447 adding 'oncoref/expression_builders.py' 2026-10-19T05:07:27,450 adding 'oncoref/expression_contract.py' 2026-10-19T05:07:27,454 adding 'oncoref/expression_engine.py' 2026-10-19T05:07:27,456 adding 'oncoref/expression_provenance_plots.py' 2026-10-19T05:07:27,458 adding 'oncoref/expression_registry.py' 2026-10-19T05:07:27,471 adding 'oncoref/expression_source_adapters.py' 2026-10-19T05:07:27,474 adding 'oncoref/figure_output.py' 2026-10-19T05:07:27,476 adding 'oncoref/figure_style.py' 2026-10-19T05:07:27,479 adding 'oncoref/fusions.py' 2026-10-19T05:07:27,481 adding 'oncoref/gene_families.py' 2026-10-19T05:07:27,483 adding 'oncoref/gene_identity.py' 2026-10-19T05:07:27,486 adding 'oncoref/gene_ids.py' 2026-10-19T05:07:27,488 adding 'oncoref/gene_qc.py' 2026-10-19T05:07:27,490 adding 'oncoref/genome.py' 2026-10-19T05:07:27,491 adding 'oncoref/gse304066.py' 2026-10-19T05:07:27,494 adding 'oncoref/hpa.py' 2026-10-19T05:07:27,496 adding 'oncoref/hpa_cancer.py' 2026-10-19T05:07:27,497 adding 'oncoref/human.py' 2026-10-19T05:07:27,499 adding 'oncoref/human_cta_snapshot.py' 2026-10-19T05:07:27,500 adding 'oncoref/human_protein_atlas.py' 2026-10-19T05:07:27,507 adding 'oncoref/ici.py' 2026-10-19T05:07:27,509 adding 'oncoref/ici_response.py' 2026-10-19T05:07:27,510 adding 'oncoref/incidence.py' 2026-10-19T05:07:27,512 adding 'oncoref/legacy.py' 2026-10-19T05:07:27,514 adding 'oncoref/load_dataset.py' 2026-10-19T05:07:27,515 adding 'oncoref/mouse.py' 2026-10-19T05:07:27,521 adding 'oncoref/normalization.py' 2026-10-19T05:07:27,523 adding 'oncoref/peptides.py' 2026-10-19T05:07:27,524 adding 'oncoref/pfizer_canine_protein.py' 2026-10-19T05:07:27,526 adding 'oncoref/pfizer_canine_rna.py' 2026-10-19T05:07:27,535 adding 'oncoref/plots.py' 2026-10-19T05:07:27,538 adding 'oncoref/proteoforms.py' 2026-10-19T05:07:27,541 adding 'oncoref/reference_data.py' 2026-10-19T05:07:27,542 adding 'oncoref/reference_identity.py' 2026-10-19T05:07:27,544 adding 'oncoref/representative_partitions.py' 2026-10-19T05:07:27,546 adding 'oncoref/response_signatures.py' 2026-10-19T05:07:27,549 adding 'oncoref/rna_protein.py' 2026-10-19T05:07:27,550 adding 'oncoref/samples.py' 2026-10-19T05:07:27,552 adding 'oncoref/sequence_groups.py' 2026-10-19T05:07:27,555 adding 'oncoref/source_matrices.py' 2026-10-19T05:07:27,557 adding 'oncoref/species.py' 2026-10-19T05:07:27,559 adding 'oncoref/species_antigens.py' 2026-10-19T05:07:27,562 adding 'oncoref/species_assets.py' 2026-10-19T05:07:27,564 adding 'oncoref/species_expression.py' 2026-10-19T05:07:27,566 adding 'oncoref/therapy_evidence.py' 2026-10-19T05:07:27,569 adding 'oncoref/tmb.py' 2026-10-19T05:07:27,571 adding 'oncoref/tumor_references.py' 2026-10-19T05:07:27,573 adding 'oncoref/version.py' 2026-10-19T05:07:27,578 adding 'oncoref/data/cancer-apd1-response.csv' 2026-10-19T05:07:27,579 adding 'oncoref/data/cancer-code-burden-map.csv' 2026-10-19T05:07:27,581 adding 'oncoref/data/cancer-cohort-aggregates.csv' 2026-10-19T05:07:27,586 adding 'oncoref/data/cancer-driver-genes.csv' 2026-10-19T05:07:27,588 adding 'oncoref/data/cancer-driver-variants.csv' 2026-10-19T05:07:27,590 adding 'oncoref/data/cancer-entity-driver-spectrum.csv' 2026-10-19T05:07:27,594 adding 'oncoref/data/cancer-expression-source-candidates.csv' 2026-10-19T05:07:27,596 adding 'oncoref/data/cancer-frameshift-burden.csv' 2026-10-19T05:07:27,599 adding 'oncoref/data/cancer-fusion-citation-audit.csv' 2026-10-19T05:07:27,603 adding 'oncoref/data/cancer-fusions.csv' 2026-10-19T05:07:27,628 adding 'oncoref/data/cancer-ici-response-estimates.csv' 2026-10-19T05:07:27,634 adding 'oncoref/data/cancer-ici-response.csv' 2026-10-19T05:07:27,642 adding 'oncoref/data/cancer-ici-source-locator-audit.csv' 2026-10-19T05:07:27,644 adding 'oncoref/data/cancer-incidence-mortality.csv' 2026-10-19T05:07:27,659 adding 'oncoref/data/cancer-key-gene-citation-audit.csv' 2026-10-19T05:07:27,673 adding 'oncoref/data/cancer-key-genes.csv' 2026-10-19T05:07:27,675 adding 'oncoref/data/cancer-lineage-group-overrides.csv' 2026-10-19T05:07:27,677 adding 'oncoref/data/cancer-lineage-groups.csv' 2026-10-19T05:07:27,678 adding 'oncoref/data/cancer-mismatch-repair-statuses.csv' 2026-10-19T05:07:27,680 adding 'oncoref/data/cancer-normal-tissue-map.csv' 2026-10-19T05:07:27,688 adding 'oncoref/data/cancer-reference-expression-availability.csv' 2026-10-19T05:07:27,720 adding 'oncoref/data/cancer-reference-expression-samples.csv.gz' 2026-10-19T05:07:27,728 adding 'oncoref/data/cancer-reference-sample-molecular-provenance.csv' 2026-10-19T05:07:27,731 adding 'oncoref/data/cancer-response-signatures.csv' 2026-10-19T05:07:27,734 adding 'oncoref/data/cancer-subtype-groupings.csv' 2026-10-19T05:07:27,811 adding 'oncoref/data/cancer-testis-antigens-extended.csv' 2026-10-19T05:07:27,894 adding 'oncoref/data/cancer-testis-antigens.csv' 2026-10-19T05:07:27,906 adding 'oncoref/data/cancer-tmb-source-audit.csv' 2026-10-19T05:07:27,911 adding 'oncoref/data/cancer-tmb.csv' 2026-10-19T05:07:27,913 adding 'oncoref/data/cancer-type-genes.csv' 2026-10-19T05:07:27,919 adding 'oncoref/data/cancer-type-registry.csv' 2026-10-19T05:07:27,921 adding 'oncoref/data/cancer-viral-antigens.csv' 2026-10-19T05:07:27,923 adding 'oncoref/data/cancer-who-soft-tissue-bone-audit.csv' 2026-10-19T05:07:27,976 adding 'oncoref/data/canonical-gene-space.csv.gz' 2026-10-19T05:07:27,981 adding 'oncoref/data/cdna-identical-gene-groups.csv' 2026-10-19T05:07:27,991 adding 'oncoref/data/censored-gene-reference-tpm.csv' 2026-10-19T05:07:27,993 adding 'oncoref/data/clean-tpm-biological-housekeeping-genes.csv' 2026-10-19T05:07:28,028 adding 'oncoref/data/clean-tpm-censored-genes.csv' 2026-10-19T05:07:28,036 adding 'oncoref/data/cohort-registry.csv' 2026-10-19T05:07:28,038 adding 'oncoref/data/cta-candidate-references.csv' 2026-10-19T05:07:28,039 adding 'oncoref/data/cta-clinical-targets.csv' 2026-10-19T05:07:28,041 adding 'oncoref/data/cta-gene-publication-evidence.csv' 2026-10-19T05:07:28,042 adding 'oncoref/data/cta-ihc-unreliable.csv' 2026-10-19T05:07:28,142 adding 'oncoref/data/cta-publication-membership.csv' 2026-10-19T05:07:28,160 adding 'oncoref/data/cta-publication-sources.csv' 2026-10-19T05:07:28,162 adding 'oncoref/data/cta-reviewed-evidence.csv' 2026-10-19T05:07:28,163 adding 'oncoref/data/cta-specificity-audit.csv' 2026-10-19T05:07:28,164 adding 'oncoref/data/cta-warning-reviews.csv' 2026-10-19T05:07:28,166 adding 'oncoref/data/degenerate-subtype-pairs.csv' 2026-10-19T05:07:28,167 adding 'oncoref/data/disease-state-rules.csv' 2026-10-19T05:07:28,176 adding 'oncoref/data/driver-gene-evidence.csv' 2026-10-19T05:07:28,184 adding 'oncoref/data/driver-variant-evidence.csv' 2026-10-19T05:07:28,212 adding 'oncoref/data/ensembl-id-aliases.csv' 2026-10-19T05:07:28,226 adding 'oncoref/data/expression-artifact-gene-universe-deltas.csv' 2026-10-19T05:07:28,238 adding 'oncoref/data/expression_sources.yaml' 2026-10-19T05:07:28,240 adding 'oncoref/data/extra-tx-mappings.csv' 2026-10-19T05:07:28,241 adding 'oncoref/data/family-burden-map.csv' 2026-10-19T05:07:28,242 adding 'oncoref/data/fusion-expression-effects.csv' 2026-10-19T05:07:28,244 adding 'oncoref/data/fusion-surrogate-expression.csv' 2026-10-19T05:07:28,246 adding 'oncoref/data/gse294016-sample-diagnoses.csv' 2026-10-19T05:07:28,247 adding 'oncoref/data/hemoglobin-genes.csv' 2026-10-19T05:07:28,249 adding 'oncoref/data/histone-genes.csv' 2026-10-19T05:07:28,250 adding 'oncoref/data/housekeeping-genes.csv' 2026-10-19T05:07:28,251 adding 'oncoref/data/hpa-cancer-crosswalk.csv' 2026-10-19T05:07:28,253 adding 'oncoref/data/hpa-cancer-rna-cohorts.csv' 2026-10-19T05:07:28,255 adding 'oncoref/data/hpa-cancer-sources.json' 2026-10-19T05:07:28,256 adding 'oncoref/data/hpa-safety-tissue-map.csv' 2026-10-19T05:07:28,257 adding 'oncoref/data/legacy-dataset-dispositions.csv' 2026-10-19T05:07:28,259 adding 'oncoref/data/mitochondrial-genes.csv' 2026-10-19T05:07:28,260 adding 'oncoref/data/narrative-gene-sets.csv' 2026-10-19T05:07:28,362 adding 'oncoref/data/ncbi-entrez-gene-mappings.csv.gz' 2026-10-19T05:07:28,409 adding 'oncoref/data/ncbi-symbol-synonyms.csv.gz' 2026-10-19T05:07:28,412 adding 'oncoref/data/nuclear-retained-lncrnas.csv' 2026-10-19T05:07:28,414 adding 'oncoref/data/numt-pseudogenes.csv' 2026-10-19T05:07:28,416 adding 'oncoref/data/proteoform-collapse-overrides.csv' 2026-10-19T05:07:28,418 adding 'oncoref/data/proteoform-groups-genome.csv' 2026-10-19T05:07:28,420 adding 'oncoref/data/proteoform-groups.csv' 2026-10-19T05:07:28,422 adding 'oncoref/data/rare-cancer-fusion-rules.csv' 2026-10-19T05:07:28,423 adding 'oncoref/data/representative-source-adjudications.csv' 2026-10-19T05:07:28,425 adding 'oncoref/data/ribosomal-protein-genes.csv' 2026-10-19T05:07:28,431 adding 'oncoref/data/ribosomal-protein-pseudogenes.csv' 2026-10-19T05:07:28,433 adding 'oncoref/data/rna-protein-calibration-samples.csv.gz' 2026-10-19T05:07:28,435 adding 'oncoref/data/rna-protein-calibration-sources.csv' 2026-10-19T05:07:29,602 adding 'oncoref/data/rna-protein-calibrations.csv.gz' 2026-10-19T05:07:29,665 adding 'oncoref/data/rna-protein-hpa-prior-sources.csv' 2026-10-19T05:07:29,754 adding 'oncoref/data/rna-protein-hpa-priors.csv.gz' 2026-10-19T05:07:29,761 adding 'oncoref/data/rrna-and-pseudogenes.csv' 2026-10-19T05:07:29,779 adding 'oncoref/data/small-noncoding-rnas.csv' 2026-10-19T05:07:29,782 adding 'oncoref/data/source-matrices.csv' 2026-10-19T05:07:29,783 adding 'oncoref/data/therapy-benefit-toxicity-evidence.csv' 2026-10-19T05:07:29,785 adding 'oncoref/data/tissue-burden-map.csv' 2026-10-19T05:07:29,788 adding 'oncoref/data/species/dog/assets.json' 2026-10-19T05:07:29,794 adding 'oncoref/data/species/dog/barkbase-samples.json' 2026-10-19T05:07:29,797 adding 'oncoref/data/species/dog/bgee-srp009687-samples.json' 2026-10-19T05:07:29,803 adding 'oncoref/data/species/dog/bgee-srp181218-samples.json' 2026-10-19T05:07:29,812 adding 'oncoref/data/species/dog/cta-evidence.json' 2026-10-19T05:07:29,815 adding 'oncoref/data/species/dog/expression_sources.yaml' 2026-10-19T05:07:29,817 adding 'oncoref/data/species/dog/lineage_overlaps.json' 2026-10-19T05:07:29,820 adding 'oncoref/data/species/dog/pfizer-dog-protein-samples.json' 2026-10-19T05:07:29,823 adding 'oncoref-1.9.14.dist-info/licenses/LICENSE' 2026-10-19T05:07:29,826 adding 'oncoref-1.9.14.dist-info/METADATA' 2026-10-19T05:07:29,827 adding 'oncoref-1.9.14.dist-info/WHEEL' 2026-10-19T05:07:29,828 adding 'oncoref-1.9.14.dist-info/entry_points.txt' 2026-10-19T05:07:29,829 adding 'oncoref-1.9.14.dist-info/top_level.txt' 2026-10-19T05:07:29,832 adding 'oncoref-1.9.14.dist-info/RECORD' 2026-10-19T05:07:30,119 removing build/bdist.linux-armv7l/wheel 2026-10-19T05:07:30,264 Building wheel for oncoref (pyproject.toml): finished with status 'done' 2026-10-19T05:07:30,606 Created wheel for oncoref: filename=oncoref-1.9.14-py3-none-any.whl size=14217237 sha256=15a23500de897db77370f42fb01282b4f20cf99a19aa9c6a96fa55939e4b3e04 2026-10-19T05:07:30,607 Stored in directory: /tmp/pip-ephem-wheel-cache-odttlzy5/wheels/78/1f/81/154bce9245e7cd4a3f0daac6e2a4d955eb047345180833b77f 2026-10-19T05:07:30,630 Successfully built oncoref 2026-10-19T05:07:30,976 Removed build tracker: '/tmp/pip-build-tracker-nw0xh8a2'