2026-07-01T03:21:14,496 Created temporary directory: /tmp/pip-ephem-wheel-cache-ny95srsb 2026-07-01T03:21:14,498 Created temporary directory: /tmp/pip-build-tracker-pfs2idqs 2026-07-01T03:21:14,499 Initialized build tracking at /tmp/pip-build-tracker-pfs2idqs 2026-07-01T03:21:14,499 Created build tracker: /tmp/pip-build-tracker-pfs2idqs 2026-07-01T03:21:14,499 Entered build tracker: /tmp/pip-build-tracker-pfs2idqs 2026-07-01T03:21:14,500 Created temporary directory: /tmp/pip-wheel-8ctgkr83 2026-07-01T03:21:14,503 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 2026-07-01T03:21:14,506 Created temporary directory: /tmp/pip-ephem-wheel-cache-jbmd0459 2026-07-01T03:21:14,528 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-07-01T03:21:14,531 2 location(s) to search for versions of oncoref: 2026-07-01T03:21:14,531 * https://pypi.org/simple/oncoref/ 2026-07-01T03:21:14,531 * https://www.piwheels.org/simple/oncoref/ 2026-07-01T03:21:14,532 Fetching project page and analyzing links: https://pypi.org/simple/oncoref/ 2026-07-01T03:21:14,533 Getting page https://pypi.org/simple/oncoref/ 2026-07-01T03:21:14,534 Found index url https://pypi.org/simple 2026-07-01T03:21:14,685 Fetched page https://pypi.org/simple/oncoref/ as application/vnd.pypi.simple.v1+json 2026-07-01T03:21:14,701 Skipping link: No binaries permitted for oncoref: 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https://www.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) 2026-07-01T03:21:14,990 Skipping link: No binaries permitted for oncoref: https://www.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) 2026-07-01T03:21:14,991 Skipping link: No binaries permitted for oncoref: https://www.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) 2026-07-01T03:21:14,991 Skipping link: No binaries permitted for oncoref: https://www.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) 2026-07-01T03:21:14,992 Skipping link: No binaries permitted for oncoref: https://www.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) 2026-07-01T03:21:14,992 Skipping link: No binaries permitted for oncoref: https://www.piwheels.org/simple/oncoref/oncoref-1.8.4-py3-none-any.whl#sha256=d649c7a749c099fe67033ecbdbafe4bf8bcd93bd71d9830ce2a6127a1c093cad (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-07-01T03:21:14,993 Skipping link: No binaries permitted for oncoref: https://www.piwheels.org/simple/oncoref/oncoref-1.8.3-py3-none-any.whl#sha256=bf75676ac99a0d1c144249b8cf320ac292b65716c9ffdc50ad27b55db1153821 (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-07-01T03:21:14,993 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) 2026-07-01T03:21:14,994 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) 2026-07-01T03:21:14,995 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) 2026-07-01T03:21:14,995 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) 2026-07-01T03:21:14,996 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) 2026-07-01T03:21:14,996 Skipping link: not a file: https://www.piwheels.org/simple/oncoref/ 2026-07-01T03:21:14,997 Skipping link: not a file: https://pypi.org/simple/oncoref/ 2026-07-01T03:21:15,021 Given no hashes to check 1 links for project 'oncoref': discarding no candidates 2026-07-01T03:21:15,038 Collecting oncoref==1.8.39 2026-07-01T03:21:15,040 Created temporary directory: /tmp/pip-unpack-tuut_5mq 2026-07-01T03:21:15,276 Downloading oncoref-1.8.39.tar.gz (1.8 MB) 2026-07-01T03:21:16,008 Added oncoref==1.8.39 from https://files.pythonhosted.org/packages/12/4e/6bb3e440d16d94f6fc3fc6fb9dd2410a00c521d4d47b0fc712122a4b8c4b/oncoref-1.8.39.tar.gz to build tracker '/tmp/pip-build-tracker-pfs2idqs' 2026-07-01T03:21:16,015 Created temporary directory: /tmp/pip-build-env-8rsct6lq 2026-07-01T03:21:16,019 Installing build dependencies: started 2026-07-01T03:21:16,021 Running command pip subprocess to install build dependencies 2026-07-01T03:21:17,182 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-07-01T03:21:17,658 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 2026-07-01T03:21:17,681 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-07-01T03:21:19,462 Collecting setuptools>=61.0 2026-07-01T03:21:19,463 Obtaining dependency information for setuptools>=61.0 from https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl.metadata 2026-07-01T03:21:19,478 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl.metadata (6.5 kB) 2026-07-01T03:21:19,711 Collecting wheel 2026-07-01T03:21:19,712 Obtaining dependency information for wheel from https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata 2026-07-01T03:21:19,726 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB) 2026-07-01T03:21:19,907 Collecting packaging>=24.0 2026-07-01T03:21:19,908 Obtaining dependency information for packaging>=24.0 from https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata 2026-07-01T03:21:19,921 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata (3.5 kB) 2026-07-01T03:21:20,114 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB) 2026-07-01T03:21:20,134 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB) 2026-07-01T03:21:20,224 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-07-01T03:21:20,259 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB) 2026-07-01T03:21:20,285 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB) 2026-07-01T03:21:20,386 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-07-01T03:21:23,128 Installing collected packages: setuptools, packaging, wheel 2026-07-01T03:21:26,544 Creating /tmp/pip-build-env-8rsct6lq/overlay/local/bin 2026-07-01T03:21:26,546 changing mode of /tmp/pip-build-env-8rsct6lq/overlay/local/bin/wheel to 755 2026-07-01T03:21:26,566 Successfully installed packaging-26.2 setuptools-82.0.1 wheel-0.47.0 2026-07-01T03:21:26,849 Installing build dependencies: finished with status 'done' 2026-07-01T03:21:26,855 Getting requirements to build wheel: started 2026-07-01T03:21:26,857 Running command Getting requirements to build wheel 2026-07-01T03:21:27,550 running egg_info 2026-07-01T03:21:27,557 writing oncoref.egg-info/PKG-INFO 2026-07-01T03:21:27,565 writing dependency_links to oncoref.egg-info/dependency_links.txt 2026-07-01T03:21:27,567 writing entry points to oncoref.egg-info/entry_points.txt 2026-07-01T03:21:27,569 writing requirements to oncoref.egg-info/requires.txt 2026-07-01T03:21:27,570 writing top-level names to oncoref.egg-info/top_level.txt 2026-07-01T03:21:27,605 reading manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-01T03:21:27,614 reading manifest template 'MANIFEST.in' 2026-07-01T03:21:27,616 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-07-01T03:21:27,617 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-07-01T03:21:27,618 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-07-01T03:21:27,619 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-07-01T03:21:27,620 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-07-01T03:21:27,621 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-07-01T03:21:27,622 adding license file 'LICENSE' 2026-07-01T03:21:27,630 writing manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-01T03:21:27,728 Getting requirements to build wheel: finished with status 'done' 2026-07-01T03:21:27,732 Created temporary directory: /tmp/pip-modern-metadata-rdnu5947 2026-07-01T03:21:27,734 Preparing metadata (pyproject.toml): started 2026-07-01T03:21:27,736 Running command Preparing metadata (pyproject.toml) 2026-07-01T03:21:28,373 running dist_info 2026-07-01T03:21:28,383 creating /tmp/pip-modern-metadata-rdnu5947/oncoref.egg-info 2026-07-01T03:21:28,385 writing /tmp/pip-modern-metadata-rdnu5947/oncoref.egg-info/PKG-INFO 2026-07-01T03:21:28,390 writing dependency_links to /tmp/pip-modern-metadata-rdnu5947/oncoref.egg-info/dependency_links.txt 2026-07-01T03:21:28,392 writing entry points to /tmp/pip-modern-metadata-rdnu5947/oncoref.egg-info/entry_points.txt 2026-07-01T03:21:28,395 writing requirements to /tmp/pip-modern-metadata-rdnu5947/oncoref.egg-info/requires.txt 2026-07-01T03:21:28,396 writing top-level names to /tmp/pip-modern-metadata-rdnu5947/oncoref.egg-info/top_level.txt 2026-07-01T03:21:28,397 writing manifest file '/tmp/pip-modern-metadata-rdnu5947/oncoref.egg-info/SOURCES.txt' 2026-07-01T03:21:28,438 reading manifest file '/tmp/pip-modern-metadata-rdnu5947/oncoref.egg-info/SOURCES.txt' 2026-07-01T03:21:28,440 reading manifest template 'MANIFEST.in' 2026-07-01T03:21:28,441 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-07-01T03:21:28,442 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-07-01T03:21:28,444 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-07-01T03:21:28,445 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-07-01T03:21:28,445 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-07-01T03:21:28,446 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-07-01T03:21:28,447 adding license file 'LICENSE' 2026-07-01T03:21:28,454 writing manifest file '/tmp/pip-modern-metadata-rdnu5947/oncoref.egg-info/SOURCES.txt' 2026-07-01T03:21:28,456 creating '/tmp/pip-modern-metadata-rdnu5947/oncoref-1.8.39.dist-info' 2026-07-01T03:21:28,583 Preparing metadata (pyproject.toml): finished with status 'done' 2026-07-01T03:21:28,588 Source in /tmp/pip-wheel-8ctgkr83/oncoref_d530f180a7264367985f4bd1543fa811 has version 1.8.39, which satisfies requirement oncoref==1.8.39 from https://files.pythonhosted.org/packages/12/4e/6bb3e440d16d94f6fc3fc6fb9dd2410a00c521d4d47b0fc712122a4b8c4b/oncoref-1.8.39.tar.gz 2026-07-01T03:21:28,589 Removed oncoref==1.8.39 from https://files.pythonhosted.org/packages/12/4e/6bb3e440d16d94f6fc3fc6fb9dd2410a00c521d4d47b0fc712122a4b8c4b/oncoref-1.8.39.tar.gz from build tracker '/tmp/pip-build-tracker-pfs2idqs' 2026-07-01T03:21:28,595 Created temporary directory: /tmp/pip-unpack-mjyj7ak1 2026-07-01T03:21:28,596 Building wheels for collected packages: oncoref 2026-07-01T03:21:28,600 Created temporary directory: /tmp/pip-wheel-s2jgsnq4 2026-07-01T03:21:28,601 Destination directory: /tmp/pip-wheel-s2jgsnq4 2026-07-01T03:21:28,603 Building wheel for oncoref (pyproject.toml): started 2026-07-01T03:21:28,604 Running command Building wheel for oncoref (pyproject.toml) 2026-07-01T03:21:29,252 running bdist_wheel 2026-07-01T03:21:29,269 running build 2026-07-01T03:21:29,270 running build_py 2026-07-01T03:21:29,277 creating build/lib/oncoref 2026-07-01T03:21:29,279 copying oncoref/antigen_coverage.py -> build/lib/oncoref 2026-07-01T03:21:29,281 copying oncoref/samples.py -> build/lib/oncoref 2026-07-01T03:21:29,283 copying oncoref/coverage.py -> build/lib/oncoref 2026-07-01T03:21:29,285 copying oncoref/plots.py -> build/lib/oncoref 2026-07-01T03:21:29,288 copying oncoref/genome.py -> build/lib/oncoref 2026-07-01T03:21:29,291 copying oncoref/ici_response.py -> build/lib/oncoref 2026-07-01T03:21:29,293 copying oncoref/version.py -> build/lib/oncoref 2026-07-01T03:21:29,295 copying oncoref/cta_curation_plots.py -> build/lib/oncoref 2026-07-01T03:21:29,297 copying oncoref/cancer_types.py -> build/lib/oncoref 2026-07-01T03:21:29,300 copying oncoref/ici.py -> build/lib/oncoref 2026-07-01T03:21:29,303 copying oncoref/tmb.py -> build/lib/oncoref 2026-07-01T03:21:29,305 copying oncoref/expression_registry.py -> build/lib/oncoref 2026-07-01T03:21:29,307 copying oncoref/apd1.py -> build/lib/oncoref 2026-07-01T03:21:29,309 copying oncoref/expression.py -> build/lib/oncoref 2026-07-01T03:21:29,313 copying oncoref/cta.py -> build/lib/oncoref 2026-07-01T03:21:29,315 copying oncoref/expression_engine.py -> build/lib/oncoref 2026-07-01T03:21:29,318 copying oncoref/fusions.py -> build/lib/oncoref 2026-07-01T03:21:29,320 copying oncoref/cohorts.py -> build/lib/oncoref 2026-07-01T03:21:29,322 copying oncoref/data_manifest.py -> build/lib/oncoref 2026-07-01T03:21:29,325 copying oncoref/catalog.py -> build/lib/oncoref 2026-07-01T03:21:29,328 copying oncoref/source_matrices.py -> build/lib/oncoref 2026-07-01T03:21:29,330 copying oncoref/cli.py -> build/lib/oncoref 2026-07-01T03:21:29,333 copying oncoref/gene_ids.py -> build/lib/oncoref 2026-07-01T03:21:29,335 copying oncoref/hpa.py -> build/lib/oncoref 2026-07-01T03:21:29,337 copying oncoref/cta_peptides.py -> build/lib/oncoref 2026-07-01T03:21:29,339 copying oncoref/__init__.py -> build/lib/oncoref 2026-07-01T03:21:29,341 copying oncoref/load_dataset.py -> build/lib/oncoref 2026-07-01T03:21:29,343 copying oncoref/gene_qc.py -> build/lib/oncoref 2026-07-01T03:21:29,346 copying oncoref/proteoforms.py -> build/lib/oncoref 2026-07-01T03:21:29,348 copying oncoref/incidence.py -> build/lib/oncoref 2026-07-01T03:21:29,350 copying oncoref/cancer_genes.py -> build/lib/oncoref 2026-07-01T03:21:29,352 copying oncoref/reference_data.py -> build/lib/oncoref 2026-07-01T03:21:29,355 copying oncoref/peptides.py -> build/lib/oncoref 2026-07-01T03:21:29,357 copying oncoref/cancer_ontology.py -> build/lib/oncoref 2026-07-01T03:21:29,359 copying oncoref/data_bundle.py -> build/lib/oncoref 2026-07-01T03:21:29,361 copying oncoref/response_signatures.py -> build/lib/oncoref 2026-07-01T03:21:29,363 copying oncoref/gene_families.py -> build/lib/oncoref 2026-07-01T03:21:29,366 copying oncoref/normalization.py -> build/lib/oncoref 2026-07-01T03:21:29,368 copying oncoref/cta_coverage.py -> build/lib/oncoref 2026-07-01T03:21:29,370 copying oncoref/cta_tissues.py -> build/lib/oncoref 2026-07-01T03:21:29,372 copying oncoref/expression_builders.py -> build/lib/oncoref 2026-07-01T03:21:29,375 copying oncoref/cta_regen.py -> build/lib/oncoref 2026-07-01T03:21:29,389 creating build/lib/oncoref/data 2026-07-01T03:21:29,390 copying oncoref/data/clean-tpm-biological-housekeeping-genes.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,393 copying oncoref/data/clean-tpm-censored-genes.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,397 copying oncoref/data/cancer-lineage-groups.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,399 copying oncoref/data/proteoform-collapse-overrides.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,401 copying oncoref/data/cancer-driver-genes.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,404 copying oncoref/data/cancer-response-signatures.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,407 copying oncoref/data/cancer-normal-tissue-map.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,409 copying oncoref/data/cancer-ici-response.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,412 copying oncoref/data/cdna-identical-gene-groups.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,414 copying oncoref/data/ribosomal-protein-pseudogenes.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,417 copying oncoref/data/narrative-gene-sets.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,420 copying oncoref/data/cancer-key-genes.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,425 copying oncoref/data/cancer-type-registry.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,428 copying oncoref/data/degenerate-subtype-pairs.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,431 copying oncoref/data/histone-genes.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,433 copying oncoref/data/family-burden-map.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,435 copying oncoref/data/hemoglobin-genes.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,437 copying oncoref/data/cancer-apd1-response.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,440 copying oncoref/data/cancer-code-burden-map.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,442 copying oncoref/data/cancer-testis-antigens.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,449 copying oncoref/data/cancer-cohort-aggregates.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,451 copying oncoref/data/cancer-tmb.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,454 copying oncoref/data/proteoform-groups.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,456 copying oncoref/data/numt-pseudogenes.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,459 copying oncoref/data/cancer-ici-response-estimates.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,468 copying oncoref/data/cancer-frameshift-burden.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,470 copying oncoref/data/cta-ihc-unreliable.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,473 copying oncoref/data/cta-candidate-references.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,475 copying oncoref/data/cohort-registry.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,478 copying oncoref/data/tissue-burden-map.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,480 copying oncoref/data/cancer-expression-source-candidates.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,483 copying oncoref/data/ensembl-id-aliases.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,491 copying oncoref/data/ribosomal-protein-genes.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,494 copying oncoref/data/expression-artifact-gene-universe-deltas.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,502 copying oncoref/data/rare-cancer-fusion-rules.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,504 copying oncoref/data/extra-tx-mappings.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,507 copying oncoref/data/fusion-expression-effects.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,509 copying oncoref/data/mitochondrial-genes.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,511 copying oncoref/data/small-noncoding-rnas.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,516 copying oncoref/data/cancer-lineage-group-overrides.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,518 copying oncoref/data/proteoform-groups-genome.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,521 copying oncoref/data/nuclear-retained-lncrnas.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,523 copying oncoref/data/cancer-type-genes.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,525 copying oncoref/data/disease-state-rules.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,527 copying oncoref/data/housekeeping-genes.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,529 copying oncoref/data/cancer-viral-antigens.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,532 copying oncoref/data/cancer-incidence-mortality.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,534 copying oncoref/data/fusion-surrogate-expression.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,536 copying oncoref/data/rrna-and-pseudogenes.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,539 copying oncoref/data/cancer-driver-variants.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,541 copying oncoref/data/censored-gene-reference-tpm.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,544 copying oncoref/data/cancer-subtype-groupings.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,546 copying oncoref/data/cancer-fusions.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,549 copying oncoref/data/source-matrices.csv -> build/lib/oncoref/data 2026-07-01T03:21:29,551 copying oncoref/data/cancer-reference-expression-samples.csv.gz -> build/lib/oncoref/data 2026-07-01T03:21:29,557 copying oncoref/data/canonical-gene-space.csv.gz -> build/lib/oncoref/data 2026-07-01T03:21:29,570 copying oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/lib/oncoref/data 2026-07-01T03:21:29,578 copying oncoref/data/expression_sources.yaml -> build/lib/oncoref/data 2026-07-01T03:21:29,592 installing to build/bdist.linux-armv7l/wheel 2026-07-01T03:21:29,593 running install 2026-07-01T03:21:29,616 running install_lib 2026-07-01T03:21:29,622 creating build/bdist.linux-armv7l/wheel 2026-07-01T03:21:29,624 creating build/bdist.linux-armv7l/wheel/oncoref 2026-07-01T03:21:29,626 copying build/lib/oncoref/antigen_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,628 copying build/lib/oncoref/samples.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,629 copying build/lib/oncoref/coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,632 copying build/lib/oncoref/plots.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,635 copying build/lib/oncoref/genome.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,637 copying build/lib/oncoref/ici_response.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,639 copying build/lib/oncoref/version.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,642 copying build/lib/oncoref/cta_curation_plots.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,644 copying build/lib/oncoref/cancer_types.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,648 copying build/lib/oncoref/ici.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,651 copying build/lib/oncoref/tmb.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,654 copying build/lib/oncoref/expression_registry.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,656 copying build/lib/oncoref/apd1.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,659 copying build/lib/oncoref/expression.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,663 copying build/lib/oncoref/cta.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,666 copying build/lib/oncoref/expression_engine.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,669 copying build/lib/oncoref/fusions.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,672 copying build/lib/oncoref/cohorts.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,674 copying build/lib/oncoref/data_manifest.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,677 copying build/lib/oncoref/catalog.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,680 copying build/lib/oncoref/source_matrices.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,684 copying build/lib/oncoref/cli.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,691 copying build/lib/oncoref/gene_ids.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,733 copying build/lib/oncoref/hpa.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,735 copying build/lib/oncoref/cta_peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,737 copying build/lib/oncoref/__init__.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,739 copying build/lib/oncoref/load_dataset.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,742 copying build/lib/oncoref/gene_qc.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,744 copying build/lib/oncoref/proteoforms.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,746 copying build/lib/oncoref/incidence.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,748 copying build/lib/oncoref/cancer_genes.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,750 copying build/lib/oncoref/reference_data.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,753 copying build/lib/oncoref/peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,755 copying build/lib/oncoref/cancer_ontology.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,757 copying build/lib/oncoref/data_bundle.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,760 copying build/lib/oncoref/response_signatures.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,762 copying build/lib/oncoref/gene_families.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,764 copying build/lib/oncoref/normalization.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,767 copying build/lib/oncoref/cta_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,769 copying build/lib/oncoref/cta_tissues.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,771 copying build/lib/oncoref/expression_builders.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,773 copying build/lib/oncoref/cta_regen.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-01T03:21:29,778 creating build/bdist.linux-armv7l/wheel/oncoref/data 2026-07-01T03:21:29,779 copying build/lib/oncoref/data/clean-tpm-biological-housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,781 copying build/lib/oncoref/data/clean-tpm-censored-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,785 copying build/lib/oncoref/data/cancer-lineage-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,787 copying build/lib/oncoref/data/proteoform-collapse-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,789 copying build/lib/oncoref/data/cancer-driver-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,793 copying build/lib/oncoref/data/cancer-response-signatures.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,796 copying build/lib/oncoref/data/cancer-reference-expression-samples.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,804 copying build/lib/oncoref/data/cancer-normal-tissue-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,806 copying build/lib/oncoref/data/cancer-ici-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,809 copying build/lib/oncoref/data/cdna-identical-gene-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,812 copying build/lib/oncoref/data/ribosomal-protein-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,816 copying build/lib/oncoref/data/narrative-gene-sets.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,818 copying build/lib/oncoref/data/cancer-key-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,824 copying build/lib/oncoref/data/cancer-type-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,828 copying build/lib/oncoref/data/degenerate-subtype-pairs.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,830 copying build/lib/oncoref/data/canonical-gene-space.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,843 copying build/lib/oncoref/data/histone-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,846 copying build/lib/oncoref/data/family-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,848 copying build/lib/oncoref/data/hemoglobin-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,850 copying build/lib/oncoref/data/cancer-apd1-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,853 copying build/lib/oncoref/data/cancer-code-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,855 copying build/lib/oncoref/data/cancer-testis-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,861 copying build/lib/oncoref/data/cancer-cohort-aggregates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,864 copying build/lib/oncoref/data/cancer-tmb.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,867 copying build/lib/oncoref/data/proteoform-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,870 copying build/lib/oncoref/data/numt-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,873 copying build/lib/oncoref/data/cancer-ici-response-estimates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,884 copying build/lib/oncoref/data/cancer-frameshift-burden.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,886 copying build/lib/oncoref/data/cta-ihc-unreliable.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,889 copying build/lib/oncoref/data/cta-candidate-references.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,892 copying build/lib/oncoref/data/expression_sources.yaml -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,896 copying build/lib/oncoref/data/cohort-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,900 copying build/lib/oncoref/data/tissue-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,903 copying build/lib/oncoref/data/cancer-expression-source-candidates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,907 copying build/lib/oncoref/data/ensembl-id-aliases.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,922 copying build/lib/oncoref/data/ribosomal-protein-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,927 copying build/lib/oncoref/data/expression-artifact-gene-universe-deltas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,941 copying build/lib/oncoref/data/rare-cancer-fusion-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,944 copying build/lib/oncoref/data/extra-tx-mappings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,947 copying build/lib/oncoref/data/fusion-expression-effects.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,950 copying build/lib/oncoref/data/mitochondrial-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,952 copying build/lib/oncoref/data/small-noncoding-rnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,958 copying build/lib/oncoref/data/cancer-lineage-group-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,960 copying build/lib/oncoref/data/proteoform-groups-genome.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,963 copying build/lib/oncoref/data/nuclear-retained-lncrnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,966 copying build/lib/oncoref/data/cancer-type-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,969 copying build/lib/oncoref/data/disease-state-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,971 copying build/lib/oncoref/data/housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,973 copying build/lib/oncoref/data/cancer-viral-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,975 copying build/lib/oncoref/data/cancer-incidence-mortality.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,977 copying build/lib/oncoref/data/fusion-surrogate-expression.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,980 copying build/lib/oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,990 copying build/lib/oncoref/data/rrna-and-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,993 copying build/lib/oncoref/data/cancer-driver-variants.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:29,997 copying build/lib/oncoref/data/censored-gene-reference-tpm.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:30,001 copying build/lib/oncoref/data/cancer-subtype-groupings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:30,003 copying build/lib/oncoref/data/cancer-fusions.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:30,007 copying build/lib/oncoref/data/source-matrices.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-01T03:21:30,010 running install_egg_info 2026-07-01T03:21:30,024 running egg_info 2026-07-01T03:21:30,031 writing oncoref.egg-info/PKG-INFO 2026-07-01T03:21:30,038 writing dependency_links to oncoref.egg-info/dependency_links.txt 2026-07-01T03:21:30,041 writing entry points to oncoref.egg-info/entry_points.txt 2026-07-01T03:21:30,044 writing requirements to oncoref.egg-info/requires.txt 2026-07-01T03:21:30,045 writing top-level names to oncoref.egg-info/top_level.txt 2026-07-01T03:21:30,073 reading manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-01T03:21:30,087 reading manifest template 'MANIFEST.in' 2026-07-01T03:21:30,089 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-07-01T03:21:30,091 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-07-01T03:21:30,092 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-07-01T03:21:30,093 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-07-01T03:21:30,094 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-07-01T03:21:30,095 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-07-01T03:21:30,095 adding license file 'LICENSE' 2026-07-01T03:21:30,103 writing manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-01T03:21:30,105 Copying oncoref.egg-info to build/bdist.linux-armv7l/wheel/./oncoref-1.8.39-py3.11.egg-info 2026-07-01T03:21:30,118 running install_scripts 2026-07-01T03:21:30,132 creating build/bdist.linux-armv7l/wheel/oncoref-1.8.39.dist-info/WHEEL 2026-07-01T03:21:30,135 creating '/tmp/pip-wheel-s2jgsnq4/.tmp-_bmmdeqk/oncoref-1.8.39-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-07-01T03:21:30,139 adding 'oncoref/__init__.py' 2026-07-01T03:21:30,141 adding 'oncoref/antigen_coverage.py' 2026-07-01T03:21:30,142 adding 'oncoref/apd1.py' 2026-07-01T03:21:30,144 adding 'oncoref/cancer_genes.py' 2026-07-01T03:21:30,146 adding 'oncoref/cancer_ontology.py' 2026-07-01T03:21:30,153 adding 'oncoref/cancer_types.py' 2026-07-01T03:21:30,155 adding 'oncoref/catalog.py' 2026-07-01T03:21:30,158 adding 'oncoref/cli.py' 2026-07-01T03:21:30,160 adding 'oncoref/cohorts.py' 2026-07-01T03:21:30,163 adding 'oncoref/coverage.py' 2026-07-01T03:21:30,166 adding 'oncoref/cta.py' 2026-07-01T03:21:30,167 adding 'oncoref/cta_coverage.py' 2026-07-01T03:21:30,169 adding 'oncoref/cta_curation_plots.py' 2026-07-01T03:21:30,170 adding 'oncoref/cta_peptides.py' 2026-07-01T03:21:30,174 adding 'oncoref/cta_regen.py' 2026-07-01T03:21:30,175 adding 'oncoref/cta_tissues.py' 2026-07-01T03:21:30,179 adding 'oncoref/data_bundle.py' 2026-07-01T03:21:30,182 adding 'oncoref/data_manifest.py' 2026-07-01T03:21:30,196 adding 'oncoref/expression.py' 2026-07-01T03:21:30,199 adding 'oncoref/expression_builders.py' 2026-07-01T03:21:30,203 adding 'oncoref/expression_engine.py' 2026-07-01T03:21:30,204 adding 'oncoref/expression_registry.py' 2026-07-01T03:21:30,206 adding 'oncoref/fusions.py' 2026-07-01T03:21:30,209 adding 'oncoref/gene_families.py' 2026-07-01T03:21:30,211 adding 'oncoref/gene_ids.py' 2026-07-01T03:21:30,213 adding 'oncoref/gene_qc.py' 2026-07-01T03:21:30,215 adding 'oncoref/genome.py' 2026-07-01T03:21:30,217 adding 'oncoref/hpa.py' 2026-07-01T03:21:30,221 adding 'oncoref/ici.py' 2026-07-01T03:21:30,222 adding 'oncoref/ici_response.py' 2026-07-01T03:21:30,224 adding 'oncoref/incidence.py' 2026-07-01T03:21:30,226 adding 'oncoref/load_dataset.py' 2026-07-01T03:21:30,230 adding 'oncoref/normalization.py' 2026-07-01T03:21:30,233 adding 'oncoref/peptides.py' 2026-07-01T03:21:30,240 adding 'oncoref/plots.py' 2026-07-01T03:21:30,243 adding 'oncoref/proteoforms.py' 2026-07-01T03:21:30,245 adding 'oncoref/reference_data.py' 2026-07-01T03:21:30,247 adding 'oncoref/response_signatures.py' 2026-07-01T03:21:30,248 adding 'oncoref/samples.py' 2026-07-01T03:21:30,250 adding 'oncoref/source_matrices.py' 2026-07-01T03:21:30,252 adding 'oncoref/tmb.py' 2026-07-01T03:21:30,253 adding 'oncoref/version.py' 2026-07-01T03:21:30,257 adding 'oncoref/data/cancer-apd1-response.csv' 2026-07-01T03:21:30,259 adding 'oncoref/data/cancer-code-burden-map.csv' 2026-07-01T03:21:30,260 adding 'oncoref/data/cancer-cohort-aggregates.csv' 2026-07-01T03:21:30,265 adding 'oncoref/data/cancer-driver-genes.csv' 2026-07-01T03:21:30,268 adding 'oncoref/data/cancer-driver-variants.csv' 2026-07-01T03:21:30,270 adding 'oncoref/data/cancer-expression-source-candidates.csv' 2026-07-01T03:21:30,272 adding 'oncoref/data/cancer-frameshift-burden.csv' 2026-07-01T03:21:30,275 adding 'oncoref/data/cancer-fusions.csv' 2026-07-01T03:21:30,292 adding 'oncoref/data/cancer-ici-response-estimates.csv' 2026-07-01T03:21:30,297 adding 'oncoref/data/cancer-ici-response.csv' 2026-07-01T03:21:30,298 adding 'oncoref/data/cancer-incidence-mortality.csv' 2026-07-01T03:21:30,313 adding 'oncoref/data/cancer-key-genes.csv' 2026-07-01T03:21:30,315 adding 'oncoref/data/cancer-lineage-group-overrides.csv' 2026-07-01T03:21:30,316 adding 'oncoref/data/cancer-lineage-groups.csv' 2026-07-01T03:21:30,318 adding 'oncoref/data/cancer-normal-tissue-map.csv' 2026-07-01T03:21:30,347 adding 'oncoref/data/cancer-reference-expression-samples.csv.gz' 2026-07-01T03:21:30,350 adding 'oncoref/data/cancer-response-signatures.csv' 2026-07-01T03:21:30,351 adding 'oncoref/data/cancer-subtype-groupings.csv' 2026-07-01T03:21:30,363 adding 'oncoref/data/cancer-testis-antigens.csv' 2026-07-01T03:21:30,366 adding 'oncoref/data/cancer-tmb.csv' 2026-07-01T03:21:30,368 adding 'oncoref/data/cancer-type-genes.csv' 2026-07-01T03:21:30,372 adding 'oncoref/data/cancer-type-registry.csv' 2026-07-01T03:21:30,373 adding 'oncoref/data/cancer-viral-antigens.csv' 2026-07-01T03:21:30,426 adding 'oncoref/data/canonical-gene-space.csv.gz' 2026-07-01T03:21:30,431 adding 'oncoref/data/cdna-identical-gene-groups.csv' 2026-07-01T03:21:30,435 adding 'oncoref/data/censored-gene-reference-tpm.csv' 2026-07-01T03:21:30,437 adding 'oncoref/data/clean-tpm-biological-housekeeping-genes.csv' 2026-07-01T03:21:30,447 adding 'oncoref/data/clean-tpm-censored-genes.csv' 2026-07-01T03:21:30,450 adding 'oncoref/data/cohort-registry.csv' 2026-07-01T03:21:30,451 adding 'oncoref/data/cta-candidate-references.csv' 2026-07-01T03:21:30,452 adding 'oncoref/data/cta-ihc-unreliable.csv' 2026-07-01T03:21:30,454 adding 'oncoref/data/degenerate-subtype-pairs.csv' 2026-07-01T03:21:30,455 adding 'oncoref/data/disease-state-rules.csv' 2026-07-01T03:21:30,482 adding 'oncoref/data/ensembl-id-aliases.csv' 2026-07-01T03:21:30,495 adding 'oncoref/data/expression-artifact-gene-universe-deltas.csv' 2026-07-01T03:21:30,500 adding 'oncoref/data/expression_sources.yaml' 2026-07-01T03:21:30,502 adding 'oncoref/data/extra-tx-mappings.csv' 2026-07-01T03:21:30,504 adding 'oncoref/data/family-burden-map.csv' 2026-07-01T03:21:30,505 adding 'oncoref/data/fusion-expression-effects.csv' 2026-07-01T03:21:30,507 adding 'oncoref/data/fusion-surrogate-expression.csv' 2026-07-01T03:21:30,508 adding 'oncoref/data/hemoglobin-genes.csv' 2026-07-01T03:21:30,509 adding 'oncoref/data/histone-genes.csv' 2026-07-01T03:21:30,511 adding 'oncoref/data/housekeeping-genes.csv' 2026-07-01T03:21:30,512 adding 'oncoref/data/mitochondrial-genes.csv' 2026-07-01T03:21:30,513 adding 'oncoref/data/narrative-gene-sets.csv' 2026-07-01T03:21:30,553 adding 'oncoref/data/ncbi-symbol-synonyms.csv.gz' 2026-07-01T03:21:30,557 adding 'oncoref/data/nuclear-retained-lncrnas.csv' 2026-07-01T03:21:30,559 adding 'oncoref/data/numt-pseudogenes.csv' 2026-07-01T03:21:30,560 adding 'oncoref/data/proteoform-collapse-overrides.csv' 2026-07-01T03:21:30,563 adding 'oncoref/data/proteoform-groups-genome.csv' 2026-07-01T03:21:30,564 adding 'oncoref/data/proteoform-groups.csv' 2026-07-01T03:21:30,566 adding 'oncoref/data/rare-cancer-fusion-rules.csv' 2026-07-01T03:21:30,567 adding 'oncoref/data/ribosomal-protein-genes.csv' 2026-07-01T03:21:30,573 adding 'oncoref/data/ribosomal-protein-pseudogenes.csv' 2026-07-01T03:21:30,576 adding 'oncoref/data/rrna-and-pseudogenes.csv' 2026-07-01T03:21:30,594 adding 'oncoref/data/small-noncoding-rnas.csv' 2026-07-01T03:21:30,597 adding 'oncoref/data/source-matrices.csv' 2026-07-01T03:21:30,598 adding 'oncoref/data/tissue-burden-map.csv' 2026-07-01T03:21:30,602 adding 'oncoref-1.8.39.dist-info/licenses/LICENSE' 2026-07-01T03:21:30,604 adding 'oncoref-1.8.39.dist-info/METADATA' 2026-07-01T03:21:30,606 adding 'oncoref-1.8.39.dist-info/WHEEL' 2026-07-01T03:21:30,608 adding 'oncoref-1.8.39.dist-info/entry_points.txt' 2026-07-01T03:21:30,610 adding 'oncoref-1.8.39.dist-info/top_level.txt' 2026-07-01T03:21:30,612 adding 'oncoref-1.8.39.dist-info/RECORD' 2026-07-01T03:21:30,655 removing build/bdist.linux-armv7l/wheel 2026-07-01T03:21:30,775 Building wheel for oncoref (pyproject.toml): finished with status 'done' 2026-07-01T03:21:30,813 Created wheel for oncoref: filename=oncoref-1.8.39-py3-none-any.whl size=1699426 sha256=2b90ccf09a27b43a59ffe5e886818e1c9d9a265840ca18ca8354f805fc854873 2026-07-01T03:21:30,814 Stored in directory: /tmp/pip-ephem-wheel-cache-jbmd0459/wheels/73/de/57/591570c12566d8c00a1fb8283ddecb9b67ef1a9fcee2ac3498 2026-07-01T03:21:30,830 Successfully built oncoref 2026-07-01T03:21:30,873 Removed build tracker: '/tmp/pip-build-tracker-pfs2idqs'