2026-07-06T04:41:00,171 Created temporary directory: /tmp/pip-ephem-wheel-cache-yx3maev1 2026-07-06T04:41:00,173 Created temporary directory: /tmp/pip-build-tracker-_ki_wz6z 2026-07-06T04:41:00,173 Initialized build tracking at /tmp/pip-build-tracker-_ki_wz6z 2026-07-06T04:41:00,174 Created build tracker: /tmp/pip-build-tracker-_ki_wz6z 2026-07-06T04:41:00,174 Entered build tracker: /tmp/pip-build-tracker-_ki_wz6z 2026-07-06T04:41:00,175 Created temporary directory: /tmp/pip-wheel-r8_pgns2 2026-07-06T04:41:00,178 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 2026-07-06T04:41:00,181 Created temporary directory: /tmp/pip-ephem-wheel-cache-2yuxxhjd 2026-07-06T04:41:00,206 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-07-06T04:41:00,209 2 location(s) to search for versions of oncoref: 2026-07-06T04:41:00,209 * https://pypi.org/simple/oncoref/ 2026-07-06T04:41:00,209 * https://www.piwheels.org/simple/oncoref/ 2026-07-06T04:41:00,210 Fetching project page and analyzing links: https://pypi.org/simple/oncoref/ 2026-07-06T04:41:00,211 Getting page https://pypi.org/simple/oncoref/ 2026-07-06T04:41:00,212 Found index url https://pypi.org/simple 2026-07-06T04:41:00,478 Fetched page https://pypi.org/simple/oncoref/ as application/vnd.pypi.simple.v1+json 2026-07-06T04:41:00,505 Skipping link: No binaries permitted for oncoref: 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https://www.piwheels.org/simple/oncoref/oncoref-1.8.26-py3-none-any.whl#sha256=577cc03d90c5cc790909fba9f7a20fcbb5a1825a744ad3917b8314b33d0dc71d (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-07-06T04:41:00,962 Skipping link: No binaries permitted for oncoref: https://www.piwheels.org/simple/oncoref/oncoref-1.8.25-py3-none-any.whl#sha256=af07dfe64ba72883f3223dd56f5b55a3370d8deb1d781fcff373e4aa696cadd2 (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-07-06T04:41:00,962 Skipping link: No binaries permitted for oncoref: https://www.piwheels.org/simple/oncoref/oncoref-1.8.24-py3-none-any.whl#sha256=37eddc72a25836c04689e807b2e937964e7758be69a3c63ef6f43b079edd274b (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-07-06T04:41:00,963 Skipping link: No binaries permitted for oncoref: 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https://www.piwheels.org/simple/oncoref/oncoref-1.8.17-py3-none-any.whl#sha256=5fa3e3356c1574425d42aebe7d135c933ff623b539736554634a762eeaab4a29 (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-07-06T04:41:00,967 Skipping link: No binaries permitted for oncoref: https://www.piwheels.org/simple/oncoref/oncoref-1.8.16-py3-none-any.whl#sha256=9defcd77c3360e0675a10c0b8de4a1784c19f227a985079b95e21e462de63e97 (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-07-06T04:41:00,968 Skipping link: No binaries permitted for oncoref: https://www.piwheels.org/simple/oncoref/oncoref-1.8.15-py3-none-any.whl#sha256=4dcd40c2e5c10b8f8be0d8df8489b5f05153d465eb43ddf7f9dc158bbe6b1de3 (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-07-06T04:41:00,968 Skipping link: No binaries permitted for oncoref: https://www.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) 2026-07-06T04:41:00,969 Skipping link: No binaries permitted for oncoref: https://www.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) 2026-07-06T04:41:00,969 Skipping link: No binaries permitted for oncoref: https://www.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) 2026-07-06T04:41:00,970 Skipping link: No binaries permitted for oncoref: https://www.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) 2026-07-06T04:41:00,971 Skipping link: No binaries permitted for oncoref: https://www.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) 2026-07-06T04:41:00,971 Skipping link: No binaries permitted for oncoref: 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) 2026-07-06T04:41:00,972 Skipping link: No binaries permitted for oncoref: 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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) 2026-07-06T04:41:00,974 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) 2026-07-06T04:41:00,974 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) 2026-07-06T04:41:00,975 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) 2026-07-06T04:41:00,975 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) 2026-07-06T04:41:00,976 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) 2026-07-06T04:41:00,977 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) 2026-07-06T04:41:00,977 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) 2026-07-06T04:41:00,978 Skipping link: not a file: https://www.piwheels.org/simple/oncoref/ 2026-07-06T04:41:00,978 Skipping link: not a file: https://pypi.org/simple/oncoref/ 2026-07-06T04:41:01,008 Given no hashes to check 1 links for project 'oncoref': discarding no candidates 2026-07-06T04:41:01,028 Collecting oncoref==1.8.52 2026-07-06T04:41:01,030 Created temporary directory: /tmp/pip-unpack-ey9ajy29 2026-07-06T04:41:01,382 Downloading oncoref-1.8.52.tar.gz (1.8 MB) 2026-07-06T04:41:02,082 Added oncoref==1.8.52 from https://files.pythonhosted.org/packages/c7/ff/685bfe120a63666df2c76ecbd832b67c664c6701781fb871adc65b76c054/oncoref-1.8.52.tar.gz to build tracker '/tmp/pip-build-tracker-_ki_wz6z' 2026-07-06T04:41:02,089 Created temporary directory: /tmp/pip-build-env-e_rsrjg0 2026-07-06T04:41:02,093 Installing build dependencies: started 2026-07-06T04:41:02,095 Running command pip subprocess to install build dependencies 2026-07-06T04:41:03,227 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-07-06T04:41:03,696 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 2026-07-06T04:41:03,719 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-07-06T04:41:05,730 Collecting setuptools>=61.0 2026-07-06T04:41:05,750 Using cached setuptools-83.0.0-py3-none-any.whl (1.0 MB) 2026-07-06T04:41:06,067 Collecting wheel 2026-07-06T04:41:06,069 Obtaining dependency information for wheel from https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata 2026-07-06T04:41:06,083 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB) 2026-07-06T04:41:06,267 Collecting packaging>=24.0 2026-07-06T04:41:06,268 Obtaining dependency information for packaging>=24.0 from https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata 2026-07-06T04:41:06,287 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata (3.5 kB) 2026-07-06T04:41:06,481 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB) 2026-07-06T04:41:06,503 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB) 2026-07-06T04:41:06,521 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB) 2026-07-06T04:41:06,546 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB) 2026-07-06T04:41:09,258 Installing collected packages: setuptools, packaging, wheel 2026-07-06T04:41:13,017 Creating /tmp/pip-build-env-e_rsrjg0/overlay/local/bin 2026-07-06T04:41:13,019 changing mode of /tmp/pip-build-env-e_rsrjg0/overlay/local/bin/wheel to 755 2026-07-06T04:41:13,040 Successfully installed packaging-26.2 setuptools-83.0.0 wheel-0.47.0 2026-07-06T04:41:13,324 Installing build dependencies: finished with status 'done' 2026-07-06T04:41:13,331 Getting requirements to build wheel: started 2026-07-06T04:41:13,332 Running command Getting requirements to build wheel 2026-07-06T04:41:14,034 running egg_info 2026-07-06T04:41:14,040 writing oncoref.egg-info/PKG-INFO 2026-07-06T04:41:14,046 writing dependency_links to oncoref.egg-info/dependency_links.txt 2026-07-06T04:41:14,047 writing entry points to oncoref.egg-info/entry_points.txt 2026-07-06T04:41:14,050 writing requirements to oncoref.egg-info/requires.txt 2026-07-06T04:41:14,051 writing top-level names to oncoref.egg-info/top_level.txt 2026-07-06T04:41:14,086 reading manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-06T04:41:14,096 reading manifest template 'MANIFEST.in' 2026-07-06T04:41:14,098 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-07-06T04:41:14,099 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-07-06T04:41:14,101 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-07-06T04:41:14,102 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-07-06T04:41:14,104 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-07-06T04:41:14,105 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-07-06T04:41:14,105 adding license file 'LICENSE' 2026-07-06T04:41:14,113 writing manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-06T04:41:14,211 Getting requirements to build wheel: finished with status 'done' 2026-07-06T04:41:14,215 Created temporary directory: /tmp/pip-modern-metadata-ra779h4h 2026-07-06T04:41:14,217 Preparing metadata (pyproject.toml): started 2026-07-06T04:41:14,218 Running command Preparing metadata (pyproject.toml) 2026-07-06T04:41:14,858 running dist_info 2026-07-06T04:41:14,868 creating /tmp/pip-modern-metadata-ra779h4h/oncoref.egg-info 2026-07-06T04:41:14,869 writing /tmp/pip-modern-metadata-ra779h4h/oncoref.egg-info/PKG-INFO 2026-07-06T04:41:14,874 writing dependency_links to /tmp/pip-modern-metadata-ra779h4h/oncoref.egg-info/dependency_links.txt 2026-07-06T04:41:14,876 writing entry points to /tmp/pip-modern-metadata-ra779h4h/oncoref.egg-info/entry_points.txt 2026-07-06T04:41:14,879 writing requirements to /tmp/pip-modern-metadata-ra779h4h/oncoref.egg-info/requires.txt 2026-07-06T04:41:14,880 writing top-level names to /tmp/pip-modern-metadata-ra779h4h/oncoref.egg-info/top_level.txt 2026-07-06T04:41:14,881 writing manifest file '/tmp/pip-modern-metadata-ra779h4h/oncoref.egg-info/SOURCES.txt' 2026-07-06T04:41:14,914 reading manifest file '/tmp/pip-modern-metadata-ra779h4h/oncoref.egg-info/SOURCES.txt' 2026-07-06T04:41:14,916 reading manifest template 'MANIFEST.in' 2026-07-06T04:41:14,917 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-07-06T04:41:14,919 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-07-06T04:41:14,920 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-07-06T04:41:14,921 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-07-06T04:41:14,922 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-07-06T04:41:14,923 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-07-06T04:41:14,923 adding license file 'LICENSE' 2026-07-06T04:41:14,930 writing manifest file '/tmp/pip-modern-metadata-ra779h4h/oncoref.egg-info/SOURCES.txt' 2026-07-06T04:41:14,931 creating '/tmp/pip-modern-metadata-ra779h4h/oncoref-1.8.52.dist-info' 2026-07-06T04:41:15,057 Preparing metadata (pyproject.toml): finished with status 'done' 2026-07-06T04:41:15,062 Source in /tmp/pip-wheel-r8_pgns2/oncoref_6a59a8df82e1492ebe08130a83f07512 has version 1.8.52, which satisfies requirement oncoref==1.8.52 from https://files.pythonhosted.org/packages/c7/ff/685bfe120a63666df2c76ecbd832b67c664c6701781fb871adc65b76c054/oncoref-1.8.52.tar.gz 2026-07-06T04:41:15,063 Removed oncoref==1.8.52 from https://files.pythonhosted.org/packages/c7/ff/685bfe120a63666df2c76ecbd832b67c664c6701781fb871adc65b76c054/oncoref-1.8.52.tar.gz from build tracker '/tmp/pip-build-tracker-_ki_wz6z' 2026-07-06T04:41:15,069 Created temporary directory: /tmp/pip-unpack-4o4_6pj5 2026-07-06T04:41:15,070 Building wheels for collected packages: oncoref 2026-07-06T04:41:15,074 Created temporary directory: /tmp/pip-wheel-klimh2eg 2026-07-06T04:41:15,075 Destination directory: /tmp/pip-wheel-klimh2eg 2026-07-06T04:41:15,077 Building wheel for oncoref (pyproject.toml): started 2026-07-06T04:41:15,079 Running command Building wheel for oncoref (pyproject.toml) 2026-07-06T04:41:15,698 running bdist_wheel 2026-07-06T04:41:15,716 running build 2026-07-06T04:41:15,716 running build_py 2026-07-06T04:41:15,723 creating build/lib/oncoref 2026-07-06T04:41:15,725 copying oncoref/tmb.py -> build/lib/oncoref 2026-07-06T04:41:15,728 copying oncoref/peptides.py -> build/lib/oncoref 2026-07-06T04:41:15,730 copying oncoref/coverage.py -> build/lib/oncoref 2026-07-06T04:41:15,733 copying oncoref/gene_ids.py -> build/lib/oncoref 2026-07-06T04:41:15,735 copying oncoref/hpa.py -> build/lib/oncoref 2026-07-06T04:41:15,737 copying oncoref/cta_regen.py -> build/lib/oncoref 2026-07-06T04:41:15,740 copying oncoref/cancer_ontology.py -> build/lib/oncoref 2026-07-06T04:41:15,742 copying oncoref/cta.py -> build/lib/oncoref 2026-07-06T04:41:15,744 copying oncoref/cancer_types.py -> build/lib/oncoref 2026-07-06T04:41:15,747 copying oncoref/data_bundle.py -> build/lib/oncoref 2026-07-06T04:41:15,750 copying oncoref/gene_qc.py -> build/lib/oncoref 2026-07-06T04:41:15,752 copying oncoref/plots.py -> build/lib/oncoref 2026-07-06T04:41:15,755 copying oncoref/proteoforms.py -> build/lib/oncoref 2026-07-06T04:41:15,758 copying oncoref/response_signatures.py -> build/lib/oncoref 2026-07-06T04:41:15,760 copying oncoref/gene_families.py -> build/lib/oncoref 2026-07-06T04:41:15,762 copying oncoref/ici.py -> build/lib/oncoref 2026-07-06T04:41:15,765 copying oncoref/fusions.py -> build/lib/oncoref 2026-07-06T04:41:15,767 copying oncoref/antigen_coverage.py -> build/lib/oncoref 2026-07-06T04:41:15,769 copying oncoref/expression_registry.py -> build/lib/oncoref 2026-07-06T04:41:15,771 copying oncoref/cta_tissues.py -> build/lib/oncoref 2026-07-06T04:41:15,773 copying oncoref/genome.py -> build/lib/oncoref 2026-07-06T04:41:15,775 copying oncoref/reference_data.py -> build/lib/oncoref 2026-07-06T04:41:15,778 copying oncoref/apd1.py -> build/lib/oncoref 2026-07-06T04:41:15,779 copying oncoref/expression.py -> build/lib/oncoref 2026-07-06T04:41:15,784 copying oncoref/expression_engine.py -> build/lib/oncoref 2026-07-06T04:41:15,787 copying oncoref/cli.py -> build/lib/oncoref 2026-07-06T04:41:15,790 copying oncoref/cancer_genes.py -> build/lib/oncoref 2026-07-06T04:41:15,792 copying oncoref/expression_builders.py -> build/lib/oncoref 2026-07-06T04:41:15,794 copying oncoref/cta_coverage.py -> build/lib/oncoref 2026-07-06T04:41:15,796 copying oncoref/__init__.py -> build/lib/oncoref 2026-07-06T04:41:15,799 copying oncoref/ici_response.py -> build/lib/oncoref 2026-07-06T04:41:15,801 copying oncoref/cta_curation_plots.py -> build/lib/oncoref 2026-07-06T04:41:15,803 copying oncoref/source_matrices.py -> build/lib/oncoref 2026-07-06T04:41:15,805 copying oncoref/normalization.py -> build/lib/oncoref 2026-07-06T04:41:15,808 copying oncoref/cohorts.py -> build/lib/oncoref 2026-07-06T04:41:15,810 copying oncoref/load_dataset.py -> build/lib/oncoref 2026-07-06T04:41:15,812 copying oncoref/version.py -> build/lib/oncoref 2026-07-06T04:41:15,814 copying oncoref/catalog.py -> build/lib/oncoref 2026-07-06T04:41:15,817 copying oncoref/incidence.py -> build/lib/oncoref 2026-07-06T04:41:15,819 copying oncoref/cta_peptides.py -> build/lib/oncoref 2026-07-06T04:41:15,821 copying oncoref/data_manifest.py -> build/lib/oncoref 2026-07-06T04:41:15,823 copying oncoref/samples.py -> build/lib/oncoref 2026-07-06T04:41:15,837 creating build/lib/oncoref/data 2026-07-06T04:41:15,838 copying oncoref/data/cancer-driver-genes.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,842 copying oncoref/data/cancer-code-burden-map.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,844 copying oncoref/data/family-burden-map.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,846 copying oncoref/data/source-matrices.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,849 copying oncoref/data/proteoform-collapse-overrides.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,851 copying oncoref/data/proteoform-groups.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,853 copying oncoref/data/ribosomal-protein-pseudogenes.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,856 copying oncoref/data/rare-cancer-fusion-rules.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,859 copying oncoref/data/cancer-lineage-group-overrides.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,861 copying oncoref/data/cta-candidate-references.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,863 copying oncoref/data/cancer-testis-antigens.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,869 copying oncoref/data/cancer-ici-response.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,871 copying oncoref/data/cancer-subtype-groupings.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,873 copying oncoref/data/cohort-registry.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,876 copying oncoref/data/histone-genes.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,878 copying oncoref/data/cancer-apd1-response.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,881 copying oncoref/data/ribosomal-protein-genes.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,883 copying oncoref/data/cancer-incidence-mortality.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,886 copying oncoref/data/clean-tpm-censored-genes.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,890 copying oncoref/data/cta-ihc-unreliable.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,892 copying oncoref/data/cancer-fusions.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,895 copying oncoref/data/clean-tpm-biological-housekeeping-genes.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,898 copying oncoref/data/narrative-gene-sets.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,900 copying oncoref/data/cancer-driver-variants.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,903 copying oncoref/data/cancer-normal-tissue-map.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,905 copying oncoref/data/tissue-burden-map.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,908 copying oncoref/data/degenerate-subtype-pairs.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,910 copying oncoref/data/cancer-type-genes.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,913 copying oncoref/data/expression-artifact-gene-universe-deltas.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,921 copying oncoref/data/ensembl-id-aliases.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,929 copying oncoref/data/cancer-key-genes.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,934 copying oncoref/data/cancer-viral-antigens.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,936 copying oncoref/data/cancer-cohort-aggregates.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,939 copying oncoref/data/hemoglobin-genes.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,941 copying oncoref/data/extra-tx-mappings.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,943 copying oncoref/data/proteoform-groups-genome.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,946 copying oncoref/data/cancer-lineage-groups.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,948 copying oncoref/data/censored-gene-reference-tpm.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,951 copying oncoref/data/numt-pseudogenes.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,954 copying oncoref/data/fusion-expression-effects.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,956 copying oncoref/data/cancer-ici-response-estimates.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,963 copying oncoref/data/cancer-type-registry.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,966 copying oncoref/data/mitochondrial-genes.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,968 copying oncoref/data/housekeeping-genes.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,971 copying oncoref/data/disease-state-rules.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,973 copying oncoref/data/rrna-and-pseudogenes.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,976 copying oncoref/data/cancer-response-signatures.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,978 copying oncoref/data/small-noncoding-rnas.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,983 copying oncoref/data/cancer-frameshift-burden.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,985 copying oncoref/data/nuclear-retained-lncrnas.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,987 copying oncoref/data/cdna-identical-gene-groups.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,990 copying oncoref/data/cancer-expression-source-candidates.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,992 copying oncoref/data/fusion-surrogate-expression.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,995 copying oncoref/data/cancer-tmb.csv -> build/lib/oncoref/data 2026-07-06T04:41:15,998 copying oncoref/data/canonical-gene-space.csv.gz -> build/lib/oncoref/data 2026-07-06T04:41:16,008 copying oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/lib/oncoref/data 2026-07-06T04:41:16,016 copying oncoref/data/cancer-reference-expression-samples.csv.gz -> build/lib/oncoref/data 2026-07-06T04:41:16,023 copying oncoref/data/expression_sources.yaml -> build/lib/oncoref/data 2026-07-06T04:41:16,037 installing to build/bdist.linux-armv7l/wheel 2026-07-06T04:41:16,038 running install 2026-07-06T04:41:16,061 running install_lib 2026-07-06T04:41:16,067 creating build/bdist.linux-armv7l/wheel 2026-07-06T04:41:16,070 creating build/bdist.linux-armv7l/wheel/oncoref 2026-07-06T04:41:16,072 copying build/lib/oncoref/tmb.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,075 copying build/lib/oncoref/peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,078 copying build/lib/oncoref/coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,297 copying build/lib/oncoref/gene_ids.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,301 copying build/lib/oncoref/hpa.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,304 copying build/lib/oncoref/cta_regen.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,308 copying build/lib/oncoref/cancer_ontology.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,311 copying build/lib/oncoref/cta.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,315 copying build/lib/oncoref/cancer_types.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,321 copying build/lib/oncoref/data_bundle.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,325 copying build/lib/oncoref/gene_qc.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,328 copying build/lib/oncoref/plots.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,334 copying build/lib/oncoref/proteoforms.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,338 copying build/lib/oncoref/response_signatures.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,340 copying build/lib/oncoref/gene_families.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,344 copying build/lib/oncoref/ici.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,349 copying build/lib/oncoref/fusions.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,353 copying build/lib/oncoref/antigen_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,356 copying build/lib/oncoref/expression_registry.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,360 copying build/lib/oncoref/cta_tissues.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,363 copying build/lib/oncoref/genome.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,367 copying build/lib/oncoref/reference_data.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,370 copying build/lib/oncoref/apd1.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,373 copying build/lib/oncoref/expression.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,382 copying build/lib/oncoref/expression_engine.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,387 creating build/bdist.linux-armv7l/wheel/oncoref/data 2026-07-06T04:41:16,389 copying build/lib/oncoref/data/cancer-driver-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,395 copying build/lib/oncoref/data/cancer-code-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,398 copying build/lib/oncoref/data/family-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,400 copying build/lib/oncoref/data/source-matrices.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,403 copying build/lib/oncoref/data/proteoform-collapse-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,405 copying build/lib/oncoref/data/proteoform-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,407 copying build/lib/oncoref/data/ribosomal-protein-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,411 copying build/lib/oncoref/data/canonical-gene-space.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,429 copying build/lib/oncoref/data/rare-cancer-fusion-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,431 copying build/lib/oncoref/data/cancer-lineage-group-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,433 copying build/lib/oncoref/data/cta-candidate-references.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,436 copying build/lib/oncoref/data/cancer-testis-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,442 copying build/lib/oncoref/data/expression_sources.yaml -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,446 copying build/lib/oncoref/data/cancer-ici-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,449 copying build/lib/oncoref/data/cancer-subtype-groupings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,451 copying build/lib/oncoref/data/cohort-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,454 copying build/lib/oncoref/data/histone-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,456 copying build/lib/oncoref/data/cancer-apd1-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,459 copying build/lib/oncoref/data/ribosomal-protein-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,462 copying build/lib/oncoref/data/cancer-incidence-mortality.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,464 copying build/lib/oncoref/data/clean-tpm-censored-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,507 copying build/lib/oncoref/data/cta-ihc-unreliable.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,509 copying build/lib/oncoref/data/cancer-fusions.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,512 copying build/lib/oncoref/data/clean-tpm-biological-housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,514 copying build/lib/oncoref/data/narrative-gene-sets.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,516 copying build/lib/oncoref/data/cancer-driver-variants.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,518 copying build/lib/oncoref/data/cancer-normal-tissue-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,521 copying build/lib/oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,529 copying build/lib/oncoref/data/tissue-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,531 copying build/lib/oncoref/data/degenerate-subtype-pairs.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,533 copying build/lib/oncoref/data/cancer-type-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,535 copying build/lib/oncoref/data/expression-artifact-gene-universe-deltas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,544 copying build/lib/oncoref/data/ensembl-id-aliases.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,552 copying build/lib/oncoref/data/cancer-key-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,556 copying build/lib/oncoref/data/cancer-viral-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,558 copying build/lib/oncoref/data/cancer-cohort-aggregates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,559 copying build/lib/oncoref/data/hemoglobin-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,561 copying build/lib/oncoref/data/extra-tx-mappings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,563 copying build/lib/oncoref/data/proteoform-groups-genome.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,565 copying build/lib/oncoref/data/cancer-lineage-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,567 copying build/lib/oncoref/data/censored-gene-reference-tpm.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,570 copying build/lib/oncoref/data/numt-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,572 copying build/lib/oncoref/data/fusion-expression-effects.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,574 copying build/lib/oncoref/data/cancer-ici-response-estimates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,579 copying build/lib/oncoref/data/cancer-type-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,582 copying build/lib/oncoref/data/mitochondrial-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,584 copying build/lib/oncoref/data/housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,586 copying build/lib/oncoref/data/disease-state-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,588 copying build/lib/oncoref/data/rrna-and-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,590 copying build/lib/oncoref/data/cancer-response-signatures.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,592 copying build/lib/oncoref/data/small-noncoding-rnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,597 copying build/lib/oncoref/data/cancer-frameshift-burden.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,599 copying build/lib/oncoref/data/nuclear-retained-lncrnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,600 copying build/lib/oncoref/data/cdna-identical-gene-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,603 copying build/lib/oncoref/data/cancer-expression-source-candidates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,605 copying build/lib/oncoref/data/fusion-surrogate-expression.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,608 copying build/lib/oncoref/data/cancer-reference-expression-samples.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,615 copying build/lib/oncoref/data/cancer-tmb.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-06T04:41:16,617 copying build/lib/oncoref/cli.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,620 copying build/lib/oncoref/cancer_genes.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,622 copying build/lib/oncoref/expression_builders.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,624 copying build/lib/oncoref/cta_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,626 copying build/lib/oncoref/__init__.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,629 copying build/lib/oncoref/ici_response.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,631 copying build/lib/oncoref/cta_curation_plots.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,633 copying build/lib/oncoref/source_matrices.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,635 copying build/lib/oncoref/normalization.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,638 copying build/lib/oncoref/cohorts.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,639 copying build/lib/oncoref/load_dataset.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,642 copying build/lib/oncoref/version.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,643 copying build/lib/oncoref/catalog.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,646 copying build/lib/oncoref/incidence.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,648 copying build/lib/oncoref/cta_peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,649 copying build/lib/oncoref/data_manifest.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,652 copying build/lib/oncoref/samples.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-06T04:41:16,653 running install_egg_info 2026-07-06T04:41:16,663 running egg_info 2026-07-06T04:41:16,668 writing oncoref.egg-info/PKG-INFO 2026-07-06T04:41:16,673 writing dependency_links to oncoref.egg-info/dependency_links.txt 2026-07-06T04:41:16,675 writing entry points to oncoref.egg-info/entry_points.txt 2026-07-06T04:41:16,677 writing requirements to oncoref.egg-info/requires.txt 2026-07-06T04:41:16,678 writing top-level names to oncoref.egg-info/top_level.txt 2026-07-06T04:41:16,697 reading manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-06T04:41:16,706 reading manifest template 'MANIFEST.in' 2026-07-06T04:41:16,708 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-07-06T04:41:16,709 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-07-06T04:41:16,711 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-07-06T04:41:16,712 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-07-06T04:41:16,713 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-07-06T04:41:16,714 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-07-06T04:41:16,715 adding license file 'LICENSE' 2026-07-06T04:41:16,723 writing manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-06T04:41:16,725 Copying oncoref.egg-info to build/bdist.linux-armv7l/wheel/./oncoref-1.8.52-py3.11.egg-info 2026-07-06T04:41:16,739 running install_scripts 2026-07-06T04:41:16,752 creating build/bdist.linux-armv7l/wheel/oncoref-1.8.52.dist-info/WHEEL 2026-07-06T04:41:16,755 creating '/tmp/pip-wheel-klimh2eg/.tmp-ju31yhbl/oncoref-1.8.52-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-07-06T04:41:16,759 adding 'oncoref/__init__.py' 2026-07-06T04:41:16,760 adding 'oncoref/antigen_coverage.py' 2026-07-06T04:41:16,762 adding 'oncoref/apd1.py' 2026-07-06T04:41:16,764 adding 'oncoref/cancer_genes.py' 2026-07-06T04:41:16,766 adding 'oncoref/cancer_ontology.py' 2026-07-06T04:41:16,773 adding 'oncoref/cancer_types.py' 2026-07-06T04:41:16,775 adding 'oncoref/catalog.py' 2026-07-06T04:41:16,779 adding 'oncoref/cli.py' 2026-07-06T04:41:16,780 adding 'oncoref/cohorts.py' 2026-07-06T04:41:16,783 adding 'oncoref/coverage.py' 2026-07-06T04:41:16,786 adding 'oncoref/cta.py' 2026-07-06T04:41:16,787 adding 'oncoref/cta_coverage.py' 2026-07-06T04:41:16,789 adding 'oncoref/cta_curation_plots.py' 2026-07-06T04:41:16,790 adding 'oncoref/cta_peptides.py' 2026-07-06T04:41:16,793 adding 'oncoref/cta_regen.py' 2026-07-06T04:41:16,795 adding 'oncoref/cta_tissues.py' 2026-07-06T04:41:16,799 adding 'oncoref/data_bundle.py' 2026-07-06T04:41:16,801 adding 'oncoref/data_manifest.py' 2026-07-06T04:41:16,815 adding 'oncoref/expression.py' 2026-07-06T04:41:16,818 adding 'oncoref/expression_builders.py' 2026-07-06T04:41:16,821 adding 'oncoref/expression_engine.py' 2026-07-06T04:41:16,836 adding 'oncoref/expression_registry.py' 2026-07-06T04:41:16,837 adding 'oncoref/fusions.py' 2026-07-06T04:41:16,840 adding 'oncoref/gene_families.py' 2026-07-06T04:41:16,842 adding 'oncoref/gene_ids.py' 2026-07-06T04:41:16,843 adding 'oncoref/gene_qc.py' 2026-07-06T04:41:16,846 adding 'oncoref/genome.py' 2026-07-06T04:41:16,847 adding 'oncoref/hpa.py' 2026-07-06T04:41:16,851 adding 'oncoref/ici.py' 2026-07-06T04:41:16,853 adding 'oncoref/ici_response.py' 2026-07-06T04:41:16,861 adding 'oncoref/incidence.py' 2026-07-06T04:41:16,863 adding 'oncoref/load_dataset.py' 2026-07-06T04:41:16,867 adding 'oncoref/normalization.py' 2026-07-06T04:41:16,869 adding 'oncoref/peptides.py' 2026-07-06T04:41:16,876 adding 'oncoref/plots.py' 2026-07-06T04:41:16,879 adding 'oncoref/proteoforms.py' 2026-07-06T04:41:16,881 adding 'oncoref/reference_data.py' 2026-07-06T04:41:16,882 adding 'oncoref/response_signatures.py' 2026-07-06T04:41:16,883 adding 'oncoref/samples.py' 2026-07-06T04:41:16,885 adding 'oncoref/source_matrices.py' 2026-07-06T04:41:16,887 adding 'oncoref/tmb.py' 2026-07-06T04:41:16,888 adding 'oncoref/version.py' 2026-07-06T04:41:16,892 adding 'oncoref/data/cancer-apd1-response.csv' 2026-07-06T04:41:16,893 adding 'oncoref/data/cancer-code-burden-map.csv' 2026-07-06T04:41:16,895 adding 'oncoref/data/cancer-cohort-aggregates.csv' 2026-07-06T04:41:16,900 adding 'oncoref/data/cancer-driver-genes.csv' 2026-07-06T04:41:16,902 adding 'oncoref/data/cancer-driver-variants.csv' 2026-07-06T04:41:16,905 adding 'oncoref/data/cancer-expression-source-candidates.csv' 2026-07-06T04:41:16,906 adding 'oncoref/data/cancer-frameshift-burden.csv' 2026-07-06T04:41:16,909 adding 'oncoref/data/cancer-fusions.csv' 2026-07-06T04:41:16,926 adding 'oncoref/data/cancer-ici-response-estimates.csv' 2026-07-06T04:41:16,930 adding 'oncoref/data/cancer-ici-response.csv' 2026-07-06T04:41:16,931 adding 'oncoref/data/cancer-incidence-mortality.csv' 2026-07-06T04:41:16,945 adding 'oncoref/data/cancer-key-genes.csv' 2026-07-06T04:41:16,948 adding 'oncoref/data/cancer-lineage-group-overrides.csv' 2026-07-06T04:41:16,949 adding 'oncoref/data/cancer-lineage-groups.csv' 2026-07-06T04:41:16,954 adding 'oncoref/data/cancer-normal-tissue-map.csv' 2026-07-06T04:41:16,983 adding 'oncoref/data/cancer-reference-expression-samples.csv.gz' 2026-07-06T04:41:16,986 adding 'oncoref/data/cancer-response-signatures.csv' 2026-07-06T04:41:16,987 adding 'oncoref/data/cancer-subtype-groupings.csv' 2026-07-06T04:41:16,999 adding 'oncoref/data/cancer-testis-antigens.csv' 2026-07-06T04:41:17,002 adding 'oncoref/data/cancer-tmb.csv' 2026-07-06T04:41:17,005 adding 'oncoref/data/cancer-type-genes.csv' 2026-07-06T04:41:17,009 adding 'oncoref/data/cancer-type-registry.csv' 2026-07-06T04:41:17,010 adding 'oncoref/data/cancer-viral-antigens.csv' 2026-07-06T04:41:17,063 adding 'oncoref/data/canonical-gene-space.csv.gz' 2026-07-06T04:41:17,069 adding 'oncoref/data/cdna-identical-gene-groups.csv' 2026-07-06T04:41:17,073 adding 'oncoref/data/censored-gene-reference-tpm.csv' 2026-07-06T04:41:17,075 adding 'oncoref/data/clean-tpm-biological-housekeeping-genes.csv' 2026-07-06T04:41:17,085 adding 'oncoref/data/clean-tpm-censored-genes.csv' 2026-07-06T04:41:17,088 adding 'oncoref/data/cohort-registry.csv' 2026-07-06T04:41:17,089 adding 'oncoref/data/cta-candidate-references.csv' 2026-07-06T04:41:17,090 adding 'oncoref/data/cta-ihc-unreliable.csv' 2026-07-06T04:41:17,091 adding 'oncoref/data/degenerate-subtype-pairs.csv' 2026-07-06T04:41:17,092 adding 'oncoref/data/disease-state-rules.csv' 2026-07-06T04:41:17,119 adding 'oncoref/data/ensembl-id-aliases.csv' 2026-07-06T04:41:17,133 adding 'oncoref/data/expression-artifact-gene-universe-deltas.csv' 2026-07-06T04:41:17,139 adding 'oncoref/data/expression_sources.yaml' 2026-07-06T04:41:17,140 adding 'oncoref/data/extra-tx-mappings.csv' 2026-07-06T04:41:17,141 adding 'oncoref/data/family-burden-map.csv' 2026-07-06T04:41:17,143 adding 'oncoref/data/fusion-expression-effects.csv' 2026-07-06T04:41:17,144 adding 'oncoref/data/fusion-surrogate-expression.csv' 2026-07-06T04:41:17,145 adding 'oncoref/data/hemoglobin-genes.csv' 2026-07-06T04:41:17,147 adding 'oncoref/data/histone-genes.csv' 2026-07-06T04:41:17,148 adding 'oncoref/data/housekeeping-genes.csv' 2026-07-06T04:41:17,149 adding 'oncoref/data/mitochondrial-genes.csv' 2026-07-06T04:41:17,151 adding 'oncoref/data/narrative-gene-sets.csv' 2026-07-06T04:41:17,191 adding 'oncoref/data/ncbi-symbol-synonyms.csv.gz' 2026-07-06T04:41:17,195 adding 'oncoref/data/nuclear-retained-lncrnas.csv' 2026-07-06T04:41:17,197 adding 'oncoref/data/numt-pseudogenes.csv' 2026-07-06T04:41:17,198 adding 'oncoref/data/proteoform-collapse-overrides.csv' 2026-07-06T04:41:17,201 adding 'oncoref/data/proteoform-groups-genome.csv' 2026-07-06T04:41:17,202 adding 'oncoref/data/proteoform-groups.csv' 2026-07-06T04:41:17,204 adding 'oncoref/data/rare-cancer-fusion-rules.csv' 2026-07-06T04:41:17,205 adding 'oncoref/data/ribosomal-protein-genes.csv' 2026-07-06T04:41:17,212 adding 'oncoref/data/ribosomal-protein-pseudogenes.csv' 2026-07-06T04:41:17,214 adding 'oncoref/data/rrna-and-pseudogenes.csv' 2026-07-06T04:41:17,233 adding 'oncoref/data/small-noncoding-rnas.csv' 2026-07-06T04:41:17,236 adding 'oncoref/data/source-matrices.csv' 2026-07-06T04:41:17,237 adding 'oncoref/data/tissue-burden-map.csv' 2026-07-06T04:41:17,241 adding 'oncoref-1.8.52.dist-info/licenses/LICENSE' 2026-07-06T04:41:17,243 adding 'oncoref-1.8.52.dist-info/METADATA' 2026-07-06T04:41:17,244 adding 'oncoref-1.8.52.dist-info/WHEEL' 2026-07-06T04:41:17,245 adding 'oncoref-1.8.52.dist-info/entry_points.txt' 2026-07-06T04:41:17,246 adding 'oncoref-1.8.52.dist-info/top_level.txt' 2026-07-06T04:41:17,248 adding 'oncoref-1.8.52.dist-info/RECORD' 2026-07-06T04:41:17,286 removing build/bdist.linux-armv7l/wheel 2026-07-06T04:41:17,406 Building wheel for oncoref (pyproject.toml): finished with status 'done' 2026-07-06T04:41:17,448 Created wheel for oncoref: filename=oncoref-1.8.52-py3-none-any.whl size=1699707 sha256=b08315342b3f3e336b905892278f5b7fa4531dc90e4f55ae268aa22ad5d1a512 2026-07-06T04:41:17,449 Stored in directory: /tmp/pip-ephem-wheel-cache-2yuxxhjd/wheels/7a/e3/32/0fb52e1b1516ad3852fb6dfd613b5899183400ed142c5f8ea8 2026-07-06T04:41:17,464 Successfully built oncoref 2026-07-06T04:41:17,502 Removed build tracker: '/tmp/pip-build-tracker-_ki_wz6z'