2026-07-26T16:55:06,133 Created temporary directory: /tmp/pip-ephem-wheel-cache-nmwhotsz 2026-07-26T16:55:06,135 Created temporary directory: /tmp/pip-build-tracker-0o3up7w6 2026-07-26T16:55:06,135 Initialized build tracking at /tmp/pip-build-tracker-0o3up7w6 2026-07-26T16:55:06,136 Created build tracker: /tmp/pip-build-tracker-0o3up7w6 2026-07-26T16:55:06,136 Entered build tracker: /tmp/pip-build-tracker-0o3up7w6 2026-07-26T16:55:06,137 Created temporary directory: /tmp/pip-wheel-mjxqw6ae 2026-07-26T16:55:06,139 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 2026-07-26T16:55:06,142 Created temporary directory: /tmp/pip-ephem-wheel-cache-1isyfgdw 2026-07-26T16:55:06,166 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-07-26T16:55:06,169 2 location(s) to search for versions of oncoref: 2026-07-26T16:55:06,169 * https://pypi.org/simple/oncoref/ 2026-07-26T16:55:06,169 * https://www.piwheels.org/simple/oncoref/ 2026-07-26T16:55:06,170 Fetching project page and analyzing links: https://pypi.org/simple/oncoref/ 2026-07-26T16:55:06,171 Getting page https://pypi.org/simple/oncoref/ 2026-07-26T16:55:06,172 Found index url https://pypi.org/simple 2026-07-26T16:55:06,365 Fetched page https://pypi.org/simple/oncoref/ as application/vnd.pypi.simple.v1+json 2026-07-26T16:55:06,419 Skipping link: No binaries permitted for oncoref: 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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) 2026-07-26T16:55:06,979 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) 2026-07-26T16:55:06,979 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) 2026-07-26T16:55:06,980 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) 2026-07-26T16:55:06,980 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) 2026-07-26T16:55:06,981 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) 2026-07-26T16:55:06,982 Skipping link: not a file: https://www.piwheels.org/simple/oncoref/ 2026-07-26T16:55:06,982 Skipping link: not a file: https://pypi.org/simple/oncoref/ 2026-07-26T16:55:07,020 Given no hashes to check 1 links for project 'oncoref': discarding no candidates 2026-07-26T16:55:07,039 Collecting oncoref==1.8.148 2026-07-26T16:55:07,041 Created temporary directory: /tmp/pip-unpack-p49at0qi 2026-07-26T16:55:07,277 Downloading oncoref-1.8.148.tar.gz (2.9 MB) 2026-07-26T16:55:08,242 Added oncoref==1.8.148 from https://files.pythonhosted.org/packages/90/5c/ab53bb26ead72fd02c538b5433266353e307fac29b32cc248bcd502cabce/oncoref-1.8.148.tar.gz to build tracker '/tmp/pip-build-tracker-0o3up7w6' 2026-07-26T16:55:08,249 Created temporary directory: /tmp/pip-build-env-xn_2sqas 2026-07-26T16:55:08,254 Installing build dependencies: started 2026-07-26T16:55:08,255 Running command pip subprocess to install build dependencies 2026-07-26T16:55:09,396 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-07-26T16:55:09,847 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 2026-07-26T16:55:09,870 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-07-26T16:55:11,732 Collecting setuptools>=61.0 2026-07-26T16:55:11,733 Obtaining dependency information for setuptools>=61.0 from https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl.metadata 2026-07-26T16:55:11,751 Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl.metadata (6.6 kB) 2026-07-26T16:55:11,990 Collecting wheel 2026-07-26T16:55:11,992 Obtaining dependency information for wheel from https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata 2026-07-26T16:55:12,006 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB) 2026-07-26T16:55:12,193 Collecting packaging>=24.0 2026-07-26T16:55:12,195 Obtaining dependency information for packaging>=24.0 from https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata 2026-07-26T16:55:12,208 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata (3.5 kB) 2026-07-26T16:55:12,399 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB) 2026-07-26T16:55:12,419 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB) 2026-07-26T16:55:12,509 Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl (1.0 MB) 2026-07-26T16:55:12,543 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB) 2026-07-26T16:55:12,567 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB) 2026-07-26T16:55:12,656 Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl (1.0 MB) 2026-07-26T16:55:15,420 Installing collected packages: setuptools, packaging, wheel 2026-07-26T16:55:18,913 Creating /tmp/pip-build-env-xn_2sqas/overlay/local/bin 2026-07-26T16:55:18,915 changing mode of /tmp/pip-build-env-xn_2sqas/overlay/local/bin/wheel to 755 2026-07-26T16:55:18,936 Successfully installed packaging-26.2 setuptools-83.0.0 wheel-0.47.0 2026-07-26T16:55:19,229 Installing build dependencies: finished with status 'done' 2026-07-26T16:55:19,236 Getting requirements to build wheel: started 2026-07-26T16:55:19,237 Running command Getting requirements to build wheel 2026-07-26T16:55:19,913 running egg_info 2026-07-26T16:55:19,919 writing oncoref.egg-info/PKG-INFO 2026-07-26T16:55:19,925 writing dependency_links to oncoref.egg-info/dependency_links.txt 2026-07-26T16:55:19,927 writing entry points to oncoref.egg-info/entry_points.txt 2026-07-26T16:55:19,930 writing requirements to oncoref.egg-info/requires.txt 2026-07-26T16:55:19,931 writing top-level names to oncoref.egg-info/top_level.txt 2026-07-26T16:55:19,967 reading manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-26T16:55:19,977 reading manifest template 'MANIFEST.in' 2026-07-26T16:55:19,979 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-07-26T16:55:19,980 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-07-26T16:55:19,981 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-07-26T16:55:19,983 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-07-26T16:55:19,984 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-07-26T16:55:19,985 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-07-26T16:55:19,986 adding license file 'LICENSE' 2026-07-26T16:55:19,994 writing manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-26T16:55:20,095 Getting requirements to build wheel: finished with status 'done' 2026-07-26T16:55:20,099 Created temporary directory: /tmp/pip-modern-metadata-_p9f43qy 2026-07-26T16:55:20,101 Preparing metadata (pyproject.toml): started 2026-07-26T16:55:20,102 Running command Preparing metadata (pyproject.toml) 2026-07-26T16:55:20,735 running dist_info 2026-07-26T16:55:20,745 creating /tmp/pip-modern-metadata-_p9f43qy/oncoref.egg-info 2026-07-26T16:55:20,746 writing /tmp/pip-modern-metadata-_p9f43qy/oncoref.egg-info/PKG-INFO 2026-07-26T16:55:20,752 writing dependency_links to /tmp/pip-modern-metadata-_p9f43qy/oncoref.egg-info/dependency_links.txt 2026-07-26T16:55:20,754 writing entry points to /tmp/pip-modern-metadata-_p9f43qy/oncoref.egg-info/entry_points.txt 2026-07-26T16:55:20,757 writing requirements to /tmp/pip-modern-metadata-_p9f43qy/oncoref.egg-info/requires.txt 2026-07-26T16:55:20,758 writing top-level names to /tmp/pip-modern-metadata-_p9f43qy/oncoref.egg-info/top_level.txt 2026-07-26T16:55:20,759 writing manifest file '/tmp/pip-modern-metadata-_p9f43qy/oncoref.egg-info/SOURCES.txt' 2026-07-26T16:55:20,793 reading manifest file '/tmp/pip-modern-metadata-_p9f43qy/oncoref.egg-info/SOURCES.txt' 2026-07-26T16:55:20,795 reading manifest template 'MANIFEST.in' 2026-07-26T16:55:20,796 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-07-26T16:55:20,797 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-07-26T16:55:20,798 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-07-26T16:55:20,800 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-07-26T16:55:20,800 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-07-26T16:55:20,801 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-07-26T16:55:20,802 adding license file 'LICENSE' 2026-07-26T16:55:20,809 writing manifest file '/tmp/pip-modern-metadata-_p9f43qy/oncoref.egg-info/SOURCES.txt' 2026-07-26T16:55:20,810 creating '/tmp/pip-modern-metadata-_p9f43qy/oncoref-1.8.148.dist-info' 2026-07-26T16:55:20,939 Preparing metadata (pyproject.toml): finished with status 'done' 2026-07-26T16:55:20,944 Source in /tmp/pip-wheel-mjxqw6ae/oncoref_4d81593594504139bf5c7c4b51938f63 has version 1.8.148, which satisfies requirement oncoref==1.8.148 from https://files.pythonhosted.org/packages/90/5c/ab53bb26ead72fd02c538b5433266353e307fac29b32cc248bcd502cabce/oncoref-1.8.148.tar.gz 2026-07-26T16:55:20,945 Removed oncoref==1.8.148 from https://files.pythonhosted.org/packages/90/5c/ab53bb26ead72fd02c538b5433266353e307fac29b32cc248bcd502cabce/oncoref-1.8.148.tar.gz from build tracker '/tmp/pip-build-tracker-0o3up7w6' 2026-07-26T16:55:20,951 Created temporary directory: /tmp/pip-unpack-yx22a8ct 2026-07-26T16:55:20,952 Building wheels for collected packages: oncoref 2026-07-26T16:55:20,956 Created temporary directory: /tmp/pip-wheel-vtsxi86s 2026-07-26T16:55:20,957 Destination directory: /tmp/pip-wheel-vtsxi86s 2026-07-26T16:55:20,959 Building wheel for oncoref (pyproject.toml): started 2026-07-26T16:55:20,960 Running command Building wheel for oncoref (pyproject.toml) 2026-07-26T16:55:21,573 running bdist_wheel 2026-07-26T16:55:21,591 running build 2026-07-26T16:55:21,591 running build_py 2026-07-26T16:55:21,598 creating build/lib/oncoref 2026-07-26T16:55:21,601 copying oncoref/cta_peptides.py -> build/lib/oncoref 2026-07-26T16:55:21,603 copying oncoref/hpa.py -> build/lib/oncoref 2026-07-26T16:55:21,605 copying oncoref/data_manifest.py -> build/lib/oncoref 2026-07-26T16:55:21,608 copying oncoref/gene_ids.py -> build/lib/oncoref 2026-07-26T16:55:21,611 copying oncoref/ici.py -> build/lib/oncoref 2026-07-26T16:55:21,614 copying oncoref/antigen_coverage.py -> build/lib/oncoref 2026-07-26T16:55:21,616 copying oncoref/tmb.py -> build/lib/oncoref 2026-07-26T16:55:21,619 copying oncoref/coverage.py -> build/lib/oncoref 2026-07-26T16:55:21,622 copying oncoref/proteoforms.py -> build/lib/oncoref 2026-07-26T16:55:21,626 copying oncoref/ici_response.py -> build/lib/oncoref 2026-07-26T16:55:21,628 copying oncoref/__init__.py -> build/lib/oncoref 2026-07-26T16:55:21,631 copying oncoref/samples.py -> build/lib/oncoref 2026-07-26T16:55:21,633 copying oncoref/fusions.py -> build/lib/oncoref 2026-07-26T16:55:21,635 copying oncoref/reference_data.py -> build/lib/oncoref 2026-07-26T16:55:21,638 copying oncoref/response_signatures.py -> build/lib/oncoref 2026-07-26T16:55:21,641 copying oncoref/expression_builders.py -> build/lib/oncoref 2026-07-26T16:55:21,736 copying oncoref/incidence.py -> build/lib/oncoref 2026-07-26T16:55:21,738 copying oncoref/plots.py -> build/lib/oncoref 2026-07-26T16:55:21,742 copying oncoref/_reference_sources.py -> build/lib/oncoref 2026-07-26T16:55:21,744 copying oncoref/cancer_ontology.py -> build/lib/oncoref 2026-07-26T16:55:21,746 copying oncoref/cta_regen.py -> build/lib/oncoref 2026-07-26T16:55:21,749 copying oncoref/cta_coverage.py -> build/lib/oncoref 2026-07-26T16:55:21,750 copying oncoref/catalog.py -> build/lib/oncoref 2026-07-26T16:55:21,753 copying oncoref/cancer_types.py -> build/lib/oncoref 2026-07-26T16:55:21,756 copying oncoref/apd1.py -> build/lib/oncoref 2026-07-26T16:55:21,758 copying oncoref/genome.py -> build/lib/oncoref 2026-07-26T16:55:21,761 copying oncoref/expression_engine.py -> build/lib/oncoref 2026-07-26T16:55:21,764 copying oncoref/source_matrices.py -> build/lib/oncoref 2026-07-26T16:55:21,766 copying oncoref/normalization.py -> build/lib/oncoref 2026-07-26T16:55:21,769 copying oncoref/cli.py -> build/lib/oncoref 2026-07-26T16:55:21,771 copying oncoref/gene_families.py -> build/lib/oncoref 2026-07-26T16:55:21,774 copying oncoref/expression_registry.py -> build/lib/oncoref 2026-07-26T16:55:21,776 copying oncoref/cta_curation_plots.py -> build/lib/oncoref 2026-07-26T16:55:21,778 copying oncoref/cta.py -> build/lib/oncoref 2026-07-26T16:55:21,781 copying oncoref/peptides.py -> build/lib/oncoref 2026-07-26T16:55:21,783 copying oncoref/cohorts.py -> build/lib/oncoref 2026-07-26T16:55:21,785 copying oncoref/gene_qc.py -> build/lib/oncoref 2026-07-26T16:55:21,788 copying oncoref/data_bundle.py -> build/lib/oncoref 2026-07-26T16:55:21,790 copying oncoref/expression.py -> build/lib/oncoref 2026-07-26T16:55:21,798 copying oncoref/cancer_genes.py -> build/lib/oncoref 2026-07-26T16:55:21,800 copying oncoref/load_dataset.py -> build/lib/oncoref 2026-07-26T16:55:21,803 copying oncoref/cta_tissues.py -> build/lib/oncoref 2026-07-26T16:55:21,805 copying oncoref/version.py -> build/lib/oncoref 2026-07-26T16:55:21,819 creating build/lib/oncoref/data 2026-07-26T16:55:21,821 copying oncoref/data/cancer-who-soft-tissue-bone-audit.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,826 copying oncoref/data/source-matrices.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,828 copying oncoref/data/cancer-mismatch-repair-statuses.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,830 copying oncoref/data/ensembl-id-aliases.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,841 copying oncoref/data/rrna-and-pseudogenes.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,844 copying oncoref/data/cancer-ici-response-estimates.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,852 copying oncoref/data/cta-candidate-references.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,854 copying oncoref/data/cta-ihc-unreliable.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,857 copying oncoref/data/cancer-type-registry.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,861 copying oncoref/data/cancer-expression-source-candidates.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,864 copying oncoref/data/histone-genes.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,866 copying oncoref/data/cancer-frameshift-burden.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,868 copying oncoref/data/cancer-driver-variants.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,872 copying oncoref/data/gse294016-sample-diagnoses.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,874 copying oncoref/data/rare-cancer-fusion-rules.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,877 copying oncoref/data/cancer-viral-antigens.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,879 copying oncoref/data/cancer-key-genes.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,884 copying oncoref/data/clean-tpm-biological-housekeeping-genes.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,887 copying oncoref/data/cta-clinical-targets.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,889 copying oncoref/data/cancer-reference-expression-availability.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,894 copying oncoref/data/numt-pseudogenes.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,897 copying oncoref/data/cancer-ici-response.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,900 copying oncoref/data/cancer-apd1-response.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,902 copying oncoref/data/cta-specificity-audit.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,904 copying oncoref/data/narrative-gene-sets.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,906 copying oncoref/data/cohort-registry.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,909 copying oncoref/data/cancer-lineage-group-overrides.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,911 copying oncoref/data/clean-tpm-censored-genes.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,915 copying oncoref/data/extra-tx-mappings.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,917 copying oncoref/data/cdna-identical-gene-groups.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,920 copying oncoref/data/cancer-key-gene-citation-audit.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,926 copying oncoref/data/fusion-expression-effects.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,929 copying oncoref/data/cancer-response-signatures.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,931 copying oncoref/data/degenerate-subtype-pairs.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,933 copying oncoref/data/cancer-code-burden-map.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,935 copying oncoref/data/family-burden-map.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,937 copying oncoref/data/cancer-type-genes.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,940 copying oncoref/data/cancer-driver-genes.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,943 copying oncoref/data/hemoglobin-genes.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,945 copying oncoref/data/ribosomal-protein-genes.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,947 copying oncoref/data/cancer-cohort-aggregates.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,949 copying oncoref/data/ribosomal-protein-pseudogenes.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,952 copying oncoref/data/cancer-normal-tissue-map.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,955 copying oncoref/data/cancer-fusions.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,958 copying oncoref/data/housekeeping-genes.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,960 copying oncoref/data/cancer-tmb.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,963 copying oncoref/data/small-noncoding-rnas.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,969 copying oncoref/data/mitochondrial-genes.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,971 copying oncoref/data/expression-artifact-gene-universe-deltas.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,979 copying oncoref/data/cancer-lineage-groups.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,982 copying oncoref/data/proteoform-groups-genome.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,985 copying oncoref/data/proteoform-groups.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,987 copying oncoref/data/censored-gene-reference-tpm.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,990 copying oncoref/data/cancer-fusion-citation-audit.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,993 copying oncoref/data/proteoform-collapse-overrides.csv -> build/lib/oncoref/data 2026-07-26T16:55:21,995 copying oncoref/data/cancer-testis-antigens.csv -> build/lib/oncoref/data 2026-07-26T16:55:22,000 copying oncoref/data/tissue-burden-map.csv -> build/lib/oncoref/data 2026-07-26T16:55:22,002 copying oncoref/data/disease-state-rules.csv -> build/lib/oncoref/data 2026-07-26T16:55:22,004 copying oncoref/data/cancer-subtype-groupings.csv -> build/lib/oncoref/data 2026-07-26T16:55:22,006 copying oncoref/data/cancer-incidence-mortality.csv -> build/lib/oncoref/data 2026-07-26T16:55:22,008 copying oncoref/data/fusion-surrogate-expression.csv -> build/lib/oncoref/data 2026-07-26T16:55:22,011 copying oncoref/data/nuclear-retained-lncrnas.csv -> build/lib/oncoref/data 2026-07-26T16:55:22,013 copying oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/lib/oncoref/data 2026-07-26T16:55:22,021 copying oncoref/data/ncbi-entrez-gene-mappings.csv.gz -> build/lib/oncoref/data 2026-07-26T16:55:22,045 copying oncoref/data/canonical-gene-space.csv.gz -> build/lib/oncoref/data 2026-07-26T16:55:22,057 copying oncoref/data/cancer-reference-expression-samples.csv.gz -> build/lib/oncoref/data 2026-07-26T16:55:22,065 copying oncoref/data/expression_sources.yaml -> build/lib/oncoref/data 2026-07-26T16:55:22,079 installing to build/bdist.linux-armv7l/wheel 2026-07-26T16:55:22,080 running install 2026-07-26T16:55:22,103 running install_lib 2026-07-26T16:55:22,108 creating build/bdist.linux-armv7l/wheel 2026-07-26T16:55:22,110 creating build/bdist.linux-armv7l/wheel/oncoref 2026-07-26T16:55:22,111 copying build/lib/oncoref/cta_peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,113 copying build/lib/oncoref/hpa.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,115 copying build/lib/oncoref/data_manifest.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,117 copying build/lib/oncoref/gene_ids.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,120 copying build/lib/oncoref/ici.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,122 copying build/lib/oncoref/antigen_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,124 copying build/lib/oncoref/tmb.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,127 copying build/lib/oncoref/coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,129 copying build/lib/oncoref/proteoforms.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,132 copying build/lib/oncoref/ici_response.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,134 copying build/lib/oncoref/__init__.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,137 copying build/lib/oncoref/samples.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,139 copying build/lib/oncoref/fusions.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,141 copying build/lib/oncoref/reference_data.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,144 copying build/lib/oncoref/response_signatures.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,145 copying build/lib/oncoref/expression_builders.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,149 copying build/lib/oncoref/incidence.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,152 copying build/lib/oncoref/plots.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,155 copying build/lib/oncoref/_reference_sources.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,156 copying build/lib/oncoref/cancer_ontology.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,159 copying build/lib/oncoref/cta_regen.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,161 copying build/lib/oncoref/cta_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,163 copying build/lib/oncoref/catalog.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,165 copying build/lib/oncoref/cancer_types.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,169 copying build/lib/oncoref/apd1.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,172 copying build/lib/oncoref/genome.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,174 copying build/lib/oncoref/expression_engine.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,177 copying build/lib/oncoref/source_matrices.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,179 copying build/lib/oncoref/normalization.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,183 copying build/lib/oncoref/cli.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,185 copying build/lib/oncoref/gene_families.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,188 copying build/lib/oncoref/expression_registry.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,190 copying build/lib/oncoref/cta_curation_plots.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,192 copying build/lib/oncoref/cta.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,195 copying build/lib/oncoref/peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,197 copying build/lib/oncoref/cohorts.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,198 copying build/lib/oncoref/gene_qc.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,200 copying build/lib/oncoref/data_bundle.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,203 copying build/lib/oncoref/expression.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,208 copying build/lib/oncoref/cancer_genes.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,210 copying build/lib/oncoref/load_dataset.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,212 copying build/lib/oncoref/cta_tissues.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,216 creating build/bdist.linux-armv7l/wheel/oncoref/data 2026-07-26T16:55:22,217 copying build/lib/oncoref/data/cancer-who-soft-tissue-bone-audit.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,219 copying build/lib/oncoref/data/source-matrices.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,222 copying build/lib/oncoref/data/cancer-mismatch-repair-statuses.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,223 copying build/lib/oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,232 copying build/lib/oncoref/data/ensembl-id-aliases.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,239 copying build/lib/oncoref/data/rrna-and-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,242 copying build/lib/oncoref/data/cancer-ici-response-estimates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,248 copying build/lib/oncoref/data/cta-candidate-references.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,250 copying build/lib/oncoref/data/cta-ihc-unreliable.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,252 copying build/lib/oncoref/data/cancer-type-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,255 copying build/lib/oncoref/data/cancer-expression-source-candidates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,258 copying build/lib/oncoref/data/histone-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,260 copying build/lib/oncoref/data/cancer-frameshift-burden.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,262 copying build/lib/oncoref/data/cancer-driver-variants.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,265 copying build/lib/oncoref/data/gse294016-sample-diagnoses.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,266 copying build/lib/oncoref/data/rare-cancer-fusion-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,269 copying build/lib/oncoref/data/cancer-viral-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,271 copying build/lib/oncoref/data/cancer-key-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,276 copying build/lib/oncoref/data/clean-tpm-biological-housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,278 copying build/lib/oncoref/data/cta-clinical-targets.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,280 copying build/lib/oncoref/data/cancer-reference-expression-availability.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,285 copying build/lib/oncoref/data/numt-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,288 copying build/lib/oncoref/data/cancer-ici-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,291 copying build/lib/oncoref/data/cancer-apd1-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,293 copying build/lib/oncoref/data/cta-specificity-audit.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,295 copying build/lib/oncoref/data/narrative-gene-sets.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,297 copying build/lib/oncoref/data/ncbi-entrez-gene-mappings.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,318 copying build/lib/oncoref/data/cohort-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,321 copying build/lib/oncoref/data/cancer-lineage-group-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,323 copying build/lib/oncoref/data/clean-tpm-censored-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,328 copying build/lib/oncoref/data/canonical-gene-space.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,338 copying build/lib/oncoref/data/extra-tx-mappings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,340 copying build/lib/oncoref/data/cdna-identical-gene-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,343 copying build/lib/oncoref/data/cancer-key-gene-citation-audit.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,349 copying build/lib/oncoref/data/fusion-expression-effects.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,352 copying build/lib/oncoref/data/cancer-response-signatures.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,354 copying build/lib/oncoref/data/cancer-reference-expression-samples.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,365 copying build/lib/oncoref/data/degenerate-subtype-pairs.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,367 copying build/lib/oncoref/data/cancer-code-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,369 copying build/lib/oncoref/data/family-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,371 copying build/lib/oncoref/data/cancer-type-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,374 copying build/lib/oncoref/data/cancer-driver-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,378 copying build/lib/oncoref/data/hemoglobin-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,380 copying build/lib/oncoref/data/ribosomal-protein-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,382 copying build/lib/oncoref/data/cancer-cohort-aggregates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,384 copying build/lib/oncoref/data/ribosomal-protein-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,388 copying build/lib/oncoref/data/cancer-normal-tissue-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,391 copying build/lib/oncoref/data/cancer-fusions.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,394 copying build/lib/oncoref/data/housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,397 copying build/lib/oncoref/data/cancer-tmb.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,400 copying build/lib/oncoref/data/small-noncoding-rnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,406 copying build/lib/oncoref/data/mitochondrial-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,408 copying build/lib/oncoref/data/expression-artifact-gene-universe-deltas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,417 copying build/lib/oncoref/data/cancer-lineage-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,419 copying build/lib/oncoref/data/proteoform-groups-genome.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,422 copying build/lib/oncoref/data/proteoform-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,424 copying build/lib/oncoref/data/censored-gene-reference-tpm.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,428 copying build/lib/oncoref/data/cancer-fusion-citation-audit.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,431 copying build/lib/oncoref/data/proteoform-collapse-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,434 copying build/lib/oncoref/data/cancer-testis-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,440 copying build/lib/oncoref/data/tissue-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,442 copying build/lib/oncoref/data/expression_sources.yaml -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,446 copying build/lib/oncoref/data/disease-state-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,448 copying build/lib/oncoref/data/cancer-subtype-groupings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,450 copying build/lib/oncoref/data/cancer-incidence-mortality.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,452 copying build/lib/oncoref/data/fusion-surrogate-expression.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,454 copying build/lib/oncoref/data/nuclear-retained-lncrnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-26T16:55:22,456 copying build/lib/oncoref/version.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-26T16:55:22,458 running install_egg_info 2026-07-26T16:55:22,467 running egg_info 2026-07-26T16:55:22,473 writing oncoref.egg-info/PKG-INFO 2026-07-26T16:55:22,479 writing dependency_links to oncoref.egg-info/dependency_links.txt 2026-07-26T16:55:22,480 writing entry points to oncoref.egg-info/entry_points.txt 2026-07-26T16:55:22,483 writing requirements to oncoref.egg-info/requires.txt 2026-07-26T16:55:22,484 writing top-level names to oncoref.egg-info/top_level.txt 2026-07-26T16:55:22,504 reading manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-26T16:55:22,514 reading manifest template 'MANIFEST.in' 2026-07-26T16:55:22,516 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-07-26T16:55:22,517 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-07-26T16:55:22,519 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-07-26T16:55:22,520 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-07-26T16:55:22,521 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-07-26T16:55:22,522 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-07-26T16:55:22,523 adding license file 'LICENSE' 2026-07-26T16:55:22,532 writing manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-26T16:55:22,534 Copying oncoref.egg-info to build/bdist.linux-armv7l/wheel/./oncoref-1.8.148-py3.11.egg-info 2026-07-26T16:55:22,546 running install_scripts 2026-07-26T16:55:22,780 creating build/bdist.linux-armv7l/wheel/oncoref-1.8.148.dist-info/WHEEL 2026-07-26T16:55:22,782 creating '/tmp/pip-wheel-vtsxi86s/.tmp-0td0ymgi/oncoref-1.8.148-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-07-26T16:55:22,786 adding 'oncoref/__init__.py' 2026-07-26T16:55:22,788 adding 'oncoref/_reference_sources.py' 2026-07-26T16:55:22,789 adding 'oncoref/antigen_coverage.py' 2026-07-26T16:55:22,791 adding 'oncoref/apd1.py' 2026-07-26T16:55:22,793 adding 'oncoref/cancer_genes.py' 2026-07-26T16:55:22,794 adding 'oncoref/cancer_ontology.py' 2026-07-26T16:55:22,806 adding 'oncoref/cancer_types.py' 2026-07-26T16:55:22,809 adding 'oncoref/catalog.py' 2026-07-26T16:55:22,811 adding 'oncoref/cli.py' 2026-07-26T16:55:22,813 adding 'oncoref/cohorts.py' 2026-07-26T16:55:22,816 adding 'oncoref/coverage.py' 2026-07-26T16:55:22,820 adding 'oncoref/cta.py' 2026-07-26T16:55:22,821 adding 'oncoref/cta_coverage.py' 2026-07-26T16:55:22,823 adding 'oncoref/cta_curation_plots.py' 2026-07-26T16:55:22,825 adding 'oncoref/cta_peptides.py' 2026-07-26T16:55:22,828 adding 'oncoref/cta_regen.py' 2026-07-26T16:55:22,829 adding 'oncoref/cta_tissues.py' 2026-07-26T16:55:22,834 adding 'oncoref/data_bundle.py' 2026-07-26T16:55:22,836 adding 'oncoref/data_manifest.py' 2026-07-26T16:55:22,863 adding 'oncoref/expression.py' 2026-07-26T16:55:22,880 adding 'oncoref/expression_builders.py' 2026-07-26T16:55:22,884 adding 'oncoref/expression_engine.py' 2026-07-26T16:55:22,886 adding 'oncoref/expression_registry.py' 2026-07-26T16:55:22,887 adding 'oncoref/fusions.py' 2026-07-26T16:55:22,890 adding 'oncoref/gene_families.py' 2026-07-26T16:55:22,893 adding 'oncoref/gene_ids.py' 2026-07-26T16:55:22,894 adding 'oncoref/gene_qc.py' 2026-07-26T16:55:22,897 adding 'oncoref/genome.py' 2026-07-26T16:55:22,898 adding 'oncoref/hpa.py' 2026-07-26T16:55:22,903 adding 'oncoref/ici.py' 2026-07-26T16:55:22,905 adding 'oncoref/ici_response.py' 2026-07-26T16:55:22,907 adding 'oncoref/incidence.py' 2026-07-26T16:55:22,909 adding 'oncoref/load_dataset.py' 2026-07-26T16:55:22,914 adding 'oncoref/normalization.py' 2026-07-26T16:55:22,916 adding 'oncoref/peptides.py' 2026-07-26T16:55:22,923 adding 'oncoref/plots.py' 2026-07-26T16:55:22,926 adding 'oncoref/proteoforms.py' 2026-07-26T16:55:22,928 adding 'oncoref/reference_data.py' 2026-07-26T16:55:22,930 adding 'oncoref/response_signatures.py' 2026-07-26T16:55:22,931 adding 'oncoref/samples.py' 2026-07-26T16:55:22,933 adding 'oncoref/source_matrices.py' 2026-07-26T16:55:22,935 adding 'oncoref/tmb.py' 2026-07-26T16:55:22,937 adding 'oncoref/version.py' 2026-07-26T16:55:22,941 adding 'oncoref/data/cancer-apd1-response.csv' 2026-07-26T16:55:22,942 adding 'oncoref/data/cancer-code-burden-map.csv' 2026-07-26T16:55:22,944 adding 'oncoref/data/cancer-cohort-aggregates.csv' 2026-07-26T16:55:22,949 adding 'oncoref/data/cancer-driver-genes.csv' 2026-07-26T16:55:22,952 adding 'oncoref/data/cancer-driver-variants.csv' 2026-07-26T16:55:22,955 adding 'oncoref/data/cancer-expression-source-candidates.csv' 2026-07-26T16:55:22,956 adding 'oncoref/data/cancer-frameshift-burden.csv' 2026-07-26T16:55:22,960 adding 'oncoref/data/cancer-fusion-citation-audit.csv' 2026-07-26T16:55:22,963 adding 'oncoref/data/cancer-fusions.csv' 2026-07-26T16:55:22,983 adding 'oncoref/data/cancer-ici-response-estimates.csv' 2026-07-26T16:55:22,988 adding 'oncoref/data/cancer-ici-response.csv' 2026-07-26T16:55:22,990 adding 'oncoref/data/cancer-incidence-mortality.csv' 2026-07-26T16:55:23,008 adding 'oncoref/data/cancer-key-gene-citation-audit.csv' 2026-07-26T16:55:23,021 adding 'oncoref/data/cancer-key-genes.csv' 2026-07-26T16:55:23,023 adding 'oncoref/data/cancer-lineage-group-overrides.csv' 2026-07-26T16:55:23,024 adding 'oncoref/data/cancer-lineage-groups.csv' 2026-07-26T16:55:23,026 adding 'oncoref/data/cancer-mismatch-repair-statuses.csv' 2026-07-26T16:55:23,027 adding 'oncoref/data/cancer-normal-tissue-map.csv' 2026-07-26T16:55:23,034 adding 'oncoref/data/cancer-reference-expression-availability.csv' 2026-07-26T16:55:23,064 adding 'oncoref/data/cancer-reference-expression-samples.csv.gz' 2026-07-26T16:55:23,067 adding 'oncoref/data/cancer-response-signatures.csv' 2026-07-26T16:55:23,068 adding 'oncoref/data/cancer-subtype-groupings.csv' 2026-07-26T16:55:23,079 adding 'oncoref/data/cancer-testis-antigens.csv' 2026-07-26T16:55:23,082 adding 'oncoref/data/cancer-tmb.csv' 2026-07-26T16:55:23,085 adding 'oncoref/data/cancer-type-genes.csv' 2026-07-26T16:55:23,090 adding 'oncoref/data/cancer-type-registry.csv' 2026-07-26T16:55:23,092 adding 'oncoref/data/cancer-viral-antigens.csv' 2026-07-26T16:55:23,094 adding 'oncoref/data/cancer-who-soft-tissue-bone-audit.csv' 2026-07-26T16:55:23,147 adding 'oncoref/data/canonical-gene-space.csv.gz' 2026-07-26T16:55:23,152 adding 'oncoref/data/cdna-identical-gene-groups.csv' 2026-07-26T16:55:23,156 adding 'oncoref/data/censored-gene-reference-tpm.csv' 2026-07-26T16:55:23,157 adding 'oncoref/data/clean-tpm-biological-housekeeping-genes.csv' 2026-07-26T16:55:23,168 adding 'oncoref/data/clean-tpm-censored-genes.csv' 2026-07-26T16:55:23,170 adding 'oncoref/data/cohort-registry.csv' 2026-07-26T16:55:23,172 adding 'oncoref/data/cta-candidate-references.csv' 2026-07-26T16:55:23,173 adding 'oncoref/data/cta-clinical-targets.csv' 2026-07-26T16:55:23,174 adding 'oncoref/data/cta-ihc-unreliable.csv' 2026-07-26T16:55:23,176 adding 'oncoref/data/cta-specificity-audit.csv' 2026-07-26T16:55:23,177 adding 'oncoref/data/degenerate-subtype-pairs.csv' 2026-07-26T16:55:23,179 adding 'oncoref/data/disease-state-rules.csv' 2026-07-26T16:55:23,206 adding 'oncoref/data/ensembl-id-aliases.csv' 2026-07-26T16:55:23,220 adding 'oncoref/data/expression-artifact-gene-universe-deltas.csv' 2026-07-26T16:55:23,229 adding 'oncoref/data/expression_sources.yaml' 2026-07-26T16:55:23,231 adding 'oncoref/data/extra-tx-mappings.csv' 2026-07-26T16:55:23,232 adding 'oncoref/data/family-burden-map.csv' 2026-07-26T16:55:23,234 adding 'oncoref/data/fusion-expression-effects.csv' 2026-07-26T16:55:23,236 adding 'oncoref/data/fusion-surrogate-expression.csv' 2026-07-26T16:55:23,237 adding 'oncoref/data/gse294016-sample-diagnoses.csv' 2026-07-26T16:55:23,238 adding 'oncoref/data/hemoglobin-genes.csv' 2026-07-26T16:55:23,240 adding 'oncoref/data/histone-genes.csv' 2026-07-26T16:55:23,241 adding 'oncoref/data/housekeeping-genes.csv' 2026-07-26T16:55:23,242 adding 'oncoref/data/mitochondrial-genes.csv' 2026-07-26T16:55:23,243 adding 'oncoref/data/narrative-gene-sets.csv' 2026-07-26T16:55:23,349 adding 'oncoref/data/ncbi-entrez-gene-mappings.csv.gz' 2026-07-26T16:55:23,395 adding 'oncoref/data/ncbi-symbol-synonyms.csv.gz' 2026-07-26T16:55:23,399 adding 'oncoref/data/nuclear-retained-lncrnas.csv' 2026-07-26T16:55:23,401 adding 'oncoref/data/numt-pseudogenes.csv' 2026-07-26T16:55:23,402 adding 'oncoref/data/proteoform-collapse-overrides.csv' 2026-07-26T16:55:23,405 adding 'oncoref/data/proteoform-groups-genome.csv' 2026-07-26T16:55:23,407 adding 'oncoref/data/proteoform-groups.csv' 2026-07-26T16:55:23,409 adding 'oncoref/data/rare-cancer-fusion-rules.csv' 2026-07-26T16:55:23,410 adding 'oncoref/data/ribosomal-protein-genes.csv' 2026-07-26T16:55:23,416 adding 'oncoref/data/ribosomal-protein-pseudogenes.csv' 2026-07-26T16:55:23,419 adding 'oncoref/data/rrna-and-pseudogenes.csv' 2026-07-26T16:55:23,438 adding 'oncoref/data/small-noncoding-rnas.csv' 2026-07-26T16:55:23,440 adding 'oncoref/data/source-matrices.csv' 2026-07-26T16:55:23,442 adding 'oncoref/data/tissue-burden-map.csv' 2026-07-26T16:55:23,445 adding 'oncoref-1.8.148.dist-info/licenses/LICENSE' 2026-07-26T16:55:23,448 adding 'oncoref-1.8.148.dist-info/METADATA' 2026-07-26T16:55:23,449 adding 'oncoref-1.8.148.dist-info/WHEEL' 2026-07-26T16:55:23,450 adding 'oncoref-1.8.148.dist-info/entry_points.txt' 2026-07-26T16:55:23,451 adding 'oncoref-1.8.148.dist-info/top_level.txt' 2026-07-26T16:55:23,453 adding 'oncoref-1.8.148.dist-info/RECORD' 2026-07-26T16:55:23,490 removing build/bdist.linux-armv7l/wheel 2026-07-26T16:55:23,620 Building wheel for oncoref (pyproject.toml): finished with status 'done' 2026-07-26T16:55:23,679 Created wheel for oncoref: filename=oncoref-1.8.148-py3-none-any.whl size=2785506 sha256=52b48b7f13e1b5690b40fd974709e382ec090ebb83c158f5aa53560b575905d0 2026-07-26T16:55:23,681 Stored in directory: /tmp/pip-ephem-wheel-cache-1isyfgdw/wheels/34/22/07/349c8962c05cd9b7df729266413984ca87e00959d4db076bb1 2026-07-26T16:55:23,698 Successfully built oncoref 2026-07-26T16:55:23,767 Removed build tracker: '/tmp/pip-build-tracker-0o3up7w6'