2026-07-08T20:49:49,366 Created temporary directory: /tmp/pip-ephem-wheel-cache-k1ah9sy6 2026-07-08T20:49:49,368 Created temporary directory: /tmp/pip-build-tracker-ivgbhvao 2026-07-08T20:49:49,368 Initialized build tracking at /tmp/pip-build-tracker-ivgbhvao 2026-07-08T20:49:49,369 Created build tracker: /tmp/pip-build-tracker-ivgbhvao 2026-07-08T20:49:49,369 Entered build tracker: /tmp/pip-build-tracker-ivgbhvao 2026-07-08T20:49:49,370 Created temporary directory: /tmp/pip-wheel-xzvzy35u 2026-07-08T20:49:49,373 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 2026-07-08T20:49:49,375 Created temporary directory: /tmp/pip-ephem-wheel-cache-w3uy0xpn 2026-07-08T20:49:49,399 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-07-08T20:49:49,403 2 location(s) to search for versions of oncoref: 2026-07-08T20:49:49,403 * https://pypi.org/simple/oncoref/ 2026-07-08T20:49:49,403 * https://www.piwheels.org/simple/oncoref/ 2026-07-08T20:49:49,404 Fetching project page and analyzing links: https://pypi.org/simple/oncoref/ 2026-07-08T20:49:49,404 Getting page https://pypi.org/simple/oncoref/ 2026-07-08T20:49:49,406 Found index url https://pypi.org/simple 2026-07-08T20:49:49,692 Fetched page https://pypi.org/simple/oncoref/ as application/vnd.pypi.simple.v1+json 2026-07-08T20:49:49,726 Skipping link: No binaries permitted for oncoref: 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2026-07-08T20:49:50,295 Given no hashes to check 1 links for project 'oncoref': discarding no candidates 2026-07-08T20:49:50,314 Collecting oncoref==1.8.84 2026-07-08T20:49:50,317 Created temporary directory: /tmp/pip-unpack-j_g2tt9g 2026-07-08T20:49:50,658 Downloading oncoref-1.8.84.tar.gz (2.7 MB) 2026-07-08T20:49:51,590 Added oncoref==1.8.84 from https://files.pythonhosted.org/packages/aa/5b/c531a85d7111918d43e4f6c34c2e2ac6d9cc3f01d159ff1f67a44babdc99/oncoref-1.8.84.tar.gz to build tracker '/tmp/pip-build-tracker-ivgbhvao' 2026-07-08T20:49:51,597 Created temporary directory: /tmp/pip-build-env-8virdlfy 2026-07-08T20:49:51,602 Installing build dependencies: started 2026-07-08T20:49:51,603 Running command pip subprocess to install build dependencies 2026-07-08T20:49:52,739 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-07-08T20:49:53,210 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 2026-07-08T20:49:53,233 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-07-08T20:49:55,241 Collecting setuptools>=61.0 2026-07-08T20:49:55,242 Obtaining dependency information for setuptools>=61.0 from https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl.metadata 2026-07-08T20:49:55,256 Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl.metadata (6.6 kB) 2026-07-08T20:49:55,491 Collecting wheel 2026-07-08T20:49:55,492 Obtaining dependency information for wheel from https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata 2026-07-08T20:49:55,505 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB) 2026-07-08T20:49:55,691 Collecting packaging>=24.0 2026-07-08T20:49:55,692 Obtaining dependency information for packaging>=24.0 from https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata 2026-07-08T20:49:55,704 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata (3.5 kB) 2026-07-08T20:49:55,894 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB) 2026-07-08T20:49:55,914 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB) 2026-07-08T20:49:55,993 Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl (1.0 MB) 2026-07-08T20:49:56,025 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB) 2026-07-08T20:49:56,052 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB) 2026-07-08T20:49:56,147 Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl (1.0 MB) 2026-07-08T20:49:58,918 Installing collected packages: setuptools, packaging, wheel 2026-07-08T20:50:02,392 Creating /tmp/pip-build-env-8virdlfy/overlay/local/bin 2026-07-08T20:50:02,395 changing mode of /tmp/pip-build-env-8virdlfy/overlay/local/bin/wheel to 755 2026-07-08T20:50:02,416 Successfully installed packaging-26.2 setuptools-83.0.0 wheel-0.47.0 2026-07-08T20:50:02,703 Installing build dependencies: finished with status 'done' 2026-07-08T20:50:02,709 Getting requirements to build wheel: started 2026-07-08T20:50:02,711 Running command Getting requirements to build wheel 2026-07-08T20:50:03,418 running egg_info 2026-07-08T20:50:03,423 writing oncoref.egg-info/PKG-INFO 2026-07-08T20:50:03,429 writing dependency_links to oncoref.egg-info/dependency_links.txt 2026-07-08T20:50:03,431 writing entry points to oncoref.egg-info/entry_points.txt 2026-07-08T20:50:03,434 writing requirements to oncoref.egg-info/requires.txt 2026-07-08T20:50:03,435 writing top-level names to oncoref.egg-info/top_level.txt 2026-07-08T20:50:03,470 reading manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-08T20:50:03,480 reading manifest template 'MANIFEST.in' 2026-07-08T20:50:03,482 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-07-08T20:50:03,483 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-07-08T20:50:03,484 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-07-08T20:50:03,486 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-07-08T20:50:03,487 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-07-08T20:50:03,488 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-07-08T20:50:03,489 adding license file 'LICENSE' 2026-07-08T20:50:03,497 writing manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-08T20:50:03,595 Getting requirements to build wheel: finished with status 'done' 2026-07-08T20:50:03,599 Created temporary directory: /tmp/pip-modern-metadata-nkwb8a2t 2026-07-08T20:50:03,601 Preparing metadata (pyproject.toml): started 2026-07-08T20:50:03,603 Running command Preparing metadata (pyproject.toml) 2026-07-08T20:50:04,249 running dist_info 2026-07-08T20:50:04,259 creating /tmp/pip-modern-metadata-nkwb8a2t/oncoref.egg-info 2026-07-08T20:50:04,260 writing /tmp/pip-modern-metadata-nkwb8a2t/oncoref.egg-info/PKG-INFO 2026-07-08T20:50:04,266 writing dependency_links to /tmp/pip-modern-metadata-nkwb8a2t/oncoref.egg-info/dependency_links.txt 2026-07-08T20:50:04,268 writing entry points to /tmp/pip-modern-metadata-nkwb8a2t/oncoref.egg-info/entry_points.txt 2026-07-08T20:50:04,271 writing requirements to /tmp/pip-modern-metadata-nkwb8a2t/oncoref.egg-info/requires.txt 2026-07-08T20:50:04,272 writing top-level names to /tmp/pip-modern-metadata-nkwb8a2t/oncoref.egg-info/top_level.txt 2026-07-08T20:50:04,273 writing manifest file '/tmp/pip-modern-metadata-nkwb8a2t/oncoref.egg-info/SOURCES.txt' 2026-07-08T20:50:04,306 reading manifest file '/tmp/pip-modern-metadata-nkwb8a2t/oncoref.egg-info/SOURCES.txt' 2026-07-08T20:50:04,308 reading manifest template 'MANIFEST.in' 2026-07-08T20:50:04,310 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-07-08T20:50:04,311 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-07-08T20:50:04,312 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-07-08T20:50:04,313 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-07-08T20:50:04,314 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-07-08T20:50:04,315 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-07-08T20:50:04,315 adding license file 'LICENSE' 2026-07-08T20:50:04,322 writing manifest file '/tmp/pip-modern-metadata-nkwb8a2t/oncoref.egg-info/SOURCES.txt' 2026-07-08T20:50:04,323 creating '/tmp/pip-modern-metadata-nkwb8a2t/oncoref-1.8.84.dist-info' 2026-07-08T20:50:04,452 Preparing metadata (pyproject.toml): finished with status 'done' 2026-07-08T20:50:04,458 Source in /tmp/pip-wheel-xzvzy35u/oncoref_bdc9bee393ff464a8ca3c3b0af3ea3ac has version 1.8.84, which satisfies requirement oncoref==1.8.84 from https://files.pythonhosted.org/packages/aa/5b/c531a85d7111918d43e4f6c34c2e2ac6d9cc3f01d159ff1f67a44babdc99/oncoref-1.8.84.tar.gz 2026-07-08T20:50:04,459 Removed oncoref==1.8.84 from https://files.pythonhosted.org/packages/aa/5b/c531a85d7111918d43e4f6c34c2e2ac6d9cc3f01d159ff1f67a44babdc99/oncoref-1.8.84.tar.gz from build tracker '/tmp/pip-build-tracker-ivgbhvao' 2026-07-08T20:50:04,465 Created temporary directory: /tmp/pip-unpack-wdjxq6k7 2026-07-08T20:50:04,466 Building wheels for collected packages: oncoref 2026-07-08T20:50:04,471 Created temporary directory: /tmp/pip-wheel-cg8vnhh7 2026-07-08T20:50:04,471 Destination directory: /tmp/pip-wheel-cg8vnhh7 2026-07-08T20:50:04,473 Building wheel for oncoref (pyproject.toml): started 2026-07-08T20:50:04,474 Running command Building wheel for oncoref (pyproject.toml) 2026-07-08T20:50:05,131 running bdist_wheel 2026-07-08T20:50:05,149 running build 2026-07-08T20:50:05,149 running build_py 2026-07-08T20:50:05,156 creating build/lib/oncoref 2026-07-08T20:50:05,159 copying oncoref/tmb.py -> build/lib/oncoref 2026-07-08T20:50:05,161 copying oncoref/peptides.py -> build/lib/oncoref 2026-07-08T20:50:05,164 copying oncoref/coverage.py -> build/lib/oncoref 2026-07-08T20:50:05,166 copying oncoref/gene_ids.py -> build/lib/oncoref 2026-07-08T20:50:05,169 copying oncoref/hpa.py -> build/lib/oncoref 2026-07-08T20:50:05,171 copying oncoref/cta_regen.py -> build/lib/oncoref 2026-07-08T20:50:05,174 copying oncoref/cancer_ontology.py -> build/lib/oncoref 2026-07-08T20:50:05,176 copying oncoref/cta.py -> build/lib/oncoref 2026-07-08T20:50:05,179 copying oncoref/cancer_types.py -> build/lib/oncoref 2026-07-08T20:50:05,182 copying oncoref/data_bundle.py -> build/lib/oncoref 2026-07-08T20:50:05,185 copying oncoref/gene_qc.py -> build/lib/oncoref 2026-07-08T20:50:05,187 copying oncoref/plots.py -> build/lib/oncoref 2026-07-08T20:50:05,190 copying oncoref/proteoforms.py -> build/lib/oncoref 2026-07-08T20:50:05,194 copying oncoref/response_signatures.py -> build/lib/oncoref 2026-07-08T20:50:05,196 copying oncoref/gene_families.py -> build/lib/oncoref 2026-07-08T20:50:05,198 copying oncoref/ici.py -> build/lib/oncoref 2026-07-08T20:50:05,201 copying oncoref/fusions.py -> build/lib/oncoref 2026-07-08T20:50:05,204 copying oncoref/antigen_coverage.py -> build/lib/oncoref 2026-07-08T20:50:05,206 copying oncoref/expression_registry.py -> build/lib/oncoref 2026-07-08T20:50:05,208 copying oncoref/cta_tissues.py -> build/lib/oncoref 2026-07-08T20:50:05,210 copying oncoref/genome.py -> build/lib/oncoref 2026-07-08T20:50:05,213 copying oncoref/reference_data.py -> build/lib/oncoref 2026-07-08T20:50:05,215 copying oncoref/apd1.py -> build/lib/oncoref 2026-07-08T20:50:05,217 copying oncoref/expression.py -> build/lib/oncoref 2026-07-08T20:50:05,222 copying oncoref/expression_engine.py -> build/lib/oncoref 2026-07-08T20:50:05,224 copying oncoref/cli.py -> build/lib/oncoref 2026-07-08T20:50:05,227 copying oncoref/cancer_genes.py -> build/lib/oncoref 2026-07-08T20:50:05,229 copying oncoref/expression_builders.py -> build/lib/oncoref 2026-07-08T20:50:05,232 copying oncoref/cta_coverage.py -> build/lib/oncoref 2026-07-08T20:50:05,234 copying oncoref/__init__.py -> build/lib/oncoref 2026-07-08T20:50:05,237 copying oncoref/ici_response.py -> build/lib/oncoref 2026-07-08T20:50:05,239 copying oncoref/cta_curation_plots.py -> build/lib/oncoref 2026-07-08T20:50:05,241 copying oncoref/source_matrices.py -> build/lib/oncoref 2026-07-08T20:50:05,243 copying oncoref/normalization.py -> build/lib/oncoref 2026-07-08T20:50:05,246 copying oncoref/cohorts.py -> build/lib/oncoref 2026-07-08T20:50:05,248 copying oncoref/load_dataset.py -> build/lib/oncoref 2026-07-08T20:50:05,250 copying oncoref/version.py -> build/lib/oncoref 2026-07-08T20:50:05,252 copying oncoref/catalog.py -> build/lib/oncoref 2026-07-08T20:50:05,255 copying oncoref/incidence.py -> build/lib/oncoref 2026-07-08T20:50:05,257 copying oncoref/cta_peptides.py -> build/lib/oncoref 2026-07-08T20:50:05,259 copying oncoref/data_manifest.py -> build/lib/oncoref 2026-07-08T20:50:05,261 copying oncoref/samples.py -> build/lib/oncoref 2026-07-08T20:50:05,275 creating build/lib/oncoref/data 2026-07-08T20:50:05,276 copying oncoref/data/cancer-driver-genes.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,280 copying oncoref/data/cancer-code-burden-map.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,282 copying oncoref/data/family-burden-map.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,284 copying oncoref/data/source-matrices.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,286 copying oncoref/data/proteoform-collapse-overrides.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,289 copying oncoref/data/proteoform-groups.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,291 copying oncoref/data/ribosomal-protein-pseudogenes.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,294 copying oncoref/data/rare-cancer-fusion-rules.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,297 copying oncoref/data/cancer-lineage-group-overrides.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,299 copying oncoref/data/cta-candidate-references.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,301 copying oncoref/data/cancer-testis-antigens.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,306 copying oncoref/data/cancer-ici-response.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,309 copying oncoref/data/cancer-subtype-groupings.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,311 copying oncoref/data/cohort-registry.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,313 copying oncoref/data/histone-genes.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,316 copying oncoref/data/cancer-apd1-response.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,319 copying oncoref/data/ribosomal-protein-genes.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,322 copying oncoref/data/cancer-incidence-mortality.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,324 copying oncoref/data/cta-specificity-audit.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,326 copying oncoref/data/clean-tpm-censored-genes.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,331 copying oncoref/data/cta-ihc-unreliable.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,333 copying oncoref/data/cancer-fusions.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,337 copying oncoref/data/clean-tpm-biological-housekeeping-genes.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,340 copying oncoref/data/narrative-gene-sets.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,342 copying oncoref/data/cancer-driver-variants.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,345 copying oncoref/data/cancer-normal-tissue-map.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,348 copying oncoref/data/tissue-burden-map.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,351 copying oncoref/data/degenerate-subtype-pairs.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,355 copying oncoref/data/cancer-type-genes.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,358 copying oncoref/data/expression-artifact-gene-universe-deltas.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,368 copying oncoref/data/ensembl-id-aliases.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,378 copying oncoref/data/cancer-key-genes.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,384 copying oncoref/data/cancer-viral-antigens.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,386 copying oncoref/data/cancer-cohort-aggregates.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,389 copying oncoref/data/hemoglobin-genes.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,391 copying oncoref/data/extra-tx-mappings.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,393 copying oncoref/data/proteoform-groups-genome.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,396 copying oncoref/data/cancer-lineage-groups.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,399 copying oncoref/data/censored-gene-reference-tpm.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,401 copying oncoref/data/numt-pseudogenes.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,404 copying oncoref/data/fusion-expression-effects.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,407 copying oncoref/data/cancer-mismatch-repair-statuses.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,409 copying oncoref/data/cancer-ici-response-estimates.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,414 copying oncoref/data/cancer-type-registry.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,417 copying oncoref/data/mitochondrial-genes.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,420 copying oncoref/data/housekeeping-genes.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,422 copying oncoref/data/cta-clinical-targets.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,424 copying oncoref/data/disease-state-rules.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,427 copying oncoref/data/rrna-and-pseudogenes.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,429 copying oncoref/data/cancer-response-signatures.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,432 copying oncoref/data/small-noncoding-rnas.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,437 copying oncoref/data/cancer-frameshift-burden.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,439 copying oncoref/data/nuclear-retained-lncrnas.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,441 copying oncoref/data/cdna-identical-gene-groups.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,444 copying oncoref/data/cancer-expression-source-candidates.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,447 copying oncoref/data/fusion-surrogate-expression.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,450 copying oncoref/data/cancer-tmb.csv -> build/lib/oncoref/data 2026-07-08T20:50:05,453 copying oncoref/data/canonical-gene-space.csv.gz -> build/lib/oncoref/data 2026-07-08T20:50:05,464 copying oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/lib/oncoref/data 2026-07-08T20:50:05,473 copying oncoref/data/cancer-reference-expression-samples.csv.gz -> build/lib/oncoref/data 2026-07-08T20:50:05,482 copying oncoref/data/ncbi-entrez-gene-mappings.csv.gz -> build/lib/oncoref/data 2026-07-08T20:50:05,506 copying oncoref/data/expression_sources.yaml -> build/lib/oncoref/data 2026-07-08T20:50:05,521 installing to build/bdist.linux-armv7l/wheel 2026-07-08T20:50:05,521 running install 2026-07-08T20:50:05,545 running install_lib 2026-07-08T20:50:05,551 creating build/bdist.linux-armv7l/wheel 2026-07-08T20:50:05,554 creating build/bdist.linux-armv7l/wheel/oncoref 2026-07-08T20:50:05,555 copying build/lib/oncoref/tmb.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,558 copying build/lib/oncoref/peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,561 copying build/lib/oncoref/coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,564 copying build/lib/oncoref/gene_ids.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,567 copying build/lib/oncoref/hpa.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,570 copying build/lib/oncoref/cta_regen.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,573 copying build/lib/oncoref/cancer_ontology.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,575 copying build/lib/oncoref/cta.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,578 copying build/lib/oncoref/cancer_types.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,581 copying build/lib/oncoref/data_bundle.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,585 copying build/lib/oncoref/gene_qc.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,587 copying build/lib/oncoref/plots.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,591 copying build/lib/oncoref/proteoforms.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,594 copying build/lib/oncoref/response_signatures.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,596 copying build/lib/oncoref/gene_families.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,598 copying build/lib/oncoref/ici.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,602 copying build/lib/oncoref/fusions.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,604 copying build/lib/oncoref/antigen_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,607 copying build/lib/oncoref/expression_registry.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,609 copying build/lib/oncoref/cta_tissues.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,611 copying build/lib/oncoref/genome.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,614 copying build/lib/oncoref/reference_data.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,617 copying build/lib/oncoref/apd1.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,619 copying build/lib/oncoref/expression.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,625 copying build/lib/oncoref/expression_engine.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,629 creating build/bdist.linux-armv7l/wheel/oncoref/data 2026-07-08T20:50:05,631 copying build/lib/oncoref/data/cancer-driver-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,635 copying build/lib/oncoref/data/cancer-code-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,637 copying build/lib/oncoref/data/family-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,639 copying build/lib/oncoref/data/source-matrices.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,641 copying build/lib/oncoref/data/proteoform-collapse-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,643 copying build/lib/oncoref/data/proteoform-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,646 copying build/lib/oncoref/data/ribosomal-protein-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,650 copying build/lib/oncoref/data/canonical-gene-space.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,663 copying build/lib/oncoref/data/rare-cancer-fusion-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,666 copying build/lib/oncoref/data/cancer-lineage-group-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,668 copying build/lib/oncoref/data/cta-candidate-references.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,671 copying build/lib/oncoref/data/cancer-testis-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,676 copying build/lib/oncoref/data/expression_sources.yaml -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,679 copying build/lib/oncoref/data/cancer-ici-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,681 copying build/lib/oncoref/data/cancer-subtype-groupings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,683 copying build/lib/oncoref/data/cohort-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,686 copying build/lib/oncoref/data/histone-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,688 copying build/lib/oncoref/data/cancer-apd1-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,690 copying build/lib/oncoref/data/ribosomal-protein-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,692 copying build/lib/oncoref/data/cancer-incidence-mortality.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,694 copying build/lib/oncoref/data/cta-specificity-audit.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,696 copying build/lib/oncoref/data/clean-tpm-censored-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,700 copying build/lib/oncoref/data/cta-ihc-unreliable.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,701 copying build/lib/oncoref/data/cancer-fusions.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,704 copying build/lib/oncoref/data/clean-tpm-biological-housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,706 copying build/lib/oncoref/data/narrative-gene-sets.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,708 copying build/lib/oncoref/data/cancer-driver-variants.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,711 copying build/lib/oncoref/data/cancer-normal-tissue-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,713 copying build/lib/oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,721 copying build/lib/oncoref/data/tissue-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,723 copying build/lib/oncoref/data/degenerate-subtype-pairs.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,725 copying build/lib/oncoref/data/cancer-type-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,728 copying build/lib/oncoref/data/expression-artifact-gene-universe-deltas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,737 copying build/lib/oncoref/data/ensembl-id-aliases.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,747 copying build/lib/oncoref/data/cancer-key-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,753 copying build/lib/oncoref/data/cancer-viral-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,755 copying build/lib/oncoref/data/cancer-cohort-aggregates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,757 copying build/lib/oncoref/data/hemoglobin-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,759 copying build/lib/oncoref/data/extra-tx-mappings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,762 copying build/lib/oncoref/data/proteoform-groups-genome.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,765 copying build/lib/oncoref/data/cancer-lineage-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,767 copying build/lib/oncoref/data/censored-gene-reference-tpm.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,770 copying build/lib/oncoref/data/numt-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,773 copying build/lib/oncoref/data/fusion-expression-effects.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,775 copying build/lib/oncoref/data/cancer-mismatch-repair-statuses.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,778 copying build/lib/oncoref/data/cancer-ici-response-estimates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,787 copying build/lib/oncoref/data/cancer-type-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,791 copying build/lib/oncoref/data/mitochondrial-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,793 copying build/lib/oncoref/data/housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,795 copying build/lib/oncoref/data/cta-clinical-targets.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,797 copying build/lib/oncoref/data/disease-state-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,799 copying build/lib/oncoref/data/rrna-and-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,802 copying build/lib/oncoref/data/cancer-response-signatures.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,804 copying build/lib/oncoref/data/small-noncoding-rnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,810 copying build/lib/oncoref/data/cancer-frameshift-burden.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,812 copying build/lib/oncoref/data/nuclear-retained-lncrnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,814 copying build/lib/oncoref/data/cdna-identical-gene-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,818 copying build/lib/oncoref/data/cancer-expression-source-candidates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,821 copying build/lib/oncoref/data/fusion-surrogate-expression.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,824 copying build/lib/oncoref/data/cancer-reference-expression-samples.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,831 copying build/lib/oncoref/data/cancer-tmb.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,833 copying build/lib/oncoref/data/ncbi-entrez-gene-mappings.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T20:50:05,851 copying build/lib/oncoref/cli.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,854 copying build/lib/oncoref/cancer_genes.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,857 copying build/lib/oncoref/expression_builders.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,860 copying build/lib/oncoref/cta_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,861 copying build/lib/oncoref/__init__.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,864 copying build/lib/oncoref/ici_response.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,866 copying build/lib/oncoref/cta_curation_plots.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,869 copying build/lib/oncoref/source_matrices.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,871 copying build/lib/oncoref/normalization.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,874 copying build/lib/oncoref/cohorts.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,876 copying build/lib/oncoref/load_dataset.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,879 copying build/lib/oncoref/version.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,881 copying build/lib/oncoref/catalog.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,884 copying build/lib/oncoref/incidence.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,886 copying build/lib/oncoref/cta_peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,888 copying build/lib/oncoref/data_manifest.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,891 copying build/lib/oncoref/samples.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T20:50:05,892 running install_egg_info 2026-07-08T20:50:05,902 running egg_info 2026-07-08T20:50:05,907 writing oncoref.egg-info/PKG-INFO 2026-07-08T20:50:05,912 writing dependency_links to oncoref.egg-info/dependency_links.txt 2026-07-08T20:50:05,914 writing entry points to oncoref.egg-info/entry_points.txt 2026-07-08T20:50:05,916 writing requirements to oncoref.egg-info/requires.txt 2026-07-08T20:50:05,917 writing top-level names to oncoref.egg-info/top_level.txt 2026-07-08T20:50:05,937 reading manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-08T20:50:05,946 reading manifest template 'MANIFEST.in' 2026-07-08T20:50:05,948 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-07-08T20:50:05,950 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-07-08T20:50:05,951 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-07-08T20:50:05,952 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-07-08T20:50:05,953 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-07-08T20:50:05,954 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-07-08T20:50:05,955 adding license file 'LICENSE' 2026-07-08T20:50:05,963 writing manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-08T20:50:05,965 Copying oncoref.egg-info to build/bdist.linux-armv7l/wheel/./oncoref-1.8.84-py3.11.egg-info 2026-07-08T20:50:05,977 running install_scripts 2026-07-08T20:50:05,990 creating build/bdist.linux-armv7l/wheel/oncoref-1.8.84.dist-info/WHEEL 2026-07-08T20:50:05,993 creating '/tmp/pip-wheel-cg8vnhh7/.tmp-prhk8yqu/oncoref-1.8.84-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-07-08T20:50:05,997 adding 'oncoref/__init__.py' 2026-07-08T20:50:05,999 adding 'oncoref/antigen_coverage.py' 2026-07-08T20:50:06,001 adding 'oncoref/apd1.py' 2026-07-08T20:50:06,003 adding 'oncoref/cancer_genes.py' 2026-07-08T20:50:06,004 adding 'oncoref/cancer_ontology.py' 2026-07-08T20:50:06,013 adding 'oncoref/cancer_types.py' 2026-07-08T20:50:06,016 adding 'oncoref/catalog.py' 2026-07-08T20:50:06,019 adding 'oncoref/cli.py' 2026-07-08T20:50:06,021 adding 'oncoref/cohorts.py' 2026-07-08T20:50:06,024 adding 'oncoref/coverage.py' 2026-07-08T20:50:06,028 adding 'oncoref/cta.py' 2026-07-08T20:50:06,030 adding 'oncoref/cta_coverage.py' 2026-07-08T20:50:06,032 adding 'oncoref/cta_curation_plots.py' 2026-07-08T20:50:06,033 adding 'oncoref/cta_peptides.py' 2026-07-08T20:50:06,036 adding 'oncoref/cta_regen.py' 2026-07-08T20:50:06,038 adding 'oncoref/cta_tissues.py' 2026-07-08T20:50:06,042 adding 'oncoref/data_bundle.py' 2026-07-08T20:50:06,045 adding 'oncoref/data_manifest.py' 2026-07-08T20:50:06,062 adding 'oncoref/expression.py' 2026-07-08T20:50:06,070 adding 'oncoref/expression_builders.py' 2026-07-08T20:50:06,074 adding 'oncoref/expression_engine.py' 2026-07-08T20:50:06,076 adding 'oncoref/expression_registry.py' 2026-07-08T20:50:06,078 adding 'oncoref/fusions.py' 2026-07-08T20:50:06,080 adding 'oncoref/gene_families.py' 2026-07-08T20:50:06,083 adding 'oncoref/gene_ids.py' 2026-07-08T20:50:06,085 adding 'oncoref/gene_qc.py' 2026-07-08T20:50:06,087 adding 'oncoref/genome.py' 2026-07-08T20:50:06,089 adding 'oncoref/hpa.py' 2026-07-08T20:50:06,093 adding 'oncoref/ici.py' 2026-07-08T20:50:06,095 adding 'oncoref/ici_response.py' 2026-07-08T20:50:06,097 adding 'oncoref/incidence.py' 2026-07-08T20:50:06,099 adding 'oncoref/load_dataset.py' 2026-07-08T20:50:06,104 adding 'oncoref/normalization.py' 2026-07-08T20:50:06,106 adding 'oncoref/peptides.py' 2026-07-08T20:50:06,113 adding 'oncoref/plots.py' 2026-07-08T20:50:06,116 adding 'oncoref/proteoforms.py' 2026-07-08T20:50:06,118 adding 'oncoref/reference_data.py' 2026-07-08T20:50:06,119 adding 'oncoref/response_signatures.py' 2026-07-08T20:50:06,120 adding 'oncoref/samples.py' 2026-07-08T20:50:06,122 adding 'oncoref/source_matrices.py' 2026-07-08T20:50:06,124 adding 'oncoref/tmb.py' 2026-07-08T20:50:06,125 adding 'oncoref/version.py' 2026-07-08T20:50:06,129 adding 'oncoref/data/cancer-apd1-response.csv' 2026-07-08T20:50:06,130 adding 'oncoref/data/cancer-code-burden-map.csv' 2026-07-08T20:50:06,131 adding 'oncoref/data/cancer-cohort-aggregates.csv' 2026-07-08T20:50:06,136 adding 'oncoref/data/cancer-driver-genes.csv' 2026-07-08T20:50:06,139 adding 'oncoref/data/cancer-driver-variants.csv' 2026-07-08T20:50:06,142 adding 'oncoref/data/cancer-expression-source-candidates.csv' 2026-07-08T20:50:06,144 adding 'oncoref/data/cancer-frameshift-burden.csv' 2026-07-08T20:50:06,147 adding 'oncoref/data/cancer-fusions.csv' 2026-07-08T20:50:06,164 adding 'oncoref/data/cancer-ici-response-estimates.csv' 2026-07-08T20:50:06,170 adding 'oncoref/data/cancer-ici-response.csv' 2026-07-08T20:50:06,171 adding 'oncoref/data/cancer-incidence-mortality.csv' 2026-07-08T20:50:06,186 adding 'oncoref/data/cancer-key-genes.csv' 2026-07-08T20:50:06,188 adding 'oncoref/data/cancer-lineage-group-overrides.csv' 2026-07-08T20:50:06,190 adding 'oncoref/data/cancer-lineage-groups.csv' 2026-07-08T20:50:06,191 adding 'oncoref/data/cancer-mismatch-repair-statuses.csv' 2026-07-08T20:50:06,193 adding 'oncoref/data/cancer-normal-tissue-map.csv' 2026-07-08T20:50:06,221 adding 'oncoref/data/cancer-reference-expression-samples.csv.gz' 2026-07-08T20:50:06,225 adding 'oncoref/data/cancer-response-signatures.csv' 2026-07-08T20:50:06,226 adding 'oncoref/data/cancer-subtype-groupings.csv' 2026-07-08T20:50:06,238 adding 'oncoref/data/cancer-testis-antigens.csv' 2026-07-08T20:50:06,241 adding 'oncoref/data/cancer-tmb.csv' 2026-07-08T20:50:06,243 adding 'oncoref/data/cancer-type-genes.csv' 2026-07-08T20:50:06,248 adding 'oncoref/data/cancer-type-registry.csv' 2026-07-08T20:50:06,249 adding 'oncoref/data/cancer-viral-antigens.csv' 2026-07-08T20:50:06,302 adding 'oncoref/data/canonical-gene-space.csv.gz' 2026-07-08T20:50:06,319 adding 'oncoref/data/cdna-identical-gene-groups.csv' 2026-07-08T20:50:06,325 adding 'oncoref/data/censored-gene-reference-tpm.csv' 2026-07-08T20:50:06,327 adding 'oncoref/data/clean-tpm-biological-housekeeping-genes.csv' 2026-07-08T20:50:06,337 adding 'oncoref/data/clean-tpm-censored-genes.csv' 2026-07-08T20:50:06,340 adding 'oncoref/data/cohort-registry.csv' 2026-07-08T20:50:06,341 adding 'oncoref/data/cta-candidate-references.csv' 2026-07-08T20:50:06,342 adding 'oncoref/data/cta-clinical-targets.csv' 2026-07-08T20:50:06,346 adding 'oncoref/data/cta-ihc-unreliable.csv' 2026-07-08T20:50:06,348 adding 'oncoref/data/cta-specificity-audit.csv' 2026-07-08T20:50:06,349 adding 'oncoref/data/degenerate-subtype-pairs.csv' 2026-07-08T20:50:06,351 adding 'oncoref/data/disease-state-rules.csv' 2026-07-08T20:50:06,378 adding 'oncoref/data/ensembl-id-aliases.csv' 2026-07-08T20:50:06,391 adding 'oncoref/data/expression-artifact-gene-universe-deltas.csv' 2026-07-08T20:50:06,397 adding 'oncoref/data/expression_sources.yaml' 2026-07-08T20:50:06,399 adding 'oncoref/data/extra-tx-mappings.csv' 2026-07-08T20:50:06,400 adding 'oncoref/data/family-burden-map.csv' 2026-07-08T20:50:06,401 adding 'oncoref/data/fusion-expression-effects.csv' 2026-07-08T20:50:06,403 adding 'oncoref/data/fusion-surrogate-expression.csv' 2026-07-08T20:50:06,404 adding 'oncoref/data/hemoglobin-genes.csv' 2026-07-08T20:50:06,406 adding 'oncoref/data/histone-genes.csv' 2026-07-08T20:50:06,407 adding 'oncoref/data/housekeeping-genes.csv' 2026-07-08T20:50:06,408 adding 'oncoref/data/mitochondrial-genes.csv' 2026-07-08T20:50:06,409 adding 'oncoref/data/narrative-gene-sets.csv' 2026-07-08T20:50:06,511 adding 'oncoref/data/ncbi-entrez-gene-mappings.csv.gz' 2026-07-08T20:50:06,569 adding 'oncoref/data/ncbi-symbol-synonyms.csv.gz' 2026-07-08T20:50:06,575 adding 'oncoref/data/nuclear-retained-lncrnas.csv' 2026-07-08T20:50:06,578 adding 'oncoref/data/numt-pseudogenes.csv' 2026-07-08T20:50:06,579 adding 'oncoref/data/proteoform-collapse-overrides.csv' 2026-07-08T20:50:06,583 adding 'oncoref/data/proteoform-groups-genome.csv' 2026-07-08T20:50:06,585 adding 'oncoref/data/proteoform-groups.csv' 2026-07-08T20:50:06,587 adding 'oncoref/data/rare-cancer-fusion-rules.csv' 2026-07-08T20:50:06,589 adding 'oncoref/data/ribosomal-protein-genes.csv' 2026-07-08T20:50:06,598 adding 'oncoref/data/ribosomal-protein-pseudogenes.csv' 2026-07-08T20:50:06,602 adding 'oncoref/data/rrna-and-pseudogenes.csv' 2026-07-08T20:50:06,630 adding 'oncoref/data/small-noncoding-rnas.csv' 2026-07-08T20:50:06,633 adding 'oncoref/data/source-matrices.csv' 2026-07-08T20:50:06,635 adding 'oncoref/data/tissue-burden-map.csv' 2026-07-08T20:50:06,639 adding 'oncoref-1.8.84.dist-info/licenses/LICENSE' 2026-07-08T20:50:06,641 adding 'oncoref-1.8.84.dist-info/METADATA' 2026-07-08T20:50:06,642 adding 'oncoref-1.8.84.dist-info/WHEEL' 2026-07-08T20:50:06,643 adding 'oncoref-1.8.84.dist-info/entry_points.txt' 2026-07-08T20:50:06,644 adding 'oncoref-1.8.84.dist-info/top_level.txt' 2026-07-08T20:50:06,646 adding 'oncoref-1.8.84.dist-info/RECORD' 2026-07-08T20:50:06,673 removing build/bdist.linux-armv7l/wheel 2026-07-08T20:50:06,794 Building wheel for oncoref (pyproject.toml): finished with status 'done' 2026-07-08T20:50:06,852 Created wheel for oncoref: filename=oncoref-1.8.84-py3-none-any.whl size=2660992 sha256=860bd3f0a41a9234a6601c6da23257b5665ac15aed369267c5c1558c52d6b61a 2026-07-08T20:50:06,853 Stored in directory: /tmp/pip-ephem-wheel-cache-w3uy0xpn/wheels/c1/68/47/7f77b16c4329412799c39c24adb25c4bc79c1b32c37c44e72f 2026-07-08T20:50:06,869 Successfully built oncoref 2026-07-08T20:50:06,952 Removed build tracker: '/tmp/pip-build-tracker-ivgbhvao'