2026-07-07T06:54:46,447 Created temporary directory: /tmp/pip-ephem-wheel-cache-2k5ew3jj 2026-07-07T06:54:46,449 Created temporary directory: /tmp/pip-build-tracker-45ajore3 2026-07-07T06:54:46,450 Initialized build tracking at /tmp/pip-build-tracker-45ajore3 2026-07-07T06:54:46,450 Created build tracker: /tmp/pip-build-tracker-45ajore3 2026-07-07T06:54:46,451 Entered build tracker: /tmp/pip-build-tracker-45ajore3 2026-07-07T06:54:46,452 Created temporary directory: /tmp/pip-wheel-8klbfw2w 2026-07-07T06:54:46,455 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 2026-07-07T06:54:46,457 Created temporary directory: /tmp/pip-ephem-wheel-cache-dr8ziphm 2026-07-07T06:54:46,482 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-07-07T06:54:46,486 2 location(s) to search for versions of oncoref: 2026-07-07T06:54:46,486 * https://pypi.org/simple/oncoref/ 2026-07-07T06:54:46,486 * https://www.piwheels.org/simple/oncoref/ 2026-07-07T06:54:46,487 Fetching project page and analyzing links: https://pypi.org/simple/oncoref/ 2026-07-07T06:54:46,488 Getting page https://pypi.org/simple/oncoref/ 2026-07-07T06:54:46,489 Found index url https://pypi.org/simple 2026-07-07T06:54:46,775 Fetched page https://pypi.org/simple/oncoref/ as application/vnd.pypi.simple.v1+json 2026-07-07T06:54:46,804 Skipping link: No binaries permitted for oncoref: 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link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/3d/cf/214dbe1e3f3ca56d6354d7f2f87283085238025685b7287be5a3020db87c/oncoref-1.8.0-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9) 2026-07-07T06:54:46,808 Found link https://files.pythonhosted.org/packages/10/a1/9b3e573b2e9ce5903eef398c68d06cd3d1425a88c87c3f5d8dbe79cbfb3c/oncoref-1.8.0.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.8.0 2026-07-07T06:54:46,809 Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/56/b4/103c9511736de31d6182b47aaf4f03da47c52933be96ea7a060ad7478ae3/oncoref-1.8.1-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9) 2026-07-07T06:54:46,810 Found link https://files.pythonhosted.org/packages/21/3e/8080dbac7eaa58029775dd4937cb7dc70d1e65b52e358ccb75b5dd8ed63e/oncoref-1.8.1.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 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Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/5e/38/d4f824676b3d280e159182422711e46a9be12a1078869b3b3da846a959d6/oncoref-1.8.13-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9) 2026-07-07T06:54:46,830 Found link https://files.pythonhosted.org/packages/53/53/a8ca36b70ca14b5654f882f5a6fec1709a385bc2cc18d4bde37a2f32d454/oncoref-1.8.13.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.8.13 2026-07-07T06:54:46,831 Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/2f/c1/703bd890ae830651eae083a090278ba8254ac89bae1c0bfefed061c3e2eb/oncoref-1.8.14-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9) 2026-07-07T06:54:46,832 Found link https://files.pythonhosted.org/packages/72/05/f82628c00d880f035d82572d1160a43c00ca2e7c45b010b4a9f300a5a863/oncoref-1.8.14.tar.gz (from https://pypi.org/simple/oncoref/) 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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) 2026-07-07T06:54:47,303 Skipping link: not a file: https://www.piwheels.org/simple/oncoref/ 2026-07-07T06:54:47,303 Skipping link: not a file: https://pypi.org/simple/oncoref/ 2026-07-07T06:54:47,333 Given no hashes to check 1 links for project 'oncoref': discarding no candidates 2026-07-07T06:54:47,353 Collecting oncoref==1.8.66 2026-07-07T06:54:47,355 Created temporary directory: /tmp/pip-unpack-cw474tm_ 2026-07-07T06:54:47,684 Downloading oncoref-1.8.66.tar.gz (1.8 MB) 2026-07-07T06:54:48,494 Added oncoref==1.8.66 from https://files.pythonhosted.org/packages/6e/02/92a7469d50bdfd44c6ff1df2ccb750b828cbac3c1dc9c7ab574d14e29785/oncoref-1.8.66.tar.gz to build tracker '/tmp/pip-build-tracker-45ajore3' 2026-07-07T06:54:48,501 Created temporary directory: /tmp/pip-build-env-rci6kx4d 2026-07-07T06:54:48,506 Installing build dependencies: started 2026-07-07T06:54:48,507 Running command pip subprocess to install build dependencies 2026-07-07T06:54:49,656 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-07-07T06:54:50,113 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 2026-07-07T06:54:50,137 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-07-07T06:54:52,167 Collecting setuptools>=61.0 2026-07-07T06:54:52,187 Using cached setuptools-83.0.0-py3-none-any.whl (1.0 MB) 2026-07-07T06:54:52,469 Collecting wheel 2026-07-07T06:54:52,470 Obtaining dependency information for wheel from https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata 2026-07-07T06:54:52,485 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB) 2026-07-07T06:54:52,669 Collecting packaging>=24.0 2026-07-07T06:54:52,670 Obtaining dependency information for packaging>=24.0 from https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata 2026-07-07T06:54:52,683 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata (3.5 kB) 2026-07-07T06:54:52,875 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB) 2026-07-07T06:54:52,899 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB) 2026-07-07T06:54:52,921 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB) 2026-07-07T06:54:52,985 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB) 2026-07-07T06:54:55,740 Installing collected packages: setuptools, packaging, wheel 2026-07-07T06:54:59,263 Creating /tmp/pip-build-env-rci6kx4d/overlay/local/bin 2026-07-07T06:54:59,265 changing mode of /tmp/pip-build-env-rci6kx4d/overlay/local/bin/wheel to 755 2026-07-07T06:54:59,285 Successfully installed packaging-26.2 setuptools-83.0.0 wheel-0.47.0 2026-07-07T06:54:59,571 Installing build dependencies: finished with status 'done' 2026-07-07T06:54:59,578 Getting requirements to build wheel: started 2026-07-07T06:54:59,579 Running command Getting requirements to build wheel 2026-07-07T06:55:00,294 running egg_info 2026-07-07T06:55:00,300 writing oncoref.egg-info/PKG-INFO 2026-07-07T06:55:00,306 writing dependency_links to oncoref.egg-info/dependency_links.txt 2026-07-07T06:55:00,308 writing entry points to oncoref.egg-info/entry_points.txt 2026-07-07T06:55:00,311 writing requirements to oncoref.egg-info/requires.txt 2026-07-07T06:55:00,312 writing top-level names to oncoref.egg-info/top_level.txt 2026-07-07T06:55:00,347 reading manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-07T06:55:00,357 reading manifest template 'MANIFEST.in' 2026-07-07T06:55:00,359 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-07-07T06:55:00,360 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-07-07T06:55:00,362 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-07-07T06:55:00,363 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-07-07T06:55:00,365 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-07-07T06:55:00,366 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-07-07T06:55:00,367 adding license file 'LICENSE' 2026-07-07T06:55:00,375 writing manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-07T06:55:00,473 Getting requirements to build wheel: finished with status 'done' 2026-07-07T06:55:00,477 Created temporary directory: /tmp/pip-modern-metadata-6e98oojz 2026-07-07T06:55:00,479 Preparing metadata (pyproject.toml): started 2026-07-07T06:55:00,480 Running command Preparing metadata (pyproject.toml) 2026-07-07T06:55:01,129 running dist_info 2026-07-07T06:55:01,140 creating /tmp/pip-modern-metadata-6e98oojz/oncoref.egg-info 2026-07-07T06:55:01,141 writing /tmp/pip-modern-metadata-6e98oojz/oncoref.egg-info/PKG-INFO 2026-07-07T06:55:01,147 writing dependency_links to /tmp/pip-modern-metadata-6e98oojz/oncoref.egg-info/dependency_links.txt 2026-07-07T06:55:01,149 writing entry points to /tmp/pip-modern-metadata-6e98oojz/oncoref.egg-info/entry_points.txt 2026-07-07T06:55:01,152 writing requirements to /tmp/pip-modern-metadata-6e98oojz/oncoref.egg-info/requires.txt 2026-07-07T06:55:01,153 writing top-level names to /tmp/pip-modern-metadata-6e98oojz/oncoref.egg-info/top_level.txt 2026-07-07T06:55:01,155 writing manifest file '/tmp/pip-modern-metadata-6e98oojz/oncoref.egg-info/SOURCES.txt' 2026-07-07T06:55:01,188 reading manifest file '/tmp/pip-modern-metadata-6e98oojz/oncoref.egg-info/SOURCES.txt' 2026-07-07T06:55:01,190 reading manifest template 'MANIFEST.in' 2026-07-07T06:55:01,192 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-07-07T06:55:01,194 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-07-07T06:55:01,195 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-07-07T06:55:01,197 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-07-07T06:55:01,198 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-07-07T06:55:01,199 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-07-07T06:55:01,199 adding license file 'LICENSE' 2026-07-07T06:55:01,206 writing manifest file '/tmp/pip-modern-metadata-6e98oojz/oncoref.egg-info/SOURCES.txt' 2026-07-07T06:55:01,208 creating '/tmp/pip-modern-metadata-6e98oojz/oncoref-1.8.66.dist-info' 2026-07-07T06:55:01,347 Preparing metadata (pyproject.toml): finished with status 'done' 2026-07-07T06:55:01,354 Source in /tmp/pip-wheel-8klbfw2w/oncoref_c83fa34c892b4bbeb5b669daec356bac has version 1.8.66, which satisfies requirement oncoref==1.8.66 from https://files.pythonhosted.org/packages/6e/02/92a7469d50bdfd44c6ff1df2ccb750b828cbac3c1dc9c7ab574d14e29785/oncoref-1.8.66.tar.gz 2026-07-07T06:55:01,355 Removed oncoref==1.8.66 from https://files.pythonhosted.org/packages/6e/02/92a7469d50bdfd44c6ff1df2ccb750b828cbac3c1dc9c7ab574d14e29785/oncoref-1.8.66.tar.gz from build tracker '/tmp/pip-build-tracker-45ajore3' 2026-07-07T06:55:01,363 Created temporary directory: /tmp/pip-unpack-izrzfklc 2026-07-07T06:55:01,364 Building wheels for collected packages: oncoref 2026-07-07T06:55:01,370 Created temporary directory: /tmp/pip-wheel-ykmsk65g 2026-07-07T06:55:01,370 Destination directory: /tmp/pip-wheel-ykmsk65g 2026-07-07T06:55:01,373 Building wheel for oncoref (pyproject.toml): started 2026-07-07T06:55:01,375 Running command Building wheel for oncoref (pyproject.toml) 2026-07-07T06:55:02,008 running bdist_wheel 2026-07-07T06:55:02,026 running build 2026-07-07T06:55:02,026 running build_py 2026-07-07T06:55:02,034 creating build/lib/oncoref 2026-07-07T06:55:02,036 copying oncoref/expression.py -> build/lib/oncoref 2026-07-07T06:55:02,041 copying oncoref/cta_coverage.py -> build/lib/oncoref 2026-07-07T06:55:02,043 copying oncoref/antigen_coverage.py -> build/lib/oncoref 2026-07-07T06:55:02,045 copying oncoref/cli.py -> build/lib/oncoref 2026-07-07T06:55:02,048 copying oncoref/catalog.py -> build/lib/oncoref 2026-07-07T06:55:02,050 copying oncoref/cta_curation_plots.py -> build/lib/oncoref 2026-07-07T06:55:02,053 copying oncoref/response_signatures.py -> build/lib/oncoref 2026-07-07T06:55:02,055 copying oncoref/gene_qc.py -> build/lib/oncoref 2026-07-07T06:55:02,057 copying oncoref/cancer_ontology.py -> build/lib/oncoref 2026-07-07T06:55:02,060 copying oncoref/coverage.py -> build/lib/oncoref 2026-07-07T06:55:02,062 copying oncoref/samples.py -> build/lib/oncoref 2026-07-07T06:55:02,065 copying oncoref/expression_engine.py -> build/lib/oncoref 2026-07-07T06:55:02,068 copying oncoref/cohorts.py -> build/lib/oncoref 2026-07-07T06:55:02,069 copying oncoref/tmb.py -> build/lib/oncoref 2026-07-07T06:55:02,072 copying oncoref/plots.py -> build/lib/oncoref 2026-07-07T06:55:02,075 copying oncoref/genome.py -> build/lib/oncoref 2026-07-07T06:55:02,077 copying oncoref/expression_builders.py -> build/lib/oncoref 2026-07-07T06:55:02,079 copying oncoref/gene_families.py -> build/lib/oncoref 2026-07-07T06:55:02,082 copying oncoref/proteoforms.py -> build/lib/oncoref 2026-07-07T06:55:02,084 copying oncoref/cta_tissues.py -> build/lib/oncoref 2026-07-07T06:55:02,087 copying oncoref/load_dataset.py -> build/lib/oncoref 2026-07-07T06:55:02,089 copying oncoref/incidence.py -> build/lib/oncoref 2026-07-07T06:55:02,091 copying oncoref/fusions.py -> build/lib/oncoref 2026-07-07T06:55:02,093 copying oncoref/cancer_genes.py -> build/lib/oncoref 2026-07-07T06:55:02,096 copying oncoref/data_bundle.py -> build/lib/oncoref 2026-07-07T06:55:02,098 copying oncoref/apd1.py -> build/lib/oncoref 2026-07-07T06:55:02,101 copying oncoref/cta_peptides.py -> build/lib/oncoref 2026-07-07T06:55:02,103 copying oncoref/cancer_types.py -> build/lib/oncoref 2026-07-07T06:55:02,106 copying oncoref/cta_regen.py -> build/lib/oncoref 2026-07-07T06:55:02,109 copying oncoref/data_manifest.py -> build/lib/oncoref 2026-07-07T06:55:02,112 copying oncoref/peptides.py -> build/lib/oncoref 2026-07-07T06:55:02,114 copying oncoref/__init__.py -> build/lib/oncoref 2026-07-07T06:55:02,117 copying oncoref/gene_ids.py -> build/lib/oncoref 2026-07-07T06:55:02,119 copying oncoref/ici_response.py -> build/lib/oncoref 2026-07-07T06:55:02,121 copying oncoref/hpa.py -> build/lib/oncoref 2026-07-07T06:55:02,123 copying oncoref/expression_registry.py -> build/lib/oncoref 2026-07-07T06:55:02,125 copying oncoref/cta.py -> build/lib/oncoref 2026-07-07T06:55:02,128 copying oncoref/reference_data.py -> build/lib/oncoref 2026-07-07T06:55:02,131 copying oncoref/source_matrices.py -> build/lib/oncoref 2026-07-07T06:55:02,133 copying oncoref/version.py -> build/lib/oncoref 2026-07-07T06:55:02,135 copying oncoref/ici.py -> build/lib/oncoref 2026-07-07T06:55:02,138 copying oncoref/normalization.py -> build/lib/oncoref 2026-07-07T06:55:02,153 creating build/lib/oncoref/data 2026-07-07T06:55:02,154 copying oncoref/data/cancer-ici-response.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,157 copying oncoref/data/cancer-ici-response-estimates.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,164 copying oncoref/data/cancer-driver-genes.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,168 copying oncoref/data/histone-genes.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,170 copying oncoref/data/disease-state-rules.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,172 copying oncoref/data/proteoform-collapse-overrides.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,175 copying oncoref/data/censored-gene-reference-tpm.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,178 copying oncoref/data/fusion-surrogate-expression.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,181 copying oncoref/data/nuclear-retained-lncrnas.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,183 copying oncoref/data/clean-tpm-biological-housekeeping-genes.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,185 copying oncoref/data/cancer-testis-antigens.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,190 copying oncoref/data/rrna-and-pseudogenes.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,193 copying oncoref/data/housekeeping-genes.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,195 copying oncoref/data/mitochondrial-genes.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,197 copying oncoref/data/cancer-subtype-groupings.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,199 copying oncoref/data/cancer-cohort-aggregates.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,201 copying oncoref/data/cancer-viral-antigens.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,203 copying oncoref/data/cancer-lineage-groups.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,205 copying oncoref/data/ensembl-id-aliases.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,215 copying oncoref/data/cancer-code-burden-map.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,217 copying oncoref/data/cancer-type-registry.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,220 copying oncoref/data/cancer-fusions.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,223 copying oncoref/data/cancer-incidence-mortality.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,225 copying oncoref/data/cancer-driver-variants.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,228 copying oncoref/data/proteoform-groups-genome.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,232 copying oncoref/data/cancer-lineage-group-overrides.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,234 copying oncoref/data/cohort-registry.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,237 copying oncoref/data/narrative-gene-sets.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,239 copying oncoref/data/cta-ihc-unreliable.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,241 copying oncoref/data/cdna-identical-gene-groups.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,244 copying oncoref/data/small-noncoding-rnas.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,250 copying oncoref/data/extra-tx-mappings.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,253 copying oncoref/data/source-matrices.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,255 copying oncoref/data/proteoform-groups.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,257 copying oncoref/data/cancer-normal-tissue-map.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,259 copying oncoref/data/cancer-expression-source-candidates.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,262 copying oncoref/data/hemoglobin-genes.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,264 copying oncoref/data/cancer-key-genes.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,269 copying oncoref/data/family-burden-map.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,271 copying oncoref/data/rare-cancer-fusion-rules.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,274 copying oncoref/data/cancer-response-signatures.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,276 copying oncoref/data/cancer-apd1-response.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,279 copying oncoref/data/degenerate-subtype-pairs.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,281 copying oncoref/data/ribosomal-protein-genes.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,283 copying oncoref/data/cancer-frameshift-burden.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,285 copying oncoref/data/cancer-type-genes.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,288 copying oncoref/data/numt-pseudogenes.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,291 copying oncoref/data/expression-artifact-gene-universe-deltas.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,298 copying oncoref/data/tissue-burden-map.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,300 copying oncoref/data/clean-tpm-censored-genes.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,304 copying oncoref/data/cta-candidate-references.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,306 copying oncoref/data/fusion-expression-effects.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,308 copying oncoref/data/ribosomal-protein-pseudogenes.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,311 copying oncoref/data/cancer-tmb.csv -> build/lib/oncoref/data 2026-07-07T06:55:02,314 copying oncoref/data/canonical-gene-space.csv.gz -> build/lib/oncoref/data 2026-07-07T06:55:02,324 copying oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/lib/oncoref/data 2026-07-07T06:55:02,332 copying oncoref/data/cancer-reference-expression-samples.csv.gz -> build/lib/oncoref/data 2026-07-07T06:55:02,339 copying oncoref/data/expression_sources.yaml -> build/lib/oncoref/data 2026-07-07T06:55:02,353 installing to build/bdist.linux-armv7l/wheel 2026-07-07T06:55:02,353 running install 2026-07-07T06:55:02,376 running install_lib 2026-07-07T06:55:02,382 creating build/bdist.linux-armv7l/wheel 2026-07-07T06:55:02,385 creating build/bdist.linux-armv7l/wheel/oncoref 2026-07-07T06:55:02,386 copying build/lib/oncoref/expression.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,392 copying build/lib/oncoref/cta_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,394 copying build/lib/oncoref/antigen_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,396 copying build/lib/oncoref/cli.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,399 copying build/lib/oncoref/catalog.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,402 copying build/lib/oncoref/cta_curation_plots.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,405 copying build/lib/oncoref/response_signatures.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,407 copying build/lib/oncoref/gene_qc.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,409 copying build/lib/oncoref/cancer_ontology.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,412 copying build/lib/oncoref/coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,415 copying build/lib/oncoref/samples.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,417 copying build/lib/oncoref/expression_engine.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,420 copying build/lib/oncoref/cohorts.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,422 copying build/lib/oncoref/tmb.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,425 copying build/lib/oncoref/plots.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,428 copying build/lib/oncoref/genome.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,431 copying build/lib/oncoref/expression_builders.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,434 copying build/lib/oncoref/gene_families.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,437 copying build/lib/oncoref/proteoforms.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,439 copying build/lib/oncoref/cta_tissues.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,442 copying build/lib/oncoref/load_dataset.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,445 copying build/lib/oncoref/incidence.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,447 copying build/lib/oncoref/fusions.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,450 copying build/lib/oncoref/cancer_genes.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,452 copying build/lib/oncoref/data_bundle.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,455 copying build/lib/oncoref/apd1.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,458 copying build/lib/oncoref/cta_peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,460 copying build/lib/oncoref/cancer_types.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,464 copying build/lib/oncoref/cta_regen.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,468 creating build/bdist.linux-armv7l/wheel/oncoref/data 2026-07-07T06:55:02,469 copying build/lib/oncoref/data/cancer-ici-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,472 copying build/lib/oncoref/data/cancer-ici-response-estimates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,479 copying build/lib/oncoref/data/cancer-driver-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,483 copying build/lib/oncoref/data/histone-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,485 copying build/lib/oncoref/data/disease-state-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,487 copying build/lib/oncoref/data/proteoform-collapse-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,489 copying build/lib/oncoref/data/censored-gene-reference-tpm.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,492 copying build/lib/oncoref/data/fusion-surrogate-expression.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,495 copying build/lib/oncoref/data/nuclear-retained-lncrnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,497 copying build/lib/oncoref/data/clean-tpm-biological-housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,499 copying build/lib/oncoref/data/cancer-testis-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,505 copying build/lib/oncoref/data/rrna-and-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,507 copying build/lib/oncoref/data/housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,510 copying build/lib/oncoref/data/mitochondrial-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,512 copying build/lib/oncoref/data/cancer-subtype-groupings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,514 copying build/lib/oncoref/data/cancer-cohort-aggregates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,516 copying build/lib/oncoref/data/cancer-viral-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,518 copying build/lib/oncoref/data/cancer-lineage-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,520 copying build/lib/oncoref/data/ensembl-id-aliases.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,531 copying build/lib/oncoref/data/cancer-code-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,533 copying build/lib/oncoref/data/cancer-type-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,536 copying build/lib/oncoref/data/expression_sources.yaml -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,539 copying build/lib/oncoref/data/cancer-fusions.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,543 copying build/lib/oncoref/data/cancer-incidence-mortality.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,545 copying build/lib/oncoref/data/cancer-driver-variants.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,548 copying build/lib/oncoref/data/proteoform-groups-genome.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,551 copying build/lib/oncoref/data/cancer-lineage-group-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,553 copying build/lib/oncoref/data/canonical-gene-space.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,566 copying build/lib/oncoref/data/cohort-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,569 copying build/lib/oncoref/data/narrative-gene-sets.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,571 copying build/lib/oncoref/data/cta-ihc-unreliable.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,573 copying build/lib/oncoref/data/cdna-identical-gene-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,576 copying build/lib/oncoref/data/small-noncoding-rnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,582 copying build/lib/oncoref/data/extra-tx-mappings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,584 copying build/lib/oncoref/data/source-matrices.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,586 copying build/lib/oncoref/data/proteoform-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,588 copying build/lib/oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,597 copying build/lib/oncoref/data/cancer-normal-tissue-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,599 copying build/lib/oncoref/data/cancer-expression-source-candidates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,602 copying build/lib/oncoref/data/hemoglobin-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,604 copying build/lib/oncoref/data/cancer-key-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,609 copying build/lib/oncoref/data/family-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,611 copying build/lib/oncoref/data/rare-cancer-fusion-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,614 copying build/lib/oncoref/data/cancer-response-signatures.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,616 copying build/lib/oncoref/data/cancer-apd1-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,619 copying build/lib/oncoref/data/degenerate-subtype-pairs.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,621 copying build/lib/oncoref/data/ribosomal-protein-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,623 copying build/lib/oncoref/data/cancer-frameshift-burden.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,625 copying build/lib/oncoref/data/cancer-type-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,628 copying build/lib/oncoref/data/numt-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,631 copying build/lib/oncoref/data/expression-artifact-gene-universe-deltas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,640 copying build/lib/oncoref/data/tissue-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,643 copying build/lib/oncoref/data/clean-tpm-censored-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,648 copying build/lib/oncoref/data/cta-candidate-references.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,650 copying build/lib/oncoref/data/fusion-expression-effects.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,653 copying build/lib/oncoref/data/ribosomal-protein-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,656 copying build/lib/oncoref/data/cancer-reference-expression-samples.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,664 copying build/lib/oncoref/data/cancer-tmb.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-07T06:55:02,667 copying build/lib/oncoref/data_manifest.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,670 copying build/lib/oncoref/peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,673 copying build/lib/oncoref/__init__.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,677 copying build/lib/oncoref/gene_ids.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,679 copying build/lib/oncoref/ici_response.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,682 copying build/lib/oncoref/hpa.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,684 copying build/lib/oncoref/expression_registry.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,687 copying build/lib/oncoref/cta.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,690 copying build/lib/oncoref/reference_data.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,693 copying build/lib/oncoref/source_matrices.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,695 copying build/lib/oncoref/version.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,697 copying build/lib/oncoref/ici.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,700 copying build/lib/oncoref/normalization.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-07T06:55:02,703 running install_egg_info 2026-07-07T06:55:02,712 running egg_info 2026-07-07T06:55:02,718 writing oncoref.egg-info/PKG-INFO 2026-07-07T06:55:02,723 writing dependency_links to oncoref.egg-info/dependency_links.txt 2026-07-07T06:55:02,725 writing entry points to oncoref.egg-info/entry_points.txt 2026-07-07T06:55:02,727 writing requirements to oncoref.egg-info/requires.txt 2026-07-07T06:55:02,729 writing top-level names to oncoref.egg-info/top_level.txt 2026-07-07T06:55:02,748 reading manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-07T06:55:02,757 reading manifest template 'MANIFEST.in' 2026-07-07T06:55:02,759 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-07-07T06:55:02,761 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-07-07T06:55:02,763 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-07-07T06:55:02,765 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-07-07T06:55:02,766 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-07-07T06:55:02,767 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-07-07T06:55:02,768 adding license file 'LICENSE' 2026-07-07T06:55:02,777 writing manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-07T06:55:02,779 Copying oncoref.egg-info to build/bdist.linux-armv7l/wheel/./oncoref-1.8.66-py3.11.egg-info 2026-07-07T06:55:02,791 running install_scripts 2026-07-07T06:55:02,803 creating build/bdist.linux-armv7l/wheel/oncoref-1.8.66.dist-info/WHEEL 2026-07-07T06:55:02,806 creating '/tmp/pip-wheel-ykmsk65g/.tmp-ujrzva2z/oncoref-1.8.66-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-07-07T06:55:02,810 adding 'oncoref/__init__.py' 2026-07-07T06:55:02,812 adding 'oncoref/antigen_coverage.py' 2026-07-07T06:55:02,814 adding 'oncoref/apd1.py' 2026-07-07T06:55:02,816 adding 'oncoref/cancer_genes.py' 2026-07-07T06:55:02,818 adding 'oncoref/cancer_ontology.py' 2026-07-07T06:55:02,826 adding 'oncoref/cancer_types.py' 2026-07-07T06:55:02,829 adding 'oncoref/catalog.py' 2026-07-07T06:55:02,833 adding 'oncoref/cli.py' 2026-07-07T06:55:02,835 adding 'oncoref/cohorts.py' 2026-07-07T06:55:02,839 adding 'oncoref/coverage.py' 2026-07-07T06:55:02,842 adding 'oncoref/cta.py' 2026-07-07T06:55:02,844 adding 'oncoref/cta_coverage.py' 2026-07-07T06:55:02,846 adding 'oncoref/cta_curation_plots.py' 2026-07-07T06:55:02,848 adding 'oncoref/cta_peptides.py' 2026-07-07T06:55:02,851 adding 'oncoref/cta_regen.py' 2026-07-07T06:55:02,853 adding 'oncoref/cta_tissues.py' 2026-07-07T06:55:02,857 adding 'oncoref/data_bundle.py' 2026-07-07T06:55:02,860 adding 'oncoref/data_manifest.py' 2026-07-07T06:55:02,875 adding 'oncoref/expression.py' 2026-07-07T06:55:02,879 adding 'oncoref/expression_builders.py' 2026-07-07T06:55:02,883 adding 'oncoref/expression_engine.py' 2026-07-07T06:55:02,885 adding 'oncoref/expression_registry.py' 2026-07-07T06:55:02,887 adding 'oncoref/fusions.py' 2026-07-07T06:55:02,889 adding 'oncoref/gene_families.py' 2026-07-07T06:55:02,892 adding 'oncoref/gene_ids.py' 2026-07-07T06:55:02,893 adding 'oncoref/gene_qc.py' 2026-07-07T06:55:02,895 adding 'oncoref/genome.py' 2026-07-07T06:55:02,897 adding 'oncoref/hpa.py' 2026-07-07T06:55:02,901 adding 'oncoref/ici.py' 2026-07-07T06:55:02,903 adding 'oncoref/ici_response.py' 2026-07-07T06:55:02,904 adding 'oncoref/incidence.py' 2026-07-07T06:55:02,906 adding 'oncoref/load_dataset.py' 2026-07-07T06:55:02,911 adding 'oncoref/normalization.py' 2026-07-07T06:55:02,913 adding 'oncoref/peptides.py' 2026-07-07T06:55:02,920 adding 'oncoref/plots.py' 2026-07-07T06:55:02,923 adding 'oncoref/proteoforms.py' 2026-07-07T06:55:02,925 adding 'oncoref/reference_data.py' 2026-07-07T06:55:02,927 adding 'oncoref/response_signatures.py' 2026-07-07T06:55:02,928 adding 'oncoref/samples.py' 2026-07-07T06:55:02,929 adding 'oncoref/source_matrices.py' 2026-07-07T06:55:02,931 adding 'oncoref/tmb.py' 2026-07-07T06:55:02,933 adding 'oncoref/version.py' 2026-07-07T06:55:02,936 adding 'oncoref/data/cancer-apd1-response.csv' 2026-07-07T06:55:02,938 adding 'oncoref/data/cancer-code-burden-map.csv' 2026-07-07T06:55:02,939 adding 'oncoref/data/cancer-cohort-aggregates.csv' 2026-07-07T06:55:02,944 adding 'oncoref/data/cancer-driver-genes.csv' 2026-07-07T06:55:02,946 adding 'oncoref/data/cancer-driver-variants.csv' 2026-07-07T06:55:02,949 adding 'oncoref/data/cancer-expression-source-candidates.csv' 2026-07-07T06:55:02,950 adding 'oncoref/data/cancer-frameshift-burden.csv' 2026-07-07T06:55:02,953 adding 'oncoref/data/cancer-fusions.csv' 2026-07-07T06:55:02,969 adding 'oncoref/data/cancer-ici-response-estimates.csv' 2026-07-07T06:55:02,974 adding 'oncoref/data/cancer-ici-response.csv' 2026-07-07T06:55:02,975 adding 'oncoref/data/cancer-incidence-mortality.csv' 2026-07-07T06:55:02,990 adding 'oncoref/data/cancer-key-genes.csv' 2026-07-07T06:55:02,992 adding 'oncoref/data/cancer-lineage-group-overrides.csv' 2026-07-07T06:55:02,994 adding 'oncoref/data/cancer-lineage-groups.csv' 2026-07-07T06:55:02,995 adding 'oncoref/data/cancer-normal-tissue-map.csv' 2026-07-07T06:55:03,024 adding 'oncoref/data/cancer-reference-expression-samples.csv.gz' 2026-07-07T06:55:03,027 adding 'oncoref/data/cancer-response-signatures.csv' 2026-07-07T06:55:03,028 adding 'oncoref/data/cancer-subtype-groupings.csv' 2026-07-07T06:55:03,040 adding 'oncoref/data/cancer-testis-antigens.csv' 2026-07-07T06:55:03,043 adding 'oncoref/data/cancer-tmb.csv' 2026-07-07T06:55:03,046 adding 'oncoref/data/cancer-type-genes.csv' 2026-07-07T06:55:03,050 adding 'oncoref/data/cancer-type-registry.csv' 2026-07-07T06:55:03,052 adding 'oncoref/data/cancer-viral-antigens.csv' 2026-07-07T06:55:03,104 adding 'oncoref/data/canonical-gene-space.csv.gz' 2026-07-07T06:55:03,113 adding 'oncoref/data/cdna-identical-gene-groups.csv' 2026-07-07T06:55:03,121 adding 'oncoref/data/censored-gene-reference-tpm.csv' 2026-07-07T06:55:03,126 adding 'oncoref/data/clean-tpm-biological-housekeeping-genes.csv' 2026-07-07T06:55:03,139 adding 'oncoref/data/clean-tpm-censored-genes.csv' 2026-07-07T06:55:03,144 adding 'oncoref/data/cohort-registry.csv' 2026-07-07T06:55:03,148 adding 'oncoref/data/cta-candidate-references.csv' 2026-07-07T06:55:03,152 adding 'oncoref/data/cta-ihc-unreliable.csv' 2026-07-07T06:55:03,155 adding 'oncoref/data/degenerate-subtype-pairs.csv' 2026-07-07T06:55:03,159 adding 'oncoref/data/disease-state-rules.csv' 2026-07-07T06:55:03,186 adding 'oncoref/data/ensembl-id-aliases.csv' 2026-07-07T06:55:03,199 adding 'oncoref/data/expression-artifact-gene-universe-deltas.csv' 2026-07-07T06:55:03,205 adding 'oncoref/data/expression_sources.yaml' 2026-07-07T06:55:03,207 adding 'oncoref/data/extra-tx-mappings.csv' 2026-07-07T06:55:03,208 adding 'oncoref/data/family-burden-map.csv' 2026-07-07T06:55:03,209 adding 'oncoref/data/fusion-expression-effects.csv' 2026-07-07T06:55:03,210 adding 'oncoref/data/fusion-surrogate-expression.csv' 2026-07-07T06:55:03,212 adding 'oncoref/data/hemoglobin-genes.csv' 2026-07-07T06:55:03,213 adding 'oncoref/data/histone-genes.csv' 2026-07-07T06:55:03,214 adding 'oncoref/data/housekeeping-genes.csv' 2026-07-07T06:55:03,216 adding 'oncoref/data/mitochondrial-genes.csv' 2026-07-07T06:55:03,217 adding 'oncoref/data/narrative-gene-sets.csv' 2026-07-07T06:55:03,257 adding 'oncoref/data/ncbi-symbol-synonyms.csv.gz' 2026-07-07T06:55:03,261 adding 'oncoref/data/nuclear-retained-lncrnas.csv' 2026-07-07T06:55:03,263 adding 'oncoref/data/numt-pseudogenes.csv' 2026-07-07T06:55:03,265 adding 'oncoref/data/proteoform-collapse-overrides.csv' 2026-07-07T06:55:03,267 adding 'oncoref/data/proteoform-groups-genome.csv' 2026-07-07T06:55:03,269 adding 'oncoref/data/proteoform-groups.csv' 2026-07-07T06:55:03,271 adding 'oncoref/data/rare-cancer-fusion-rules.csv' 2026-07-07T06:55:03,272 adding 'oncoref/data/ribosomal-protein-genes.csv' 2026-07-07T06:55:03,279 adding 'oncoref/data/ribosomal-protein-pseudogenes.csv' 2026-07-07T06:55:03,281 adding 'oncoref/data/rrna-and-pseudogenes.csv' 2026-07-07T06:55:03,300 adding 'oncoref/data/small-noncoding-rnas.csv' 2026-07-07T06:55:03,302 adding 'oncoref/data/source-matrices.csv' 2026-07-07T06:55:03,304 adding 'oncoref/data/tissue-burden-map.csv' 2026-07-07T06:55:03,307 adding 'oncoref-1.8.66.dist-info/licenses/LICENSE' 2026-07-07T06:55:03,310 adding 'oncoref-1.8.66.dist-info/METADATA' 2026-07-07T06:55:03,311 adding 'oncoref-1.8.66.dist-info/WHEEL' 2026-07-07T06:55:03,312 adding 'oncoref-1.8.66.dist-info/entry_points.txt' 2026-07-07T06:55:03,313 adding 'oncoref-1.8.66.dist-info/top_level.txt' 2026-07-07T06:55:03,315 adding 'oncoref-1.8.66.dist-info/RECORD' 2026-07-07T06:55:03,342 removing build/bdist.linux-armv7l/wheel 2026-07-07T06:55:03,465 Building wheel for oncoref (pyproject.toml): finished with status 'done' 2026-07-07T06:55:03,504 Created wheel for oncoref: filename=oncoref-1.8.66-py3-none-any.whl size=1708418 sha256=dc4b497443f4614935e5240b85202cde7f0e695c9f21a4bb634057d527287764 2026-07-07T06:55:03,505 Stored in directory: /tmp/pip-ephem-wheel-cache-dr8ziphm/wheels/99/7e/70/ff4cc53696cfcd5db4829a2f9fb3f770882f1806d471440edc 2026-07-07T06:55:03,520 Successfully built oncoref 2026-07-07T06:55:03,562 Removed build tracker: '/tmp/pip-build-tracker-45ajore3'