2026-07-10T16:53:07,287 Created temporary directory: /tmp/pip-ephem-wheel-cache-tvoxmtpw 2026-07-10T16:53:07,290 Created temporary directory: /tmp/pip-build-tracker-fhghdweo 2026-07-10T16:53:07,290 Initialized build tracking at /tmp/pip-build-tracker-fhghdweo 2026-07-10T16:53:07,291 Created build tracker: /tmp/pip-build-tracker-fhghdweo 2026-07-10T16:53:07,291 Entered build tracker: /tmp/pip-build-tracker-fhghdweo 2026-07-10T16:53:07,292 Created temporary directory: /tmp/pip-wheel-ikkj8o1o 2026-07-10T16:53:07,295 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 2026-07-10T16:53:07,297 Created temporary directory: /tmp/pip-ephem-wheel-cache-uk3zksap 2026-07-10T16:53:07,320 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-07-10T16:53:07,323 2 location(s) to search for versions of oncoref: 2026-07-10T16:53:07,323 * https://pypi.org/simple/oncoref/ 2026-07-10T16:53:07,323 * https://www.piwheels.org/simple/oncoref/ 2026-07-10T16:53:07,324 Fetching project page and analyzing links: https://pypi.org/simple/oncoref/ 2026-07-10T16:53:07,325 Getting page https://pypi.org/simple/oncoref/ 2026-07-10T16:53:07,326 Found index url https://pypi.org/simple 2026-07-10T16:53:07,612 Fetched page https://pypi.org/simple/oncoref/ as application/vnd.pypi.simple.v1+json 2026-07-10T16:53:07,653 Skipping link: No binaries permitted for oncoref: 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https://www.piwheels.org/simple/oncoref/oncoref-1.8.8-py3-none-any.whl#sha256=f1b7351039ce534abc9d36a03b53fd9479b1629b4a6fd8698bc500162f1cd362 (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-07-10T16:53:08,237 Skipping link: No binaries permitted for oncoref: https://www.piwheels.org/simple/oncoref/oncoref-1.8.7-py3-none-any.whl#sha256=84f80af8afa25d02579e67983b74fd2e515df1ce6d0cb602ecb6808e994f8f63 (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-07-10T16:53:08,237 Skipping link: No binaries permitted for oncoref: https://www.piwheels.org/simple/oncoref/oncoref-1.8.6-py3-none-any.whl#sha256=460f281fc846e410a5992e3a87193febdfac8bf81f3e5497a5e5d72ae58176bf (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-07-10T16:53:08,238 Skipping link: No binaries permitted for oncoref: https://www.piwheels.org/simple/oncoref/oncoref-1.8.5-py3-none-any.whl#sha256=cfedb20aa2c2593dfb010bc01a13d5b6c732ec5cf013fd70b65c71d1adb71f7e (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-07-10T16:53:08,238 Skipping link: No binaries permitted for oncoref: https://www.piwheels.org/simple/oncoref/oncoref-1.8.4-py3-none-any.whl#sha256=d649c7a749c099fe67033ecbdbafe4bf8bcd93bd71d9830ce2a6127a1c093cad (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-07-10T16:53:08,239 Skipping link: No binaries permitted for oncoref: https://www.piwheels.org/simple/oncoref/oncoref-1.8.3-py3-none-any.whl#sha256=bf75676ac99a0d1c144249b8cf320ac292b65716c9ffdc50ad27b55db1153821 (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-07-10T16:53:08,240 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) 2026-07-10T16:53:08,240 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) 2026-07-10T16:53:08,241 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) 2026-07-10T16:53:08,241 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) 2026-07-10T16:53:08,242 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) 2026-07-10T16:53:08,242 Skipping link: not a file: https://www.piwheels.org/simple/oncoref/ 2026-07-10T16:53:08,243 Skipping link: not a file: https://pypi.org/simple/oncoref/ 2026-07-10T16:53:08,277 Given no hashes to check 1 links for project 'oncoref': discarding no candidates 2026-07-10T16:53:08,297 Collecting oncoref==1.8.115 2026-07-10T16:53:08,299 Created temporary directory: /tmp/pip-unpack-fcy3msp2 2026-07-10T16:53:08,562 Downloading oncoref-1.8.115.tar.gz (2.8 MB) 2026-07-10T16:53:09,417 Added oncoref==1.8.115 from https://files.pythonhosted.org/packages/6c/e3/be946cca3bc4f19fb9af2ce91c21516d2ce48729197615428e66f41ce88e/oncoref-1.8.115.tar.gz to build tracker '/tmp/pip-build-tracker-fhghdweo' 2026-07-10T16:53:09,424 Created temporary directory: /tmp/pip-build-env-s3oe2xa6 2026-07-10T16:53:09,429 Installing build dependencies: started 2026-07-10T16:53:09,431 Running command pip subprocess to install build dependencies 2026-07-10T16:53:10,617 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-07-10T16:53:11,041 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 2026-07-10T16:53:11,064 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-07-10T16:53:13,085 Collecting setuptools>=61.0 2026-07-10T16:53:13,086 Obtaining dependency information for setuptools>=61.0 from https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl.metadata 2026-07-10T16:53:13,101 Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl.metadata (6.6 kB) 2026-07-10T16:53:13,334 Collecting wheel 2026-07-10T16:53:13,335 Obtaining dependency information for wheel from https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata 2026-07-10T16:53:13,347 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB) 2026-07-10T16:53:13,532 Collecting packaging>=24.0 2026-07-10T16:53:13,533 Obtaining dependency information for packaging>=24.0 from https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata 2026-07-10T16:53:13,547 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata (3.5 kB) 2026-07-10T16:53:13,740 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB) 2026-07-10T16:53:13,761 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB) 2026-07-10T16:53:13,840 Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl (1.0 MB) 2026-07-10T16:53:13,878 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB) 2026-07-10T16:53:13,905 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB) 2026-07-10T16:53:14,013 Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl (1.0 MB) 2026-07-10T16:53:16,792 Installing collected packages: setuptools, packaging, wheel 2026-07-10T16:53:20,351 Creating /tmp/pip-build-env-s3oe2xa6/overlay/local/bin 2026-07-10T16:53:20,353 changing mode of /tmp/pip-build-env-s3oe2xa6/overlay/local/bin/wheel to 755 2026-07-10T16:53:20,374 Successfully installed packaging-26.2 setuptools-83.0.0 wheel-0.47.0 2026-07-10T16:53:20,662 Installing build dependencies: finished with status 'done' 2026-07-10T16:53:20,669 Getting requirements to build wheel: started 2026-07-10T16:53:20,671 Running command Getting requirements to build wheel 2026-07-10T16:53:21,369 running egg_info 2026-07-10T16:53:21,374 writing oncoref.egg-info/PKG-INFO 2026-07-10T16:53:21,380 writing dependency_links to oncoref.egg-info/dependency_links.txt 2026-07-10T16:53:21,382 writing entry points to oncoref.egg-info/entry_points.txt 2026-07-10T16:53:21,385 writing requirements to oncoref.egg-info/requires.txt 2026-07-10T16:53:21,386 writing top-level names to oncoref.egg-info/top_level.txt 2026-07-10T16:53:21,422 reading manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-10T16:53:21,431 reading manifest template 'MANIFEST.in' 2026-07-10T16:53:21,433 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-07-10T16:53:21,435 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-07-10T16:53:21,436 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-07-10T16:53:21,437 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-07-10T16:53:21,438 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-07-10T16:53:21,440 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-07-10T16:53:21,440 adding license file 'LICENSE' 2026-07-10T16:53:21,448 writing manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-10T16:53:21,546 Getting requirements to build wheel: finished with status 'done' 2026-07-10T16:53:21,550 Created temporary directory: /tmp/pip-modern-metadata-aw9fl1h_ 2026-07-10T16:53:21,552 Preparing metadata (pyproject.toml): started 2026-07-10T16:53:21,553 Running command Preparing metadata (pyproject.toml) 2026-07-10T16:53:22,200 running dist_info 2026-07-10T16:53:22,211 creating /tmp/pip-modern-metadata-aw9fl1h_/oncoref.egg-info 2026-07-10T16:53:22,212 writing /tmp/pip-modern-metadata-aw9fl1h_/oncoref.egg-info/PKG-INFO 2026-07-10T16:53:22,219 writing dependency_links to /tmp/pip-modern-metadata-aw9fl1h_/oncoref.egg-info/dependency_links.txt 2026-07-10T16:53:22,221 writing entry points to /tmp/pip-modern-metadata-aw9fl1h_/oncoref.egg-info/entry_points.txt 2026-07-10T16:53:22,224 writing requirements to /tmp/pip-modern-metadata-aw9fl1h_/oncoref.egg-info/requires.txt 2026-07-10T16:53:22,225 writing top-level names to /tmp/pip-modern-metadata-aw9fl1h_/oncoref.egg-info/top_level.txt 2026-07-10T16:53:22,227 writing manifest file '/tmp/pip-modern-metadata-aw9fl1h_/oncoref.egg-info/SOURCES.txt' 2026-07-10T16:53:22,261 reading manifest file '/tmp/pip-modern-metadata-aw9fl1h_/oncoref.egg-info/SOURCES.txt' 2026-07-10T16:53:22,263 reading manifest template 'MANIFEST.in' 2026-07-10T16:53:22,265 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-07-10T16:53:22,267 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-07-10T16:53:22,269 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-07-10T16:53:22,270 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-07-10T16:53:22,272 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-07-10T16:53:22,273 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-07-10T16:53:22,274 adding license file 'LICENSE' 2026-07-10T16:53:22,281 writing manifest file '/tmp/pip-modern-metadata-aw9fl1h_/oncoref.egg-info/SOURCES.txt' 2026-07-10T16:53:22,283 creating '/tmp/pip-modern-metadata-aw9fl1h_/oncoref-1.8.115.dist-info' 2026-07-10T16:53:22,411 Preparing metadata (pyproject.toml): finished with status 'done' 2026-07-10T16:53:22,416 Source in /tmp/pip-wheel-ikkj8o1o/oncoref_83ff4527e48b45a296329ce0eff000a0 has version 1.8.115, which satisfies requirement oncoref==1.8.115 from https://files.pythonhosted.org/packages/6c/e3/be946cca3bc4f19fb9af2ce91c21516d2ce48729197615428e66f41ce88e/oncoref-1.8.115.tar.gz 2026-07-10T16:53:22,418 Removed oncoref==1.8.115 from https://files.pythonhosted.org/packages/6c/e3/be946cca3bc4f19fb9af2ce91c21516d2ce48729197615428e66f41ce88e/oncoref-1.8.115.tar.gz from build tracker '/tmp/pip-build-tracker-fhghdweo' 2026-07-10T16:53:22,424 Created temporary directory: /tmp/pip-unpack-go7ku2ff 2026-07-10T16:53:22,425 Building wheels for collected packages: oncoref 2026-07-10T16:53:22,430 Created temporary directory: /tmp/pip-wheel-gtun9qos 2026-07-10T16:53:22,430 Destination directory: /tmp/pip-wheel-gtun9qos 2026-07-10T16:53:22,432 Building wheel for oncoref (pyproject.toml): started 2026-07-10T16:53:22,433 Running command Building wheel for oncoref (pyproject.toml) 2026-07-10T16:53:23,067 running bdist_wheel 2026-07-10T16:53:23,084 running build 2026-07-10T16:53:23,085 running build_py 2026-07-10T16:53:23,092 creating build/lib/oncoref 2026-07-10T16:53:23,094 copying oncoref/load_dataset.py -> build/lib/oncoref 2026-07-10T16:53:23,096 copying oncoref/catalog.py -> build/lib/oncoref 2026-07-10T16:53:23,099 copying oncoref/ici.py -> build/lib/oncoref 2026-07-10T16:53:23,102 copying oncoref/gene_ids.py -> build/lib/oncoref 2026-07-10T16:53:23,104 copying oncoref/apd1.py -> build/lib/oncoref 2026-07-10T16:53:23,107 copying oncoref/cancer_types.py -> build/lib/oncoref 2026-07-10T16:53:23,111 copying oncoref/expression_engine.py -> build/lib/oncoref 2026-07-10T16:53:23,114 copying oncoref/cta_curation_plots.py -> build/lib/oncoref 2026-07-10T16:53:23,116 copying oncoref/reference_data.py -> build/lib/oncoref 2026-07-10T16:53:23,119 copying oncoref/version.py -> build/lib/oncoref 2026-07-10T16:53:23,120 copying oncoref/expression_builders.py -> build/lib/oncoref 2026-07-10T16:53:23,124 copying oncoref/plots.py -> build/lib/oncoref 2026-07-10T16:53:23,127 copying oncoref/ici_response.py -> build/lib/oncoref 2026-07-10T16:53:23,129 copying oncoref/cta_regen.py -> build/lib/oncoref 2026-07-10T16:53:23,132 copying oncoref/data_manifest.py -> build/lib/oncoref 2026-07-10T16:53:23,134 copying oncoref/cancer_genes.py -> build/lib/oncoref 2026-07-10T16:53:23,137 copying oncoref/cli.py -> build/lib/oncoref 2026-07-10T16:53:23,140 copying oncoref/cta.py -> build/lib/oncoref 2026-07-10T16:53:23,142 copying oncoref/cta_coverage.py -> build/lib/oncoref 2026-07-10T16:53:23,145 copying oncoref/gene_families.py -> build/lib/oncoref 2026-07-10T16:53:23,147 copying oncoref/proteoforms.py -> build/lib/oncoref 2026-07-10T16:53:23,150 copying oncoref/data_bundle.py -> build/lib/oncoref 2026-07-10T16:53:23,153 copying oncoref/response_signatures.py -> build/lib/oncoref 2026-07-10T16:53:23,155 copying oncoref/expression_registry.py -> build/lib/oncoref 2026-07-10T16:53:23,157 copying oncoref/normalization.py -> build/lib/oncoref 2026-07-10T16:53:23,160 copying oncoref/incidence.py -> build/lib/oncoref 2026-07-10T16:53:23,162 copying oncoref/__init__.py -> build/lib/oncoref 2026-07-10T16:53:23,165 copying oncoref/cancer_ontology.py -> build/lib/oncoref 2026-07-10T16:53:23,167 copying oncoref/peptides.py -> build/lib/oncoref 2026-07-10T16:53:23,169 copying oncoref/antigen_coverage.py -> build/lib/oncoref 2026-07-10T16:53:23,171 copying oncoref/tmb.py -> build/lib/oncoref 2026-07-10T16:53:23,173 copying oncoref/source_matrices.py -> build/lib/oncoref 2026-07-10T16:53:23,175 copying oncoref/genome.py -> build/lib/oncoref 2026-07-10T16:53:23,178 copying oncoref/gene_qc.py -> build/lib/oncoref 2026-07-10T16:53:23,180 copying oncoref/hpa.py -> build/lib/oncoref 2026-07-10T16:53:23,182 copying oncoref/cta_peptides.py -> build/lib/oncoref 2026-07-10T16:53:23,184 copying oncoref/coverage.py -> build/lib/oncoref 2026-07-10T16:53:23,187 copying oncoref/expression.py -> build/lib/oncoref 2026-07-10T16:53:23,191 copying oncoref/fusions.py -> build/lib/oncoref 2026-07-10T16:53:23,194 copying oncoref/samples.py -> build/lib/oncoref 2026-07-10T16:53:23,196 copying oncoref/cta_tissues.py -> build/lib/oncoref 2026-07-10T16:53:23,198 copying oncoref/cohorts.py -> build/lib/oncoref 2026-07-10T16:53:23,212 creating build/lib/oncoref/data 2026-07-10T16:53:23,213 copying oncoref/data/cohort-registry.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,216 copying oncoref/data/expression-artifact-gene-universe-deltas.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,223 copying oncoref/data/cancer-incidence-mortality.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,225 copying oncoref/data/histone-genes.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,227 copying oncoref/data/cta-candidate-references.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,230 copying oncoref/data/cancer-driver-genes.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,233 copying oncoref/data/cancer-lineage-groups.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,235 copying oncoref/data/cancer-cohort-aggregates.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,237 copying oncoref/data/cancer-subtype-groupings.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,239 copying oncoref/data/small-noncoding-rnas.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,244 copying oncoref/data/clean-tpm-biological-housekeeping-genes.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,247 copying oncoref/data/numt-pseudogenes.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,249 copying oncoref/data/cancer-response-signatures.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,251 copying oncoref/data/hemoglobin-genes.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,253 copying oncoref/data/narrative-gene-sets.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,255 copying oncoref/data/cancer-fusions.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,258 copying oncoref/data/proteoform-groups.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,261 copying oncoref/data/cancer-type-registry.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,264 copying oncoref/data/cancer-testis-antigens.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,269 copying oncoref/data/extra-tx-mappings.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,272 copying oncoref/data/mitochondrial-genes.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,274 copying oncoref/data/rare-cancer-fusion-rules.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,276 copying oncoref/data/cancer-viral-antigens.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,278 copying oncoref/data/fusion-surrogate-expression.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,281 copying oncoref/data/cancer-mismatch-repair-statuses.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,283 copying oncoref/data/cancer-type-genes.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,286 copying oncoref/data/nuclear-retained-lncrnas.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,288 copying oncoref/data/degenerate-subtype-pairs.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,290 copying oncoref/data/cta-clinical-targets.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,292 copying oncoref/data/cancer-frameshift-burden.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,295 copying oncoref/data/family-burden-map.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,297 copying oncoref/data/censored-gene-reference-tpm.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,300 copying oncoref/data/rrna-and-pseudogenes.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,302 copying oncoref/data/ensembl-id-aliases.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,310 copying oncoref/data/cancer-apd1-response.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,313 copying oncoref/data/cancer-expression-source-candidates.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,316 copying oncoref/data/cancer-ici-response-estimates.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,321 copying oncoref/data/cancer-key-genes.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,326 copying oncoref/data/ribosomal-protein-genes.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,328 copying oncoref/data/tissue-burden-map.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,330 copying oncoref/data/cancer-lineage-group-overrides.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,332 copying oncoref/data/clean-tpm-censored-genes.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,336 copying oncoref/data/cancer-code-burden-map.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,338 copying oncoref/data/cta-specificity-audit.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,340 copying oncoref/data/cancer-ici-response.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,343 copying oncoref/data/housekeeping-genes.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,345 copying oncoref/data/cta-ihc-unreliable.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,347 copying oncoref/data/disease-state-rules.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,349 copying oncoref/data/proteoform-groups-genome.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,352 copying oncoref/data/ribosomal-protein-pseudogenes.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,355 copying oncoref/data/cancer-tmb.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,357 copying oncoref/data/cdna-identical-gene-groups.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,360 copying oncoref/data/cancer-driver-variants.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,363 copying oncoref/data/cancer-normal-tissue-map.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,365 copying oncoref/data/fusion-expression-effects.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,367 copying oncoref/data/source-matrices.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,369 copying oncoref/data/proteoform-collapse-overrides.csv -> build/lib/oncoref/data 2026-07-10T16:53:23,371 copying oncoref/data/cancer-reference-expression-samples.csv.gz -> build/lib/oncoref/data 2026-07-10T16:53:23,377 copying oncoref/data/canonical-gene-space.csv.gz -> build/lib/oncoref/data 2026-07-10T16:53:23,388 copying oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/lib/oncoref/data 2026-07-10T16:53:23,397 copying oncoref/data/ncbi-entrez-gene-mappings.csv.gz -> build/lib/oncoref/data 2026-07-10T16:53:23,415 copying oncoref/data/expression_sources.yaml -> build/lib/oncoref/data 2026-07-10T16:53:23,428 installing to build/bdist.linux-armv7l/wheel 2026-07-10T16:53:23,429 running install 2026-07-10T16:53:23,451 running install_lib 2026-07-10T16:53:23,457 creating build/bdist.linux-armv7l/wheel 2026-07-10T16:53:23,459 creating build/bdist.linux-armv7l/wheel/oncoref 2026-07-10T16:53:23,461 copying build/lib/oncoref/load_dataset.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,463 copying build/lib/oncoref/catalog.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,465 copying build/lib/oncoref/ici.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,468 copying build/lib/oncoref/gene_ids.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,470 copying build/lib/oncoref/apd1.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,473 copying build/lib/oncoref/cancer_types.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,476 copying build/lib/oncoref/expression_engine.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,478 copying build/lib/oncoref/cta_curation_plots.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,481 copying build/lib/oncoref/reference_data.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,483 copying build/lib/oncoref/version.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,485 copying build/lib/oncoref/expression_builders.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,488 copying build/lib/oncoref/plots.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,491 copying build/lib/oncoref/ici_response.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,494 copying build/lib/oncoref/cta_regen.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,497 copying build/lib/oncoref/data_manifest.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,499 copying build/lib/oncoref/cancer_genes.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,501 copying build/lib/oncoref/cli.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,503 copying build/lib/oncoref/cta.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,506 copying build/lib/oncoref/cta_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,508 copying build/lib/oncoref/gene_families.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,510 copying build/lib/oncoref/proteoforms.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,512 copying build/lib/oncoref/data_bundle.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,515 copying build/lib/oncoref/response_signatures.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,517 copying build/lib/oncoref/expression_registry.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,519 copying build/lib/oncoref/normalization.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,522 copying build/lib/oncoref/incidence.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,524 copying build/lib/oncoref/__init__.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,526 copying build/lib/oncoref/cancer_ontology.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,528 copying build/lib/oncoref/peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,530 copying build/lib/oncoref/antigen_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,532 copying build/lib/oncoref/tmb.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,536 creating build/bdist.linux-armv7l/wheel/oncoref/data 2026-07-10T16:53:23,537 copying build/lib/oncoref/data/cohort-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,539 copying build/lib/oncoref/data/expression-artifact-gene-universe-deltas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,546 copying build/lib/oncoref/data/cancer-incidence-mortality.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,548 copying build/lib/oncoref/data/histone-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,550 copying build/lib/oncoref/data/cta-candidate-references.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,552 copying build/lib/oncoref/data/cancer-driver-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,555 copying build/lib/oncoref/data/cancer-reference-expression-samples.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,561 copying build/lib/oncoref/data/cancer-lineage-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,563 copying build/lib/oncoref/data/canonical-gene-space.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,571 copying build/lib/oncoref/data/cancer-cohort-aggregates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,573 copying build/lib/oncoref/data/cancer-subtype-groupings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,575 copying build/lib/oncoref/data/small-noncoding-rnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,580 copying build/lib/oncoref/data/clean-tpm-biological-housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,583 copying build/lib/oncoref/data/numt-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,585 copying build/lib/oncoref/data/cancer-response-signatures.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,587 copying build/lib/oncoref/data/hemoglobin-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,589 copying build/lib/oncoref/data/narrative-gene-sets.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,590 copying build/lib/oncoref/data/cancer-fusions.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,593 copying build/lib/oncoref/data/proteoform-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,595 copying build/lib/oncoref/data/cancer-type-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,598 copying build/lib/oncoref/data/cancer-testis-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,602 copying build/lib/oncoref/data/extra-tx-mappings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,604 copying build/lib/oncoref/data/mitochondrial-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,606 copying build/lib/oncoref/data/rare-cancer-fusion-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,609 copying build/lib/oncoref/data/cancer-viral-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,610 copying build/lib/oncoref/data/fusion-surrogate-expression.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,612 copying build/lib/oncoref/data/cancer-mismatch-repair-statuses.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,614 copying build/lib/oncoref/data/cancer-type-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,617 copying build/lib/oncoref/data/nuclear-retained-lncrnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,618 copying build/lib/oncoref/data/degenerate-subtype-pairs.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,620 copying build/lib/oncoref/data/cta-clinical-targets.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,622 copying build/lib/oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,630 copying build/lib/oncoref/data/cancer-frameshift-burden.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,632 copying build/lib/oncoref/data/family-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,634 copying build/lib/oncoref/data/censored-gene-reference-tpm.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,636 copying build/lib/oncoref/data/rrna-and-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,639 copying build/lib/oncoref/data/ensembl-id-aliases.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,647 copying build/lib/oncoref/data/cancer-apd1-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,650 copying build/lib/oncoref/data/cancer-expression-source-candidates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,652 copying build/lib/oncoref/data/cancer-ici-response-estimates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,659 copying build/lib/oncoref/data/cancer-key-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,663 copying build/lib/oncoref/data/ribosomal-protein-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,665 copying build/lib/oncoref/data/tissue-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,667 copying build/lib/oncoref/data/cancer-lineage-group-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,669 copying build/lib/oncoref/data/clean-tpm-censored-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,673 copying build/lib/oncoref/data/cancer-code-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,674 copying build/lib/oncoref/data/ncbi-entrez-gene-mappings.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,697 copying build/lib/oncoref/data/cta-specificity-audit.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,698 copying build/lib/oncoref/data/cancer-ici-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,701 copying build/lib/oncoref/data/housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,703 copying build/lib/oncoref/data/cta-ihc-unreliable.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,705 copying build/lib/oncoref/data/disease-state-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,707 copying build/lib/oncoref/data/proteoform-groups-genome.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,709 copying build/lib/oncoref/data/ribosomal-protein-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,712 copying build/lib/oncoref/data/expression_sources.yaml -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,715 copying build/lib/oncoref/data/cancer-tmb.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,718 copying build/lib/oncoref/data/cdna-identical-gene-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,720 copying build/lib/oncoref/data/cancer-driver-variants.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,723 copying build/lib/oncoref/data/cancer-normal-tissue-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,725 copying build/lib/oncoref/data/fusion-expression-effects.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,727 copying build/lib/oncoref/data/source-matrices.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,729 copying build/lib/oncoref/data/proteoform-collapse-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-10T16:53:23,730 copying build/lib/oncoref/source_matrices.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,732 copying build/lib/oncoref/genome.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,735 copying build/lib/oncoref/gene_qc.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,737 copying build/lib/oncoref/hpa.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,739 copying build/lib/oncoref/cta_peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,741 copying build/lib/oncoref/coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,744 copying build/lib/oncoref/expression.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,749 copying build/lib/oncoref/fusions.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,751 copying build/lib/oncoref/samples.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,753 copying build/lib/oncoref/cta_tissues.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,755 copying build/lib/oncoref/cohorts.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-10T16:53:23,757 running install_egg_info 2026-07-10T16:53:23,766 running egg_info 2026-07-10T16:53:23,771 writing oncoref.egg-info/PKG-INFO 2026-07-10T16:53:23,776 writing dependency_links to oncoref.egg-info/dependency_links.txt 2026-07-10T16:53:23,778 writing entry points to oncoref.egg-info/entry_points.txt 2026-07-10T16:53:23,780 writing requirements to oncoref.egg-info/requires.txt 2026-07-10T16:53:23,781 writing top-level names to oncoref.egg-info/top_level.txt 2026-07-10T16:53:23,800 reading manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-10T16:53:23,810 reading manifest template 'MANIFEST.in' 2026-07-10T16:53:23,812 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-07-10T16:53:23,813 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-07-10T16:53:23,814 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-07-10T16:53:23,816 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-07-10T16:53:23,817 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-07-10T16:53:23,818 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-07-10T16:53:23,819 adding license file 'LICENSE' 2026-07-10T16:53:23,827 writing manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-10T16:53:23,829 Copying oncoref.egg-info to build/bdist.linux-armv7l/wheel/./oncoref-1.8.115-py3.11.egg-info 2026-07-10T16:53:23,840 running install_scripts 2026-07-10T16:53:23,852 creating build/bdist.linux-armv7l/wheel/oncoref-1.8.115.dist-info/WHEEL 2026-07-10T16:53:23,854 creating '/tmp/pip-wheel-gtun9qos/.tmp-ro9hobk4/oncoref-1.8.115-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-07-10T16:53:23,858 adding 'oncoref/__init__.py' 2026-07-10T16:53:23,860 adding 'oncoref/antigen_coverage.py' 2026-07-10T16:53:23,862 adding 'oncoref/apd1.py' 2026-07-10T16:53:23,864 adding 'oncoref/cancer_genes.py' 2026-07-10T16:53:23,865 adding 'oncoref/cancer_ontology.py' 2026-07-10T16:53:23,875 adding 'oncoref/cancer_types.py' 2026-07-10T16:53:23,878 adding 'oncoref/catalog.py' 2026-07-10T16:53:23,881 adding 'oncoref/cli.py' 2026-07-10T16:53:23,883 adding 'oncoref/cohorts.py' 2026-07-10T16:53:23,886 adding 'oncoref/coverage.py' 2026-07-10T16:53:23,890 adding 'oncoref/cta.py' 2026-07-10T16:53:23,892 adding 'oncoref/cta_coverage.py' 2026-07-10T16:53:23,893 adding 'oncoref/cta_curation_plots.py' 2026-07-10T16:53:23,895 adding 'oncoref/cta_peptides.py' 2026-07-10T16:53:23,898 adding 'oncoref/cta_regen.py' 2026-07-10T16:53:23,899 adding 'oncoref/cta_tissues.py' 2026-07-10T16:53:23,903 adding 'oncoref/data_bundle.py' 2026-07-10T16:53:23,906 adding 'oncoref/data_manifest.py' 2026-07-10T16:53:23,928 adding 'oncoref/expression.py' 2026-07-10T16:53:23,940 adding 'oncoref/expression_builders.py' 2026-07-10T16:53:23,944 adding 'oncoref/expression_engine.py' 2026-07-10T16:53:23,945 adding 'oncoref/expression_registry.py' 2026-07-10T16:53:23,947 adding 'oncoref/fusions.py' 2026-07-10T16:53:23,950 adding 'oncoref/gene_families.py' 2026-07-10T16:53:23,952 adding 'oncoref/gene_ids.py' 2026-07-10T16:53:23,954 adding 'oncoref/gene_qc.py' 2026-07-10T16:53:23,957 adding 'oncoref/genome.py' 2026-07-10T16:53:23,958 adding 'oncoref/hpa.py' 2026-07-10T16:53:23,963 adding 'oncoref/ici.py' 2026-07-10T16:53:23,965 adding 'oncoref/ici_response.py' 2026-07-10T16:53:23,967 adding 'oncoref/incidence.py' 2026-07-10T16:53:23,968 adding 'oncoref/load_dataset.py' 2026-07-10T16:53:23,973 adding 'oncoref/normalization.py' 2026-07-10T16:53:23,975 adding 'oncoref/peptides.py' 2026-07-10T16:53:23,982 adding 'oncoref/plots.py' 2026-07-10T16:53:23,985 adding 'oncoref/proteoforms.py' 2026-07-10T16:53:23,988 adding 'oncoref/reference_data.py' 2026-07-10T16:53:23,989 adding 'oncoref/response_signatures.py' 2026-07-10T16:53:23,991 adding 'oncoref/samples.py' 2026-07-10T16:53:23,992 adding 'oncoref/source_matrices.py' 2026-07-10T16:53:23,994 adding 'oncoref/tmb.py' 2026-07-10T16:53:23,996 adding 'oncoref/version.py' 2026-07-10T16:53:24,000 adding 'oncoref/data/cancer-apd1-response.csv' 2026-07-10T16:53:24,001 adding 'oncoref/data/cancer-code-burden-map.csv' 2026-07-10T16:53:24,002 adding 'oncoref/data/cancer-cohort-aggregates.csv' 2026-07-10T16:53:24,007 adding 'oncoref/data/cancer-driver-genes.csv' 2026-07-10T16:53:24,010 adding 'oncoref/data/cancer-driver-variants.csv' 2026-07-10T16:53:24,012 adding 'oncoref/data/cancer-expression-source-candidates.csv' 2026-07-10T16:53:24,014 adding 'oncoref/data/cancer-frameshift-burden.csv' 2026-07-10T16:53:24,017 adding 'oncoref/data/cancer-fusions.csv' 2026-07-10T16:53:24,033 adding 'oncoref/data/cancer-ici-response-estimates.csv' 2026-07-10T16:53:24,038 adding 'oncoref/data/cancer-ici-response.csv' 2026-07-10T16:53:24,039 adding 'oncoref/data/cancer-incidence-mortality.csv' 2026-07-10T16:53:24,054 adding 'oncoref/data/cancer-key-genes.csv' 2026-07-10T16:53:24,056 adding 'oncoref/data/cancer-lineage-group-overrides.csv' 2026-07-10T16:53:24,057 adding 'oncoref/data/cancer-lineage-groups.csv' 2026-07-10T16:53:24,059 adding 'oncoref/data/cancer-mismatch-repair-statuses.csv' 2026-07-10T16:53:24,060 adding 'oncoref/data/cancer-normal-tissue-map.csv' 2026-07-10T16:53:24,089 adding 'oncoref/data/cancer-reference-expression-samples.csv.gz' 2026-07-10T16:53:24,092 adding 'oncoref/data/cancer-response-signatures.csv' 2026-07-10T16:53:24,093 adding 'oncoref/data/cancer-subtype-groupings.csv' 2026-07-10T16:53:24,105 adding 'oncoref/data/cancer-testis-antigens.csv' 2026-07-10T16:53:24,108 adding 'oncoref/data/cancer-tmb.csv' 2026-07-10T16:53:24,110 adding 'oncoref/data/cancer-type-genes.csv' 2026-07-10T16:53:24,115 adding 'oncoref/data/cancer-type-registry.csv' 2026-07-10T16:53:24,116 adding 'oncoref/data/cancer-viral-antigens.csv' 2026-07-10T16:53:24,169 adding 'oncoref/data/canonical-gene-space.csv.gz' 2026-07-10T16:53:24,175 adding 'oncoref/data/cdna-identical-gene-groups.csv' 2026-07-10T16:53:24,179 adding 'oncoref/data/censored-gene-reference-tpm.csv' 2026-07-10T16:53:24,180 adding 'oncoref/data/clean-tpm-biological-housekeeping-genes.csv' 2026-07-10T16:53:24,191 adding 'oncoref/data/clean-tpm-censored-genes.csv' 2026-07-10T16:53:24,193 adding 'oncoref/data/cohort-registry.csv' 2026-07-10T16:53:24,194 adding 'oncoref/data/cta-candidate-references.csv' 2026-07-10T16:53:24,196 adding 'oncoref/data/cta-clinical-targets.csv' 2026-07-10T16:53:24,197 adding 'oncoref/data/cta-ihc-unreliable.csv' 2026-07-10T16:53:24,198 adding 'oncoref/data/cta-specificity-audit.csv' 2026-07-10T16:53:24,200 adding 'oncoref/data/degenerate-subtype-pairs.csv' 2026-07-10T16:53:24,201 adding 'oncoref/data/disease-state-rules.csv' 2026-07-10T16:53:24,228 adding 'oncoref/data/ensembl-id-aliases.csv' 2026-07-10T16:53:24,242 adding 'oncoref/data/expression-artifact-gene-universe-deltas.csv' 2026-07-10T16:53:24,250 adding 'oncoref/data/expression_sources.yaml' 2026-07-10T16:53:24,252 adding 'oncoref/data/extra-tx-mappings.csv' 2026-07-10T16:53:24,253 adding 'oncoref/data/family-burden-map.csv' 2026-07-10T16:53:24,254 adding 'oncoref/data/fusion-expression-effects.csv' 2026-07-10T16:53:24,256 adding 'oncoref/data/fusion-surrogate-expression.csv' 2026-07-10T16:53:24,257 adding 'oncoref/data/hemoglobin-genes.csv' 2026-07-10T16:53:24,259 adding 'oncoref/data/histone-genes.csv' 2026-07-10T16:53:24,260 adding 'oncoref/data/housekeeping-genes.csv' 2026-07-10T16:53:24,261 adding 'oncoref/data/mitochondrial-genes.csv' 2026-07-10T16:53:24,262 adding 'oncoref/data/narrative-gene-sets.csv' 2026-07-10T16:53:24,365 adding 'oncoref/data/ncbi-entrez-gene-mappings.csv.gz' 2026-07-10T16:53:24,414 adding 'oncoref/data/ncbi-symbol-synonyms.csv.gz' 2026-07-10T16:53:24,419 adding 'oncoref/data/nuclear-retained-lncrnas.csv' 2026-07-10T16:53:24,421 adding 'oncoref/data/numt-pseudogenes.csv' 2026-07-10T16:53:24,422 adding 'oncoref/data/proteoform-collapse-overrides.csv' 2026-07-10T16:53:24,425 adding 'oncoref/data/proteoform-groups-genome.csv' 2026-07-10T16:53:24,426 adding 'oncoref/data/proteoform-groups.csv' 2026-07-10T16:53:24,428 adding 'oncoref/data/rare-cancer-fusion-rules.csv' 2026-07-10T16:53:24,430 adding 'oncoref/data/ribosomal-protein-genes.csv' 2026-07-10T16:53:24,437 adding 'oncoref/data/ribosomal-protein-pseudogenes.csv' 2026-07-10T16:53:24,440 adding 'oncoref/data/rrna-and-pseudogenes.csv' 2026-07-10T16:53:24,459 adding 'oncoref/data/small-noncoding-rnas.csv' 2026-07-10T16:53:24,462 adding 'oncoref/data/source-matrices.csv' 2026-07-10T16:53:24,463 adding 'oncoref/data/tissue-burden-map.csv' 2026-07-10T16:53:24,467 adding 'oncoref-1.8.115.dist-info/licenses/LICENSE' 2026-07-10T16:53:24,469 adding 'oncoref-1.8.115.dist-info/METADATA' 2026-07-10T16:53:24,470 adding 'oncoref-1.8.115.dist-info/WHEEL' 2026-07-10T16:53:24,471 adding 'oncoref-1.8.115.dist-info/entry_points.txt' 2026-07-10T16:53:24,472 adding 'oncoref-1.8.115.dist-info/top_level.txt' 2026-07-10T16:53:24,474 adding 'oncoref-1.8.115.dist-info/RECORD' 2026-07-10T16:53:24,504 removing build/bdist.linux-armv7l/wheel 2026-07-10T16:53:24,627 Building wheel for oncoref (pyproject.toml): finished with status 'done' 2026-07-10T16:53:24,687 Created wheel for oncoref: filename=oncoref-1.8.115-py3-none-any.whl size=2686835 sha256=74e603ffcc5f4fe490cf8951682db7339294957cbff23c464d0bc0432f2f0536 2026-07-10T16:53:24,689 Stored in directory: /tmp/pip-ephem-wheel-cache-uk3zksap/wheels/be/5e/fd/e9e95617eed245b41b9078a418db6b17cd403d8c021aee80d2 2026-07-10T16:53:24,705 Successfully built oncoref 2026-07-10T16:53:24,771 Removed build tracker: '/tmp/pip-build-tracker-fhghdweo'