2026-07-08T09:01:27,304 Created temporary directory: /tmp/pip-ephem-wheel-cache-ujvt9vze 2026-07-08T09:01:27,305 Created temporary directory: /tmp/pip-build-tracker-ce2q9rp4 2026-07-08T09:01:27,306 Initialized build tracking at /tmp/pip-build-tracker-ce2q9rp4 2026-07-08T09:01:27,307 Created build tracker: /tmp/pip-build-tracker-ce2q9rp4 2026-07-08T09:01:27,307 Entered build tracker: /tmp/pip-build-tracker-ce2q9rp4 2026-07-08T09:01:27,308 Created temporary directory: /tmp/pip-wheel-t89i5e5t 2026-07-08T09:01:27,311 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 2026-07-08T09:01:27,313 Created temporary directory: /tmp/pip-ephem-wheel-cache-ne_oidju 2026-07-08T09:01:27,338 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-07-08T09:01:27,342 2 location(s) to search for versions of oncoref: 2026-07-08T09:01:27,342 * https://pypi.org/simple/oncoref/ 2026-07-08T09:01:27,342 * https://www.piwheels.org/simple/oncoref/ 2026-07-08T09:01:27,342 Fetching project page and analyzing links: https://pypi.org/simple/oncoref/ 2026-07-08T09:01:27,343 Getting page https://pypi.org/simple/oncoref/ 2026-07-08T09:01:27,345 Found index url https://pypi.org/simple 2026-07-08T09:01:27,632 Fetched page https://pypi.org/simple/oncoref/ as application/vnd.pypi.simple.v1+json 2026-07-08T09:01:27,665 Skipping link: No binaries permitted for oncoref: 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(requires-python:>=3.9) 2026-07-08T09:01:27,820 Found link https://files.pythonhosted.org/packages/55/ba/dd4289da065810c3d1133c2dc85ad2b1e07aa0ae7657cb08f691533f2cef/oncoref-1.8.90.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.8.90 2026-07-08T09:01:27,821 Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/79/5a/b8271cb56a390290a254488f31bf8cc9c82e3eded3780ebb7c6817c6b2f4/oncoref-1.8.91-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9) 2026-07-08T09:01:27,821 Found link https://files.pythonhosted.org/packages/c8/f0/2e307c26822b2bb8a62b4c64ad6414b01389b822041b625fc6fab2c53886/oncoref-1.8.91.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.8.91 2026-07-08T09:01:27,822 Fetching project page and analyzing links: https://www.piwheels.org/simple/oncoref/ 2026-07-08T09:01:27,823 Getting page https://www.piwheels.org/simple/oncoref/ 2026-07-08T09:01:27,824 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2026-07-08T09:01:28,230 Given no hashes to check 1 links for project 'oncoref': discarding no candidates 2026-07-08T09:01:28,248 Collecting oncoref==1.8.76 2026-07-08T09:01:28,250 Created temporary directory: /tmp/pip-unpack-eij0dafp 2026-07-08T09:01:28,500 Downloading oncoref-1.8.76.tar.gz (2.7 MB) 2026-07-08T09:01:29,336 Added oncoref==1.8.76 from https://files.pythonhosted.org/packages/30/c2/956670f34940b2c734ebb252bf865ead4b2e4b178c96c894b1e7bb048dab/oncoref-1.8.76.tar.gz to build tracker '/tmp/pip-build-tracker-ce2q9rp4' 2026-07-08T09:01:29,347 Created temporary directory: /tmp/pip-build-env-skyn79xq 2026-07-08T09:01:29,354 Installing build dependencies: started 2026-07-08T09:01:29,355 Running command pip subprocess to install build dependencies 2026-07-08T09:01:30,540 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-07-08T09:01:30,954 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 2026-07-08T09:01:30,977 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-07-08T09:01:32,985 Collecting setuptools>=61.0 2026-07-08T09:01:32,986 Obtaining dependency information for setuptools>=61.0 from https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl.metadata 2026-07-08T09:01:33,004 Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl.metadata (6.6 kB) 2026-07-08T09:01:33,241 Collecting wheel 2026-07-08T09:01:33,242 Obtaining dependency information for wheel from https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata 2026-07-08T09:01:33,257 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB) 2026-07-08T09:01:33,447 Collecting packaging>=24.0 2026-07-08T09:01:33,448 Obtaining dependency information for packaging>=24.0 from https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata 2026-07-08T09:01:33,467 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata (3.5 kB) 2026-07-08T09:01:33,662 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB) 2026-07-08T09:01:33,682 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB) 2026-07-08T09:01:33,759 Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl (1.0 MB) 2026-07-08T09:01:33,792 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB) 2026-07-08T09:01:33,819 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB) 2026-07-08T09:01:33,911 Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl (1.0 MB) 2026-07-08T09:01:36,664 Installing collected packages: setuptools, packaging, wheel 2026-07-08T09:01:40,214 Creating /tmp/pip-build-env-skyn79xq/overlay/local/bin 2026-07-08T09:01:40,217 changing mode of /tmp/pip-build-env-skyn79xq/overlay/local/bin/wheel to 755 2026-07-08T09:01:40,239 Successfully installed packaging-26.2 setuptools-83.0.0 wheel-0.47.0 2026-07-08T09:01:40,529 Installing build dependencies: finished with status 'done' 2026-07-08T09:01:40,538 Getting requirements to build wheel: started 2026-07-08T09:01:40,540 Running command Getting requirements to build wheel 2026-07-08T09:01:41,232 running egg_info 2026-07-08T09:01:41,237 writing oncoref.egg-info/PKG-INFO 2026-07-08T09:01:41,243 writing dependency_links to oncoref.egg-info/dependency_links.txt 2026-07-08T09:01:41,246 writing entry points to oncoref.egg-info/entry_points.txt 2026-07-08T09:01:41,249 writing requirements to oncoref.egg-info/requires.txt 2026-07-08T09:01:41,250 writing top-level names to oncoref.egg-info/top_level.txt 2026-07-08T09:01:41,285 reading manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-08T09:01:41,295 reading manifest template 'MANIFEST.in' 2026-07-08T09:01:41,297 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-07-08T09:01:41,299 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-07-08T09:01:41,301 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-07-08T09:01:41,303 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-07-08T09:01:41,304 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-07-08T09:01:41,306 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-07-08T09:01:41,307 adding license file 'LICENSE' 2026-07-08T09:01:41,316 writing manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-08T09:01:41,415 Getting requirements to build wheel: finished with status 'done' 2026-07-08T09:01:41,419 Created temporary directory: /tmp/pip-modern-metadata-wk9c9no7 2026-07-08T09:01:41,421 Preparing metadata (pyproject.toml): started 2026-07-08T09:01:41,422 Running command Preparing metadata (pyproject.toml) 2026-07-08T09:01:42,071 running dist_info 2026-07-08T09:01:42,081 creating /tmp/pip-modern-metadata-wk9c9no7/oncoref.egg-info 2026-07-08T09:01:42,082 writing /tmp/pip-modern-metadata-wk9c9no7/oncoref.egg-info/PKG-INFO 2026-07-08T09:01:42,088 writing dependency_links to /tmp/pip-modern-metadata-wk9c9no7/oncoref.egg-info/dependency_links.txt 2026-07-08T09:01:42,090 writing entry points to /tmp/pip-modern-metadata-wk9c9no7/oncoref.egg-info/entry_points.txt 2026-07-08T09:01:42,092 writing requirements to /tmp/pip-modern-metadata-wk9c9no7/oncoref.egg-info/requires.txt 2026-07-08T09:01:42,094 writing top-level names to /tmp/pip-modern-metadata-wk9c9no7/oncoref.egg-info/top_level.txt 2026-07-08T09:01:42,095 writing manifest file '/tmp/pip-modern-metadata-wk9c9no7/oncoref.egg-info/SOURCES.txt' 2026-07-08T09:01:42,127 reading manifest file '/tmp/pip-modern-metadata-wk9c9no7/oncoref.egg-info/SOURCES.txt' 2026-07-08T09:01:42,129 reading manifest template 'MANIFEST.in' 2026-07-08T09:01:42,131 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-07-08T09:01:42,132 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-07-08T09:01:42,133 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-07-08T09:01:42,134 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-07-08T09:01:42,135 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-07-08T09:01:42,136 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-07-08T09:01:42,137 adding license file 'LICENSE' 2026-07-08T09:01:42,143 writing manifest file '/tmp/pip-modern-metadata-wk9c9no7/oncoref.egg-info/SOURCES.txt' 2026-07-08T09:01:42,145 creating '/tmp/pip-modern-metadata-wk9c9no7/oncoref-1.8.76.dist-info' 2026-07-08T09:01:42,271 Preparing metadata (pyproject.toml): finished with status 'done' 2026-07-08T09:01:42,276 Source in /tmp/pip-wheel-t89i5e5t/oncoref_51bf4b3fe3c24bcdb4eed672758d7d26 has version 1.8.76, which satisfies requirement oncoref==1.8.76 from https://files.pythonhosted.org/packages/30/c2/956670f34940b2c734ebb252bf865ead4b2e4b178c96c894b1e7bb048dab/oncoref-1.8.76.tar.gz 2026-07-08T09:01:42,277 Removed oncoref==1.8.76 from https://files.pythonhosted.org/packages/30/c2/956670f34940b2c734ebb252bf865ead4b2e4b178c96c894b1e7bb048dab/oncoref-1.8.76.tar.gz from build tracker '/tmp/pip-build-tracker-ce2q9rp4' 2026-07-08T09:01:42,283 Created temporary directory: /tmp/pip-unpack-3bglt0jr 2026-07-08T09:01:42,284 Building wheels for collected packages: oncoref 2026-07-08T09:01:42,288 Created temporary directory: /tmp/pip-wheel-m0glq940 2026-07-08T09:01:42,289 Destination directory: /tmp/pip-wheel-m0glq940 2026-07-08T09:01:42,291 Building wheel for oncoref (pyproject.toml): started 2026-07-08T09:01:42,292 Running command Building wheel for oncoref (pyproject.toml) 2026-07-08T09:01:42,912 running bdist_wheel 2026-07-08T09:01:42,930 running build 2026-07-08T09:01:42,930 running build_py 2026-07-08T09:01:42,938 creating build/lib/oncoref 2026-07-08T09:01:42,940 copying oncoref/coverage.py -> build/lib/oncoref 2026-07-08T09:01:42,943 copying oncoref/cta_coverage.py -> build/lib/oncoref 2026-07-08T09:01:42,944 copying oncoref/catalog.py -> build/lib/oncoref 2026-07-08T09:01:42,947 copying oncoref/version.py -> build/lib/oncoref 2026-07-08T09:01:42,949 copying oncoref/gene_ids.py -> build/lib/oncoref 2026-07-08T09:01:42,951 copying oncoref/load_dataset.py -> build/lib/oncoref 2026-07-08T09:01:42,954 copying oncoref/expression_registry.py -> build/lib/oncoref 2026-07-08T09:01:42,956 copying oncoref/cta.py -> build/lib/oncoref 2026-07-08T09:01:42,959 copying oncoref/reference_data.py -> build/lib/oncoref 2026-07-08T09:01:42,961 copying oncoref/ici.py -> build/lib/oncoref 2026-07-08T09:01:42,964 copying oncoref/expression_builders.py -> build/lib/oncoref 2026-07-08T09:01:42,967 copying oncoref/cli.py -> build/lib/oncoref 2026-07-08T09:01:42,970 copying oncoref/hpa.py -> build/lib/oncoref 2026-07-08T09:01:42,972 copying oncoref/normalization.py -> build/lib/oncoref 2026-07-08T09:01:42,975 copying oncoref/__init__.py -> build/lib/oncoref 2026-07-08T09:01:42,977 copying oncoref/cta_peptides.py -> build/lib/oncoref 2026-07-08T09:01:42,979 copying oncoref/expression.py -> build/lib/oncoref 2026-07-08T09:01:42,984 copying oncoref/antigen_coverage.py -> build/lib/oncoref 2026-07-08T09:01:42,986 copying oncoref/incidence.py -> build/lib/oncoref 2026-07-08T09:01:42,988 copying oncoref/expression_engine.py -> build/lib/oncoref 2026-07-08T09:01:42,991 copying oncoref/source_matrices.py -> build/lib/oncoref 2026-07-08T09:01:42,993 copying oncoref/cancer_types.py -> build/lib/oncoref 2026-07-08T09:01:42,997 copying oncoref/data_bundle.py -> build/lib/oncoref 2026-07-08T09:01:42,999 copying oncoref/cta_tissues.py -> build/lib/oncoref 2026-07-08T09:01:43,002 copying oncoref/cta_regen.py -> build/lib/oncoref 2026-07-08T09:01:43,005 copying oncoref/cohorts.py -> build/lib/oncoref 2026-07-08T09:01:43,006 copying oncoref/proteoforms.py -> build/lib/oncoref 2026-07-08T09:01:43,009 copying oncoref/gene_qc.py -> build/lib/oncoref 2026-07-08T09:01:43,011 copying oncoref/genome.py -> build/lib/oncoref 2026-07-08T09:01:43,014 copying oncoref/samples.py -> build/lib/oncoref 2026-07-08T09:01:43,016 copying oncoref/data_manifest.py -> build/lib/oncoref 2026-07-08T09:01:43,019 copying oncoref/response_signatures.py -> build/lib/oncoref 2026-07-08T09:01:43,021 copying oncoref/peptides.py -> build/lib/oncoref 2026-07-08T09:01:43,023 copying oncoref/ici_response.py -> build/lib/oncoref 2026-07-08T09:01:43,025 copying oncoref/apd1.py -> build/lib/oncoref 2026-07-08T09:01:43,028 copying oncoref/cancer_genes.py -> build/lib/oncoref 2026-07-08T09:01:43,030 copying oncoref/gene_families.py -> build/lib/oncoref 2026-07-08T09:01:43,032 copying oncoref/fusions.py -> build/lib/oncoref 2026-07-08T09:01:43,034 copying oncoref/plots.py -> build/lib/oncoref 2026-07-08T09:01:43,037 copying oncoref/tmb.py -> build/lib/oncoref 2026-07-08T09:01:43,039 copying oncoref/cancer_ontology.py -> build/lib/oncoref 2026-07-08T09:01:43,041 copying oncoref/cta_curation_plots.py -> build/lib/oncoref 2026-07-08T09:01:43,055 creating build/lib/oncoref/data 2026-07-08T09:01:43,056 copying oncoref/data/expression-artifact-gene-universe-deltas.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,063 copying oncoref/data/cancer-type-genes.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,066 copying oncoref/data/disease-state-rules.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,068 copying oncoref/data/cancer-lineage-groups.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,070 copying oncoref/data/fusion-expression-effects.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,072 copying oncoref/data/cancer-ici-response.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,075 copying oncoref/data/cta-ihc-unreliable.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,077 copying oncoref/data/degenerate-subtype-pairs.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,079 copying oncoref/data/housekeeping-genes.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,081 copying oncoref/data/cancer-expression-source-candidates.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,084 copying oncoref/data/cancer-driver-genes.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,087 copying oncoref/data/histone-genes.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,089 copying oncoref/data/cancer-apd1-response.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,092 copying oncoref/data/numt-pseudogenes.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,095 copying oncoref/data/proteoform-groups.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,097 copying oncoref/data/rrna-and-pseudogenes.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,099 copying oncoref/data/cancer-response-signatures.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,101 copying oncoref/data/cancer-key-genes.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,106 copying oncoref/data/censored-gene-reference-tpm.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,108 copying oncoref/data/cancer-type-registry.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,112 copying oncoref/data/small-noncoding-rnas.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,116 copying oncoref/data/cohort-registry.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,119 copying oncoref/data/cancer-subtype-groupings.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,121 copying oncoref/data/cancer-driver-variants.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,124 copying oncoref/data/cancer-testis-antigens.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,129 copying oncoref/data/cancer-tmb.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,131 copying oncoref/data/cancer-cohort-aggregates.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,133 copying oncoref/data/cancer-ici-response-estimates.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,139 copying oncoref/data/nuclear-retained-lncrnas.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,141 copying oncoref/data/cancer-lineage-group-overrides.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,144 copying oncoref/data/ensembl-id-aliases.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,152 copying oncoref/data/fusion-surrogate-expression.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,155 copying oncoref/data/cta-candidate-references.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,157 copying oncoref/data/ribosomal-protein-genes.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,159 copying oncoref/data/cancer-incidence-mortality.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,161 copying oncoref/data/proteoform-groups-genome.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,164 copying oncoref/data/cancer-viral-antigens.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,166 copying oncoref/data/proteoform-collapse-overrides.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,168 copying oncoref/data/hemoglobin-genes.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,170 copying oncoref/data/narrative-gene-sets.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,172 copying oncoref/data/cancer-fusions.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,175 copying oncoref/data/cancer-code-burden-map.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,177 copying oncoref/data/extra-tx-mappings.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,180 copying oncoref/data/family-burden-map.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,182 copying oncoref/data/rare-cancer-fusion-rules.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,184 copying oncoref/data/cancer-normal-tissue-map.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,187 copying oncoref/data/ribosomal-protein-pseudogenes.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,190 copying oncoref/data/mitochondrial-genes.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,193 copying oncoref/data/tissue-burden-map.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,196 copying oncoref/data/cancer-frameshift-burden.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,199 copying oncoref/data/clean-tpm-biological-housekeeping-genes.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,202 copying oncoref/data/clean-tpm-censored-genes.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,206 copying oncoref/data/source-matrices.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,208 copying oncoref/data/cdna-identical-gene-groups.csv -> build/lib/oncoref/data 2026-07-08T09:01:43,211 copying oncoref/data/canonical-gene-space.csv.gz -> build/lib/oncoref/data 2026-07-08T09:01:43,222 copying oncoref/data/ncbi-entrez-gene-mappings.csv.gz -> build/lib/oncoref/data 2026-07-08T09:01:43,244 copying oncoref/data/cancer-reference-expression-samples.csv.gz -> build/lib/oncoref/data 2026-07-08T09:01:43,251 copying oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/lib/oncoref/data 2026-07-08T09:01:43,261 copying oncoref/data/expression_sources.yaml -> build/lib/oncoref/data 2026-07-08T09:01:43,275 installing to build/bdist.linux-armv7l/wheel 2026-07-08T09:01:43,275 running install 2026-07-08T09:01:43,299 running install_lib 2026-07-08T09:01:43,306 creating build/bdist.linux-armv7l/wheel 2026-07-08T09:01:43,309 creating build/bdist.linux-armv7l/wheel/oncoref 2026-07-08T09:01:43,310 copying build/lib/oncoref/coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,313 copying build/lib/oncoref/cta_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,316 copying build/lib/oncoref/catalog.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,318 copying build/lib/oncoref/version.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,321 copying build/lib/oncoref/gene_ids.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,324 copying build/lib/oncoref/load_dataset.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,326 copying build/lib/oncoref/expression_registry.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,329 copying build/lib/oncoref/cta.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,332 copying build/lib/oncoref/reference_data.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,334 copying build/lib/oncoref/ici.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,339 creating build/bdist.linux-armv7l/wheel/oncoref/data 2026-07-08T09:01:43,340 copying build/lib/oncoref/data/expression-artifact-gene-universe-deltas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,348 copying build/lib/oncoref/data/cancer-type-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,351 copying build/lib/oncoref/data/disease-state-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,353 copying build/lib/oncoref/data/cancer-lineage-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,355 copying build/lib/oncoref/data/fusion-expression-effects.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,357 copying build/lib/oncoref/data/cancer-ici-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,360 copying build/lib/oncoref/data/cta-ihc-unreliable.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,362 copying build/lib/oncoref/data/degenerate-subtype-pairs.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,364 copying build/lib/oncoref/data/housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,366 copying build/lib/oncoref/data/cancer-expression-source-candidates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,369 copying build/lib/oncoref/data/cancer-driver-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,372 copying build/lib/oncoref/data/histone-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,375 copying build/lib/oncoref/data/cancer-apd1-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,378 copying build/lib/oncoref/data/numt-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,381 copying build/lib/oncoref/data/canonical-gene-space.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,392 copying build/lib/oncoref/data/ncbi-entrez-gene-mappings.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,410 copying build/lib/oncoref/data/proteoform-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,412 copying build/lib/oncoref/data/rrna-and-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,416 copying build/lib/oncoref/data/cancer-response-signatures.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,418 copying build/lib/oncoref/data/cancer-key-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,426 copying build/lib/oncoref/data/censored-gene-reference-tpm.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,429 copying build/lib/oncoref/data/expression_sources.yaml -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,433 copying build/lib/oncoref/data/cancer-type-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,438 copying build/lib/oncoref/data/small-noncoding-rnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,446 copying build/lib/oncoref/data/cohort-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,449 copying build/lib/oncoref/data/cancer-subtype-groupings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,451 copying build/lib/oncoref/data/cancer-driver-variants.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,454 copying build/lib/oncoref/data/cancer-testis-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,460 copying build/lib/oncoref/data/cancer-tmb.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,463 copying build/lib/oncoref/data/cancer-cohort-aggregates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,465 copying build/lib/oncoref/data/cancer-ici-response-estimates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,473 copying build/lib/oncoref/data/nuclear-retained-lncrnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,475 copying build/lib/oncoref/data/cancer-lineage-group-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,478 copying build/lib/oncoref/data/ensembl-id-aliases.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,490 copying build/lib/oncoref/data/fusion-surrogate-expression.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,492 copying build/lib/oncoref/data/cta-candidate-references.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,494 copying build/lib/oncoref/data/ribosomal-protein-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,496 copying build/lib/oncoref/data/cancer-incidence-mortality.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,499 copying build/lib/oncoref/data/proteoform-groups-genome.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,502 copying build/lib/oncoref/data/cancer-viral-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,504 copying build/lib/oncoref/data/proteoform-collapse-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,506 copying build/lib/oncoref/data/hemoglobin-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,508 copying build/lib/oncoref/data/narrative-gene-sets.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,510 copying build/lib/oncoref/data/cancer-fusions.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,513 copying build/lib/oncoref/data/cancer-code-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,515 copying build/lib/oncoref/data/extra-tx-mappings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,517 copying build/lib/oncoref/data/family-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,519 copying build/lib/oncoref/data/rare-cancer-fusion-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,522 copying build/lib/oncoref/data/cancer-normal-tissue-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,525 copying build/lib/oncoref/data/ribosomal-protein-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,528 copying build/lib/oncoref/data/mitochondrial-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,530 copying build/lib/oncoref/data/cancer-reference-expression-samples.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,538 copying build/lib/oncoref/data/tissue-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,541 copying build/lib/oncoref/data/cancer-frameshift-burden.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,543 copying build/lib/oncoref/data/clean-tpm-biological-housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,545 copying build/lib/oncoref/data/clean-tpm-censored-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,550 copying build/lib/oncoref/data/source-matrices.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,553 copying build/lib/oncoref/data/cdna-identical-gene-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,556 copying build/lib/oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-08T09:01:43,564 copying build/lib/oncoref/expression_builders.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,567 copying build/lib/oncoref/cli.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,570 copying build/lib/oncoref/hpa.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,572 copying build/lib/oncoref/normalization.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,575 copying build/lib/oncoref/__init__.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,577 copying build/lib/oncoref/cta_peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,579 copying build/lib/oncoref/expression.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,584 copying build/lib/oncoref/antigen_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,585 copying build/lib/oncoref/incidence.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,588 copying build/lib/oncoref/expression_engine.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,590 copying build/lib/oncoref/source_matrices.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,592 copying build/lib/oncoref/cancer_types.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,595 copying build/lib/oncoref/data_bundle.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,598 copying build/lib/oncoref/cta_tissues.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,601 copying build/lib/oncoref/cta_regen.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,603 copying build/lib/oncoref/cohorts.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,605 copying build/lib/oncoref/proteoforms.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,608 copying build/lib/oncoref/gene_qc.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,610 copying build/lib/oncoref/genome.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,612 copying build/lib/oncoref/samples.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,614 copying build/lib/oncoref/data_manifest.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,617 copying build/lib/oncoref/response_signatures.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,619 copying build/lib/oncoref/peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,621 copying build/lib/oncoref/ici_response.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,624 copying build/lib/oncoref/apd1.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,626 copying build/lib/oncoref/cancer_genes.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,628 copying build/lib/oncoref/gene_families.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,631 copying build/lib/oncoref/fusions.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,633 copying build/lib/oncoref/plots.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,636 copying build/lib/oncoref/tmb.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,639 copying build/lib/oncoref/cancer_ontology.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,641 copying build/lib/oncoref/cta_curation_plots.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-08T09:01:43,643 running install_egg_info 2026-07-08T09:01:43,652 running egg_info 2026-07-08T09:01:43,658 writing oncoref.egg-info/PKG-INFO 2026-07-08T09:01:43,664 writing dependency_links to oncoref.egg-info/dependency_links.txt 2026-07-08T09:01:43,665 writing entry points to oncoref.egg-info/entry_points.txt 2026-07-08T09:01:43,667 writing requirements to oncoref.egg-info/requires.txt 2026-07-08T09:01:43,668 writing top-level names to oncoref.egg-info/top_level.txt 2026-07-08T09:01:43,687 reading manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-08T09:01:43,698 reading manifest template 'MANIFEST.in' 2026-07-08T09:01:43,700 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-07-08T09:01:43,702 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-07-08T09:01:43,703 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-07-08T09:01:43,704 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-07-08T09:01:43,705 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-07-08T09:01:43,706 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-07-08T09:01:43,707 adding license file 'LICENSE' 2026-07-08T09:01:43,715 writing manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-08T09:01:43,717 Copying oncoref.egg-info to build/bdist.linux-armv7l/wheel/./oncoref-1.8.76-py3.11.egg-info 2026-07-08T09:01:43,729 running install_scripts 2026-07-08T09:01:43,744 creating build/bdist.linux-armv7l/wheel/oncoref-1.8.76.dist-info/WHEEL 2026-07-08T09:01:43,747 creating '/tmp/pip-wheel-m0glq940/.tmp-fg2wh_n0/oncoref-1.8.76-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-07-08T09:01:43,753 adding 'oncoref/__init__.py' 2026-07-08T09:01:43,755 adding 'oncoref/antigen_coverage.py' 2026-07-08T09:01:43,757 adding 'oncoref/apd1.py' 2026-07-08T09:01:43,760 adding 'oncoref/cancer_genes.py' 2026-07-08T09:01:43,762 adding 'oncoref/cancer_ontology.py' 2026-07-08T09:01:43,773 adding 'oncoref/cancer_types.py' 2026-07-08T09:01:43,776 adding 'oncoref/catalog.py' 2026-07-08T09:01:43,780 adding 'oncoref/cli.py' 2026-07-08T09:01:43,782 adding 'oncoref/cohorts.py' 2026-07-08T09:01:43,787 adding 'oncoref/coverage.py' 2026-07-08T09:01:43,791 adding 'oncoref/cta.py' 2026-07-08T09:01:43,793 adding 'oncoref/cta_coverage.py' 2026-07-08T09:01:43,795 adding 'oncoref/cta_curation_plots.py' 2026-07-08T09:01:43,797 adding 'oncoref/cta_peptides.py' 2026-07-08T09:01:43,801 adding 'oncoref/cta_regen.py' 2026-07-08T09:01:43,803 adding 'oncoref/cta_tissues.py' 2026-07-08T09:01:43,809 adding 'oncoref/data_bundle.py' 2026-07-08T09:01:43,812 adding 'oncoref/data_manifest.py' 2026-07-08T09:01:43,836 adding 'oncoref/expression.py' 2026-07-08T09:01:43,842 adding 'oncoref/expression_builders.py' 2026-07-08T09:01:43,846 adding 'oncoref/expression_engine.py' 2026-07-08T09:01:43,848 adding 'oncoref/expression_registry.py' 2026-07-08T09:01:43,850 adding 'oncoref/fusions.py' 2026-07-08T09:01:43,853 adding 'oncoref/gene_families.py' 2026-07-08T09:01:43,855 adding 'oncoref/gene_ids.py' 2026-07-08T09:01:43,857 adding 'oncoref/gene_qc.py' 2026-07-08T09:01:43,859 adding 'oncoref/genome.py' 2026-07-08T09:01:43,861 adding 'oncoref/hpa.py' 2026-07-08T09:01:43,865 adding 'oncoref/ici.py' 2026-07-08T09:01:43,867 adding 'oncoref/ici_response.py' 2026-07-08T09:01:43,869 adding 'oncoref/incidence.py' 2026-07-08T09:01:43,870 adding 'oncoref/load_dataset.py' 2026-07-08T09:01:43,875 adding 'oncoref/normalization.py' 2026-07-08T09:01:43,877 adding 'oncoref/peptides.py' 2026-07-08T09:01:43,884 adding 'oncoref/plots.py' 2026-07-08T09:01:43,887 adding 'oncoref/proteoforms.py' 2026-07-08T09:01:43,890 adding 'oncoref/reference_data.py' 2026-07-08T09:01:43,891 adding 'oncoref/response_signatures.py' 2026-07-08T09:01:43,892 adding 'oncoref/samples.py' 2026-07-08T09:01:43,894 adding 'oncoref/source_matrices.py' 2026-07-08T09:01:43,896 adding 'oncoref/tmb.py' 2026-07-08T09:01:43,897 adding 'oncoref/version.py' 2026-07-08T09:01:43,901 adding 'oncoref/data/cancer-apd1-response.csv' 2026-07-08T09:01:43,903 adding 'oncoref/data/cancer-code-burden-map.csv' 2026-07-08T09:01:43,904 adding 'oncoref/data/cancer-cohort-aggregates.csv' 2026-07-08T09:01:43,909 adding 'oncoref/data/cancer-driver-genes.csv' 2026-07-08T09:01:43,912 adding 'oncoref/data/cancer-driver-variants.csv' 2026-07-08T09:01:43,914 adding 'oncoref/data/cancer-expression-source-candidates.csv' 2026-07-08T09:01:43,916 adding 'oncoref/data/cancer-frameshift-burden.csv' 2026-07-08T09:01:43,919 adding 'oncoref/data/cancer-fusions.csv' 2026-07-08T09:01:43,936 adding 'oncoref/data/cancer-ici-response-estimates.csv' 2026-07-08T09:01:43,940 adding 'oncoref/data/cancer-ici-response.csv' 2026-07-08T09:01:43,942 adding 'oncoref/data/cancer-incidence-mortality.csv' 2026-07-08T09:01:43,956 adding 'oncoref/data/cancer-key-genes.csv' 2026-07-08T09:01:43,959 adding 'oncoref/data/cancer-lineage-group-overrides.csv' 2026-07-08T09:01:43,960 adding 'oncoref/data/cancer-lineage-groups.csv' 2026-07-08T09:01:43,961 adding 'oncoref/data/cancer-normal-tissue-map.csv' 2026-07-08T09:01:43,990 adding 'oncoref/data/cancer-reference-expression-samples.csv.gz' 2026-07-08T09:01:43,993 adding 'oncoref/data/cancer-response-signatures.csv' 2026-07-08T09:01:43,994 adding 'oncoref/data/cancer-subtype-groupings.csv' 2026-07-08T09:01:44,006 adding 'oncoref/data/cancer-testis-antigens.csv' 2026-07-08T09:01:44,009 adding 'oncoref/data/cancer-tmb.csv' 2026-07-08T09:01:44,011 adding 'oncoref/data/cancer-type-genes.csv' 2026-07-08T09:01:44,015 adding 'oncoref/data/cancer-type-registry.csv' 2026-07-08T09:01:44,017 adding 'oncoref/data/cancer-viral-antigens.csv' 2026-07-08T09:01:44,069 adding 'oncoref/data/canonical-gene-space.csv.gz' 2026-07-08T09:01:44,075 adding 'oncoref/data/cdna-identical-gene-groups.csv' 2026-07-08T09:01:44,079 adding 'oncoref/data/censored-gene-reference-tpm.csv' 2026-07-08T09:01:44,081 adding 'oncoref/data/clean-tpm-biological-housekeeping-genes.csv' 2026-07-08T09:01:44,091 adding 'oncoref/data/clean-tpm-censored-genes.csv' 2026-07-08T09:01:44,094 adding 'oncoref/data/cohort-registry.csv' 2026-07-08T09:01:44,095 adding 'oncoref/data/cta-candidate-references.csv' 2026-07-08T09:01:44,096 adding 'oncoref/data/cta-ihc-unreliable.csv' 2026-07-08T09:01:44,098 adding 'oncoref/data/degenerate-subtype-pairs.csv' 2026-07-08T09:01:44,099 adding 'oncoref/data/disease-state-rules.csv' 2026-07-08T09:01:44,126 adding 'oncoref/data/ensembl-id-aliases.csv' 2026-07-08T09:01:44,139 adding 'oncoref/data/expression-artifact-gene-universe-deltas.csv' 2026-07-08T09:01:44,145 adding 'oncoref/data/expression_sources.yaml' 2026-07-08T09:01:44,147 adding 'oncoref/data/extra-tx-mappings.csv' 2026-07-08T09:01:44,148 adding 'oncoref/data/family-burden-map.csv' 2026-07-08T09:01:44,149 adding 'oncoref/data/fusion-expression-effects.csv' 2026-07-08T09:01:44,151 adding 'oncoref/data/fusion-surrogate-expression.csv' 2026-07-08T09:01:44,152 adding 'oncoref/data/hemoglobin-genes.csv' 2026-07-08T09:01:44,154 adding 'oncoref/data/histone-genes.csv' 2026-07-08T09:01:44,155 adding 'oncoref/data/housekeeping-genes.csv' 2026-07-08T09:01:44,156 adding 'oncoref/data/mitochondrial-genes.csv' 2026-07-08T09:01:44,157 adding 'oncoref/data/narrative-gene-sets.csv' 2026-07-08T09:01:44,259 adding 'oncoref/data/ncbi-entrez-gene-mappings.csv.gz' 2026-07-08T09:01:44,307 adding 'oncoref/data/ncbi-symbol-synonyms.csv.gz' 2026-07-08T09:01:44,311 adding 'oncoref/data/nuclear-retained-lncrnas.csv' 2026-07-08T09:01:44,313 adding 'oncoref/data/numt-pseudogenes.csv' 2026-07-08T09:01:44,314 adding 'oncoref/data/proteoform-collapse-overrides.csv' 2026-07-08T09:01:44,317 adding 'oncoref/data/proteoform-groups-genome.csv' 2026-07-08T09:01:44,318 adding 'oncoref/data/proteoform-groups.csv' 2026-07-08T09:01:44,320 adding 'oncoref/data/rare-cancer-fusion-rules.csv' 2026-07-08T09:01:44,322 adding 'oncoref/data/ribosomal-protein-genes.csv' 2026-07-08T09:01:44,328 adding 'oncoref/data/ribosomal-protein-pseudogenes.csv' 2026-07-08T09:01:44,331 adding 'oncoref/data/rrna-and-pseudogenes.csv' 2026-07-08T09:01:44,350 adding 'oncoref/data/small-noncoding-rnas.csv' 2026-07-08T09:01:44,352 adding 'oncoref/data/source-matrices.csv' 2026-07-08T09:01:44,354 adding 'oncoref/data/tissue-burden-map.csv' 2026-07-08T09:01:44,358 adding 'oncoref-1.8.76.dist-info/licenses/LICENSE' 2026-07-08T09:01:44,360 adding 'oncoref-1.8.76.dist-info/METADATA' 2026-07-08T09:01:44,361 adding 'oncoref-1.8.76.dist-info/WHEEL' 2026-07-08T09:01:44,362 adding 'oncoref-1.8.76.dist-info/entry_points.txt' 2026-07-08T09:01:44,363 adding 'oncoref-1.8.76.dist-info/top_level.txt' 2026-07-08T09:01:44,364 adding 'oncoref-1.8.76.dist-info/RECORD' 2026-07-08T09:01:44,392 removing build/bdist.linux-armv7l/wheel 2026-07-08T09:01:44,514 Building wheel for oncoref (pyproject.toml): finished with status 'done' 2026-07-08T09:01:44,576 Created wheel for oncoref: filename=oncoref-1.8.76-py3-none-any.whl size=2642997 sha256=711d662219d27bfa2a94675d44d635d50c63e9b25ab95276ab9b1a2e79fc366c 2026-07-08T09:01:44,578 Stored in directory: /tmp/pip-ephem-wheel-cache-ne_oidju/wheels/f3/c5/6e/fca178c72509a20e92943bf0e03f0fc4ca74f1243fb2665485 2026-07-08T09:01:44,593 Successfully built oncoref 2026-07-08T09:01:44,664 Removed build tracker: '/tmp/pip-build-tracker-ce2q9rp4'