2026-07-31T19:00:25,898 Created temporary directory: /tmp/pip-ephem-wheel-cache-8l17lo_c 2026-07-31T19:00:25,900 Created temporary directory: /tmp/pip-build-tracker-7yixrxe3 2026-07-31T19:00:25,900 Initialized build tracking at /tmp/pip-build-tracker-7yixrxe3 2026-07-31T19:00:25,901 Created build tracker: /tmp/pip-build-tracker-7yixrxe3 2026-07-31T19:00:25,901 Entered build tracker: /tmp/pip-build-tracker-7yixrxe3 2026-07-31T19:00:25,902 Created temporary directory: /tmp/pip-wheel-lv6gmqso 2026-07-31T19:00:25,905 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 2026-07-31T19:00:25,908 Created temporary directory: /tmp/pip-ephem-wheel-cache-jx7sbvom 2026-07-31T19:00:25,931 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-07-31T19:00:25,935 2 location(s) to search for versions of oncoref: 2026-07-31T19:00:25,935 * https://pypi.org/simple/oncoref/ 2026-07-31T19:00:25,935 * https://www.piwheels.org/simple/oncoref/ 2026-07-31T19:00:25,936 Fetching project page and analyzing links: https://pypi.org/simple/oncoref/ 2026-07-31T19:00:25,936 Getting page https://pypi.org/simple/oncoref/ 2026-07-31T19:00:25,938 Found index url https://pypi.org/simple 2026-07-31T19:00:26,219 Fetched page https://pypi.org/simple/oncoref/ as application/vnd.pypi.simple.v1+json 2026-07-31T19:00:26,278 Skipping link: No binaries permitted for oncoref: 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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) 2026-07-31T19:00:26,885 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) 2026-07-31T19:00:26,886 Skipping link: not a file: https://www.piwheels.org/simple/oncoref/ 2026-07-31T19:00:26,886 Skipping link: not a file: https://pypi.org/simple/oncoref/ 2026-07-31T19:00:26,925 Given no hashes to check 1 links for project 'oncoref': discarding no candidates 2026-07-31T19:00:26,944 Collecting oncoref==1.8.164 2026-07-31T19:00:26,946 Created temporary directory: /tmp/pip-unpack-55hzxa38 2026-07-31T19:00:27,100 Downloading oncoref-1.8.164.tar.gz (3.0 MB) 2026-07-31T19:00:28,037 Added oncoref==1.8.164 from https://files.pythonhosted.org/packages/6a/ad/3a399e6a73eb114de42686813c45c4b7b2adf00829167dccc55b8227fcb6/oncoref-1.8.164.tar.gz to build tracker '/tmp/pip-build-tracker-7yixrxe3' 2026-07-31T19:00:28,044 Created temporary directory: /tmp/pip-build-env-f15_l2ez 2026-07-31T19:00:28,048 Installing build dependencies: started 2026-07-31T19:00:28,049 Running command pip subprocess to install build dependencies 2026-07-31T19:00:29,465 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-07-31T19:00:29,990 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 2026-07-31T19:00:30,013 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-07-31T19:00:31,806 Collecting setuptools>=77.0.0 2026-07-31T19:00:31,807 Obtaining dependency information for setuptools>=77.0.0 from https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl.metadata 2026-07-31T19:00:31,824 Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl.metadata (6.6 kB) 2026-07-31T19:00:32,059 Collecting wheel 2026-07-31T19:00:32,060 Obtaining dependency information for wheel from https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata 2026-07-31T19:00:32,074 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB) 2026-07-31T19:00:32,258 Collecting packaging>=24.0 2026-07-31T19:00:32,258 Obtaining dependency information for packaging>=24.0 from https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata 2026-07-31T19:00:32,273 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata (3.5 kB) 2026-07-31T19:00:32,466 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB) 2026-07-31T19:00:32,486 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB) 2026-07-31T19:00:32,600 Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl (1.0 MB) 2026-07-31T19:00:32,639 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB) 2026-07-31T19:00:32,670 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB) 2026-07-31T19:00:32,763 Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl (1.0 MB) 2026-07-31T19:00:35,560 Installing collected packages: setuptools, packaging, wheel 2026-07-31T19:00:38,989 Creating /tmp/pip-build-env-f15_l2ez/overlay/local/bin 2026-07-31T19:00:38,991 changing mode of /tmp/pip-build-env-f15_l2ez/overlay/local/bin/wheel to 755 2026-07-31T19:00:39,012 Successfully installed packaging-26.2 setuptools-83.0.0 wheel-0.47.0 2026-07-31T19:00:39,292 Installing build dependencies: finished with status 'done' 2026-07-31T19:00:39,298 Getting requirements to build wheel: started 2026-07-31T19:00:39,300 Running command Getting requirements to build wheel 2026-07-31T19:00:39,998 running egg_info 2026-07-31T19:00:40,006 writing oncoref.egg-info/PKG-INFO 2026-07-31T19:00:40,012 writing dependency_links to oncoref.egg-info/dependency_links.txt 2026-07-31T19:00:40,014 writing entry points to oncoref.egg-info/entry_points.txt 2026-07-31T19:00:40,016 writing requirements to oncoref.egg-info/requires.txt 2026-07-31T19:00:40,018 writing top-level names to oncoref.egg-info/top_level.txt 2026-07-31T19:00:40,054 reading manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-31T19:00:40,066 reading manifest template 'MANIFEST.in' 2026-07-31T19:00:40,079 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-07-31T19:00:40,080 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-07-31T19:00:40,082 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-07-31T19:00:40,084 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-07-31T19:00:40,085 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-07-31T19:00:40,086 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-07-31T19:00:40,087 adding license file 'LICENSE' 2026-07-31T19:00:40,097 writing manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-31T19:00:40,196 Getting requirements to build wheel: finished with status 'done' 2026-07-31T19:00:40,200 Created temporary directory: /tmp/pip-modern-metadata-6co98yqk 2026-07-31T19:00:40,202 Preparing metadata (pyproject.toml): started 2026-07-31T19:00:40,203 Running command Preparing metadata (pyproject.toml) 2026-07-31T19:00:41,137 running dist_info 2026-07-31T19:00:41,147 creating /tmp/pip-modern-metadata-6co98yqk/oncoref.egg-info 2026-07-31T19:00:41,148 writing /tmp/pip-modern-metadata-6co98yqk/oncoref.egg-info/PKG-INFO 2026-07-31T19:00:41,155 writing dependency_links to /tmp/pip-modern-metadata-6co98yqk/oncoref.egg-info/dependency_links.txt 2026-07-31T19:00:41,157 writing entry points to /tmp/pip-modern-metadata-6co98yqk/oncoref.egg-info/entry_points.txt 2026-07-31T19:00:41,160 writing requirements to /tmp/pip-modern-metadata-6co98yqk/oncoref.egg-info/requires.txt 2026-07-31T19:00:41,161 writing top-level names to /tmp/pip-modern-metadata-6co98yqk/oncoref.egg-info/top_level.txt 2026-07-31T19:00:41,163 writing manifest file '/tmp/pip-modern-metadata-6co98yqk/oncoref.egg-info/SOURCES.txt' 2026-07-31T19:00:41,197 reading manifest file '/tmp/pip-modern-metadata-6co98yqk/oncoref.egg-info/SOURCES.txt' 2026-07-31T19:00:41,199 reading manifest template 'MANIFEST.in' 2026-07-31T19:00:41,215 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-07-31T19:00:41,217 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-07-31T19:00:41,218 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-07-31T19:00:41,219 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-07-31T19:00:41,220 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-07-31T19:00:41,221 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-07-31T19:00:41,222 adding license file 'LICENSE' 2026-07-31T19:00:41,229 writing manifest file '/tmp/pip-modern-metadata-6co98yqk/oncoref.egg-info/SOURCES.txt' 2026-07-31T19:00:41,231 creating '/tmp/pip-modern-metadata-6co98yqk/oncoref-1.8.164.dist-info' 2026-07-31T19:00:41,361 Preparing metadata (pyproject.toml): finished with status 'done' 2026-07-31T19:00:41,367 Source in /tmp/pip-wheel-lv6gmqso/oncoref_842976fb25df477ebe7687c155fc613b has version 1.8.164, which satisfies requirement oncoref==1.8.164 from https://files.pythonhosted.org/packages/6a/ad/3a399e6a73eb114de42686813c45c4b7b2adf00829167dccc55b8227fcb6/oncoref-1.8.164.tar.gz 2026-07-31T19:00:41,368 Removed oncoref==1.8.164 from https://files.pythonhosted.org/packages/6a/ad/3a399e6a73eb114de42686813c45c4b7b2adf00829167dccc55b8227fcb6/oncoref-1.8.164.tar.gz from build tracker '/tmp/pip-build-tracker-7yixrxe3' 2026-07-31T19:00:41,374 Created temporary directory: /tmp/pip-unpack-3t1x53oo 2026-07-31T19:00:41,375 Building wheels for collected packages: oncoref 2026-07-31T19:00:41,380 Created temporary directory: /tmp/pip-wheel-qas_4e_3 2026-07-31T19:00:41,381 Destination directory: /tmp/pip-wheel-qas_4e_3 2026-07-31T19:00:41,383 Building wheel for oncoref (pyproject.toml): started 2026-07-31T19:00:41,385 Running command Building wheel for oncoref (pyproject.toml) 2026-07-31T19:00:42,012 running bdist_wheel 2026-07-31T19:00:42,030 running build 2026-07-31T19:00:42,030 running build_py 2026-07-31T19:00:42,038 creating build/lib/oncoref 2026-07-31T19:00:42,041 copying oncoref/version.py -> build/lib/oncoref 2026-07-31T19:00:42,043 copying oncoref/data_manifest.py -> build/lib/oncoref 2026-07-31T19:00:42,046 copying oncoref/coverage.py -> build/lib/oncoref 2026-07-31T19:00:42,049 copying oncoref/cta.py -> build/lib/oncoref 2026-07-31T19:00:42,052 copying oncoref/incidence.py -> build/lib/oncoref 2026-07-31T19:00:42,055 copying oncoref/fusions.py -> build/lib/oncoref 2026-07-31T19:00:42,058 copying oncoref/expression_source_adapters.py -> build/lib/oncoref 2026-07-31T19:00:42,061 copying oncoref/peptides.py -> build/lib/oncoref 2026-07-31T19:00:42,063 copying oncoref/ici.py -> build/lib/oncoref 2026-07-31T19:00:42,066 copying oncoref/antigen_coverage.py -> build/lib/oncoref 2026-07-31T19:00:42,069 copying oncoref/ici_response.py -> build/lib/oncoref 2026-07-31T19:00:42,071 copying oncoref/normalization.py -> build/lib/oncoref 2026-07-31T19:00:42,074 copying oncoref/cancer_ontology.py -> build/lib/oncoref 2026-07-31T19:00:42,077 copying oncoref/genome.py -> build/lib/oncoref 2026-07-31T19:00:42,080 copying oncoref/cancer_types.py -> build/lib/oncoref 2026-07-31T19:00:42,084 copying oncoref/_reference_sources.py -> build/lib/oncoref 2026-07-31T19:00:42,085 copying oncoref/plots.py -> build/lib/oncoref 2026-07-31T19:00:42,088 copying oncoref/data_bundle.py -> build/lib/oncoref 2026-07-31T19:00:42,091 copying oncoref/cta_peptides.py -> build/lib/oncoref 2026-07-31T19:00:42,093 copying oncoref/source_matrices.py -> build/lib/oncoref 2026-07-31T19:00:42,096 copying oncoref/cancer_genes.py -> build/lib/oncoref 2026-07-31T19:00:42,098 copying oncoref/representative_partitions.py -> build/lib/oncoref 2026-07-31T19:00:42,101 copying oncoref/expression_builders.py -> build/lib/oncoref 2026-07-31T19:00:42,107 copying oncoref/hpa.py -> build/lib/oncoref 2026-07-31T19:00:42,109 copying oncoref/gene_ids.py -> build/lib/oncoref 2026-07-31T19:00:42,112 copying oncoref/reference_data.py -> build/lib/oncoref 2026-07-31T19:00:42,114 copying oncoref/expression.py -> build/lib/oncoref 2026-07-31T19:00:42,120 copying oncoref/tmb.py -> build/lib/oncoref 2026-07-31T19:00:42,123 copying oncoref/expression_engine.py -> build/lib/oncoref 2026-07-31T19:00:42,125 copying oncoref/cta_coverage.py -> build/lib/oncoref 2026-07-31T19:00:42,127 copying oncoref/cta_curation_plots.py -> build/lib/oncoref 2026-07-31T19:00:42,130 copying oncoref/cta_tissues.py -> build/lib/oncoref 2026-07-31T19:00:42,132 copying oncoref/__init__.py -> build/lib/oncoref 2026-07-31T19:00:42,135 copying oncoref/catalog.py -> build/lib/oncoref 2026-07-31T19:00:42,137 copying oncoref/cta_regen.py -> build/lib/oncoref 2026-07-31T19:00:42,140 copying oncoref/gene_families.py -> build/lib/oncoref 2026-07-31T19:00:42,142 copying oncoref/apd1.py -> build/lib/oncoref 2026-07-31T19:00:42,145 copying oncoref/cli.py -> build/lib/oncoref 2026-07-31T19:00:42,147 copying oncoref/expression_registry.py -> build/lib/oncoref 2026-07-31T19:00:42,150 copying oncoref/proteoforms.py -> build/lib/oncoref 2026-07-31T19:00:42,152 copying oncoref/samples.py -> build/lib/oncoref 2026-07-31T19:00:42,154 copying oncoref/gene_qc.py -> build/lib/oncoref 2026-07-31T19:00:42,157 copying oncoref/cohorts.py -> build/lib/oncoref 2026-07-31T19:00:42,158 copying oncoref/response_signatures.py -> build/lib/oncoref 2026-07-31T19:00:42,160 copying oncoref/load_dataset.py -> build/lib/oncoref 2026-07-31T19:00:42,176 creating build/lib/oncoref/data 2026-07-31T19:00:42,177 copying oncoref/data/clean-tpm-censored-genes.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,182 copying oncoref/data/cancer-cohort-aggregates.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,185 copying oncoref/data/cta-ihc-unreliable.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,188 copying oncoref/data/proteoform-groups.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,191 copying oncoref/data/mitochondrial-genes.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,193 copying oncoref/data/cancer-frameshift-burden.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,195 copying oncoref/data/cancer-expression-source-candidates.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,199 copying oncoref/data/cta-clinical-targets.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,201 copying oncoref/data/cancer-incidence-mortality.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,204 copying oncoref/data/numt-pseudogenes.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,206 copying oncoref/data/ensembl-id-aliases.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,217 copying oncoref/data/rare-cancer-fusion-rules.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,220 copying oncoref/data/cta-specificity-audit.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,222 copying oncoref/data/ribosomal-protein-genes.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,224 copying oncoref/data/cancer-subtype-groupings.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,226 copying oncoref/data/degenerate-subtype-pairs.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,228 copying oncoref/data/cancer-apd1-response.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,231 copying oncoref/data/cancer-type-registry.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,235 copying oncoref/data/cancer-lineage-groups.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,237 copying oncoref/data/expression-artifact-gene-universe-deltas.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,247 copying oncoref/data/cancer-normal-tissue-map.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,250 copying oncoref/data/nuclear-retained-lncrnas.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,252 copying oncoref/data/cancer-mismatch-repair-statuses.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,254 copying oncoref/data/representative-source-adjudications.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,256 copying oncoref/data/cta-candidate-references.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,259 copying oncoref/data/disease-state-rules.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,261 copying oncoref/data/cancer-reference-expression-availability.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,266 copying oncoref/data/cancer-response-signatures.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,268 copying oncoref/data/gse294016-sample-diagnoses.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,271 copying oncoref/data/clean-tpm-biological-housekeeping-genes.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,273 copying oncoref/data/ribosomal-protein-pseudogenes.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,276 copying oncoref/data/cancer-ici-source-locator-audit.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,282 copying oncoref/data/tissue-burden-map.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,284 copying oncoref/data/cancer-fusion-citation-audit.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,287 copying oncoref/data/cancer-key-gene-citation-audit.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,293 copying oncoref/data/fusion-surrogate-expression.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,295 copying oncoref/data/cancer-type-genes.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,298 copying oncoref/data/cancer-testis-antigens.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,303 copying oncoref/data/source-matrices.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,306 copying oncoref/data/small-noncoding-rnas.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,312 copying oncoref/data/cdna-identical-gene-groups.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,315 copying oncoref/data/fusion-expression-effects.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,317 copying oncoref/data/cancer-who-soft-tissue-bone-audit.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,320 copying oncoref/data/cancer-code-burden-map.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,322 copying oncoref/data/cancer-lineage-group-overrides.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,324 copying oncoref/data/cancer-viral-antigens.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,326 copying oncoref/data/cancer-ici-response.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,329 copying oncoref/data/rrna-and-pseudogenes.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,332 copying oncoref/data/cancer-driver-genes.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,335 copying oncoref/data/hemoglobin-genes.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,338 copying oncoref/data/proteoform-groups-genome.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,340 copying oncoref/data/housekeeping-genes.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,343 copying oncoref/data/cancer-ici-response-estimates.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,353 copying oncoref/data/cancer-driver-variants.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,356 copying oncoref/data/family-burden-map.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,358 copying oncoref/data/cancer-tmb.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,361 copying oncoref/data/censored-gene-reference-tpm.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,364 copying oncoref/data/cancer-key-genes.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,369 copying oncoref/data/histone-genes.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,372 copying oncoref/data/extra-tx-mappings.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,374 copying oncoref/data/proteoform-collapse-overrides.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,377 copying oncoref/data/cohort-registry.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,379 copying oncoref/data/cancer-fusions.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,382 copying oncoref/data/narrative-gene-sets.csv -> build/lib/oncoref/data 2026-07-31T19:00:42,385 copying oncoref/data/cancer-reference-expression-samples.csv.gz -> build/lib/oncoref/data 2026-07-31T19:00:42,391 copying oncoref/data/ncbi-entrez-gene-mappings.csv.gz -> build/lib/oncoref/data 2026-07-31T19:00:42,414 copying oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/lib/oncoref/data 2026-07-31T19:00:42,423 copying oncoref/data/canonical-gene-space.csv.gz -> build/lib/oncoref/data 2026-07-31T19:00:42,433 copying oncoref/data/expression_sources.yaml -> build/lib/oncoref/data 2026-07-31T19:00:42,448 installing to build/bdist.linux-armv7l/wheel 2026-07-31T19:00:42,449 running install 2026-07-31T19:00:42,471 running install_lib 2026-07-31T19:00:42,476 creating build/bdist.linux-armv7l/wheel 2026-07-31T19:00:42,479 creating build/bdist.linux-armv7l/wheel/oncoref 2026-07-31T19:00:42,480 copying build/lib/oncoref/version.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,482 copying build/lib/oncoref/data_manifest.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,484 copying build/lib/oncoref/coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,487 copying build/lib/oncoref/cta.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,490 copying build/lib/oncoref/incidence.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,492 copying build/lib/oncoref/fusions.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,494 copying build/lib/oncoref/expression_source_adapters.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,497 copying build/lib/oncoref/peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,500 copying build/lib/oncoref/ici.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,502 copying build/lib/oncoref/antigen_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,504 copying build/lib/oncoref/ici_response.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,506 copying build/lib/oncoref/normalization.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,509 copying build/lib/oncoref/cancer_ontology.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,511 copying build/lib/oncoref/genome.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,514 copying build/lib/oncoref/cancer_types.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,518 copying build/lib/oncoref/_reference_sources.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,520 copying build/lib/oncoref/plots.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,523 copying build/lib/oncoref/data_bundle.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,526 copying build/lib/oncoref/cta_peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,528 copying build/lib/oncoref/source_matrices.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,531 copying build/lib/oncoref/cancer_genes.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,533 copying build/lib/oncoref/representative_partitions.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,535 copying build/lib/oncoref/expression_builders.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,541 copying build/lib/oncoref/hpa.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,543 copying build/lib/oncoref/gene_ids.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,546 copying build/lib/oncoref/reference_data.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,548 copying build/lib/oncoref/expression.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,554 copying build/lib/oncoref/tmb.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,557 creating build/bdist.linux-armv7l/wheel/oncoref/data 2026-07-31T19:00:42,558 copying build/lib/oncoref/data/clean-tpm-censored-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,563 copying build/lib/oncoref/data/cancer-cohort-aggregates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,565 copying build/lib/oncoref/data/cta-ihc-unreliable.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,567 copying build/lib/oncoref/data/cancer-reference-expression-samples.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,575 copying build/lib/oncoref/data/proteoform-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,577 copying build/lib/oncoref/data/mitochondrial-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,578 copying build/lib/oncoref/data/cancer-frameshift-burden.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,580 copying build/lib/oncoref/data/cancer-expression-source-candidates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,583 copying build/lib/oncoref/data/cta-clinical-targets.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,585 copying build/lib/oncoref/data/cancer-incidence-mortality.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,587 copying build/lib/oncoref/data/numt-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,589 copying build/lib/oncoref/data/ensembl-id-aliases.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,599 copying build/lib/oncoref/data/rare-cancer-fusion-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,601 copying build/lib/oncoref/data/cta-specificity-audit.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,603 copying build/lib/oncoref/data/ribosomal-protein-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,605 copying build/lib/oncoref/data/cancer-subtype-groupings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,607 copying build/lib/oncoref/data/degenerate-subtype-pairs.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,609 copying build/lib/oncoref/data/cancer-apd1-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,611 copying build/lib/oncoref/data/expression_sources.yaml -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,615 copying build/lib/oncoref/data/cancer-type-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,619 copying build/lib/oncoref/data/cancer-lineage-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,621 copying build/lib/oncoref/data/expression-artifact-gene-universe-deltas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,628 copying build/lib/oncoref/data/ncbi-entrez-gene-mappings.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,644 copying build/lib/oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,654 copying build/lib/oncoref/data/cancer-normal-tissue-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,656 copying build/lib/oncoref/data/nuclear-retained-lncrnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,658 copying build/lib/oncoref/data/cancer-mismatch-repair-statuses.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,660 copying build/lib/oncoref/data/representative-source-adjudications.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,662 copying build/lib/oncoref/data/cta-candidate-references.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,664 copying build/lib/oncoref/data/disease-state-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,666 copying build/lib/oncoref/data/cancer-reference-expression-availability.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,669 copying build/lib/oncoref/data/cancer-response-signatures.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,671 copying build/lib/oncoref/data/gse294016-sample-diagnoses.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,673 copying build/lib/oncoref/data/clean-tpm-biological-housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,675 copying build/lib/oncoref/data/ribosomal-protein-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,678 copying build/lib/oncoref/data/cancer-ici-source-locator-audit.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,682 copying build/lib/oncoref/data/tissue-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,684 copying build/lib/oncoref/data/cancer-fusion-citation-audit.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,686 copying build/lib/oncoref/data/cancer-key-gene-citation-audit.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,690 copying build/lib/oncoref/data/fusion-surrogate-expression.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,693 copying build/lib/oncoref/data/cancer-type-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,695 copying build/lib/oncoref/data/cancer-testis-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,699 copying build/lib/oncoref/data/source-matrices.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,701 copying build/lib/oncoref/data/small-noncoding-rnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,705 copying build/lib/oncoref/data/cdna-identical-gene-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,708 copying build/lib/oncoref/data/fusion-expression-effects.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,710 copying build/lib/oncoref/data/cancer-who-soft-tissue-bone-audit.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,712 copying build/lib/oncoref/data/cancer-code-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,714 copying build/lib/oncoref/data/cancer-lineage-group-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,716 copying build/lib/oncoref/data/cancer-viral-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,718 copying build/lib/oncoref/data/cancer-ici-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,720 copying build/lib/oncoref/data/rrna-and-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,722 copying build/lib/oncoref/data/cancer-driver-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,725 copying build/lib/oncoref/data/canonical-gene-space.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,735 copying build/lib/oncoref/data/hemoglobin-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,737 copying build/lib/oncoref/data/proteoform-groups-genome.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,740 copying build/lib/oncoref/data/housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,742 copying build/lib/oncoref/data/cancer-ici-response-estimates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,755 copying build/lib/oncoref/data/cancer-driver-variants.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,758 copying build/lib/oncoref/data/family-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,760 copying build/lib/oncoref/data/cancer-tmb.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,763 copying build/lib/oncoref/data/censored-gene-reference-tpm.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,767 copying build/lib/oncoref/data/cancer-key-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,774 copying build/lib/oncoref/data/histone-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,776 copying build/lib/oncoref/data/extra-tx-mappings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,779 copying build/lib/oncoref/data/proteoform-collapse-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,781 copying build/lib/oncoref/data/cohort-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,783 copying build/lib/oncoref/data/cancer-fusions.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,787 copying build/lib/oncoref/data/narrative-gene-sets.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-07-31T19:00:42,789 copying build/lib/oncoref/expression_engine.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,792 copying build/lib/oncoref/cta_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,794 copying build/lib/oncoref/cta_curation_plots.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,796 copying build/lib/oncoref/cta_tissues.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,798 copying build/lib/oncoref/__init__.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,801 copying build/lib/oncoref/catalog.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,804 copying build/lib/oncoref/cta_regen.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,807 copying build/lib/oncoref/gene_families.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,810 copying build/lib/oncoref/apd1.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,812 copying build/lib/oncoref/cli.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,815 copying build/lib/oncoref/expression_registry.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,817 copying build/lib/oncoref/proteoforms.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,820 copying build/lib/oncoref/samples.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,821 copying build/lib/oncoref/gene_qc.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,824 copying build/lib/oncoref/cohorts.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,826 copying build/lib/oncoref/response_signatures.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,828 copying build/lib/oncoref/load_dataset.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-07-31T19:00:42,830 running install_egg_info 2026-07-31T19:00:42,839 running egg_info 2026-07-31T19:00:42,845 writing oncoref.egg-info/PKG-INFO 2026-07-31T19:00:42,850 writing dependency_links to oncoref.egg-info/dependency_links.txt 2026-07-31T19:00:42,851 writing entry points to oncoref.egg-info/entry_points.txt 2026-07-31T19:00:42,854 writing requirements to oncoref.egg-info/requires.txt 2026-07-31T19:00:42,855 writing top-level names to oncoref.egg-info/top_level.txt 2026-07-31T19:00:42,876 reading manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-31T19:00:42,889 reading manifest template 'MANIFEST.in' 2026-07-31T19:00:42,902 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-07-31T19:00:42,903 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-07-31T19:00:42,904 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-07-31T19:00:42,906 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-07-31T19:00:42,907 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-07-31T19:00:42,908 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-07-31T19:00:42,909 adding license file 'LICENSE' 2026-07-31T19:00:42,920 writing manifest file 'oncoref.egg-info/SOURCES.txt' 2026-07-31T19:00:42,922 Copying oncoref.egg-info to build/bdist.linux-armv7l/wheel/./oncoref-1.8.164-py3.11.egg-info 2026-07-31T19:00:42,934 running install_scripts 2026-07-31T19:00:42,945 creating build/bdist.linux-armv7l/wheel/oncoref-1.8.164.dist-info/WHEEL 2026-07-31T19:00:42,948 creating '/tmp/pip-wheel-qas_4e_3/.tmp-4q6ye9nm/oncoref-1.8.164-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-07-31T19:00:42,952 adding 'oncoref/__init__.py' 2026-07-31T19:00:42,954 adding 'oncoref/_reference_sources.py' 2026-07-31T19:00:42,956 adding 'oncoref/antigen_coverage.py' 2026-07-31T19:00:42,958 adding 'oncoref/apd1.py' 2026-07-31T19:00:42,960 adding 'oncoref/cancer_genes.py' 2026-07-31T19:00:42,961 adding 'oncoref/cancer_ontology.py' 2026-07-31T19:00:42,978 adding 'oncoref/cancer_types.py' 2026-07-31T19:00:42,982 adding 'oncoref/catalog.py' 2026-07-31T19:00:42,986 adding 'oncoref/cli.py' 2026-07-31T19:00:42,988 adding 'oncoref/cohorts.py' 2026-07-31T19:00:42,993 adding 'oncoref/coverage.py' 2026-07-31T19:00:42,998 adding 'oncoref/cta.py' 2026-07-31T19:00:43,000 adding 'oncoref/cta_coverage.py' 2026-07-31T19:00:43,003 adding 'oncoref/cta_curation_plots.py' 2026-07-31T19:00:43,005 adding 'oncoref/cta_peptides.py' 2026-07-31T19:00:43,009 adding 'oncoref/cta_regen.py' 2026-07-31T19:00:43,011 adding 'oncoref/cta_tissues.py' 2026-07-31T19:00:43,017 adding 'oncoref/data_bundle.py' 2026-07-31T19:00:43,020 adding 'oncoref/data_manifest.py' 2026-07-31T19:00:43,061 adding 'oncoref/expression.py' 2026-07-31T19:00:43,088 adding 'oncoref/expression_builders.py' 2026-07-31T19:00:43,092 adding 'oncoref/expression_engine.py' 2026-07-31T19:00:43,094 adding 'oncoref/expression_registry.py' 2026-07-31T19:00:43,100 adding 'oncoref/expression_source_adapters.py' 2026-07-31T19:00:43,102 adding 'oncoref/fusions.py' 2026-07-31T19:00:43,105 adding 'oncoref/gene_families.py' 2026-07-31T19:00:43,107 adding 'oncoref/gene_ids.py' 2026-07-31T19:00:43,109 adding 'oncoref/gene_qc.py' 2026-07-31T19:00:43,111 adding 'oncoref/genome.py' 2026-07-31T19:00:43,113 adding 'oncoref/hpa.py' 2026-07-31T19:00:43,118 adding 'oncoref/ici.py' 2026-07-31T19:00:43,119 adding 'oncoref/ici_response.py' 2026-07-31T19:00:43,121 adding 'oncoref/incidence.py' 2026-07-31T19:00:43,123 adding 'oncoref/load_dataset.py' 2026-07-31T19:00:43,128 adding 'oncoref/normalization.py' 2026-07-31T19:00:43,130 adding 'oncoref/peptides.py' 2026-07-31T19:00:43,137 adding 'oncoref/plots.py' 2026-07-31T19:00:43,140 adding 'oncoref/proteoforms.py' 2026-07-31T19:00:43,142 adding 'oncoref/reference_data.py' 2026-07-31T19:00:43,144 adding 'oncoref/representative_partitions.py' 2026-07-31T19:00:43,145 adding 'oncoref/response_signatures.py' 2026-07-31T19:00:43,147 adding 'oncoref/samples.py' 2026-07-31T19:00:43,149 adding 'oncoref/source_matrices.py' 2026-07-31T19:00:43,151 adding 'oncoref/tmb.py' 2026-07-31T19:00:43,153 adding 'oncoref/version.py' 2026-07-31T19:00:43,157 adding 'oncoref/data/cancer-apd1-response.csv' 2026-07-31T19:00:43,158 adding 'oncoref/data/cancer-code-burden-map.csv' 2026-07-31T19:00:43,160 adding 'oncoref/data/cancer-cohort-aggregates.csv' 2026-07-31T19:00:43,165 adding 'oncoref/data/cancer-driver-genes.csv' 2026-07-31T19:00:43,167 adding 'oncoref/data/cancer-driver-variants.csv' 2026-07-31T19:00:43,170 adding 'oncoref/data/cancer-expression-source-candidates.csv' 2026-07-31T19:00:43,172 adding 'oncoref/data/cancer-frameshift-burden.csv' 2026-07-31T19:00:43,175 adding 'oncoref/data/cancer-fusion-citation-audit.csv' 2026-07-31T19:00:43,178 adding 'oncoref/data/cancer-fusions.csv' 2026-07-31T19:00:43,203 adding 'oncoref/data/cancer-ici-response-estimates.csv' 2026-07-31T19:00:43,208 adding 'oncoref/data/cancer-ici-response.csv' 2026-07-31T19:00:43,215 adding 'oncoref/data/cancer-ici-source-locator-audit.csv' 2026-07-31T19:00:43,218 adding 'oncoref/data/cancer-incidence-mortality.csv' 2026-07-31T19:00:43,233 adding 'oncoref/data/cancer-key-gene-citation-audit.csv' 2026-07-31T19:00:43,247 adding 'oncoref/data/cancer-key-genes.csv' 2026-07-31T19:00:43,249 adding 'oncoref/data/cancer-lineage-group-overrides.csv' 2026-07-31T19:00:43,251 adding 'oncoref/data/cancer-lineage-groups.csv' 2026-07-31T19:00:43,252 adding 'oncoref/data/cancer-mismatch-repair-statuses.csv' 2026-07-31T19:00:43,253 adding 'oncoref/data/cancer-normal-tissue-map.csv' 2026-07-31T19:00:43,260 adding 'oncoref/data/cancer-reference-expression-availability.csv' 2026-07-31T19:00:43,289 adding 'oncoref/data/cancer-reference-expression-samples.csv.gz' 2026-07-31T19:00:43,292 adding 'oncoref/data/cancer-response-signatures.csv' 2026-07-31T19:00:43,294 adding 'oncoref/data/cancer-subtype-groupings.csv' 2026-07-31T19:00:43,305 adding 'oncoref/data/cancer-testis-antigens.csv' 2026-07-31T19:00:43,308 adding 'oncoref/data/cancer-tmb.csv' 2026-07-31T19:00:43,311 adding 'oncoref/data/cancer-type-genes.csv' 2026-07-31T19:00:43,316 adding 'oncoref/data/cancer-type-registry.csv' 2026-07-31T19:00:43,318 adding 'oncoref/data/cancer-viral-antigens.csv' 2026-07-31T19:00:43,320 adding 'oncoref/data/cancer-who-soft-tissue-bone-audit.csv' 2026-07-31T19:00:43,372 adding 'oncoref/data/canonical-gene-space.csv.gz' 2026-07-31T19:00:43,377 adding 'oncoref/data/cdna-identical-gene-groups.csv' 2026-07-31T19:00:43,381 adding 'oncoref/data/censored-gene-reference-tpm.csv' 2026-07-31T19:00:43,383 adding 'oncoref/data/clean-tpm-biological-housekeeping-genes.csv' 2026-07-31T19:00:43,393 adding 'oncoref/data/clean-tpm-censored-genes.csv' 2026-07-31T19:00:43,396 adding 'oncoref/data/cohort-registry.csv' 2026-07-31T19:00:43,397 adding 'oncoref/data/cta-candidate-references.csv' 2026-07-31T19:00:43,399 adding 'oncoref/data/cta-clinical-targets.csv' 2026-07-31T19:00:43,400 adding 'oncoref/data/cta-ihc-unreliable.csv' 2026-07-31T19:00:43,401 adding 'oncoref/data/cta-specificity-audit.csv' 2026-07-31T19:00:43,403 adding 'oncoref/data/degenerate-subtype-pairs.csv' 2026-07-31T19:00:43,404 adding 'oncoref/data/disease-state-rules.csv' 2026-07-31T19:00:43,431 adding 'oncoref/data/ensembl-id-aliases.csv' 2026-07-31T19:00:43,445 adding 'oncoref/data/expression-artifact-gene-universe-deltas.csv' 2026-07-31T19:00:43,454 adding 'oncoref/data/expression_sources.yaml' 2026-07-31T19:00:43,456 adding 'oncoref/data/extra-tx-mappings.csv' 2026-07-31T19:00:43,457 adding 'oncoref/data/family-burden-map.csv' 2026-07-31T19:00:43,459 adding 'oncoref/data/fusion-expression-effects.csv' 2026-07-31T19:00:43,460 adding 'oncoref/data/fusion-surrogate-expression.csv' 2026-07-31T19:00:43,462 adding 'oncoref/data/gse294016-sample-diagnoses.csv' 2026-07-31T19:00:43,463 adding 'oncoref/data/hemoglobin-genes.csv' 2026-07-31T19:00:43,465 adding 'oncoref/data/histone-genes.csv' 2026-07-31T19:00:43,466 adding 'oncoref/data/housekeeping-genes.csv' 2026-07-31T19:00:43,468 adding 'oncoref/data/mitochondrial-genes.csv' 2026-07-31T19:00:43,469 adding 'oncoref/data/narrative-gene-sets.csv' 2026-07-31T19:00:43,570 adding 'oncoref/data/ncbi-entrez-gene-mappings.csv.gz' 2026-07-31T19:00:43,616 adding 'oncoref/data/ncbi-symbol-synonyms.csv.gz' 2026-07-31T19:00:43,620 adding 'oncoref/data/nuclear-retained-lncrnas.csv' 2026-07-31T19:00:43,622 adding 'oncoref/data/numt-pseudogenes.csv' 2026-07-31T19:00:43,623 adding 'oncoref/data/proteoform-collapse-overrides.csv' 2026-07-31T19:00:43,626 adding 'oncoref/data/proteoform-groups-genome.csv' 2026-07-31T19:00:43,627 adding 'oncoref/data/proteoform-groups.csv' 2026-07-31T19:00:43,629 adding 'oncoref/data/rare-cancer-fusion-rules.csv' 2026-07-31T19:00:43,630 adding 'oncoref/data/representative-source-adjudications.csv' 2026-07-31T19:00:43,632 adding 'oncoref/data/ribosomal-protein-genes.csv' 2026-07-31T19:00:43,638 adding 'oncoref/data/ribosomal-protein-pseudogenes.csv' 2026-07-31T19:00:43,640 adding 'oncoref/data/rrna-and-pseudogenes.csv' 2026-07-31T19:00:43,659 adding 'oncoref/data/small-noncoding-rnas.csv' 2026-07-31T19:00:43,661 adding 'oncoref/data/source-matrices.csv' 2026-07-31T19:00:43,662 adding 'oncoref/data/tissue-burden-map.csv' 2026-07-31T19:00:43,666 adding 'oncoref-1.8.164.dist-info/licenses/LICENSE' 2026-07-31T19:00:43,667 adding 'oncoref-1.8.164.dist-info/METADATA' 2026-07-31T19:00:43,669 adding 'oncoref-1.8.164.dist-info/WHEEL' 2026-07-31T19:00:43,669 adding 'oncoref-1.8.164.dist-info/entry_points.txt' 2026-07-31T19:00:43,670 adding 'oncoref-1.8.164.dist-info/top_level.txt' 2026-07-31T19:00:43,672 adding 'oncoref-1.8.164.dist-info/RECORD' 2026-07-31T19:00:43,709 removing build/bdist.linux-armv7l/wheel 2026-07-31T19:00:43,830 Building wheel for oncoref (pyproject.toml): finished with status 'done' 2026-07-31T19:00:43,895 Created wheel for oncoref: filename=oncoref-1.8.164-py3-none-any.whl size=2849032 sha256=444d383ef8c52b25d050517ccc2d0af529e655d47e5d8f8f9593a26e58d53c16 2026-07-31T19:00:43,896 Stored in directory: /tmp/pip-ephem-wheel-cache-jx7sbvom/wheels/82/ee/82/5153f93e6c631eecc693430a3a69f9cb0c801314f3e631deb2 2026-07-31T19:00:43,912 Successfully built oncoref 2026-07-31T19:00:43,983 Removed build tracker: '/tmp/pip-build-tracker-7yixrxe3'