2026-06-21T16:26:19,924 Created temporary directory: /tmp/pip-ephem-wheel-cache-i1fadbi0
2026-06-21T16:26:19,926 Created temporary directory: /tmp/pip-build-tracker-puatlm3g
2026-06-21T16:26:19,927 Initialized build tracking at /tmp/pip-build-tracker-puatlm3g
2026-06-21T16:26:19,927 Created build tracker: /tmp/pip-build-tracker-puatlm3g
2026-06-21T16:26:19,928 Entered build tracker: /tmp/pip-build-tracker-puatlm3g
2026-06-21T16:26:19,928 Created temporary directory: /tmp/pip-wheel-kxwllzdg
2026-06-21T16:26:19,932 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
2026-06-21T16:26:19,934 Created temporary directory: /tmp/pip-ephem-wheel-cache-d59ngf27
2026-06-21T16:26:19,956 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-06-21T16:26:19,959 2 location(s) to search for versions of oncoref:
2026-06-21T16:26:19,959 * https://pypi.org/simple/oncoref/
2026-06-21T16:26:19,959 * https://www.piwheels.org/simple/oncoref/
2026-06-21T16:26:19,960 Fetching project page and analyzing links: https://pypi.org/simple/oncoref/
2026-06-21T16:26:19,961 Getting page https://pypi.org/simple/oncoref/
2026-06-21T16:26:19,962 Found index url https://pypi.org/simple
2026-06-21T16:26:20,291 Fetched page https://pypi.org/simple/oncoref/ as application/vnd.pypi.simple.v1+json
2026-06-21T16:26:20,294   Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/28/98/3c08853ca8c6e4f7ea1625192d883f4890b4482814b60c92972610af6a91/oncoref-1.6.0-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-21T16:26:20,295   Found link https://files.pythonhosted.org/packages/d3/fa/b1f2479c8c9b44597623ab898f37be9f1c317250cac13115edb09adf0bd0/oncoref-1.6.0.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.6.0
2026-06-21T16:26:20,295   Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/00/bc/d076f0b5f3ab5d26840cd8eee073af59210bb90aba8a7826d64980c08e70/oncoref-1.7.0-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-21T16:26:20,296   Found link https://files.pythonhosted.org/packages/6b/4f/2b9be7b2858be7ca1c850ea67261cfe41c9595b7d57ed818b20af88c815c/oncoref-1.7.0.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.7.0
2026-06-21T16:26:20,297   Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/3d/cf/214dbe1e3f3ca56d6354d7f2f87283085238025685b7287be5a3020db87c/oncoref-1.8.0-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-21T16:26:20,298   Found link https://files.pythonhosted.org/packages/10/a1/9b3e573b2e9ce5903eef398c68d06cd3d1425a88c87c3f5d8dbe79cbfb3c/oncoref-1.8.0.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.8.0
2026-06-21T16:26:20,299   Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/56/b4/103c9511736de31d6182b47aaf4f03da47c52933be96ea7a060ad7478ae3/oncoref-1.8.1-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-21T16:26:20,300   Found link https://files.pythonhosted.org/packages/21/3e/8080dbac7eaa58029775dd4937cb7dc70d1e65b52e358ccb75b5dd8ed63e/oncoref-1.8.1.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.8.1
2026-06-21T16:26:20,301   Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/02/4f/03495de60734a5fb8a50476fd036af4b0262949e609827f759349cc1ff6b/oncoref-1.8.2-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-21T16:26:20,302   Found link https://files.pythonhosted.org/packages/e6/18/5ee9311af10f46d71490d6563884c80cb170f106e31164d3a2cf7e47d1e8/oncoref-1.8.2.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.8.2
2026-06-21T16:26:20,303 Fetching project page and analyzing links: https://www.piwheels.org/simple/oncoref/
2026-06-21T16:26:20,304 Getting page https://www.piwheels.org/simple/oncoref/
2026-06-21T16:26:20,305 Found index url https://www.piwheels.org/simple
2026-06-21T16:26:20,592 Fetched page https://www.piwheels.org/simple/oncoref/ as text/html
2026-06-21T16:26:20,595   Skipping link: No binaries permitted for oncoref: https://www.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)
2026-06-21T16:26:20,595   Skipping link: No binaries permitted for oncoref: https://www.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)
2026-06-21T16:26:20,596   Skipping link: No binaries permitted for oncoref: https://www.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)
2026-06-21T16:26:20,596   Skipping link: No binaries permitted for oncoref: https://www.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)
2026-06-21T16:26:20,596 Skipping link: not a file: https://www.piwheels.org/simple/oncoref/
2026-06-21T16:26:20,597 Skipping link: not a file: https://pypi.org/simple/oncoref/
2026-06-21T16:26:20,617 Given no hashes to check 1 links for project 'oncoref': discarding no candidates
2026-06-21T16:26:20,636 Collecting oncoref==1.8.2
2026-06-21T16:26:20,638   Created temporary directory: /tmp/pip-unpack-wzptcl2r
2026-06-21T16:26:20,887   Downloading oncoref-1.8.2.tar.gz (1.7 MB)
2026-06-21T16:26:21,560   Added oncoref==1.8.2 from https://files.pythonhosted.org/packages/e6/18/5ee9311af10f46d71490d6563884c80cb170f106e31164d3a2cf7e47d1e8/oncoref-1.8.2.tar.gz to build tracker '/tmp/pip-build-tracker-puatlm3g'
2026-06-21T16:26:21,567   Created temporary directory: /tmp/pip-build-env-49_c_wva
2026-06-21T16:26:21,572   Installing build dependencies: started
2026-06-21T16:26:21,573   Running command pip subprocess to install build dependencies
2026-06-21T16:26:22,759   Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11)
2026-06-21T16:26:23,229   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
2026-06-21T16:26:23,252   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-06-21T16:26:25,219   Collecting setuptools>=61.0
2026-06-21T16:26:25,220     Obtaining dependency information for setuptools>=61.0 from https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl.metadata
2026-06-21T16:26:25,237     Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl.metadata (6.5 kB)
2026-06-21T16:26:25,468   Collecting wheel
2026-06-21T16:26:25,469     Obtaining dependency information for wheel from https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata
2026-06-21T16:26:25,490     Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB)
2026-06-21T16:26:25,675   Collecting packaging>=24.0
2026-06-21T16:26:25,676     Obtaining dependency information for packaging>=24.0 from https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata
2026-06-21T16:26:25,693     Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata (3.5 kB)
2026-06-21T16:26:25,883   Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB)
2026-06-21T16:26:25,902   Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB)
2026-06-21T16:26:25,985   Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB)
2026-06-21T16:26:26,029   Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB)
2026-06-21T16:26:26,056   Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB)
2026-06-21T16:26:26,158   Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB)
2026-06-21T16:26:28,910   Installing collected packages: setuptools, packaging, wheel
2026-06-21T16:26:32,331     Creating /tmp/pip-build-env-49_c_wva/overlay/local/bin
2026-06-21T16:26:32,334     changing mode of /tmp/pip-build-env-49_c_wva/overlay/local/bin/wheel to 755
2026-06-21T16:26:32,354   Successfully installed packaging-26.2 setuptools-82.0.1 wheel-0.47.0
2026-06-21T16:26:32,641   Installing build dependencies: finished with status 'done'
2026-06-21T16:26:32,648   Getting requirements to build wheel: started
2026-06-21T16:26:32,649   Running command Getting requirements to build wheel
2026-06-21T16:26:33,334   running egg_info
2026-06-21T16:26:33,340   writing oncoref.egg-info/PKG-INFO
2026-06-21T16:26:33,345   writing dependency_links to oncoref.egg-info/dependency_links.txt
2026-06-21T16:26:33,347   writing entry points to oncoref.egg-info/entry_points.txt
2026-06-21T16:26:33,350   writing requirements to oncoref.egg-info/requires.txt
2026-06-21T16:26:33,351   writing top-level names to oncoref.egg-info/top_level.txt
2026-06-21T16:26:33,385   reading manifest file 'oncoref.egg-info/SOURCES.txt'
2026-06-21T16:26:33,393   reading manifest template 'MANIFEST.in'
2026-06-21T16:26:33,395   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression'
2026-06-21T16:26:33,396   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles'
2026-06-21T16:26:33,397   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives'
2026-06-21T16:26:33,398   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5'
2026-06-21T16:26:33,399   warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv'
2026-06-21T16:26:33,400   warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv'
2026-06-21T16:26:33,401   adding license file 'LICENSE'
2026-06-21T16:26:33,408   writing manifest file 'oncoref.egg-info/SOURCES.txt'
2026-06-21T16:26:33,506   Getting requirements to build wheel: finished with status 'done'
2026-06-21T16:26:33,509   Created temporary directory: /tmp/pip-modern-metadata-mzh27wkp
2026-06-21T16:26:33,512   Preparing metadata (pyproject.toml): started
2026-06-21T16:26:33,513   Running command Preparing metadata (pyproject.toml)
2026-06-21T16:26:34,150   running dist_info
2026-06-21T16:26:34,160   creating /tmp/pip-modern-metadata-mzh27wkp/oncoref.egg-info
2026-06-21T16:26:34,161   writing /tmp/pip-modern-metadata-mzh27wkp/oncoref.egg-info/PKG-INFO
2026-06-21T16:26:34,167   writing dependency_links to /tmp/pip-modern-metadata-mzh27wkp/oncoref.egg-info/dependency_links.txt
2026-06-21T16:26:34,168   writing entry points to /tmp/pip-modern-metadata-mzh27wkp/oncoref.egg-info/entry_points.txt
2026-06-21T16:26:34,171   writing requirements to /tmp/pip-modern-metadata-mzh27wkp/oncoref.egg-info/requires.txt
2026-06-21T16:26:34,172   writing top-level names to /tmp/pip-modern-metadata-mzh27wkp/oncoref.egg-info/top_level.txt
2026-06-21T16:26:34,174   writing manifest file '/tmp/pip-modern-metadata-mzh27wkp/oncoref.egg-info/SOURCES.txt'
2026-06-21T16:26:34,205   reading manifest file '/tmp/pip-modern-metadata-mzh27wkp/oncoref.egg-info/SOURCES.txt'
2026-06-21T16:26:34,207   reading manifest template 'MANIFEST.in'
2026-06-21T16:26:34,208   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression'
2026-06-21T16:26:34,209   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles'
2026-06-21T16:26:34,210   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives'
2026-06-21T16:26:34,211   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5'
2026-06-21T16:26:34,212   warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv'
2026-06-21T16:26:34,213   warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv'
2026-06-21T16:26:34,213   adding license file 'LICENSE'
2026-06-21T16:26:34,219   writing manifest file '/tmp/pip-modern-metadata-mzh27wkp/oncoref.egg-info/SOURCES.txt'
2026-06-21T16:26:34,220   creating '/tmp/pip-modern-metadata-mzh27wkp/oncoref-1.8.2.dist-info'
2026-06-21T16:26:34,346   Preparing metadata (pyproject.toml): finished with status 'done'
2026-06-21T16:26:34,351   Source in /tmp/pip-wheel-kxwllzdg/oncoref_7028ef824a0f48a4897688db02cf81b9 has version 1.8.2, which satisfies requirement oncoref==1.8.2 from https://files.pythonhosted.org/packages/e6/18/5ee9311af10f46d71490d6563884c80cb170f106e31164d3a2cf7e47d1e8/oncoref-1.8.2.tar.gz
2026-06-21T16:26:34,352   Removed oncoref==1.8.2 from https://files.pythonhosted.org/packages/e6/18/5ee9311af10f46d71490d6563884c80cb170f106e31164d3a2cf7e47d1e8/oncoref-1.8.2.tar.gz from build tracker '/tmp/pip-build-tracker-puatlm3g'
2026-06-21T16:26:34,358 Created temporary directory: /tmp/pip-unpack-xw_vv4a1
2026-06-21T16:26:34,359 Building wheels for collected packages: oncoref
2026-06-21T16:26:34,364   Created temporary directory: /tmp/pip-wheel-c7zdp_cl
2026-06-21T16:26:34,364   Destination directory: /tmp/pip-wheel-c7zdp_cl
2026-06-21T16:26:34,366   Building wheel for oncoref (pyproject.toml): started
2026-06-21T16:26:34,368   Running command Building wheel for oncoref (pyproject.toml)
2026-06-21T16:26:34,985   running bdist_wheel
2026-06-21T16:26:35,002   running build
2026-06-21T16:26:35,003   running build_py
2026-06-21T16:26:35,009   creating build/lib/oncoref
2026-06-21T16:26:35,012   copying oncoref/expression.py -> build/lib/oncoref
2026-06-21T16:26:35,015   copying oncoref/cli.py -> build/lib/oncoref
2026-06-21T16:26:35,018   copying oncoref/catalog.py -> build/lib/oncoref
2026-06-21T16:26:35,020   copying oncoref/cta_curation_plots.py -> build/lib/oncoref
2026-06-21T16:26:35,022   copying oncoref/response_signatures.py -> build/lib/oncoref
2026-06-21T16:26:35,024   copying oncoref/gene_qc.py -> build/lib/oncoref
2026-06-21T16:26:35,027   copying oncoref/coverage.py -> build/lib/oncoref
2026-06-21T16:26:35,029   copying oncoref/samples.py -> build/lib/oncoref
2026-06-21T16:26:35,031   copying oncoref/expression_engine.py -> build/lib/oncoref
2026-06-21T16:26:35,033   copying oncoref/tmb.py -> build/lib/oncoref
2026-06-21T16:26:35,036   copying oncoref/plots.py -> build/lib/oncoref
2026-06-21T16:26:35,039   copying oncoref/genome.py -> build/lib/oncoref
2026-06-21T16:26:35,041   copying oncoref/expression_builders.py -> build/lib/oncoref
2026-06-21T16:26:35,044   copying oncoref/gene_families.py -> build/lib/oncoref
2026-06-21T16:26:35,046   copying oncoref/proteoforms.py -> build/lib/oncoref
2026-06-21T16:26:35,049   copying oncoref/cta_tissues.py -> build/lib/oncoref
2026-06-21T16:26:35,051   copying oncoref/load_dataset.py -> build/lib/oncoref
2026-06-21T16:26:35,053   copying oncoref/incidence.py -> build/lib/oncoref
2026-06-21T16:26:35,055   copying oncoref/fusions.py -> build/lib/oncoref
2026-06-21T16:26:35,057   copying oncoref/cancer_genes.py -> build/lib/oncoref
2026-06-21T16:26:35,059   copying oncoref/data_bundle.py -> build/lib/oncoref
2026-06-21T16:26:35,062   copying oncoref/apd1.py -> build/lib/oncoref
2026-06-21T16:26:35,064   copying oncoref/cancer_types.py -> build/lib/oncoref
2026-06-21T16:26:35,066   copying oncoref/cta_regen.py -> build/lib/oncoref
2026-06-21T16:26:35,069   copying oncoref/data_manifest.py -> build/lib/oncoref
2026-06-21T16:26:35,071   copying oncoref/peptides.py -> build/lib/oncoref
2026-06-21T16:26:35,073   copying oncoref/__init__.py -> build/lib/oncoref
2026-06-21T16:26:35,075   copying oncoref/gene_ids.py -> build/lib/oncoref
2026-06-21T16:26:35,077   copying oncoref/hpa.py -> build/lib/oncoref
2026-06-21T16:26:35,079   copying oncoref/expression_registry.py -> build/lib/oncoref
2026-06-21T16:26:35,081   copying oncoref/cta.py -> build/lib/oncoref
2026-06-21T16:26:35,084   copying oncoref/reference_data.py -> build/lib/oncoref
2026-06-21T16:26:35,086   copying oncoref/source_matrices.py -> build/lib/oncoref
2026-06-21T16:26:35,088   copying oncoref/version.py -> build/lib/oncoref
2026-06-21T16:26:35,089   copying oncoref/ici.py -> build/lib/oncoref
2026-06-21T16:26:35,092   copying oncoref/normalization.py -> build/lib/oncoref
2026-06-21T16:26:35,106   creating build/lib/oncoref/data
2026-06-21T16:26:35,107   copying oncoref/data/cancer-ici-response.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,110   copying oncoref/data/cancer-ici-response-estimates.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,116   copying oncoref/data/cancer-driver-genes.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,119   copying oncoref/data/histone-genes.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,122   copying oncoref/data/disease-state-rules.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,124   copying oncoref/data/proteoform-collapse-overrides.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,126   copying oncoref/data/censored-gene-reference-tpm.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,129   copying oncoref/data/fusion-surrogate-expression.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,131   copying oncoref/data/nuclear-retained-lncrnas.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,133   copying oncoref/data/cancer-testis-antigens.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,138   copying oncoref/data/rrna-and-pseudogenes.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,141   copying oncoref/data/housekeeping-genes.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,143   copying oncoref/data/mitochondrial-genes.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,145   copying oncoref/data/cancer-subtype-groupings.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,147   copying oncoref/data/cancer-cohort-aggregates.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,149   copying oncoref/data/cancer-viral-antigens.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,151   copying oncoref/data/cancer-lineage-groups.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,153   copying oncoref/data/ensembl-id-aliases.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,161   copying oncoref/data/cancer-code-burden-map.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,163   copying oncoref/data/cancer-type-registry.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,166   copying oncoref/data/cancer-fusions.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,168   copying oncoref/data/cancer-incidence-mortality.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,171   copying oncoref/data/cancer-driver-variants.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,173   copying oncoref/data/proteoform-groups-genome.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,176   copying oncoref/data/cancer-lineage-group-overrides.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,178   copying oncoref/data/cohort-registry.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,181   copying oncoref/data/narrative-gene-sets.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,183   copying oncoref/data/cta-ihc-unreliable.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,185   copying oncoref/data/cdna-identical-gene-groups.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,188   copying oncoref/data/small-noncoding-rnas.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,192   copying oncoref/data/extra-tx-mappings.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,195   copying oncoref/data/source-matrices.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,197   copying oncoref/data/proteoform-groups.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,199   copying oncoref/data/cancer-expression-source-candidates.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,202   copying oncoref/data/hemoglobin-genes.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,203   copying oncoref/data/cancer-key-genes.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,208   copying oncoref/data/family-burden-map.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,210   copying oncoref/data/rare-cancer-fusion-rules.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,212   copying oncoref/data/cancer-response-signatures.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,214   copying oncoref/data/cancer-apd1-response.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,217   copying oncoref/data/degenerate-subtype-pairs.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,219   copying oncoref/data/ribosomal-protein-genes.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,221   copying oncoref/data/cancer-frameshift-burden.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,223   copying oncoref/data/cancer-type-genes.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,226   copying oncoref/data/numt-pseudogenes.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,229   copying oncoref/data/tissue-burden-map.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,231   copying oncoref/data/clean-tpm-censored-genes.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,236   copying oncoref/data/cta-candidate-references.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,238   copying oncoref/data/fusion-expression-effects.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,241   copying oncoref/data/ribosomal-protein-pseudogenes.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,244   copying oncoref/data/cancer-tmb.csv -> build/lib/oncoref/data
2026-06-21T16:26:35,247   copying oncoref/data/canonical-gene-space.csv.gz -> build/lib/oncoref/data
2026-06-21T16:26:35,256   copying oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/lib/oncoref/data
2026-06-21T16:26:35,264   copying oncoref/data/cancer-reference-expression-samples.csv.gz -> build/lib/oncoref/data
2026-06-21T16:26:35,271   copying oncoref/data/expression_sources.yaml -> build/lib/oncoref/data
2026-06-21T16:26:35,285   installing to build/bdist.linux-armv7l/wheel
2026-06-21T16:26:35,286   running install
2026-06-21T16:26:35,308   running install_lib
2026-06-21T16:26:35,314   creating build/bdist.linux-armv7l/wheel
2026-06-21T16:26:35,317   creating build/bdist.linux-armv7l/wheel/oncoref
2026-06-21T16:26:35,318   copying build/lib/oncoref/expression.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,321   copying build/lib/oncoref/cli.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,324   copying build/lib/oncoref/catalog.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,326   copying build/lib/oncoref/cta_curation_plots.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,328   copying build/lib/oncoref/response_signatures.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,330   copying build/lib/oncoref/gene_qc.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,332   copying build/lib/oncoref/coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,335   copying build/lib/oncoref/samples.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,337   copying build/lib/oncoref/expression_engine.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,339   copying build/lib/oncoref/tmb.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,341   copying build/lib/oncoref/plots.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,346   copying build/lib/oncoref/genome.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,348   copying build/lib/oncoref/expression_builders.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,350   copying build/lib/oncoref/gene_families.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,352   copying build/lib/oncoref/proteoforms.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,355   copying build/lib/oncoref/cta_tissues.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,357   copying build/lib/oncoref/load_dataset.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,359   copying build/lib/oncoref/incidence.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,362   copying build/lib/oncoref/fusions.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,364   copying build/lib/oncoref/cancer_genes.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,366   copying build/lib/oncoref/data_bundle.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,368   copying build/lib/oncoref/apd1.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,370   copying build/lib/oncoref/cancer_types.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,373   copying build/lib/oncoref/cta_regen.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,377   creating build/bdist.linux-armv7l/wheel/oncoref/data
2026-06-21T16:26:35,378   copying build/lib/oncoref/data/cancer-ici-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,380   copying build/lib/oncoref/data/cancer-ici-response-estimates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,386   copying build/lib/oncoref/data/cancer-driver-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,389   copying build/lib/oncoref/data/histone-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,391   copying build/lib/oncoref/data/disease-state-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,393   copying build/lib/oncoref/data/proteoform-collapse-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,395   copying build/lib/oncoref/data/censored-gene-reference-tpm.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,397   copying build/lib/oncoref/data/fusion-surrogate-expression.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,400   copying build/lib/oncoref/data/nuclear-retained-lncrnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,401   copying build/lib/oncoref/data/cancer-testis-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,406   copying build/lib/oncoref/data/rrna-and-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,408   copying build/lib/oncoref/data/housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,410   copying build/lib/oncoref/data/mitochondrial-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,412   copying build/lib/oncoref/data/cancer-subtype-groupings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,414   copying build/lib/oncoref/data/cancer-cohort-aggregates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,416   copying build/lib/oncoref/data/cancer-viral-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,417   copying build/lib/oncoref/data/cancer-lineage-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,419   copying build/lib/oncoref/data/ensembl-id-aliases.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,427   copying build/lib/oncoref/data/cancer-code-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,429   copying build/lib/oncoref/data/cancer-type-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,432   copying build/lib/oncoref/data/expression_sources.yaml -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,435   copying build/lib/oncoref/data/cancer-fusions.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,438   copying build/lib/oncoref/data/cancer-incidence-mortality.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,439   copying build/lib/oncoref/data/cancer-driver-variants.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,442   copying build/lib/oncoref/data/proteoform-groups-genome.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,445   copying build/lib/oncoref/data/cancer-lineage-group-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,447   copying build/lib/oncoref/data/canonical-gene-space.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,456   copying build/lib/oncoref/data/cohort-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,459   copying build/lib/oncoref/data/narrative-gene-sets.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,460   copying build/lib/oncoref/data/cta-ihc-unreliable.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,462   copying build/lib/oncoref/data/cdna-identical-gene-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,465   copying build/lib/oncoref/data/small-noncoding-rnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,469   copying build/lib/oncoref/data/extra-tx-mappings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,472   copying build/lib/oncoref/data/source-matrices.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,474   copying build/lib/oncoref/data/proteoform-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,476   copying build/lib/oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,483   copying build/lib/oncoref/data/cancer-expression-source-candidates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,486   copying build/lib/oncoref/data/hemoglobin-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,487   copying build/lib/oncoref/data/cancer-key-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,492   copying build/lib/oncoref/data/family-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,494   copying build/lib/oncoref/data/rare-cancer-fusion-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,496   copying build/lib/oncoref/data/cancer-response-signatures.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,497   copying build/lib/oncoref/data/cancer-apd1-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,500   copying build/lib/oncoref/data/degenerate-subtype-pairs.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,502   copying build/lib/oncoref/data/ribosomal-protein-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,504   copying build/lib/oncoref/data/cancer-frameshift-burden.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,506   copying build/lib/oncoref/data/cancer-type-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,508   copying build/lib/oncoref/data/numt-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,510   copying build/lib/oncoref/data/tissue-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,512   copying build/lib/oncoref/data/clean-tpm-censored-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,516   copying build/lib/oncoref/data/cta-candidate-references.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,518   copying build/lib/oncoref/data/fusion-expression-effects.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,520   copying build/lib/oncoref/data/ribosomal-protein-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,522   copying build/lib/oncoref/data/cancer-reference-expression-samples.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,529   copying build/lib/oncoref/data/cancer-tmb.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-21T16:26:35,531   copying build/lib/oncoref/data_manifest.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,533   copying build/lib/oncoref/peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,536   copying build/lib/oncoref/__init__.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,538   copying build/lib/oncoref/gene_ids.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,540   copying build/lib/oncoref/hpa.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,542   copying build/lib/oncoref/expression_registry.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,544   copying build/lib/oncoref/cta.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,546   copying build/lib/oncoref/reference_data.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,549   copying build/lib/oncoref/source_matrices.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,551   copying build/lib/oncoref/version.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,553   copying build/lib/oncoref/ici.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,555   copying build/lib/oncoref/normalization.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-21T16:26:35,558   running install_egg_info
2026-06-21T16:26:35,567   running egg_info
2026-06-21T16:26:35,572   writing oncoref.egg-info/PKG-INFO
2026-06-21T16:26:35,577   writing dependency_links to oncoref.egg-info/dependency_links.txt
2026-06-21T16:26:35,579   writing entry points to oncoref.egg-info/entry_points.txt
2026-06-21T16:26:35,581   writing requirements to oncoref.egg-info/requires.txt
2026-06-21T16:26:35,582   writing top-level names to oncoref.egg-info/top_level.txt
2026-06-21T16:26:35,600   reading manifest file 'oncoref.egg-info/SOURCES.txt'
2026-06-21T16:26:35,609   reading manifest template 'MANIFEST.in'
2026-06-21T16:26:35,611   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression'
2026-06-21T16:26:35,612   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles'
2026-06-21T16:26:35,613   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives'
2026-06-21T16:26:35,614   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5'
2026-06-21T16:26:35,615   warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv'
2026-06-21T16:26:35,616   warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv'
2026-06-21T16:26:35,617   adding license file 'LICENSE'
2026-06-21T16:26:35,625   writing manifest file 'oncoref.egg-info/SOURCES.txt'
2026-06-21T16:26:35,627   Copying oncoref.egg-info to build/bdist.linux-armv7l/wheel/./oncoref-1.8.2-py3.11.egg-info
2026-06-21T16:26:35,639   running install_scripts
2026-06-21T16:26:35,651   creating build/bdist.linux-armv7l/wheel/oncoref-1.8.2.dist-info/WHEEL
2026-06-21T16:26:35,654   creating '/tmp/pip-wheel-c7zdp_cl/.tmp-_4_a13ga/oncoref-1.8.2-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2026-06-21T16:26:35,658   adding 'oncoref/__init__.py'
2026-06-21T16:26:35,659   adding 'oncoref/apd1.py'
2026-06-21T16:26:35,661   adding 'oncoref/cancer_genes.py'
2026-06-21T16:26:35,665   adding 'oncoref/cancer_types.py'
2026-06-21T16:26:35,668   adding 'oncoref/catalog.py'
2026-06-21T16:26:35,671   adding 'oncoref/cli.py'
2026-06-21T16:26:35,675   adding 'oncoref/coverage.py'
2026-06-21T16:26:35,677   adding 'oncoref/cta.py'
2026-06-21T16:26:35,679   adding 'oncoref/cta_curation_plots.py'
2026-06-21T16:26:35,682   adding 'oncoref/cta_regen.py'
2026-06-21T16:26:35,684   adding 'oncoref/cta_tissues.py'
2026-06-21T16:26:35,686   adding 'oncoref/data_bundle.py'
2026-06-21T16:26:35,688   adding 'oncoref/data_manifest.py'
2026-06-21T16:26:35,696   adding 'oncoref/expression.py'
2026-06-21T16:26:35,699   adding 'oncoref/expression_builders.py'
2026-06-21T16:26:35,701   adding 'oncoref/expression_engine.py'
2026-06-21T16:26:35,702   adding 'oncoref/expression_registry.py'
2026-06-21T16:26:35,704   adding 'oncoref/fusions.py'
2026-06-21T16:26:35,706   adding 'oncoref/gene_families.py'
2026-06-21T16:26:35,707   adding 'oncoref/gene_ids.py'
2026-06-21T16:26:35,709   adding 'oncoref/gene_qc.py'
2026-06-21T16:26:35,711   adding 'oncoref/genome.py'
2026-06-21T16:26:35,713   adding 'oncoref/hpa.py'
2026-06-21T16:26:35,716   adding 'oncoref/ici.py'
2026-06-21T16:26:35,717   adding 'oncoref/incidence.py'
2026-06-21T16:26:35,719   adding 'oncoref/load_dataset.py'
2026-06-21T16:26:35,723   adding 'oncoref/normalization.py'
2026-06-21T16:26:35,725   adding 'oncoref/peptides.py'
2026-06-21T16:26:35,732   adding 'oncoref/plots.py'
2026-06-21T16:26:35,735   adding 'oncoref/proteoforms.py'
2026-06-21T16:26:35,737   adding 'oncoref/reference_data.py'
2026-06-21T16:26:35,738   adding 'oncoref/response_signatures.py'
2026-06-21T16:26:35,740   adding 'oncoref/samples.py'
2026-06-21T16:26:35,741   adding 'oncoref/source_matrices.py'
2026-06-21T16:26:35,743   adding 'oncoref/tmb.py'
2026-06-21T16:26:35,744   adding 'oncoref/version.py'
2026-06-21T16:26:35,748   adding 'oncoref/data/cancer-apd1-response.csv'
2026-06-21T16:26:35,749   adding 'oncoref/data/cancer-code-burden-map.csv'
2026-06-21T16:26:35,750   adding 'oncoref/data/cancer-cohort-aggregates.csv'
2026-06-21T16:26:35,755   adding 'oncoref/data/cancer-driver-genes.csv'
2026-06-21T16:26:35,758   adding 'oncoref/data/cancer-driver-variants.csv'
2026-06-21T16:26:35,760   adding 'oncoref/data/cancer-expression-source-candidates.csv'
2026-06-21T16:26:35,762   adding 'oncoref/data/cancer-frameshift-burden.csv'
2026-06-21T16:26:35,765   adding 'oncoref/data/cancer-fusions.csv'
2026-06-21T16:26:35,782   adding 'oncoref/data/cancer-ici-response-estimates.csv'
2026-06-21T16:26:35,786   adding 'oncoref/data/cancer-ici-response.csv'
2026-06-21T16:26:35,788   adding 'oncoref/data/cancer-incidence-mortality.csv'
2026-06-21T16:26:35,802   adding 'oncoref/data/cancer-key-genes.csv'
2026-06-21T16:26:35,805   adding 'oncoref/data/cancer-lineage-group-overrides.csv'
2026-06-21T16:26:35,806   adding 'oncoref/data/cancer-lineage-groups.csv'
2026-06-21T16:26:35,835   adding 'oncoref/data/cancer-reference-expression-samples.csv.gz'
2026-06-21T16:26:35,838   adding 'oncoref/data/cancer-response-signatures.csv'
2026-06-21T16:26:35,839   adding 'oncoref/data/cancer-subtype-groupings.csv'
2026-06-21T16:26:35,851   adding 'oncoref/data/cancer-testis-antigens.csv'
2026-06-21T16:26:35,854   adding 'oncoref/data/cancer-tmb.csv'
2026-06-21T16:26:35,856   adding 'oncoref/data/cancer-type-genes.csv'
2026-06-21T16:26:35,860   adding 'oncoref/data/cancer-type-registry.csv'
2026-06-21T16:26:35,862   adding 'oncoref/data/cancer-viral-antigens.csv'
2026-06-21T16:26:35,914   adding 'oncoref/data/canonical-gene-space.csv.gz'
2026-06-21T16:26:35,920   adding 'oncoref/data/cdna-identical-gene-groups.csv'
2026-06-21T16:26:35,924   adding 'oncoref/data/censored-gene-reference-tpm.csv'
2026-06-21T16:26:35,935   adding 'oncoref/data/clean-tpm-censored-genes.csv'
2026-06-21T16:26:35,938   adding 'oncoref/data/cohort-registry.csv'
2026-06-21T16:26:35,939   adding 'oncoref/data/cta-candidate-references.csv'
2026-06-21T16:26:35,941   adding 'oncoref/data/cta-ihc-unreliable.csv'
2026-06-21T16:26:35,942   adding 'oncoref/data/degenerate-subtype-pairs.csv'
2026-06-21T16:26:35,943   adding 'oncoref/data/disease-state-rules.csv'
2026-06-21T16:26:35,970   adding 'oncoref/data/ensembl-id-aliases.csv'
2026-06-21T16:26:35,977   adding 'oncoref/data/expression_sources.yaml'
2026-06-21T16:26:35,979   adding 'oncoref/data/extra-tx-mappings.csv'
2026-06-21T16:26:35,980   adding 'oncoref/data/family-burden-map.csv'
2026-06-21T16:26:35,981   adding 'oncoref/data/fusion-expression-effects.csv'
2026-06-21T16:26:35,983   adding 'oncoref/data/fusion-surrogate-expression.csv'
2026-06-21T16:26:35,984   adding 'oncoref/data/hemoglobin-genes.csv'
2026-06-21T16:26:35,985   adding 'oncoref/data/histone-genes.csv'
2026-06-21T16:26:35,987   adding 'oncoref/data/housekeeping-genes.csv'
2026-06-21T16:26:35,988   adding 'oncoref/data/mitochondrial-genes.csv'
2026-06-21T16:26:35,989   adding 'oncoref/data/narrative-gene-sets.csv'
2026-06-21T16:26:36,030   adding 'oncoref/data/ncbi-symbol-synonyms.csv.gz'
2026-06-21T16:26:36,034   adding 'oncoref/data/nuclear-retained-lncrnas.csv'
2026-06-21T16:26:36,036   adding 'oncoref/data/numt-pseudogenes.csv'
2026-06-21T16:26:36,037   adding 'oncoref/data/proteoform-collapse-overrides.csv'
2026-06-21T16:26:36,040   adding 'oncoref/data/proteoform-groups-genome.csv'
2026-06-21T16:26:36,041   adding 'oncoref/data/proteoform-groups.csv'
2026-06-21T16:26:36,043   adding 'oncoref/data/rare-cancer-fusion-rules.csv'
2026-06-21T16:26:36,045   adding 'oncoref/data/ribosomal-protein-genes.csv'
2026-06-21T16:26:36,051   adding 'oncoref/data/ribosomal-protein-pseudogenes.csv'
2026-06-21T16:26:36,054   adding 'oncoref/data/rrna-and-pseudogenes.csv'
2026-06-21T16:26:36,072   adding 'oncoref/data/small-noncoding-rnas.csv'
2026-06-21T16:26:36,075   adding 'oncoref/data/source-matrices.csv'
2026-06-21T16:26:36,076   adding 'oncoref/data/tissue-burden-map.csv'
2026-06-21T16:26:36,080   adding 'oncoref-1.8.2.dist-info/licenses/LICENSE'
2026-06-21T16:26:36,082   adding 'oncoref-1.8.2.dist-info/METADATA'
2026-06-21T16:26:36,083   adding 'oncoref-1.8.2.dist-info/WHEEL'
2026-06-21T16:26:36,084   adding 'oncoref-1.8.2.dist-info/entry_points.txt'
2026-06-21T16:26:36,084   adding 'oncoref-1.8.2.dist-info/top_level.txt'
2026-06-21T16:26:36,086   adding 'oncoref-1.8.2.dist-info/RECORD'
2026-06-21T16:26:36,114   removing build/bdist.linux-armv7l/wheel
2026-06-21T16:26:36,235   Building wheel for oncoref (pyproject.toml): finished with status 'done'
2026-06-21T16:26:36,279   Created wheel for oncoref: filename=oncoref-1.8.2-py3-none-any.whl size=1636183 sha256=9f47ca1a637e6255fbf29fd252834c85e5d19238a980add71843cd860b39777e
2026-06-21T16:26:36,280   Stored in directory: /tmp/pip-ephem-wheel-cache-d59ngf27/wheels/9b/3b/92/cc991b831d31e5e01d52de5cfc650e1b3af89128849e442e67
2026-06-21T16:26:36,295 Successfully built oncoref
2026-06-21T16:26:36,341 Removed build tracker: '/tmp/pip-build-tracker-puatlm3g'