2026-06-23T17:19:28,063 Created temporary directory: /tmp/pip-ephem-wheel-cache-kfcv55_1
2026-06-23T17:19:28,065 Created temporary directory: /tmp/pip-build-tracker-u66j_sdd
2026-06-23T17:19:28,066 Initialized build tracking at /tmp/pip-build-tracker-u66j_sdd
2026-06-23T17:19:28,066 Created build tracker: /tmp/pip-build-tracker-u66j_sdd
2026-06-23T17:19:28,066 Entered build tracker: /tmp/pip-build-tracker-u66j_sdd
2026-06-23T17:19:28,067 Created temporary directory: /tmp/pip-wheel-59wu3_lb
2026-06-23T17:19:28,070 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
2026-06-23T17:19:28,072 Created temporary directory: /tmp/pip-ephem-wheel-cache-w4_zcqn1
2026-06-23T17:19:28,094 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-06-23T17:19:28,097 2 location(s) to search for versions of oncoref:
2026-06-23T17:19:28,097 * https://pypi.org/simple/oncoref/
2026-06-23T17:19:28,097 * https://www.piwheels.org/simple/oncoref/
2026-06-23T17:19:28,098 Fetching project page and analyzing links: https://pypi.org/simple/oncoref/
2026-06-23T17:19:28,099 Getting page https://pypi.org/simple/oncoref/
2026-06-23T17:19:28,100 Found index url https://pypi.org/simple
2026-06-23T17:19:28,350 Fetched page https://pypi.org/simple/oncoref/ as application/vnd.pypi.simple.v1+json
2026-06-23T17:19:28,354   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)
2026-06-23T17:19:28,355   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
2026-06-23T17:19:28,355   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)
2026-06-23T17:19:28,356   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
2026-06-23T17:19:28,357   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)
2026-06-23T17:19:28,358   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
2026-06-23T17:19:28,359   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)
2026-06-23T17:19:28,360   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
2026-06-23T17:19:28,360   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)
2026-06-23T17:19:28,362   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
2026-06-23T17:19:28,362   Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/9b/4f/60a3e4e56d57a916f462597f08c5c4915e19cb97fc1cd0b85c110e41659e/oncoref-1.8.3-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-23T17:19:28,363   Found link https://files.pythonhosted.org/packages/e7/7d/22a2797b33413bfe0f46708f396b9b1f9ad9dbc253d94fcbeb6ccf9ad5ff/oncoref-1.8.3.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.8.3
2026-06-23T17:19:28,364   Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/ca/bb/0981e424fd20641c70c1607dc7e707ff53036f90e7482b18ef4f2b100bba/oncoref-1.8.4-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-23T17:19:28,365   Found link https://files.pythonhosted.org/packages/da/8f/e45e879798fcad2b21996a64d69c0034e947ca8c07b2668b484580bcccd2/oncoref-1.8.4.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.8.4
2026-06-23T17:19:28,366 Fetching project page and analyzing links: https://www.piwheels.org/simple/oncoref/
2026-06-23T17:19:28,366 Getting page https://www.piwheels.org/simple/oncoref/
2026-06-23T17:19:28,367 Found index url https://www.piwheels.org/simple
2026-06-23T17:19:28,668 Fetched page https://www.piwheels.org/simple/oncoref/ as text/html
2026-06-23T17:19:28,671   Skipping link: No binaries permitted for oncoref: https://www.piwheels.org/simple/oncoref/oncoref-1.8.3-py3-none-any.whl#sha256=bf75676ac99a0d1c144249b8cf320ac292b65716c9ffdc50ad27b55db1153821 (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-23T17:19:28,671   Skipping link: No binaries permitted for oncoref: https://archive1.piwheels.org/simple/oncoref/oncoref-1.8.2-py3-none-any.whl#sha256=9f47ca1a637e6255fbf29fd252834c85e5d19238a980add71843cd860b39777e (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-23T17:19:28,672   Skipping link: No binaries permitted for oncoref: https://archive1.piwheels.org/simple/oncoref/oncoref-1.8.1-py3-none-any.whl#sha256=12f0eb28c115080796010095a4032b844d9ea4383bc0ea2e2b75a3e5f21c9392 (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-23T17:19:28,673   Skipping link: No binaries permitted for oncoref: https://archive1.piwheels.org/simple/oncoref/oncoref-1.8.0-py3-none-any.whl#sha256=6f9be6d1511d7e84166b02f2cd219b977025db68916073cb4bd1ebdfc8919914 (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-23T17:19:28,673   Skipping link: No binaries permitted for oncoref: https://archive1.piwheels.org/simple/oncoref/oncoref-1.7.0-py3-none-any.whl#sha256=249750fecb30a99d715c221ca1ca76a4ff790891f0051782cd528395d14db6ed (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-23T17:19:28,674   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)
2026-06-23T17:19:28,675 Skipping link: not a file: https://www.piwheels.org/simple/oncoref/
2026-06-23T17:19:28,675 Skipping link: not a file: https://pypi.org/simple/oncoref/
2026-06-23T17:19:28,694 Given no hashes to check 1 links for project 'oncoref': discarding no candidates
2026-06-23T17:19:28,711 Collecting oncoref==1.8.4
2026-06-23T17:19:28,714   Created temporary directory: /tmp/pip-unpack-e7nsuv48
2026-06-23T17:19:29,044   Downloading oncoref-1.8.4.tar.gz (1.7 MB)
2026-06-23T17:19:29,714   Added oncoref==1.8.4 from https://files.pythonhosted.org/packages/da/8f/e45e879798fcad2b21996a64d69c0034e947ca8c07b2668b484580bcccd2/oncoref-1.8.4.tar.gz to build tracker '/tmp/pip-build-tracker-u66j_sdd'
2026-06-23T17:19:29,721   Created temporary directory: /tmp/pip-build-env-gzqgh6by
2026-06-23T17:19:29,725   Installing build dependencies: started
2026-06-23T17:19:29,727   Running command pip subprocess to install build dependencies
2026-06-23T17:19:30,857   Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11)
2026-06-23T17:19:31,265   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
2026-06-23T17:19:31,288   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-06-23T17:19:33,291   Collecting setuptools>=61.0
2026-06-23T17:19:33,292     Obtaining dependency information for setuptools>=61.0 from https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl.metadata
2026-06-23T17:19:33,307     Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl.metadata (6.5 kB)
2026-06-23T17:19:33,542   Collecting wheel
2026-06-23T17:19:33,543     Obtaining dependency information for wheel from https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata
2026-06-23T17:19:33,559     Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB)
2026-06-23T17:19:33,742   Collecting packaging>=24.0
2026-06-23T17:19:33,743     Obtaining dependency information for packaging>=24.0 from https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata
2026-06-23T17:19:33,758     Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata (3.5 kB)
2026-06-23T17:19:33,949   Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB)
2026-06-23T17:19:33,971   Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB)
2026-06-23T17:19:34,051   Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB)
2026-06-23T17:19:34,088   Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB)
2026-06-23T17:19:34,114   Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB)
2026-06-23T17:19:34,196   Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB)
2026-06-23T17:19:36,959   Installing collected packages: setuptools, packaging, wheel
2026-06-23T17:19:40,378     Creating /tmp/pip-build-env-gzqgh6by/overlay/local/bin
2026-06-23T17:19:40,380     changing mode of /tmp/pip-build-env-gzqgh6by/overlay/local/bin/wheel to 755
2026-06-23T17:19:40,401   Successfully installed packaging-26.2 setuptools-82.0.1 wheel-0.47.0
2026-06-23T17:19:40,689   Installing build dependencies: finished with status 'done'
2026-06-23T17:19:40,696   Getting requirements to build wheel: started
2026-06-23T17:19:40,697   Running command Getting requirements to build wheel
2026-06-23T17:19:41,432   running egg_info
2026-06-23T17:19:41,438   writing oncoref.egg-info/PKG-INFO
2026-06-23T17:19:41,443   writing dependency_links to oncoref.egg-info/dependency_links.txt
2026-06-23T17:19:41,445   writing entry points to oncoref.egg-info/entry_points.txt
2026-06-23T17:19:41,449   writing requirements to oncoref.egg-info/requires.txt
2026-06-23T17:19:41,450   writing top-level names to oncoref.egg-info/top_level.txt
2026-06-23T17:19:41,484   reading manifest file 'oncoref.egg-info/SOURCES.txt'
2026-06-23T17:19:41,493   reading manifest template 'MANIFEST.in'
2026-06-23T17:19:41,495   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression'
2026-06-23T17:19:41,496   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles'
2026-06-23T17:19:41,498   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives'
2026-06-23T17:19:41,500   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5'
2026-06-23T17:19:41,501   warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv'
2026-06-23T17:19:41,502   warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv'
2026-06-23T17:19:41,503   adding license file 'LICENSE'
2026-06-23T17:19:41,511   writing manifest file 'oncoref.egg-info/SOURCES.txt'
2026-06-23T17:19:41,610   Getting requirements to build wheel: finished with status 'done'
2026-06-23T17:19:41,614   Created temporary directory: /tmp/pip-modern-metadata-vpx_u782
2026-06-23T17:19:41,617   Preparing metadata (pyproject.toml): started
2026-06-23T17:19:41,618   Running command Preparing metadata (pyproject.toml)
2026-06-23T17:19:42,276   running dist_info
2026-06-23T17:19:42,286   creating /tmp/pip-modern-metadata-vpx_u782/oncoref.egg-info
2026-06-23T17:19:42,287   writing /tmp/pip-modern-metadata-vpx_u782/oncoref.egg-info/PKG-INFO
2026-06-23T17:19:42,293   writing dependency_links to /tmp/pip-modern-metadata-vpx_u782/oncoref.egg-info/dependency_links.txt
2026-06-23T17:19:42,294   writing entry points to /tmp/pip-modern-metadata-vpx_u782/oncoref.egg-info/entry_points.txt
2026-06-23T17:19:42,297   writing requirements to /tmp/pip-modern-metadata-vpx_u782/oncoref.egg-info/requires.txt
2026-06-23T17:19:42,298   writing top-level names to /tmp/pip-modern-metadata-vpx_u782/oncoref.egg-info/top_level.txt
2026-06-23T17:19:42,299   writing manifest file '/tmp/pip-modern-metadata-vpx_u782/oncoref.egg-info/SOURCES.txt'
2026-06-23T17:19:42,331   reading manifest file '/tmp/pip-modern-metadata-vpx_u782/oncoref.egg-info/SOURCES.txt'
2026-06-23T17:19:42,332   reading manifest template 'MANIFEST.in'
2026-06-23T17:19:42,334   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression'
2026-06-23T17:19:42,335   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles'
2026-06-23T17:19:42,336   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives'
2026-06-23T17:19:42,337   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5'
2026-06-23T17:19:42,338   warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv'
2026-06-23T17:19:42,339   warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv'
2026-06-23T17:19:42,339   adding license file 'LICENSE'
2026-06-23T17:19:42,345   writing manifest file '/tmp/pip-modern-metadata-vpx_u782/oncoref.egg-info/SOURCES.txt'
2026-06-23T17:19:42,347   creating '/tmp/pip-modern-metadata-vpx_u782/oncoref-1.8.4.dist-info'
2026-06-23T17:19:42,473   Preparing metadata (pyproject.toml): finished with status 'done'
2026-06-23T17:19:42,478   Source in /tmp/pip-wheel-59wu3_lb/oncoref_6a16d80c9d6448ddaf4da0720062e18f has version 1.8.4, which satisfies requirement oncoref==1.8.4 from https://files.pythonhosted.org/packages/da/8f/e45e879798fcad2b21996a64d69c0034e947ca8c07b2668b484580bcccd2/oncoref-1.8.4.tar.gz
2026-06-23T17:19:42,479   Removed oncoref==1.8.4 from https://files.pythonhosted.org/packages/da/8f/e45e879798fcad2b21996a64d69c0034e947ca8c07b2668b484580bcccd2/oncoref-1.8.4.tar.gz from build tracker '/tmp/pip-build-tracker-u66j_sdd'
2026-06-23T17:19:42,485 Created temporary directory: /tmp/pip-unpack-sn3cl2cn
2026-06-23T17:19:42,485 Building wheels for collected packages: oncoref
2026-06-23T17:19:42,490   Created temporary directory: /tmp/pip-wheel-ozliof3o
2026-06-23T17:19:42,490   Destination directory: /tmp/pip-wheel-ozliof3o
2026-06-23T17:19:42,493   Building wheel for oncoref (pyproject.toml): started
2026-06-23T17:19:42,494   Running command Building wheel for oncoref (pyproject.toml)
2026-06-23T17:19:43,119   running bdist_wheel
2026-06-23T17:19:43,136   running build
2026-06-23T17:19:43,137   running build_py
2026-06-23T17:19:43,144   creating build/lib/oncoref
2026-06-23T17:19:43,146   copying oncoref/coverage.py -> build/lib/oncoref
2026-06-23T17:19:43,149   copying oncoref/catalog.py -> build/lib/oncoref
2026-06-23T17:19:43,152   copying oncoref/version.py -> build/lib/oncoref
2026-06-23T17:19:43,154   copying oncoref/gene_ids.py -> build/lib/oncoref
2026-06-23T17:19:43,156   copying oncoref/load_dataset.py -> build/lib/oncoref
2026-06-23T17:19:43,158   copying oncoref/expression_registry.py -> build/lib/oncoref
2026-06-23T17:19:43,160   copying oncoref/cta.py -> build/lib/oncoref
2026-06-23T17:19:43,163   copying oncoref/reference_data.py -> build/lib/oncoref
2026-06-23T17:19:43,166   copying oncoref/ici.py -> build/lib/oncoref
2026-06-23T17:19:43,168   copying oncoref/expression_builders.py -> build/lib/oncoref
2026-06-23T17:19:43,171   copying oncoref/cli.py -> build/lib/oncoref
2026-06-23T17:19:43,173   copying oncoref/hpa.py -> build/lib/oncoref
2026-06-23T17:19:43,175   copying oncoref/normalization.py -> build/lib/oncoref
2026-06-23T17:19:43,178   copying oncoref/__init__.py -> build/lib/oncoref
2026-06-23T17:19:43,181   copying oncoref/expression.py -> build/lib/oncoref
2026-06-23T17:19:43,184   copying oncoref/incidence.py -> build/lib/oncoref
2026-06-23T17:19:43,187   copying oncoref/expression_engine.py -> build/lib/oncoref
2026-06-23T17:19:43,189   copying oncoref/source_matrices.py -> build/lib/oncoref
2026-06-23T17:19:43,191   copying oncoref/cancer_types.py -> build/lib/oncoref
2026-06-23T17:19:43,194   copying oncoref/data_bundle.py -> build/lib/oncoref
2026-06-23T17:19:43,196   copying oncoref/cta_tissues.py -> build/lib/oncoref
2026-06-23T17:19:43,199   copying oncoref/cta_regen.py -> build/lib/oncoref
2026-06-23T17:19:43,201   copying oncoref/proteoforms.py -> build/lib/oncoref
2026-06-23T17:19:43,204   copying oncoref/gene_qc.py -> build/lib/oncoref
2026-06-23T17:19:43,206   copying oncoref/genome.py -> build/lib/oncoref
2026-06-23T17:19:43,209   copying oncoref/samples.py -> build/lib/oncoref
2026-06-23T17:19:43,210   copying oncoref/data_manifest.py -> build/lib/oncoref
2026-06-23T17:19:43,213   copying oncoref/response_signatures.py -> build/lib/oncoref
2026-06-23T17:19:43,215   copying oncoref/peptides.py -> build/lib/oncoref
2026-06-23T17:19:43,217   copying oncoref/apd1.py -> build/lib/oncoref
2026-06-23T17:19:43,219   copying oncoref/cancer_genes.py -> build/lib/oncoref
2026-06-23T17:19:43,221   copying oncoref/gene_families.py -> build/lib/oncoref
2026-06-23T17:19:43,224   copying oncoref/fusions.py -> build/lib/oncoref
2026-06-23T17:19:43,226   copying oncoref/plots.py -> build/lib/oncoref
2026-06-23T17:19:43,229   copying oncoref/tmb.py -> build/lib/oncoref
2026-06-23T17:19:43,231   copying oncoref/cta_curation_plots.py -> build/lib/oncoref
2026-06-23T17:19:43,245   creating build/lib/oncoref/data
2026-06-23T17:19:43,246   copying oncoref/data/cancer-type-genes.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,249   copying oncoref/data/disease-state-rules.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,252   copying oncoref/data/cancer-lineage-groups.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,254   copying oncoref/data/fusion-expression-effects.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,256   copying oncoref/data/cancer-ici-response.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,259   copying oncoref/data/cta-ihc-unreliable.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,261   copying oncoref/data/degenerate-subtype-pairs.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,264   copying oncoref/data/housekeeping-genes.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,266   copying oncoref/data/cancer-expression-source-candidates.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,269   copying oncoref/data/cancer-driver-genes.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,272   copying oncoref/data/histone-genes.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,275   copying oncoref/data/cancer-apd1-response.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,278   copying oncoref/data/numt-pseudogenes.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,280   copying oncoref/data/proteoform-groups.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,283   copying oncoref/data/rrna-and-pseudogenes.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,286   copying oncoref/data/cancer-response-signatures.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,288   copying oncoref/data/cancer-key-genes.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,293   copying oncoref/data/censored-gene-reference-tpm.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,296   copying oncoref/data/cancer-type-registry.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,299   copying oncoref/data/small-noncoding-rnas.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,304   copying oncoref/data/cohort-registry.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,306   copying oncoref/data/cancer-subtype-groupings.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,308   copying oncoref/data/cancer-driver-variants.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,311   copying oncoref/data/cancer-testis-antigens.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,316   copying oncoref/data/cancer-tmb.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,319   copying oncoref/data/cancer-cohort-aggregates.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,321   copying oncoref/data/cancer-ici-response-estimates.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,327   copying oncoref/data/nuclear-retained-lncrnas.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,329   copying oncoref/data/cancer-lineage-group-overrides.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,331   copying oncoref/data/ensembl-id-aliases.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,340   copying oncoref/data/fusion-surrogate-expression.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,342   copying oncoref/data/cta-candidate-references.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,344   copying oncoref/data/ribosomal-protein-genes.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,347   copying oncoref/data/cancer-incidence-mortality.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,349   copying oncoref/data/proteoform-groups-genome.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,352   copying oncoref/data/cancer-viral-antigens.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,354   copying oncoref/data/proteoform-collapse-overrides.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,356   copying oncoref/data/hemoglobin-genes.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,358   copying oncoref/data/narrative-gene-sets.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,360   copying oncoref/data/cancer-fusions.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,363   copying oncoref/data/cancer-code-burden-map.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,365   copying oncoref/data/extra-tx-mappings.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,367   copying oncoref/data/family-burden-map.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,369   copying oncoref/data/rare-cancer-fusion-rules.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,372   copying oncoref/data/ribosomal-protein-pseudogenes.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,375   copying oncoref/data/mitochondrial-genes.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,377   copying oncoref/data/tissue-burden-map.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,379   copying oncoref/data/cancer-frameshift-burden.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,382   copying oncoref/data/clean-tpm-censored-genes.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,387   copying oncoref/data/source-matrices.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,390   copying oncoref/data/cdna-identical-gene-groups.csv -> build/lib/oncoref/data
2026-06-23T17:19:43,392   copying oncoref/data/canonical-gene-space.csv.gz -> build/lib/oncoref/data
2026-06-23T17:19:43,405   copying oncoref/data/cancer-reference-expression-samples.csv.gz -> build/lib/oncoref/data
2026-06-23T17:19:43,413   copying oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/lib/oncoref/data
2026-06-23T17:19:43,422   copying oncoref/data/expression_sources.yaml -> build/lib/oncoref/data
2026-06-23T17:19:43,436   installing to build/bdist.linux-armv7l/wheel
2026-06-23T17:19:43,437   running install
2026-06-23T17:19:43,459   running install_lib
2026-06-23T17:19:43,465   creating build/bdist.linux-armv7l/wheel
2026-06-23T17:19:43,468   creating build/bdist.linux-armv7l/wheel/oncoref
2026-06-23T17:19:43,469   copying build/lib/oncoref/coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,472   copying build/lib/oncoref/catalog.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,474   copying build/lib/oncoref/version.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,476   copying build/lib/oncoref/gene_ids.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,478   copying build/lib/oncoref/load_dataset.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,480   copying build/lib/oncoref/expression_registry.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,482   copying build/lib/oncoref/cta.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,484   copying build/lib/oncoref/reference_data.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,487   copying build/lib/oncoref/ici.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,491   creating build/bdist.linux-armv7l/wheel/oncoref/data
2026-06-23T17:19:43,492   copying build/lib/oncoref/data/cancer-type-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,494   copying build/lib/oncoref/data/disease-state-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,496   copying build/lib/oncoref/data/cancer-lineage-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,498   copying build/lib/oncoref/data/fusion-expression-effects.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,500   copying build/lib/oncoref/data/cancer-ici-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,502   copying build/lib/oncoref/data/cta-ihc-unreliable.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,504   copying build/lib/oncoref/data/degenerate-subtype-pairs.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,506   copying build/lib/oncoref/data/housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,508   copying build/lib/oncoref/data/cancer-expression-source-candidates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,511   copying build/lib/oncoref/data/cancer-driver-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,513   copying build/lib/oncoref/data/histone-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,516   copying build/lib/oncoref/data/cancer-apd1-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,518   copying build/lib/oncoref/data/numt-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,520   copying build/lib/oncoref/data/canonical-gene-space.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,530   copying build/lib/oncoref/data/proteoform-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,532   copying build/lib/oncoref/data/rrna-and-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,534   copying build/lib/oncoref/data/cancer-response-signatures.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,536   copying build/lib/oncoref/data/cancer-key-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,540   copying build/lib/oncoref/data/censored-gene-reference-tpm.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,543   copying build/lib/oncoref/data/expression_sources.yaml -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,545   copying build/lib/oncoref/data/cancer-type-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,548   copying build/lib/oncoref/data/small-noncoding-rnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,553   copying build/lib/oncoref/data/cohort-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,555   copying build/lib/oncoref/data/cancer-subtype-groupings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,556   copying build/lib/oncoref/data/cancer-driver-variants.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,559   copying build/lib/oncoref/data/cancer-testis-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,564   copying build/lib/oncoref/data/cancer-tmb.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,566   copying build/lib/oncoref/data/cancer-cohort-aggregates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,568   copying build/lib/oncoref/data/cancer-ici-response-estimates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,573   copying build/lib/oncoref/data/nuclear-retained-lncrnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,575   copying build/lib/oncoref/data/cancer-lineage-group-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,577   copying build/lib/oncoref/data/ensembl-id-aliases.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,585   copying build/lib/oncoref/data/fusion-surrogate-expression.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,587   copying build/lib/oncoref/data/cta-candidate-references.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,589   copying build/lib/oncoref/data/ribosomal-protein-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,591   copying build/lib/oncoref/data/cancer-incidence-mortality.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,593   copying build/lib/oncoref/data/proteoform-groups-genome.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,596   copying build/lib/oncoref/data/cancer-viral-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,597   copying build/lib/oncoref/data/proteoform-collapse-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,599   copying build/lib/oncoref/data/hemoglobin-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,601   copying build/lib/oncoref/data/narrative-gene-sets.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,603   copying build/lib/oncoref/data/cancer-fusions.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,605   copying build/lib/oncoref/data/cancer-code-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,607   copying build/lib/oncoref/data/extra-tx-mappings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,609   copying build/lib/oncoref/data/family-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,611   copying build/lib/oncoref/data/rare-cancer-fusion-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,614   copying build/lib/oncoref/data/ribosomal-protein-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,617   copying build/lib/oncoref/data/mitochondrial-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,619   copying build/lib/oncoref/data/cancer-reference-expression-samples.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,625   copying build/lib/oncoref/data/tissue-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,627   copying build/lib/oncoref/data/cancer-frameshift-burden.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,629   copying build/lib/oncoref/data/clean-tpm-censored-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,633   copying build/lib/oncoref/data/source-matrices.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,635   copying build/lib/oncoref/data/cdna-identical-gene-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,637   copying build/lib/oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-23T17:19:43,646   copying build/lib/oncoref/expression_builders.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,648   copying build/lib/oncoref/cli.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,651   copying build/lib/oncoref/hpa.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,653   copying build/lib/oncoref/normalization.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,656   copying build/lib/oncoref/__init__.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,658   copying build/lib/oncoref/expression.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,661   copying build/lib/oncoref/incidence.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,663   copying build/lib/oncoref/expression_engine.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,666   copying build/lib/oncoref/source_matrices.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,668   copying build/lib/oncoref/cancer_types.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,671   copying build/lib/oncoref/data_bundle.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,673   copying build/lib/oncoref/cta_tissues.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,675   copying build/lib/oncoref/cta_regen.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,677   copying build/lib/oncoref/proteoforms.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,680   copying build/lib/oncoref/gene_qc.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,682   copying build/lib/oncoref/genome.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,684   copying build/lib/oncoref/samples.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,687   copying build/lib/oncoref/data_manifest.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,689   copying build/lib/oncoref/response_signatures.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,691   copying build/lib/oncoref/peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,693   copying build/lib/oncoref/apd1.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,695   copying build/lib/oncoref/cancer_genes.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,698   copying build/lib/oncoref/gene_families.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,700   copying build/lib/oncoref/fusions.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,702   copying build/lib/oncoref/plots.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,705   copying build/lib/oncoref/tmb.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,707   copying build/lib/oncoref/cta_curation_plots.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-23T17:19:43,710   running install_egg_info
2026-06-23T17:19:43,719   running egg_info
2026-06-23T17:19:43,724   writing oncoref.egg-info/PKG-INFO
2026-06-23T17:19:43,729   writing dependency_links to oncoref.egg-info/dependency_links.txt
2026-06-23T17:19:43,731   writing entry points to oncoref.egg-info/entry_points.txt
2026-06-23T17:19:43,733   writing requirements to oncoref.egg-info/requires.txt
2026-06-23T17:19:43,734   writing top-level names to oncoref.egg-info/top_level.txt
2026-06-23T17:19:43,752   reading manifest file 'oncoref.egg-info/SOURCES.txt'
2026-06-23T17:19:43,761   reading manifest template 'MANIFEST.in'
2026-06-23T17:19:43,762   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression'
2026-06-23T17:19:43,764   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles'
2026-06-23T17:19:43,765   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives'
2026-06-23T17:19:43,766   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5'
2026-06-23T17:19:43,767   warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv'
2026-06-23T17:19:43,768   warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv'
2026-06-23T17:19:43,769   adding license file 'LICENSE'
2026-06-23T17:19:43,777   writing manifest file 'oncoref.egg-info/SOURCES.txt'
2026-06-23T17:19:43,778   Copying oncoref.egg-info to build/bdist.linux-armv7l/wheel/./oncoref-1.8.4-py3.11.egg-info
2026-06-23T17:19:43,790   running install_scripts
2026-06-23T17:19:43,803   creating build/bdist.linux-armv7l/wheel/oncoref-1.8.4.dist-info/WHEEL
2026-06-23T17:19:43,806   creating '/tmp/pip-wheel-ozliof3o/.tmp-h6g1qy02/oncoref-1.8.4-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2026-06-23T17:19:43,810   adding 'oncoref/__init__.py'
2026-06-23T17:19:43,811   adding 'oncoref/apd1.py'
2026-06-23T17:19:43,813   adding 'oncoref/cancer_genes.py'
2026-06-23T17:19:43,817   adding 'oncoref/cancer_types.py'
2026-06-23T17:19:43,820   adding 'oncoref/catalog.py'
2026-06-23T17:19:43,823   adding 'oncoref/cli.py'
2026-06-23T17:19:43,827   adding 'oncoref/coverage.py'
2026-06-23T17:19:43,830   adding 'oncoref/cta.py'
2026-06-23T17:19:43,832   adding 'oncoref/cta_curation_plots.py'
2026-06-23T17:19:43,835   adding 'oncoref/cta_regen.py'
2026-06-23T17:19:43,837   adding 'oncoref/cta_tissues.py'
2026-06-23T17:19:43,839   adding 'oncoref/data_bundle.py'
2026-06-23T17:19:43,841   adding 'oncoref/data_manifest.py'
2026-06-23T17:19:43,850   adding 'oncoref/expression.py'
2026-06-23T17:19:43,852   adding 'oncoref/expression_builders.py'
2026-06-23T17:19:43,854   adding 'oncoref/expression_engine.py'
2026-06-23T17:19:43,856   adding 'oncoref/expression_registry.py'
2026-06-23T17:19:43,858   adding 'oncoref/fusions.py'
2026-06-23T17:19:43,859   adding 'oncoref/gene_families.py'
2026-06-23T17:19:43,861   adding 'oncoref/gene_ids.py'
2026-06-23T17:19:43,863   adding 'oncoref/gene_qc.py'
2026-06-23T17:19:43,865   adding 'oncoref/genome.py'
2026-06-23T17:19:43,867   adding 'oncoref/hpa.py'
2026-06-23T17:19:43,870   adding 'oncoref/ici.py'
2026-06-23T17:19:43,871   adding 'oncoref/incidence.py'
2026-06-23T17:19:43,873   adding 'oncoref/load_dataset.py'
2026-06-23T17:19:43,877   adding 'oncoref/normalization.py'
2026-06-23T17:19:43,879   adding 'oncoref/peptides.py'
2026-06-23T17:19:43,887   adding 'oncoref/plots.py'
2026-06-23T17:19:43,889   adding 'oncoref/proteoforms.py'
2026-06-23T17:19:43,892   adding 'oncoref/reference_data.py'
2026-06-23T17:19:43,893   adding 'oncoref/response_signatures.py'
2026-06-23T17:19:43,895   adding 'oncoref/samples.py'
2026-06-23T17:19:43,897   adding 'oncoref/source_matrices.py'
2026-06-23T17:19:43,898   adding 'oncoref/tmb.py'
2026-06-23T17:19:43,900   adding 'oncoref/version.py'
2026-06-23T17:19:43,903   adding 'oncoref/data/cancer-apd1-response.csv'
2026-06-23T17:19:43,905   adding 'oncoref/data/cancer-code-burden-map.csv'
2026-06-23T17:19:43,906   adding 'oncoref/data/cancer-cohort-aggregates.csv'
2026-06-23T17:19:43,911   adding 'oncoref/data/cancer-driver-genes.csv'
2026-06-23T17:19:43,914   adding 'oncoref/data/cancer-driver-variants.csv'
2026-06-23T17:19:43,916   adding 'oncoref/data/cancer-expression-source-candidates.csv'
2026-06-23T17:19:43,917   adding 'oncoref/data/cancer-frameshift-burden.csv'
2026-06-23T17:19:43,920   adding 'oncoref/data/cancer-fusions.csv'
2026-06-23T17:19:43,938   adding 'oncoref/data/cancer-ici-response-estimates.csv'
2026-06-23T17:19:43,942   adding 'oncoref/data/cancer-ici-response.csv'
2026-06-23T17:19:43,944   adding 'oncoref/data/cancer-incidence-mortality.csv'
2026-06-23T17:19:43,958   adding 'oncoref/data/cancer-key-genes.csv'
2026-06-23T17:19:43,961   adding 'oncoref/data/cancer-lineage-group-overrides.csv'
2026-06-23T17:19:43,962   adding 'oncoref/data/cancer-lineage-groups.csv'
2026-06-23T17:19:43,990   adding 'oncoref/data/cancer-reference-expression-samples.csv.gz'
2026-06-23T17:19:43,994   adding 'oncoref/data/cancer-response-signatures.csv'
2026-06-23T17:19:43,995   adding 'oncoref/data/cancer-subtype-groupings.csv'
2026-06-23T17:19:44,007   adding 'oncoref/data/cancer-testis-antigens.csv'
2026-06-23T17:19:44,010   adding 'oncoref/data/cancer-tmb.csv'
2026-06-23T17:19:44,012   adding 'oncoref/data/cancer-type-genes.csv'
2026-06-23T17:19:44,016   adding 'oncoref/data/cancer-type-registry.csv'
2026-06-23T17:19:44,018   adding 'oncoref/data/cancer-viral-antigens.csv'
2026-06-23T17:19:44,070   adding 'oncoref/data/canonical-gene-space.csv.gz'
2026-06-23T17:19:44,077   adding 'oncoref/data/cdna-identical-gene-groups.csv'
2026-06-23T17:19:44,081   adding 'oncoref/data/censored-gene-reference-tpm.csv'
2026-06-23T17:19:44,091   adding 'oncoref/data/clean-tpm-censored-genes.csv'
2026-06-23T17:19:44,094   adding 'oncoref/data/cohort-registry.csv'
2026-06-23T17:19:44,095   adding 'oncoref/data/cta-candidate-references.csv'
2026-06-23T17:19:44,097   adding 'oncoref/data/cta-ihc-unreliable.csv'
2026-06-23T17:19:44,098   adding 'oncoref/data/degenerate-subtype-pairs.csv'
2026-06-23T17:19:44,100   adding 'oncoref/data/disease-state-rules.csv'
2026-06-23T17:19:44,126   adding 'oncoref/data/ensembl-id-aliases.csv'
2026-06-23T17:19:44,133   adding 'oncoref/data/expression_sources.yaml'
2026-06-23T17:19:44,135   adding 'oncoref/data/extra-tx-mappings.csv'
2026-06-23T17:19:44,137   adding 'oncoref/data/family-burden-map.csv'
2026-06-23T17:19:44,138   adding 'oncoref/data/fusion-expression-effects.csv'
2026-06-23T17:19:44,140   adding 'oncoref/data/fusion-surrogate-expression.csv'
2026-06-23T17:19:44,141   adding 'oncoref/data/hemoglobin-genes.csv'
2026-06-23T17:19:44,142   adding 'oncoref/data/histone-genes.csv'
2026-06-23T17:19:44,143   adding 'oncoref/data/housekeeping-genes.csv'
2026-06-23T17:19:44,145   adding 'oncoref/data/mitochondrial-genes.csv'
2026-06-23T17:19:44,146   adding 'oncoref/data/narrative-gene-sets.csv'
2026-06-23T17:19:44,186   adding 'oncoref/data/ncbi-symbol-synonyms.csv.gz'
2026-06-23T17:19:44,190   adding 'oncoref/data/nuclear-retained-lncrnas.csv'
2026-06-23T17:19:44,192   adding 'oncoref/data/numt-pseudogenes.csv'
2026-06-23T17:19:44,194   adding 'oncoref/data/proteoform-collapse-overrides.csv'
2026-06-23T17:19:44,196   adding 'oncoref/data/proteoform-groups-genome.csv'
2026-06-23T17:19:44,198   adding 'oncoref/data/proteoform-groups.csv'
2026-06-23T17:19:44,200   adding 'oncoref/data/rare-cancer-fusion-rules.csv'
2026-06-23T17:19:44,201   adding 'oncoref/data/ribosomal-protein-genes.csv'
2026-06-23T17:19:44,207   adding 'oncoref/data/ribosomal-protein-pseudogenes.csv'
2026-06-23T17:19:44,210   adding 'oncoref/data/rrna-and-pseudogenes.csv'
2026-06-23T17:19:44,229   adding 'oncoref/data/small-noncoding-rnas.csv'
2026-06-23T17:19:44,231   adding 'oncoref/data/source-matrices.csv'
2026-06-23T17:19:44,233   adding 'oncoref/data/tissue-burden-map.csv'
2026-06-23T17:19:44,236   adding 'oncoref-1.8.4.dist-info/licenses/LICENSE'
2026-06-23T17:19:44,238   adding 'oncoref-1.8.4.dist-info/METADATA'
2026-06-23T17:19:44,239   adding 'oncoref-1.8.4.dist-info/WHEEL'
2026-06-23T17:19:44,240   adding 'oncoref-1.8.4.dist-info/entry_points.txt'
2026-06-23T17:19:44,241   adding 'oncoref-1.8.4.dist-info/top_level.txt'
2026-06-23T17:19:44,243   adding 'oncoref-1.8.4.dist-info/RECORD'
2026-06-23T17:19:44,267   removing build/bdist.linux-armv7l/wheel
2026-06-23T17:19:44,386   Building wheel for oncoref (pyproject.toml): finished with status 'done'
2026-06-23T17:19:44,425   Created wheel for oncoref: filename=oncoref-1.8.4-py3-none-any.whl size=1640541 sha256=d649c7a749c099fe67033ecbdbafe4bf8bcd93bd71d9830ce2a6127a1c093cad
2026-06-23T17:19:44,426   Stored in directory: /tmp/pip-ephem-wheel-cache-w4_zcqn1/wheels/28/ee/3d/d5771d7e9f845c5c01f32624a7f8654011873dac25d43a909e
2026-06-23T17:19:44,441 Successfully built oncoref
2026-06-23T17:19:44,482 Removed build tracker: '/tmp/pip-build-tracker-u66j_sdd'