2026-06-24T19:49:21,751 Created temporary directory: /tmp/pip-ephem-wheel-cache-i3fv2vog
2026-06-24T19:49:21,753 Created temporary directory: /tmp/pip-build-tracker-tclpduki
2026-06-24T19:49:21,753 Initialized build tracking at /tmp/pip-build-tracker-tclpduki
2026-06-24T19:49:21,754 Created build tracker: /tmp/pip-build-tracker-tclpduki
2026-06-24T19:49:21,754 Entered build tracker: /tmp/pip-build-tracker-tclpduki
2026-06-24T19:49:21,755 Created temporary directory: /tmp/pip-wheel-e5bab36r
2026-06-24T19:49:21,758 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
2026-06-24T19:49:21,760 Created temporary directory: /tmp/pip-ephem-wheel-cache-0ob58ppc
2026-06-24T19:49:21,784 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-06-24T19:49:21,787 2 location(s) to search for versions of oncoref:
2026-06-24T19:49:21,787 * https://pypi.org/simple/oncoref/
2026-06-24T19:49:21,787 * https://www.piwheels.org/simple/oncoref/
2026-06-24T19:49:21,788 Fetching project page and analyzing links: https://pypi.org/simple/oncoref/
2026-06-24T19:49:21,789 Getting page https://pypi.org/simple/oncoref/
2026-06-24T19:49:21,790 Found index url https://pypi.org/simple
2026-06-24T19:49:22,019 Fetched page https://pypi.org/simple/oncoref/ as application/vnd.pypi.simple.v1+json
2026-06-24T19:49:22,024   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)
2026-06-24T19:49:22,025   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
2026-06-24T19:49:22,026   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)
2026-06-24T19:49:22,027   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
2026-06-24T19:49:22,028   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)
2026-06-24T19:49:22,029   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
2026-06-24T19:49:22,030   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)
2026-06-24T19:49:22,030   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
2026-06-24T19:49:22,031   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)
2026-06-24T19:49:22,032   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
2026-06-24T19:49:22,033   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)
2026-06-24T19:49:22,034   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
2026-06-24T19:49:22,035   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)
2026-06-24T19:49:22,035   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
2026-06-24T19:49:22,036   Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/b8/72/7cb35a084c989d648fc0ef20be3c0b9d888092e0e13aabc75710797dfbbd/oncoref-1.8.5-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-24T19:49:22,037   Found link https://files.pythonhosted.org/packages/0a/e2/de65c5e1582fe009b3f640e94e6ecd5cf2f139d490750374cdad3af0e14c/oncoref-1.8.5.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.8.5
2026-06-24T19:49:22,037   Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/71/92/3cd4d589831ccb90b12732347718e54d84097a6c780ced1810f52e3b302a/oncoref-1.8.6-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-24T19:49:22,038   Found link https://files.pythonhosted.org/packages/fe/29/0640ff92bcb51841b69a4d04ccf94a5173a18ee10c54786b959026ca4362/oncoref-1.8.6.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.8.6
2026-06-24T19:49:22,039   Skipping link: No binaries permitted for oncoref: https://files.pythonhosted.org/packages/f2/29/f869b37c956b8836b9c9b45e89ab7dad98a93270e6bd395b45a7ca5657ad/oncoref-1.8.7-py3-none-any.whl (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-24T19:49:22,040   Found link https://files.pythonhosted.org/packages/62/2d/434129dfb4157eb2bf8c4f89ff3f5c74e65b2a62e619fcd1154388d70aa4/oncoref-1.8.7.tar.gz (from https://pypi.org/simple/oncoref/) (requires-python:>=3.9), version: 1.8.7
2026-06-24T19:49:22,041 Fetching project page and analyzing links: https://www.piwheels.org/simple/oncoref/
2026-06-24T19:49:22,042 Getting page https://www.piwheels.org/simple/oncoref/
2026-06-24T19:49:22,043 Found index url https://www.piwheels.org/simple
2026-06-24T19:49:22,227 Fetched page https://www.piwheels.org/simple/oncoref/ as text/html
2026-06-24T19:49:22,231   Skipping link: No binaries permitted for oncoref: https://www.piwheels.org/simple/oncoref/oncoref-1.8.6-py3-none-any.whl#sha256=460f281fc846e410a5992e3a87193febdfac8bf81f3e5497a5e5d72ae58176bf (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-24T19:49:22,232   Skipping link: No binaries permitted for oncoref: https://www.piwheels.org/simple/oncoref/oncoref-1.8.5-py3-none-any.whl#sha256=cfedb20aa2c2593dfb010bc01a13d5b6c732ec5cf013fd70b65c71d1adb71f7e (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-24T19:49:22,232   Skipping link: No binaries permitted for oncoref: https://www.piwheels.org/simple/oncoref/oncoref-1.8.4-py3-none-any.whl#sha256=d649c7a749c099fe67033ecbdbafe4bf8bcd93bd71d9830ce2a6127a1c093cad (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9)
2026-06-24T19:49:22,233   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)
2026-06-24T19:49:22,233   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)
2026-06-24T19:49:22,234   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)
2026-06-24T19:49:22,235   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)
2026-06-24T19:49:22,235   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)
2026-06-24T19:49:22,235   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)
2026-06-24T19:49:22,236 Skipping link: not a file: https://www.piwheels.org/simple/oncoref/
2026-06-24T19:49:22,237 Skipping link: not a file: https://pypi.org/simple/oncoref/
2026-06-24T19:49:22,256 Given no hashes to check 1 links for project 'oncoref': discarding no candidates
2026-06-24T19:49:22,274 Collecting oncoref==1.8.7
2026-06-24T19:49:22,276   Created temporary directory: /tmp/pip-unpack-yw2eg5f4
2026-06-24T19:49:22,505   Downloading oncoref-1.8.7.tar.gz (1.7 MB)
2026-06-24T19:49:23,134   Added oncoref==1.8.7 from https://files.pythonhosted.org/packages/62/2d/434129dfb4157eb2bf8c4f89ff3f5c74e65b2a62e619fcd1154388d70aa4/oncoref-1.8.7.tar.gz to build tracker '/tmp/pip-build-tracker-tclpduki'
2026-06-24T19:49:23,141   Created temporary directory: /tmp/pip-build-env-x99losqh
2026-06-24T19:49:23,146   Installing build dependencies: started
2026-06-24T19:49:23,147   Running command pip subprocess to install build dependencies
2026-06-24T19:49:24,271   Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11)
2026-06-24T19:49:24,737   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
2026-06-24T19:49:24,760   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-06-24T19:49:26,555   Collecting setuptools>=61.0
2026-06-24T19:49:26,556     Obtaining dependency information for setuptools>=61.0 from https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl.metadata
2026-06-24T19:49:26,569     Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl.metadata (6.5 kB)
2026-06-24T19:49:26,827   Collecting wheel
2026-06-24T19:49:26,829     Obtaining dependency information for wheel from https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata
2026-06-24T19:49:26,843     Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB)
2026-06-24T19:49:27,026   Collecting packaging>=24.0
2026-06-24T19:49:27,027     Obtaining dependency information for packaging>=24.0 from https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata
2026-06-24T19:49:27,041     Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata (3.5 kB)
2026-06-24T19:49:27,230   Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB)
2026-06-24T19:49:27,251   Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB)
2026-06-24T19:49:27,329   Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB)
2026-06-24T19:49:27,361   Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB)
2026-06-24T19:49:27,387   Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB)
2026-06-24T19:49:27,484   Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB)
2026-06-24T19:49:30,216   Installing collected packages: setuptools, packaging, wheel
2026-06-24T19:49:34,233     Creating /tmp/pip-build-env-x99losqh/overlay/local/bin
2026-06-24T19:49:34,237     changing mode of /tmp/pip-build-env-x99losqh/overlay/local/bin/wheel to 755
2026-06-24T19:49:34,257   Successfully installed packaging-26.2 setuptools-82.0.1 wheel-0.47.0
2026-06-24T19:49:34,542   Installing build dependencies: finished with status 'done'
2026-06-24T19:49:34,765   Getting requirements to build wheel: started
2026-06-24T19:49:34,767   Running command Getting requirements to build wheel
2026-06-24T19:49:35,530   running egg_info
2026-06-24T19:49:35,537   writing oncoref.egg-info/PKG-INFO
2026-06-24T19:49:35,544   writing dependency_links to oncoref.egg-info/dependency_links.txt
2026-06-24T19:49:35,546   writing entry points to oncoref.egg-info/entry_points.txt
2026-06-24T19:49:35,548   writing requirements to oncoref.egg-info/requires.txt
2026-06-24T19:49:35,549   writing top-level names to oncoref.egg-info/top_level.txt
2026-06-24T19:49:35,584   reading manifest file 'oncoref.egg-info/SOURCES.txt'
2026-06-24T19:49:35,595   reading manifest template 'MANIFEST.in'
2026-06-24T19:49:35,597   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression'
2026-06-24T19:49:35,599   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles'
2026-06-24T19:49:35,600   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives'
2026-06-24T19:49:35,601   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5'
2026-06-24T19:49:35,602   warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv'
2026-06-24T19:49:35,603   warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv'
2026-06-24T19:49:35,604   adding license file 'LICENSE'
2026-06-24T19:49:35,612   writing manifest file 'oncoref.egg-info/SOURCES.txt'
2026-06-24T19:49:35,711   Getting requirements to build wheel: finished with status 'done'
2026-06-24T19:49:35,715   Created temporary directory: /tmp/pip-modern-metadata-i9ju6k95
2026-06-24T19:49:35,717   Preparing metadata (pyproject.toml): started
2026-06-24T19:49:35,718   Running command Preparing metadata (pyproject.toml)
2026-06-24T19:49:36,817   running dist_info
2026-06-24T19:49:36,827   creating /tmp/pip-modern-metadata-i9ju6k95/oncoref.egg-info
2026-06-24T19:49:36,828   writing /tmp/pip-modern-metadata-i9ju6k95/oncoref.egg-info/PKG-INFO
2026-06-24T19:49:36,834   writing dependency_links to /tmp/pip-modern-metadata-i9ju6k95/oncoref.egg-info/dependency_links.txt
2026-06-24T19:49:36,836   writing entry points to /tmp/pip-modern-metadata-i9ju6k95/oncoref.egg-info/entry_points.txt
2026-06-24T19:49:36,838   writing requirements to /tmp/pip-modern-metadata-i9ju6k95/oncoref.egg-info/requires.txt
2026-06-24T19:49:36,840   writing top-level names to /tmp/pip-modern-metadata-i9ju6k95/oncoref.egg-info/top_level.txt
2026-06-24T19:49:36,841   writing manifest file '/tmp/pip-modern-metadata-i9ju6k95/oncoref.egg-info/SOURCES.txt'
2026-06-24T19:49:36,874   reading manifest file '/tmp/pip-modern-metadata-i9ju6k95/oncoref.egg-info/SOURCES.txt'
2026-06-24T19:49:36,876   reading manifest template 'MANIFEST.in'
2026-06-24T19:49:36,877   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression'
2026-06-24T19:49:36,878   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles'
2026-06-24T19:49:36,879   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives'
2026-06-24T19:49:36,880   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5'
2026-06-24T19:49:36,881   warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv'
2026-06-24T19:49:36,882   warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv'
2026-06-24T19:49:36,882   adding license file 'LICENSE'
2026-06-24T19:49:36,888   writing manifest file '/tmp/pip-modern-metadata-i9ju6k95/oncoref.egg-info/SOURCES.txt'
2026-06-24T19:49:36,890   creating '/tmp/pip-modern-metadata-i9ju6k95/oncoref-1.8.7.dist-info'
2026-06-24T19:49:37,017   Preparing metadata (pyproject.toml): finished with status 'done'
2026-06-24T19:49:37,022   Source in /tmp/pip-wheel-e5bab36r/oncoref_0398a11bc430445eac6049f4b00f3988 has version 1.8.7, which satisfies requirement oncoref==1.8.7 from https://files.pythonhosted.org/packages/62/2d/434129dfb4157eb2bf8c4f89ff3f5c74e65b2a62e619fcd1154388d70aa4/oncoref-1.8.7.tar.gz
2026-06-24T19:49:37,023   Removed oncoref==1.8.7 from https://files.pythonhosted.org/packages/62/2d/434129dfb4157eb2bf8c4f89ff3f5c74e65b2a62e619fcd1154388d70aa4/oncoref-1.8.7.tar.gz from build tracker '/tmp/pip-build-tracker-tclpduki'
2026-06-24T19:49:37,029 Created temporary directory: /tmp/pip-unpack-mtadu0lo
2026-06-24T19:49:37,030 Building wheels for collected packages: oncoref
2026-06-24T19:49:37,034   Created temporary directory: /tmp/pip-wheel-80ky0prc
2026-06-24T19:49:37,035   Destination directory: /tmp/pip-wheel-80ky0prc
2026-06-24T19:49:37,037   Building wheel for oncoref (pyproject.toml): started
2026-06-24T19:49:37,038   Running command Building wheel for oncoref (pyproject.toml)
2026-06-24T19:49:37,726   running bdist_wheel
2026-06-24T19:49:37,743   running build
2026-06-24T19:49:37,744   running build_py
2026-06-24T19:49:37,751   creating build/lib/oncoref
2026-06-24T19:49:37,753   copying oncoref/cta.py -> build/lib/oncoref
2026-06-24T19:49:37,757   copying oncoref/cohorts.py -> build/lib/oncoref
2026-06-24T19:49:37,759   copying oncoref/expression.py -> build/lib/oncoref
2026-06-24T19:49:37,764   copying oncoref/response_signatures.py -> build/lib/oncoref
2026-06-24T19:49:37,766   copying oncoref/data_bundle.py -> build/lib/oncoref
2026-06-24T19:49:37,768   copying oncoref/tmb.py -> build/lib/oncoref
2026-06-24T19:49:37,770   copying oncoref/cta_tissues.py -> build/lib/oncoref
2026-06-24T19:49:37,773   copying oncoref/gene_ids.py -> build/lib/oncoref
2026-06-24T19:49:37,776   copying oncoref/source_matrices.py -> build/lib/oncoref
2026-06-24T19:49:37,778   copying oncoref/gene_qc.py -> build/lib/oncoref
2026-06-24T19:49:37,780   copying oncoref/cli.py -> build/lib/oncoref
2026-06-24T19:49:37,783   copying oncoref/peptides.py -> build/lib/oncoref
2026-06-24T19:49:37,786   copying oncoref/expression_builders.py -> build/lib/oncoref
2026-06-24T19:49:37,788   copying oncoref/proteoforms.py -> build/lib/oncoref
2026-06-24T19:49:37,791   copying oncoref/samples.py -> build/lib/oncoref
2026-06-24T19:49:37,793   copying oncoref/cancer_genes.py -> build/lib/oncoref
2026-06-24T19:49:37,795   copying oncoref/expression_engine.py -> build/lib/oncoref
2026-06-24T19:49:37,798   copying oncoref/ici_response.py -> build/lib/oncoref
2026-06-24T19:49:37,800   copying oncoref/reference_data.py -> build/lib/oncoref
2026-06-24T19:49:37,802   copying oncoref/normalization.py -> build/lib/oncoref
2026-06-24T19:49:37,806   copying oncoref/apd1.py -> build/lib/oncoref
2026-06-24T19:49:37,807   copying oncoref/catalog.py -> build/lib/oncoref
2026-06-24T19:49:37,810   copying oncoref/antigen_coverage.py -> build/lib/oncoref
2026-06-24T19:49:37,812   copying oncoref/plots.py -> build/lib/oncoref
2026-06-24T19:49:37,815   copying oncoref/data_manifest.py -> build/lib/oncoref
2026-06-24T19:49:37,818   copying oncoref/hpa.py -> build/lib/oncoref
2026-06-24T19:49:37,820   copying oncoref/genome.py -> build/lib/oncoref
2026-06-24T19:49:37,822   copying oncoref/incidence.py -> build/lib/oncoref
2026-06-24T19:49:37,824   copying oncoref/cancer_types.py -> build/lib/oncoref
2026-06-24T19:49:37,827   copying oncoref/cta_curation_plots.py -> build/lib/oncoref
2026-06-24T19:49:37,830   copying oncoref/load_dataset.py -> build/lib/oncoref
2026-06-24T19:49:37,832   copying oncoref/cta_regen.py -> build/lib/oncoref
2026-06-24T19:49:37,834   copying oncoref/__init__.py -> build/lib/oncoref
2026-06-24T19:49:37,837   copying oncoref/cta_coverage.py -> build/lib/oncoref
2026-06-24T19:49:37,839   copying oncoref/fusions.py -> build/lib/oncoref
2026-06-24T19:49:37,841   copying oncoref/coverage.py -> build/lib/oncoref
2026-06-24T19:49:37,844   copying oncoref/version.py -> build/lib/oncoref
2026-06-24T19:49:37,846   copying oncoref/cancer_ontology.py -> build/lib/oncoref
2026-06-24T19:49:37,848   copying oncoref/ici.py -> build/lib/oncoref
2026-06-24T19:49:37,850   copying oncoref/cta_peptides.py -> build/lib/oncoref
2026-06-24T19:49:37,852   copying oncoref/expression_registry.py -> build/lib/oncoref
2026-06-24T19:49:37,854   copying oncoref/gene_families.py -> build/lib/oncoref
2026-06-24T19:49:37,868   creating build/lib/oncoref/data
2026-06-24T19:49:37,869   copying oncoref/data/nuclear-retained-lncrnas.csv -> build/lib/oncoref/data
2026-06-24T19:49:37,872   copying oncoref/data/cancer-apd1-response.csv -> build/lib/oncoref/data
2026-06-24T19:49:37,878   copying oncoref/data/cancer-code-burden-map.csv -> build/lib/oncoref/data
2026-06-24T19:49:37,880   copying oncoref/data/cancer-type-registry.csv -> build/lib/oncoref/data
2026-06-24T19:49:37,888   copying oncoref/data/clean-tpm-biological-housekeeping-genes.csv -> build/lib/oncoref/data
2026-06-24T19:49:37,901   copying oncoref/data/rare-cancer-fusion-rules.csv -> build/lib/oncoref/data
2026-06-24T19:49:37,917   copying oncoref/data/small-noncoding-rnas.csv -> build/lib/oncoref/data
2026-06-24T19:49:37,945   copying oncoref/data/clean-tpm-censored-genes.csv -> build/lib/oncoref/data
2026-06-24T19:49:37,963   copying oncoref/data/cohort-registry.csv -> build/lib/oncoref/data
2026-06-24T19:49:37,975   copying oncoref/data/housekeeping-genes.csv -> build/lib/oncoref/data
2026-06-24T19:49:37,986   copying oncoref/data/rrna-and-pseudogenes.csv -> build/lib/oncoref/data
2026-06-24T19:49:37,990   copying oncoref/data/cancer-ici-response.csv -> build/lib/oncoref/data
2026-06-24T19:49:37,995   copying oncoref/data/extra-tx-mappings.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,004   copying oncoref/data/cancer-lineage-groups.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,011   copying oncoref/data/numt-pseudogenes.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,019   copying oncoref/data/fusion-surrogate-expression.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,022   copying oncoref/data/disease-state-rules.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,024   copying oncoref/data/tissue-burden-map.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,027   copying oncoref/data/proteoform-groups.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,029   copying oncoref/data/cancer-fusions.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,033   copying oncoref/data/proteoform-groups-genome.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,036   copying oncoref/data/fusion-expression-effects.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,041   copying oncoref/data/cancer-driver-variants.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,046   copying oncoref/data/cancer-key-genes.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,051   copying oncoref/data/cdna-identical-gene-groups.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,054   copying oncoref/data/censored-gene-reference-tpm.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,058   copying oncoref/data/cta-ihc-unreliable.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,060   copying oncoref/data/proteoform-collapse-overrides.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,062   copying oncoref/data/cancer-testis-antigens.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,068   copying oncoref/data/cancer-type-genes.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,070   copying oncoref/data/cancer-tmb.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,075   copying oncoref/data/histone-genes.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,078   copying oncoref/data/cancer-frameshift-burden.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,081   copying oncoref/data/degenerate-subtype-pairs.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,083   copying oncoref/data/cancer-driver-genes.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,087   copying oncoref/data/narrative-gene-sets.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,089   copying oncoref/data/cancer-expression-source-candidates.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,092   copying oncoref/data/cta-candidate-references.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,095   copying oncoref/data/hemoglobin-genes.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,097   copying oncoref/data/cancer-incidence-mortality.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,099   copying oncoref/data/cancer-response-signatures.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,102   copying oncoref/data/family-burden-map.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,104   copying oncoref/data/ensembl-id-aliases.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,125   copying oncoref/data/ribosomal-protein-genes.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,127   copying oncoref/data/cancer-lineage-group-overrides.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,129   copying oncoref/data/cancer-viral-antigens.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,131   copying oncoref/data/mitochondrial-genes.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,134   copying oncoref/data/source-matrices.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,136   copying oncoref/data/cancer-ici-response-estimates.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,147   copying oncoref/data/ribosomal-protein-pseudogenes.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,151   copying oncoref/data/cancer-cohort-aggregates.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,153   copying oncoref/data/cancer-subtype-groupings.csv -> build/lib/oncoref/data
2026-06-24T19:49:38,155   copying oncoref/data/canonical-gene-space.csv.gz -> build/lib/oncoref/data
2026-06-24T19:49:38,175   copying oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/lib/oncoref/data
2026-06-24T19:49:38,188   copying oncoref/data/cancer-reference-expression-samples.csv.gz -> build/lib/oncoref/data
2026-06-24T19:49:38,198   copying oncoref/data/expression_sources.yaml -> build/lib/oncoref/data
2026-06-24T19:49:38,212   installing to build/bdist.linux-armv7l/wheel
2026-06-24T19:49:38,213   running install
2026-06-24T19:49:38,234   running install_lib
2026-06-24T19:49:38,240   creating build/bdist.linux-armv7l/wheel
2026-06-24T19:49:38,243   creating build/bdist.linux-armv7l/wheel/oncoref
2026-06-24T19:49:38,244   copying build/lib/oncoref/cta.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,247   copying build/lib/oncoref/cohorts.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,249   copying build/lib/oncoref/expression.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,254   copying build/lib/oncoref/response_signatures.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,256   copying build/lib/oncoref/data_bundle.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,259   copying build/lib/oncoref/tmb.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,262   copying build/lib/oncoref/cta_tissues.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,267   copying build/lib/oncoref/gene_ids.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,272   copying build/lib/oncoref/source_matrices.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,274   copying build/lib/oncoref/gene_qc.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,276   copying build/lib/oncoref/cli.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,281   copying build/lib/oncoref/peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,286   copying build/lib/oncoref/expression_builders.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,293   copying build/lib/oncoref/proteoforms.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,304   copying build/lib/oncoref/samples.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,318   copying build/lib/oncoref/cancer_genes.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,330   copying build/lib/oncoref/expression_engine.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,342   copying build/lib/oncoref/ici_response.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,354   copying build/lib/oncoref/reference_data.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,369   copying build/lib/oncoref/normalization.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,386   copying build/lib/oncoref/apd1.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,389   copying build/lib/oncoref/catalog.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,394   copying build/lib/oncoref/antigen_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,400   copying build/lib/oncoref/plots.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,453   copying build/lib/oncoref/data_manifest.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,456   copying build/lib/oncoref/hpa.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,458   copying build/lib/oncoref/genome.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,461   copying build/lib/oncoref/incidence.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,464   copying build/lib/oncoref/cancer_types.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,467   copying build/lib/oncoref/cta_curation_plots.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:38,471   creating build/bdist.linux-armv7l/wheel/oncoref/data
2026-06-24T19:49:38,472   copying build/lib/oncoref/data/nuclear-retained-lncrnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:38,474   copying build/lib/oncoref/data/cancer-apd1-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:38,933   copying build/lib/oncoref/data/cancer-code-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:38,936   copying build/lib/oncoref/data/expression_sources.yaml -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:38,941   copying build/lib/oncoref/data/cancer-type-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:38,947   copying build/lib/oncoref/data/clean-tpm-biological-housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:38,951   copying build/lib/oncoref/data/rare-cancer-fusion-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:38,955   copying build/lib/oncoref/data/small-noncoding-rnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,006   copying build/lib/oncoref/data/clean-tpm-censored-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,054   copying build/lib/oncoref/data/cohort-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,059   copying build/lib/oncoref/data/housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,063   copying build/lib/oncoref/data/rrna-and-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,068   copying build/lib/oncoref/data/cancer-ici-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,073   copying build/lib/oncoref/data/canonical-gene-space.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,109   copying build/lib/oncoref/data/extra-tx-mappings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,113   copying build/lib/oncoref/data/cancer-lineage-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,116   copying build/lib/oncoref/data/numt-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,120   copying build/lib/oncoref/data/fusion-surrogate-expression.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,124   copying build/lib/oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,139   copying build/lib/oncoref/data/disease-state-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,142   copying build/lib/oncoref/data/tissue-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,145   copying build/lib/oncoref/data/proteoform-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,147   copying build/lib/oncoref/data/cancer-fusions.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,151   copying build/lib/oncoref/data/proteoform-groups-genome.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,154   copying build/lib/oncoref/data/fusion-expression-effects.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,157   copying build/lib/oncoref/data/cancer-driver-variants.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,161   copying build/lib/oncoref/data/cancer-key-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,168   copying build/lib/oncoref/data/cdna-identical-gene-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,171   copying build/lib/oncoref/data/censored-gene-reference-tpm.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,174   copying build/lib/oncoref/data/cta-ihc-unreliable.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,177   copying build/lib/oncoref/data/proteoform-collapse-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,180   copying build/lib/oncoref/data/cancer-testis-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,187   copying build/lib/oncoref/data/cancer-type-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,192   copying build/lib/oncoref/data/cancer-reference-expression-samples.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,204   copying build/lib/oncoref/data/cancer-tmb.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,209   copying build/lib/oncoref/data/histone-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,214   copying build/lib/oncoref/data/cancer-frameshift-burden.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,217   copying build/lib/oncoref/data/degenerate-subtype-pairs.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,222   copying build/lib/oncoref/data/cancer-driver-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,226   copying build/lib/oncoref/data/narrative-gene-sets.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,229   copying build/lib/oncoref/data/cancer-expression-source-candidates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,233   copying build/lib/oncoref/data/cta-candidate-references.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,236   copying build/lib/oncoref/data/hemoglobin-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,453   copying build/lib/oncoref/data/cancer-incidence-mortality.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,454   copying build/lib/oncoref/data/cancer-response-signatures.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,456   copying build/lib/oncoref/data/family-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,458   copying build/lib/oncoref/data/ensembl-id-aliases.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,466   copying build/lib/oncoref/data/ribosomal-protein-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,468   copying build/lib/oncoref/data/cancer-lineage-group-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,469   copying build/lib/oncoref/data/cancer-viral-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,471   copying build/lib/oncoref/data/mitochondrial-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,473   copying build/lib/oncoref/data/source-matrices.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,475   copying build/lib/oncoref/data/cancer-ici-response-estimates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,482   copying build/lib/oncoref/data/ribosomal-protein-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,485   copying build/lib/oncoref/data/cancer-cohort-aggregates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,487   copying build/lib/oncoref/data/cancer-subtype-groupings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data
2026-06-24T19:49:39,489   copying build/lib/oncoref/load_dataset.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:39,491   copying build/lib/oncoref/cta_regen.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:39,494   copying build/lib/oncoref/__init__.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:39,496   copying build/lib/oncoref/cta_coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:39,498   copying build/lib/oncoref/fusions.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:39,500   copying build/lib/oncoref/coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:39,503   copying build/lib/oncoref/version.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:39,505   copying build/lib/oncoref/cancer_ontology.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:39,507   copying build/lib/oncoref/ici.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:39,510   copying build/lib/oncoref/cta_peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:39,511   copying build/lib/oncoref/expression_registry.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:39,514   copying build/lib/oncoref/gene_families.py -> build/bdist.linux-armv7l/wheel/./oncoref
2026-06-24T19:49:39,516   running install_egg_info
2026-06-24T19:49:39,525   running egg_info
2026-06-24T19:49:39,530   writing oncoref.egg-info/PKG-INFO
2026-06-24T19:49:39,536   writing dependency_links to oncoref.egg-info/dependency_links.txt
2026-06-24T19:49:39,537   writing entry points to oncoref.egg-info/entry_points.txt
2026-06-24T19:49:39,540   writing requirements to oncoref.egg-info/requires.txt
2026-06-24T19:49:39,541   writing top-level names to oncoref.egg-info/top_level.txt
2026-06-24T19:49:39,560   reading manifest file 'oncoref.egg-info/SOURCES.txt'
2026-06-24T19:49:39,569   reading manifest template 'MANIFEST.in'
2026-06-24T19:49:39,571   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression'
2026-06-24T19:49:39,572   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles'
2026-06-24T19:49:39,573   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives'
2026-06-24T19:49:39,574   warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5'
2026-06-24T19:49:39,575   warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv'
2026-06-24T19:49:39,576   warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv'
2026-06-24T19:49:39,576   adding license file 'LICENSE'
2026-06-24T19:49:39,584   writing manifest file 'oncoref.egg-info/SOURCES.txt'
2026-06-24T19:49:39,586   Copying oncoref.egg-info to build/bdist.linux-armv7l/wheel/./oncoref-1.8.7-py3.11.egg-info
2026-06-24T19:49:39,599   running install_scripts
2026-06-24T19:49:39,612   creating build/bdist.linux-armv7l/wheel/oncoref-1.8.7.dist-info/WHEEL
2026-06-24T19:49:39,615   creating '/tmp/pip-wheel-80ky0prc/.tmp-1l9xfpiz/oncoref-1.8.7-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2026-06-24T19:49:39,619   adding 'oncoref/__init__.py'
2026-06-24T19:49:39,620   adding 'oncoref/antigen_coverage.py'
2026-06-24T19:49:39,622   adding 'oncoref/apd1.py'
2026-06-24T19:49:39,624   adding 'oncoref/cancer_genes.py'
2026-06-24T19:49:39,625   adding 'oncoref/cancer_ontology.py'
2026-06-24T19:49:39,629   adding 'oncoref/cancer_types.py'
2026-06-24T19:49:39,632   adding 'oncoref/catalog.py'
2026-06-24T19:49:39,635   adding 'oncoref/cli.py'
2026-06-24T19:49:39,637   adding 'oncoref/cohorts.py'
2026-06-24T19:49:39,640   adding 'oncoref/coverage.py'
2026-06-24T19:49:39,643   adding 'oncoref/cta.py'
2026-06-24T19:49:39,644   adding 'oncoref/cta_coverage.py'
2026-06-24T19:49:39,646   adding 'oncoref/cta_curation_plots.py'
2026-06-24T19:49:39,648   adding 'oncoref/cta_peptides.py'
2026-06-24T19:49:39,651   adding 'oncoref/cta_regen.py'
2026-06-24T19:49:39,652   adding 'oncoref/cta_tissues.py'
2026-06-24T19:49:39,655   adding 'oncoref/data_bundle.py'
2026-06-24T19:49:39,657   adding 'oncoref/data_manifest.py'
2026-06-24T19:49:39,665   adding 'oncoref/expression.py'
2026-06-24T19:49:39,668   adding 'oncoref/expression_builders.py'
2026-06-24T19:49:39,670   adding 'oncoref/expression_engine.py'
2026-06-24T19:49:39,671   adding 'oncoref/expression_registry.py'
2026-06-24T19:49:39,673   adding 'oncoref/fusions.py'
2026-06-24T19:49:39,676   adding 'oncoref/gene_families.py'
2026-06-24T19:49:39,678   adding 'oncoref/gene_ids.py'
2026-06-24T19:49:39,680   adding 'oncoref/gene_qc.py'
2026-06-24T19:49:39,682   adding 'oncoref/genome.py'
2026-06-24T19:49:39,684   adding 'oncoref/hpa.py'
2026-06-24T19:49:39,687   adding 'oncoref/ici.py'
2026-06-24T19:49:39,688   adding 'oncoref/ici_response.py'
2026-06-24T19:49:39,690   adding 'oncoref/incidence.py'
2026-06-24T19:49:39,693   adding 'oncoref/load_dataset.py'
2026-06-24T19:49:39,696   adding 'oncoref/normalization.py'
2026-06-24T19:49:39,699   adding 'oncoref/peptides.py'
2026-06-24T19:49:39,705   adding 'oncoref/plots.py'
2026-06-24T19:49:39,708   adding 'oncoref/proteoforms.py'
2026-06-24T19:49:39,710   adding 'oncoref/reference_data.py'
2026-06-24T19:49:39,712   adding 'oncoref/response_signatures.py'
2026-06-24T19:49:39,713   adding 'oncoref/samples.py'
2026-06-24T19:49:39,715   adding 'oncoref/source_matrices.py'
2026-06-24T19:49:39,717   adding 'oncoref/tmb.py'
2026-06-24T19:49:39,718   adding 'oncoref/version.py'
2026-06-24T19:49:39,722   adding 'oncoref/data/cancer-apd1-response.csv'
2026-06-24T19:49:39,723   adding 'oncoref/data/cancer-code-burden-map.csv'
2026-06-24T19:49:39,725   adding 'oncoref/data/cancer-cohort-aggregates.csv'
2026-06-24T19:49:39,730   adding 'oncoref/data/cancer-driver-genes.csv'
2026-06-24T19:49:39,732   adding 'oncoref/data/cancer-driver-variants.csv'
2026-06-24T19:49:39,735   adding 'oncoref/data/cancer-expression-source-candidates.csv'
2026-06-24T19:49:39,736   adding 'oncoref/data/cancer-frameshift-burden.csv'
2026-06-24T19:49:39,739   adding 'oncoref/data/cancer-fusions.csv'
2026-06-24T19:49:39,756   adding 'oncoref/data/cancer-ici-response-estimates.csv'
2026-06-24T19:49:39,760   adding 'oncoref/data/cancer-ici-response.csv'
2026-06-24T19:49:39,762   adding 'oncoref/data/cancer-incidence-mortality.csv'
2026-06-24T19:49:39,776   adding 'oncoref/data/cancer-key-genes.csv'
2026-06-24T19:49:39,778   adding 'oncoref/data/cancer-lineage-group-overrides.csv'
2026-06-24T19:49:39,779   adding 'oncoref/data/cancer-lineage-groups.csv'
2026-06-24T19:49:39,808   adding 'oncoref/data/cancer-reference-expression-samples.csv.gz'
2026-06-24T19:49:39,811   adding 'oncoref/data/cancer-response-signatures.csv'
2026-06-24T19:49:39,812   adding 'oncoref/data/cancer-subtype-groupings.csv'
2026-06-24T19:49:39,823   adding 'oncoref/data/cancer-testis-antigens.csv'
2026-06-24T19:49:39,827   adding 'oncoref/data/cancer-tmb.csv'
2026-06-24T19:49:39,829   adding 'oncoref/data/cancer-type-genes.csv'
2026-06-24T19:49:39,833   adding 'oncoref/data/cancer-type-registry.csv'
2026-06-24T19:49:39,835   adding 'oncoref/data/cancer-viral-antigens.csv'
2026-06-24T19:49:39,887   adding 'oncoref/data/canonical-gene-space.csv.gz'
2026-06-24T19:49:39,893   adding 'oncoref/data/cdna-identical-gene-groups.csv'
2026-06-24T19:49:39,896   adding 'oncoref/data/censored-gene-reference-tpm.csv'
2026-06-24T19:49:39,898   adding 'oncoref/data/clean-tpm-biological-housekeeping-genes.csv'
2026-06-24T19:49:39,908   adding 'oncoref/data/clean-tpm-censored-genes.csv'
2026-06-24T19:49:39,911   adding 'oncoref/data/cohort-registry.csv'
2026-06-24T19:49:39,912   adding 'oncoref/data/cta-candidate-references.csv'
2026-06-24T19:49:39,914   adding 'oncoref/data/cta-ihc-unreliable.csv'
2026-06-24T19:49:39,915   adding 'oncoref/data/degenerate-subtype-pairs.csv'
2026-06-24T19:49:39,916   adding 'oncoref/data/disease-state-rules.csv'
2026-06-24T19:49:39,944   adding 'oncoref/data/ensembl-id-aliases.csv'
2026-06-24T19:49:39,950   adding 'oncoref/data/expression_sources.yaml'
2026-06-24T19:49:39,952   adding 'oncoref/data/extra-tx-mappings.csv'
2026-06-24T19:49:39,953   adding 'oncoref/data/family-burden-map.csv'
2026-06-24T19:49:39,954   adding 'oncoref/data/fusion-expression-effects.csv'
2026-06-24T19:49:39,956   adding 'oncoref/data/fusion-surrogate-expression.csv'
2026-06-24T19:49:39,957   adding 'oncoref/data/hemoglobin-genes.csv'
2026-06-24T19:49:39,958   adding 'oncoref/data/histone-genes.csv'
2026-06-24T19:49:39,959   adding 'oncoref/data/housekeeping-genes.csv'
2026-06-24T19:49:39,961   adding 'oncoref/data/mitochondrial-genes.csv'
2026-06-24T19:49:39,962   adding 'oncoref/data/narrative-gene-sets.csv'
2026-06-24T19:49:40,004   adding 'oncoref/data/ncbi-symbol-synonyms.csv.gz'
2026-06-24T19:49:40,007   adding 'oncoref/data/nuclear-retained-lncrnas.csv'
2026-06-24T19:49:40,009   adding 'oncoref/data/numt-pseudogenes.csv'
2026-06-24T19:49:40,011   adding 'oncoref/data/proteoform-collapse-overrides.csv'
2026-06-24T19:49:40,013   adding 'oncoref/data/proteoform-groups-genome.csv'
2026-06-24T19:49:40,015   adding 'oncoref/data/proteoform-groups.csv'
2026-06-24T19:49:40,017   adding 'oncoref/data/rare-cancer-fusion-rules.csv'
2026-06-24T19:49:40,018   adding 'oncoref/data/ribosomal-protein-genes.csv'
2026-06-24T19:49:40,025   adding 'oncoref/data/ribosomal-protein-pseudogenes.csv'
2026-06-24T19:49:40,027   adding 'oncoref/data/rrna-and-pseudogenes.csv'
2026-06-24T19:49:40,047   adding 'oncoref/data/small-noncoding-rnas.csv'
2026-06-24T19:49:40,050   adding 'oncoref/data/source-matrices.csv'
2026-06-24T19:49:40,051   adding 'oncoref/data/tissue-burden-map.csv'
2026-06-24T19:49:40,055   adding 'oncoref-1.8.7.dist-info/licenses/LICENSE'
2026-06-24T19:49:40,057   adding 'oncoref-1.8.7.dist-info/METADATA'
2026-06-24T19:49:40,058   adding 'oncoref-1.8.7.dist-info/WHEEL'
2026-06-24T19:49:40,059   adding 'oncoref-1.8.7.dist-info/entry_points.txt'
2026-06-24T19:49:40,060   adding 'oncoref-1.8.7.dist-info/top_level.txt'
2026-06-24T19:49:40,062   adding 'oncoref-1.8.7.dist-info/RECORD'
2026-06-24T19:49:40,090   removing build/bdist.linux-armv7l/wheel
2026-06-24T19:49:40,212   Building wheel for oncoref (pyproject.toml): finished with status 'done'
2026-06-24T19:49:40,253   Created wheel for oncoref: filename=oncoref-1.8.7-py3-none-any.whl size=1652325 sha256=84f80af8afa25d02579e67983b74fd2e515df1ce6d0cb602ecb6808e994f8f63
2026-06-24T19:49:40,254   Stored in directory: /tmp/pip-ephem-wheel-cache-0ob58ppc/wheels/88/44/d5/da995827fbe55ffdd5e32563dff262d13842e889f01fce3b51
2026-06-24T19:49:40,269 Successfully built oncoref
2026-06-24T19:49:40,374 Removed build tracker: '/tmp/pip-build-tracker-tclpduki'