2026-06-20T15:25:07,872 Created temporary directory: /tmp/pip-ephem-wheel-cache-45oc8i7o 2026-06-20T15:25:07,873 Created temporary directory: /tmp/pip-build-tracker-nndqtw3_ 2026-06-20T15:25:07,874 Initialized build tracking at /tmp/pip-build-tracker-nndqtw3_ 2026-06-20T15:25:07,874 Created build tracker: /tmp/pip-build-tracker-nndqtw3_ 2026-06-20T15:25:07,875 Entered build tracker: /tmp/pip-build-tracker-nndqtw3_ 2026-06-20T15:25:07,876 Created temporary directory: /tmp/pip-wheel-nvhh8y7s 2026-06-20T15:25:07,878 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 2026-06-20T15:25:07,881 Created temporary directory: /tmp/pip-ephem-wheel-cache-86be343o 2026-06-20T15:25:07,904 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-06-20T15:25:07,908 2 location(s) to search for versions of oncoref: 2026-06-20T15:25:07,908 * https://pypi.org/simple/oncoref/ 2026-06-20T15:25:07,908 * https://www.piwheels.org/simple/oncoref/ 2026-06-20T15:25:07,909 Fetching project page and analyzing links: https://pypi.org/simple/oncoref/ 2026-06-20T15:25:07,909 Getting page https://pypi.org/simple/oncoref/ 2026-06-20T15:25:07,911 Found index url https://pypi.org/simple 2026-06-20T15:25:08,140 Fetched page https://pypi.org/simple/oncoref/ as application/vnd.pypi.simple.v1+json 2026-06-20T15:25:08,143 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) 2026-06-20T15:25:08,144 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 2026-06-20T15:25:08,144 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) 2026-06-20T15:25:08,145 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 2026-06-20T15:25:08,146 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) 2026-06-20T15:25:08,147 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 2026-06-20T15:25:08,148 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) 2026-06-20T15:25:08,149 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 2026-06-20T15:25:08,150 Fetching project page and analyzing links: https://www.piwheels.org/simple/oncoref/ 2026-06-20T15:25:08,151 Getting page https://www.piwheels.org/simple/oncoref/ 2026-06-20T15:25:08,152 Found index url https://www.piwheels.org/simple 2026-06-20T15:25:08,340 Fetched page https://www.piwheels.org/simple/oncoref/ as text/html 2026-06-20T15:25:08,342 Skipping link: No binaries permitted for oncoref: https://www.piwheels.org/simple/oncoref/oncoref-1.8.0-py3-none-any.whl#sha256=6f9be6d1511d7e84166b02f2cd219b977025db68916073cb4bd1ebdfc8919914 (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-06-20T15:25:08,343 Skipping link: No binaries permitted for oncoref: https://www.piwheels.org/simple/oncoref/oncoref-1.7.0-py3-none-any.whl#sha256=249750fecb30a99d715c221ca1ca76a4ff790891f0051782cd528395d14db6ed (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-06-20T15:25:08,344 Skipping link: No binaries permitted for oncoref: https://www.piwheels.org/simple/oncoref/oncoref-1.6.0-py3-none-any.whl#sha256=e8383754a89924adfeb524e978f9d8e304fe5f179989515ee7ee4ae3eaa3d997 (from https://www.piwheels.org/simple/oncoref/) (requires-python:>=3.9) 2026-06-20T15:25:08,344 Skipping link: not a file: https://www.piwheels.org/simple/oncoref/ 2026-06-20T15:25:08,344 Skipping link: not a file: https://pypi.org/simple/oncoref/ 2026-06-20T15:25:08,363 Given no hashes to check 1 links for project 'oncoref': discarding no candidates 2026-06-20T15:25:08,381 Collecting oncoref==1.8.1 2026-06-20T15:25:08,384 Created temporary directory: /tmp/pip-unpack-aywzcej5 2026-06-20T15:25:08,532 Downloading oncoref-1.8.1.tar.gz (1.7 MB) 2026-06-20T15:25:09,104 Added oncoref==1.8.1 from https://files.pythonhosted.org/packages/21/3e/8080dbac7eaa58029775dd4937cb7dc70d1e65b52e358ccb75b5dd8ed63e/oncoref-1.8.1.tar.gz to build tracker '/tmp/pip-build-tracker-nndqtw3_' 2026-06-20T15:25:09,111 Created temporary directory: /tmp/pip-build-env-0jk_l45k 2026-06-20T15:25:09,115 Installing build dependencies: started 2026-06-20T15:25:09,116 Running command pip subprocess to install build dependencies 2026-06-20T15:25:10,248 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-06-20T15:25:10,719 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 2026-06-20T15:25:10,742 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-06-20T15:25:12,532 Collecting setuptools>=61.0 2026-06-20T15:25:12,534 Obtaining dependency information for setuptools>=61.0 from https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl.metadata 2026-06-20T15:25:12,550 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl.metadata (6.5 kB) 2026-06-20T15:25:12,789 Collecting wheel 2026-06-20T15:25:12,790 Obtaining dependency information for wheel from https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata 2026-06-20T15:25:12,804 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB) 2026-06-20T15:25:12,989 Collecting packaging>=24.0 2026-06-20T15:25:12,990 Obtaining dependency information for packaging>=24.0 from https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata 2026-06-20T15:25:13,035 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata (3.5 kB) 2026-06-20T15:25:13,223 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB) 2026-06-20T15:25:13,243 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB) 2026-06-20T15:25:13,326 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-06-20T15:25:13,363 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB) 2026-06-20T15:25:13,388 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB) 2026-06-20T15:25:13,475 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-06-20T15:25:16,227 Installing collected packages: setuptools, packaging, wheel 2026-06-20T15:25:19,765 Creating /tmp/pip-build-env-0jk_l45k/overlay/local/bin 2026-06-20T15:25:19,767 changing mode of /tmp/pip-build-env-0jk_l45k/overlay/local/bin/wheel to 755 2026-06-20T15:25:19,788 Successfully installed packaging-26.2 setuptools-82.0.1 wheel-0.47.0 2026-06-20T15:25:20,076 Installing build dependencies: finished with status 'done' 2026-06-20T15:25:20,083 Getting requirements to build wheel: started 2026-06-20T15:25:20,084 Running command Getting requirements to build wheel 2026-06-20T15:25:20,760 running egg_info 2026-06-20T15:25:20,765 writing oncoref.egg-info/PKG-INFO 2026-06-20T15:25:20,771 writing dependency_links to oncoref.egg-info/dependency_links.txt 2026-06-20T15:25:20,772 writing entry points to oncoref.egg-info/entry_points.txt 2026-06-20T15:25:20,775 writing requirements to oncoref.egg-info/requires.txt 2026-06-20T15:25:20,776 writing top-level names to oncoref.egg-info/top_level.txt 2026-06-20T15:25:20,810 reading manifest file 'oncoref.egg-info/SOURCES.txt' 2026-06-20T15:25:20,819 reading manifest template 'MANIFEST.in' 2026-06-20T15:25:20,820 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-06-20T15:25:20,822 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-06-20T15:25:20,823 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-06-20T15:25:20,824 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-06-20T15:25:20,825 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-06-20T15:25:20,826 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-06-20T15:25:20,826 adding license file 'LICENSE' 2026-06-20T15:25:20,834 writing manifest file 'oncoref.egg-info/SOURCES.txt' 2026-06-20T15:25:20,933 Getting requirements to build wheel: finished with status 'done' 2026-06-20T15:25:20,936 Created temporary directory: /tmp/pip-modern-metadata-suau3me2 2026-06-20T15:25:20,938 Preparing metadata (pyproject.toml): started 2026-06-20T15:25:20,939 Running command Preparing metadata (pyproject.toml) 2026-06-20T15:25:21,587 running dist_info 2026-06-20T15:25:21,597 creating /tmp/pip-modern-metadata-suau3me2/oncoref.egg-info 2026-06-20T15:25:21,598 writing /tmp/pip-modern-metadata-suau3me2/oncoref.egg-info/PKG-INFO 2026-06-20T15:25:21,603 writing dependency_links to /tmp/pip-modern-metadata-suau3me2/oncoref.egg-info/dependency_links.txt 2026-06-20T15:25:21,605 writing entry points to /tmp/pip-modern-metadata-suau3me2/oncoref.egg-info/entry_points.txt 2026-06-20T15:25:21,608 writing requirements to /tmp/pip-modern-metadata-suau3me2/oncoref.egg-info/requires.txt 2026-06-20T15:25:21,609 writing top-level names to /tmp/pip-modern-metadata-suau3me2/oncoref.egg-info/top_level.txt 2026-06-20T15:25:21,610 writing manifest file '/tmp/pip-modern-metadata-suau3me2/oncoref.egg-info/SOURCES.txt' 2026-06-20T15:25:21,642 reading manifest file '/tmp/pip-modern-metadata-suau3me2/oncoref.egg-info/SOURCES.txt' 2026-06-20T15:25:21,644 reading manifest template 'MANIFEST.in' 2026-06-20T15:25:21,646 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-06-20T15:25:21,647 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-06-20T15:25:21,648 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-06-20T15:25:21,649 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-06-20T15:25:21,650 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-06-20T15:25:21,651 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-06-20T15:25:21,651 adding license file 'LICENSE' 2026-06-20T15:25:21,657 writing manifest file '/tmp/pip-modern-metadata-suau3me2/oncoref.egg-info/SOURCES.txt' 2026-06-20T15:25:21,658 creating '/tmp/pip-modern-metadata-suau3me2/oncoref-1.8.1.dist-info' 2026-06-20T15:25:21,788 Preparing metadata (pyproject.toml): finished with status 'done' 2026-06-20T15:25:21,793 Source in /tmp/pip-wheel-nvhh8y7s/oncoref_3e36c61af03f482a97595791d1483344 has version 1.8.1, which satisfies requirement oncoref==1.8.1 from https://files.pythonhosted.org/packages/21/3e/8080dbac7eaa58029775dd4937cb7dc70d1e65b52e358ccb75b5dd8ed63e/oncoref-1.8.1.tar.gz 2026-06-20T15:25:21,794 Removed oncoref==1.8.1 from https://files.pythonhosted.org/packages/21/3e/8080dbac7eaa58029775dd4937cb7dc70d1e65b52e358ccb75b5dd8ed63e/oncoref-1.8.1.tar.gz from build tracker '/tmp/pip-build-tracker-nndqtw3_' 2026-06-20T15:25:21,800 Created temporary directory: /tmp/pip-unpack-9prnujm9 2026-06-20T15:25:21,801 Building wheels for collected packages: oncoref 2026-06-20T15:25:21,812 Created temporary directory: /tmp/pip-wheel-nfe0ixab 2026-06-20T15:25:21,812 Destination directory: /tmp/pip-wheel-nfe0ixab 2026-06-20T15:25:21,814 Building wheel for oncoref (pyproject.toml): started 2026-06-20T15:25:21,815 Running command Building wheel for oncoref (pyproject.toml) 2026-06-20T15:25:22,438 running bdist_wheel 2026-06-20T15:25:22,455 running build 2026-06-20T15:25:22,456 running build_py 2026-06-20T15:25:22,463 creating build/lib/oncoref 2026-06-20T15:25:22,465 copying oncoref/expression_registry.py -> build/lib/oncoref 2026-06-20T15:25:22,467 copying oncoref/expression.py -> build/lib/oncoref 2026-06-20T15:25:22,471 copying oncoref/fusions.py -> build/lib/oncoref 2026-06-20T15:25:22,473 copying oncoref/cta_tissues.py -> build/lib/oncoref 2026-06-20T15:25:22,476 copying oncoref/cancer_genes.py -> build/lib/oncoref 2026-06-20T15:25:22,479 copying oncoref/gene_qc.py -> build/lib/oncoref 2026-06-20T15:25:22,481 copying oncoref/normalization.py -> build/lib/oncoref 2026-06-20T15:25:22,484 copying oncoref/expression_engine.py -> build/lib/oncoref 2026-06-20T15:25:22,487 copying oncoref/source_matrices.py -> build/lib/oncoref 2026-06-20T15:25:22,489 copying oncoref/load_dataset.py -> build/lib/oncoref 2026-06-20T15:25:22,491 copying oncoref/data_bundle.py -> build/lib/oncoref 2026-06-20T15:25:22,494 copying oncoref/apd1.py -> build/lib/oncoref 2026-06-20T15:25:22,496 copying oncoref/peptides.py -> build/lib/oncoref 2026-06-20T15:25:22,498 copying oncoref/samples.py -> build/lib/oncoref 2026-06-20T15:25:22,500 copying oncoref/catalog.py -> build/lib/oncoref 2026-06-20T15:25:22,503 copying oncoref/version.py -> build/lib/oncoref 2026-06-20T15:25:22,505 copying oncoref/tmb.py -> build/lib/oncoref 2026-06-20T15:25:22,507 copying oncoref/proteoforms.py -> build/lib/oncoref 2026-06-20T15:25:22,509 copying oncoref/cta_curation_plots.py -> build/lib/oncoref 2026-06-20T15:25:22,512 copying oncoref/reference_data.py -> build/lib/oncoref 2026-06-20T15:25:22,514 copying oncoref/plots.py -> build/lib/oncoref 2026-06-20T15:25:22,517 copying oncoref/__init__.py -> build/lib/oncoref 2026-06-20T15:25:22,519 copying oncoref/expression_builders.py -> build/lib/oncoref 2026-06-20T15:25:22,522 copying oncoref/gene_ids.py -> build/lib/oncoref 2026-06-20T15:25:22,524 copying oncoref/genome.py -> build/lib/oncoref 2026-06-20T15:25:22,527 copying oncoref/coverage.py -> build/lib/oncoref 2026-06-20T15:25:22,530 copying oncoref/data_manifest.py -> build/lib/oncoref 2026-06-20T15:25:22,532 copying oncoref/gene_families.py -> build/lib/oncoref 2026-06-20T15:25:22,535 copying oncoref/cta.py -> build/lib/oncoref 2026-06-20T15:25:22,537 copying oncoref/hpa.py -> build/lib/oncoref 2026-06-20T15:25:22,539 copying oncoref/response_signatures.py -> build/lib/oncoref 2026-06-20T15:25:22,541 copying oncoref/cli.py -> build/lib/oncoref 2026-06-20T15:25:22,544 copying oncoref/ici.py -> build/lib/oncoref 2026-06-20T15:25:22,547 copying oncoref/cancer_types.py -> build/lib/oncoref 2026-06-20T15:25:22,550 copying oncoref/incidence.py -> build/lib/oncoref 2026-06-20T15:25:22,552 copying oncoref/cta_regen.py -> build/lib/oncoref 2026-06-20T15:25:22,566 creating build/lib/oncoref/data 2026-06-20T15:25:22,567 copying oncoref/data/hemoglobin-genes.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,570 copying oncoref/data/nuclear-retained-lncrnas.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,572 copying oncoref/data/cancer-frameshift-burden.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,574 copying oncoref/data/disease-state-rules.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,576 copying oncoref/data/extra-tx-mappings.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,579 copying oncoref/data/cancer-response-signatures.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,581 copying oncoref/data/ensembl-id-aliases.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,591 copying oncoref/data/censored-gene-reference-tpm.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,594 copying oncoref/data/cancer-driver-genes.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,597 copying oncoref/data/fusion-surrogate-expression.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,600 copying oncoref/data/cancer-cohort-aggregates.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,602 copying oncoref/data/cancer-viral-antigens.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,605 copying oncoref/data/cancer-expression-source-candidates.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,608 copying oncoref/data/rrna-and-pseudogenes.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,611 copying oncoref/data/cdna-identical-gene-groups.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,614 copying oncoref/data/cancer-incidence-mortality.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,616 copying oncoref/data/cancer-subtype-groupings.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,619 copying oncoref/data/cancer-fusions.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,622 copying oncoref/data/source-matrices.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,624 copying oncoref/data/proteoform-groups-genome.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,627 copying oncoref/data/cancer-lineage-group-overrides.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,630 copying oncoref/data/cohort-registry.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,633 copying oncoref/data/cancer-type-genes.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,636 copying oncoref/data/histone-genes.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,639 copying oncoref/data/cancer-ici-response-estimates.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,645 copying oncoref/data/cta-ihc-unreliable.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,647 copying oncoref/data/cancer-tmb.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,650 copying oncoref/data/numt-pseudogenes.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,653 copying oncoref/data/cancer-key-genes.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,658 copying oncoref/data/degenerate-subtype-pairs.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,660 copying oncoref/data/cancer-type-registry.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,664 copying oncoref/data/narrative-gene-sets.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,667 copying oncoref/data/cancer-lineage-groups.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,669 copying oncoref/data/housekeeping-genes.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,671 copying oncoref/data/tissue-burden-map.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,682 copying oncoref/data/cancer-driver-variants.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,686 copying oncoref/data/mitochondrial-genes.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,688 copying oncoref/data/ribosomal-protein-pseudogenes.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,692 copying oncoref/data/clean-tpm-censored-genes.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,697 copying oncoref/data/rare-cancer-fusion-rules.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,700 copying oncoref/data/family-burden-map.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,702 copying oncoref/data/cancer-apd1-response.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,706 copying oncoref/data/proteoform-groups.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,708 copying oncoref/data/small-noncoding-rnas.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,714 copying oncoref/data/cancer-ici-response.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,717 copying oncoref/data/cancer-code-burden-map.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,719 copying oncoref/data/fusion-expression-effects.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,722 copying oncoref/data/proteoform-collapse-overrides.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,725 copying oncoref/data/cta-candidate-references.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,727 copying oncoref/data/cancer-testis-antigens.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,732 copying oncoref/data/ribosomal-protein-genes.csv -> build/lib/oncoref/data 2026-06-20T15:25:22,734 copying oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/lib/oncoref/data 2026-06-20T15:25:22,742 copying oncoref/data/cancer-reference-expression-samples.csv.gz -> build/lib/oncoref/data 2026-06-20T15:25:22,749 copying oncoref/data/canonical-gene-space.csv.gz -> build/lib/oncoref/data 2026-06-20T15:25:22,761 copying oncoref/data/expression_sources.yaml -> build/lib/oncoref/data 2026-06-20T15:25:22,774 installing to build/bdist.linux-armv7l/wheel 2026-06-20T15:25:22,775 running install 2026-06-20T15:25:22,798 running install_lib 2026-06-20T15:25:22,804 creating build/bdist.linux-armv7l/wheel 2026-06-20T15:25:22,807 creating build/bdist.linux-armv7l/wheel/oncoref 2026-06-20T15:25:22,809 copying build/lib/oncoref/expression_registry.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:22,811 copying build/lib/oncoref/expression.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:22,815 copying build/lib/oncoref/fusions.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:22,818 copying build/lib/oncoref/cta_tissues.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:22,820 copying build/lib/oncoref/cancer_genes.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:22,822 copying build/lib/oncoref/gene_qc.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:22,825 copying build/lib/oncoref/normalization.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:22,828 copying build/lib/oncoref/expression_engine.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:22,830 copying build/lib/oncoref/source_matrices.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:22,833 copying build/lib/oncoref/load_dataset.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:22,835 copying build/lib/oncoref/data_bundle.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:22,838 copying build/lib/oncoref/apd1.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:22,840 copying build/lib/oncoref/peptides.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:22,843 copying build/lib/oncoref/samples.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:22,845 copying build/lib/oncoref/catalog.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:22,848 copying build/lib/oncoref/version.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:22,850 copying build/lib/oncoref/tmb.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:22,852 copying build/lib/oncoref/proteoforms.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:22,855 copying build/lib/oncoref/cta_curation_plots.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:22,858 copying build/lib/oncoref/reference_data.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:22,860 copying build/lib/oncoref/plots.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:22,863 copying build/lib/oncoref/__init__.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:22,866 copying build/lib/oncoref/expression_builders.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:22,870 creating build/bdist.linux-armv7l/wheel/oncoref/data 2026-06-20T15:25:22,871 copying build/lib/oncoref/data/hemoglobin-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,873 copying build/lib/oncoref/data/nuclear-retained-lncrnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,875 copying build/lib/oncoref/data/cancer-frameshift-burden.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,877 copying build/lib/oncoref/data/disease-state-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,880 copying build/lib/oncoref/data/extra-tx-mappings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,882 copying build/lib/oncoref/data/cancer-response-signatures.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,885 copying build/lib/oncoref/data/ensembl-id-aliases.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,893 copying build/lib/oncoref/data/censored-gene-reference-tpm.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,896 copying build/lib/oncoref/data/cancer-driver-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,899 copying build/lib/oncoref/data/fusion-surrogate-expression.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,902 copying build/lib/oncoref/data/cancer-cohort-aggregates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,905 copying build/lib/oncoref/data/cancer-viral-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,907 copying build/lib/oncoref/data/cancer-expression-source-candidates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,910 copying build/lib/oncoref/data/rrna-and-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,913 copying build/lib/oncoref/data/cdna-identical-gene-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,916 copying build/lib/oncoref/data/cancer-incidence-mortality.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,918 copying build/lib/oncoref/data/cancer-subtype-groupings.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,920 copying build/lib/oncoref/data/cancer-fusions.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,923 copying build/lib/oncoref/data/source-matrices.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,926 copying build/lib/oncoref/data/proteoform-groups-genome.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,928 copying build/lib/oncoref/data/cancer-lineage-group-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,931 copying build/lib/oncoref/data/ncbi-symbol-synonyms.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,939 copying build/lib/oncoref/data/cohort-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,942 copying build/lib/oncoref/data/cancer-type-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,944 copying build/lib/oncoref/data/cancer-reference-expression-samples.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,950 copying build/lib/oncoref/data/histone-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,953 copying build/lib/oncoref/data/cancer-ici-response-estimates.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,960 copying build/lib/oncoref/data/cta-ihc-unreliable.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,962 copying build/lib/oncoref/data/cancer-tmb.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,964 copying build/lib/oncoref/data/numt-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,967 copying build/lib/oncoref/data/cancer-key-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,972 copying build/lib/oncoref/data/degenerate-subtype-pairs.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,975 copying build/lib/oncoref/data/cancer-type-registry.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,978 copying build/lib/oncoref/data/expression_sources.yaml -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,981 copying build/lib/oncoref/data/canonical-gene-space.csv.gz -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,995 copying build/lib/oncoref/data/narrative-gene-sets.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,997 copying build/lib/oncoref/data/cancer-lineage-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:22,999 copying build/lib/oncoref/data/housekeeping-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:23,002 copying build/lib/oncoref/data/tissue-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:23,004 copying build/lib/oncoref/data/cancer-driver-variants.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:23,007 copying build/lib/oncoref/data/mitochondrial-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:23,009 copying build/lib/oncoref/data/ribosomal-protein-pseudogenes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:23,012 copying build/lib/oncoref/data/clean-tpm-censored-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:23,018 copying build/lib/oncoref/data/rare-cancer-fusion-rules.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:23,021 copying build/lib/oncoref/data/family-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:23,023 copying build/lib/oncoref/data/cancer-apd1-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:23,026 copying build/lib/oncoref/data/proteoform-groups.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:23,028 copying build/lib/oncoref/data/small-noncoding-rnas.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:23,034 copying build/lib/oncoref/data/cancer-ici-response.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:23,037 copying build/lib/oncoref/data/cancer-code-burden-map.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:23,039 copying build/lib/oncoref/data/fusion-expression-effects.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:23,041 copying build/lib/oncoref/data/proteoform-collapse-overrides.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:23,043 copying build/lib/oncoref/data/cta-candidate-references.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:23,045 copying build/lib/oncoref/data/cancer-testis-antigens.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:23,050 copying build/lib/oncoref/data/ribosomal-protein-genes.csv -> build/bdist.linux-armv7l/wheel/./oncoref/data 2026-06-20T15:25:23,053 copying build/lib/oncoref/gene_ids.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:23,055 copying build/lib/oncoref/genome.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:23,058 copying build/lib/oncoref/coverage.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:23,061 copying build/lib/oncoref/data_manifest.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:23,064 copying build/lib/oncoref/gene_families.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:23,066 copying build/lib/oncoref/cta.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:23,069 copying build/lib/oncoref/hpa.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:23,071 copying build/lib/oncoref/response_signatures.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:23,073 copying build/lib/oncoref/cli.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:23,076 copying build/lib/oncoref/ici.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:23,079 copying build/lib/oncoref/cancer_types.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:23,082 copying build/lib/oncoref/incidence.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:23,085 copying build/lib/oncoref/cta_regen.py -> build/bdist.linux-armv7l/wheel/./oncoref 2026-06-20T15:25:23,088 running install_egg_info 2026-06-20T15:25:23,097 running egg_info 2026-06-20T15:25:23,102 writing oncoref.egg-info/PKG-INFO 2026-06-20T15:25:23,108 writing dependency_links to oncoref.egg-info/dependency_links.txt 2026-06-20T15:25:23,110 writing entry points to oncoref.egg-info/entry_points.txt 2026-06-20T15:25:23,112 writing requirements to oncoref.egg-info/requires.txt 2026-06-20T15:25:23,114 writing top-level names to oncoref.egg-info/top_level.txt 2026-06-20T15:25:23,132 reading manifest file 'oncoref.egg-info/SOURCES.txt' 2026-06-20T15:25:23,141 reading manifest template 'MANIFEST.in' 2026-06-20T15:25:23,143 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression' 2026-06-20T15:25:23,144 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-percentiles' 2026-06-20T15:25:23,146 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-representatives' 2026-06-20T15:25:23,147 warning: no previously-included files matching '*' found under directory 'oncoref/data/cancer-reference-expression-within-sample-top5' 2026-06-20T15:25:23,149 warning: no previously-included files found matching 'oncoref/data/pan-cancer-expression.csv' 2026-06-20T15:25:23,150 warning: no previously-included files found matching 'oncoref/data/hpa-cell-type-expression.csv' 2026-06-20T15:25:23,150 adding license file 'LICENSE' 2026-06-20T15:25:23,158 writing manifest file 'oncoref.egg-info/SOURCES.txt' 2026-06-20T15:25:23,160 Copying oncoref.egg-info to build/bdist.linux-armv7l/wheel/./oncoref-1.8.1-py3.11.egg-info 2026-06-20T15:25:23,172 running install_scripts 2026-06-20T15:25:23,185 creating build/bdist.linux-armv7l/wheel/oncoref-1.8.1.dist-info/WHEEL 2026-06-20T15:25:23,188 creating '/tmp/pip-wheel-nfe0ixab/.tmp-3hggqy9t/oncoref-1.8.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-06-20T15:25:23,192 adding 'oncoref/__init__.py' 2026-06-20T15:25:23,193 adding 'oncoref/apd1.py' 2026-06-20T15:25:23,195 adding 'oncoref/cancer_genes.py' 2026-06-20T15:25:23,200 adding 'oncoref/cancer_types.py' 2026-06-20T15:25:23,203 adding 'oncoref/catalog.py' 2026-06-20T15:25:23,207 adding 'oncoref/cli.py' 2026-06-20T15:25:23,210 adding 'oncoref/coverage.py' 2026-06-20T15:25:23,213 adding 'oncoref/cta.py' 2026-06-20T15:25:23,215 adding 'oncoref/cta_curation_plots.py' 2026-06-20T15:25:23,219 adding 'oncoref/cta_regen.py' 2026-06-20T15:25:23,221 adding 'oncoref/cta_tissues.py' 2026-06-20T15:25:23,223 adding 'oncoref/data_bundle.py' 2026-06-20T15:25:23,226 adding 'oncoref/data_manifest.py' 2026-06-20T15:25:23,234 adding 'oncoref/expression.py' 2026-06-20T15:25:23,237 adding 'oncoref/expression_builders.py' 2026-06-20T15:25:23,239 adding 'oncoref/expression_engine.py' 2026-06-20T15:25:23,241 adding 'oncoref/expression_registry.py' 2026-06-20T15:25:23,244 adding 'oncoref/fusions.py' 2026-06-20T15:25:23,246 adding 'oncoref/gene_families.py' 2026-06-20T15:25:23,248 adding 'oncoref/gene_ids.py' 2026-06-20T15:25:23,250 adding 'oncoref/gene_qc.py' 2026-06-20T15:25:23,252 adding 'oncoref/genome.py' 2026-06-20T15:25:23,254 adding 'oncoref/hpa.py' 2026-06-20T15:25:23,258 adding 'oncoref/ici.py' 2026-06-20T15:25:23,260 adding 'oncoref/incidence.py' 2026-06-20T15:25:23,262 adding 'oncoref/load_dataset.py' 2026-06-20T15:25:23,266 adding 'oncoref/normalization.py' 2026-06-20T15:25:23,268 adding 'oncoref/peptides.py' 2026-06-20T15:25:23,275 adding 'oncoref/plots.py' 2026-06-20T15:25:23,279 adding 'oncoref/proteoforms.py' 2026-06-20T15:25:23,281 adding 'oncoref/reference_data.py' 2026-06-20T15:25:23,283 adding 'oncoref/response_signatures.py' 2026-06-20T15:25:23,285 adding 'oncoref/samples.py' 2026-06-20T15:25:23,287 adding 'oncoref/source_matrices.py' 2026-06-20T15:25:23,289 adding 'oncoref/tmb.py' 2026-06-20T15:25:23,290 adding 'oncoref/version.py' 2026-06-20T15:25:23,294 adding 'oncoref/data/cancer-apd1-response.csv' 2026-06-20T15:25:23,296 adding 'oncoref/data/cancer-code-burden-map.csv' 2026-06-20T15:25:23,297 adding 'oncoref/data/cancer-cohort-aggregates.csv' 2026-06-20T15:25:23,303 adding 'oncoref/data/cancer-driver-genes.csv' 2026-06-20T15:25:23,306 adding 'oncoref/data/cancer-driver-variants.csv' 2026-06-20T15:25:23,308 adding 'oncoref/data/cancer-expression-source-candidates.csv' 2026-06-20T15:25:23,310 adding 'oncoref/data/cancer-frameshift-burden.csv' 2026-06-20T15:25:23,314 adding 'oncoref/data/cancer-fusions.csv' 2026-06-20T15:25:23,331 adding 'oncoref/data/cancer-ici-response-estimates.csv' 2026-06-20T15:25:23,336 adding 'oncoref/data/cancer-ici-response.csv' 2026-06-20T15:25:23,338 adding 'oncoref/data/cancer-incidence-mortality.csv' 2026-06-20T15:25:23,353 adding 'oncoref/data/cancer-key-genes.csv' 2026-06-20T15:25:23,355 adding 'oncoref/data/cancer-lineage-group-overrides.csv' 2026-06-20T15:25:23,356 adding 'oncoref/data/cancer-lineage-groups.csv' 2026-06-20T15:25:23,385 adding 'oncoref/data/cancer-reference-expression-samples.csv.gz' 2026-06-20T15:25:23,388 adding 'oncoref/data/cancer-response-signatures.csv' 2026-06-20T15:25:23,389 adding 'oncoref/data/cancer-subtype-groupings.csv' 2026-06-20T15:25:23,400 adding 'oncoref/data/cancer-testis-antigens.csv' 2026-06-20T15:25:23,403 adding 'oncoref/data/cancer-tmb.csv' 2026-06-20T15:25:23,406 adding 'oncoref/data/cancer-type-genes.csv' 2026-06-20T15:25:23,409 adding 'oncoref/data/cancer-type-registry.csv' 2026-06-20T15:25:23,411 adding 'oncoref/data/cancer-viral-antigens.csv' 2026-06-20T15:25:23,464 adding 'oncoref/data/canonical-gene-space.csv.gz' 2026-06-20T15:25:23,469 adding 'oncoref/data/cdna-identical-gene-groups.csv' 2026-06-20T15:25:23,473 adding 'oncoref/data/censored-gene-reference-tpm.csv' 2026-06-20T15:25:23,483 adding 'oncoref/data/clean-tpm-censored-genes.csv' 2026-06-20T15:25:23,486 adding 'oncoref/data/cohort-registry.csv' 2026-06-20T15:25:23,487 adding 'oncoref/data/cta-candidate-references.csv' 2026-06-20T15:25:23,488 adding 'oncoref/data/cta-ihc-unreliable.csv' 2026-06-20T15:25:23,490 adding 'oncoref/data/degenerate-subtype-pairs.csv' 2026-06-20T15:25:23,491 adding 'oncoref/data/disease-state-rules.csv' 2026-06-20T15:25:23,518 adding 'oncoref/data/ensembl-id-aliases.csv' 2026-06-20T15:25:23,524 adding 'oncoref/data/expression_sources.yaml' 2026-06-20T15:25:23,525 adding 'oncoref/data/extra-tx-mappings.csv' 2026-06-20T15:25:23,527 adding 'oncoref/data/family-burden-map.csv' 2026-06-20T15:25:23,528 adding 'oncoref/data/fusion-expression-effects.csv' 2026-06-20T15:25:23,530 adding 'oncoref/data/fusion-surrogate-expression.csv' 2026-06-20T15:25:23,531 adding 'oncoref/data/hemoglobin-genes.csv' 2026-06-20T15:25:23,532 adding 'oncoref/data/histone-genes.csv' 2026-06-20T15:25:23,533 adding 'oncoref/data/housekeeping-genes.csv' 2026-06-20T15:25:23,534 adding 'oncoref/data/mitochondrial-genes.csv' 2026-06-20T15:25:23,535 adding 'oncoref/data/narrative-gene-sets.csv' 2026-06-20T15:25:23,576 adding 'oncoref/data/ncbi-symbol-synonyms.csv.gz' 2026-06-20T15:25:23,579 adding 'oncoref/data/nuclear-retained-lncrnas.csv' 2026-06-20T15:25:23,581 adding 'oncoref/data/numt-pseudogenes.csv' 2026-06-20T15:25:23,582 adding 'oncoref/data/proteoform-collapse-overrides.csv' 2026-06-20T15:25:23,585 adding 'oncoref/data/proteoform-groups-genome.csv' 2026-06-20T15:25:23,586 adding 'oncoref/data/proteoform-groups.csv' 2026-06-20T15:25:23,588 adding 'oncoref/data/rare-cancer-fusion-rules.csv' 2026-06-20T15:25:23,589 adding 'oncoref/data/ribosomal-protein-genes.csv' 2026-06-20T15:25:23,596 adding 'oncoref/data/ribosomal-protein-pseudogenes.csv' 2026-06-20T15:25:23,598 adding 'oncoref/data/rrna-and-pseudogenes.csv' 2026-06-20T15:25:23,617 adding 'oncoref/data/small-noncoding-rnas.csv' 2026-06-20T15:25:23,619 adding 'oncoref/data/source-matrices.csv' 2026-06-20T15:25:23,620 adding 'oncoref/data/tissue-burden-map.csv' 2026-06-20T15:25:23,624 adding 'oncoref-1.8.1.dist-info/licenses/LICENSE' 2026-06-20T15:25:23,626 adding 'oncoref-1.8.1.dist-info/METADATA' 2026-06-20T15:25:23,627 adding 'oncoref-1.8.1.dist-info/WHEEL' 2026-06-20T15:25:23,628 adding 'oncoref-1.8.1.dist-info/entry_points.txt' 2026-06-20T15:25:23,629 adding 'oncoref-1.8.1.dist-info/top_level.txt' 2026-06-20T15:25:23,630 adding 'oncoref-1.8.1.dist-info/RECORD' 2026-06-20T15:25:23,660 removing build/bdist.linux-armv7l/wheel 2026-06-20T15:25:23,782 Building wheel for oncoref (pyproject.toml): finished with status 'done' 2026-06-20T15:25:23,826 Created wheel for oncoref: filename=oncoref-1.8.1-py3-none-any.whl size=1634863 sha256=12f0eb28c115080796010095a4032b844d9ea4383bc0ea2e2b75a3e5f21c9392 2026-06-20T15:25:23,827 Stored in directory: /tmp/pip-ephem-wheel-cache-86be343o/wheels/ab/92/e0/13c64a4cf2c9505a60617398ca32496c9ec8680b65f375859b 2026-06-20T15:25:23,842 Successfully built oncoref 2026-06-20T15:25:23,890 Removed build tracker: '/tmp/pip-build-tracker-nndqtw3_'