2025-12-11T03:52:03,115 Created temporary directory: /tmp/pip-ephem-wheel-cache-isl6p253
2025-12-11T03:52:03,117 Created temporary directory: /tmp/pip-build-tracker-l07j542s
2025-12-11T03:52:03,118 Initialized build tracking at /tmp/pip-build-tracker-l07j542s
2025-12-11T03:52:03,118 Created build tracker: /tmp/pip-build-tracker-l07j542s
2025-12-11T03:52:03,119 Entered build tracker: /tmp/pip-build-tracker-l07j542s
2025-12-11T03:52:03,120 Created temporary directory: /tmp/pip-wheel-cy335btf
2025-12-11T03:52:03,122 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
2025-12-11T03:52:03,125 Created temporary directory: /tmp/pip-ephem-wheel-cache-lfyng6r_
2025-12-11T03:52:03,146 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-12-11T03:52:03,150 2 location(s) to search for versions of ragbio:
2025-12-11T03:52:03,150 * https://pypi.org/simple/ragbio/
2025-12-11T03:52:03,150 * https://www.piwheels.org/simple/ragbio/
2025-12-11T03:52:03,151 Fetching project page and analyzing links: https://pypi.org/simple/ragbio/
2025-12-11T03:52:03,151 Getting page https://pypi.org/simple/ragbio/
2025-12-11T03:52:03,153 Found index url https://pypi.org/simple
2025-12-11T03:52:03,365 Fetched page https://pypi.org/simple/ragbio/ as application/vnd.pypi.simple.v1+json
2025-12-11T03:52:03,366   Skipping link: No binaries permitted for ragbio: https://files.pythonhosted.org/packages/49/ef/b76938c77f3c7b1ea66f2f25e49ae4b169e1f8050de61183a14e6ac4d4fe/ragbio-0.1.12-py3-none-any.whl (from https://pypi.org/simple/ragbio/) (requires-python:>=3.9)
2025-12-11T03:52:03,367   Found link https://files.pythonhosted.org/packages/34/53/62f7f4e6ea6e004f8ef0bcfe3006736331f55847fa6dea5ab395b84f1663/ragbio-0.1.12.tar.gz (from https://pypi.org/simple/ragbio/) (requires-python:>=3.9), version: 0.1.12
2025-12-11T03:52:03,368 Fetching project page and analyzing links: https://www.piwheels.org/simple/ragbio/
2025-12-11T03:52:03,369 Getting page https://www.piwheels.org/simple/ragbio/
2025-12-11T03:52:03,370 Found index url https://www.piwheels.org/simple
2025-12-11T03:52:03,527 Fetched page https://www.piwheels.org/simple/ragbio/ as text/html
2025-12-11T03:52:03,528 Skipping link: not a file: https://www.piwheels.org/simple/ragbio/
2025-12-11T03:52:03,528 Skipping link: not a file: https://pypi.org/simple/ragbio/
2025-12-11T03:52:03,547 Given no hashes to check 1 links for project 'ragbio': discarding no candidates
2025-12-11T03:52:03,565 Collecting ragbio==0.1.12
2025-12-11T03:52:03,567   Created temporary directory: /tmp/pip-unpack-thznpy0r
2025-12-11T03:52:03,777   Downloading ragbio-0.1.12.tar.gz (315 kB)
2025-12-11T03:52:03,934   Added ragbio==0.1.12 from https://files.pythonhosted.org/packages/34/53/62f7f4e6ea6e004f8ef0bcfe3006736331f55847fa6dea5ab395b84f1663/ragbio-0.1.12.tar.gz to build tracker '/tmp/pip-build-tracker-l07j542s'
2025-12-11T03:52:03,939   Created temporary directory: /tmp/pip-build-env-dltqr6yc
2025-12-11T03:52:03,943   Installing build dependencies: started
2025-12-11T03:52:03,945   Running command pip subprocess to install build dependencies
2025-12-11T03:52:05,081   Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11)
2025-12-11T03:52:05,686   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
2025-12-11T03:52:05,711   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-12-11T03:52:07,450   Collecting setuptools>=61.0
2025-12-11T03:52:07,546     Using cached https://www.piwheels.org/simple/setuptools/setuptools-80.9.0-py3-none-any.whl (1.2 MB)
2025-12-11T03:52:07,812   Collecting wheel
2025-12-11T03:52:07,828     Using cached https://www.piwheels.org/simple/wheel/wheel-0.45.1-py3-none-any.whl (72 kB)
2025-12-11T03:52:10,741   Installing collected packages: wheel, setuptools
2025-12-11T03:52:10,984     Creating /tmp/pip-build-env-dltqr6yc/overlay/local/bin
2025-12-11T03:52:10,986     changing mode of /tmp/pip-build-env-dltqr6yc/overlay/local/bin/wheel to 755
2025-12-11T03:52:14,657   Successfully installed setuptools-80.9.0 wheel-0.45.1
2025-12-11T03:52:14,929   Installing build dependencies: finished with status 'done'
2025-12-11T03:52:14,936   Getting requirements to build wheel: started
2025-12-11T03:52:14,937   Running command Getting requirements to build wheel
2025-12-11T03:52:15,541   /tmp/pip-build-env-dltqr6yc/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
2025-12-11T03:52:15,541   !!

2025-12-11T03:52:15,543           ********************************************************************************
2025-12-11T03:52:15,543           Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0).

2025-12-11T03:52:15,544           By 2026-Feb-18, you need to update your project and remove deprecated calls
2025-12-11T03:52:15,544           or your builds will no longer be supported.

2025-12-11T03:52:15,546           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-12-11T03:52:15,546           ********************************************************************************

2025-12-11T03:52:15,547   !!
2025-12-11T03:52:15,548     corresp(dist, value, root_dir)
2025-12-11T03:52:15,633   running egg_info
2025-12-11T03:52:15,640   writing ragbio.egg-info/PKG-INFO
2025-12-11T03:52:15,643   writing dependency_links to ragbio.egg-info/dependency_links.txt
2025-12-11T03:52:15,646   writing requirements to ragbio.egg-info/requires.txt
2025-12-11T03:52:15,647   writing top-level names to ragbio.egg-info/top_level.txt
2025-12-11T03:52:15,675   reading manifest file 'ragbio.egg-info/SOURCES.txt'
2025-12-11T03:52:15,678   reading manifest template 'MANIFEST.in'
2025-12-11T03:52:15,679   adding license file 'LICENSE'
2025-12-11T03:52:15,683   writing manifest file 'ragbio.egg-info/SOURCES.txt'
2025-12-11T03:52:15,779   Getting requirements to build wheel: finished with status 'done'
2025-12-11T03:52:15,783   Created temporary directory: /tmp/pip-modern-metadata-r71q2j2b
2025-12-11T03:52:15,785   Preparing metadata (pyproject.toml): started
2025-12-11T03:52:15,786   Running command Preparing metadata (pyproject.toml)
2025-12-11T03:52:16,367   /tmp/pip-build-env-dltqr6yc/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
2025-12-11T03:52:16,367   !!

2025-12-11T03:52:16,369           ********************************************************************************
2025-12-11T03:52:16,369           Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0).

2025-12-11T03:52:16,370           By 2026-Feb-18, you need to update your project and remove deprecated calls
2025-12-11T03:52:16,371           or your builds will no longer be supported.

2025-12-11T03:52:16,372           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-12-11T03:52:16,373           ********************************************************************************

2025-12-11T03:52:16,374   !!
2025-12-11T03:52:16,375     corresp(dist, value, root_dir)
2025-12-11T03:52:16,461   running dist_info
2025-12-11T03:52:16,474   creating /tmp/pip-modern-metadata-r71q2j2b/ragbio.egg-info
2025-12-11T03:52:16,475   writing /tmp/pip-modern-metadata-r71q2j2b/ragbio.egg-info/PKG-INFO
2025-12-11T03:52:16,478   writing dependency_links to /tmp/pip-modern-metadata-r71q2j2b/ragbio.egg-info/dependency_links.txt
2025-12-11T03:52:16,480   writing requirements to /tmp/pip-modern-metadata-r71q2j2b/ragbio.egg-info/requires.txt
2025-12-11T03:52:16,481   writing top-level names to /tmp/pip-modern-metadata-r71q2j2b/ragbio.egg-info/top_level.txt
2025-12-11T03:52:16,483   writing manifest file '/tmp/pip-modern-metadata-r71q2j2b/ragbio.egg-info/SOURCES.txt'
2025-12-11T03:52:16,509   reading manifest file '/tmp/pip-modern-metadata-r71q2j2b/ragbio.egg-info/SOURCES.txt'
2025-12-11T03:52:16,511   reading manifest template 'MANIFEST.in'
2025-12-11T03:52:16,512   adding license file 'LICENSE'
2025-12-11T03:52:16,515   writing manifest file '/tmp/pip-modern-metadata-r71q2j2b/ragbio.egg-info/SOURCES.txt'
2025-12-11T03:52:16,516   creating '/tmp/pip-modern-metadata-r71q2j2b/ragbio-0.1.12.dist-info'
2025-12-11T03:52:16,638   Preparing metadata (pyproject.toml): finished with status 'done'
2025-12-11T03:52:16,643   Source in /tmp/pip-wheel-cy335btf/ragbio_191c864c52a641de9741e335accaa428 has version 0.1.12, which satisfies requirement ragbio==0.1.12 from https://files.pythonhosted.org/packages/34/53/62f7f4e6ea6e004f8ef0bcfe3006736331f55847fa6dea5ab395b84f1663/ragbio-0.1.12.tar.gz
2025-12-11T03:52:16,644   Removed ragbio==0.1.12 from https://files.pythonhosted.org/packages/34/53/62f7f4e6ea6e004f8ef0bcfe3006736331f55847fa6dea5ab395b84f1663/ragbio-0.1.12.tar.gz from build tracker '/tmp/pip-build-tracker-l07j542s'
2025-12-11T03:52:16,650 Created temporary directory: /tmp/pip-unpack-tks9d5w7
2025-12-11T03:52:16,651 Building wheels for collected packages: ragbio
2025-12-11T03:52:16,655   Created temporary directory: /tmp/pip-wheel-2cetylfb
2025-12-11T03:52:16,656   Destination directory: /tmp/pip-wheel-2cetylfb
2025-12-11T03:52:16,658   Building wheel for ragbio (pyproject.toml): started
2025-12-11T03:52:16,659   Running command Building wheel for ragbio (pyproject.toml)
2025-12-11T03:52:17,212   /tmp/pip-build-env-dltqr6yc/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
2025-12-11T03:52:17,212   !!

2025-12-11T03:52:17,214           ********************************************************************************
2025-12-11T03:52:17,214           Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0).

2025-12-11T03:52:17,215           By 2026-Feb-18, you need to update your project and remove deprecated calls
2025-12-11T03:52:17,216           or your builds will no longer be supported.

2025-12-11T03:52:17,217           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-12-11T03:52:17,218           ********************************************************************************

2025-12-11T03:52:17,219   !!
2025-12-11T03:52:17,219     corresp(dist, value, root_dir)
2025-12-11T03:52:17,297   running bdist_wheel
2025-12-11T03:52:17,319   running build
2025-12-11T03:52:17,320   running build_py
2025-12-11T03:52:17,327   creating build/lib/ragbio
2025-12-11T03:52:17,330   copying ragbio/__init__.py -> build/lib/ragbio
2025-12-11T03:52:17,333   copying ragbio/config.py -> build/lib/ragbio
2025-12-11T03:52:17,335   creating build/lib/ragbio/pipeline
2025-12-11T03:52:17,337   copying ragbio/pipeline/rag_pipeline.py -> build/lib/ragbio/pipeline
2025-12-11T03:52:17,339   copying ragbio/pipeline/rag_cytoscape_streamlit.py -> build/lib/ragbio/pipeline
2025-12-11T03:52:17,342   copying ragbio/pipeline/rag_neo4j_visualization.py -> build/lib/ragbio/pipeline
2025-12-11T03:52:17,345   creating build/lib/ragbio/embeddings
2025-12-11T03:52:17,346   copying ragbio/embeddings/__init__.py -> build/lib/ragbio/embeddings
2025-12-11T03:52:17,348   copying ragbio/embeddings/embedding_engine.py -> build/lib/ragbio/embeddings
2025-12-11T03:52:17,351   creating build/lib/ragbio/knowledge_graph
2025-12-11T03:52:17,352   copying ragbio/knowledge_graph/structured_drug_kg.py -> build/lib/ragbio/knowledge_graph
2025-12-11T03:52:17,356   creating build/lib/ragbio/utils
2025-12-11T03:52:17,357   copying ragbio/utils/data_loader.py -> build/lib/ragbio/utils
2025-12-11T03:52:17,359   copying ragbio/utils/update_config.py -> build/lib/ragbio/utils
2025-12-11T03:52:17,362   copying ragbio/utils/__init__.py -> build/lib/ragbio/utils
2025-12-11T03:52:17,363   copying ragbio/utils/delete_neo4j_graph.py -> build/lib/ragbio/utils
2025-12-11T03:52:17,365   running egg_info
2025-12-11T03:52:17,377   writing ragbio.egg-info/PKG-INFO
2025-12-11T03:52:17,380   writing dependency_links to ragbio.egg-info/dependency_links.txt
2025-12-11T03:52:17,381   writing requirements to ragbio.egg-info/requires.txt
2025-12-11T03:52:17,382   writing top-level names to ragbio.egg-info/top_level.txt
2025-12-11T03:52:17,397   reading manifest file 'ragbio.egg-info/SOURCES.txt'
2025-12-11T03:52:17,400   reading manifest template 'MANIFEST.in'
2025-12-11T03:52:17,401   adding license file 'LICENSE'
2025-12-11T03:52:17,405   writing manifest file 'ragbio.egg-info/SOURCES.txt'
2025-12-11T03:52:17,410   creating build/lib/ragbio/images
2025-12-11T03:52:17,411   copying ragbio/images/network_graph.png -> build/lib/ragbio/images
2025-12-11T03:52:17,431   installing to build/bdist.linux-armv7l/wheel
2025-12-11T03:52:17,432   running install
2025-12-11T03:52:17,456   running install_lib
2025-12-11T03:52:17,463   creating build/bdist.linux-armv7l/wheel
2025-12-11T03:52:17,465   creating build/bdist.linux-armv7l/wheel/ragbio
2025-12-11T03:52:17,467   creating build/bdist.linux-armv7l/wheel/ragbio/pipeline
2025-12-11T03:52:17,469   copying build/lib/ragbio/pipeline/rag_pipeline.py -> build/bdist.linux-armv7l/wheel/./ragbio/pipeline
2025-12-11T03:52:17,472   copying build/lib/ragbio/pipeline/rag_cytoscape_streamlit.py -> build/bdist.linux-armv7l/wheel/./ragbio/pipeline
2025-12-11T03:52:17,475   copying build/lib/ragbio/pipeline/rag_neo4j_visualization.py -> build/bdist.linux-armv7l/wheel/./ragbio/pipeline
2025-12-11T03:52:17,478   creating build/bdist.linux-armv7l/wheel/ragbio/embeddings
2025-12-11T03:52:17,480   copying build/lib/ragbio/embeddings/__init__.py -> build/bdist.linux-armv7l/wheel/./ragbio/embeddings
2025-12-11T03:52:17,482   copying build/lib/ragbio/embeddings/embedding_engine.py -> build/bdist.linux-armv7l/wheel/./ragbio/embeddings
2025-12-11T03:52:17,485   creating build/bdist.linux-armv7l/wheel/ragbio/knowledge_graph
2025-12-11T03:52:17,487   copying build/lib/ragbio/knowledge_graph/structured_drug_kg.py -> build/bdist.linux-armv7l/wheel/./ragbio/knowledge_graph
2025-12-11T03:52:17,490   creating build/bdist.linux-armv7l/wheel/ragbio/images
2025-12-11T03:52:17,492   copying build/lib/ragbio/images/network_graph.png -> build/bdist.linux-armv7l/wheel/./ragbio/images
2025-12-11T03:52:17,501   copying build/lib/ragbio/__init__.py -> build/bdist.linux-armv7l/wheel/./ragbio
2025-12-11T03:52:17,503   copying build/lib/ragbio/config.py -> build/bdist.linux-armv7l/wheel/./ragbio
2025-12-11T03:52:17,506   creating build/bdist.linux-armv7l/wheel/ragbio/utils
2025-12-11T03:52:17,508   copying build/lib/ragbio/utils/data_loader.py -> build/bdist.linux-armv7l/wheel/./ragbio/utils
2025-12-11T03:52:17,511   copying build/lib/ragbio/utils/update_config.py -> build/bdist.linux-armv7l/wheel/./ragbio/utils
2025-12-11T03:52:17,513   copying build/lib/ragbio/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./ragbio/utils
2025-12-11T03:52:17,515   copying build/lib/ragbio/utils/delete_neo4j_graph.py -> build/bdist.linux-armv7l/wheel/./ragbio/utils
2025-12-11T03:52:17,517   running install_egg_info
2025-12-11T03:52:17,523   Copying ragbio.egg-info to build/bdist.linux-armv7l/wheel/./ragbio-0.1.12-py3.11.egg-info
2025-12-11T03:52:17,533   running install_scripts
2025-12-11T03:52:17,542   creating build/bdist.linux-armv7l/wheel/ragbio-0.1.12.dist-info/WHEEL
2025-12-11T03:52:17,545   creating '/tmp/pip-wheel-2cetylfb/.tmp-6_x5bvbr/ragbio-0.1.12-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-12-11T03:52:17,548   adding 'ragbio/__init__.py'
2025-12-11T03:52:17,550   adding 'ragbio/config.py'
2025-12-11T03:52:17,552   adding 'ragbio/embeddings/__init__.py'
2025-12-11T03:52:17,553   adding 'ragbio/embeddings/embedding_engine.py'
2025-12-11T03:52:17,587   adding 'ragbio/images/network_graph.png'
2025-12-11T03:52:17,590   adding 'ragbio/knowledge_graph/structured_drug_kg.py'
2025-12-11T03:52:17,592   adding 'ragbio/pipeline/rag_cytoscape_streamlit.py'
2025-12-11T03:52:17,594   adding 'ragbio/pipeline/rag_neo4j_visualization.py'
2025-12-11T03:52:17,596   adding 'ragbio/pipeline/rag_pipeline.py'
2025-12-11T03:52:17,598   adding 'ragbio/utils/__init__.py'
2025-12-11T03:52:17,599   adding 'ragbio/utils/data_loader.py'
2025-12-11T03:52:17,601   adding 'ragbio/utils/delete_neo4j_graph.py'
2025-12-11T03:52:17,602   adding 'ragbio/utils/update_config.py'
2025-12-11T03:52:17,604   adding 'ragbio-0.1.12.dist-info/licenses/LICENSE'
2025-12-11T03:52:17,605   adding 'ragbio-0.1.12.dist-info/METADATA'
2025-12-11T03:52:17,606   adding 'ragbio-0.1.12.dist-info/WHEEL'
2025-12-11T03:52:17,607   adding 'ragbio-0.1.12.dist-info/top_level.txt'
2025-12-11T03:52:17,608   adding 'ragbio-0.1.12.dist-info/RECORD'
2025-12-11T03:52:17,613   removing build/bdist.linux-armv7l/wheel
2025-12-11T03:52:17,719   Building wheel for ragbio (pyproject.toml): finished with status 'done'
2025-12-11T03:52:17,731   Created wheel for ragbio: filename=ragbio-0.1.12-py3-none-any.whl size=311368 sha256=1342160fe2f337fa22045a27acec4b081fa922939b65d47324ece873fd3618be
2025-12-11T03:52:17,732   Stored in directory: /tmp/pip-ephem-wheel-cache-lfyng6r_/wheels/4a/f0/7d/93ce12d1a9c21dfacb0809a3cf0279a09f7ed7ef7d5afb4130
2025-12-11T03:52:17,744 Successfully built ragbio
2025-12-11T03:52:17,755 Removed build tracker: '/tmp/pip-build-tracker-l07j542s'