2024-11-18T22:35:28,315 Created temporary directory: /tmp/pip-build-tracker-w5xybx6y 2024-11-18T22:35:28,316 Initialized build tracking at /tmp/pip-build-tracker-w5xybx6y 2024-11-18T22:35:28,317 Created build tracker: /tmp/pip-build-tracker-w5xybx6y 2024-11-18T22:35:28,317 Entered build tracker: /tmp/pip-build-tracker-w5xybx6y 2024-11-18T22:35:28,318 Created temporary directory: /tmp/pip-wheel-7abne6ex 2024-11-18T22:35:28,322 Created temporary directory: /tmp/pip-ephem-wheel-cache-jepnz5jy 2024-11-18T22:35:28,368 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-11-18T22:35:28,371 2 location(s) to search for versions of isb-miner3: 2024-11-18T22:35:28,371 * https://pypi.org/simple/isb-miner3/ 2024-11-18T22:35:28,371 * https://www.piwheels.org/simple/isb-miner3/ 2024-11-18T22:35:28,371 Fetching project page and analyzing links: https://pypi.org/simple/isb-miner3/ 2024-11-18T22:35:28,372 Getting page https://pypi.org/simple/isb-miner3/ 2024-11-18T22:35:28,374 Found index url https://pypi.org/simple/ 2024-11-18T22:35:28,597 Fetched page https://pypi.org/simple/isb-miner3/ as application/vnd.pypi.simple.v1+json 2024-11-18T22:35:28,600 Skipping link: No binaries permitted for isb-miner3: https://files.pythonhosted.org/packages/fc/d2/2c0f85359a956acfd34ede78b02ade01b5baf71414cde8525f99631fdfd5/isb_miner3-1.1.7-py2.py3-none-any.whl (from https://pypi.org/simple/isb-miner3/) 2024-11-18T22:35:28,601 Found link https://files.pythonhosted.org/packages/66/8e/e3717b386457b3c131cbb0473957a075283003c16d31b952fbfe07495ca5/isb_miner3-1.1.7.tar.gz (from https://pypi.org/simple/isb-miner3/), version: 1.1.7 2024-11-18T22:35:28,601 Skipping link: No binaries permitted for isb-miner3: https://files.pythonhosted.org/packages/4f/1d/14f1f37e98c2e0c58a4ddae1abc37a289359a606b5bcd027bba303f4bc40/isb_miner3-1.1.8-py2.py3-none-any.whl (from https://pypi.org/simple/isb-miner3/) 2024-11-18T22:35:28,602 Found link https://files.pythonhosted.org/packages/83/21/532c2745a075eb267f58e1a2a660d97e4d119825f59aec481596c277f72b/isb_miner3-1.1.8.tar.gz (from https://pypi.org/simple/isb-miner3/), version: 1.1.8 2024-11-18T22:35:28,602 Skipping link: No binaries permitted for isb-miner3: https://files.pythonhosted.org/packages/f0/35/8d730f4589b554ec1867709ae5965597d9063736f7cb372d9d65c5af12f2/isb_miner3-1.1.9-py2.py3-none-any.whl (from https://pypi.org/simple/isb-miner3/) 2024-11-18T22:35:28,603 Found link https://files.pythonhosted.org/packages/85/1f/812f39de5bbf5a3eace02297e71067f6e4b0a072386546e2c777947708bb/isb_miner3-1.1.9.tar.gz (from https://pypi.org/simple/isb-miner3/), version: 1.1.9 2024-11-18T22:35:28,604 Skipping link: No binaries permitted for isb-miner3: https://files.pythonhosted.org/packages/0f/0b/5559cfa162a4cf86cbd2a6ffc45b22a2c8a0a55573cb6035b65fea813718/isb_miner3-1.2.0-py2.py3-none-any.whl (from https://pypi.org/simple/isb-miner3/) 2024-11-18T22:35:28,605 Found link https://files.pythonhosted.org/packages/32/47/e5abc991a3dc9df61490a24e1f1186833ca15ff6ae77dd74df892da7a444/isb_miner3-1.2.0.tar.gz (from https://pypi.org/simple/isb-miner3/), version: 1.2.0 2024-11-18T22:35:28,605 Skipping link: No binaries permitted for isb-miner3: https://files.pythonhosted.org/packages/45/45/8d7b22e6b011fa7524ca09e0e02e01cac3a42215c1c932b8bcabe0f4f345/isb_miner3-1.2.3-py2.py3-none-any.whl (from https://pypi.org/simple/isb-miner3/) 2024-11-18T22:35:28,606 Found link https://files.pythonhosted.org/packages/09/ab/308f2cb85066df362c7367a91e18d7a7075d25343d5efbe36a90f4ced951/isb_miner3-1.2.3.tar.gz (from https://pypi.org/simple/isb-miner3/), version: 1.2.3 2024-11-18T22:35:28,607 Fetching project page and analyzing links: https://www.piwheels.org/simple/isb-miner3/ 2024-11-18T22:35:28,607 Getting page https://www.piwheels.org/simple/isb-miner3/ 2024-11-18T22:35:28,609 Found index url https://www.piwheels.org/simple/ 2024-11-18T22:35:28,779 Fetched page https://www.piwheels.org/simple/isb-miner3/ as text/html 2024-11-18T22:35:28,782 Skipping link: No binaries permitted for isb-miner3: https://www.piwheels.org/simple/isb-miner3/isb_miner3-1.2.0-py2.py3-none-any.whl#sha256=49273f79eacbb4b2b03f58133483a7667d085f744e9f750889c301e7f8f72ecc (from https://www.piwheels.org/simple/isb-miner3/) 2024-11-18T22:35:28,782 Skipping link: No binaries permitted for isb-miner3: https://www.piwheels.org/simple/isb-miner3/isb_miner3-1.1.9-py2.py3-none-any.whl#sha256=bb90d39bd00b29b3fa8f6eba96684cb7cc9adfc8f9291818db10b6c591b163b3 (from https://www.piwheels.org/simple/isb-miner3/) 2024-11-18T22:35:28,783 Skipping link: No binaries permitted for isb-miner3: https://www.piwheels.org/simple/isb-miner3/isb_miner3-1.1.8-py2.py3-none-any.whl#sha256=57a3dac4be4867d7f4d2ddf49e1f65c5156bea78768d6d9bb84c92c457c68185 (from https://www.piwheels.org/simple/isb-miner3/) 2024-11-18T22:35:28,784 Skipping link: No binaries permitted for isb-miner3: https://www.piwheels.org/simple/isb-miner3/isb_miner3-1.1.7-py2.py3-none-any.whl#sha256=2357f7fc658c9b30c987c6a6c1450f000deb907d355c7b04dd989733af6799ef (from https://www.piwheels.org/simple/isb-miner3/) 2024-11-18T22:35:28,784 Skipping link: not a file: https://www.piwheels.org/simple/isb-miner3/ 2024-11-18T22:35:28,784 Skipping link: not a file: https://pypi.org/simple/isb-miner3/ 2024-11-18T22:35:28,804 Given no hashes to check 1 links for project 'isb-miner3': discarding no candidates 2024-11-18T22:35:28,806 Collecting isb-miner3==1.2.3 2024-11-18T22:35:28,808 Created temporary directory: /tmp/pip-unpack-7rcfwsxo 2024-11-18T22:35:29,990 Downloading isb_miner3-1.2.3.tar.gz (47.6 MB) 2024-11-18T22:35:43,989 Added isb-miner3==1.2.3 from https://files.pythonhosted.org/packages/09/ab/308f2cb85066df362c7367a91e18d7a7075d25343d5efbe36a90f4ced951/isb_miner3-1.2.3.tar.gz to build tracker '/tmp/pip-build-tracker-w5xybx6y' 2024-11-18T22:35:43,991 Running setup.py (path:/tmp/pip-wheel-7abne6ex/isb-miner3_a8eb80765c0744b8b252fb1005eeac26/setup.py) egg_info for package isb-miner3 2024-11-18T22:35:43,992 Created temporary directory: /tmp/pip-pip-egg-info-fwjz7n53 2024-11-18T22:35:43,992 Preparing metadata (setup.py): started 2024-11-18T22:35:43,993 Running command python setup.py egg_info 2024-11-18T22:35:45,040 running egg_info 2024-11-18T22:35:45,067 creating /tmp/pip-pip-egg-info-fwjz7n53/isb_miner3.egg-info 2024-11-18T22:35:45,068 writing /tmp/pip-pip-egg-info-fwjz7n53/isb_miner3.egg-info/PKG-INFO 2024-11-18T22:35:45,072 writing dependency_links to /tmp/pip-pip-egg-info-fwjz7n53/isb_miner3.egg-info/dependency_links.txt 2024-11-18T22:35:45,074 writing requirements to /tmp/pip-pip-egg-info-fwjz7n53/isb_miner3.egg-info/requires.txt 2024-11-18T22:35:45,075 writing top-level names to /tmp/pip-pip-egg-info-fwjz7n53/isb_miner3.egg-info/top_level.txt 2024-11-18T22:35:45,076 writing manifest file '/tmp/pip-pip-egg-info-fwjz7n53/isb_miner3.egg-info/SOURCES.txt' 2024-11-18T22:35:45,192 reading manifest file '/tmp/pip-pip-egg-info-fwjz7n53/isb_miner3.egg-info/SOURCES.txt' 2024-11-18T22:35:45,194 adding license file 'LICENSE' 2024-11-18T22:35:45,197 writing manifest file '/tmp/pip-pip-egg-info-fwjz7n53/isb_miner3.egg-info/SOURCES.txt' 2024-11-18T22:35:45,306 Preparing metadata (setup.py): finished with status 'done' 2024-11-18T22:35:45,310 Source in /tmp/pip-wheel-7abne6ex/isb-miner3_a8eb80765c0744b8b252fb1005eeac26 has version 1.2.3, which satisfies requirement isb-miner3==1.2.3 from https://files.pythonhosted.org/packages/09/ab/308f2cb85066df362c7367a91e18d7a7075d25343d5efbe36a90f4ced951/isb_miner3-1.2.3.tar.gz 2024-11-18T22:35:45,311 Removed isb-miner3==1.2.3 from https://files.pythonhosted.org/packages/09/ab/308f2cb85066df362c7367a91e18d7a7075d25343d5efbe36a90f4ced951/isb_miner3-1.2.3.tar.gz from build tracker '/tmp/pip-build-tracker-w5xybx6y' 2024-11-18T22:35:45,319 Created temporary directory: /tmp/pip-unpack-xd62zjd7 2024-11-18T22:35:45,320 Created temporary directory: /tmp/pip-unpack-yb63aa1v 2024-11-18T22:35:45,321 Building wheels for collected packages: isb-miner3 2024-11-18T22:35:45,325 Created temporary directory: /tmp/pip-wheel-_lv9vyt_ 2024-11-18T22:35:45,326 Building wheel for isb-miner3 (setup.py): started 2024-11-18T22:35:45,327 Destination directory: /tmp/pip-wheel-_lv9vyt_ 2024-11-18T22:35:45,328 Running command python setup.py bdist_wheel 2024-11-18T22:35:46,346 running bdist_wheel 2024-11-18T22:35:46,426 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:111: SetuptoolsDeprecationWarning: bdist_wheel.universal is deprecated 2024-11-18T22:35:46,427 !! 2024-11-18T22:35:46,428 ******************************************************************************** 2024-11-18T22:35:46,428 With Python 2.7 end-of-life, support for building universal wheels 2024-11-18T22:35:46,428 (i.e., wheels that support both Python 2 and Python 3) 2024-11-18T22:35:46,429 is being obviated. 2024-11-18T22:35:46,430 Please discontinue using this option, or if you still need it, 2024-11-18T22:35:46,430 file an issue with pypa/setuptools describing your use case. 2024-11-18T22:35:46,431 By 2025-Aug-30, you need to update your project and remove deprecated calls 2024-11-18T22:35:46,431 or your builds will no longer be supported. 2024-11-18T22:35:46,432 ******************************************************************************** 2024-11-18T22:35:46,433 !! 2024-11-18T22:35:46,433 self.finalize_options() 2024-11-18T22:35:46,486 running build 2024-11-18T22:35:46,487 running build_py 2024-11-18T22:35:46,518 creating build/lib/miner 2024-11-18T22:35:46,520 copying miner/subtypes.py -> build/lib/miner 2024-11-18T22:35:46,523 copying miner/progressbar.py -> build/lib/miner 2024-11-18T22:35:46,525 copying miner/coexpression.py -> build/lib/miner 2024-11-18T22:35:46,528 copying miner/bcmembers.py -> build/lib/miner 2024-11-18T22:35:46,530 copying miner/validation.py -> build/lib/miner 2024-11-18T22:35:46,534 copying miner/mechinf.py -> build/lib/miner 2024-11-18T22:35:46,536 copying miner/__init__.py -> build/lib/miner 2024-11-18T22:35:46,539 copying miner/miner.py -> build/lib/miner 2024-11-18T22:35:46,546 copying miner/opentargets.py -> build/lib/miner 2024-11-18T22:35:46,549 copying miner/causal_inference.py -> build/lib/miner 2024-11-18T22:35:46,553 copying miner/util.py -> build/lib/miner 2024-11-18T22:35:46,555 copying miner/miner_working_frequency_matrix.py -> build/lib/miner 2024-11-18T22:35:46,563 running egg_info 2024-11-18T22:35:46,594 writing isb_miner3.egg-info/PKG-INFO 2024-11-18T22:35:46,598 writing dependency_links to isb_miner3.egg-info/dependency_links.txt 2024-11-18T22:35:46,600 writing requirements to isb_miner3.egg-info/requires.txt 2024-11-18T22:35:46,602 writing top-level names to isb_miner3.egg-info/top_level.txt 2024-11-18T22:35:46,635 reading manifest file 'isb_miner3.egg-info/SOURCES.txt' 2024-11-18T22:35:46,640 adding license file 'LICENSE' 2024-11-18T22:35:46,645 writing manifest file 'isb_miner3.egg-info/SOURCES.txt' 2024-11-18T22:35:46,648 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'miner.data' is absent from the `packages` configuration. 2024-11-18T22:35:46,649 !! 2024-11-18T22:35:46,650 ******************************************************************************** 2024-11-18T22:35:46,651 ############################ 2024-11-18T22:35:46,651 # Package would be ignored # 2024-11-18T22:35:46,652 ############################ 2024-11-18T22:35:46,652 Python recognizes 'miner.data' as an importable package[^1], 2024-11-18T22:35:46,653 but it is absent from setuptools' `packages` configuration. 2024-11-18T22:35:46,654 This leads to an ambiguous overall configuration. If you want to distribute this 2024-11-18T22:35:46,655 package, please make sure that 'miner.data' is explicitly added 2024-11-18T22:35:46,655 to the `packages` configuration field. 2024-11-18T22:35:46,656 Alternatively, you can also rely on setuptools' discovery methods 2024-11-18T22:35:46,657 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-11-18T22:35:46,657 instead of `find_packages(...)`/`find:`). 2024-11-18T22:35:46,658 You can read more about "package discovery" on setuptools documentation page: 2024-11-18T22:35:46,659 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-11-18T22:35:46,660 If you don't want 'miner.data' to be distributed and are 2024-11-18T22:35:46,660 already explicitly excluding 'miner.data' via 2024-11-18T22:35:46,661 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-11-18T22:35:46,661 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-11-18T22:35:46,661 combination with a more fine grained `package-data` configuration. 2024-11-18T22:35:46,662 You can read more about "package data files" on setuptools documentation page: 2024-11-18T22:35:46,663 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-11-18T22:35:46,664 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-11-18T22:35:46,665 even if it does not contain any `.py` files. 2024-11-18T22:35:46,665 On the other hand, currently there is no concept of package data 2024-11-18T22:35:46,666 directory, all directories are treated like packages. 2024-11-18T22:35:46,666 ******************************************************************************** 2024-11-18T22:35:46,667 !! 2024-11-18T22:35:46,667 check.warn(importable) 2024-11-18T22:35:46,668 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'miner.data.network_dictionaries' is absent from the `packages` configuration. 2024-11-18T22:35:46,668 !! 2024-11-18T22:35:46,669 ******************************************************************************** 2024-11-18T22:35:46,670 ############################ 2024-11-18T22:35:46,670 # Package would be ignored # 2024-11-18T22:35:46,671 ############################ 2024-11-18T22:35:46,671 Python recognizes 'miner.data.network_dictionaries' as an importable package[^1], 2024-11-18T22:35:46,672 but it is absent from setuptools' `packages` configuration. 2024-11-18T22:35:46,673 This leads to an ambiguous overall configuration. If you want to distribute this 2024-11-18T22:35:46,674 package, please make sure that 'miner.data.network_dictionaries' is explicitly added 2024-11-18T22:35:46,676 to the `packages` configuration field. 2024-11-18T22:35:46,679 Alternatively, you can also rely on setuptools' discovery methods 2024-11-18T22:35:46,679 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-11-18T22:35:46,680 instead of `find_packages(...)`/`find:`). 2024-11-18T22:35:46,681 You can read more about "package discovery" on setuptools documentation page: 2024-11-18T22:35:46,682 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-11-18T22:35:46,683 If you don't want 'miner.data.network_dictionaries' to be distributed and are 2024-11-18T22:35:46,683 already explicitly excluding 'miner.data.network_dictionaries' via 2024-11-18T22:35:46,684 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-11-18T22:35:46,684 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-11-18T22:35:46,685 combination with a more fine grained `package-data` configuration. 2024-11-18T22:35:46,686 You can read more about "package data files" on setuptools documentation page: 2024-11-18T22:35:46,687 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-11-18T22:35:46,689 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-11-18T22:35:46,690 even if it does not contain any `.py` files. 2024-11-18T22:35:46,690 On the other hand, currently there is no concept of package data 2024-11-18T22:35:46,691 directory, all directories are treated like packages. 2024-11-18T22:35:46,692 ******************************************************************************** 2024-11-18T22:35:46,692 !! 2024-11-18T22:35:46,693 check.warn(importable) 2024-11-18T22:35:46,693 creating build/lib/miner/data 2024-11-18T22:35:46,694 copying miner/data/all_tfs_to_motifs.pkl -> build/lib/miner/data 2024-11-18T22:35:46,694 copying miner/data/epigenes.txt -> build/lib/miner/data 2024-11-18T22:35:46,695 copying miner/data/identifier_mappings.txt -> build/lib/miner/data 2024-11-18T22:35:46,878 creating build/lib/miner/data/network_dictionaries 2024-11-18T22:35:46,879 copying miner/data/network_dictionaries/GO_bio.pkl -> build/lib/miner/data/network_dictionaries 2024-11-18T22:35:46,955 copying miner/data/network_dictionaries/GO_bio_reciprocal.pkl -> build/lib/miner/data/network_dictionaries 2024-11-18T22:35:46,985 copying miner/data/network_dictionaries/chea_reciprocal.pkl -> build/lib/miner/data/network_dictionaries 2024-11-18T22:35:47,027 copying miner/data/network_dictionaries/chea_seq.pkl -> build/lib/miner/data/network_dictionaries 2024-11-18T22:35:47,080 copying miner/data/network_dictionaries/hallmarks.pkl -> build/lib/miner/data/network_dictionaries 2024-11-18T22:35:47,082 copying miner/data/network_dictionaries/hallmarks_reciprocal.pkl -> build/lib/miner/data/network_dictionaries 2024-11-18T22:35:47,085 copying miner/data/network_dictionaries/mirna.pkl -> build/lib/miner/data/network_dictionaries 2024-11-18T22:35:47,093 copying miner/data/network_dictionaries/mirna_reciprocal.pkl -> build/lib/miner/data/network_dictionaries 2024-11-18T22:35:47,101 copying miner/data/network_dictionaries/motif_to_primary_tf.pkl -> build/lib/miner/data/network_dictionaries 2024-11-18T22:35:47,106 copying miner/data/network_dictionaries/pathways.pkl -> build/lib/miner/data/network_dictionaries 2024-11-18T22:35:47,119 copying miner/data/network_dictionaries/pathways_reciprocal.pkl -> build/lib/miner/data/network_dictionaries 2024-11-18T22:35:47,133 copying miner/data/network_dictionaries/primary_tf_to_motif.pkl -> build/lib/miner/data/network_dictionaries 2024-11-18T22:35:47,138 copying miner/data/network_dictionaries/protein_interactions.pkl -> build/lib/miner/data/network_dictionaries 2024-11-18T22:35:47,153 copying miner/data/network_dictionaries/reciprocal_tfbsdb_ensembl.pkl -> build/lib/miner/data/network_dictionaries 2024-11-18T22:35:47,499 copying miner/data/network_dictionaries/tf2genes1.json -> build/lib/miner/data/network_dictionaries 2024-11-18T22:35:48,127 copying miner/data/network_dictionaries/tf2genes2.json -> build/lib/miner/data/network_dictionaries 2024-11-18T22:35:48,434 copying miner/data/network_dictionaries/tf2genes_jsonified.zip -> build/lib/miner/data/network_dictionaries 2024-11-18T22:35:48,616 copying miner/data/network_dictionaries/tfbsdb2_all_tfs_to_motifs.pkl -> build/lib/miner/data/network_dictionaries 2024-11-18T22:35:48,622 copying miner/data/network_dictionaries/tfbsdb2_genes_to_tf.pkl -> build/lib/miner/data/network_dictionaries 2024-11-18T22:35:48,729 copying miner/data/network_dictionaries/tfbsdb2_tf_to_genes.pkl -> build/lib/miner/data/network_dictionaries 2024-11-18T22:35:48,868 copying miner/data/network_dictionaries/tfbsdb_genes_to_tf.pkl -> build/lib/miner/data/network_dictionaries 2024-11-18T22:35:49,055 copying miner/data/network_dictionaries/tfbsdb_tf_to_genes.pkl -> build/lib/miner/data/network_dictionaries 2024-11-18T22:35:49,308 running build_scripts 2024-11-18T22:35:49,309 creating build/scripts-3.11 2024-11-18T22:35:49,310 copying and adjusting bin/miner3-coexpr -> build/scripts-3.11 2024-11-18T22:35:49,312 copying and adjusting bin/miner3-mechinf -> build/scripts-3.11 2024-11-18T22:35:49,314 copying and adjusting bin/miner3-subtypes -> build/scripts-3.11 2024-11-18T22:35:49,316 copying and adjusting bin/miner3-survival -> build/scripts-3.11 2024-11-18T22:35:49,319 copying and adjusting bin/miner3-causalinference -> build/scripts-3.11 2024-11-18T22:35:49,321 copying and adjusting bin/miner3-riskpredict -> build/scripts-3.11 2024-11-18T22:35:49,323 copying and adjusting bin/gene2opentargets -> build/scripts-3.11 2024-11-18T22:35:49,325 copying and adjusting bin/drug2opentargets -> build/scripts-3.11 2024-11-18T22:35:49,326 changing mode of build/scripts-3.11/miner3-coexpr from 644 to 755 2024-11-18T22:35:49,327 changing mode of build/scripts-3.11/miner3-mechinf from 644 to 755 2024-11-18T22:35:49,327 changing mode of build/scripts-3.11/miner3-subtypes from 644 to 755 2024-11-18T22:35:49,328 changing mode of build/scripts-3.11/miner3-survival from 644 to 755 2024-11-18T22:35:49,328 changing mode of build/scripts-3.11/miner3-causalinference from 644 to 755 2024-11-18T22:35:49,329 changing mode of build/scripts-3.11/miner3-riskpredict from 644 to 755 2024-11-18T22:35:49,330 changing mode of build/scripts-3.11/gene2opentargets from 644 to 755 2024-11-18T22:35:49,330 changing mode of build/scripts-3.11/drug2opentargets from 644 to 755 2024-11-18T22:35:49,355 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-11-18T22:35:49,356 !! 2024-11-18T22:35:49,357 ******************************************************************************** 2024-11-18T22:35:49,358 Please avoid running ``setup.py`` directly. 2024-11-18T22:35:49,358 Instead, use pypa/build, pypa/installer or other 2024-11-18T22:35:49,359 standards-based tools. 2024-11-18T22:35:49,360 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-11-18T22:35:49,361 ******************************************************************************** 2024-11-18T22:35:49,362 !! 2024-11-18T22:35:49,362 self.initialize_options() 2024-11-18T22:35:49,384 installing to build/bdist.linux-armv7l/wheel 2024-11-18T22:35:49,384 running install 2024-11-18T22:35:49,408 running install_lib 2024-11-18T22:35:49,435 creating build/bdist.linux-armv7l/wheel 2024-11-18T22:35:49,437 creating build/bdist.linux-armv7l/wheel/miner 2024-11-18T22:35:49,439 copying build/lib/miner/subtypes.py -> build/bdist.linux-armv7l/wheel/./miner 2024-11-18T22:35:49,441 copying build/lib/miner/progressbar.py -> build/bdist.linux-armv7l/wheel/./miner 2024-11-18T22:35:49,443 copying build/lib/miner/coexpression.py -> build/bdist.linux-armv7l/wheel/./miner 2024-11-18T22:35:49,445 copying build/lib/miner/bcmembers.py -> build/bdist.linux-armv7l/wheel/./miner 2024-11-18T22:35:49,447 copying build/lib/miner/validation.py -> build/bdist.linux-armv7l/wheel/./miner 2024-11-18T22:35:49,450 creating build/bdist.linux-armv7l/wheel/miner/data 2024-11-18T22:35:49,451 copying build/lib/miner/data/all_tfs_to_motifs.pkl -> build/bdist.linux-armv7l/wheel/./miner/data 2024-11-18T22:35:49,459 copying build/lib/miner/data/identifier_mappings.txt -> build/bdist.linux-armv7l/wheel/./miner/data 2024-11-18T22:35:49,656 copying build/lib/miner/data/epigenes.txt -> build/bdist.linux-armv7l/wheel/./miner/data 2024-11-18T22:35:49,660 creating build/bdist.linux-armv7l/wheel/miner/data/network_dictionaries 2024-11-18T22:35:49,661 copying build/lib/miner/data/network_dictionaries/GO_bio.pkl -> build/bdist.linux-armv7l/wheel/./miner/data/network_dictionaries 2024-11-18T22:35:49,739 copying build/lib/miner/data/network_dictionaries/chea_seq.pkl -> build/bdist.linux-armv7l/wheel/./miner/data/network_dictionaries 2024-11-18T22:35:49,795 copying build/lib/miner/data/network_dictionaries/pathways_reciprocal.pkl -> build/bdist.linux-armv7l/wheel/./miner/data/network_dictionaries 2024-11-18T22:35:49,810 copying build/lib/miner/data/network_dictionaries/reciprocal_tfbsdb_ensembl.pkl -> build/bdist.linux-armv7l/wheel/./miner/data/network_dictionaries 2024-11-18T22:35:50,186 copying build/lib/miner/data/network_dictionaries/tfbsdb2_all_tfs_to_motifs.pkl -> build/bdist.linux-armv7l/wheel/./miner/data/network_dictionaries 2024-11-18T22:35:50,191 copying build/lib/miner/data/network_dictionaries/tf2genes1.json -> build/bdist.linux-armv7l/wheel/./miner/data/network_dictionaries 2024-11-18T22:35:50,776 copying build/lib/miner/data/network_dictionaries/mirna_reciprocal.pkl -> build/bdist.linux-armv7l/wheel/./miner/data/network_dictionaries 2024-11-18T22:35:50,797 copying build/lib/miner/data/network_dictionaries/tfbsdb_tf_to_genes.pkl -> build/bdist.linux-armv7l/wheel/./miner/data/network_dictionaries 2024-11-18T22:35:51,060 copying build/lib/miner/data/network_dictionaries/tf2genes_jsonified.zip -> build/bdist.linux-armv7l/wheel/./miner/data/network_dictionaries 2024-11-18T22:35:51,236 copying build/lib/miner/data/network_dictionaries/mirna.pkl -> build/bdist.linux-armv7l/wheel/./miner/data/network_dictionaries 2024-11-18T22:35:51,243 copying build/lib/miner/data/network_dictionaries/protein_interactions.pkl -> build/bdist.linux-armv7l/wheel/./miner/data/network_dictionaries 2024-11-18T22:35:51,257 copying build/lib/miner/data/network_dictionaries/tfbsdb2_tf_to_genes.pkl -> build/bdist.linux-armv7l/wheel/./miner/data/network_dictionaries 2024-11-18T22:35:51,419 copying build/lib/miner/data/network_dictionaries/GO_bio_reciprocal.pkl -> build/bdist.linux-armv7l/wheel/./miner/data/network_dictionaries 2024-11-18T22:35:51,474 copying build/lib/miner/data/network_dictionaries/hallmarks.pkl -> build/bdist.linux-armv7l/wheel/./miner/data/network_dictionaries 2024-11-18T22:35:51,479 copying build/lib/miner/data/network_dictionaries/tf2genes2.json -> build/bdist.linux-armv7l/wheel/./miner/data/network_dictionaries 2024-11-18T22:35:51,911 copying build/lib/miner/data/network_dictionaries/tfbsdb_genes_to_tf.pkl -> build/bdist.linux-armv7l/wheel/./miner/data/network_dictionaries 2024-11-18T22:35:52,105 copying build/lib/miner/data/network_dictionaries/hallmarks_reciprocal.pkl -> build/bdist.linux-armv7l/wheel/./miner/data/network_dictionaries 2024-11-18T22:35:52,107 copying build/lib/miner/data/network_dictionaries/primary_tf_to_motif.pkl -> build/bdist.linux-armv7l/wheel/./miner/data/network_dictionaries 2024-11-18T22:35:52,111 copying build/lib/miner/data/network_dictionaries/pathways.pkl -> build/bdist.linux-armv7l/wheel/./miner/data/network_dictionaries 2024-11-18T22:35:52,127 copying build/lib/miner/data/network_dictionaries/motif_to_primary_tf.pkl -> build/bdist.linux-armv7l/wheel/./miner/data/network_dictionaries 2024-11-18T22:35:52,131 copying build/lib/miner/data/network_dictionaries/chea_reciprocal.pkl -> build/bdist.linux-armv7l/wheel/./miner/data/network_dictionaries 2024-11-18T22:35:52,179 copying build/lib/miner/data/network_dictionaries/tfbsdb2_genes_to_tf.pkl -> build/bdist.linux-armv7l/wheel/./miner/data/network_dictionaries 2024-11-18T22:35:52,284 copying build/lib/miner/mechinf.py -> build/bdist.linux-armv7l/wheel/./miner 2024-11-18T22:35:52,287 copying build/lib/miner/__init__.py -> build/bdist.linux-armv7l/wheel/./miner 2024-11-18T22:35:52,288 copying build/lib/miner/miner.py -> build/bdist.linux-armv7l/wheel/./miner 2024-11-18T22:35:52,345 copying build/lib/miner/opentargets.py -> build/bdist.linux-armv7l/wheel/./miner 2024-11-18T22:35:52,348 copying build/lib/miner/causal_inference.py -> build/bdist.linux-armv7l/wheel/./miner 2024-11-18T22:35:52,351 copying build/lib/miner/util.py -> build/bdist.linux-armv7l/wheel/./miner 2024-11-18T22:35:52,353 copying build/lib/miner/miner_working_frequency_matrix.py -> build/bdist.linux-armv7l/wheel/./miner 2024-11-18T22:35:52,359 running install_egg_info 2024-11-18T22:35:52,393 Copying isb_miner3.egg-info to build/bdist.linux-armv7l/wheel/./isb_miner3-1.2.3-py3.11.egg-info 2024-11-18T22:35:52,403 running install_scripts 2024-11-18T22:35:52,404 creating build/bdist.linux-armv7l/wheel/isb_miner3-1.2.3.data/scripts 2024-11-18T22:35:52,406 copying build/scripts-3.11/miner3-survival -> build/bdist.linux-armv7l/wheel/isb_miner3-1.2.3.data/scripts 2024-11-18T22:35:52,409 copying build/scripts-3.11/drug2opentargets -> build/bdist.linux-armv7l/wheel/isb_miner3-1.2.3.data/scripts 2024-11-18T22:35:52,411 copying build/scripts-3.11/miner3-subtypes -> build/bdist.linux-armv7l/wheel/isb_miner3-1.2.3.data/scripts 2024-11-18T22:35:52,414 copying build/scripts-3.11/miner3-causalinference -> build/bdist.linux-armv7l/wheel/isb_miner3-1.2.3.data/scripts 2024-11-18T22:35:52,416 copying build/scripts-3.11/miner3-coexpr -> build/bdist.linux-armv7l/wheel/isb_miner3-1.2.3.data/scripts 2024-11-18T22:35:52,418 copying build/scripts-3.11/miner3-riskpredict -> build/bdist.linux-armv7l/wheel/isb_miner3-1.2.3.data/scripts 2024-11-18T22:35:52,421 copying build/scripts-3.11/miner3-mechinf -> build/bdist.linux-armv7l/wheel/isb_miner3-1.2.3.data/scripts 2024-11-18T22:35:52,423 copying build/scripts-3.11/gene2opentargets -> build/bdist.linux-armv7l/wheel/isb_miner3-1.2.3.data/scripts 2024-11-18T22:35:52,425 changing mode of build/bdist.linux-armv7l/wheel/isb_miner3-1.2.3.data/scripts/miner3-survival to 755 2024-11-18T22:35:52,426 changing mode of build/bdist.linux-armv7l/wheel/isb_miner3-1.2.3.data/scripts/drug2opentargets to 755 2024-11-18T22:35:52,427 changing mode of build/bdist.linux-armv7l/wheel/isb_miner3-1.2.3.data/scripts/miner3-subtypes to 755 2024-11-18T22:35:52,427 changing mode of build/bdist.linux-armv7l/wheel/isb_miner3-1.2.3.data/scripts/miner3-causalinference to 755 2024-11-18T22:35:52,428 changing mode of build/bdist.linux-armv7l/wheel/isb_miner3-1.2.3.data/scripts/miner3-coexpr to 755 2024-11-18T22:35:52,429 changing mode of build/bdist.linux-armv7l/wheel/isb_miner3-1.2.3.data/scripts/miner3-riskpredict to 755 2024-11-18T22:35:52,429 changing mode of build/bdist.linux-armv7l/wheel/isb_miner3-1.2.3.data/scripts/miner3-mechinf to 755 2024-11-18T22:35:52,430 changing mode of build/bdist.linux-armv7l/wheel/isb_miner3-1.2.3.data/scripts/gene2opentargets to 755 2024-11-18T22:35:52,448 creating build/bdist.linux-armv7l/wheel/isb_miner3-1.2.3.dist-info/WHEEL 2024-11-18T22:35:52,451 creating '/tmp/pip-wheel-_lv9vyt_/isb_miner3-1.2.3-py2.py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-11-18T22:35:52,454 adding 'isb_miner3-1.2.3.data/scripts/drug2opentargets' 2024-11-18T22:35:52,456 adding 'isb_miner3-1.2.3.data/scripts/gene2opentargets' 2024-11-18T22:35:52,458 adding 'isb_miner3-1.2.3.data/scripts/miner3-causalinference' 2024-11-18T22:35:52,460 adding 'isb_miner3-1.2.3.data/scripts/miner3-coexpr' 2024-11-18T22:35:52,462 adding 'isb_miner3-1.2.3.data/scripts/miner3-mechinf' 2024-11-18T22:35:52,465 adding 'isb_miner3-1.2.3.data/scripts/miner3-riskpredict' 2024-11-18T22:35:52,467 adding 'isb_miner3-1.2.3.data/scripts/miner3-subtypes' 2024-11-18T22:35:52,469 adding 'isb_miner3-1.2.3.data/scripts/miner3-survival' 2024-11-18T22:35:52,472 adding 'miner/__init__.py' 2024-11-18T22:35:52,474 adding 'miner/bcmembers.py' 2024-11-18T22:35:52,479 adding 'miner/causal_inference.py' 2024-11-18T22:35:52,481 adding 'miner/coexpression.py' 2024-11-18T22:35:52,482 adding 'miner/mechinf.py' 2024-11-18T22:35:52,506 adding 'miner/miner.py' 2024-11-18T22:35:52,536 adding 'miner/miner_working_frequency_matrix.py' 2024-11-18T22:35:52,540 adding 'miner/opentargets.py' 2024-11-18T22:35:52,541 adding 'miner/progressbar.py' 2024-11-18T22:35:52,543 adding 'miner/subtypes.py' 2024-11-18T22:35:52,544 adding 'miner/util.py' 2024-11-18T22:35:52,548 adding 'miner/validation.py' 2024-11-18T22:35:52,609 adding 'miner/data/all_tfs_to_motifs.pkl' 2024-11-18T22:35:52,613 adding 'miner/data/epigenes.txt' 2024-11-18T22:35:53,560 adding 'miner/data/identifier_mappings.txt' 2024-11-18T22:35:54,395 adding 'miner/data/network_dictionaries/GO_bio.pkl' 2024-11-18T22:35:54,857 adding 'miner/data/network_dictionaries/GO_bio_reciprocal.pkl' 2024-11-18T22:35:55,394 adding 'miner/data/network_dictionaries/chea_reciprocal.pkl' 2024-11-18T22:35:56,188 adding 'miner/data/network_dictionaries/chea_seq.pkl' 2024-11-18T22:35:56,208 adding 'miner/data/network_dictionaries/hallmarks.pkl' 2024-11-18T22:35:56,210 adding 'miner/data/network_dictionaries/hallmarks_reciprocal.pkl' 2024-11-18T22:35:56,289 adding 'miner/data/network_dictionaries/mirna.pkl' 2024-11-18T22:35:56,380 adding 'miner/data/network_dictionaries/mirna_reciprocal.pkl' 2024-11-18T22:35:56,405 adding 'miner/data/network_dictionaries/motif_to_primary_tf.pkl' 2024-11-18T22:35:56,582 adding 'miner/data/network_dictionaries/pathways.pkl' 2024-11-18T22:35:56,748 adding 'miner/data/network_dictionaries/pathways_reciprocal.pkl' 2024-11-18T22:35:56,771 adding 'miner/data/network_dictionaries/primary_tf_to_motif.pkl' 2024-11-18T22:35:56,974 adding 'miner/data/network_dictionaries/protein_interactions.pkl' 2024-11-18T22:36:03,749 adding 'miner/data/network_dictionaries/reciprocal_tfbsdb_ensembl.pkl' 2024-11-18T22:36:07,376 adding 'miner/data/network_dictionaries/tf2genes1.json' 2024-11-18T22:36:09,403 adding 'miner/data/network_dictionaries/tf2genes2.json' 2024-11-18T22:36:10,768 adding 'miner/data/network_dictionaries/tf2genes_jsonified.zip' 2024-11-18T22:36:10,874 adding 'miner/data/network_dictionaries/tfbsdb2_all_tfs_to_motifs.pkl' 2024-11-18T22:36:12,837 adding 'miner/data/network_dictionaries/tfbsdb2_genes_to_tf.pkl' 2024-11-18T22:36:15,080 adding 'miner/data/network_dictionaries/tfbsdb2_tf_to_genes.pkl' 2024-11-18T22:36:17,652 adding 'miner/data/network_dictionaries/tfbsdb_genes_to_tf.pkl' 2024-11-18T22:36:21,885 adding 'miner/data/network_dictionaries/tfbsdb_tf_to_genes.pkl' 2024-11-18T22:36:21,989 adding 'isb_miner3-1.2.3.dist-info/LICENSE' 2024-11-18T22:36:21,990 adding 'isb_miner3-1.2.3.dist-info/METADATA' 2024-11-18T22:36:21,991 adding 'isb_miner3-1.2.3.dist-info/WHEEL' 2024-11-18T22:36:21,992 adding 'isb_miner3-1.2.3.dist-info/top_level.txt' 2024-11-18T22:36:21,994 adding 'isb_miner3-1.2.3.dist-info/RECORD' 2024-11-18T22:36:22,466 removing build/bdist.linux-armv7l/wheel 2024-11-18T22:36:22,652 Building wheel for isb-miner3 (setup.py): finished with status 'done' 2024-11-18T22:36:23,137 Created wheel for isb-miner3: filename=isb_miner3-1.2.3-py2.py3-none-any.whl size=49387813 sha256=501e48af5ad5023a87ea8c4e121e41f9443732e7a6779372c4a9a268fd8fc37c 2024-11-18T22:36:23,139 Stored in directory: /tmp/pip-ephem-wheel-cache-jepnz5jy/wheels/f4/21/03/554c5bcc5f49031b51746dea04963d2c50ae65e8f2be90bdb0 2024-11-18T22:36:23,167 Successfully built isb-miner3 2024-11-18T22:36:24,306 Removed build tracker: '/tmp/pip-build-tracker-w5xybx6y'