2023-10-19T22:46:11,141 Created temporary directory: /tmp/pip-build-tracker-tg80l8e7 2023-10-19T22:46:11,142 Initialized build tracking at /tmp/pip-build-tracker-tg80l8e7 2023-10-19T22:46:11,143 Created build tracker: /tmp/pip-build-tracker-tg80l8e7 2023-10-19T22:46:11,143 Entered build tracker: /tmp/pip-build-tracker-tg80l8e7 2023-10-19T22:46:11,144 Created temporary directory: /tmp/pip-wheel-dvwnt9in 2023-10-19T22:46:11,147 Created temporary directory: /tmp/pip-ephem-wheel-cache-k9uo8y6r 2023-10-19T22:46:11,169 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-10-19T22:46:11,173 2 location(s) to search for versions of hydra-rbp: 2023-10-19T22:46:11,173 * https://pypi.org/simple/hydra-rbp/ 2023-10-19T22:46:11,173 * https://www.piwheels.org/simple/hydra-rbp/ 2023-10-19T22:46:11,173 Fetching project page and analyzing links: https://pypi.org/simple/hydra-rbp/ 2023-10-19T22:46:11,174 Getting page https://pypi.org/simple/hydra-rbp/ 2023-10-19T22:46:11,176 Found index url https://pypi.org/simple/ 2023-10-19T22:46:11,404 Fetched page https://pypi.org/simple/hydra-rbp/ as application/vnd.pypi.simple.v1+json 2023-10-19T22:46:11,406 Found link https://files.pythonhosted.org/packages/c5/09/447109100c21cdb2df7a02685baa6324ffad284da0f14a3cfb6ce4b64972/hydra_rbp-0.1.21.27.tar.gz (from https://pypi.org/simple/hydra-rbp/) (requires-python:>=3.6), version: 0.1.21.27 2023-10-19T22:46:11,406 Fetching project page and analyzing links: https://www.piwheels.org/simple/hydra-rbp/ 2023-10-19T22:46:11,407 Getting page https://www.piwheels.org/simple/hydra-rbp/ 2023-10-19T22:46:11,408 Found index url https://www.piwheels.org/simple/ 2023-10-19T22:46:11,565 Fetched page https://www.piwheels.org/simple/hydra-rbp/ as text/html 2023-10-19T22:46:11,566 Skipping link: not a file: https://www.piwheels.org/simple/hydra-rbp/ 2023-10-19T22:46:11,567 Skipping link: not a file: https://pypi.org/simple/hydra-rbp/ 2023-10-19T22:46:11,586 Given no hashes to check 1 links for project 'hydra-rbp': discarding no candidates 2023-10-19T22:46:11,606 Collecting hydra-rbp==0.1.21.27 2023-10-19T22:46:11,608 Created temporary directory: /tmp/pip-unpack-4bofbuf4 2023-10-19T22:46:11,872 Downloading hydra_rbp-0.1.21.27.tar.gz (52.4 MB) 2023-10-19T22:46:30,477 Added hydra-rbp==0.1.21.27 from https://files.pythonhosted.org/packages/c5/09/447109100c21cdb2df7a02685baa6324ffad284da0f14a3cfb6ce4b64972/hydra_rbp-0.1.21.27.tar.gz to build tracker '/tmp/pip-build-tracker-tg80l8e7' 2023-10-19T22:46:30,479 Running setup.py (path:/tmp/pip-wheel-dvwnt9in/hydra-rbp_3822b312d7504221abde707d060d091b/setup.py) egg_info for package hydra-rbp 2023-10-19T22:46:30,480 Created temporary directory: /tmp/pip-pip-egg-info-wxq7qonw 2023-10-19T22:46:30,481 Preparing metadata (setup.py): started 2023-10-19T22:46:30,482 Running command python setup.py egg_info 2023-10-19T22:46:31,210 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2023-10-19T22:46:31,210 !! 2023-10-19T22:46:31,211 ******************************************************************************** 2023-10-19T22:46:31,212 Requirements should be satisfied by a PEP 517 installer. 2023-10-19T22:46:31,212 If you are using pip, you can try `pip install --use-pep517`. 2023-10-19T22:46:31,213 ******************************************************************************** 2023-10-19T22:46:31,214 !! 2023-10-19T22:46:31,215 dist.fetch_build_eggs(dist.setup_requires) 2023-10-19T22:46:33,870 running egg_info 2023-10-19T22:46:33,872 creating /tmp/pip-pip-egg-info-wxq7qonw/hydra_rbp.egg-info 2023-10-19T22:46:33,898 writing /tmp/pip-pip-egg-info-wxq7qonw/hydra_rbp.egg-info/PKG-INFO 2023-10-19T22:46:33,902 writing dependency_links to /tmp/pip-pip-egg-info-wxq7qonw/hydra_rbp.egg-info/dependency_links.txt 2023-10-19T22:46:33,904 writing entry points to /tmp/pip-pip-egg-info-wxq7qonw/hydra_rbp.egg-info/entry_points.txt 2023-10-19T22:46:33,906 writing requirements to /tmp/pip-pip-egg-info-wxq7qonw/hydra_rbp.egg-info/requires.txt 2023-10-19T22:46:33,907 writing top-level names to /tmp/pip-pip-egg-info-wxq7qonw/hydra_rbp.egg-info/top_level.txt 2023-10-19T22:46:33,909 writing manifest file '/tmp/pip-pip-egg-info-wxq7qonw/hydra_rbp.egg-info/SOURCES.txt' 2023-10-19T22:46:34,016 reading manifest file '/tmp/pip-pip-egg-info-wxq7qonw/hydra_rbp.egg-info/SOURCES.txt' 2023-10-19T22:46:34,017 reading manifest template 'MANIFEST.in' 2023-10-19T22:46:34,021 adding license file 'LICENSE' 2023-10-19T22:46:34,025 writing manifest file '/tmp/pip-pip-egg-info-wxq7qonw/hydra_rbp.egg-info/SOURCES.txt' 2023-10-19T22:46:34,135 Preparing metadata (setup.py): finished with status 'done' 2023-10-19T22:46:34,139 Source in /tmp/pip-wheel-dvwnt9in/hydra-rbp_3822b312d7504221abde707d060d091b has version 0.1.21.27, which satisfies requirement hydra-rbp==0.1.21.27 from https://files.pythonhosted.org/packages/c5/09/447109100c21cdb2df7a02685baa6324ffad284da0f14a3cfb6ce4b64972/hydra_rbp-0.1.21.27.tar.gz 2023-10-19T22:46:34,140 Removed hydra-rbp==0.1.21.27 from https://files.pythonhosted.org/packages/c5/09/447109100c21cdb2df7a02685baa6324ffad284da0f14a3cfb6ce4b64972/hydra_rbp-0.1.21.27.tar.gz from build tracker '/tmp/pip-build-tracker-tg80l8e7' 2023-10-19T22:46:34,147 Created temporary directory: /tmp/pip-unpack-pwr1dnl1 2023-10-19T22:46:34,148 Created temporary directory: /tmp/pip-unpack-iv1f4nzf 2023-10-19T22:46:34,161 Building wheels for collected packages: hydra-rbp 2023-10-19T22:46:34,165 Created temporary directory: /tmp/pip-wheel-j2kmvq6d 2023-10-19T22:46:34,165 Building wheel for hydra-rbp (setup.py): started 2023-10-19T22:46:34,166 Destination directory: /tmp/pip-wheel-j2kmvq6d 2023-10-19T22:46:34,167 Running command python setup.py bdist_wheel 2023-10-19T22:46:34,872 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2023-10-19T22:46:34,873 !! 2023-10-19T22:46:34,874 ******************************************************************************** 2023-10-19T22:46:34,875 Requirements should be satisfied by a PEP 517 installer. 2023-10-19T22:46:34,875 If you are using pip, you can try `pip install --use-pep517`. 2023-10-19T22:46:34,876 ******************************************************************************** 2023-10-19T22:46:34,877 !! 2023-10-19T22:46:34,878 dist.fetch_build_eggs(dist.setup_requires) 2023-10-19T22:46:35,380 running bdist_wheel 2023-10-19T22:46:35,485 running build 2023-10-19T22:46:35,486 running build_py 2023-10-19T22:46:35,516 creating build 2023-10-19T22:46:35,516 creating build/lib 2023-10-19T22:46:35,517 creating build/lib/HydRa 2023-10-19T22:46:35,518 copying HydRa/__init__.py -> build/lib/HydRa 2023-10-19T22:46:35,520 copying HydRa/HydRa2_0_predict.py -> build/lib/HydRa 2023-10-19T22:46:35,524 copying HydRa/test_data_load.py -> build/lib/HydRa 2023-10-19T22:46:35,526 copying HydRa/HydRa_predict.py -> build/lib/HydRa 2023-10-19T22:46:35,530 creating build/lib/HydRa/predictions 2023-10-19T22:46:35,531 copying HydRa/predictions/Occlusion_map_v3_HydRa2_0.py -> build/lib/HydRa/predictions 2023-10-19T22:46:35,537 copying HydRa/predictions/__init__.py -> build/lib/HydRa/predictions 2023-10-19T22:46:35,540 copying HydRa/predictions/Occlusion_1D_analysis_SONARplus_intrinsic_on_WuhanVirus_20200124_ensScore.py -> build/lib/HydRa/predictions 2023-10-19T22:46:35,543 copying HydRa/predictions/Occlusion_map_v2.py -> build/lib/HydRa/predictions 2023-10-19T22:46:35,548 copying HydRa/predictions/Occlusion_map.py -> build/lib/HydRa/predictions 2023-10-19T22:46:35,553 copying HydRa/predictions/Occlusion_1D_analysis_SONARplus_intrinsic_on_WuhanVirus_20200124.py -> build/lib/HydRa/predictions 2023-10-19T22:46:35,559 copying HydRa/predictions/Occlusion_1D_analysis_2.py -> build/lib/HydRa/predictions 2023-10-19T22:46:35,562 copying HydRa/predictions/Occlusion_map_v2_HydRa2_0.py -> build/lib/HydRa/predictions 2023-10-19T22:46:35,573 creating build/lib/HydRa/training 2023-10-19T22:46:35,578 copying HydRa/training/__init__.py -> build/lib/HydRa/training 2023-10-19T22:46:35,584 copying HydRa/training/train_and_evaluate_HydRa2_0.py -> build/lib/HydRa/training 2023-10-19T22:46:35,590 copying HydRa/training/train_and_evaluate_HydRa.py -> build/lib/HydRa/training 2023-10-19T22:46:35,597 copying HydRa/training/train_and_evaluate_HydRa_bk.py -> build/lib/HydRa/training 2023-10-19T22:46:35,604 copying HydRa/training/train_HydRa2_0.py -> build/lib/HydRa/training 2023-10-19T22:46:35,612 copying HydRa/training/train_HydRa.py -> build/lib/HydRa/training 2023-10-19T22:46:35,620 creating build/lib/HydRa/evaluation 2023-10-19T22:46:35,621 copying HydRa/evaluation/__init__.py -> build/lib/HydRa/evaluation 2023-10-19T22:46:35,624 copying HydRa/evaluation/ROC_PR_AUC_analysis.py -> build/lib/HydRa/evaluation 2023-10-19T22:46:35,627 creating build/lib/HydRa/models 2023-10-19T22:46:35,628 copying HydRa/models/__init__.py -> build/lib/HydRa/models 2023-10-19T22:46:35,630 copying HydRa/models/DNN_seq.py -> build/lib/HydRa/models 2023-10-19T22:46:35,636 copying HydRa/models/Sequence_class.py -> build/lib/HydRa/models 2023-10-19T22:46:35,642 creating build/lib/HydRa/preprocessing 2023-10-19T22:46:35,643 copying HydRa/preprocessing/__init__.py -> build/lib/HydRa/preprocessing 2023-10-19T22:46:35,646 copying HydRa/preprocessing/predict_SS.py -> build/lib/HydRa/preprocessing 2023-10-19T22:46:35,648 copying HydRa/preprocessing/Get_All_selected_SVM_features.py -> build/lib/HydRa/preprocessing 2023-10-19T22:46:35,650 copying HydRa/preprocessing/get_SVM_seq_features.py -> build/lib/HydRa/preprocessing 2023-10-19T22:46:35,653 copying HydRa/preprocessing/PPI_feature_generation.py -> build/lib/HydRa/preprocessing 2023-10-19T22:46:35,655 creating build/lib/HydRa/preprocessing/Feature_selection 2023-10-19T22:46:35,656 copying HydRa/preprocessing/Feature_selection/__init__.py -> build/lib/HydRa/preprocessing/Feature_selection 2023-10-19T22:46:35,658 copying HydRa/preprocessing/Feature_selection/Feature_selection_for_each_feature_after_chi2Filtering_forFinalTraining.py -> build/lib/HydRa/preprocessing/Feature_selection 2023-10-19T22:46:35,661 creating build/lib/HydRa/preprocessing/Feature_generation 2023-10-19T22:46:35,662 copying HydRa/preprocessing/Feature_generation/__init__.py -> build/lib/HydRa/preprocessing/Feature_generation 2023-10-19T22:46:35,664 copying HydRa/preprocessing/Feature_generation/get_PPI_feature_mat_MB_STRING.py -> build/lib/HydRa/preprocessing/Feature_generation 2023-10-19T22:46:35,666 copying HydRa/preprocessing/Feature_generation/PPI_feature_generation.py -> build/lib/HydRa/preprocessing/Feature_generation 2023-10-19T22:46:35,669 copying HydRa/preprocessing/Feature_generation/run_get_PPI_feature_mat_MB_STRING_addingOOPSXRNAXlabelsV2.py -> build/lib/HydRa/preprocessing/Feature_generation 2023-10-19T22:46:35,670 copying HydRa/preprocessing/Feature_generation/AAC_feature_table_generation.py -> build/lib/HydRa/preprocessing/Feature_generation 2023-10-19T22:46:35,672 copying HydRa/preprocessing/Feature_generation/kmer_table_generation.py -> build/lib/HydRa/preprocessing/Feature_generation 2023-10-19T22:46:35,674 copying HydRa/preprocessing/Feature_generation/Secondary_structure_prediction.py -> build/lib/HydRa/preprocessing/Feature_generation 2023-10-19T22:46:35,676 running egg_info 2023-10-19T22:46:35,731 writing hydra_rbp.egg-info/PKG-INFO 2023-10-19T22:46:35,735 writing dependency_links to hydra_rbp.egg-info/dependency_links.txt 2023-10-19T22:46:35,738 writing entry points to hydra_rbp.egg-info/entry_points.txt 2023-10-19T22:46:35,739 writing requirements to hydra_rbp.egg-info/requires.txt 2023-10-19T22:46:35,740 writing top-level names to hydra_rbp.egg-info/top_level.txt 2023-10-19T22:46:35,783 reading manifest file 'hydra_rbp.egg-info/SOURCES.txt' 2023-10-19T22:46:35,786 reading manifest template 'MANIFEST.in' 2023-10-19T22:46:35,789 adding license file 'LICENSE' 2023-10-19T22:46:35,795 writing manifest file 'hydra_rbp.egg-info/SOURCES.txt' 2023-10-19T22:46:35,797 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'HydRa.data' is absent from the `packages` configuration. 2023-10-19T22:46:35,798 !! 2023-10-19T22:46:35,799 ******************************************************************************** 2023-10-19T22:46:35,799 ############################ 2023-10-19T22:46:35,800 # Package would be ignored # 2023-10-19T22:46:35,800 ############################ 2023-10-19T22:46:35,800 Python recognizes 'HydRa.data' as an importable package[^1], 2023-10-19T22:46:35,801 but it is absent from setuptools' `packages` configuration. 2023-10-19T22:46:35,802 This leads to an ambiguous overall configuration. If you want to distribute this 2023-10-19T22:46:35,802 package, please make sure that 'HydRa.data' is explicitly added 2023-10-19T22:46:35,803 to the `packages` configuration field. 2023-10-19T22:46:35,804 Alternatively, you can also rely on setuptools' discovery methods 2023-10-19T22:46:35,804 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-10-19T22:46:35,804 instead of `find_packages(...)`/`find:`). 2023-10-19T22:46:35,805 You can read more about "package discovery" on setuptools documentation page: 2023-10-19T22:46:35,806 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-10-19T22:46:35,807 If you don't want 'HydRa.data' to be distributed and are 2023-10-19T22:46:35,808 already explicitly excluding 'HydRa.data' via 2023-10-19T22:46:35,808 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-10-19T22:46:35,808 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-10-19T22:46:35,809 combination with a more fine grained `package-data` configuration. 2023-10-19T22:46:35,810 You can read more about "package data files" on setuptools documentation page: 2023-10-19T22:46:35,811 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-10-19T22:46:35,813 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-10-19T22:46:35,814 even if it does not contain any `.py` files. 2023-10-19T22:46:35,815 On the other hand, currently there is no concept of package data 2023-10-19T22:46:35,815 directory, all directories are treated like packages. 2023-10-19T22:46:35,816 ******************************************************************************** 2023-10-19T22:46:35,817 !! 2023-10-19T22:46:35,818 check.warn(importable) 2023-10-19T22:46:35,819 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'HydRa.pre_trained' is absent from the `packages` configuration. 2023-10-19T22:46:35,819 !! 2023-10-19T22:46:35,820 ******************************************************************************** 2023-10-19T22:46:35,821 ############################ 2023-10-19T22:46:35,821 # Package would be ignored # 2023-10-19T22:46:35,822 ############################ 2023-10-19T22:46:35,824 Python recognizes 'HydRa.pre_trained' as an importable package[^1], 2023-10-19T22:46:35,831 but it is absent from setuptools' `packages` configuration. 2023-10-19T22:46:35,839 This leads to an ambiguous overall configuration. If you want to distribute this 2023-10-19T22:46:35,840 package, please make sure that 'HydRa.pre_trained' is explicitly added 2023-10-19T22:46:35,840 to the `packages` configuration field. 2023-10-19T22:46:35,841 Alternatively, you can also rely on setuptools' discovery methods 2023-10-19T22:46:35,842 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-10-19T22:46:35,843 instead of `find_packages(...)`/`find:`). 2023-10-19T22:46:35,844 You can read more about "package discovery" on setuptools documentation page: 2023-10-19T22:46:35,845 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-10-19T22:46:35,846 If you don't want 'HydRa.pre_trained' to be distributed and are 2023-10-19T22:46:35,846 already explicitly excluding 'HydRa.pre_trained' via 2023-10-19T22:46:35,847 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-10-19T22:46:35,847 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-10-19T22:46:35,848 combination with a more fine grained `package-data` configuration. 2023-10-19T22:46:35,852 You can read more about "package data files" on setuptools documentation page: 2023-10-19T22:46:35,862 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-10-19T22:46:35,863 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-10-19T22:46:35,864 even if it does not contain any `.py` files. 2023-10-19T22:46:35,864 On the other hand, currently there is no concept of package data 2023-10-19T22:46:35,865 directory, all directories are treated like packages. 2023-10-19T22:46:35,865 ******************************************************************************** 2023-10-19T22:46:35,866 !! 2023-10-19T22:46:35,867 check.warn(importable) 2023-10-19T22:46:35,867 creating build/lib/HydRa/data 2023-10-19T22:46:35,868 copying HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_menthaBioPlex_STRING.tsv -> build/lib/HydRa/data 2023-10-19T22:46:35,868 copying HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_noSS_menthaBioPlex_STRING.tsv -> build/lib/HydRa/data 2023-10-19T22:46:35,869 copying HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_AddNoSS_trainedWithWholeDataset.xls -> build/lib/HydRa/data 2023-10-19T22:46:35,986 copying HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_noSS_trainedWithWholeDataset.tsv -> build/lib/HydRa/data 2023-10-19T22:46:36,012 copying HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_trainedWithWholeDataset.tsv -> build/lib/HydRa/data 2023-10-19T22:46:36,049 copying HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv -> build/lib/HydRa/data 2023-10-19T22:46:36,221 copying HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv -> build/lib/HydRa/data 2023-10-19T22:46:36,295 copying HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv.bk -> build/lib/HydRa/data 2023-10-19T22:46:36,469 copying HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv -> build/lib/HydRa/data 2023-10-19T22:46:36,503 copying HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv -> build/lib/HydRa/data 2023-10-19T22:46:36,542 copying HydRa/data/Combined10RBPlist_uniprotID_20190716.txt -> build/lib/HydRa/data 2023-10-19T22:46:36,549 copying HydRa/data/Combined8RBPlist_plusOOPSXRNAXsharedRBPs_uniprotID_20190717.txt -> build/lib/HydRa/data 2023-10-19T22:46:36,555 copying HydRa/data/FromOrelOcclRun_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl -> build/lib/HydRa/data 2023-10-19T22:46:36,558 copying HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_avg_zscores_statistics.pkl -> build/lib/HydRa/data 2023-10-19T22:46:36,560 copying HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_scores_statistics.pkl -> build/lib/HydRa/data 2023-10-19T22:46:36,562 copying HydRa/data/HydRa2.0_proteins_with_RBP_categories_RBPflagCorrected_Nov2021_new.tsv -> build/lib/HydRa/data 2023-10-19T22:46:36,656 copying HydRa/data/HydRa_v4_7_3_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl -> build/lib/HydRa/data 2023-10-19T22:46:36,658 copying HydRa/data/STRING_v10.5_uniprot_edgelist_withoutExperimentalData.txt -> build/lib/HydRa/data 2023-10-19T22:46:36,813 copying HydRa/data/SVM_AAC_chi2_alpha0.01_selected_features_From_WholeDataSet_AACname.txt -> build/lib/HydRa/data 2023-10-19T22:46:36,815 copying HydRa/data/SVM_SS_11mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/lib/HydRa/data 2023-10-19T22:46:36,817 copying HydRa/data/SVM_SS_15mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/lib/HydRa/data 2023-10-19T22:46:36,819 copying HydRa/data/SVM_SeqFeature_table_comined_all_selected_features_From_WholeDataset_12Apr_AACname.txt -> build/lib/HydRa/data 2023-10-19T22:46:37,447 copying HydRa/data/SVM_mer3_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/lib/HydRa/data 2023-10-19T22:46:37,449 copying HydRa/data/SVM_mer4_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/lib/HydRa/data 2023-10-19T22:46:37,450 copying HydRa/data/mentha20180108_BioPlex2.0_edgelist.txt -> build/lib/HydRa/data 2023-10-19T22:46:37,516 copying HydRa/data/menthaBioPlex_feature_table_combined10RBPlist.xls -> build/lib/HydRa/data 2023-10-19T22:46:37,545 copying HydRa/data/menthaBioPlex_separatedSTRING_feature_table_combined8RBPlistAddingOOPSXRNAX.xls -> build/lib/HydRa/data 2023-10-19T22:46:37,585 copying HydRa/data/protVec_100d_3grams.csv -> build/lib/HydRa/data 2023-10-19T22:46:37,804 creating build/lib/HydRa/pre_trained 2023-10-19T22:46:37,805 copying HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5 -> build/lib/HydRa/pre_trained 2023-10-19T22:46:37,834 copying HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5 -> build/lib/HydRa/pre_trained 2023-10-19T22:46:37,862 copying HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_model_structure.json -> build/lib/HydRa/pre_trained 2023-10-19T22:46:37,864 copying HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_model_weights.h5 -> build/lib/HydRa/pre_trained 2023-10-19T22:46:37,928 copying HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_model_structure.json -> build/lib/HydRa/pre_trained 2023-10-19T22:46:37,931 copying HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_model_weights.h5 -> build/lib/HydRa/pre_trained 2023-10-19T22:46:38,034 copying HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5 -> build/lib/HydRa/pre_trained 2023-10-19T22:46:38,038 copying HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5 -> build/lib/HydRa/pre_trained 2023-10-19T22:46:38,042 copying HydRa/pre_trained/SVM_PPI_MB-S_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pkl -> build/lib/HydRa/pre_trained 2023-10-19T22:46:38,059 copying HydRa/pre_trained/SVM_PPI_MB_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pkl -> build/lib/HydRa/pre_trained 2023-10-19T22:46:38,075 copying HydRa/pre_trained/SVM_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pickle.pkl -> build/lib/HydRa/pre_trained 2023-10-19T22:46:41,203 copying HydRa/pre_trained/SVM_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_ModelFile.pickle.pkl -> build/lib/HydRa/pre_trained 2023-10-19T22:46:42,932 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-10-19T22:46:42,932 !! 2023-10-19T22:46:42,935 ******************************************************************************** 2023-10-19T22:46:42,937 Please avoid running ``setup.py`` directly. 2023-10-19T22:46:42,938 Instead, use pypa/build, pypa/installer or other 2023-10-19T22:46:42,938 standards-based tools. 2023-10-19T22:46:42,939 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-10-19T22:46:42,940 ******************************************************************************** 2023-10-19T22:46:42,941 !! 2023-10-19T22:46:42,942 self.initialize_options() 2023-10-19T22:46:42,960 installing to build/bdist.linux-armv7l/wheel 2023-10-19T22:46:42,961 running install 2023-10-19T22:46:42,984 running install_lib 2023-10-19T22:46:43,012 creating build/bdist.linux-armv7l 2023-10-19T22:46:43,012 creating build/bdist.linux-armv7l/wheel 2023-10-19T22:46:43,014 creating build/bdist.linux-armv7l/wheel/HydRa 2023-10-19T22:46:43,016 creating build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:43,017 copying build/lib/HydRa/data/HydRa2.0_proteins_with_RBP_categories_RBPflagCorrected_Nov2021_new.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:43,099 copying build/lib/HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_noSS_trainedWithWholeDataset.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:43,127 copying build/lib/HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:43,293 copying build/lib/HydRa/data/SVM_AAC_chi2_alpha0.01_selected_features_From_WholeDataSet_AACname.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:43,295 copying build/lib/HydRa/data/Combined8RBPlist_plusOOPSXRNAXsharedRBPs_uniprotID_20190717.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:43,299 copying build/lib/HydRa/data/SVM_SS_15mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:43,301 copying build/lib/HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_trainedWithWholeDataset.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:43,344 copying build/lib/HydRa/data/SVM_SS_11mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:43,346 copying build/lib/HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_scores_statistics.pkl -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:43,348 copying build/lib/HydRa/data/Combined10RBPlist_uniprotID_20190716.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:43,352 copying build/lib/HydRa/data/menthaBioPlex_separatedSTRING_feature_table_combined8RBPlistAddingOOPSXRNAX.xls -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:43,387 copying build/lib/HydRa/data/menthaBioPlex_feature_table_combined10RBPlist.xls -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:43,416 copying build/lib/HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:43,453 copying build/lib/HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv.bk -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:43,617 copying build/lib/HydRa/data/SVM_mer3_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:43,618 copying build/lib/HydRa/data/protVec_100d_3grams.csv -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:43,757 copying build/lib/HydRa/data/HydRa_v4_7_3_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:43,759 copying build/lib/HydRa/data/FromOrelOcclRun_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:43,761 copying build/lib/HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_menthaBioPlex_STRING.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:43,783 copying build/lib/HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_noSS_menthaBioPlex_STRING.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:43,803 copying build/lib/HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_AddNoSS_trainedWithWholeDataset.xls -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:43,926 copying build/lib/HydRa/data/mentha20180108_BioPlex2.0_edgelist.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:44,094 copying build/lib/HydRa/data/STRING_v10.5_uniprot_edgelist_withoutExperimentalData.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:44,242 copying build/lib/HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:44,312 copying build/lib/HydRa/data/SVM_mer4_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:44,313 copying build/lib/HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_avg_zscores_statistics.pkl -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:44,315 copying build/lib/HydRa/data/SVM_SeqFeature_table_comined_all_selected_features_From_WholeDataset_12Apr_AACname.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:44,883 copying build/lib/HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-19T22:46:44,920 copying build/lib/HydRa/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa 2023-10-19T22:46:44,922 creating build/bdist.linux-armv7l/wheel/HydRa/predictions 2023-10-19T22:46:44,924 copying build/lib/HydRa/predictions/Occlusion_map_v3_HydRa2_0.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2023-10-19T22:46:44,928 copying build/lib/HydRa/predictions/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2023-10-19T22:46:44,930 copying build/lib/HydRa/predictions/Occlusion_1D_analysis_SONARplus_intrinsic_on_WuhanVirus_20200124_ensScore.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2023-10-19T22:46:44,932 copying build/lib/HydRa/predictions/Occlusion_map_v2.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2023-10-19T22:46:44,936 copying build/lib/HydRa/predictions/Occlusion_map.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2023-10-19T22:46:44,939 copying build/lib/HydRa/predictions/Occlusion_1D_analysis_SONARplus_intrinsic_on_WuhanVirus_20200124.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2023-10-19T22:46:44,942 copying build/lib/HydRa/predictions/Occlusion_1D_analysis_2.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2023-10-19T22:46:44,944 copying build/lib/HydRa/predictions/Occlusion_map_v2_HydRa2_0.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2023-10-19T22:46:44,948 creating build/bdist.linux-armv7l/wheel/HydRa/training 2023-10-19T22:46:44,949 copying build/lib/HydRa/training/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2023-10-19T22:46:44,951 copying build/lib/HydRa/training/train_and_evaluate_HydRa2_0.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2023-10-19T22:46:44,954 copying build/lib/HydRa/training/train_and_evaluate_HydRa.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2023-10-19T22:46:44,957 copying build/lib/HydRa/training/train_and_evaluate_HydRa_bk.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2023-10-19T22:46:44,960 copying build/lib/HydRa/training/train_HydRa2_0.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2023-10-19T22:46:44,962 copying build/lib/HydRa/training/train_HydRa.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2023-10-19T22:46:44,965 copying build/lib/HydRa/HydRa2_0_predict.py -> build/bdist.linux-armv7l/wheel/HydRa 2023-10-19T22:46:44,968 creating build/bdist.linux-armv7l/wheel/HydRa/evaluation 2023-10-19T22:46:44,969 copying build/lib/HydRa/evaluation/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/evaluation 2023-10-19T22:46:44,971 copying build/lib/HydRa/evaluation/ROC_PR_AUC_analysis.py -> build/bdist.linux-armv7l/wheel/HydRa/evaluation 2023-10-19T22:46:44,973 creating build/bdist.linux-armv7l/wheel/HydRa/models 2023-10-19T22:46:44,974 copying build/lib/HydRa/models/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/models 2023-10-19T22:46:44,976 copying build/lib/HydRa/models/DNN_seq.py -> build/bdist.linux-armv7l/wheel/HydRa/models 2023-10-19T22:46:44,979 copying build/lib/HydRa/models/Sequence_class.py -> build/bdist.linux-armv7l/wheel/HydRa/models 2023-10-19T22:46:44,982 copying build/lib/HydRa/test_data_load.py -> build/bdist.linux-armv7l/wheel/HydRa 2023-10-19T22:46:44,984 creating build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2023-10-19T22:46:44,985 copying build/lib/HydRa/preprocessing/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2023-10-19T22:46:44,987 copying build/lib/HydRa/preprocessing/predict_SS.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2023-10-19T22:46:44,988 copying build/lib/HydRa/preprocessing/Get_All_selected_SVM_features.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2023-10-19T22:46:44,991 copying build/lib/HydRa/preprocessing/get_SVM_seq_features.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2023-10-19T22:46:44,993 creating build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_selection 2023-10-19T22:46:44,994 copying build/lib/HydRa/preprocessing/Feature_selection/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_selection 2023-10-19T22:46:44,996 copying build/lib/HydRa/preprocessing/Feature_selection/Feature_selection_for_each_feature_after_chi2Filtering_forFinalTraining.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_selection 2023-10-19T22:46:44,998 copying build/lib/HydRa/preprocessing/PPI_feature_generation.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2023-10-19T22:46:45,001 creating build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2023-10-19T22:46:45,002 copying build/lib/HydRa/preprocessing/Feature_generation/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2023-10-19T22:46:45,004 copying build/lib/HydRa/preprocessing/Feature_generation/get_PPI_feature_mat_MB_STRING.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2023-10-19T22:46:45,007 copying build/lib/HydRa/preprocessing/Feature_generation/PPI_feature_generation.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2023-10-19T22:46:45,009 copying build/lib/HydRa/preprocessing/Feature_generation/run_get_PPI_feature_mat_MB_STRING_addingOOPSXRNAXlabelsV2.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2023-10-19T22:46:45,011 copying build/lib/HydRa/preprocessing/Feature_generation/AAC_feature_table_generation.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2023-10-19T22:46:45,013 copying build/lib/HydRa/preprocessing/Feature_generation/kmer_table_generation.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2023-10-19T22:46:45,015 copying build/lib/HydRa/preprocessing/Feature_generation/Secondary_structure_prediction.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2023-10-19T22:46:45,016 copying build/lib/HydRa/HydRa_predict.py -> build/bdist.linux-armv7l/wheel/HydRa 2023-10-19T22:46:45,019 creating build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-10-19T22:46:45,020 copying build/lib/HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_model_structure.json -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-10-19T22:46:45,023 copying build/lib/HydRa/pre_trained/SVM_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pickle.pkl -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-10-19T22:46:48,495 copying build/lib/HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_model_weights.h5 -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-10-19T22:46:48,556 copying build/lib/HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_model_weights.h5 -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-10-19T22:46:48,618 copying build/lib/HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5 -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-10-19T22:46:48,622 copying build/lib/HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5 -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-10-19T22:46:48,648 copying build/lib/HydRa/pre_trained/SVM_PPI_MB-S_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pkl -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-10-19T22:46:48,666 copying build/lib/HydRa/pre_trained/SVM_PPI_MB_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pkl -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-10-19T22:46:48,683 copying build/lib/HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_model_structure.json -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-10-19T22:46:48,686 copying build/lib/HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5 -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-10-19T22:46:48,689 copying build/lib/HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5 -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-10-19T22:46:48,715 copying build/lib/HydRa/pre_trained/SVM_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_ModelFile.pickle.pkl -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-10-19T22:46:49,597 running install_egg_info 2023-10-19T22:46:49,626 Copying hydra_rbp.egg-info to build/bdist.linux-armv7l/wheel/hydra_rbp-0.1.21.27-py3.11.egg-info 2023-10-19T22:46:49,639 running install_scripts 2023-10-19T22:46:49,657 creating build/bdist.linux-armv7l/wheel/hydra_rbp-0.1.21.27.dist-info/WHEEL 2023-10-19T22:46:49,659 creating '/tmp/pip-wheel-j2kmvq6d/hydra_rbp-0.1.21.27-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-10-19T22:46:49,665 adding 'HydRa/HydRa2_0_predict.py' 2023-10-19T22:46:49,669 adding 'HydRa/HydRa_predict.py' 2023-10-19T22:46:49,670 adding 'HydRa/__init__.py' 2023-10-19T22:46:49,671 adding 'HydRa/test_data_load.py' 2023-10-19T22:46:50,058 adding 'HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_menthaBioPlex_STRING.tsv' 2023-10-19T22:46:50,427 adding 'HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_noSS_menthaBioPlex_STRING.tsv' 2023-10-19T22:46:52,596 adding 'HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_AddNoSS_trainedWithWholeDataset.xls' 2023-10-19T22:46:53,164 adding 'HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_noSS_trainedWithWholeDataset.tsv' 2023-10-19T22:46:53,909 adding 'HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_trainedWithWholeDataset.tsv' 2023-10-19T22:46:57,276 adding 'HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv' 2023-10-19T22:46:58,482 adding 'HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv' 2023-10-19T22:47:01,866 adding 'HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv.bk' 2023-10-19T22:47:02,522 adding 'HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv' 2023-10-19T22:47:03,102 adding 'HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv' 2023-10-19T22:47:03,161 adding 'HydRa/data/Combined10RBPlist_uniprotID_20190716.txt' 2023-10-19T22:47:03,206 adding 'HydRa/data/Combined8RBPlist_plusOOPSXRNAXsharedRBPs_uniprotID_20190717.txt' 2023-10-19T22:47:03,209 adding 'HydRa/data/FromOrelOcclRun_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl' 2023-10-19T22:47:03,211 adding 'HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_avg_zscores_statistics.pkl' 2023-10-19T22:47:03,212 adding 'HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_scores_statistics.pkl' 2023-10-19T22:47:04,327 adding 'HydRa/data/HydRa2.0_proteins_with_RBP_categories_RBPflagCorrected_Nov2021_new.tsv' 2023-10-19T22:47:04,367 adding 'HydRa/data/HydRa_v4_7_3_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl' 2023-10-19T22:47:06,059 adding 'HydRa/data/STRING_v10.5_uniprot_edgelist_withoutExperimentalData.txt' 2023-10-19T22:47:06,139 adding 'HydRa/data/SVM_AAC_chi2_alpha0.01_selected_features_From_WholeDataSet_AACname.txt' 2023-10-19T22:47:06,141 adding 'HydRa/data/SVM_SS_11mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt' 2023-10-19T22:47:06,144 adding 'HydRa/data/SVM_SS_15mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt' 2023-10-19T22:47:09,470 adding 'HydRa/data/SVM_SeqFeature_table_comined_all_selected_features_From_WholeDataset_12Apr_AACname.txt' 2023-10-19T22:47:09,789 adding 'HydRa/data/SVM_mer3_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt' 2023-10-19T22:47:09,791 adding 'HydRa/data/SVM_mer4_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt' 2023-10-19T22:47:11,255 adding 'HydRa/data/mentha20180108_BioPlex2.0_edgelist.txt' 2023-10-19T22:47:11,769 adding 'HydRa/data/menthaBioPlex_feature_table_combined10RBPlist.xls' 2023-10-19T22:47:12,350 adding 'HydRa/data/menthaBioPlex_separatedSTRING_feature_table_combined8RBPlistAddingOOPSXRNAX.xls' 2023-10-19T22:47:14,714 adding 'HydRa/data/protVec_100d_3grams.csv' 2023-10-19T22:47:14,784 adding 'HydRa/evaluation/ROC_PR_AUC_analysis.py' 2023-10-19T22:47:14,786 adding 'HydRa/evaluation/__init__.py' 2023-10-19T22:47:14,791 adding 'HydRa/models/DNN_seq.py' 2023-10-19T22:47:14,794 adding 'HydRa/models/Sequence_class.py' 2023-10-19T22:47:14,796 adding 'HydRa/models/__init__.py' 2023-10-19T22:47:15,026 adding 'HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5' 2023-10-19T22:47:15,265 adding 'HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5' 2023-10-19T22:47:15,280 adding 'HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_model_structure.json' 2023-10-19T22:47:15,892 adding 'HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_model_weights.h5' 2023-10-19T22:47:15,927 adding 'HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_model_structure.json' 2023-10-19T22:47:16,537 adding 'HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_model_weights.h5' 2023-10-19T22:47:16,575 adding 'HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5' 2023-10-19T22:47:16,581 adding 'HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5' 2023-10-19T22:47:16,678 adding 'HydRa/pre_trained/SVM_PPI_MB-S_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pkl' 2023-10-19T22:47:16,785 adding 'HydRa/pre_trained/SVM_PPI_MB_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pkl' 2023-10-19T22:47:23,066 adding 'HydRa/pre_trained/SVM_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pickle.pkl' 2023-10-19T22:47:27,017 adding 'HydRa/pre_trained/SVM_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_ModelFile.pickle.pkl' 2023-10-19T22:47:27,557 adding 'HydRa/predictions/Occlusion_1D_analysis_2.py' 2023-10-19T22:47:27,562 adding 'HydRa/predictions/Occlusion_1D_analysis_SONARplus_intrinsic_on_WuhanVirus_20200124.py' 2023-10-19T22:47:27,564 adding 'HydRa/predictions/Occlusion_1D_analysis_SONARplus_intrinsic_on_WuhanVirus_20200124_ensScore.py' 2023-10-19T22:47:27,568 adding 'HydRa/predictions/Occlusion_map.py' 2023-10-19T22:47:27,575 adding 'HydRa/predictions/Occlusion_map_v2.py' 2023-10-19T22:47:27,583 adding 'HydRa/predictions/Occlusion_map_v2_HydRa2_0.py' 2023-10-19T22:47:27,593 adding 'HydRa/predictions/Occlusion_map_v3_HydRa2_0.py' 2023-10-19T22:47:27,595 adding 'HydRa/predictions/__init__.py' 2023-10-19T22:47:27,598 adding 'HydRa/preprocessing/Get_All_selected_SVM_features.py' 2023-10-19T22:47:27,599 adding 'HydRa/preprocessing/PPI_feature_generation.py' 2023-10-19T22:47:27,600 adding 'HydRa/preprocessing/__init__.py' 2023-10-19T22:47:27,602 adding 'HydRa/preprocessing/get_SVM_seq_features.py' 2023-10-19T22:47:27,603 adding 'HydRa/preprocessing/predict_SS.py' 2023-10-19T22:47:27,605 adding 'HydRa/preprocessing/Feature_generation/AAC_feature_table_generation.py' 2023-10-19T22:47:27,607 adding 'HydRa/preprocessing/Feature_generation/PPI_feature_generation.py' 2023-10-19T22:47:27,608 adding 'HydRa/preprocessing/Feature_generation/Secondary_structure_prediction.py' 2023-10-19T22:47:27,609 adding 'HydRa/preprocessing/Feature_generation/__init__.py' 2023-10-19T22:47:27,611 adding 'HydRa/preprocessing/Feature_generation/get_PPI_feature_mat_MB_STRING.py' 2023-10-19T22:47:27,612 adding 'HydRa/preprocessing/Feature_generation/kmer_table_generation.py' 2023-10-19T22:47:27,614 adding 'HydRa/preprocessing/Feature_generation/run_get_PPI_feature_mat_MB_STRING_addingOOPSXRNAXlabelsV2.py' 2023-10-19T22:47:27,616 adding 'HydRa/preprocessing/Feature_selection/Feature_selection_for_each_feature_after_chi2Filtering_forFinalTraining.py' 2023-10-19T22:47:27,617 adding 'HydRa/preprocessing/Feature_selection/__init__.py' 2023-10-19T22:47:27,619 adding 'HydRa/training/__init__.py' 2023-10-19T22:47:27,622 adding 'HydRa/training/train_HydRa.py' 2023-10-19T22:47:27,627 adding 'HydRa/training/train_HydRa2_0.py' 2023-10-19T22:47:27,632 adding 'HydRa/training/train_and_evaluate_HydRa.py' 2023-10-19T22:47:27,638 adding 'HydRa/training/train_and_evaluate_HydRa2_0.py' 2023-10-19T22:47:27,642 adding 'HydRa/training/train_and_evaluate_HydRa_bk.py' 2023-10-19T22:47:27,645 adding 'hydra_rbp-0.1.21.27.dist-info/LICENSE' 2023-10-19T22:47:27,647 adding 'hydra_rbp-0.1.21.27.dist-info/METADATA' 2023-10-19T22:47:27,648 adding 'hydra_rbp-0.1.21.27.dist-info/WHEEL' 2023-10-19T22:47:27,649 adding 'hydra_rbp-0.1.21.27.dist-info/entry_points.txt' 2023-10-19T22:47:27,650 adding 'hydra_rbp-0.1.21.27.dist-info/top_level.txt' 2023-10-19T22:47:27,652 adding 'hydra_rbp-0.1.21.27.dist-info/RECORD' 2023-10-19T22:47:27,681 removing build/bdist.linux-armv7l/wheel 2023-10-19T22:47:27,940 Building wheel for hydra-rbp (setup.py): finished with status 'done' 2023-10-19T22:47:29,182 Created wheel for hydra-rbp: filename=hydra_rbp-0.1.21.27-py3-none-any.whl size=53774376 sha256=c9ac5819931db90ef2e745d6179b24dc2bdc396044ae3c6ceaef7dbadbe6a45a 2023-10-19T22:47:29,183 Stored in directory: /tmp/pip-ephem-wheel-cache-k9uo8y6r/wheels/03/af/b4/faea35ecc7e8380e1953954e7c527f37bfc61cf8b9455c110f 2023-10-19T22:47:29,213 Successfully built hydra-rbp 2023-10-19T22:47:30,484 Removed build tracker: '/tmp/pip-build-tracker-tg80l8e7'