2023-10-20T23:56:24,630 Created temporary directory: /tmp/pip-build-tracker-vvhyt6zk 2023-10-20T23:56:24,631 Initialized build tracking at /tmp/pip-build-tracker-vvhyt6zk 2023-10-20T23:56:24,632 Created build tracker: /tmp/pip-build-tracker-vvhyt6zk 2023-10-20T23:56:24,632 Entered build tracker: /tmp/pip-build-tracker-vvhyt6zk 2023-10-20T23:56:24,633 Created temporary directory: /tmp/pip-wheel-ce6wx2v9 2023-10-20T23:56:24,636 Created temporary directory: /tmp/pip-ephem-wheel-cache-i9t_xor1 2023-10-20T23:56:24,658 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-10-20T23:56:24,662 2 location(s) to search for versions of hydra-rbp: 2023-10-20T23:56:24,662 * https://pypi.org/simple/hydra-rbp/ 2023-10-20T23:56:24,662 * https://www.piwheels.org/simple/hydra-rbp/ 2023-10-20T23:56:24,663 Fetching project page and analyzing links: https://pypi.org/simple/hydra-rbp/ 2023-10-20T23:56:24,664 Getting page https://pypi.org/simple/hydra-rbp/ 2023-10-20T23:56:24,665 Found index url https://pypi.org/simple/ 2023-10-20T23:56:24,882 Fetched page https://pypi.org/simple/hydra-rbp/ as application/vnd.pypi.simple.v1+json 2023-10-20T23:56:24,884 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 2023-10-20T23:56:24,885 Found link https://files.pythonhosted.org/packages/f3/d2/ff965058796232582106702bd93d72d0bdce3920bd9ae52773bfd8a8db71/hydra_rbp-0.1.21.28.tar.gz (from https://pypi.org/simple/hydra-rbp/) (requires-python:>=3.6), version: 0.1.21.28 2023-10-20T23:56:24,885 Fetching project page and analyzing links: https://www.piwheels.org/simple/hydra-rbp/ 2023-10-20T23:56:24,886 Getting page https://www.piwheels.org/simple/hydra-rbp/ 2023-10-20T23:56:24,888 Found index url https://www.piwheels.org/simple/ 2023-10-20T23:56:25,060 Fetched page https://www.piwheels.org/simple/hydra-rbp/ as text/html 2023-10-20T23:56:25,062 Skipping link: No binaries permitted for hydra-rbp: https://www.piwheels.org/simple/hydra-rbp/hydra_rbp-0.1.21.27-py3-none-any.whl#sha256=c9ac5819931db90ef2e745d6179b24dc2bdc396044ae3c6ceaef7dbadbe6a45a (from https://www.piwheels.org/simple/hydra-rbp/) (requires-python:>=3.6) 2023-10-20T23:56:25,062 Skipping link: not a file: https://www.piwheels.org/simple/hydra-rbp/ 2023-10-20T23:56:25,063 Skipping link: not a file: https://pypi.org/simple/hydra-rbp/ 2023-10-20T23:56:25,082 Given no hashes to check 1 links for project 'hydra-rbp': discarding no candidates 2023-10-20T23:56:25,100 Collecting hydra-rbp==0.1.21.28 2023-10-20T23:56:25,102 Created temporary directory: /tmp/pip-unpack-xy1smpzf 2023-10-20T23:56:25,325 Downloading hydra_rbp-0.1.21.28.tar.gz (52.4 MB) 2023-10-20T23:56:42,809 Added hydra-rbp==0.1.21.28 from https://files.pythonhosted.org/packages/f3/d2/ff965058796232582106702bd93d72d0bdce3920bd9ae52773bfd8a8db71/hydra_rbp-0.1.21.28.tar.gz to build tracker '/tmp/pip-build-tracker-vvhyt6zk' 2023-10-20T23:56:42,812 Running setup.py (path:/tmp/pip-wheel-ce6wx2v9/hydra-rbp_c9499285815d4c48b410b85cbb1f3ea5/setup.py) egg_info for package hydra-rbp 2023-10-20T23:56:42,813 Created temporary directory: /tmp/pip-pip-egg-info-33rs0gnm 2023-10-20T23:56:42,814 Preparing metadata (setup.py): started 2023-10-20T23:56:42,815 Running command python setup.py egg_info 2023-10-20T23:56:43,534 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2023-10-20T23:56:43,534 !! 2023-10-20T23:56:43,535 ******************************************************************************** 2023-10-20T23:56:43,536 Requirements should be satisfied by a PEP 517 installer. 2023-10-20T23:56:43,537 If you are using pip, you can try `pip install --use-pep517`. 2023-10-20T23:56:43,537 ******************************************************************************** 2023-10-20T23:56:43,538 !! 2023-10-20T23:56:43,539 dist.fetch_build_eggs(dist.setup_requires) 2023-10-20T23:56:46,870 running egg_info 2023-10-20T23:56:46,872 creating /tmp/pip-pip-egg-info-33rs0gnm/hydra_rbp.egg-info 2023-10-20T23:56:46,898 writing /tmp/pip-pip-egg-info-33rs0gnm/hydra_rbp.egg-info/PKG-INFO 2023-10-20T23:56:46,901 writing dependency_links to /tmp/pip-pip-egg-info-33rs0gnm/hydra_rbp.egg-info/dependency_links.txt 2023-10-20T23:56:46,903 writing entry points to /tmp/pip-pip-egg-info-33rs0gnm/hydra_rbp.egg-info/entry_points.txt 2023-10-20T23:56:46,905 writing requirements to /tmp/pip-pip-egg-info-33rs0gnm/hydra_rbp.egg-info/requires.txt 2023-10-20T23:56:46,906 writing top-level names to /tmp/pip-pip-egg-info-33rs0gnm/hydra_rbp.egg-info/top_level.txt 2023-10-20T23:56:46,907 writing manifest file '/tmp/pip-pip-egg-info-33rs0gnm/hydra_rbp.egg-info/SOURCES.txt' 2023-10-20T23:56:47,015 reading manifest file '/tmp/pip-pip-egg-info-33rs0gnm/hydra_rbp.egg-info/SOURCES.txt' 2023-10-20T23:56:47,016 reading manifest template 'MANIFEST.in' 2023-10-20T23:56:47,020 adding license file 'LICENSE' 2023-10-20T23:56:47,024 writing manifest file '/tmp/pip-pip-egg-info-33rs0gnm/hydra_rbp.egg-info/SOURCES.txt' 2023-10-20T23:56:47,133 Preparing metadata (setup.py): finished with status 'done' 2023-10-20T23:56:47,137 Source in /tmp/pip-wheel-ce6wx2v9/hydra-rbp_c9499285815d4c48b410b85cbb1f3ea5 has version 0.1.21.28, which satisfies requirement hydra-rbp==0.1.21.28 from https://files.pythonhosted.org/packages/f3/d2/ff965058796232582106702bd93d72d0bdce3920bd9ae52773bfd8a8db71/hydra_rbp-0.1.21.28.tar.gz 2023-10-20T23:56:47,138 Removed hydra-rbp==0.1.21.28 from https://files.pythonhosted.org/packages/f3/d2/ff965058796232582106702bd93d72d0bdce3920bd9ae52773bfd8a8db71/hydra_rbp-0.1.21.28.tar.gz from build tracker '/tmp/pip-build-tracker-vvhyt6zk' 2023-10-20T23:56:47,145 Created temporary directory: /tmp/pip-unpack-ivoskkor 2023-10-20T23:56:47,146 Created temporary directory: /tmp/pip-unpack-lfuvw5jf 2023-10-20T23:56:47,159 Building wheels for collected packages: hydra-rbp 2023-10-20T23:56:47,163 Created temporary directory: /tmp/pip-wheel-gaohn94a 2023-10-20T23:56:47,163 Building wheel for hydra-rbp (setup.py): started 2023-10-20T23:56:47,165 Destination directory: /tmp/pip-wheel-gaohn94a 2023-10-20T23:56:47,165 Running command python setup.py bdist_wheel 2023-10-20T23:56:47,832 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2023-10-20T23:56:47,832 !! 2023-10-20T23:56:47,833 ******************************************************************************** 2023-10-20T23:56:47,834 Requirements should be satisfied by a PEP 517 installer. 2023-10-20T23:56:47,835 If you are using pip, you can try `pip install --use-pep517`. 2023-10-20T23:56:47,835 ******************************************************************************** 2023-10-20T23:56:47,836 !! 2023-10-20T23:56:47,837 dist.fetch_build_eggs(dist.setup_requires) 2023-10-20T23:56:48,317 running bdist_wheel 2023-10-20T23:56:48,417 running build 2023-10-20T23:56:48,417 running build_py 2023-10-20T23:56:48,446 creating build 2023-10-20T23:56:48,446 creating build/lib 2023-10-20T23:56:48,447 creating build/lib/HydRa 2023-10-20T23:56:48,448 copying HydRa/test_data_load.py -> build/lib/HydRa 2023-10-20T23:56:48,450 copying HydRa/__init__.py -> build/lib/HydRa 2023-10-20T23:56:48,452 copying HydRa/HydRa2_0_predict.py -> build/lib/HydRa 2023-10-20T23:56:48,454 copying HydRa/HydRa_predict.py -> build/lib/HydRa 2023-10-20T23:56:48,458 creating build/lib/HydRa/training 2023-10-20T23:56:48,458 copying HydRa/training/train_and_evaluate_HydRa2_0.py -> build/lib/HydRa/training 2023-10-20T23:56:48,462 copying HydRa/training/train_and_evaluate_HydRa_bk.py -> build/lib/HydRa/training 2023-10-20T23:56:48,464 copying HydRa/training/train_HydRa.py -> build/lib/HydRa/training 2023-10-20T23:56:48,467 copying HydRa/training/train_and_evaluate_HydRa.py -> build/lib/HydRa/training 2023-10-20T23:56:48,470 copying HydRa/training/train_HydRa2_0.py -> build/lib/HydRa/training 2023-10-20T23:56:48,473 copying HydRa/training/__init__.py -> build/lib/HydRa/training 2023-10-20T23:56:48,474 creating build/lib/HydRa/preprocessing 2023-10-20T23:56:48,475 copying HydRa/preprocessing/PPI_feature_generation.py -> build/lib/HydRa/preprocessing 2023-10-20T23:56:48,477 copying HydRa/preprocessing/predict_SS.py -> build/lib/HydRa/preprocessing 2023-10-20T23:56:48,479 copying HydRa/preprocessing/__init__.py -> build/lib/HydRa/preprocessing 2023-10-20T23:56:48,480 copying HydRa/preprocessing/get_SVM_seq_features.py -> build/lib/HydRa/preprocessing 2023-10-20T23:56:48,482 copying HydRa/preprocessing/Get_All_selected_SVM_features.py -> build/lib/HydRa/preprocessing 2023-10-20T23:56:48,484 creating build/lib/HydRa/predictions 2023-10-20T23:56:48,485 copying HydRa/predictions/Occlusion_map_v2_HydRa2_0.py -> build/lib/HydRa/predictions 2023-10-20T23:56:48,489 copying HydRa/predictions/Occlusion_1D_analysis_2.py -> build/lib/HydRa/predictions 2023-10-20T23:56:48,490 copying HydRa/predictions/Occlusion_map_v2.py -> build/lib/HydRa/predictions 2023-10-20T23:56:48,493 copying HydRa/predictions/Occlusion_map_v3_HydRa2_0.py -> build/lib/HydRa/predictions 2023-10-20T23:56:48,497 copying HydRa/predictions/Occlusion_map.py -> build/lib/HydRa/predictions 2023-10-20T23:56:48,499 copying HydRa/predictions/Occlusion_1D_analysis_SONARplus_intrinsic_on_WuhanVirus_20200124_ensScore.py -> build/lib/HydRa/predictions 2023-10-20T23:56:48,501 copying HydRa/predictions/__init__.py -> build/lib/HydRa/predictions 2023-10-20T23:56:48,503 copying HydRa/predictions/Occlusion_1D_analysis_SONARplus_intrinsic_on_WuhanVirus_20200124.py -> build/lib/HydRa/predictions 2023-10-20T23:56:48,506 creating build/lib/HydRa/models 2023-10-20T23:56:48,507 copying HydRa/models/Sequence_class.py -> build/lib/HydRa/models 2023-10-20T23:56:48,510 copying HydRa/models/__init__.py -> build/lib/HydRa/models 2023-10-20T23:56:48,511 copying HydRa/models/DNN_seq.py -> build/lib/HydRa/models 2023-10-20T23:56:48,515 creating build/lib/HydRa/evaluation 2023-10-20T23:56:48,515 copying HydRa/evaluation/ROC_PR_AUC_analysis.py -> build/lib/HydRa/evaluation 2023-10-20T23:56:48,517 copying HydRa/evaluation/__init__.py -> build/lib/HydRa/evaluation 2023-10-20T23:56:48,519 creating build/lib/HydRa/preprocessing/Feature_selection 2023-10-20T23:56:48,520 copying HydRa/preprocessing/Feature_selection/Feature_selection_for_each_feature_after_chi2Filtering_forFinalTraining.py -> build/lib/HydRa/preprocessing/Feature_selection 2023-10-20T23:56:48,523 copying HydRa/preprocessing/Feature_selection/__init__.py -> build/lib/HydRa/preprocessing/Feature_selection 2023-10-20T23:56:48,525 creating build/lib/HydRa/preprocessing/Feature_generation 2023-10-20T23:56:48,526 copying HydRa/preprocessing/Feature_generation/PPI_feature_generation.py -> build/lib/HydRa/preprocessing/Feature_generation 2023-10-20T23:56:48,528 copying HydRa/preprocessing/Feature_generation/Secondary_structure_prediction.py -> build/lib/HydRa/preprocessing/Feature_generation 2023-10-20T23:56:48,529 copying HydRa/preprocessing/Feature_generation/kmer_table_generation.py -> build/lib/HydRa/preprocessing/Feature_generation 2023-10-20T23:56:48,531 copying HydRa/preprocessing/Feature_generation/run_get_PPI_feature_mat_MB_STRING_addingOOPSXRNAXlabelsV2.py -> build/lib/HydRa/preprocessing/Feature_generation 2023-10-20T23:56:48,533 copying HydRa/preprocessing/Feature_generation/get_PPI_feature_mat_MB_STRING.py -> build/lib/HydRa/preprocessing/Feature_generation 2023-10-20T23:56:48,535 copying HydRa/preprocessing/Feature_generation/__init__.py -> build/lib/HydRa/preprocessing/Feature_generation 2023-10-20T23:56:48,537 copying HydRa/preprocessing/Feature_generation/AAC_feature_table_generation.py -> build/lib/HydRa/preprocessing/Feature_generation 2023-10-20T23:56:48,538 running egg_info 2023-10-20T23:56:48,591 writing hydra_rbp.egg-info/PKG-INFO 2023-10-20T23:56:48,594 writing dependency_links to hydra_rbp.egg-info/dependency_links.txt 2023-10-20T23:56:48,596 writing entry points to hydra_rbp.egg-info/entry_points.txt 2023-10-20T23:56:48,597 writing requirements to hydra_rbp.egg-info/requires.txt 2023-10-20T23:56:48,598 writing top-level names to hydra_rbp.egg-info/top_level.txt 2023-10-20T23:56:48,638 reading manifest file 'hydra_rbp.egg-info/SOURCES.txt' 2023-10-20T23:56:48,641 reading manifest template 'MANIFEST.in' 2023-10-20T23:56:48,644 adding license file 'LICENSE' 2023-10-20T23:56:48,649 writing manifest file 'hydra_rbp.egg-info/SOURCES.txt' 2023-10-20T23:56:48,652 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'HydRa.data' is absent from the `packages` configuration. 2023-10-20T23:56:48,652 !! 2023-10-20T23:56:48,653 ******************************************************************************** 2023-10-20T23:56:48,653 ############################ 2023-10-20T23:56:48,654 # Package would be ignored # 2023-10-20T23:56:48,654 ############################ 2023-10-20T23:56:48,655 Python recognizes 'HydRa.data' as an importable package[^1], 2023-10-20T23:56:48,655 but it is absent from setuptools' `packages` configuration. 2023-10-20T23:56:48,656 This leads to an ambiguous overall configuration. If you want to distribute this 2023-10-20T23:56:48,656 package, please make sure that 'HydRa.data' is explicitly added 2023-10-20T23:56:48,657 to the `packages` configuration field. 2023-10-20T23:56:48,658 Alternatively, you can also rely on setuptools' discovery methods 2023-10-20T23:56:48,658 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-10-20T23:56:48,659 instead of `find_packages(...)`/`find:`). 2023-10-20T23:56:48,660 You can read more about "package discovery" on setuptools documentation page: 2023-10-20T23:56:48,661 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-10-20T23:56:48,663 If you don't want 'HydRa.data' to be distributed and are 2023-10-20T23:56:48,663 already explicitly excluding 'HydRa.data' via 2023-10-20T23:56:48,664 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-10-20T23:56:48,664 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-10-20T23:56:48,665 combination with a more fine grained `package-data` configuration. 2023-10-20T23:56:48,676 You can read more about "package data files" on setuptools documentation page: 2023-10-20T23:56:48,680 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-10-20T23:56:48,682 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-10-20T23:56:48,682 even if it does not contain any `.py` files. 2023-10-20T23:56:48,683 On the other hand, currently there is no concept of package data 2023-10-20T23:56:48,683 directory, all directories are treated like packages. 2023-10-20T23:56:48,684 ******************************************************************************** 2023-10-20T23:56:48,685 !! 2023-10-20T23:56:48,686 check.warn(importable) 2023-10-20T23:56:48,686 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'HydRa.pre_trained' is absent from the `packages` configuration. 2023-10-20T23:56:48,687 !! 2023-10-20T23:56:48,700 ******************************************************************************** 2023-10-20T23:56:48,700 ############################ 2023-10-20T23:56:48,701 # Package would be ignored # 2023-10-20T23:56:48,701 ############################ 2023-10-20T23:56:48,702 Python recognizes 'HydRa.pre_trained' as an importable package[^1], 2023-10-20T23:56:48,703 but it is absent from setuptools' `packages` configuration. 2023-10-20T23:56:48,704 This leads to an ambiguous overall configuration. If you want to distribute this 2023-10-20T23:56:48,704 package, please make sure that 'HydRa.pre_trained' is explicitly added 2023-10-20T23:56:48,705 to the `packages` configuration field. 2023-10-20T23:56:48,706 Alternatively, you can also rely on setuptools' discovery methods 2023-10-20T23:56:48,706 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-10-20T23:56:48,707 instead of `find_packages(...)`/`find:`). 2023-10-20T23:56:48,707 You can read more about "package discovery" on setuptools documentation page: 2023-10-20T23:56:48,708 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-10-20T23:56:48,709 If you don't want 'HydRa.pre_trained' to be distributed and are 2023-10-20T23:56:48,710 already explicitly excluding 'HydRa.pre_trained' via 2023-10-20T23:56:48,710 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-10-20T23:56:48,711 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-10-20T23:56:48,711 combination with a more fine grained `package-data` configuration. 2023-10-20T23:56:48,712 You can read more about "package data files" on setuptools documentation page: 2023-10-20T23:56:48,713 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-10-20T23:56:48,714 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-10-20T23:56:48,715 even if it does not contain any `.py` files. 2023-10-20T23:56:48,715 On the other hand, currently there is no concept of package data 2023-10-20T23:56:48,716 directory, all directories are treated like packages. 2023-10-20T23:56:48,717 ******************************************************************************** 2023-10-20T23:56:48,718 !! 2023-10-20T23:56:48,719 check.warn(importable) 2023-10-20T23:56:48,719 creating build/lib/HydRa/data 2023-10-20T23:56:48,720 copying HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_menthaBioPlex_STRING.tsv -> build/lib/HydRa/data 2023-10-20T23:56:48,721 copying HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_noSS_menthaBioPlex_STRING.tsv -> build/lib/HydRa/data 2023-10-20T23:56:48,721 copying HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_AddNoSS_trainedWithWholeDataset.xls -> build/lib/HydRa/data 2023-10-20T23:56:48,808 copying HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_noSS_trainedWithWholeDataset.tsv -> build/lib/HydRa/data 2023-10-20T23:56:48,836 copying HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_trainedWithWholeDataset.tsv -> build/lib/HydRa/data 2023-10-20T23:56:48,875 copying HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv -> build/lib/HydRa/data 2023-10-20T23:56:49,046 copying HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv -> build/lib/HydRa/data 2023-10-20T23:56:49,121 copying HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv.bk -> build/lib/HydRa/data 2023-10-20T23:56:49,318 copying HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv -> build/lib/HydRa/data 2023-10-20T23:56:49,349 copying HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv -> build/lib/HydRa/data 2023-10-20T23:56:49,387 copying HydRa/data/Combined10RBPlist_uniprotID_20190716.txt -> build/lib/HydRa/data 2023-10-20T23:56:49,392 copying HydRa/data/Combined8RBPlist_plusOOPSXRNAXsharedRBPs_uniprotID_20190717.txt -> build/lib/HydRa/data 2023-10-20T23:56:49,397 copying HydRa/data/FromOrelOcclRun_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl -> build/lib/HydRa/data 2023-10-20T23:56:49,398 copying HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_avg_zscores_statistics.pkl -> build/lib/HydRa/data 2023-10-20T23:56:49,400 copying HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_scores_statistics.pkl -> build/lib/HydRa/data 2023-10-20T23:56:49,402 copying HydRa/data/HydRa2.0_proteins_with_RBP_categories_RBPflagCorrected_Nov2021_new.tsv -> build/lib/HydRa/data 2023-10-20T23:56:49,480 copying HydRa/data/HydRa_v4_7_3_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl -> build/lib/HydRa/data 2023-10-20T23:56:49,482 copying HydRa/data/STRING_v10.5_uniprot_edgelist_withoutExperimentalData.txt -> build/lib/HydRa/data 2023-10-20T23:56:49,634 copying HydRa/data/SVM_AAC_chi2_alpha0.01_selected_features_From_WholeDataSet_AACname.txt -> build/lib/HydRa/data 2023-10-20T23:56:49,636 copying HydRa/data/SVM_SS_11mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/lib/HydRa/data 2023-10-20T23:56:49,638 copying HydRa/data/SVM_SS_15mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/lib/HydRa/data 2023-10-20T23:56:49,640 copying HydRa/data/SVM_SeqFeature_table_comined_all_selected_features_From_WholeDataset_12Apr_AACname.txt -> build/lib/HydRa/data 2023-10-20T23:56:50,607 copying HydRa/data/SVM_mer3_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/lib/HydRa/data 2023-10-20T23:56:50,608 copying HydRa/data/SVM_mer4_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/lib/HydRa/data 2023-10-20T23:56:50,610 copying HydRa/data/mentha20180108_BioPlex2.0_edgelist.txt -> build/lib/HydRa/data 2023-10-20T23:56:50,679 copying HydRa/data/menthaBioPlex_feature_table_combined10RBPlist.xls -> build/lib/HydRa/data 2023-10-20T23:56:50,706 copying HydRa/data/menthaBioPlex_separatedSTRING_feature_table_combined8RBPlistAddingOOPSXRNAX.xls -> build/lib/HydRa/data 2023-10-20T23:56:50,746 copying HydRa/data/protVec_100d_3grams.csv -> build/lib/HydRa/data 2023-10-20T23:56:50,867 creating build/lib/HydRa/pre_trained 2023-10-20T23:56:50,868 copying HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5 -> build/lib/HydRa/pre_trained 2023-10-20T23:56:50,894 copying HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5 -> build/lib/HydRa/pre_trained 2023-10-20T23:56:50,918 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 2023-10-20T23:56:50,920 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 2023-10-20T23:56:50,981 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 2023-10-20T23:56:50,984 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 2023-10-20T23:56:51,043 copying HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5 -> build/lib/HydRa/pre_trained 2023-10-20T23:56:51,046 copying HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5 -> build/lib/HydRa/pre_trained 2023-10-20T23:56:51,050 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 2023-10-20T23:56:51,068 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 2023-10-20T23:56:51,085 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 2023-10-20T23:56:54,135 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 2023-10-20T23:56:55,779 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-10-20T23:56:55,779 !! 2023-10-20T23:56:55,780 ******************************************************************************** 2023-10-20T23:56:55,781 Please avoid running ``setup.py`` directly. 2023-10-20T23:56:55,781 Instead, use pypa/build, pypa/installer or other 2023-10-20T23:56:55,782 standards-based tools. 2023-10-20T23:56:55,783 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-10-20T23:56:55,783 ******************************************************************************** 2023-10-20T23:56:55,784 !! 2023-10-20T23:56:55,785 self.initialize_options() 2023-10-20T23:56:55,806 installing to build/bdist.linux-armv7l/wheel 2023-10-20T23:56:55,806 running install 2023-10-20T23:56:55,830 running install_lib 2023-10-20T23:56:55,856 creating build/bdist.linux-armv7l 2023-10-20T23:56:55,857 creating build/bdist.linux-armv7l/wheel 2023-10-20T23:56:55,858 creating build/bdist.linux-armv7l/wheel/HydRa 2023-10-20T23:56:55,859 copying build/lib/HydRa/test_data_load.py -> build/bdist.linux-armv7l/wheel/HydRa 2023-10-20T23:56:55,862 creating build/bdist.linux-armv7l/wheel/HydRa/training 2023-10-20T23:56:55,863 copying build/lib/HydRa/training/train_and_evaluate_HydRa2_0.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2023-10-20T23:56:55,866 copying build/lib/HydRa/training/train_and_evaluate_HydRa_bk.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2023-10-20T23:56:55,869 copying build/lib/HydRa/training/train_HydRa.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2023-10-20T23:56:55,872 copying build/lib/HydRa/training/train_and_evaluate_HydRa.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2023-10-20T23:56:55,874 copying build/lib/HydRa/training/train_HydRa2_0.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2023-10-20T23:56:55,877 copying build/lib/HydRa/training/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/training 2023-10-20T23:56:55,879 creating build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-10-20T23:56:55,880 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 2023-10-20T23:56:55,895 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 2023-10-20T23:56:55,913 copying build/lib/HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5 -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-10-20T23:56:55,916 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 2023-10-20T23:56:59,013 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 2023-10-20T23:56:59,872 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 2023-10-20T23:56:59,928 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 2023-10-20T23:56:59,931 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 2023-10-20T23:56:59,934 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 2023-10-20T23:57:00,337 copying build/lib/HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5 -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-10-20T23:57:00,363 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 2023-10-20T23:57:00,365 copying build/lib/HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5 -> build/bdist.linux-armv7l/wheel/HydRa/pre_trained 2023-10-20T23:57:00,396 creating build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-20T23:57:00,397 copying build/lib/HydRa/data/HydRa2.0_proteins_with_RBP_categories_RBPflagCorrected_Nov2021_new.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-20T23:57:00,475 copying build/lib/HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-20T23:57:00,507 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 2023-10-20T23:57:00,654 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 2023-10-20T23:57:00,819 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 2023-10-20T23:57:00,843 copying build/lib/HydRa/data/mentha20180108_BioPlex2.0_edgelist.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-20T23:57:00,915 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 2023-10-20T23:57:00,955 copying build/lib/HydRa/data/SVM_AAC_chi2_alpha0.01_selected_features_From_WholeDataSet_AACname.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-20T23:57:00,956 copying build/lib/HydRa/data/SVM_SeqFeature_table_comined_all_selected_features_From_WholeDataset_12Apr_AACname.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-20T23:57:01,480 copying build/lib/HydRa/data/SVM_mer4_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-20T23:57:01,482 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 2023-10-20T23:57:01,562 copying build/lib/HydRa/data/FromOrelOcclRun_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-20T23:57:01,564 copying build/lib/HydRa/data/menthaBioPlex_feature_table_combined10RBPlist.xls -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-20T23:57:01,601 copying build/lib/HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_scores_statistics.pkl -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-20T23:57:01,602 copying build/lib/HydRa/data/Combined8RBPlist_plusOOPSXRNAXsharedRBPs_uniprotID_20190717.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-20T23:57:01,608 copying build/lib/HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_trainedWithWholeDataset.tsv -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-20T23:57:01,652 copying build/lib/HydRa/data/protVec_100d_3grams.csv -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-20T23:57:01,775 copying build/lib/HydRa/data/Combined10RBPlist_uniprotID_20190716.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-20T23:57:01,779 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 2023-10-20T23:57:01,807 copying build/lib/HydRa/data/STRING_v10.5_uniprot_edgelist_withoutExperimentalData.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-20T23:57:01,948 copying build/lib/HydRa/data/HydRa_v4_7_3_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-20T23:57:01,949 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 2023-10-20T23:57:01,951 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 2023-10-20T23:57:01,971 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 2023-10-20T23:57:01,974 copying build/lib/HydRa/data/SVM_mer3_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-20T23:57:01,976 copying build/lib/HydRa/data/menthaBioPlex_separatedSTRING_feature_table_combined8RBPlistAddingOOPSXRNAX.xls -> build/bdist.linux-armv7l/wheel/HydRa/data 2023-10-20T23:57:02,011 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 2023-10-20T23:57:02,013 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 2023-10-20T23:57:02,170 creating build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2023-10-20T23:57:02,171 copying build/lib/HydRa/preprocessing/PPI_feature_generation.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2023-10-20T23:57:02,174 copying build/lib/HydRa/preprocessing/predict_SS.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2023-10-20T23:57:02,176 creating build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_selection 2023-10-20T23:57:02,177 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 2023-10-20T23:57:02,179 copying build/lib/HydRa/preprocessing/Feature_selection/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_selection 2023-10-20T23:57:02,181 copying build/lib/HydRa/preprocessing/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2023-10-20T23:57:02,183 copying build/lib/HydRa/preprocessing/get_SVM_seq_features.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2023-10-20T23:57:02,185 creating build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2023-10-20T23:57:02,186 copying build/lib/HydRa/preprocessing/Feature_generation/PPI_feature_generation.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2023-10-20T23:57:02,188 copying build/lib/HydRa/preprocessing/Feature_generation/Secondary_structure_prediction.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2023-10-20T23:57:02,190 copying build/lib/HydRa/preprocessing/Feature_generation/kmer_table_generation.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2023-10-20T23:57:02,191 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 2023-10-20T23:57:02,193 copying build/lib/HydRa/preprocessing/Feature_generation/get_PPI_feature_mat_MB_STRING.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2023-10-20T23:57:02,195 copying build/lib/HydRa/preprocessing/Feature_generation/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2023-10-20T23:57:02,197 copying build/lib/HydRa/preprocessing/Feature_generation/AAC_feature_table_generation.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing/Feature_generation 2023-10-20T23:57:02,198 copying build/lib/HydRa/preprocessing/Get_All_selected_SVM_features.py -> build/bdist.linux-armv7l/wheel/HydRa/preprocessing 2023-10-20T23:57:02,201 creating build/bdist.linux-armv7l/wheel/HydRa/predictions 2023-10-20T23:57:02,202 copying build/lib/HydRa/predictions/Occlusion_map_v2_HydRa2_0.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2023-10-20T23:57:02,206 copying build/lib/HydRa/predictions/Occlusion_1D_analysis_2.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2023-10-20T23:57:02,208 copying build/lib/HydRa/predictions/Occlusion_map_v2.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2023-10-20T23:57:02,211 copying build/lib/HydRa/predictions/Occlusion_map_v3_HydRa2_0.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2023-10-20T23:57:02,215 copying build/lib/HydRa/predictions/Occlusion_map.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2023-10-20T23:57:02,217 copying build/lib/HydRa/predictions/Occlusion_1D_analysis_SONARplus_intrinsic_on_WuhanVirus_20200124_ensScore.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2023-10-20T23:57:02,219 copying build/lib/HydRa/predictions/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2023-10-20T23:57:02,221 copying build/lib/HydRa/predictions/Occlusion_1D_analysis_SONARplus_intrinsic_on_WuhanVirus_20200124.py -> build/bdist.linux-armv7l/wheel/HydRa/predictions 2023-10-20T23:57:02,224 copying build/lib/HydRa/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa 2023-10-20T23:57:02,226 creating build/bdist.linux-armv7l/wheel/HydRa/models 2023-10-20T23:57:02,227 copying build/lib/HydRa/models/Sequence_class.py -> build/bdist.linux-armv7l/wheel/HydRa/models 2023-10-20T23:57:02,230 copying build/lib/HydRa/models/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/models 2023-10-20T23:57:02,232 copying build/lib/HydRa/models/DNN_seq.py -> build/bdist.linux-armv7l/wheel/HydRa/models 2023-10-20T23:57:02,235 copying build/lib/HydRa/HydRa2_0_predict.py -> build/bdist.linux-armv7l/wheel/HydRa 2023-10-20T23:57:02,238 creating build/bdist.linux-armv7l/wheel/HydRa/evaluation 2023-10-20T23:57:02,239 copying build/lib/HydRa/evaluation/ROC_PR_AUC_analysis.py -> build/bdist.linux-armv7l/wheel/HydRa/evaluation 2023-10-20T23:57:02,241 copying build/lib/HydRa/evaluation/__init__.py -> build/bdist.linux-armv7l/wheel/HydRa/evaluation 2023-10-20T23:57:02,243 copying build/lib/HydRa/HydRa_predict.py -> build/bdist.linux-armv7l/wheel/HydRa 2023-10-20T23:57:02,245 running install_egg_info 2023-10-20T23:57:02,273 Copying hydra_rbp.egg-info to build/bdist.linux-armv7l/wheel/hydra_rbp-0.1.21.28-py3.11.egg-info 2023-10-20T23:57:02,285 running install_scripts 2023-10-20T23:57:02,302 creating build/bdist.linux-armv7l/wheel/hydra_rbp-0.1.21.28.dist-info/WHEEL 2023-10-20T23:57:02,305 creating '/tmp/pip-wheel-gaohn94a/hydra_rbp-0.1.21.28-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-10-20T23:57:02,310 adding 'HydRa/HydRa2_0_predict.py' 2023-10-20T23:57:02,314 adding 'HydRa/HydRa_predict.py' 2023-10-20T23:57:02,315 adding 'HydRa/__init__.py' 2023-10-20T23:57:02,316 adding 'HydRa/test_data_load.py' 2023-10-20T23:57:02,704 adding 'HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_menthaBioPlex_STRING.tsv' 2023-10-20T23:57:03,073 adding 'HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_noSS_menthaBioPlex_STRING.tsv' 2023-10-20T23:57:05,248 adding 'HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_AddNoSS_trainedWithWholeDataset.xls' 2023-10-20T23:57:05,823 adding 'HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_noSS_trainedWithWholeDataset.tsv' 2023-10-20T23:57:06,570 adding 'HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_trainedWithWholeDataset.tsv' 2023-10-20T23:57:09,971 adding 'HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv' 2023-10-20T23:57:11,177 adding 'HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv' 2023-10-20T23:57:14,581 adding 'HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv.bk' 2023-10-20T23:57:15,239 adding 'HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv' 2023-10-20T23:57:15,823 adding 'HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv' 2023-10-20T23:57:15,901 adding 'HydRa/data/Combined10RBPlist_uniprotID_20190716.txt' 2023-10-20T23:57:15,945 adding 'HydRa/data/Combined8RBPlist_plusOOPSXRNAXsharedRBPs_uniprotID_20190717.txt' 2023-10-20T23:57:15,947 adding 'HydRa/data/FromOrelOcclRun_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl' 2023-10-20T23:57:15,949 adding 'HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_avg_zscores_statistics.pkl' 2023-10-20T23:57:15,950 adding 'HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_scores_statistics.pkl' 2023-10-20T23:57:17,089 adding 'HydRa/data/HydRa2.0_proteins_with_RBP_categories_RBPflagCorrected_Nov2021_new.tsv' 2023-10-20T23:57:17,160 adding 'HydRa/data/HydRa_v4_7_3_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl' 2023-10-20T23:57:18,920 adding 'HydRa/data/STRING_v10.5_uniprot_edgelist_withoutExperimentalData.txt' 2023-10-20T23:57:19,001 adding 'HydRa/data/SVM_AAC_chi2_alpha0.01_selected_features_From_WholeDataSet_AACname.txt' 2023-10-20T23:57:19,003 adding 'HydRa/data/SVM_SS_11mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt' 2023-10-20T23:57:19,005 adding 'HydRa/data/SVM_SS_15mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt' 2023-10-20T23:57:22,386 adding 'HydRa/data/SVM_SeqFeature_table_comined_all_selected_features_From_WholeDataset_12Apr_AACname.txt' 2023-10-20T23:57:22,707 adding 'HydRa/data/SVM_mer3_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt' 2023-10-20T23:57:22,709 adding 'HydRa/data/SVM_mer4_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt' 2023-10-20T23:57:24,185 adding 'HydRa/data/mentha20180108_BioPlex2.0_edgelist.txt' 2023-10-20T23:57:24,702 adding 'HydRa/data/menthaBioPlex_feature_table_combined10RBPlist.xls' 2023-10-20T23:57:25,287 adding 'HydRa/data/menthaBioPlex_separatedSTRING_feature_table_combined8RBPlistAddingOOPSXRNAX.xls' 2023-10-20T23:57:27,663 adding 'HydRa/data/protVec_100d_3grams.csv' 2023-10-20T23:57:27,734 adding 'HydRa/evaluation/ROC_PR_AUC_analysis.py' 2023-10-20T23:57:27,736 adding 'HydRa/evaluation/__init__.py' 2023-10-20T23:57:27,740 adding 'HydRa/models/DNN_seq.py' 2023-10-20T23:57:27,744 adding 'HydRa/models/Sequence_class.py' 2023-10-20T23:57:27,746 adding 'HydRa/models/__init__.py' 2023-10-20T23:57:27,975 adding 'HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5' 2023-10-20T23:57:28,213 adding 'HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5' 2023-10-20T23:57:28,228 adding 'HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_model_structure.json' 2023-10-20T23:57:28,839 adding 'HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_model_weights.h5' 2023-10-20T23:57:28,873 adding 'HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_model_structure.json' 2023-10-20T23:57:29,481 adding 'HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_model_weights.h5' 2023-10-20T23:57:29,582 adding 'HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5' 2023-10-20T23:57:29,589 adding 'HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5' 2023-10-20T23:57:29,689 adding 'HydRa/pre_trained/SVM_PPI_MB-S_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pkl' 2023-10-20T23:57:29,796 adding 'HydRa/pre_trained/SVM_PPI_MB_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pkl' 2023-10-20T23:57:36,054 adding 'HydRa/pre_trained/SVM_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pickle.pkl' 2023-10-20T23:57:39,591 adding 'HydRa/pre_trained/SVM_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_ModelFile.pickle.pkl' 2023-10-20T23:57:40,129 adding 'HydRa/predictions/Occlusion_1D_analysis_2.py' 2023-10-20T23:57:40,134 adding 'HydRa/predictions/Occlusion_1D_analysis_SONARplus_intrinsic_on_WuhanVirus_20200124.py' 2023-10-20T23:57:40,136 adding 'HydRa/predictions/Occlusion_1D_analysis_SONARplus_intrinsic_on_WuhanVirus_20200124_ensScore.py' 2023-10-20T23:57:40,140 adding 'HydRa/predictions/Occlusion_map.py' 2023-10-20T23:57:40,147 adding 'HydRa/predictions/Occlusion_map_v2.py' 2023-10-20T23:57:40,156 adding 'HydRa/predictions/Occlusion_map_v2_HydRa2_0.py' 2023-10-20T23:57:40,165 adding 'HydRa/predictions/Occlusion_map_v3_HydRa2_0.py' 2023-10-20T23:57:40,167 adding 'HydRa/predictions/__init__.py' 2023-10-20T23:57:40,169 adding 'HydRa/preprocessing/Get_All_selected_SVM_features.py' 2023-10-20T23:57:40,171 adding 'HydRa/preprocessing/PPI_feature_generation.py' 2023-10-20T23:57:40,172 adding 'HydRa/preprocessing/__init__.py' 2023-10-20T23:57:40,174 adding 'HydRa/preprocessing/get_SVM_seq_features.py' 2023-10-20T23:57:40,175 adding 'HydRa/preprocessing/predict_SS.py' 2023-10-20T23:57:40,177 adding 'HydRa/preprocessing/Feature_generation/AAC_feature_table_generation.py' 2023-10-20T23:57:40,178 adding 'HydRa/preprocessing/Feature_generation/PPI_feature_generation.py' 2023-10-20T23:57:40,179 adding 'HydRa/preprocessing/Feature_generation/Secondary_structure_prediction.py' 2023-10-20T23:57:40,180 adding 'HydRa/preprocessing/Feature_generation/__init__.py' 2023-10-20T23:57:40,182 adding 'HydRa/preprocessing/Feature_generation/get_PPI_feature_mat_MB_STRING.py' 2023-10-20T23:57:40,183 adding 'HydRa/preprocessing/Feature_generation/kmer_table_generation.py' 2023-10-20T23:57:40,184 adding 'HydRa/preprocessing/Feature_generation/run_get_PPI_feature_mat_MB_STRING_addingOOPSXRNAXlabelsV2.py' 2023-10-20T23:57:40,186 adding 'HydRa/preprocessing/Feature_selection/Feature_selection_for_each_feature_after_chi2Filtering_forFinalTraining.py' 2023-10-20T23:57:40,187 adding 'HydRa/preprocessing/Feature_selection/__init__.py' 2023-10-20T23:57:40,189 adding 'HydRa/training/__init__.py' 2023-10-20T23:57:40,192 adding 'HydRa/training/train_HydRa.py' 2023-10-20T23:57:40,197 adding 'HydRa/training/train_HydRa2_0.py' 2023-10-20T23:57:40,202 adding 'HydRa/training/train_and_evaluate_HydRa.py' 2023-10-20T23:57:40,208 adding 'HydRa/training/train_and_evaluate_HydRa2_0.py' 2023-10-20T23:57:40,212 adding 'HydRa/training/train_and_evaluate_HydRa_bk.py' 2023-10-20T23:57:40,215 adding 'hydra_rbp-0.1.21.28.dist-info/LICENSE' 2023-10-20T23:57:40,216 adding 'hydra_rbp-0.1.21.28.dist-info/METADATA' 2023-10-20T23:57:40,218 adding 'hydra_rbp-0.1.21.28.dist-info/WHEEL' 2023-10-20T23:57:40,219 adding 'hydra_rbp-0.1.21.28.dist-info/entry_points.txt' 2023-10-20T23:57:40,219 adding 'hydra_rbp-0.1.21.28.dist-info/top_level.txt' 2023-10-20T23:57:40,221 adding 'hydra_rbp-0.1.21.28.dist-info/RECORD' 2023-10-20T23:57:40,306 removing build/bdist.linux-armv7l/wheel 2023-10-20T23:57:40,556 Building wheel for hydra-rbp (setup.py): finished with status 'done' 2023-10-20T23:57:41,179 Created wheel for hydra-rbp: filename=hydra_rbp-0.1.21.28-py3-none-any.whl size=53774465 sha256=2dce1c5216cc6dfeb287ba82fc7ecc0f084574aebca3a134b3d2dd9c2c0bd3dc 2023-10-20T23:57:41,180 Stored in directory: /tmp/pip-ephem-wheel-cache-i9t_xor1/wheels/bf/75/d5/39f0a591b07778db8354090436e1312b79edec6a98b8bd5530 2023-10-20T23:57:41,211 Successfully built hydra-rbp 2023-10-20T23:57:42,550 Removed build tracker: '/tmp/pip-build-tracker-vvhyt6zk'