2024-11-02T17:14:46,228 Disabling truststore because Python version isn't 3.10+ 2024-11-02T17:14:46,696 Created temporary directory: /tmp/pip-build-tracker-qvnh93dn 2024-11-02T17:14:46,697 Initialized build tracking at /tmp/pip-build-tracker-qvnh93dn 2024-11-02T17:14:46,697 Created build tracker: /tmp/pip-build-tracker-qvnh93dn 2024-11-02T17:14:46,698 Entered build tracker: /tmp/pip-build-tracker-qvnh93dn 2024-11-02T17:14:46,698 Created temporary directory: /tmp/pip-wheel-m065_q1y 2024-11-02T17:14:46,704 Created temporary directory: /tmp/pip-ephem-wheel-cache-8udejcql 2024-11-02T17:14:46,745 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-11-02T17:14:46,748 2 location(s) to search for versions of proteomedataprep: 2024-11-02T17:14:46,748 * https://pypi.org/simple/proteomedataprep/ 2024-11-02T17:14:46,748 * https://www.piwheels.org/simple/proteomedataprep/ 2024-11-02T17:14:46,749 Fetching project page and analyzing links: https://pypi.org/simple/proteomedataprep/ 2024-11-02T17:14:46,749 Getting page https://pypi.org/simple/proteomedataprep/ 2024-11-02T17:14:46,751 Found index url https://pypi.org/simple/ 2024-11-02T17:14:46,906 Fetched page https://pypi.org/simple/proteomedataprep/ as application/vnd.pypi.simple.v1+json 2024-11-02T17:14:46,909 Skipping link: No binaries permitted for proteomedataprep: https://files.pythonhosted.org/packages/43/6b/4e39e06e38aaf068629784a7295f5a051bf2f045fda0d161ac781e77fed8/ProteomeDataPrep-0.1.0-py3-none-any.whl (from https://pypi.org/simple/proteomedataprep/) (requires-python:>=3.6) 2024-11-02T17:14:46,910 Found link https://files.pythonhosted.org/packages/c5/aa/27a6f70896dfb99a924f00c909a438019868aec0e1e7d48696edd83ec7c3/proteomedataprep-0.1.0.tar.gz (from https://pypi.org/simple/proteomedataprep/) (requires-python:>=3.6), version: 0.1.0 2024-11-02T17:14:46,910 Skipping link: No binaries permitted for proteomedataprep: https://files.pythonhosted.org/packages/c4/44/e6d782cb71a9efd4b62a6db38610962ba23731e2b1de6e03c3247a74db5a/ProteomeDataPrep-0.2.0-py3-none-any.whl (from https://pypi.org/simple/proteomedataprep/) (requires-python:>=3.6) 2024-11-02T17:14:46,910 Found link https://files.pythonhosted.org/packages/af/e3/f1d00196524835d572126c422fcf300df4947749200d430492580037c55a/proteomedataprep-0.2.0.tar.gz (from https://pypi.org/simple/proteomedataprep/) (requires-python:>=3.6), version: 0.2.0 2024-11-02T17:14:46,911 Skipping link: No binaries permitted for proteomedataprep: https://files.pythonhosted.org/packages/71/4d/1a0a049752b2614e34d3b027a66853f242586403db0ae623c789716c34bc/ProteomeDataPrep-0.2.1-py3-none-any.whl (from https://pypi.org/simple/proteomedataprep/) (requires-python:>=3.6) 2024-11-02T17:14:46,911 Found link https://files.pythonhosted.org/packages/d0/e3/995cdf9ab27398225e07fe4874f79bf81a27a13e52d59a55f222a94ac518/proteomedataprep-0.2.1.tar.gz (from https://pypi.org/simple/proteomedataprep/) (requires-python:>=3.6), version: 0.2.1 2024-11-02T17:14:46,911 Skipping link: No binaries permitted for proteomedataprep: https://files.pythonhosted.org/packages/ac/64/a3abb82026c082f787dfc15ba35271a8ec9f8a092e368226f5912dda8450/ProteomeDataPrep-0.2.2-py3-none-any.whl (from https://pypi.org/simple/proteomedataprep/) (requires-python:>=3.6) 2024-11-02T17:14:46,912 Found link https://files.pythonhosted.org/packages/89/e2/d0d864b83e71e2c0551230b154fb8c1898c0553927e494888be78644ba86/proteomedataprep-0.2.2.tar.gz (from https://pypi.org/simple/proteomedataprep/) (requires-python:>=3.6), version: 0.2.2 2024-11-02T17:14:46,912 Skipping link: No binaries permitted for proteomedataprep: https://files.pythonhosted.org/packages/2f/4f/34eb6fb5ef8ad1fd3183d5b9d2721dc619c7b5cd28dcb724dcdb58c0a8b7/ProteomeDataPrep-0.2.3-py3-none-any.whl (from https://pypi.org/simple/proteomedataprep/) (requires-python:>=3.6) 2024-11-02T17:14:46,913 Found link https://files.pythonhosted.org/packages/ae/d0/c6aaf2bb351ef8754e19916365ee7728d91a89627591eba8d7c1f3b0f0fd/proteomedataprep-0.2.3.tar.gz (from https://pypi.org/simple/proteomedataprep/) (requires-python:>=3.6), version: 0.2.3 2024-11-02T17:14:46,913 Skipping link: No binaries permitted for proteomedataprep: https://files.pythonhosted.org/packages/ad/04/1e3763d8b16ec3a5aed7213b2fc58f08f3fc8b6972a121b47c2405f6be47/ProteomeDataPrep-0.2.4-py3-none-any.whl (from https://pypi.org/simple/proteomedataprep/) (requires-python:>=3.6) 2024-11-02T17:14:46,913 Found link https://files.pythonhosted.org/packages/46/c2/4b16b50011de85d52c84928a3c2632c169252f9aebefb9e9629ec57c163f/proteomedataprep-0.2.4.tar.gz (from https://pypi.org/simple/proteomedataprep/) (requires-python:>=3.6), version: 0.2.4 2024-11-02T17:14:46,914 Fetching project page and analyzing links: https://www.piwheels.org/simple/proteomedataprep/ 2024-11-02T17:14:46,914 Getting page https://www.piwheels.org/simple/proteomedataprep/ 2024-11-02T17:14:46,915 Found index url https://www.piwheels.org/simple/ 2024-11-02T17:14:46,958 Fetched page https://www.piwheels.org/simple/proteomedataprep/ as text/html 2024-11-02T17:14:46,959 Skipping link: not a file: https://www.piwheels.org/simple/proteomedataprep/ 2024-11-02T17:14:46,960 Skipping link: not a file: https://pypi.org/simple/proteomedataprep/ 2024-11-02T17:14:46,975 Given no hashes to check 1 links for project 'proteomedataprep': discarding no candidates 2024-11-02T17:14:46,977 Collecting proteomedataprep==0.1.0 2024-11-02T17:14:46,980 Created temporary directory: /tmp/pip-unpack-yi4s3whi 2024-11-02T17:14:47,080 Downloading proteomedataprep-0.1.0.tar.gz (840 kB) 2024-11-02T17:14:47,609 Added proteomedataprep==0.1.0 from https://files.pythonhosted.org/packages/c5/aa/27a6f70896dfb99a924f00c909a438019868aec0e1e7d48696edd83ec7c3/proteomedataprep-0.1.0.tar.gz to build tracker '/tmp/pip-build-tracker-qvnh93dn' 2024-11-02T17:14:47,611 Running setup.py (path:/tmp/pip-wheel-m065_q1y/proteomedataprep_a337cc7163914396977ec8260945ea58/setup.py) egg_info for package proteomedataprep 2024-11-02T17:14:47,612 Created temporary directory: /tmp/pip-pip-egg-info-93mk7nxu 2024-11-02T17:14:47,612 Preparing metadata (setup.py): started 2024-11-02T17:14:47,613 Running command python setup.py egg_info 2024-11-02T17:14:50,626 running egg_info 2024-11-02T17:14:50,654 creating /tmp/pip-pip-egg-info-93mk7nxu/ProteomeDataPrep.egg-info 2024-11-02T17:14:50,656 writing /tmp/pip-pip-egg-info-93mk7nxu/ProteomeDataPrep.egg-info/PKG-INFO 2024-11-02T17:14:50,660 writing dependency_links to /tmp/pip-pip-egg-info-93mk7nxu/ProteomeDataPrep.egg-info/dependency_links.txt 2024-11-02T17:14:50,662 writing requirements to /tmp/pip-pip-egg-info-93mk7nxu/ProteomeDataPrep.egg-info/requires.txt 2024-11-02T17:14:50,664 writing top-level names to /tmp/pip-pip-egg-info-93mk7nxu/ProteomeDataPrep.egg-info/top_level.txt 2024-11-02T17:14:50,665 writing manifest file '/tmp/pip-pip-egg-info-93mk7nxu/ProteomeDataPrep.egg-info/SOURCES.txt' 2024-11-02T17:14:50,756 reading manifest file '/tmp/pip-pip-egg-info-93mk7nxu/ProteomeDataPrep.egg-info/SOURCES.txt' 2024-11-02T17:14:50,761 writing manifest file '/tmp/pip-pip-egg-info-93mk7nxu/ProteomeDataPrep.egg-info/SOURCES.txt' 2024-11-02T17:14:50,850 Preparing metadata (setup.py): finished with status 'done' 2024-11-02T17:14:50,855 Source in /tmp/pip-wheel-m065_q1y/proteomedataprep_a337cc7163914396977ec8260945ea58 has version 0.1.0, which satisfies requirement proteomedataprep==0.1.0 from https://files.pythonhosted.org/packages/c5/aa/27a6f70896dfb99a924f00c909a438019868aec0e1e7d48696edd83ec7c3/proteomedataprep-0.1.0.tar.gz 2024-11-02T17:14:51,754 Removed proteomedataprep==0.1.0 from https://files.pythonhosted.org/packages/c5/aa/27a6f70896dfb99a924f00c909a438019868aec0e1e7d48696edd83ec7c3/proteomedataprep-0.1.0.tar.gz from build tracker '/tmp/pip-build-tracker-qvnh93dn' 2024-11-02T17:14:51,762 Created temporary directory: /tmp/pip-unpack-yr5ruwo_ 2024-11-02T17:14:51,763 Created temporary directory: /tmp/pip-unpack-w74bd16s 2024-11-02T17:14:51,763 Building wheels for collected packages: proteomedataprep 2024-11-02T17:14:51,767 Created temporary directory: /tmp/pip-wheel-j87wl6o2 2024-11-02T17:14:51,767 Building wheel for proteomedataprep (setup.py): started 2024-11-02T17:14:51,768 Destination directory: /tmp/pip-wheel-j87wl6o2 2024-11-02T17:14:51,768 Running command python setup.py bdist_wheel 2024-11-02T17:14:52,834 running bdist_wheel 2024-11-02T17:14:52,968 running build 2024-11-02T17:14:52,968 running build_py 2024-11-02T17:14:52,997 creating build/lib/proteome_data_prep 2024-11-02T17:14:52,999 copying proteome_data_prep/process_utils.py -> build/lib/proteome_data_prep 2024-11-02T17:14:53,002 copying proteome_data_prep/__init__.py -> build/lib/proteome_data_prep 2024-11-02T17:14:53,003 copying proteome_data_prep/peptide_processor.py -> build/lib/proteome_data_prep 2024-11-02T17:14:53,006 copying proteome_data_prep/data_loader.py -> build/lib/proteome_data_prep 2024-11-02T17:14:53,009 copying proteome_data_prep/data_container.py -> build/lib/proteome_data_prep 2024-11-02T17:14:53,010 copying proteome_data_prep/protein_processor.py -> build/lib/proteome_data_prep 2024-11-02T17:14:53,012 running egg_info 2024-11-02T17:14:53,038 writing ProteomeDataPrep.egg-info/PKG-INFO 2024-11-02T17:14:53,041 writing dependency_links to ProteomeDataPrep.egg-info/dependency_links.txt 2024-11-02T17:14:53,043 writing requirements to ProteomeDataPrep.egg-info/requires.txt 2024-11-02T17:14:53,044 writing top-level names to ProteomeDataPrep.egg-info/top_level.txt 2024-11-02T17:14:53,074 reading manifest file 'ProteomeDataPrep.egg-info/SOURCES.txt' 2024-11-02T17:14:53,080 writing manifest file 'ProteomeDataPrep.egg-info/SOURCES.txt' 2024-11-02T17:14:53,082 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'proteome_data_prep.data' is absent from the `packages` configuration. 2024-11-02T17:14:53,083 !! 2024-11-02T17:14:53,083 ******************************************************************************** 2024-11-02T17:14:53,083 ############################ 2024-11-02T17:14:53,083 # Package would be ignored # 2024-11-02T17:14:53,083 ############################ 2024-11-02T17:14:53,083 Python recognizes 'proteome_data_prep.data' as an importable package[^1], 2024-11-02T17:14:53,084 but it is absent from setuptools' `packages` configuration. 2024-11-02T17:14:53,084 This leads to an ambiguous overall configuration. If you want to distribute this 2024-11-02T17:14:53,084 package, please make sure that 'proteome_data_prep.data' is explicitly added 2024-11-02T17:14:53,084 to the `packages` configuration field. 2024-11-02T17:14:53,084 Alternatively, you can also rely on setuptools' discovery methods 2024-11-02T17:14:53,084 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-11-02T17:14:53,085 instead of `find_packages(...)`/`find:`). 2024-11-02T17:14:53,085 You can read more about "package discovery" on setuptools documentation page: 2024-11-02T17:14:53,085 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-11-02T17:14:53,085 If you don't want 'proteome_data_prep.data' to be distributed and are 2024-11-02T17:14:53,085 already explicitly excluding 'proteome_data_prep.data' via 2024-11-02T17:14:53,086 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-11-02T17:14:53,086 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-11-02T17:14:53,086 combination with a more fine grained `package-data` configuration. 2024-11-02T17:14:53,086 You can read more about "package data files" on setuptools documentation page: 2024-11-02T17:14:53,086 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-11-02T17:14:53,087 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-11-02T17:14:53,087 even if it does not contain any `.py` files. 2024-11-02T17:14:53,087 On the other hand, currently there is no concept of package data 2024-11-02T17:14:53,087 directory, all directories are treated like packages. 2024-11-02T17:14:53,087 ******************************************************************************** 2024-11-02T17:14:53,088 !! 2024-11-02T17:14:53,088 check.warn(importable) 2024-11-02T17:14:53,088 creating build/lib/proteome_data_prep/data 2024-11-02T17:14:53,088 copying proteome_data_prep/data/acc_by_tf_gene.json -> build/lib/proteome_data_prep/data 2024-11-02T17:14:53,089 copying proteome_data_prep/data/bad_batches.txt -> build/lib/proteome_data_prep/data 2024-11-02T17:14:53,091 copying proteome_data_prep/data/gene_info_by_acc.json -> build/lib/proteome_data_prep/data 2024-11-02T17:14:53,159 copying proteome_data_prep/data/tf_proteins.txt -> build/lib/proteome_data_prep/data 2024-11-02T17:14:53,187 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-11-02T17:14:53,188 !! 2024-11-02T17:14:53,188 ******************************************************************************** 2024-11-02T17:14:53,188 Please avoid running ``setup.py`` directly. 2024-11-02T17:14:53,188 Instead, use pypa/build, pypa/installer or other 2024-11-02T17:14:53,188 standards-based tools. 2024-11-02T17:14:53,189 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-11-02T17:14:53,189 ******************************************************************************** 2024-11-02T17:14:53,189 !! 2024-11-02T17:14:53,189 self.initialize_options() 2024-11-02T17:14:53,212 installing to build/bdist.linux-armv7l/wheel 2024-11-02T17:14:53,213 running install 2024-11-02T17:14:53,238 running install_lib 2024-11-02T17:14:53,263 creating build/bdist.linux-armv7l/wheel 2024-11-02T17:14:53,265 creating build/bdist.linux-armv7l/wheel/proteome_data_prep 2024-11-02T17:14:53,266 copying build/lib/proteome_data_prep/process_utils.py -> build/bdist.linux-armv7l/wheel/./proteome_data_prep 2024-11-02T17:14:53,269 copying build/lib/proteome_data_prep/__init__.py -> build/bdist.linux-armv7l/wheel/./proteome_data_prep 2024-11-02T17:14:53,271 copying build/lib/proteome_data_prep/peptide_processor.py -> build/bdist.linux-armv7l/wheel/./proteome_data_prep 2024-11-02T17:14:53,273 copying build/lib/proteome_data_prep/data_loader.py -> build/bdist.linux-armv7l/wheel/./proteome_data_prep 2024-11-02T17:14:53,275 copying build/lib/proteome_data_prep/data_container.py -> build/bdist.linux-armv7l/wheel/./proteome_data_prep 2024-11-02T17:14:53,278 creating build/bdist.linux-armv7l/wheel/proteome_data_prep/data 2024-11-02T17:14:53,279 copying build/lib/proteome_data_prep/data/gene_info_by_acc.json -> build/bdist.linux-armv7l/wheel/./proteome_data_prep/data 2024-11-02T17:14:53,354 copying build/lib/proteome_data_prep/data/tf_proteins.txt -> build/bdist.linux-armv7l/wheel/./proteome_data_prep/data 2024-11-02T17:14:53,357 copying build/lib/proteome_data_prep/data/acc_by_tf_gene.json -> build/bdist.linux-armv7l/wheel/./proteome_data_prep/data 2024-11-02T17:14:53,359 copying build/lib/proteome_data_prep/data/bad_batches.txt -> build/bdist.linux-armv7l/wheel/./proteome_data_prep/data 2024-11-02T17:14:53,361 copying build/lib/proteome_data_prep/protein_processor.py -> build/bdist.linux-armv7l/wheel/./proteome_data_prep 2024-11-02T17:14:53,363 running install_egg_info 2024-11-02T17:14:53,394 Copying ProteomeDataPrep.egg-info to build/bdist.linux-armv7l/wheel/./ProteomeDataPrep-0.1.0-py3.9.egg-info 2024-11-02T17:14:53,403 running install_scripts 2024-11-02T17:14:53,417 creating build/bdist.linux-armv7l/wheel/ProteomeDataPrep-0.1.0.dist-info/WHEEL 2024-11-02T17:14:53,419 creating '/tmp/pip-wheel-j87wl6o2/ProteomeDataPrep-0.1.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-11-02T17:14:53,422 adding 'proteome_data_prep/__init__.py' 2024-11-02T17:14:53,423 adding 'proteome_data_prep/data_container.py' 2024-11-02T17:14:53,425 adding 'proteome_data_prep/data_loader.py' 2024-11-02T17:14:53,428 adding 'proteome_data_prep/peptide_processor.py' 2024-11-02T17:14:53,430 adding 'proteome_data_prep/process_utils.py' 2024-11-02T17:14:53,432 adding 'proteome_data_prep/protein_processor.py' 2024-11-02T17:14:53,439 adding 'proteome_data_prep/data/acc_by_tf_gene.json' 2024-11-02T17:14:53,440 adding 'proteome_data_prep/data/bad_batches.txt' 2024-11-02T17:14:53,792 adding 'proteome_data_prep/data/gene_info_by_acc.json' 2024-11-02T17:14:53,832 adding 'proteome_data_prep/data/tf_proteins.txt' 2024-11-02T17:14:53,835 adding 'ProteomeDataPrep-0.1.0.dist-info/METADATA' 2024-11-02T17:14:53,837 adding 'ProteomeDataPrep-0.1.0.dist-info/WHEEL' 2024-11-02T17:14:53,839 adding 'ProteomeDataPrep-0.1.0.dist-info/top_level.txt' 2024-11-02T17:14:53,840 adding 'ProteomeDataPrep-0.1.0.dist-info/RECORD' 2024-11-02T17:14:53,868 removing build/bdist.linux-armv7l/wheel 2024-11-02T17:14:53,977 Building wheel for proteomedataprep (setup.py): finished with status 'done' 2024-11-02T17:14:53,989 Created wheel for proteomedataprep: filename=ProteomeDataPrep-0.1.0-py3-none-any.whl size=863720 sha256=d8ad9f89b3d8739e9e7779cafe89fe7ecb1dd70716a6a1141b2f2aec90b7af6d 2024-11-02T17:14:53,990 Stored in directory: /tmp/pip-ephem-wheel-cache-8udejcql/wheels/8f/b3/c0/ddc61de2869633f4c6512b7de0045493b1d141bbbf8b430635 2024-11-02T17:14:54,001 Successfully built proteomedataprep 2024-11-02T17:14:54,024 Removed build tracker: '/tmp/pip-build-tracker-qvnh93dn'