2025-06-07T16:53:24,855 Created temporary directory: /tmp/pip-build-tracker-6667708z 2025-06-07T16:53:24,856 Initialized build tracking at /tmp/pip-build-tracker-6667708z 2025-06-07T16:53:24,856 Created build tracker: /tmp/pip-build-tracker-6667708z 2025-06-07T16:53:24,857 Entered build tracker: /tmp/pip-build-tracker-6667708z 2025-06-07T16:53:24,858 Created temporary directory: /tmp/pip-wheel-hkt07mvv 2025-06-07T16:53:24,862 Created temporary directory: /tmp/pip-ephem-wheel-cache-w8losgtx 2025-06-07T16:53:24,915 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-06-07T16:53:24,918 2 location(s) to search for versions of promb: 2025-06-07T16:53:24,918 * https://pypi.org/simple/promb/ 2025-06-07T16:53:24,918 * https://www.piwheels.org/simple/promb/ 2025-06-07T16:53:24,919 Fetching project page and analyzing links: https://pypi.org/simple/promb/ 2025-06-07T16:53:24,919 Getting page https://pypi.org/simple/promb/ 2025-06-07T16:53:24,921 Found index url https://pypi.org/simple/ 2025-06-07T16:53:25,084 Fetched page https://pypi.org/simple/promb/ as application/vnd.pypi.simple.v1+json 2025-06-07T16:53:25,086 Skipping link: No binaries permitted for promb: https://files.pythonhosted.org/packages/0b/1b/45491921d19957e516d87999d53a78912e71a9dcb1322517b6b72434ff47/promb-1.0.0-py3-none-any.whl (from https://pypi.org/simple/promb/) (requires-python:>=3.8) 2025-06-07T16:53:25,088 Found link https://files.pythonhosted.org/packages/20/e3/83d440c84b242a78be190fcf0f667118e6bc2078bda79c4ca15deb138c46/promb-1.0.0.tar.gz (from https://pypi.org/simple/promb/) (requires-python:>=3.8), version: 1.0.0 2025-06-07T16:53:25,089 Skipping link: No binaries permitted for promb: https://files.pythonhosted.org/packages/32/0b/cf021945b0642d25bdfe9881d481409699a5b19c6da16fa85f77bfdba7d7/promb-1.0.1-py3-none-any.whl (from https://pypi.org/simple/promb/) (requires-python:>=3.8) 2025-06-07T16:53:25,090 Found link https://files.pythonhosted.org/packages/47/eb/d057b212de120b65fcf9db7a340c48ff254994af13c6ecf69f06658bff68/promb-1.0.1.tar.gz (from https://pypi.org/simple/promb/) (requires-python:>=3.8), version: 1.0.1 2025-06-07T16:53:25,090 Skipping link: No binaries permitted for promb: https://files.pythonhosted.org/packages/62/b8/6315b46baf27331c4117ceb7aa3ce2c26fee9dd20719378e53717f7033a9/promb-1.0.2-py3-none-any.whl (from https://pypi.org/simple/promb/) (requires-python:>=3.8) 2025-06-07T16:53:25,091 Found link https://files.pythonhosted.org/packages/e1/bc/8a78638f65becbdc5f22c6766db489726bcaeb3720f10f3b8c03e5effd9f/promb-1.0.2.tar.gz (from https://pypi.org/simple/promb/) (requires-python:>=3.8), version: 1.0.2 2025-06-07T16:53:25,092 Fetching project page and analyzing links: https://www.piwheels.org/simple/promb/ 2025-06-07T16:53:25,093 Getting page https://www.piwheels.org/simple/promb/ 2025-06-07T16:53:25,095 Found index url https://www.piwheels.org/simple/ 2025-06-07T16:53:25,269 WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/promb/ 2025-06-07T16:53:25,931 WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/promb/ 2025-06-07T16:53:27,105 WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/promb/ 2025-06-07T16:53:29,279 WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/promb/ 2025-06-07T16:53:33,448 WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/promb/ 2025-06-07T16:53:33,620 Could not fetch URL https://www.piwheels.org/simple/promb/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='www.piwheels.org', port=443): Max retries exceeded with url: /simple/promb/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))) - skipping 2025-06-07T16:53:33,622 Skipping link: not a file: https://www.piwheels.org/simple/promb/ 2025-06-07T16:53:33,623 Skipping link: not a file: https://pypi.org/simple/promb/ 2025-06-07T16:53:33,644 Given no hashes to check 1 links for project 'promb': discarding no candidates 2025-06-07T16:53:33,646 Collecting promb==1.0.1 2025-06-07T16:53:33,649 Created temporary directory: /tmp/pip-unpack-zojswye3 2025-06-07T16:53:34,010 Downloading promb-1.0.1.tar.gz (39.3 MB) 2025-06-07T16:53:41,406 Added promb==1.0.1 from https://files.pythonhosted.org/packages/47/eb/d057b212de120b65fcf9db7a340c48ff254994af13c6ecf69f06658bff68/promb-1.0.1.tar.gz to build tracker '/tmp/pip-build-tracker-6667708z' 2025-06-07T16:53:41,408 Running setup.py (path:/tmp/pip-wheel-hkt07mvv/promb_729b6c05f35b4b8ba70def7ced17d56d/setup.py) egg_info for package promb 2025-06-07T16:53:41,409 Created temporary directory: /tmp/pip-pip-egg-info-fim8tz7u 2025-06-07T16:53:41,410 Preparing metadata (setup.py): started 2025-06-07T16:53:41,411 Running command python setup.py egg_info 2025-06-07T16:53:42,356 running egg_info 2025-06-07T16:53:42,384 creating /tmp/pip-pip-egg-info-fim8tz7u/promb.egg-info 2025-06-07T16:53:42,385 writing /tmp/pip-pip-egg-info-fim8tz7u/promb.egg-info/PKG-INFO 2025-06-07T16:53:42,389 writing dependency_links to /tmp/pip-pip-egg-info-fim8tz7u/promb.egg-info/dependency_links.txt 2025-06-07T16:53:42,391 writing entry points to /tmp/pip-pip-egg-info-fim8tz7u/promb.egg-info/entry_points.txt 2025-06-07T16:53:42,392 writing requirements to /tmp/pip-pip-egg-info-fim8tz7u/promb.egg-info/requires.txt 2025-06-07T16:53:42,393 writing top-level names to /tmp/pip-pip-egg-info-fim8tz7u/promb.egg-info/top_level.txt 2025-06-07T16:53:42,395 writing manifest file '/tmp/pip-pip-egg-info-fim8tz7u/promb.egg-info/SOURCES.txt' 2025-06-07T16:53:42,488 reading manifest file '/tmp/pip-pip-egg-info-fim8tz7u/promb.egg-info/SOURCES.txt' 2025-06-07T16:53:42,489 reading manifest template 'MANIFEST.in' 2025-06-07T16:53:42,504 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2025-06-07T16:53:42,504 warning: no previously-included files matching '*.pyo' found anywhere in distribution 2025-06-07T16:53:42,505 warning: no previously-included files matching '.git' found anywhere in distribution 2025-06-07T16:53:42,506 warning: no previously-included files matching '.DS_Store' found anywhere in distribution 2025-06-07T16:53:42,506 warning: no previously-included files matching '.ipynb_checkpoints' found anywhere in distribution 2025-06-07T16:53:42,507 no previously-included directories found matching 'tests' 2025-06-07T16:53:42,508 no previously-included directories found matching 'work' 2025-06-07T16:53:42,508 adding license file 'LICENSE' 2025-06-07T16:53:42,509 adding license file 'LICENSES_THIRD_PARTY' 2025-06-07T16:53:42,511 writing manifest file '/tmp/pip-pip-egg-info-fim8tz7u/promb.egg-info/SOURCES.txt' 2025-06-07T16:53:42,616 Preparing metadata (setup.py): finished with status 'done' 2025-06-07T16:53:42,620 Source in /tmp/pip-wheel-hkt07mvv/promb_729b6c05f35b4b8ba70def7ced17d56d has version 1.0.1, which satisfies requirement promb==1.0.1 from https://files.pythonhosted.org/packages/47/eb/d057b212de120b65fcf9db7a340c48ff254994af13c6ecf69f06658bff68/promb-1.0.1.tar.gz 2025-06-07T16:53:42,621 Removed promb==1.0.1 from https://files.pythonhosted.org/packages/47/eb/d057b212de120b65fcf9db7a340c48ff254994af13c6ecf69f06658bff68/promb-1.0.1.tar.gz from build tracker '/tmp/pip-build-tracker-6667708z' 2025-06-07T16:53:42,628 Created temporary directory: /tmp/pip-unpack-y7ljmm7q 2025-06-07T16:53:42,629 Created temporary directory: /tmp/pip-unpack-47mb35l0 2025-06-07T16:53:42,630 Building wheels for collected packages: promb 2025-06-07T16:53:42,635 Created temporary directory: /tmp/pip-wheel-d4_pz7rv 2025-06-07T16:53:42,636 DEPRECATION: Building 'promb' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'promb'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-06-07T16:53:42,638 Building wheel for promb (setup.py): started 2025-06-07T16:53:42,639 Destination directory: /tmp/pip-wheel-d4_pz7rv 2025-06-07T16:53:42,640 Running command python setup.py bdist_wheel 2025-06-07T16:53:43,477 running bdist_wheel 2025-06-07T16:53:43,610 running build 2025-06-07T16:53:43,611 running build_py 2025-06-07T16:53:43,642 creating build/lib/promb 2025-06-07T16:53:43,644 copying promb/__init__.py -> build/lib/promb 2025-06-07T16:53:43,646 copying promb/cli.py -> build/lib/promb 2025-06-07T16:53:43,649 copying promb/__version__.py -> build/lib/promb 2025-06-07T16:53:43,651 copying promb/parsing.py -> build/lib/promb 2025-06-07T16:53:43,653 copying promb/formatting.py -> build/lib/promb 2025-06-07T16:53:43,655 copying promb/netmhc.py -> build/lib/promb 2025-06-07T16:53:43,658 copying promb/db.py -> build/lib/promb 2025-06-07T16:53:43,661 running egg_info 2025-06-07T16:53:43,691 writing promb.egg-info/PKG-INFO 2025-06-07T16:53:43,695 writing dependency_links to promb.egg-info/dependency_links.txt 2025-06-07T16:53:43,696 writing entry points to promb.egg-info/entry_points.txt 2025-06-07T16:53:43,698 writing requirements to promb.egg-info/requires.txt 2025-06-07T16:53:43,699 writing top-level names to promb.egg-info/top_level.txt 2025-06-07T16:53:43,730 reading manifest file 'promb.egg-info/SOURCES.txt' 2025-06-07T16:53:43,733 reading manifest template 'MANIFEST.in' 2025-06-07T16:53:43,747 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2025-06-07T16:53:43,748 warning: no previously-included files matching '*.pyo' found anywhere in distribution 2025-06-07T16:53:43,749 warning: no previously-included files matching '.git' found anywhere in distribution 2025-06-07T16:53:43,750 warning: no previously-included files matching '.DS_Store' found anywhere in distribution 2025-06-07T16:53:43,750 warning: no previously-included files matching '.ipynb_checkpoints' found anywhere in distribution 2025-06-07T16:53:43,751 no previously-included directories found matching 'tests' 2025-06-07T16:53:43,752 no previously-included directories found matching 'work' 2025-06-07T16:53:43,752 adding license file 'LICENSE' 2025-06-07T16:53:43,753 adding license file 'LICENSES_THIRD_PARTY' 2025-06-07T16:53:43,756 writing manifest file 'promb.egg-info/SOURCES.txt' 2025-06-07T16:53:43,758 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'promb.resources' is absent from the `packages` configuration. 2025-06-07T16:53:43,759 !! 2025-06-07T16:53:43,760 ******************************************************************************** 2025-06-07T16:53:43,761 ############################ 2025-06-07T16:53:43,761 # Package would be ignored # 2025-06-07T16:53:43,762 ############################ 2025-06-07T16:53:43,762 Python recognizes 'promb.resources' as an importable package[^1], 2025-06-07T16:53:43,763 but it is absent from setuptools' `packages` configuration. 2025-06-07T16:53:43,765 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-07T16:53:43,765 package, please make sure that 'promb.resources' is explicitly added 2025-06-07T16:53:43,766 to the `packages` configuration field. 2025-06-07T16:53:43,766 Alternatively, you can also rely on setuptools' discovery methods 2025-06-07T16:53:43,767 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-07T16:53:43,767 instead of `find_packages(...)`/`find:`). 2025-06-07T16:53:43,768 You can read more about "package discovery" on setuptools documentation page: 2025-06-07T16:53:43,769 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-07T16:53:43,770 If you don't want 'promb.resources' to be distributed and are 2025-06-07T16:53:43,771 already explicitly excluding 'promb.resources' via 2025-06-07T16:53:43,771 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-07T16:53:43,772 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-07T16:53:43,772 combination with a more fine grained `package-data` configuration. 2025-06-07T16:53:43,773 You can read more about "package data files" on setuptools documentation page: 2025-06-07T16:53:43,774 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-07T16:53:43,775 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-07T16:53:43,776 even if it does not contain any `.py` files. 2025-06-07T16:53:43,777 On the other hand, currently there is no concept of package data 2025-06-07T16:53:43,777 directory, all directories are treated like packages. 2025-06-07T16:53:43,778 ******************************************************************************** 2025-06-07T16:53:43,779 !! 2025-06-07T16:53:43,780 check.warn(importable) 2025-06-07T16:53:43,781 creating build/lib/promb/resources 2025-06-07T16:53:43,781 copying promb/resources/OASis_9mers_v1_10perc_subjects.txt.gz -> build/lib/promb/resources 2025-06-07T16:53:43,969 copying promb/resources/uniprot_sprot_human.fasta.gz -> build/lib/promb/resources 2025-06-07T16:53:44,089 copying promb/resources/uniprotkb_proteome_UP000005640_2025_04_21.fasta.gz -> build/lib/promb/resources 2025-06-07T16:53:44,429 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-06-07T16:53:44,430 !! 2025-06-07T16:53:44,431 ******************************************************************************** 2025-06-07T16:53:44,432 Please avoid running ``setup.py`` directly. 2025-06-07T16:53:44,432 Instead, use pypa/build, pypa/installer or other 2025-06-07T16:53:44,433 standards-based tools. 2025-06-07T16:53:44,434 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-06-07T16:53:44,434 or your builds will no longer be supported. 2025-06-07T16:53:44,436 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-06-07T16:53:44,436 ******************************************************************************** 2025-06-07T16:53:44,438 !! 2025-06-07T16:53:44,438 self.initialize_options() 2025-06-07T16:53:44,459 installing to build/bdist.linux-armv7l/wheel 2025-06-07T16:53:44,460 running install 2025-06-07T16:53:44,484 running install_lib 2025-06-07T16:53:44,511 creating build/bdist.linux-armv7l/wheel 2025-06-07T16:53:44,513 creating build/bdist.linux-armv7l/wheel/promb 2025-06-07T16:53:44,514 copying build/lib/promb/__init__.py -> build/bdist.linux-armv7l/wheel/./promb 2025-06-07T16:53:44,516 copying build/lib/promb/cli.py -> build/bdist.linux-armv7l/wheel/./promb 2025-06-07T16:53:44,519 creating build/bdist.linux-armv7l/wheel/promb/resources 2025-06-07T16:53:44,520 copying build/lib/promb/resources/uniprotkb_proteome_UP000005640_2025_04_21.fasta.gz -> build/bdist.linux-armv7l/wheel/./promb/resources 2025-06-07T16:53:44,838 copying build/lib/promb/resources/uniprot_sprot_human.fasta.gz -> build/bdist.linux-armv7l/wheel/./promb/resources 2025-06-07T16:53:44,949 copying build/lib/promb/resources/OASis_9mers_v1_10perc_subjects.txt.gz -> build/bdist.linux-armv7l/wheel/./promb/resources 2025-06-07T16:53:45,163 copying build/lib/promb/__version__.py -> build/bdist.linux-armv7l/wheel/./promb 2025-06-07T16:53:45,165 copying build/lib/promb/parsing.py -> build/bdist.linux-armv7l/wheel/./promb 2025-06-07T16:53:45,167 copying build/lib/promb/formatting.py -> build/bdist.linux-armv7l/wheel/./promb 2025-06-07T16:53:45,168 copying build/lib/promb/netmhc.py -> build/bdist.linux-armv7l/wheel/./promb 2025-06-07T16:53:45,171 copying build/lib/promb/db.py -> build/bdist.linux-armv7l/wheel/./promb 2025-06-07T16:53:45,173 running install_egg_info 2025-06-07T16:53:45,213 Copying promb.egg-info to build/bdist.linux-armv7l/wheel/./promb-1.0.1-py3.11.egg-info 2025-06-07T16:53:45,224 running install_scripts 2025-06-07T16:53:45,240 creating build/bdist.linux-armv7l/wheel/promb-1.0.1.dist-info/WHEEL 2025-06-07T16:53:45,242 creating '/tmp/pip-wheel-d4_pz7rv/promb-1.0.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-06-07T16:53:45,245 adding 'promb/__init__.py' 2025-06-07T16:53:45,246 adding 'promb/__version__.py' 2025-06-07T16:53:45,249 adding 'promb/cli.py' 2025-06-07T16:53:45,253 adding 'promb/db.py' 2025-06-07T16:53:45,255 adding 'promb/formatting.py' 2025-06-07T16:53:45,257 adding 'promb/netmhc.py' 2025-06-07T16:53:45,259 adding 'promb/parsing.py' 2025-06-07T16:53:46,912 adding 'promb/resources/OASis_9mers_v1_10perc_subjects.txt.gz' 2025-06-07T16:53:47,733 adding 'promb/resources/uniprot_sprot_human.fasta.gz' 2025-06-07T16:53:49,813 adding 'promb/resources/uniprotkb_proteome_UP000005640_2025_04_21.fasta.gz' 2025-06-07T16:53:49,931 adding 'promb-1.0.1.dist-info/licenses/LICENSE' 2025-06-07T16:53:49,933 adding 'promb-1.0.1.dist-info/licenses/LICENSES_THIRD_PARTY' 2025-06-07T16:53:49,934 adding 'promb-1.0.1.dist-info/METADATA' 2025-06-07T16:53:49,935 adding 'promb-1.0.1.dist-info/WHEEL' 2025-06-07T16:53:49,936 adding 'promb-1.0.1.dist-info/entry_points.txt' 2025-06-07T16:53:49,937 adding 'promb-1.0.1.dist-info/top_level.txt' 2025-06-07T16:53:49,939 adding 'promb-1.0.1.dist-info/RECORD' 2025-06-07T16:53:50,347 removing build/bdist.linux-armv7l/wheel 2025-06-07T16:53:50,477 Building wheel for promb (setup.py): finished with status 'done' 2025-06-07T16:53:50,869 Created wheel for promb: filename=promb-1.0.1-py3-none-any.whl size=39339346 sha256=1e328e3e1a5b81a3eed72fcd91f1a8aea91ab0ea5345e834d41cb6d85640d122 2025-06-07T16:53:50,870 Stored in directory: /tmp/pip-ephem-wheel-cache-w8losgtx/wheels/b9/fa/d7/633fed1e786f4dca1688646d7e6024914941bf94957e10ccef 2025-06-07T16:53:50,895 Successfully built promb 2025-06-07T16:53:51,856 Removed build tracker: '/tmp/pip-build-tracker-6667708z'