2025-06-07T01:29:58,499 Created temporary directory: /tmp/pip-build-tracker-sn8o56a5
2025-06-07T01:29:58,501 Initialized build tracking at /tmp/pip-build-tracker-sn8o56a5
2025-06-07T01:29:58,501 Created build tracker: /tmp/pip-build-tracker-sn8o56a5
2025-06-07T01:29:58,501 Entered build tracker: /tmp/pip-build-tracker-sn8o56a5
2025-06-07T01:29:58,502 Created temporary directory: /tmp/pip-wheel-93f9rfdu
2025-06-07T01:29:58,506 Created temporary directory: /tmp/pip-ephem-wheel-cache-2y98ybll
2025-06-07T01:29:58,560 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-06-07T01:29:58,563 2 location(s) to search for versions of promb:
2025-06-07T01:29:58,563 * https://pypi.org/simple/promb/
2025-06-07T01:29:58,563 * https://www.piwheels.org/simple/promb/
2025-06-07T01:29:58,564 Fetching project page and analyzing links: https://pypi.org/simple/promb/
2025-06-07T01:29:58,564 Getting page https://pypi.org/simple/promb/
2025-06-07T01:29:58,566 Found index url https://pypi.org/simple/
2025-06-07T01:29:58,794 Fetched page https://pypi.org/simple/promb/ as application/vnd.pypi.simple.v1+json
2025-06-07T01:29:58,797   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)
2025-06-07T01:29:58,799   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
2025-06-07T01:29:58,800   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)
2025-06-07T01:29:58,801   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
2025-06-07T01:29:58,803   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)
2025-06-07T01:29:58,804   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
2025-06-07T01:29:58,805 Fetching project page and analyzing links: https://www.piwheels.org/simple/promb/
2025-06-07T01:29:58,807 Getting page https://www.piwheels.org/simple/promb/
2025-06-07T01:29:58,809 Found index url https://www.piwheels.org/simple/
2025-06-07T01:29:58,988 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/
2025-06-07T01:29:59,646 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/
2025-06-07T01:30:00,819 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/
2025-06-07T01:30:02,991 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/
2025-06-07T01:30:07,161 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/
2025-06-07T01:30:07,332 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
2025-06-07T01:30:07,334 Skipping link: not a file: https://www.piwheels.org/simple/promb/
2025-06-07T01:30:07,335 Skipping link: not a file: https://pypi.org/simple/promb/
2025-06-07T01:30:07,355 Given no hashes to check 1 links for project 'promb': discarding no candidates
2025-06-07T01:30:07,357 Collecting promb==1.0.0
2025-06-07T01:30:07,359   Created temporary directory: /tmp/pip-unpack-1zduyxau
2025-06-07T01:30:07,712   Downloading promb-1.0.0.tar.gz (39.3 MB)
2025-06-07T01:30:15,101   Added promb==1.0.0 from https://files.pythonhosted.org/packages/20/e3/83d440c84b242a78be190fcf0f667118e6bc2078bda79c4ca15deb138c46/promb-1.0.0.tar.gz to build tracker '/tmp/pip-build-tracker-sn8o56a5'
2025-06-07T01:30:15,104   Running setup.py (path:/tmp/pip-wheel-93f9rfdu/promb_98cc46893ddf4d6982b40f811ce01e08/setup.py) egg_info for package promb
2025-06-07T01:30:15,105   Created temporary directory: /tmp/pip-pip-egg-info-4vp_ykps
2025-06-07T01:30:15,106   Preparing metadata (setup.py): started
2025-06-07T01:30:15,107   Running command python setup.py egg_info
2025-06-07T01:30:16,043   running egg_info
2025-06-07T01:30:16,072   creating /tmp/pip-pip-egg-info-4vp_ykps/promb.egg-info
2025-06-07T01:30:16,073   writing /tmp/pip-pip-egg-info-4vp_ykps/promb.egg-info/PKG-INFO
2025-06-07T01:30:16,077   writing dependency_links to /tmp/pip-pip-egg-info-4vp_ykps/promb.egg-info/dependency_links.txt
2025-06-07T01:30:16,078   writing entry points to /tmp/pip-pip-egg-info-4vp_ykps/promb.egg-info/entry_points.txt
2025-06-07T01:30:16,080   writing requirements to /tmp/pip-pip-egg-info-4vp_ykps/promb.egg-info/requires.txt
2025-06-07T01:30:16,081   writing top-level names to /tmp/pip-pip-egg-info-4vp_ykps/promb.egg-info/top_level.txt
2025-06-07T01:30:16,082   writing manifest file '/tmp/pip-pip-egg-info-4vp_ykps/promb.egg-info/SOURCES.txt'
2025-06-07T01:30:16,176   reading manifest file '/tmp/pip-pip-egg-info-4vp_ykps/promb.egg-info/SOURCES.txt'
2025-06-07T01:30:16,178   reading manifest template 'MANIFEST.in'
2025-06-07T01:30:16,194   warning: no previously-included files matching '*.pyc' found anywhere in distribution
2025-06-07T01:30:16,195   warning: no previously-included files matching '*.pyo' found anywhere in distribution
2025-06-07T01:30:16,195   warning: no previously-included files matching '.git' found anywhere in distribution
2025-06-07T01:30:16,196   warning: no previously-included files matching '.DS_Store' found anywhere in distribution
2025-06-07T01:30:16,197   warning: no previously-included files matching '.ipynb_checkpoints' found anywhere in distribution
2025-06-07T01:30:16,198   no previously-included directories found matching 'tests'
2025-06-07T01:30:16,198   no previously-included directories found matching 'work'
2025-06-07T01:30:16,199   adding license file 'LICENSE'
2025-06-07T01:30:16,200   adding license file 'LICENSES_THIRD_PARTY'
2025-06-07T01:30:16,202   writing manifest file '/tmp/pip-pip-egg-info-4vp_ykps/promb.egg-info/SOURCES.txt'
2025-06-07T01:30:16,308   Preparing metadata (setup.py): finished with status 'done'
2025-06-07T01:30:16,312   Source in /tmp/pip-wheel-93f9rfdu/promb_98cc46893ddf4d6982b40f811ce01e08 has version 1.0.0, which satisfies requirement promb==1.0.0 from https://files.pythonhosted.org/packages/20/e3/83d440c84b242a78be190fcf0f667118e6bc2078bda79c4ca15deb138c46/promb-1.0.0.tar.gz
2025-06-07T01:30:16,313   Removed promb==1.0.0 from https://files.pythonhosted.org/packages/20/e3/83d440c84b242a78be190fcf0f667118e6bc2078bda79c4ca15deb138c46/promb-1.0.0.tar.gz from build tracker '/tmp/pip-build-tracker-sn8o56a5'
2025-06-07T01:30:16,320 Created temporary directory: /tmp/pip-unpack-z2h0vg9c
2025-06-07T01:30:16,322 Created temporary directory: /tmp/pip-unpack-f5nevm6j
2025-06-07T01:30:16,322 Building wheels for collected packages: promb
2025-06-07T01:30:16,326   Created temporary directory: /tmp/pip-wheel-jn2s368j
2025-06-07T01:30:16,327   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
2025-06-07T01:30:16,329   Building wheel for promb (setup.py): started
2025-06-07T01:30:16,330   Destination directory: /tmp/pip-wheel-jn2s368j
2025-06-07T01:30:16,331   Running command python setup.py bdist_wheel
2025-06-07T01:30:17,187   running bdist_wheel
2025-06-07T01:30:17,326   running build
2025-06-07T01:30:17,327   running build_py
2025-06-07T01:30:17,359   creating build/lib/promb
2025-06-07T01:30:17,362   copying promb/netmhc.py -> build/lib/promb
2025-06-07T01:30:17,364   copying promb/cli.py -> build/lib/promb
2025-06-07T01:30:17,367   copying promb/parsing.py -> build/lib/promb
2025-06-07T01:30:17,369   copying promb/db.py -> build/lib/promb
2025-06-07T01:30:17,372   copying promb/formatting.py -> build/lib/promb
2025-06-07T01:30:17,374   copying promb/__init__.py -> build/lib/promb
2025-06-07T01:30:17,376   copying promb/__version__.py -> build/lib/promb
2025-06-07T01:30:17,378   running egg_info
2025-06-07T01:30:17,411   writing promb.egg-info/PKG-INFO
2025-06-07T01:30:17,414   writing dependency_links to promb.egg-info/dependency_links.txt
2025-06-07T01:30:17,416   writing entry points to promb.egg-info/entry_points.txt
2025-06-07T01:30:17,417   writing requirements to promb.egg-info/requires.txt
2025-06-07T01:30:17,419   writing top-level names to promb.egg-info/top_level.txt
2025-06-07T01:30:17,451   reading manifest file 'promb.egg-info/SOURCES.txt'
2025-06-07T01:30:17,455   reading manifest template 'MANIFEST.in'
2025-06-07T01:30:17,470   warning: no previously-included files matching '*.pyc' found anywhere in distribution
2025-06-07T01:30:17,471   warning: no previously-included files matching '*.pyo' found anywhere in distribution
2025-06-07T01:30:17,472   warning: no previously-included files matching '.git' found anywhere in distribution
2025-06-07T01:30:17,473   warning: no previously-included files matching '.DS_Store' found anywhere in distribution
2025-06-07T01:30:17,473   warning: no previously-included files matching '.ipynb_checkpoints' found anywhere in distribution
2025-06-07T01:30:17,474   no previously-included directories found matching 'tests'
2025-06-07T01:30:17,475   no previously-included directories found matching 'work'
2025-06-07T01:30:17,475   adding license file 'LICENSE'
2025-06-07T01:30:17,476   adding license file 'LICENSES_THIRD_PARTY'
2025-06-07T01:30:17,478   writing manifest file 'promb.egg-info/SOURCES.txt'
2025-06-07T01:30:17,481   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'promb.resources' is absent from the `packages` configuration.
2025-06-07T01:30:17,481   !!

2025-06-07T01:30:17,483           ********************************************************************************
2025-06-07T01:30:17,483           ############################
2025-06-07T01:30:17,484           # Package would be ignored #
2025-06-07T01:30:17,484           ############################
2025-06-07T01:30:17,485           Python recognizes 'promb.resources' as an importable package[^1],
2025-06-07T01:30:17,485           but it is absent from setuptools' `packages` configuration.

2025-06-07T01:30:17,487           This leads to an ambiguous overall configuration. If you want to distribute this
2025-06-07T01:30:17,487           package, please make sure that 'promb.resources' is explicitly added
2025-06-07T01:30:17,488           to the `packages` configuration field.

2025-06-07T01:30:17,489           Alternatively, you can also rely on setuptools' discovery methods
2025-06-07T01:30:17,489           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-06-07T01:30:17,490           instead of `find_packages(...)`/`find:`).

2025-06-07T01:30:17,491           You can read more about "package discovery" on setuptools documentation page:

2025-06-07T01:30:17,492           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-06-07T01:30:17,493           If you don't want 'promb.resources' to be distributed and are
2025-06-07T01:30:17,493           already explicitly excluding 'promb.resources' via
2025-06-07T01:30:17,494           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-06-07T01:30:17,494           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-06-07T01:30:17,495           combination with a more fine grained `package-data` configuration.

2025-06-07T01:30:17,496           You can read more about "package data files" on setuptools documentation page:

2025-06-07T01:30:17,497           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-06-07T01:30:17,498           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-06-07T01:30:17,499                 even if it does not contain any `.py` files.
2025-06-07T01:30:17,499                 On the other hand, currently there is no concept of package data
2025-06-07T01:30:17,500                 directory, all directories are treated like packages.
2025-06-07T01:30:17,501           ********************************************************************************

2025-06-07T01:30:17,502   !!
2025-06-07T01:30:17,503     check.warn(importable)
2025-06-07T01:30:17,504   creating build/lib/promb/resources
2025-06-07T01:30:17,504   copying promb/resources/OASis_9mers_v1_10perc_subjects.txt.gz -> build/lib/promb/resources
2025-06-07T01:30:17,708   copying promb/resources/uniprot_sprot_human.fasta.gz -> build/lib/promb/resources
2025-06-07T01:30:17,821   copying promb/resources/uniprotkb_proteome_UP000005640_2025_04_21.fasta.gz -> build/lib/promb/resources
2025-06-07T01:30:18,121   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2025-06-07T01:30:18,122   !!

2025-06-07T01:30:18,123           ********************************************************************************
2025-06-07T01:30:18,124           Please avoid running ``setup.py`` directly.
2025-06-07T01:30:18,125           Instead, use pypa/build, pypa/installer or other
2025-06-07T01:30:18,125           standards-based tools.

2025-06-07T01:30:18,126           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-06-07T01:30:18,127           or your builds will no longer be supported.

2025-06-07T01:30:18,128           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2025-06-07T01:30:18,129           ********************************************************************************

2025-06-07T01:30:18,130   !!
2025-06-07T01:30:18,131     self.initialize_options()
2025-06-07T01:30:18,152   installing to build/bdist.linux-armv7l/wheel
2025-06-07T01:30:18,153   running install
2025-06-07T01:30:18,177   running install_lib
2025-06-07T01:30:18,205   creating build/bdist.linux-armv7l/wheel
2025-06-07T01:30:18,208   creating build/bdist.linux-armv7l/wheel/promb
2025-06-07T01:30:18,209   copying build/lib/promb/netmhc.py -> build/bdist.linux-armv7l/wheel/./promb
2025-06-07T01:30:18,212   copying build/lib/promb/cli.py -> build/bdist.linux-armv7l/wheel/./promb
2025-06-07T01:30:18,215   copying build/lib/promb/parsing.py -> build/bdist.linux-armv7l/wheel/./promb
2025-06-07T01:30:18,217   copying build/lib/promb/db.py -> build/bdist.linux-armv7l/wheel/./promb
2025-06-07T01:30:18,221   creating build/bdist.linux-armv7l/wheel/promb/resources
2025-06-07T01:30:18,222   copying build/lib/promb/resources/OASis_9mers_v1_10perc_subjects.txt.gz -> build/bdist.linux-armv7l/wheel/./promb/resources
2025-06-07T01:30:18,433   copying build/lib/promb/resources/uniprotkb_proteome_UP000005640_2025_04_21.fasta.gz -> build/bdist.linux-armv7l/wheel/./promb/resources
2025-06-07T01:30:18,707   copying build/lib/promb/resources/uniprot_sprot_human.fasta.gz -> build/bdist.linux-armv7l/wheel/./promb/resources
2025-06-07T01:30:18,805   copying build/lib/promb/formatting.py -> build/bdist.linux-armv7l/wheel/./promb
2025-06-07T01:30:18,807   copying build/lib/promb/__init__.py -> build/bdist.linux-armv7l/wheel/./promb
2025-06-07T01:30:18,809   copying build/lib/promb/__version__.py -> build/bdist.linux-armv7l/wheel/./promb
2025-06-07T01:30:18,811   running install_egg_info
2025-06-07T01:30:18,851   Copying promb.egg-info to build/bdist.linux-armv7l/wheel/./promb-1.0.0-py3.11.egg-info
2025-06-07T01:30:18,864   running install_scripts
2025-06-07T01:30:18,882   creating build/bdist.linux-armv7l/wheel/promb-1.0.0.dist-info/WHEEL
2025-06-07T01:30:18,885   creating '/tmp/pip-wheel-jn2s368j/promb-1.0.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-06-07T01:30:18,888   adding 'promb/__init__.py'
2025-06-07T01:30:18,890   adding 'promb/__version__.py'
2025-06-07T01:30:18,892   adding 'promb/cli.py'
2025-06-07T01:30:18,896   adding 'promb/db.py'
2025-06-07T01:30:18,898   adding 'promb/formatting.py'
2025-06-07T01:30:18,900   adding 'promb/netmhc.py'
2025-06-07T01:30:18,902   adding 'promb/parsing.py'
2025-06-07T01:30:20,559   adding 'promb/resources/OASis_9mers_v1_10perc_subjects.txt.gz'
2025-06-07T01:30:21,382   adding 'promb/resources/uniprot_sprot_human.fasta.gz'
2025-06-07T01:30:23,471   adding 'promb/resources/uniprotkb_proteome_UP000005640_2025_04_21.fasta.gz'
2025-06-07T01:30:23,590   adding 'promb-1.0.0.dist-info/licenses/LICENSE'
2025-06-07T01:30:23,592   adding 'promb-1.0.0.dist-info/licenses/LICENSES_THIRD_PARTY'
2025-06-07T01:30:23,593   adding 'promb-1.0.0.dist-info/METADATA'
2025-06-07T01:30:23,594   adding 'promb-1.0.0.dist-info/WHEEL'
2025-06-07T01:30:23,595   adding 'promb-1.0.0.dist-info/entry_points.txt'
2025-06-07T01:30:23,596   adding 'promb-1.0.0.dist-info/top_level.txt'
2025-06-07T01:30:23,597   adding 'promb-1.0.0.dist-info/RECORD'
2025-06-07T01:30:24,004   removing build/bdist.linux-armv7l/wheel
2025-06-07T01:30:24,136   Building wheel for promb (setup.py): finished with status 'done'
2025-06-07T01:30:24,525   Created wheel for promb: filename=promb-1.0.0-py3-none-any.whl size=39339174 sha256=d663e8ea43d72a5716b6973e5e6b5e7ddeb7b9d545ffa7a646674be54a2fde27
2025-06-07T01:30:24,527   Stored in directory: /tmp/pip-ephem-wheel-cache-2y98ybll/wheels/d7/36/0c/2113cab6166ddccb17c9675d7abee0011d3efaabe2324c4706
2025-06-07T01:30:24,553 Successfully built promb
2025-06-07T01:30:25,498 Removed build tracker: '/tmp/pip-build-tracker-sn8o56a5'