2025-06-08T00:42:06,026 Created temporary directory: /tmp/pip-build-tracker-vpsa0bp4
2025-06-08T00:42:06,027 Initialized build tracking at /tmp/pip-build-tracker-vpsa0bp4
2025-06-08T00:42:06,027 Created build tracker: /tmp/pip-build-tracker-vpsa0bp4
2025-06-08T00:42:06,028 Entered build tracker: /tmp/pip-build-tracker-vpsa0bp4
2025-06-08T00:42:06,029 Created temporary directory: /tmp/pip-wheel-ovxh819n
2025-06-08T00:42:06,033 Created temporary directory: /tmp/pip-ephem-wheel-cache-wpx6a86i
2025-06-08T00:42:06,086 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-06-08T00:42:06,088 2 location(s) to search for versions of promb:
2025-06-08T00:42:06,088 * https://pypi.org/simple/promb/
2025-06-08T00:42:06,088 * https://www.piwheels.org/simple/promb/
2025-06-08T00:42:06,089 Fetching project page and analyzing links: https://pypi.org/simple/promb/
2025-06-08T00:42:06,090 Getting page https://pypi.org/simple/promb/
2025-06-08T00:42:06,092 Found index url https://pypi.org/simple/
2025-06-08T00:42:06,250 Fetched page https://pypi.org/simple/promb/ as application/vnd.pypi.simple.v1+json
2025-06-08T00:42:06,252   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)
2025-06-08T00:42:06,254   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
2025-06-08T00:42:06,254   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)
2025-06-08T00:42:06,255   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
2025-06-08T00:42:06,256   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)
2025-06-08T00:42:06,256   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
2025-06-08T00:42:06,257 Fetching project page and analyzing links: https://www.piwheels.org/simple/promb/
2025-06-08T00:42:06,258 Getting page https://www.piwheels.org/simple/promb/
2025-06-08T00:42:06,259 Found index url https://www.piwheels.org/simple/
2025-06-08T00:42:06,425 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/
2025-06-08T00:42:07,093 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/
2025-06-08T00:42:08,263 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/
2025-06-08T00:42:10,438 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/
2025-06-08T00:42:14,619 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/
2025-06-08T00:42:14,806 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
2025-06-08T00:42:14,809 Skipping link: not a file: https://www.piwheels.org/simple/promb/
2025-06-08T00:42:14,810 Skipping link: not a file: https://pypi.org/simple/promb/
2025-06-08T00:42:14,829 Given no hashes to check 1 links for project 'promb': discarding no candidates
2025-06-08T00:42:14,830 Collecting promb==1.0.2
2025-06-08T00:42:14,833   Created temporary directory: /tmp/pip-unpack-etr5bxi8
2025-06-08T00:42:15,550   Downloading promb-1.0.2.tar.gz (39.3 MB)
2025-06-08T00:42:24,042   Added promb==1.0.2 from https://files.pythonhosted.org/packages/e1/bc/8a78638f65becbdc5f22c6766db489726bcaeb3720f10f3b8c03e5effd9f/promb-1.0.2.tar.gz to build tracker '/tmp/pip-build-tracker-vpsa0bp4'
2025-06-08T00:42:24,044   Running setup.py (path:/tmp/pip-wheel-ovxh819n/promb_abb9fd57e1bc450a841ae435f97ae05d/setup.py) egg_info for package promb
2025-06-08T00:42:24,045   Created temporary directory: /tmp/pip-pip-egg-info-ttnupi5c
2025-06-08T00:42:24,045   Preparing metadata (setup.py): started
2025-06-08T00:42:24,046   Running command python setup.py egg_info
2025-06-08T00:42:24,947   running egg_info
2025-06-08T00:42:24,976   creating /tmp/pip-pip-egg-info-ttnupi5c/promb.egg-info
2025-06-08T00:42:24,978   writing /tmp/pip-pip-egg-info-ttnupi5c/promb.egg-info/PKG-INFO
2025-06-08T00:42:24,981   writing dependency_links to /tmp/pip-pip-egg-info-ttnupi5c/promb.egg-info/dependency_links.txt
2025-06-08T00:42:24,983   writing entry points to /tmp/pip-pip-egg-info-ttnupi5c/promb.egg-info/entry_points.txt
2025-06-08T00:42:24,985   writing requirements to /tmp/pip-pip-egg-info-ttnupi5c/promb.egg-info/requires.txt
2025-06-08T00:42:24,986   writing top-level names to /tmp/pip-pip-egg-info-ttnupi5c/promb.egg-info/top_level.txt
2025-06-08T00:42:24,988   writing manifest file '/tmp/pip-pip-egg-info-ttnupi5c/promb.egg-info/SOURCES.txt'
2025-06-08T00:42:25,082   reading manifest file '/tmp/pip-pip-egg-info-ttnupi5c/promb.egg-info/SOURCES.txt'
2025-06-08T00:42:25,084   reading manifest template 'MANIFEST.in'
2025-06-08T00:42:25,099   warning: no previously-included files matching '*.pyc' found anywhere in distribution
2025-06-08T00:42:25,100   warning: no previously-included files matching '*.pyo' found anywhere in distribution
2025-06-08T00:42:25,101   warning: no previously-included files matching '.git' found anywhere in distribution
2025-06-08T00:42:25,101   warning: no previously-included files matching '.DS_Store' found anywhere in distribution
2025-06-08T00:42:25,102   warning: no previously-included files matching '.ipynb_checkpoints' found anywhere in distribution
2025-06-08T00:42:25,103   no previously-included directories found matching 'tests'
2025-06-08T00:42:25,103   no previously-included directories found matching 'work'
2025-06-08T00:42:25,104   adding license file 'LICENSE'
2025-06-08T00:42:25,105   adding license file 'LICENSES_THIRD_PARTY'
2025-06-08T00:42:25,107   writing manifest file '/tmp/pip-pip-egg-info-ttnupi5c/promb.egg-info/SOURCES.txt'
2025-06-08T00:42:25,213   Preparing metadata (setup.py): finished with status 'done'
2025-06-08T00:42:25,218   Source in /tmp/pip-wheel-ovxh819n/promb_abb9fd57e1bc450a841ae435f97ae05d has version 1.0.2, which satisfies requirement promb==1.0.2 from https://files.pythonhosted.org/packages/e1/bc/8a78638f65becbdc5f22c6766db489726bcaeb3720f10f3b8c03e5effd9f/promb-1.0.2.tar.gz
2025-06-08T00:42:25,219   Removed promb==1.0.2 from https://files.pythonhosted.org/packages/e1/bc/8a78638f65becbdc5f22c6766db489726bcaeb3720f10f3b8c03e5effd9f/promb-1.0.2.tar.gz from build tracker '/tmp/pip-build-tracker-vpsa0bp4'
2025-06-08T00:42:25,226 Created temporary directory: /tmp/pip-unpack-2j6g4k2x
2025-06-08T00:42:25,228 Created temporary directory: /tmp/pip-unpack-mft3fqc4
2025-06-08T00:42:25,228 Building wheels for collected packages: promb
2025-06-08T00:42:25,232   Created temporary directory: /tmp/pip-wheel-1zi2ktce
2025-06-08T00:42:25,233   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
2025-06-08T00:42:25,234   Building wheel for promb (setup.py): started
2025-06-08T00:42:25,236   Destination directory: /tmp/pip-wheel-1zi2ktce
2025-06-08T00:42:25,236   Running command python setup.py bdist_wheel
2025-06-08T00:42:26,090   running bdist_wheel
2025-06-08T00:42:26,230   running build
2025-06-08T00:42:26,231   running build_py
2025-06-08T00:42:26,263   creating build/lib/promb
2025-06-08T00:42:26,265   copying promb/cli.py -> build/lib/promb
2025-06-08T00:42:26,267   copying promb/__init__.py -> build/lib/promb
2025-06-08T00:42:26,269   copying promb/__version__.py -> build/lib/promb
2025-06-08T00:42:26,271   copying promb/formatting.py -> build/lib/promb
2025-06-08T00:42:26,273   copying promb/db.py -> build/lib/promb
2025-06-08T00:42:26,275   copying promb/netmhc.py -> build/lib/promb
2025-06-08T00:42:26,277   copying promb/parsing.py -> build/lib/promb
2025-06-08T00:42:26,279   running egg_info
2025-06-08T00:42:26,311   writing promb.egg-info/PKG-INFO
2025-06-08T00:42:26,315   writing dependency_links to promb.egg-info/dependency_links.txt
2025-06-08T00:42:26,317   writing entry points to promb.egg-info/entry_points.txt
2025-06-08T00:42:26,318   writing requirements to promb.egg-info/requires.txt
2025-06-08T00:42:26,320   writing top-level names to promb.egg-info/top_level.txt
2025-06-08T00:42:26,353   reading manifest file 'promb.egg-info/SOURCES.txt'
2025-06-08T00:42:26,357   reading manifest template 'MANIFEST.in'
2025-06-08T00:42:26,371   warning: no previously-included files matching '*.pyc' found anywhere in distribution
2025-06-08T00:42:26,371   warning: no previously-included files matching '*.pyo' found anywhere in distribution
2025-06-08T00:42:26,372   warning: no previously-included files matching '.git' found anywhere in distribution
2025-06-08T00:42:26,373   warning: no previously-included files matching '.DS_Store' found anywhere in distribution
2025-06-08T00:42:26,374   warning: no previously-included files matching '.ipynb_checkpoints' found anywhere in distribution
2025-06-08T00:42:26,375   no previously-included directories found matching 'tests'
2025-06-08T00:42:26,375   no previously-included directories found matching 'work'
2025-06-08T00:42:26,376   adding license file 'LICENSE'
2025-06-08T00:42:26,376   adding license file 'LICENSES_THIRD_PARTY'
2025-06-08T00:42:26,379   writing manifest file 'promb.egg-info/SOURCES.txt'
2025-06-08T00:42:26,382   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'promb.resources' is absent from the `packages` configuration.
2025-06-08T00:42:26,382   !!

2025-06-08T00:42:26,383           ********************************************************************************
2025-06-08T00:42:26,384           ############################
2025-06-08T00:42:26,385           # Package would be ignored #
2025-06-08T00:42:26,385           ############################
2025-06-08T00:42:26,386           Python recognizes 'promb.resources' as an importable package[^1],
2025-06-08T00:42:26,386           but it is absent from setuptools' `packages` configuration.

2025-06-08T00:42:26,388           This leads to an ambiguous overall configuration. If you want to distribute this
2025-06-08T00:42:26,388           package, please make sure that 'promb.resources' is explicitly added
2025-06-08T00:42:26,389           to the `packages` configuration field.

2025-06-08T00:42:26,390           Alternatively, you can also rely on setuptools' discovery methods
2025-06-08T00:42:26,390           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-06-08T00:42:26,391           instead of `find_packages(...)`/`find:`).

2025-06-08T00:42:26,392           You can read more about "package discovery" on setuptools documentation page:

2025-06-08T00:42:26,393           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-06-08T00:42:26,394           If you don't want 'promb.resources' to be distributed and are
2025-06-08T00:42:26,394           already explicitly excluding 'promb.resources' via
2025-06-08T00:42:26,395           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-06-08T00:42:26,395           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-06-08T00:42:26,396           combination with a more fine grained `package-data` configuration.

2025-06-08T00:42:26,396           You can read more about "package data files" on setuptools documentation page:

2025-06-08T00:42:26,397           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-06-08T00:42:26,399           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-06-08T00:42:26,400                 even if it does not contain any `.py` files.
2025-06-08T00:42:26,400                 On the other hand, currently there is no concept of package data
2025-06-08T00:42:26,401                 directory, all directories are treated like packages.
2025-06-08T00:42:26,402           ********************************************************************************

2025-06-08T00:42:26,403   !!
2025-06-08T00:42:26,404     check.warn(importable)
2025-06-08T00:42:26,405   creating build/lib/promb/resources
2025-06-08T00:42:26,405   copying promb/resources/OASis_9mers_v1_10perc_subjects.txt.gz -> build/lib/promb/resources
2025-06-08T00:42:26,598   copying promb/resources/uniprot_sprot_human.fasta.gz -> build/lib/promb/resources
2025-06-08T00:42:26,702   copying promb/resources/uniprotkb_proteome_UP000005640_2025_04_21.fasta.gz -> build/lib/promb/resources
2025-06-08T00:42:27,031   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2025-06-08T00:42:27,031   !!

2025-06-08T00:42:27,033           ********************************************************************************
2025-06-08T00:42:27,033           Please avoid running ``setup.py`` directly.
2025-06-08T00:42:27,034           Instead, use pypa/build, pypa/installer or other
2025-06-08T00:42:27,035           standards-based tools.

2025-06-08T00:42:27,036           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-06-08T00:42:27,036           or your builds will no longer be supported.

2025-06-08T00:42:27,037           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2025-06-08T00:42:27,038           ********************************************************************************

2025-06-08T00:42:27,039   !!
2025-06-08T00:42:27,040     self.initialize_options()
2025-06-08T00:42:27,063   installing to build/bdist.linux-armv7l/wheel
2025-06-08T00:42:27,063   running install
2025-06-08T00:42:27,088   running install_lib
2025-06-08T00:42:27,118   creating build/bdist.linux-armv7l/wheel
2025-06-08T00:42:27,120   creating build/bdist.linux-armv7l/wheel/promb
2025-06-08T00:42:27,121   copying build/lib/promb/cli.py -> build/bdist.linux-armv7l/wheel/./promb
2025-06-08T00:42:27,124   copying build/lib/promb/__init__.py -> build/bdist.linux-armv7l/wheel/./promb
2025-06-08T00:42:27,126   copying build/lib/promb/__version__.py -> build/bdist.linux-armv7l/wheel/./promb
2025-06-08T00:42:27,128   copying build/lib/promb/formatting.py -> build/bdist.linux-armv7l/wheel/./promb
2025-06-08T00:42:27,130   copying build/lib/promb/db.py -> build/bdist.linux-armv7l/wheel/./promb
2025-06-08T00:42:27,133   copying build/lib/promb/netmhc.py -> build/bdist.linux-armv7l/wheel/./promb
2025-06-08T00:42:27,136   creating build/bdist.linux-armv7l/wheel/promb/resources
2025-06-08T00:42:27,137   copying build/lib/promb/resources/uniprotkb_proteome_UP000005640_2025_04_21.fasta.gz -> build/bdist.linux-armv7l/wheel/./promb/resources
2025-06-08T00:42:27,416   copying build/lib/promb/resources/OASis_9mers_v1_10perc_subjects.txt.gz -> build/bdist.linux-armv7l/wheel/./promb/resources
2025-06-08T00:42:27,621   copying build/lib/promb/resources/uniprot_sprot_human.fasta.gz -> build/bdist.linux-armv7l/wheel/./promb/resources
2025-06-08T00:42:27,730   copying build/lib/promb/parsing.py -> build/bdist.linux-armv7l/wheel/./promb
2025-06-08T00:42:27,732   running install_egg_info
2025-06-08T00:42:27,771   Copying promb.egg-info to build/bdist.linux-armv7l/wheel/./promb-1.0.2-py3.11.egg-info
2025-06-08T00:42:27,783   running install_scripts
2025-06-08T00:42:27,800   creating build/bdist.linux-armv7l/wheel/promb-1.0.2.dist-info/WHEEL
2025-06-08T00:42:27,803   creating '/tmp/pip-wheel-1zi2ktce/promb-1.0.2-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-06-08T00:42:27,805   adding 'promb/__init__.py'
2025-06-08T00:42:27,807   adding 'promb/__version__.py'
2025-06-08T00:42:27,809   adding 'promb/cli.py'
2025-06-08T00:42:27,813   adding 'promb/db.py'
2025-06-08T00:42:27,815   adding 'promb/formatting.py'
2025-06-08T00:42:27,817   adding 'promb/netmhc.py'
2025-06-08T00:42:27,819   adding 'promb/parsing.py'
2025-06-08T00:42:29,497   adding 'promb/resources/OASis_9mers_v1_10perc_subjects.txt.gz'
2025-06-08T00:42:30,330   adding 'promb/resources/uniprot_sprot_human.fasta.gz'
2025-06-08T00:42:32,446   adding 'promb/resources/uniprotkb_proteome_UP000005640_2025_04_21.fasta.gz'
2025-06-08T00:42:32,565   adding 'promb-1.0.2.dist-info/licenses/LICENSE'
2025-06-08T00:42:32,566   adding 'promb-1.0.2.dist-info/licenses/LICENSES_THIRD_PARTY'
2025-06-08T00:42:32,568   adding 'promb-1.0.2.dist-info/METADATA'
2025-06-08T00:42:32,569   adding 'promb-1.0.2.dist-info/WHEEL'
2025-06-08T00:42:32,570   adding 'promb-1.0.2.dist-info/entry_points.txt'
2025-06-08T00:42:32,571   adding 'promb-1.0.2.dist-info/top_level.txt'
2025-06-08T00:42:32,572   adding 'promb-1.0.2.dist-info/RECORD'
2025-06-08T00:42:33,001   removing build/bdist.linux-armv7l/wheel
2025-06-08T00:42:33,132   Building wheel for promb (setup.py): finished with status 'done'
2025-06-08T00:42:33,523   Created wheel for promb: filename=promb-1.0.2-py3-none-any.whl size=39339320 sha256=02dd2df753eb0df22e96138bc56dec145350f3acff9b53ce8f137e1fb129a0c9
2025-06-08T00:42:33,524   Stored in directory: /tmp/pip-ephem-wheel-cache-wpx6a86i/wheels/07/6f/c7/517862028c7106780b288da34a42302f4eaa6186e666559197
2025-06-08T00:42:33,551 Successfully built promb
2025-06-08T00:42:34,475 Removed build tracker: '/tmp/pip-build-tracker-vpsa0bp4'