2025-06-02T00:19:56,214 Created temporary directory: /tmp/pip-build-tracker-x5xs2z6a
2025-06-02T00:19:56,215 Initialized build tracking at /tmp/pip-build-tracker-x5xs2z6a
2025-06-02T00:19:56,216 Created build tracker: /tmp/pip-build-tracker-x5xs2z6a
2025-06-02T00:19:56,216 Entered build tracker: /tmp/pip-build-tracker-x5xs2z6a
2025-06-02T00:19:56,217 Created temporary directory: /tmp/pip-wheel-vjzbzs77
2025-06-02T00:19:56,222 Created temporary directory: /tmp/pip-ephem-wheel-cache-_xrg6vdk
2025-06-02T00:19:56,273 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-06-02T00:19:56,276 2 location(s) to search for versions of jaffatools:
2025-06-02T00:19:56,276 * https://pypi.org/simple/jaffatools/
2025-06-02T00:19:56,276 * https://www.piwheels.org/simple/jaffatools/
2025-06-02T00:19:56,276 Fetching project page and analyzing links: https://pypi.org/simple/jaffatools/
2025-06-02T00:19:56,277 Getting page https://pypi.org/simple/jaffatools/
2025-06-02T00:19:56,279 Found index url https://pypi.org/simple/
2025-06-02T00:19:56,566 Fetched page https://pypi.org/simple/jaffatools/ as application/vnd.pypi.simple.v1+json
2025-06-02T00:19:56,570   Found link https://files.pythonhosted.org/packages/70/9b/10cd32313d9f27367f7966299bf7ce77a153843a6015ce0119dcb98d4d31/jaffatools-0.2.0.tar.gz (from https://pypi.org/simple/jaffatools/) (requires-python:>=3.6), version: 0.2.0
2025-06-02T00:19:56,571   Found link https://files.pythonhosted.org/packages/98/3b/7bc648568915b40b1768e1fa9348126b1448771f1021f8440e2681845f55/jaffatools-0.3.0.tar.gz (from https://pypi.org/simple/jaffatools/) (requires-python:>=3.6), version: 0.3.0
2025-06-02T00:19:56,572   Found link https://files.pythonhosted.org/packages/cf/bb/a00c6fe9bc5bfd158e3b8a02bd07f99744642cd6f5b31fcdf36e46d8db42/jaffatools-0.4.0.tar.gz (from https://pypi.org/simple/jaffatools/) (requires-python:>=3.6), version: 0.4.0
2025-06-02T00:19:56,573   Found link https://files.pythonhosted.org/packages/79/ee/b182c851028f5f94f46d753cd52a239f76d3ef36926d2e3f319bb07bd6c6/jaffatools-0.5.0.tar.gz (from https://pypi.org/simple/jaffatools/) (requires-python:>=3.6), version: 0.5.0
2025-06-02T00:19:56,574 Fetching project page and analyzing links: https://www.piwheels.org/simple/jaffatools/
2025-06-02T00:19:56,575 Getting page https://www.piwheels.org/simple/jaffatools/
2025-06-02T00:19:56,577 Found index url https://www.piwheels.org/simple/
2025-06-02T00:19:56,738 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/jaffatools/
2025-06-02T00:19:57,388 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/jaffatools/
2025-06-02T00:19:58,556 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/jaffatools/
2025-06-02T00:20:00,724 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/jaffatools/
2025-06-02T00:20:04,898 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/jaffatools/
2025-06-02T00:20:05,070 Could not fetch URL https://www.piwheels.org/simple/jaffatools/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='www.piwheels.org', port=443): Max retries exceeded with url: /simple/jaffatools/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))) - skipping
2025-06-02T00:20:05,072 Skipping link: not a file: https://www.piwheels.org/simple/jaffatools/
2025-06-02T00:20:05,073 Skipping link: not a file: https://pypi.org/simple/jaffatools/
2025-06-02T00:20:05,094 Given no hashes to check 1 links for project 'jaffatools': discarding no candidates
2025-06-02T00:20:05,096 Collecting jaffatools==0.5.0
2025-06-02T00:20:05,099   Created temporary directory: /tmp/pip-unpack-jew5es1c
2025-06-02T00:20:05,323   Downloading jaffatools-0.5.0.tar.gz (34 kB)
2025-06-02T00:20:05,411   Added jaffatools==0.5.0 from https://files.pythonhosted.org/packages/79/ee/b182c851028f5f94f46d753cd52a239f76d3ef36926d2e3f319bb07bd6c6/jaffatools-0.5.0.tar.gz to build tracker '/tmp/pip-build-tracker-x5xs2z6a'
2025-06-02T00:20:05,413   Running setup.py (path:/tmp/pip-wheel-vjzbzs77/jaffatools_702e79c99c094d31ac382dad0d1dd7e9/setup.py) egg_info for package jaffatools
2025-06-02T00:20:05,414   Created temporary directory: /tmp/pip-pip-egg-info-_xs0pk61
2025-06-02T00:20:05,415   Preparing metadata (setup.py): started
2025-06-02T00:20:05,416   Running command python setup.py egg_info
2025-06-02T00:20:06,328   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-06-02T00:20:06,329   !!

2025-06-02T00:20:06,330           ********************************************************************************
2025-06-02T00:20:06,330           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-06-02T00:20:06,331           License :: OSI Approved :: MIT License

2025-06-02T00:20:06,333           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-06-02T00:20:06,333           ********************************************************************************

2025-06-02T00:20:06,334   !!
2025-06-02T00:20:06,335     self._finalize_license_expression()
2025-06-02T00:20:06,360   running egg_info
2025-06-02T00:20:06,388   creating /tmp/pip-pip-egg-info-_xs0pk61/jaffatools.egg-info
2025-06-02T00:20:06,389   writing /tmp/pip-pip-egg-info-_xs0pk61/jaffatools.egg-info/PKG-INFO
2025-06-02T00:20:06,392   writing dependency_links to /tmp/pip-pip-egg-info-_xs0pk61/jaffatools.egg-info/dependency_links.txt
2025-06-02T00:20:06,394   writing entry points to /tmp/pip-pip-egg-info-_xs0pk61/jaffatools.egg-info/entry_points.txt
2025-06-02T00:20:06,396   writing requirements to /tmp/pip-pip-egg-info-_xs0pk61/jaffatools.egg-info/requires.txt
2025-06-02T00:20:06,397   writing top-level names to /tmp/pip-pip-egg-info-_xs0pk61/jaffatools.egg-info/top_level.txt
2025-06-02T00:20:06,398   writing manifest file '/tmp/pip-pip-egg-info-_xs0pk61/jaffatools.egg-info/SOURCES.txt'
2025-06-02T00:20:06,495   reading manifest file '/tmp/pip-pip-egg-info-_xs0pk61/jaffatools.egg-info/SOURCES.txt'
2025-06-02T00:20:06,496   reading manifest template 'MANIFEST.in'
2025-06-02T00:20:06,501   adding license file 'LICENSE'
2025-06-02T00:20:06,504   writing manifest file '/tmp/pip-pip-egg-info-_xs0pk61/jaffatools.egg-info/SOURCES.txt'
2025-06-02T00:20:06,608   Preparing metadata (setup.py): finished with status 'done'
2025-06-02T00:20:06,613   Source in /tmp/pip-wheel-vjzbzs77/jaffatools_702e79c99c094d31ac382dad0d1dd7e9 has version 0.5.0, which satisfies requirement jaffatools==0.5.0 from https://files.pythonhosted.org/packages/79/ee/b182c851028f5f94f46d753cd52a239f76d3ef36926d2e3f319bb07bd6c6/jaffatools-0.5.0.tar.gz
2025-06-02T00:20:06,614   Removed jaffatools==0.5.0 from https://files.pythonhosted.org/packages/79/ee/b182c851028f5f94f46d753cd52a239f76d3ef36926d2e3f319bb07bd6c6/jaffatools-0.5.0.tar.gz from build tracker '/tmp/pip-build-tracker-x5xs2z6a'
2025-06-02T00:20:06,621 Created temporary directory: /tmp/pip-unpack-usdeju0h
2025-06-02T00:20:06,623 Created temporary directory: /tmp/pip-unpack-q_e26lot
2025-06-02T00:20:06,623 Building wheels for collected packages: jaffatools
2025-06-02T00:20:06,628   Created temporary directory: /tmp/pip-wheel-cxh1ckxc
2025-06-02T00:20:06,629   DEPRECATION: Building 'jaffatools' 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 'jaffatools'. Discussion can be found at https://github.com/pypa/pip/issues/6334
2025-06-02T00:20:06,631   Building wheel for jaffatools (setup.py): started
2025-06-02T00:20:06,632   Destination directory: /tmp/pip-wheel-cxh1ckxc
2025-06-02T00:20:06,632   Running command python setup.py bdist_wheel
2025-06-02T00:20:07,485   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-06-02T00:20:07,485   !!

2025-06-02T00:20:07,488           ********************************************************************************
2025-06-02T00:20:07,488           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-06-02T00:20:07,489           License :: OSI Approved :: MIT License

2025-06-02T00:20:07,490           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-06-02T00:20:07,491           ********************************************************************************

2025-06-02T00:20:07,492   !!
2025-06-02T00:20:07,492     self._finalize_license_expression()
2025-06-02T00:20:07,493   running bdist_wheel
2025-06-02T00:20:07,628   running build
2025-06-02T00:20:07,629   running build_py
2025-06-02T00:20:07,662   creating build/lib/jaffatools
2025-06-02T00:20:07,665   copying jaffatools/__init__.py -> build/lib/jaffatools
2025-06-02T00:20:07,667   copying jaffatools/jaffa_runner.py -> build/lib/jaffatools
2025-06-02T00:20:07,670   copying jaffatools/bam_annotator.py -> build/lib/jaffatools
2025-06-02T00:20:07,672   copying jaffatools/fastq_filter.py -> build/lib/jaffatools
2025-06-02T00:20:07,675   creating build/lib/jaffatools/cli
2025-06-02T00:20:07,676   copying jaffatools/cli/jaffa_runner_cli.py -> build/lib/jaffatools/cli
2025-06-02T00:20:07,678   copying jaffatools/cli/jaffa_viz_cli.py -> build/lib/jaffatools/cli
2025-06-02T00:20:07,681   copying jaffatools/cli/ __init__.py -> build/lib/jaffatools/cli
2025-06-02T00:20:07,683   copying jaffatools/cli/bam_annotator_cli.py -> build/lib/jaffatools/cli
2025-06-02T00:20:07,685   copying jaffatools/cli/fastq_filter_cli.py -> build/lib/jaffatools/cli
2025-06-02T00:20:07,687   running egg_info
2025-06-02T00:20:07,719   writing jaffatools.egg-info/PKG-INFO
2025-06-02T00:20:07,723   writing dependency_links to jaffatools.egg-info/dependency_links.txt
2025-06-02T00:20:07,725   writing entry points to jaffatools.egg-info/entry_points.txt
2025-06-02T00:20:07,726   writing requirements to jaffatools.egg-info/requires.txt
2025-06-02T00:20:07,728   writing top-level names to jaffatools.egg-info/top_level.txt
2025-06-02T00:20:07,763   reading manifest file 'jaffatools.egg-info/SOURCES.txt'
2025-06-02T00:20:07,766   reading manifest template 'MANIFEST.in'
2025-06-02T00:20:07,771   adding license file 'LICENSE'
2025-06-02T00:20:07,774   writing manifest file 'jaffatools.egg-info/SOURCES.txt'
2025-06-02T00:20:07,777   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'jaffatools.data' is absent from the `packages` configuration.
2025-06-02T00:20:07,777   !!

2025-06-02T00:20:07,779           ********************************************************************************
2025-06-02T00:20:07,779           ############################
2025-06-02T00:20:07,780           # Package would be ignored #
2025-06-02T00:20:07,780           ############################
2025-06-02T00:20:07,781           Python recognizes 'jaffatools.data' as an importable package[^1],
2025-06-02T00:20:07,782           but it is absent from setuptools' `packages` configuration.

2025-06-02T00:20:07,783           This leads to an ambiguous overall configuration. If you want to distribute this
2025-06-02T00:20:07,783           package, please make sure that 'jaffatools.data' is explicitly added
2025-06-02T00:20:07,784           to the `packages` configuration field.

2025-06-02T00:20:07,785           Alternatively, you can also rely on setuptools' discovery methods
2025-06-02T00:20:07,786           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-06-02T00:20:07,786           instead of `find_packages(...)`/`find:`).

2025-06-02T00:20:07,788           You can read more about "package discovery" on setuptools documentation page:

2025-06-02T00:20:07,789           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-06-02T00:20:07,790           If you don't want 'jaffatools.data' to be distributed and are
2025-06-02T00:20:07,791           already explicitly excluding 'jaffatools.data' via
2025-06-02T00:20:07,791           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-06-02T00:20:07,792           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-06-02T00:20:07,793           combination with a more fine grained `package-data` configuration.

2025-06-02T00:20:07,794           You can read more about "package data files" on setuptools documentation page:

2025-06-02T00:20:07,795           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-06-02T00:20:07,797           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-06-02T00:20:07,798                 even if it does not contain any `.py` files.
2025-06-02T00:20:07,799                 On the other hand, currently there is no concept of package data
2025-06-02T00:20:07,800                 directory, all directories are treated like packages.
2025-06-02T00:20:07,800           ********************************************************************************

2025-06-02T00:20:07,802   !!
2025-06-02T00:20:07,803     check.warn(importable)
2025-06-02T00:20:07,805   creating build/lib/jaffatools/data
2025-06-02T00:20:07,807   copying jaffatools/data/UCSC.HG19.Human.CytoBandIdeogram.txt -> build/lib/jaffatools/data
2025-06-02T00:20:07,808   copying jaffatools/data/UCSC.HG38.Human.CytoBandIdeogram.txt -> build/lib/jaffatools/data
2025-06-02T00:20:07,810   copying jaffatools/data/UCSC.MM10.Mus.musculus.CytoBandIdeogram.txt -> build/lib/jaffatools/data
2025-06-02T00:20:07,810   copying jaffatools/data/jaffa_plots.R -> build/lib/jaffatools/data
2025-06-02T00:20:07,833   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2025-06-02T00:20:07,834   !!

2025-06-02T00:20:07,835           ********************************************************************************
2025-06-02T00:20:07,835           Please avoid running ``setup.py`` directly.
2025-06-02T00:20:07,836           Instead, use pypa/build, pypa/installer or other
2025-06-02T00:20:07,836           standards-based tools.

2025-06-02T00:20:07,838           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-06-02T00:20:07,838           or your builds will no longer be supported.

2025-06-02T00:20:07,839           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2025-06-02T00:20:07,840           ********************************************************************************

2025-06-02T00:20:07,841   !!
2025-06-02T00:20:07,842     self.initialize_options()
2025-06-02T00:20:07,867   installing to build/bdist.linux-armv7l/wheel
2025-06-02T00:20:07,867   running install
2025-06-02T00:20:07,894   running install_lib
2025-06-02T00:20:07,922   creating build/bdist.linux-armv7l/wheel
2025-06-02T00:20:07,924   creating build/bdist.linux-armv7l/wheel/jaffatools
2025-06-02T00:20:07,926   copying build/lib/jaffatools/__init__.py -> build/bdist.linux-armv7l/wheel/./jaffatools
2025-06-02T00:20:07,929   copying build/lib/jaffatools/jaffa_runner.py -> build/bdist.linux-armv7l/wheel/./jaffatools
2025-06-02T00:20:07,932   creating build/bdist.linux-armv7l/wheel/jaffatools/data
2025-06-02T00:20:07,933   copying build/lib/jaffatools/data/UCSC.HG38.Human.CytoBandIdeogram.txt -> build/bdist.linux-armv7l/wheel/./jaffatools/data
2025-06-02T00:20:07,937   copying build/lib/jaffatools/data/jaffa_plots.R -> build/bdist.linux-armv7l/wheel/./jaffatools/data
2025-06-02T00:20:07,940   copying build/lib/jaffatools/data/UCSC.MM10.Mus.musculus.CytoBandIdeogram.txt -> build/bdist.linux-armv7l/wheel/./jaffatools/data
2025-06-02T00:20:07,944   copying build/lib/jaffatools/data/UCSC.HG19.Human.CytoBandIdeogram.txt -> build/bdist.linux-armv7l/wheel/./jaffatools/data
2025-06-02T00:20:07,947   copying build/lib/jaffatools/bam_annotator.py -> build/bdist.linux-armv7l/wheel/./jaffatools
2025-06-02T00:20:07,950   creating build/bdist.linux-armv7l/wheel/jaffatools/cli
2025-06-02T00:20:07,952   copying build/lib/jaffatools/cli/jaffa_runner_cli.py -> build/bdist.linux-armv7l/wheel/./jaffatools/cli
2025-06-02T00:20:07,954   copying build/lib/jaffatools/cli/jaffa_viz_cli.py -> build/bdist.linux-armv7l/wheel/./jaffatools/cli
2025-06-02T00:20:07,957   copying build/lib/jaffatools/cli/ __init__.py -> build/bdist.linux-armv7l/wheel/./jaffatools/cli
2025-06-02T00:20:07,959   copying build/lib/jaffatools/cli/bam_annotator_cli.py -> build/bdist.linux-armv7l/wheel/./jaffatools/cli
2025-06-02T00:20:07,962   copying build/lib/jaffatools/cli/fastq_filter_cli.py -> build/bdist.linux-armv7l/wheel/./jaffatools/cli
2025-06-02T00:20:07,964   copying build/lib/jaffatools/fastq_filter.py -> build/bdist.linux-armv7l/wheel/./jaffatools
2025-06-02T00:20:07,967   running install_egg_info
2025-06-02T00:20:08,006   Copying jaffatools.egg-info to build/bdist.linux-armv7l/wheel/./jaffatools-0.5.0-py3.11.egg-info
2025-06-02T00:20:08,017   running install_scripts
2025-06-02T00:20:08,032   creating build/bdist.linux-armv7l/wheel/jaffatools-0.5.0.dist-info/WHEEL
2025-06-02T00:20:08,035   creating '/tmp/pip-wheel-cxh1ckxc/jaffatools-0.5.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-06-02T00:20:08,038   adding 'jaffatools/__init__.py'
2025-06-02T00:20:08,040   adding 'jaffatools/bam_annotator.py'
2025-06-02T00:20:08,042   adding 'jaffatools/fastq_filter.py'
2025-06-02T00:20:08,044   adding 'jaffatools/jaffa_runner.py'
2025-06-02T00:20:08,047   adding 'jaffatools/cli/ __init__.py'
2025-06-02T00:20:08,049   adding 'jaffatools/cli/bam_annotator_cli.py'
2025-06-02T00:20:08,050   adding 'jaffatools/cli/fastq_filter_cli.py'
2025-06-02T00:20:08,052   adding 'jaffatools/cli/jaffa_runner_cli.py'
2025-06-02T00:20:08,055   adding 'jaffatools/cli/jaffa_viz_cli.py'
2025-06-02T00:20:08,061   adding 'jaffatools/data/UCSC.HG19.Human.CytoBandIdeogram.txt'
2025-06-02T00:20:08,067   adding 'jaffatools/data/UCSC.HG38.Human.CytoBandIdeogram.txt'
2025-06-02T00:20:08,070   adding 'jaffatools/data/UCSC.MM10.Mus.musculus.CytoBandIdeogram.txt'
2025-06-02T00:20:08,073   adding 'jaffatools/data/jaffa_plots.R'
2025-06-02T00:20:08,076   adding 'jaffatools-0.5.0.dist-info/licenses/LICENSE'
2025-06-02T00:20:08,078   adding 'jaffatools-0.5.0.dist-info/METADATA'
2025-06-02T00:20:08,079   adding 'jaffatools-0.5.0.dist-info/WHEEL'
2025-06-02T00:20:08,081   adding 'jaffatools-0.5.0.dist-info/entry_points.txt'
2025-06-02T00:20:08,082   adding 'jaffatools-0.5.0.dist-info/top_level.txt'
2025-06-02T00:20:08,084   adding 'jaffatools-0.5.0.dist-info/RECORD'
2025-06-02T00:20:08,085   removing build/bdist.linux-armv7l/wheel
2025-06-02T00:20:08,199   Building wheel for jaffatools (setup.py): finished with status 'done'
2025-06-02T00:20:08,202   Created wheel for jaffatools: filename=jaffatools-0.5.0-py3-none-any.whl size=35307 sha256=028c3420aa80be4620c7def11c225d5de00455aa9678771becf1e6fcb3123fd2
2025-06-02T00:20:08,203   Stored in directory: /tmp/pip-ephem-wheel-cache-_xrg6vdk/wheels/4b/74/63/55b4ea3d7a555b4fa30b5b670bbe4e538c4be2dca9b3d5ef53
2025-06-02T00:20:08,216 Successfully built jaffatools
2025-06-02T00:20:08,222 Removed build tracker: '/tmp/pip-build-tracker-x5xs2z6a'