2025-06-06T06:22:40,681 Created temporary directory: /tmp/pip-build-tracker-oj6oe1xp
2025-06-06T06:22:40,682 Initialized build tracking at /tmp/pip-build-tracker-oj6oe1xp
2025-06-06T06:22:40,683 Created build tracker: /tmp/pip-build-tracker-oj6oe1xp
2025-06-06T06:22:40,683 Entered build tracker: /tmp/pip-build-tracker-oj6oe1xp
2025-06-06T06:22:40,684 Created temporary directory: /tmp/pip-wheel-gt7d7al2
2025-06-06T06:22:40,688 Created temporary directory: /tmp/pip-ephem-wheel-cache-pcbo9ds1
2025-06-06T06:22:40,743 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-06-06T06:22:40,746 2 location(s) to search for versions of pyvcf3:
2025-06-06T06:22:40,746 * https://pypi.org/simple/pyvcf3/
2025-06-06T06:22:40,746 * https://www.piwheels.org/simple/pyvcf3/
2025-06-06T06:22:40,747 Fetching project page and analyzing links: https://pypi.org/simple/pyvcf3/
2025-06-06T06:22:40,747 Getting page https://pypi.org/simple/pyvcf3/
2025-06-06T06:22:40,749 Found index url https://pypi.org/simple/
2025-06-06T06:22:40,974 Fetched page https://pypi.org/simple/pyvcf3/ as application/vnd.pypi.simple.v1+json
2025-06-06T06:22:40,978   Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/28/e4/1444bd99ba308b117583dc2424ad29fbc59e3f48b283f34ee0b525f81355/PyVCF3-1.0.0-py3.10-linux-x86_64.egg (from https://pypi.org/simple/pyvcf3/)
2025-06-06T06:22:40,979   Found link https://files.pythonhosted.org/packages/af/3a/d3c816c29dc176177067160069ac049a4bbd3c0feb96a41380b6d0e9d4bf/PyVCF3-1.0.0.tar.gz (from https://pypi.org/simple/pyvcf3/), version: 1.0.0
2025-06-06T06:22:40,980   Found link https://files.pythonhosted.org/packages/9b/f3/79dd49b0c14edb1e6845fcfcbaebc059970466deadfced075037d1862147/PyVCF3-1.0.1.tar.gz (from https://pypi.org/simple/pyvcf3/), version: 1.0.1
2025-06-06T06:22:40,981   Found link https://files.pythonhosted.org/packages/6a/0d/6d79c6ac40df1e24a8dc2df551e2f1bf93bc5defa815750910787a1f1ead/PyVCF3-1.0.2.tar.gz (from https://pypi.org/simple/pyvcf3/), version: 1.0.2
2025-06-06T06:22:40,983   Found link https://files.pythonhosted.org/packages/28/ee/5d0b0bd20762f1126b34cb15dce973fe4dbd1baf17d7ee621b18e336c0e5/PyVCF3-1.0.3.tar.gz (from https://pypi.org/simple/pyvcf3/), version: 1.0.3
2025-06-06T06:22:40,984   Skipping link: No binaries permitted for pyvcf3: https://files.pythonhosted.org/packages/67/52/e4c3d6656b94bddaf41bacffbe3e3e0e4ba1262854dde40e0d884fb2b40b/pyvcf3-1.0.4-py3-none-any.whl (from https://pypi.org/simple/pyvcf3/)
2025-06-06T06:22:40,985   Found link https://files.pythonhosted.org/packages/54/25/11d689a4c8eb8e0fe863310cccb3785ab79746896d342683e493b1308bd8/pyvcf3-1.0.4.tar.gz (from https://pypi.org/simple/pyvcf3/), version: 1.0.4
2025-06-06T06:22:40,987 Fetching project page and analyzing links: https://www.piwheels.org/simple/pyvcf3/
2025-06-06T06:22:40,988 Getting page https://www.piwheels.org/simple/pyvcf3/
2025-06-06T06:22:40,990 Found index url https://www.piwheels.org/simple/
2025-06-06T06:22:41,150 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/pyvcf3/
2025-06-06T06:22:41,811 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/pyvcf3/
2025-06-06T06:22:42,983 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/pyvcf3/
2025-06-06T06:22:45,157 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/pyvcf3/
2025-06-06T06:22:49,335 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/pyvcf3/
2025-06-06T06:22:49,509 Could not fetch URL https://www.piwheels.org/simple/pyvcf3/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='www.piwheels.org', port=443): Max retries exceeded with url: /simple/pyvcf3/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))) - skipping
2025-06-06T06:22:49,511 Skipping link: not a file: https://www.piwheels.org/simple/pyvcf3/
2025-06-06T06:22:49,512 Skipping link: not a file: https://pypi.org/simple/pyvcf3/
2025-06-06T06:22:49,532 Given no hashes to check 1 links for project 'pyvcf3': discarding no candidates
2025-06-06T06:22:49,533 Collecting pyvcf3==1.0.4
2025-06-06T06:22:49,536   Created temporary directory: /tmp/pip-unpack-uyapvocn
2025-06-06T06:22:49,780   Downloading pyvcf3-1.0.4.tar.gz (977 kB)
2025-06-06T06:22:50,120   Added pyvcf3==1.0.4 from https://files.pythonhosted.org/packages/54/25/11d689a4c8eb8e0fe863310cccb3785ab79746896d342683e493b1308bd8/pyvcf3-1.0.4.tar.gz to build tracker '/tmp/pip-build-tracker-oj6oe1xp'
2025-06-06T06:22:50,123   Running setup.py (path:/tmp/pip-wheel-gt7d7al2/pyvcf3_970ea9881c9b4f89bfe8c87eda8d57f9/setup.py) egg_info for package pyvcf3
2025-06-06T06:22:50,124   Created temporary directory: /tmp/pip-pip-egg-info-caqulyr2
2025-06-06T06:22:50,124   Preparing metadata (setup.py): started
2025-06-06T06:22:50,126   Running command python setup.py egg_info
2025-06-06T06:22:50,745   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite'
2025-06-06T06:22:50,746     warnings.warn(msg)
2025-06-06T06:22:51,040   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-06-06T06:22:51,040   !!

2025-06-06T06:22:51,042           ********************************************************************************
2025-06-06T06:22:51,042           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-06-06T06:22:51,044           License :: OSI Approved :: BSD License
2025-06-06T06:22:51,044           License :: OSI Approved :: MIT License

2025-06-06T06:22:51,046           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-06-06T06:22:51,046           ********************************************************************************

2025-06-06T06:22:51,048   !!
2025-06-06T06:22:51,048     self._finalize_license_expression()
2025-06-06T06:22:51,073   running egg_info
2025-06-06T06:22:51,102   creating /tmp/pip-pip-egg-info-caqulyr2/PyVCF3.egg-info
2025-06-06T06:22:51,103   writing /tmp/pip-pip-egg-info-caqulyr2/PyVCF3.egg-info/PKG-INFO
2025-06-06T06:22:51,106   writing dependency_links to /tmp/pip-pip-egg-info-caqulyr2/PyVCF3.egg-info/dependency_links.txt
2025-06-06T06:22:51,108   writing entry points to /tmp/pip-pip-egg-info-caqulyr2/PyVCF3.egg-info/entry_points.txt
2025-06-06T06:22:51,110   writing requirements to /tmp/pip-pip-egg-info-caqulyr2/PyVCF3.egg-info/requires.txt
2025-06-06T06:22:51,111   writing top-level names to /tmp/pip-pip-egg-info-caqulyr2/PyVCF3.egg-info/top_level.txt
2025-06-06T06:22:51,112   writing manifest file '/tmp/pip-pip-egg-info-caqulyr2/PyVCF3.egg-info/SOURCES.txt'
2025-06-06T06:22:51,244   reading manifest file '/tmp/pip-pip-egg-info-caqulyr2/PyVCF3.egg-info/SOURCES.txt'
2025-06-06T06:22:51,246   reading manifest template 'MANIFEST.in'
2025-06-06T06:22:51,264   adding license file 'LICENSE'
2025-06-06T06:22:51,269   writing manifest file '/tmp/pip-pip-egg-info-caqulyr2/PyVCF3.egg-info/SOURCES.txt'
2025-06-06T06:22:51,378   Preparing metadata (setup.py): finished with status 'done'
2025-06-06T06:22:51,383   Source in /tmp/pip-wheel-gt7d7al2/pyvcf3_970ea9881c9b4f89bfe8c87eda8d57f9 has version 1.0.4, which satisfies requirement pyvcf3==1.0.4 from https://files.pythonhosted.org/packages/54/25/11d689a4c8eb8e0fe863310cccb3785ab79746896d342683e493b1308bd8/pyvcf3-1.0.4.tar.gz
2025-06-06T06:22:51,384   Removed pyvcf3==1.0.4 from https://files.pythonhosted.org/packages/54/25/11d689a4c8eb8e0fe863310cccb3785ab79746896d342683e493b1308bd8/pyvcf3-1.0.4.tar.gz from build tracker '/tmp/pip-build-tracker-oj6oe1xp'
2025-06-06T06:22:51,389 Created temporary directory: /tmp/pip-unpack-e7g83n15
2025-06-06T06:22:51,390 Created temporary directory: /tmp/pip-unpack-tv0vv0tv
2025-06-06T06:22:51,390 Building wheels for collected packages: pyvcf3
2025-06-06T06:22:51,394   Created temporary directory: /tmp/pip-wheel-i84oj9_b
2025-06-06T06:22:51,395   DEPRECATION: Building 'pyvcf3' 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 'pyvcf3'. Discussion can be found at https://github.com/pypa/pip/issues/6334
2025-06-06T06:22:51,396   Building wheel for pyvcf3 (setup.py): started
2025-06-06T06:22:51,397   Destination directory: /tmp/pip-wheel-i84oj9_b
2025-06-06T06:22:51,398   Running command python setup.py bdist_wheel
2025-06-06T06:22:51,963   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite'
2025-06-06T06:22:51,963     warnings.warn(msg)
2025-06-06T06:22:52,246   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-06-06T06:22:52,247   !!

2025-06-06T06:22:52,248           ********************************************************************************
2025-06-06T06:22:52,249           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-06-06T06:22:52,250           License :: OSI Approved :: BSD License
2025-06-06T06:22:52,251           License :: OSI Approved :: MIT License

2025-06-06T06:22:52,252           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-06-06T06:22:52,253           ********************************************************************************

2025-06-06T06:22:52,254   !!
2025-06-06T06:22:52,255     self._finalize_license_expression()
2025-06-06T06:22:52,256   running bdist_wheel
2025-06-06T06:22:52,364   running build
2025-06-06T06:22:52,365   running build_py
2025-06-06T06:22:52,397   creating build/lib.linux-armv7l-cpython-311/vcf
2025-06-06T06:22:52,400   copying vcf/utils.py -> build/lib.linux-armv7l-cpython-311/vcf
2025-06-06T06:22:52,402   copying vcf/parser.py -> build/lib.linux-armv7l-cpython-311/vcf
2025-06-06T06:22:52,405   copying vcf/filters.py -> build/lib.linux-armv7l-cpython-311/vcf
2025-06-06T06:22:52,408   copying vcf/__init__.py -> build/lib.linux-armv7l-cpython-311/vcf
2025-06-06T06:22:52,410   copying vcf/bgzf.py -> build/lib.linux-armv7l-cpython-311/vcf
2025-06-06T06:22:52,414   copying vcf/model.py -> build/lib.linux-armv7l-cpython-311/vcf
2025-06-06T06:22:52,417   copying vcf/sample_filter.py -> build/lib.linux-armv7l-cpython-311/vcf
2025-06-06T06:22:52,421   creating build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,423   copying vcf/test/prof.py -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,426   copying vcf/test/__init__.py -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,428   copying vcf/test/test_vcf.py -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,432   running egg_info
2025-06-06T06:22:52,463   writing PyVCF3.egg-info/PKG-INFO
2025-06-06T06:22:52,466   writing dependency_links to PyVCF3.egg-info/dependency_links.txt
2025-06-06T06:22:52,469   writing entry points to PyVCF3.egg-info/entry_points.txt
2025-06-06T06:22:52,471   writing requirements to PyVCF3.egg-info/requires.txt
2025-06-06T06:22:52,472   writing top-level names to PyVCF3.egg-info/top_level.txt
2025-06-06T06:22:52,512   reading manifest file 'PyVCF3.egg-info/SOURCES.txt'
2025-06-06T06:22:52,518   reading manifest template 'MANIFEST.in'
2025-06-06T06:22:52,539   adding license file 'LICENSE'
2025-06-06T06:22:52,545   writing manifest file 'PyVCF3.egg-info/SOURCES.txt'
2025-06-06T06:22:52,554   copying vcf/cparse.pyx -> build/lib.linux-armv7l-cpython-311/vcf
2025-06-06T06:22:52,558   copying vcf/test/1kg.sites.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,562   copying vcf/test/1kg.vcf.gz -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,589   copying vcf/test/FT.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,592   copying vcf/test/bad-info-character.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,595   copying vcf/test/bcftools.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,600   copying vcf/test/contig_idonly.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,603   copying vcf/test/example-4.0.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,606   copying vcf/test/example-4.1-bnd.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,609   copying vcf/test/example-4.1-info-multiple-values.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,612   copying vcf/test/example-4.1-ploidy.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,615   copying vcf/test/example-4.1-sv.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,619   copying vcf/test/example-4.1.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,621   copying vcf/test/example-4.2.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,625   copying vcf/test/freebayes.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,630   copying vcf/test/gatk.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,634   copying vcf/test/gatk_26_meta.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,637   copying vcf/test/gonl.chr20.release4.gtc.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,641   copying vcf/test/info-type-character.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,644   copying vcf/test/issue-140-file1.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,647   copying vcf/test/issue-140-file2.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,650   copying vcf/test/issue-140-file3.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,652   copying vcf/test/issue-16.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,655   copying vcf/test/issue-201.vcf.gz -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,658   copying vcf/test/issue-201.vcf.gz.tbi -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,661   copying vcf/test/issue-214.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,664   copying vcf/test/issue-254.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,667   copying vcf/test/issue_49.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,671   copying vcf/test/metadata-whitespace.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,675   copying vcf/test/mixed-filtering.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,678   copying vcf/test/null_genotype_mono.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,682   copying vcf/test/parse-meta-line.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,684   copying vcf/test/samples-space.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,687   copying vcf/test/samtools.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,690   copying vcf/test/strelka.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,694   copying vcf/test/string_as_flag.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,697   copying vcf/test/tb.vcf.gz -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,699   copying vcf/test/tb.vcf.gz.tbi -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,702   copying vcf/test/uncalled_genotypes.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,705   copying vcf/test/walk_left.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,708   copying vcf/test/walk_refcall.vcf -> build/lib.linux-armv7l-cpython-311/vcf/test
2025-06-06T06:22:52,711   running build_ext
2025-06-06T06:22:53,129   Compiling vcf/cparse.pyx because it changed.
2025-06-06T06:22:53,130   [1/1] Cythonizing vcf/cparse.pyx
2025-06-06T06:22:54,828   building 'vcf.cparse' extension
2025-06-06T06:22:54,829   creating build/temp.linux-armv7l-cpython-311/vcf
2025-06-06T06:22:54,831   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/python3.11 -c vcf/cparse.c -o build/temp.linux-armv7l-cpython-311/vcf/cparse.o
2025-06-06T06:23:07,867   arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/vcf/cparse.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/vcf/cparse.cpython-311-arm-linux-gnueabihf.so
2025-06-06T06:23:07,994   running build_scripts
2025-06-06T06:23:07,994   creating build/scripts-3.11
2025-06-06T06:23:07,995   copying and adjusting scripts/vcf_melt -> build/scripts-3.11
2025-06-06T06:23:07,997   copying and adjusting scripts/vcf_filter.py -> build/scripts-3.11
2025-06-06T06:23:07,999   copying and adjusting scripts/vcf_sample_filter.py -> build/scripts-3.11
2025-06-06T06:23:08,000   changing mode of build/scripts-3.11/vcf_melt from 644 to 755
2025-06-06T06:23:08,001   changing mode of build/scripts-3.11/vcf_filter.py from 644 to 755
2025-06-06T06:23:08,002   changing mode of build/scripts-3.11/vcf_sample_filter.py from 644 to 755
2025-06-06T06:23:08,030   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2025-06-06T06:23:08,031   !!

2025-06-06T06:23:08,032           ********************************************************************************
2025-06-06T06:23:08,033           Please avoid running ``setup.py`` directly.
2025-06-06T06:23:08,034           Instead, use pypa/build, pypa/installer or other
2025-06-06T06:23:08,035           standards-based tools.

2025-06-06T06:23:08,036           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-06-06T06:23:08,037           or your builds will no longer be supported.

2025-06-06T06:23:08,038           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2025-06-06T06:23:08,038           ********************************************************************************

2025-06-06T06:23:08,040   !!
2025-06-06T06:23:08,040     self.initialize_options()
2025-06-06T06:23:08,061   installing to build/bdist.linux-armv7l/wheel
2025-06-06T06:23:08,062   running install
2025-06-06T06:23:08,087   running install_lib
2025-06-06T06:23:08,117   creating build/bdist.linux-armv7l/wheel
2025-06-06T06:23:08,119   creating build/bdist.linux-armv7l/wheel/vcf
2025-06-06T06:23:08,120   copying build/lib.linux-armv7l-cpython-311/vcf/utils.py -> build/bdist.linux-armv7l/wheel/./vcf
2025-06-06T06:23:08,124   creating build/bdist.linux-armv7l/wheel/vcf/test
2025-06-06T06:23:08,125   copying build/lib.linux-armv7l-cpython-311/vcf/test/example-4.1-ploidy.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,127   copying build/lib.linux-armv7l-cpython-311/vcf/test/tb.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,129   copying build/lib.linux-armv7l-cpython-311/vcf/test/info-type-character.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,131   copying build/lib.linux-armv7l-cpython-311/vcf/test/issue-140-file2.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,133   copying build/lib.linux-armv7l-cpython-311/vcf/test/walk_refcall.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,135   copying build/lib.linux-armv7l-cpython-311/vcf/test/parse-meta-line.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,137   copying build/lib.linux-armv7l-cpython-311/vcf/test/issue-201.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,139   copying build/lib.linux-armv7l-cpython-311/vcf/test/samples-space.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,141   copying build/lib.linux-armv7l-cpython-311/vcf/test/uncalled_genotypes.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,143   copying build/lib.linux-armv7l-cpython-311/vcf/test/issue-254.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,145   copying build/lib.linux-armv7l-cpython-311/vcf/test/string_as_flag.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,147   copying build/lib.linux-armv7l-cpython-311/vcf/test/gonl.chr20.release4.gtc.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,150   copying build/lib.linux-armv7l-cpython-311/vcf/test/example-4.1-info-multiple-values.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,152   copying build/lib.linux-armv7l-cpython-311/vcf/test/tb.vcf.gz -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,154   copying build/lib.linux-armv7l-cpython-311/vcf/test/prof.py -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,157   copying build/lib.linux-armv7l-cpython-311/vcf/test/mixed-filtering.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,159   copying build/lib.linux-armv7l-cpython-311/vcf/test/bcftools.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,164   copying build/lib.linux-armv7l-cpython-311/vcf/test/__init__.py -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,166   copying build/lib.linux-armv7l-cpython-311/vcf/test/example-4.0.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,168   copying build/lib.linux-armv7l-cpython-311/vcf/test/FT.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,171   copying build/lib.linux-armv7l-cpython-311/vcf/test/walk_left.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,173   copying build/lib.linux-armv7l-cpython-311/vcf/test/freebayes.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,179   copying build/lib.linux-armv7l-cpython-311/vcf/test/null_genotype_mono.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,182   copying build/lib.linux-armv7l-cpython-311/vcf/test/metadata-whitespace.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,185   copying build/lib.linux-armv7l-cpython-311/vcf/test/issue-201.vcf.gz -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,187   copying build/lib.linux-armv7l-cpython-311/vcf/test/issue_49.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,190   copying build/lib.linux-armv7l-cpython-311/vcf/test/1kg.sites.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,193   copying build/lib.linux-armv7l-cpython-311/vcf/test/gatk_26_meta.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,195   copying build/lib.linux-armv7l-cpython-311/vcf/test/issue-214.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,198   copying build/lib.linux-armv7l-cpython-311/vcf/test/example-4.1.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,200   copying build/lib.linux-armv7l-cpython-311/vcf/test/1kg.vcf.gz -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,218   copying build/lib.linux-armv7l-cpython-311/vcf/test/example-4.1-sv.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,220   copying build/lib.linux-armv7l-cpython-311/vcf/test/issue-16.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,222   copying build/lib.linux-armv7l-cpython-311/vcf/test/issue-140-file1.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,224   copying build/lib.linux-armv7l-cpython-311/vcf/test/issue-140-file3.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,226   copying build/lib.linux-armv7l-cpython-311/vcf/test/test_vcf.py -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,229   copying build/lib.linux-armv7l-cpython-311/vcf/test/example-4.1-bnd.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,231   copying build/lib.linux-armv7l-cpython-311/vcf/test/example-4.2.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,234   copying build/lib.linux-armv7l-cpython-311/vcf/test/strelka.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,237   copying build/lib.linux-armv7l-cpython-311/vcf/test/bad-info-character.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,239   copying build/lib.linux-armv7l-cpython-311/vcf/test/gatk.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,242   copying build/lib.linux-armv7l-cpython-311/vcf/test/samtools.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,244   copying build/lib.linux-armv7l-cpython-311/vcf/test/contig_idonly.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test
2025-06-06T06:23:08,246   copying build/lib.linux-armv7l-cpython-311/vcf/parser.py -> build/bdist.linux-armv7l/wheel/./vcf
2025-06-06T06:23:08,249   copying build/lib.linux-armv7l-cpython-311/vcf/cparse.pyx -> build/bdist.linux-armv7l/wheel/./vcf
2025-06-06T06:23:08,251   copying build/lib.linux-armv7l-cpython-311/vcf/filters.py -> build/bdist.linux-armv7l/wheel/./vcf
2025-06-06T06:23:08,254   copying build/lib.linux-armv7l-cpython-311/vcf/__init__.py -> build/bdist.linux-armv7l/wheel/./vcf
2025-06-06T06:23:08,256   copying build/lib.linux-armv7l-cpython-311/vcf/bgzf.py -> build/bdist.linux-armv7l/wheel/./vcf
2025-06-06T06:23:08,259   copying build/lib.linux-armv7l-cpython-311/vcf/cparse.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./vcf
2025-06-06T06:23:08,275   copying build/lib.linux-armv7l-cpython-311/vcf/model.py -> build/bdist.linux-armv7l/wheel/./vcf
2025-06-06T06:23:08,277   copying build/lib.linux-armv7l-cpython-311/vcf/sample_filter.py -> build/bdist.linux-armv7l/wheel/./vcf
2025-06-06T06:23:08,279   running install_egg_info
2025-06-06T06:23:08,318   Copying PyVCF3.egg-info to build/bdist.linux-armv7l/wheel/./PyVCF3-1.0.4-py3.11.egg-info
2025-06-06T06:23:08,331   running install_scripts
2025-06-06T06:23:08,332   creating build/bdist.linux-armv7l/wheel/pyvcf3-1.0.4.data/scripts
2025-06-06T06:23:08,334   copying build/scripts-3.11/vcf_melt -> build/bdist.linux-armv7l/wheel/pyvcf3-1.0.4.data/scripts
2025-06-06T06:23:08,336   copying build/scripts-3.11/vcf_filter.py -> build/bdist.linux-armv7l/wheel/pyvcf3-1.0.4.data/scripts
2025-06-06T06:23:08,338   copying build/scripts-3.11/vcf_sample_filter.py -> build/bdist.linux-armv7l/wheel/pyvcf3-1.0.4.data/scripts
2025-06-06T06:23:08,340   changing mode of build/bdist.linux-armv7l/wheel/pyvcf3-1.0.4.data/scripts/vcf_melt to 755
2025-06-06T06:23:08,341   changing mode of build/bdist.linux-armv7l/wheel/pyvcf3-1.0.4.data/scripts/vcf_filter.py to 755
2025-06-06T06:23:08,341   changing mode of build/bdist.linux-armv7l/wheel/pyvcf3-1.0.4.data/scripts/vcf_sample_filter.py to 755
2025-06-06T06:23:08,397   creating build/bdist.linux-armv7l/wheel/pyvcf3-1.0.4.dist-info/WHEEL
2025-06-06T06:23:08,400   creating '/tmp/pip-wheel-i84oj9_b/pyvcf3-1.0.4-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-06-06T06:23:08,403   adding 'pyvcf3-1.0.4.data/scripts/vcf_filter.py'
2025-06-06T06:23:08,405   adding 'pyvcf3-1.0.4.data/scripts/vcf_melt'
2025-06-06T06:23:08,406   adding 'pyvcf3-1.0.4.data/scripts/vcf_sample_filter.py'
2025-06-06T06:23:08,409   adding 'pyvcf3-1.0.4.dist-info/licenses/LICENSE'
2025-06-06T06:23:08,411   adding 'vcf/__init__.py'
2025-06-06T06:23:08,416   adding 'vcf/bgzf.py'
2025-06-06T06:23:08,560   adding 'vcf/cparse.cpython-311-arm-linux-gnueabihf.so'
2025-06-06T06:23:08,566   adding 'vcf/cparse.pyx'
2025-06-06T06:23:08,567   adding 'vcf/filters.py'
2025-06-06T06:23:08,570   adding 'vcf/model.py'
2025-06-06T06:23:08,574   adding 'vcf/parser.py'
2025-06-06T06:23:08,576   adding 'vcf/sample_filter.py'
2025-06-06T06:23:08,577   adding 'vcf/utils.py'
2025-06-06T06:23:08,583   adding 'vcf/test/1kg.sites.vcf'
2025-06-06T06:23:08,679   adding 'vcf/test/1kg.vcf.gz'
2025-06-06T06:23:08,686   adding 'vcf/test/FT.vcf'
2025-06-06T06:23:08,687   adding 'vcf/test/__init__.py'
2025-06-06T06:23:08,689   adding 'vcf/test/bad-info-character.vcf'
2025-06-06T06:23:08,696   adding 'vcf/test/bcftools.vcf'
2025-06-06T06:23:08,697   adding 'vcf/test/contig_idonly.vcf'
2025-06-06T06:23:08,699   adding 'vcf/test/example-4.0.vcf'
2025-06-06T06:23:08,700   adding 'vcf/test/example-4.1-bnd.vcf'
2025-06-06T06:23:08,701   adding 'vcf/test/example-4.1-info-multiple-values.vcf'
2025-06-06T06:23:08,703   adding 'vcf/test/example-4.1-ploidy.vcf'
2025-06-06T06:23:08,704   adding 'vcf/test/example-4.1-sv.vcf'
2025-06-06T06:23:08,705   adding 'vcf/test/example-4.1.vcf'
2025-06-06T06:23:08,709   adding 'vcf/test/example-4.2.vcf'
2025-06-06T06:23:08,725   adding 'vcf/test/freebayes.vcf'
2025-06-06T06:23:08,729   adding 'vcf/test/gatk.vcf'
2025-06-06T06:23:08,730   adding 'vcf/test/gatk_26_meta.vcf'
2025-06-06T06:23:08,732   adding 'vcf/test/gonl.chr20.release4.gtc.vcf'
2025-06-06T06:23:08,734   adding 'vcf/test/info-type-character.vcf'
2025-06-06T06:23:08,735   adding 'vcf/test/issue-140-file1.vcf'
2025-06-06T06:23:08,736   adding 'vcf/test/issue-140-file2.vcf'
2025-06-06T06:23:08,738   adding 'vcf/test/issue-140-file3.vcf'
2025-06-06T06:23:08,739   adding 'vcf/test/issue-16.vcf'
2025-06-06T06:23:08,740   adding 'vcf/test/issue-201.vcf.gz'
2025-06-06T06:23:08,742   adding 'vcf/test/issue-201.vcf.gz.tbi'
2025-06-06T06:23:08,743   adding 'vcf/test/issue-214.vcf'
2025-06-06T06:23:08,744   adding 'vcf/test/issue-254.vcf'
2025-06-06T06:23:08,746   adding 'vcf/test/issue_49.vcf'
2025-06-06T06:23:08,750   adding 'vcf/test/metadata-whitespace.vcf'
2025-06-06T06:23:08,751   adding 'vcf/test/mixed-filtering.vcf'
2025-06-06T06:23:08,753   adding 'vcf/test/null_genotype_mono.vcf'
2025-06-06T06:23:08,754   adding 'vcf/test/parse-meta-line.vcf'
2025-06-06T06:23:08,756   adding 'vcf/test/prof.py'
2025-06-06T06:23:08,757   adding 'vcf/test/samples-space.vcf'
2025-06-06T06:23:08,758   adding 'vcf/test/samtools.vcf'
2025-06-06T06:23:08,760   adding 'vcf/test/strelka.vcf'
2025-06-06T06:23:08,761   adding 'vcf/test/string_as_flag.vcf'
2025-06-06T06:23:08,762   adding 'vcf/test/tb.vcf.gz'
2025-06-06T06:23:08,764   adding 'vcf/test/tb.vcf.gz.tbi'
2025-06-06T06:23:08,769   adding 'vcf/test/test_vcf.py'
2025-06-06T06:23:08,771   adding 'vcf/test/uncalled_genotypes.vcf'
2025-06-06T06:23:08,772   adding 'vcf/test/walk_left.vcf'
2025-06-06T06:23:08,773   adding 'vcf/test/walk_refcall.vcf'
2025-06-06T06:23:08,774   adding 'pyvcf3-1.0.4.dist-info/METADATA'
2025-06-06T06:23:08,775   adding 'pyvcf3-1.0.4.dist-info/WHEEL'
2025-06-06T06:23:08,777   adding 'pyvcf3-1.0.4.dist-info/entry_points.txt'
2025-06-06T06:23:08,778   adding 'pyvcf3-1.0.4.dist-info/top_level.txt'
2025-06-06T06:23:08,779   adding 'pyvcf3-1.0.4.dist-info/RECORD'
2025-06-06T06:23:08,795   removing build/bdist.linux-armv7l/wheel
2025-06-06T06:23:09,050   Building wheel for pyvcf3 (setup.py): finished with status 'done'
2025-06-06T06:23:09,065   Created wheel for pyvcf3: filename=pyvcf3-1.0.4-cp311-cp311-linux_armv7l.whl size=1258643 sha256=ee39875519ab622a90403b09c1af29fc8cbf9f58e3f78c97095b5df541683645
2025-06-06T06:23:09,066   Stored in directory: /tmp/pip-ephem-wheel-cache-pcbo9ds1/wheels/aa/d2/93/24a22d6c6371f9a14e1b6d6a2cdcdb3d955d6e784fd0ed3041
2025-06-06T06:23:09,080 Successfully built pyvcf3
2025-06-06T06:23:09,117 Removed build tracker: '/tmp/pip-build-tracker-oj6oe1xp'