2025-09-19T03:08:25,628 Created temporary directory: /tmp/pip-ephem-wheel-cache-2c2dhj60 2025-09-19T03:08:25,631 Created temporary directory: /tmp/pip-req-tracker-unen9523 2025-09-19T03:08:25,631 Initialized build tracking at /tmp/pip-req-tracker-unen9523 2025-09-19T03:08:25,632 Created build tracker: /tmp/pip-req-tracker-unen9523 2025-09-19T03:08:25,632 Entered build tracker: /tmp/pip-req-tracker-unen9523 2025-09-19T03:08:25,633 Created temporary directory: /tmp/pip-wheel-c5xmfb4w 2025-09-19T03:08:25,660 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple, https://www.piwheels.org/simple 2025-09-19T03:08:25,662 2 location(s) to search for versions of pyvcf3: 2025-09-19T03:08:25,662 * https://pypi.org/simple/pyvcf3/ 2025-09-19T03:08:25,662 * https://www.piwheels.org/simple/pyvcf3/ 2025-09-19T03:08:25,663 Fetching project page and analyzing links: https://pypi.org/simple/pyvcf3/ 2025-09-19T03:08:25,663 Getting page https://pypi.org/simple/pyvcf3/ 2025-09-19T03:08:25,665 Found index url https://pypi.org/simple 2025-09-19T03:08:25,671 Starting new HTTPS connection (1): pypi.org:443 2025-09-19T03:08:25,796 https://pypi.org:443 "GET /simple/pyvcf3/ HTTP/1.1" 200 1024 2025-09-19T03:08:25,865 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/28/e4/1444bd99ba308b117583dc2424ad29fbc59e3f48b283f34ee0b525f81355/PyVCF3-1.0.0-py3.10-linux-x86_64.egg#sha256=8f69facb62dca7fcdeb2903665a00eb164f7af3f37d64d843e6fc73f3bc15b28 (from https://pypi.org/simple/pyvcf3/) 2025-09-19T03:08:25,865 Found link https://files.pythonhosted.org/packages/af/3a/d3c816c29dc176177067160069ac049a4bbd3c0feb96a41380b6d0e9d4bf/PyVCF3-1.0.0.tar.gz#sha256=7368ec0bf51e8772b2a18c25ab3e7567a3391ae3762d0d6099232a3f8fc0f2b3 (from https://pypi.org/simple/pyvcf3/), version: 1.0.0 2025-09-19T03:08:25,865 Found link https://files.pythonhosted.org/packages/9b/f3/79dd49b0c14edb1e6845fcfcbaebc059970466deadfced075037d1862147/PyVCF3-1.0.1.tar.gz#sha256=6c5da84692a61fa8ef7dcc66c4c702df489e17e0cb18773e4b1934cdc8d222b6 (from https://pypi.org/simple/pyvcf3/), version: 1.0.1 2025-09-19T03:08:25,866 Found link https://files.pythonhosted.org/packages/6a/0d/6d79c6ac40df1e24a8dc2df551e2f1bf93bc5defa815750910787a1f1ead/PyVCF3-1.0.2.tar.gz#sha256=ff6ec5e58e089e37d7c1adb41ec23f4cf81abea87cae64fafae475b806ffe338 (from https://pypi.org/simple/pyvcf3/), version: 1.0.2 2025-09-19T03:08:25,866 Found link https://files.pythonhosted.org/packages/28/ee/5d0b0bd20762f1126b34cb15dce973fe4dbd1baf17d7ee621b18e336c0e5/PyVCF3-1.0.3.tar.gz#sha256=4b16d71c8b97010487e2c939fb4d5707b7bbfa4e2b313df9dba3e372c5ba031d (from https://pypi.org/simple/pyvcf3/), version: 1.0.3 2025-09-19T03:08:25,866 Skipping link: No binaries permitted for pyvcf3: https://files.pythonhosted.org/packages/67/52/e4c3d6656b94bddaf41bacffbe3e3e0e4ba1262854dde40e0d884fb2b40b/pyvcf3-1.0.4-py3-none-any.whl#sha256=750df57ec68784d3d96d614ed149ec9bfbaea43e702b2683badb78a6282a349b (from https://pypi.org/simple/pyvcf3/) 2025-09-19T03:08:25,867 Found link https://files.pythonhosted.org/packages/54/25/11d689a4c8eb8e0fe863310cccb3785ab79746896d342683e493b1308bd8/pyvcf3-1.0.4.tar.gz#sha256=6a251582b8f226f9cf363bb27f3323ace8a1c561a14c297f4bfafe1ffdb2e3d1 (from https://pypi.org/simple/pyvcf3/), version: 1.0.4 2025-09-19T03:08:25,867 Fetching project page and analyzing links: https://www.piwheels.org/simple/pyvcf3/ 2025-09-19T03:08:25,867 Getting page https://www.piwheels.org/simple/pyvcf3/ 2025-09-19T03:08:25,868 Found index url https://www.piwheels.org/simple 2025-09-19T03:08:25,870 Starting new HTTPS connection (1): www.piwheels.org:443 2025-09-19T03:08:25,937 https://www.piwheels.org:443 "GET /simple/pyvcf3/ HTTP/1.1" 200 1368 2025-09-19T03:08:25,960 Skipping link: No binaries permitted for pyvcf3: https://archive1.piwheels.org/simple/pyvcf3/pyvcf3-1.0.4-cp311-cp311-linux_armv6l.whl#sha256=ee39875519ab622a90403b09c1af29fc8cbf9f58e3f78c97095b5df541683645 (from https://www.piwheels.org/simple/pyvcf3/) 2025-09-19T03:08:25,960 Skipping link: No binaries permitted for pyvcf3: https://archive1.piwheels.org/simple/pyvcf3/pyvcf3-1.0.4-cp311-cp311-linux_armv7l.whl#sha256=ee39875519ab622a90403b09c1af29fc8cbf9f58e3f78c97095b5df541683645 (from https://www.piwheels.org/simple/pyvcf3/) 2025-09-19T03:08:25,960 Skipping link: No binaries permitted for pyvcf3: https://archive1.piwheels.org/simple/pyvcf3/PyVCF3-1.0.3-cp35-cp35m-linux_armv6l.whl#sha256=c2bc58d6ef4d1585e4cf018a09ebb2bbcb970d5e9a7057bd8cf8428f59b7a2a3 (from https://www.piwheels.org/simple/pyvcf3/) 2025-09-19T03:08:25,960 Skipping link: No binaries permitted for pyvcf3: 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https://www.piwheels.org/simple/pyvcf3/pyvcf3-1.0.0-cp313-cp313-linux_armv7l.whl#sha256=1b51514f52da54d204e61ac906f4065ac3c0a79d5f4e011edc0c55d19185cc81 (from https://www.piwheels.org/simple/pyvcf3/) 2025-09-19T03:08:25,997 Given no hashes to check 1 links for project 'pyvcf3': discarding no candidates 2025-09-19T03:08:26,026 Collecting pyvcf3==1.0.4 2025-09-19T03:08:26,027 Created temporary directory: /tmp/pip-unpack-969x5c4e 2025-09-19T03:08:26,031 Starting new HTTPS connection (1): files.pythonhosted.org:443 2025-09-19T03:08:26,076 https://files.pythonhosted.org:443 "GET /packages/54/25/11d689a4c8eb8e0fe863310cccb3785ab79746896d342683e493b1308bd8/pyvcf3-1.0.4.tar.gz HTTP/1.1" 200 977792 2025-09-19T03:08:26,078 Downloading pyvcf3-1.0.4.tar.gz (977 kB) 2025-09-19T03:08:26,334 Added pyvcf3==1.0.4 from https://files.pythonhosted.org/packages/54/25/11d689a4c8eb8e0fe863310cccb3785ab79746896d342683e493b1308bd8/pyvcf3-1.0.4.tar.gz#sha256=6a251582b8f226f9cf363bb27f3323ace8a1c561a14c297f4bfafe1ffdb2e3d1 to build tracker '/tmp/pip-req-tracker-unen9523' 2025-09-19T03:08:26,335 Running setup.py (path:/tmp/pip-wheel-c5xmfb4w/pyvcf3_687d523b07f84929a178c73868a84eb9/setup.py) egg_info for package pyvcf3 2025-09-19T03:08:26,335 Created temporary directory: /tmp/pip-pip-egg-info-dr9z7amz 2025-09-19T03:08:26,335 Running command python setup.py egg_info 2025-09-19T03:08:26,917 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-19T03:08:26,917 warnings.warn(msg) 2025-09-19T03:08:27,213 /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-19T03:08:27,213 !! 2025-09-19T03:08:27,213 ******************************************************************************** 2025-09-19T03:08:27,214 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-19T03:08:27,214 License :: OSI Approved :: BSD License 2025-09-19T03:08:27,214 License :: OSI Approved :: MIT License 2025-09-19T03:08:27,215 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-19T03:08:27,215 ******************************************************************************** 2025-09-19T03:08:27,215 !! 2025-09-19T03:08:27,216 self._finalize_license_expression() 2025-09-19T03:08:27,242 running egg_info 2025-09-19T03:08:27,270 creating /tmp/pip-pip-egg-info-dr9z7amz/PyVCF3.egg-info 2025-09-19T03:08:27,271 writing /tmp/pip-pip-egg-info-dr9z7amz/PyVCF3.egg-info/PKG-INFO 2025-09-19T03:08:27,274 writing dependency_links to /tmp/pip-pip-egg-info-dr9z7amz/PyVCF3.egg-info/dependency_links.txt 2025-09-19T03:08:27,276 writing entry points to /tmp/pip-pip-egg-info-dr9z7amz/PyVCF3.egg-info/entry_points.txt 2025-09-19T03:08:27,278 writing requirements to /tmp/pip-pip-egg-info-dr9z7amz/PyVCF3.egg-info/requires.txt 2025-09-19T03:08:27,279 writing top-level names to /tmp/pip-pip-egg-info-dr9z7amz/PyVCF3.egg-info/top_level.txt 2025-09-19T03:08:27,280 writing manifest file '/tmp/pip-pip-egg-info-dr9z7amz/PyVCF3.egg-info/SOURCES.txt' 2025-09-19T03:08:27,405 reading manifest file '/tmp/pip-pip-egg-info-dr9z7amz/PyVCF3.egg-info/SOURCES.txt' 2025-09-19T03:08:27,407 reading manifest template 'MANIFEST.in' 2025-09-19T03:08:27,425 adding license file 'LICENSE' 2025-09-19T03:08:27,429 writing manifest file '/tmp/pip-pip-egg-info-dr9z7amz/PyVCF3.egg-info/SOURCES.txt' 2025-09-19T03:08:27,520 Source in /tmp/pip-wheel-c5xmfb4w/pyvcf3_687d523b07f84929a178c73868a84eb9 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#sha256=6a251582b8f226f9cf363bb27f3323ace8a1c561a14c297f4bfafe1ffdb2e3d1 2025-09-19T03:08:27,521 Removed pyvcf3==1.0.4 from https://files.pythonhosted.org/packages/54/25/11d689a4c8eb8e0fe863310cccb3785ab79746896d342683e493b1308bd8/pyvcf3-1.0.4.tar.gz#sha256=6a251582b8f226f9cf363bb27f3323ace8a1c561a14c297f4bfafe1ffdb2e3d1 from build tracker '/tmp/pip-req-tracker-unen9523' 2025-09-19T03:08:27,529 Created temporary directory: /tmp/pip-unpack-xbkw4c2x 2025-09-19T03:08:27,529 Building wheels for collected packages: pyvcf3 2025-09-19T03:08:27,533 Created temporary directory: /tmp/pip-wheel-vb79m5aj 2025-09-19T03:08:27,534 Building wheel for pyvcf3 (setup.py): started 2025-09-19T03:08:27,534 Destination directory: /tmp/pip-wheel-vb79m5aj 2025-09-19T03:08:27,534 Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-c5xmfb4w/pyvcf3_687d523b07f84929a178c73868a84eb9/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-c5xmfb4w/pyvcf3_687d523b07f84929a178c73868a84eb9/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-vb79m5aj 2025-09-19T03:08:28,113 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-19T03:08:28,114 warnings.warn(msg) 2025-09-19T03:08:28,422 /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-19T03:08:28,422 !! 2025-09-19T03:08:28,423 ******************************************************************************** 2025-09-19T03:08:28,423 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-19T03:08:28,423 License :: OSI Approved :: BSD License 2025-09-19T03:08:28,424 License :: OSI Approved :: MIT License 2025-09-19T03:08:28,424 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-19T03:08:28,424 ******************************************************************************** 2025-09-19T03:08:28,424 !! 2025-09-19T03:08:28,425 self._finalize_license_expression() 2025-09-19T03:08:28,425 running bdist_wheel 2025-09-19T03:08:28,541 running build 2025-09-19T03:08:28,541 running build_py 2025-09-19T03:08:28,573 creating build/lib.linux-armv7l-cpython-39/vcf 2025-09-19T03:08:28,575 copying vcf/utils.py -> build/lib.linux-armv7l-cpython-39/vcf 2025-09-19T03:08:28,577 copying vcf/bgzf.py -> build/lib.linux-armv7l-cpython-39/vcf 2025-09-19T03:08:28,580 copying vcf/sample_filter.py -> build/lib.linux-armv7l-cpython-39/vcf 2025-09-19T03:08:28,582 copying vcf/filters.py -> build/lib.linux-armv7l-cpython-39/vcf 2025-09-19T03:08:28,584 copying vcf/__init__.py -> build/lib.linux-armv7l-cpython-39/vcf 2025-09-19T03:08:28,585 copying vcf/parser.py -> build/lib.linux-armv7l-cpython-39/vcf 2025-09-19T03:08:28,588 copying vcf/model.py -> build/lib.linux-armv7l-cpython-39/vcf 2025-09-19T03:08:28,591 creating build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,592 copying vcf/test/prof.py -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,594 copying vcf/test/test_vcf.py -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,598 copying vcf/test/__init__.py -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,599 running egg_info 2025-09-19T03:08:28,626 writing PyVCF3.egg-info/PKG-INFO 2025-09-19T03:08:28,629 writing dependency_links to PyVCF3.egg-info/dependency_links.txt 2025-09-19T03:08:28,631 writing entry points to PyVCF3.egg-info/entry_points.txt 2025-09-19T03:08:28,633 writing requirements to PyVCF3.egg-info/requires.txt 2025-09-19T03:08:28,634 writing top-level names to PyVCF3.egg-info/top_level.txt 2025-09-19T03:08:28,673 reading manifest file 'PyVCF3.egg-info/SOURCES.txt' 2025-09-19T03:08:28,679 reading manifest template 'MANIFEST.in' 2025-09-19T03:08:28,696 adding license file 'LICENSE' 2025-09-19T03:08:28,702 writing manifest file 'PyVCF3.egg-info/SOURCES.txt' 2025-09-19T03:08:28,711 copying vcf/cparse.pyx -> build/lib.linux-armv7l-cpython-39/vcf 2025-09-19T03:08:28,714 copying vcf/test/1kg.sites.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,717 copying vcf/test/1kg.vcf.gz -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,737 copying vcf/test/FT.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,740 copying vcf/test/bad-info-character.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,742 copying vcf/test/bcftools.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,745 copying vcf/test/contig_idonly.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,747 copying vcf/test/example-4.0.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,749 copying vcf/test/example-4.1-bnd.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,752 copying vcf/test/example-4.1-info-multiple-values.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,754 copying vcf/test/example-4.1-ploidy.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,756 copying vcf/test/example-4.1-sv.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,758 copying vcf/test/example-4.1.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,760 copying vcf/test/example-4.2.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,763 copying vcf/test/freebayes.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,767 copying vcf/test/gatk.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,770 copying vcf/test/gatk_26_meta.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,772 copying vcf/test/gonl.chr20.release4.gtc.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,775 copying vcf/test/info-type-character.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,777 copying vcf/test/issue-140-file1.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,779 copying vcf/test/issue-140-file2.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,781 copying vcf/test/issue-140-file3.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,783 copying vcf/test/issue-16.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,785 copying vcf/test/issue-201.vcf.gz -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,787 copying vcf/test/issue-201.vcf.gz.tbi -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,789 copying vcf/test/issue-214.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,791 copying vcf/test/issue-254.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,793 copying vcf/test/issue_49.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,796 copying vcf/test/metadata-whitespace.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,799 copying vcf/test/mixed-filtering.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,801 copying vcf/test/null_genotype_mono.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,803 copying vcf/test/parse-meta-line.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,805 copying vcf/test/samples-space.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,807 copying vcf/test/samtools.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,809 copying vcf/test/strelka.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,812 copying vcf/test/string_as_flag.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,814 copying vcf/test/tb.vcf.gz -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,816 copying vcf/test/tb.vcf.gz.tbi -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,818 copying vcf/test/uncalled_genotypes.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,820 copying vcf/test/walk_left.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,822 copying vcf/test/walk_refcall.vcf -> build/lib.linux-armv7l-cpython-39/vcf/test 2025-09-19T03:08:28,825 running build_ext 2025-09-19T03:08:29,282 Compiling vcf/cparse.pyx because it changed. 2025-09-19T03:08:29,283 [1/1] Cythonizing vcf/cparse.pyx 2025-09-19T03:08:31,370 building 'vcf.cparse' extension 2025-09-19T03:08:31,372 creating build/temp.linux-armv7l-cpython-39/vcf 2025-09-19T03:08:31,373 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-eDAWto/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/python3.9 -c vcf/cparse.c -o build/temp.linux-armv7l-cpython-39/vcf/cparse.o 2025-09-19T03:08:42,625 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/vcf/cparse.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/vcf/cparse.cpython-39-arm-linux-gnueabihf.so 2025-09-19T03:08:42,859 running build_scripts 2025-09-19T03:08:42,860 creating build/scripts-3.9 2025-09-19T03:08:42,861 copying and adjusting scripts/vcf_melt -> build/scripts-3.9 2025-09-19T03:08:42,864 copying and adjusting scripts/vcf_filter.py -> build/scripts-3.9 2025-09-19T03:08:42,866 copying and adjusting scripts/vcf_sample_filter.py -> build/scripts-3.9 2025-09-19T03:08:42,867 changing mode of build/scripts-3.9/vcf_melt from 644 to 755 2025-09-19T03:08:42,867 changing mode of build/scripts-3.9/vcf_filter.py from 644 to 755 2025-09-19T03:08:42,868 changing mode of build/scripts-3.9/vcf_sample_filter.py from 644 to 755 2025-09-19T03:08:42,897 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-09-19T03:08:42,898 !! 2025-09-19T03:08:42,898 ******************************************************************************** 2025-09-19T03:08:42,898 Please avoid running ``setup.py`` directly. 2025-09-19T03:08:42,898 Instead, use pypa/build, pypa/installer or other 2025-09-19T03:08:42,899 standards-based tools. 2025-09-19T03:08:42,899 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-19T03:08:42,899 or your builds will no longer be supported. 2025-09-19T03:08:42,900 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-09-19T03:08:42,900 ******************************************************************************** 2025-09-19T03:08:42,900 !! 2025-09-19T03:08:42,901 self.initialize_options() 2025-09-19T03:08:42,925 installing to build/bdist.linux-armv7l/wheel 2025-09-19T03:08:42,926 running install 2025-09-19T03:08:42,946 running install_lib 2025-09-19T03:08:42,974 creating build/bdist.linux-armv7l/wheel 2025-09-19T03:08:42,976 creating build/bdist.linux-armv7l/wheel/vcf 2025-09-19T03:08:42,978 copying build/lib.linux-armv7l-cpython-39/vcf/cparse.pyx -> build/bdist.linux-armv7l/wheel/./vcf 2025-09-19T03:08:42,980 copying build/lib.linux-armv7l-cpython-39/vcf/utils.py -> build/bdist.linux-armv7l/wheel/./vcf 2025-09-19T03:08:42,981 copying build/lib.linux-armv7l-cpython-39/vcf/bgzf.py -> build/bdist.linux-armv7l/wheel/./vcf 2025-09-19T03:08:42,984 copying build/lib.linux-armv7l-cpython-39/vcf/sample_filter.py -> build/bdist.linux-armv7l/wheel/./vcf 2025-09-19T03:08:42,986 copying build/lib.linux-armv7l-cpython-39/vcf/filters.py -> build/bdist.linux-armv7l/wheel/./vcf 2025-09-19T03:08:42,988 copying build/lib.linux-armv7l-cpython-39/vcf/__init__.py -> build/bdist.linux-armv7l/wheel/./vcf 2025-09-19T03:08:42,990 copying build/lib.linux-armv7l-cpython-39/vcf/cparse.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./vcf 2025-09-19T03:08:43,017 creating build/bdist.linux-armv7l/wheel/vcf/test 2025-09-19T03:08:43,018 copying build/lib.linux-armv7l-cpython-39/vcf/test/gatk_26_meta.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,019 copying build/lib.linux-armv7l-cpython-39/vcf/test/string_as_flag.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,021 copying build/lib.linux-armv7l-cpython-39/vcf/test/samtools.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,023 copying build/lib.linux-armv7l-cpython-39/vcf/test/issue-140-file1.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,025 copying build/lib.linux-armv7l-cpython-39/vcf/test/issue-201.vcf.gz -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,026 copying build/lib.linux-armv7l-cpython-39/vcf/test/contig_idonly.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,028 copying build/lib.linux-armv7l-cpython-39/vcf/test/example-4.2.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,031 copying build/lib.linux-armv7l-cpython-39/vcf/test/tb.vcf.gz -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,032 copying build/lib.linux-armv7l-cpython-39/vcf/test/samples-space.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,034 copying build/lib.linux-armv7l-cpython-39/vcf/test/issue-201.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,036 copying build/lib.linux-armv7l-cpython-39/vcf/test/freebayes.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,039 copying build/lib.linux-armv7l-cpython-39/vcf/test/issue-140-file3.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,041 copying build/lib.linux-armv7l-cpython-39/vcf/test/gatk.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,046 copying build/lib.linux-armv7l-cpython-39/vcf/test/1kg.sites.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,051 copying build/lib.linux-armv7l-cpython-39/vcf/test/info-type-character.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,053 copying build/lib.linux-armv7l-cpython-39/vcf/test/issue-214.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,055 copying build/lib.linux-armv7l-cpython-39/vcf/test/metadata-whitespace.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,059 copying build/lib.linux-armv7l-cpython-39/vcf/test/walk_left.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,061 copying build/lib.linux-armv7l-cpython-39/vcf/test/example-4.1.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,063 copying build/lib.linux-armv7l-cpython-39/vcf/test/parse-meta-line.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,065 copying build/lib.linux-armv7l-cpython-39/vcf/test/uncalled_genotypes.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,067 copying build/lib.linux-armv7l-cpython-39/vcf/test/example-4.1-bnd.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,068 copying build/lib.linux-armv7l-cpython-39/vcf/test/1kg.vcf.gz -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,121 copying build/lib.linux-armv7l-cpython-39/vcf/test/tb.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,123 copying build/lib.linux-armv7l-cpython-39/vcf/test/prof.py -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,125 copying build/lib.linux-armv7l-cpython-39/vcf/test/gonl.chr20.release4.gtc.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,129 copying build/lib.linux-armv7l-cpython-39/vcf/test/example-4.1-ploidy.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,131 copying build/lib.linux-armv7l-cpython-39/vcf/test/FT.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,133 copying build/lib.linux-armv7l-cpython-39/vcf/test/issue-254.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,135 copying build/lib.linux-armv7l-cpython-39/vcf/test/test_vcf.py -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,190 copying build/lib.linux-armv7l-cpython-39/vcf/test/bad-info-character.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,193 copying build/lib.linux-armv7l-cpython-39/vcf/test/__init__.py -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,194 copying build/lib.linux-armv7l-cpython-39/vcf/test/null_genotype_mono.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,198 copying build/lib.linux-armv7l-cpython-39/vcf/test/walk_refcall.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,201 copying build/lib.linux-armv7l-cpython-39/vcf/test/issue_49.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,204 copying build/lib.linux-armv7l-cpython-39/vcf/test/bcftools.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,210 copying build/lib.linux-armv7l-cpython-39/vcf/test/issue-16.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,212 copying build/lib.linux-armv7l-cpython-39/vcf/test/issue-140-file2.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,214 copying build/lib.linux-armv7l-cpython-39/vcf/test/example-4.0.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,215 copying build/lib.linux-armv7l-cpython-39/vcf/test/example-4.1-info-multiple-values.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,217 copying build/lib.linux-armv7l-cpython-39/vcf/test/example-4.1-sv.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,219 copying build/lib.linux-armv7l-cpython-39/vcf/test/mixed-filtering.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,221 copying build/lib.linux-armv7l-cpython-39/vcf/test/strelka.vcf -> build/bdist.linux-armv7l/wheel/./vcf/test 2025-09-19T03:08:43,223 copying build/lib.linux-armv7l-cpython-39/vcf/parser.py -> build/bdist.linux-armv7l/wheel/./vcf 2025-09-19T03:08:43,228 copying build/lib.linux-armv7l-cpython-39/vcf/model.py -> build/bdist.linux-armv7l/wheel/./vcf 2025-09-19T03:08:43,233 running install_egg_info 2025-09-19T03:08:43,268 Copying PyVCF3.egg-info to build/bdist.linux-armv7l/wheel/./PyVCF3-1.0.4-py3.9.egg-info 2025-09-19T03:08:43,284 running install_scripts 2025-09-19T03:08:43,285 creating build/bdist.linux-armv7l/wheel/pyvcf3-1.0.4.data/scripts 2025-09-19T03:08:43,287 copying build/scripts-3.9/vcf_melt -> build/bdist.linux-armv7l/wheel/pyvcf3-1.0.4.data/scripts 2025-09-19T03:08:43,289 copying build/scripts-3.9/vcf_filter.py -> build/bdist.linux-armv7l/wheel/pyvcf3-1.0.4.data/scripts 2025-09-19T03:08:43,291 copying build/scripts-3.9/vcf_sample_filter.py -> build/bdist.linux-armv7l/wheel/pyvcf3-1.0.4.data/scripts 2025-09-19T03:08:43,293 changing mode of build/bdist.linux-armv7l/wheel/pyvcf3-1.0.4.data/scripts/vcf_melt to 755 2025-09-19T03:08:43,294 changing mode of build/bdist.linux-armv7l/wheel/pyvcf3-1.0.4.data/scripts/vcf_filter.py to 755 2025-09-19T03:08:43,294 changing mode of build/bdist.linux-armv7l/wheel/pyvcf3-1.0.4.data/scripts/vcf_sample_filter.py to 755 2025-09-19T03:08:43,356 creating build/bdist.linux-armv7l/wheel/pyvcf3-1.0.4.dist-info/WHEEL 2025-09-19T03:08:43,361 creating '/tmp/pip-wheel-vb79m5aj/pyvcf3-1.0.4-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-09-19T03:08:43,367 adding 'pyvcf3-1.0.4.data/scripts/vcf_filter.py' 2025-09-19T03:08:43,369 adding 'pyvcf3-1.0.4.data/scripts/vcf_melt' 2025-09-19T03:08:43,371 adding 'pyvcf3-1.0.4.data/scripts/vcf_sample_filter.py' 2025-09-19T03:08:43,374 adding 'pyvcf3-1.0.4.dist-info/licenses/LICENSE' 2025-09-19T03:08:43,376 adding 'vcf/__init__.py' 2025-09-19T03:08:43,381 adding 'vcf/bgzf.py' 2025-09-19T03:08:43,561 adding 'vcf/cparse.cpython-39-arm-linux-gnueabihf.so' 2025-09-19T03:08:43,567 adding 'vcf/cparse.pyx' 2025-09-19T03:08:43,568 adding 'vcf/filters.py' 2025-09-19T03:08:43,571 adding 'vcf/model.py' 2025-09-19T03:08:43,575 adding 'vcf/parser.py' 2025-09-19T03:08:43,577 adding 'vcf/sample_filter.py' 2025-09-19T03:08:43,579 adding 'vcf/utils.py' 2025-09-19T03:08:43,584 adding 'vcf/test/1kg.sites.vcf' 2025-09-19T03:08:43,723 adding 'vcf/test/1kg.vcf.gz' 2025-09-19T03:08:43,730 adding 'vcf/test/FT.vcf' 2025-09-19T03:08:43,731 adding 'vcf/test/__init__.py' 2025-09-19T03:08:43,732 adding 'vcf/test/bad-info-character.vcf' 2025-09-19T03:08:43,739 adding 'vcf/test/bcftools.vcf' 2025-09-19T03:08:43,741 adding 'vcf/test/contig_idonly.vcf' 2025-09-19T03:08:43,742 adding 'vcf/test/example-4.0.vcf' 2025-09-19T03:08:43,743 adding 'vcf/test/example-4.1-bnd.vcf' 2025-09-19T03:08:43,744 adding 'vcf/test/example-4.1-info-multiple-values.vcf' 2025-09-19T03:08:43,746 adding 'vcf/test/example-4.1-ploidy.vcf' 2025-09-19T03:08:43,747 adding 'vcf/test/example-4.1-sv.vcf' 2025-09-19T03:08:43,748 adding 'vcf/test/example-4.1.vcf' 2025-09-19T03:08:43,752 adding 'vcf/test/example-4.2.vcf' 2025-09-19T03:08:43,768 adding 'vcf/test/freebayes.vcf' 2025-09-19T03:08:43,772 adding 'vcf/test/gatk.vcf' 2025-09-19T03:08:43,775 adding 'vcf/test/gatk_26_meta.vcf' 2025-09-19T03:08:43,778 adding 'vcf/test/gonl.chr20.release4.gtc.vcf' 2025-09-19T03:08:43,779 adding 'vcf/test/info-type-character.vcf' 2025-09-19T03:08:43,781 adding 'vcf/test/issue-140-file1.vcf' 2025-09-19T03:08:43,782 adding 'vcf/test/issue-140-file2.vcf' 2025-09-19T03:08:43,783 adding 'vcf/test/issue-140-file3.vcf' 2025-09-19T03:08:43,785 adding 'vcf/test/issue-16.vcf' 2025-09-19T03:08:43,786 adding 'vcf/test/issue-201.vcf.gz' 2025-09-19T03:08:43,787 adding 'vcf/test/issue-201.vcf.gz.tbi' 2025-09-19T03:08:43,789 adding 'vcf/test/issue-214.vcf' 2025-09-19T03:08:43,790 adding 'vcf/test/issue-254.vcf' 2025-09-19T03:08:43,792 adding 'vcf/test/issue_49.vcf' 2025-09-19T03:08:43,795 adding 'vcf/test/metadata-whitespace.vcf' 2025-09-19T03:08:43,797 adding 'vcf/test/mixed-filtering.vcf' 2025-09-19T03:08:43,799 adding 'vcf/test/null_genotype_mono.vcf' 2025-09-19T03:08:43,800 adding 'vcf/test/parse-meta-line.vcf' 2025-09-19T03:08:43,801 adding 'vcf/test/prof.py' 2025-09-19T03:08:43,802 adding 'vcf/test/samples-space.vcf' 2025-09-19T03:08:43,804 adding 'vcf/test/samtools.vcf' 2025-09-19T03:08:43,805 adding 'vcf/test/strelka.vcf' 2025-09-19T03:08:43,807 adding 'vcf/test/string_as_flag.vcf' 2025-09-19T03:08:43,808 adding 'vcf/test/tb.vcf.gz' 2025-09-19T03:08:43,809 adding 'vcf/test/tb.vcf.gz.tbi' 2025-09-19T03:08:43,814 adding 'vcf/test/test_vcf.py' 2025-09-19T03:08:43,816 adding 'vcf/test/uncalled_genotypes.vcf' 2025-09-19T03:08:43,817 adding 'vcf/test/walk_left.vcf' 2025-09-19T03:08:43,819 adding 'vcf/test/walk_refcall.vcf' 2025-09-19T03:08:43,820 adding 'pyvcf3-1.0.4.dist-info/METADATA' 2025-09-19T03:08:43,821 adding 'pyvcf3-1.0.4.dist-info/WHEEL' 2025-09-19T03:08:43,823 adding 'pyvcf3-1.0.4.dist-info/entry_points.txt' 2025-09-19T03:08:43,824 adding 'pyvcf3-1.0.4.dist-info/top_level.txt' 2025-09-19T03:08:43,825 adding 'pyvcf3-1.0.4.dist-info/RECORD' 2025-09-19T03:08:43,848 removing build/bdist.linux-armv7l/wheel 2025-09-19T03:08:43,865 error: [Errno 39] Directory not empty: 'test' 2025-09-19T03:08:44,130 Building wheel for pyvcf3 (setup.py): finished with status 'error' 2025-09-19T03:08:44,131 ERROR: Failed building wheel for pyvcf3 2025-09-19T03:08:44,131 Running setup.py clean for pyvcf3 2025-09-19T03:08:44,132 Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-c5xmfb4w/pyvcf3_687d523b07f84929a178c73868a84eb9/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-c5xmfb4w/pyvcf3_687d523b07f84929a178c73868a84eb9/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all 2025-09-19T03:08:44,713 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-19T03:08:44,714 warnings.warn(msg) 2025-09-19T03:08:45,011 /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-19T03:08:45,012 !! 2025-09-19T03:08:45,012 ******************************************************************************** 2025-09-19T03:08:45,013 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-19T03:08:45,013 License :: OSI Approved :: BSD License 2025-09-19T03:08:45,013 License :: OSI Approved :: MIT License 2025-09-19T03:08:45,014 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-19T03:08:45,014 ******************************************************************************** 2025-09-19T03:08:45,014 !! 2025-09-19T03:08:45,014 self._finalize_license_expression() 2025-09-19T03:08:45,042 running clean 2025-09-19T03:08:45,097 removing 'build/temp.linux-armv7l-cpython-39' (and everything under it) 2025-09-19T03:08:45,104 removing 'build/lib.linux-armv7l-cpython-39' (and everything under it) 2025-09-19T03:08:45,116 removing 'build/bdist.linux-armv7l' (and everything under it) 2025-09-19T03:08:45,129 error removing build/bdist.linux-armv7l: [Errno 2] No such file or directory: 'build/bdist.linux-armv7l/wheel/vcf/test/.nfs00000000000e00fc00001e59' 2025-09-19T03:08:45,132 removing 'build/scripts-3.9' (and everything under it) 2025-09-19T03:08:45,134 removing 'build' 2025-09-19T03:08:45,244 Failed to build pyvcf3 2025-09-19T03:08:45,244 ERROR: Failed to build one or more wheels 2025-09-19T03:08:45,245 Exception information: 2025-09-19T03:08:45,245 Traceback (most recent call last): 2025-09-19T03:08:45,245 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 223, in _main 2025-09-19T03:08:45,245 status = self.run(options, args) 2025-09-19T03:08:45,245 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 180, in wrapper 2025-09-19T03:08:45,245 return func(self, options, args) 2025-09-19T03:08:45,245 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 194, in run 2025-09-19T03:08:45,245 raise CommandError( 2025-09-19T03:08:45,245 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-19T03:08:45,248 Removed build tracker: '/tmp/pip-req-tracker-unen9523'