2023-09-16T03:55:46,110 Created temporary directory: /tmp/pip-build-tracker-dhg5fg8w 2023-09-16T03:55:46,111 Initialized build tracking at /tmp/pip-build-tracker-dhg5fg8w 2023-09-16T03:55:46,112 Created build tracker: /tmp/pip-build-tracker-dhg5fg8w 2023-09-16T03:55:46,112 Entered build tracker: /tmp/pip-build-tracker-dhg5fg8w 2023-09-16T03:55:46,113 Created temporary directory: /tmp/pip-wheel-s054bbmi 2023-09-16T03:55:46,116 Created temporary directory: /tmp/pip-ephem-wheel-cache-un242ggq 2023-09-16T03:55:46,139 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-16T03:55:46,143 2 location(s) to search for versions of pyvcf3: 2023-09-16T03:55:46,143 * https://pypi.org/simple/pyvcf3/ 2023-09-16T03:55:46,143 * https://www.piwheels.org/simple/pyvcf3/ 2023-09-16T03:55:46,143 Fetching project page and analyzing links: https://pypi.org/simple/pyvcf3/ 2023-09-16T03:55:46,145 Getting page https://pypi.org/simple/pyvcf3/ 2023-09-16T03:55:46,146 Found index url https://pypi.org/simple/ 2023-09-16T03:55:46,286 Fetched page https://pypi.org/simple/pyvcf3/ as application/vnd.pypi.simple.v1+json 2023-09-16T03:55:46,288 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/) 2023-09-16T03:55:46,288 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 2023-09-16T03:55:46,289 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 2023-09-16T03:55:46,290 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 2023-09-16T03:55:46,290 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 2023-09-16T03:55:46,291 Fetching project page and analyzing links: https://www.piwheels.org/simple/pyvcf3/ 2023-09-16T03:55:46,292 Getting page https://www.piwheels.org/simple/pyvcf3/ 2023-09-16T03:55:46,293 Found index url https://www.piwheels.org/simple/ 2023-09-16T03:55:51,789 Fetched page https://www.piwheels.org/simple/pyvcf3/ as text/html 2023-09-16T03:55:51,807 Skipping link: No binaries permitted for pyvcf3: https://www.piwheels.org/simple/pyvcf3/PyVCF3-1.0.3-cp39-cp39-linux_armv7l.whl#sha256=d18221cbaa400e8c4bf62c3b3d48934d3bee2050b19d99ccc11631c8e83e5fd3 (from https://www.piwheels.org/simple/pyvcf3/) 2023-09-16T03:55:51,808 Skipping link: No binaries permitted for pyvcf3: https://www.piwheels.org/simple/pyvcf3/PyVCF3-1.0.3-cp39-cp39-linux_armv6l.whl#sha256=d18221cbaa400e8c4bf62c3b3d48934d3bee2050b19d99ccc11631c8e83e5fd3 (from https://www.piwheels.org/simple/pyvcf3/) 2023-09-16T03:55:51,809 Skipping link: No binaries permitted for pyvcf3: https://www.piwheels.org/simple/pyvcf3/PyVCF3-1.0.3-cp37-cp37m-linux_armv7l.whl#sha256=2b277f1dd4672377c2f0742abf937ea512150ca34fcd48b232bf12ccbd00351e (from https://www.piwheels.org/simple/pyvcf3/) 2023-09-16T03:55:51,810 Skipping link: No binaries permitted for pyvcf3: https://www.piwheels.org/simple/pyvcf3/PyVCF3-1.0.3-cp37-cp37m-linux_armv6l.whl#sha256=2b277f1dd4672377c2f0742abf937ea512150ca34fcd48b232bf12ccbd00351e (from https://www.piwheels.org/simple/pyvcf3/) 2023-09-16T03:55:51,811 Skipping link: No binaries permitted for pyvcf3: https://www.piwheels.org/simple/pyvcf3/PyVCF3-1.0.3-cp35-cp35m-linux_armv7l.whl#sha256=c2bc58d6ef4d1585e4cf018a09ebb2bbcb970d5e9a7057bd8cf8428f59b7a2a3 (from https://www.piwheels.org/simple/pyvcf3/) 2023-09-16T03:55:51,812 Skipping link: No binaries permitted for pyvcf3: https://www.piwheels.org/simple/pyvcf3/PyVCF3-1.0.3-cp35-cp35m-linux_armv6l.whl#sha256=c2bc58d6ef4d1585e4cf018a09ebb2bbcb970d5e9a7057bd8cf8428f59b7a2a3 (from https://www.piwheels.org/simple/pyvcf3/) 2023-09-16T03:55:51,813 Skipping link: No binaries permitted for pyvcf3: https://www.piwheels.org/simple/pyvcf3/PyVCF3-1.0.2-cp39-cp39-linux_armv7l.whl#sha256=14b855223b3226e36ef32d87963a489a07254e6d22b74024ba612b703f671b7e (from https://www.piwheels.org/simple/pyvcf3/) 2023-09-16T03:55:51,814 Skipping link: No binaries permitted for pyvcf3: https://www.piwheels.org/simple/pyvcf3/PyVCF3-1.0.2-cp39-cp39-linux_armv6l.whl#sha256=14b855223b3226e36ef32d87963a489a07254e6d22b74024ba612b703f671b7e (from https://www.piwheels.org/simple/pyvcf3/) 2023-09-16T03:55:51,815 Skipping link: No binaries permitted for pyvcf3: https://www.piwheels.org/simple/pyvcf3/PyVCF3-1.0.2-cp37-cp37m-linux_armv7l.whl#sha256=3a4fb334c31a538e67ad8c658cfab21b34169a5456600073530e5e7302fe6337 (from https://www.piwheels.org/simple/pyvcf3/) 2023-09-16T03:55:51,816 Skipping link: No binaries permitted for pyvcf3: https://www.piwheels.org/simple/pyvcf3/PyVCF3-1.0.2-cp37-cp37m-linux_armv6l.whl#sha256=3a4fb334c31a538e67ad8c658cfab21b34169a5456600073530e5e7302fe6337 (from https://www.piwheels.org/simple/pyvcf3/) 2023-09-16T03:55:51,816 Skipping link: No binaries permitted for pyvcf3: https://www.piwheels.org/simple/pyvcf3/PyVCF3-1.0.2-cp35-cp35m-linux_armv7l.whl#sha256=da4f2b44f5cfe68ddb4d162669bb5364e47cc53c2ced18ebf73636987add62f3 (from https://www.piwheels.org/simple/pyvcf3/) 2023-09-16T03:55:51,817 Skipping link: No binaries permitted for pyvcf3: https://www.piwheels.org/simple/pyvcf3/PyVCF3-1.0.2-cp35-cp35m-linux_armv6l.whl#sha256=da4f2b44f5cfe68ddb4d162669bb5364e47cc53c2ced18ebf73636987add62f3 (from https://www.piwheels.org/simple/pyvcf3/) 2023-09-16T03:55:51,818 Skipping link: No binaries permitted for pyvcf3: https://www.piwheels.org/simple/pyvcf3/PyVCF3-1.0.1-cp39-cp39-linux_armv7l.whl#sha256=b5c8fed57dd1f35872b4b6dbf824f7c9795cf7e0345ed0c7fa9014e6fb9b9b9e (from https://www.piwheels.org/simple/pyvcf3/) 2023-09-16T03:55:51,819 Skipping link: No binaries permitted for pyvcf3: https://www.piwheels.org/simple/pyvcf3/PyVCF3-1.0.1-cp39-cp39-linux_armv6l.whl#sha256=b5c8fed57dd1f35872b4b6dbf824f7c9795cf7e0345ed0c7fa9014e6fb9b9b9e (from https://www.piwheels.org/simple/pyvcf3/) 2023-09-16T03:55:51,820 Skipping link: No binaries permitted for pyvcf3: https://www.piwheels.org/simple/pyvcf3/PyVCF3-1.0.1-cp37-cp37m-linux_armv7l.whl#sha256=3308b8a1fa5bd25c337d9f6234df79b445c27005a610251d0d43ee16c417e00e (from https://www.piwheels.org/simple/pyvcf3/) 2023-09-16T03:55:51,820 Skipping link: No binaries permitted for pyvcf3: https://www.piwheels.org/simple/pyvcf3/PyVCF3-1.0.1-cp37-cp37m-linux_armv6l.whl#sha256=3308b8a1fa5bd25c337d9f6234df79b445c27005a610251d0d43ee16c417e00e (from https://www.piwheels.org/simple/pyvcf3/) 2023-09-16T03:55:51,821 Skipping link: No binaries permitted for pyvcf3: https://www.piwheels.org/simple/pyvcf3/PyVCF3-1.0.1-cp35-cp35m-linux_armv7l.whl#sha256=0883d937a95f4c19a9ada081207e8b991e1234ed0d3fd8f5f0b274ad91020033 (from https://www.piwheels.org/simple/pyvcf3/) 2023-09-16T03:55:51,822 Skipping link: No binaries permitted for pyvcf3: https://www.piwheels.org/simple/pyvcf3/PyVCF3-1.0.1-cp35-cp35m-linux_armv6l.whl#sha256=0883d937a95f4c19a9ada081207e8b991e1234ed0d3fd8f5f0b274ad91020033 (from https://www.piwheels.org/simple/pyvcf3/) 2023-09-16T03:55:51,823 Skipping link: No binaries permitted for pyvcf3: https://www.piwheels.org/simple/pyvcf3/PyVCF3-1.0.0-cp311-cp311-linux_armv7l.whl#sha256=834bc9b76b225a2870d3d35222774265acd67d1ce3822617fc45e84eb8509631 (from https://www.piwheels.org/simple/pyvcf3/) 2023-09-16T03:55:51,824 Skipping link: No binaries permitted for pyvcf3: https://www.piwheels.org/simple/pyvcf3/PyVCF3-1.0.0-cp311-cp311-linux_armv6l.whl#sha256=834bc9b76b225a2870d3d35222774265acd67d1ce3822617fc45e84eb8509631 (from https://www.piwheels.org/simple/pyvcf3/) 2023-09-16T03:55:51,825 Skipping link: No binaries permitted for pyvcf3: https://www.piwheels.org/simple/pyvcf3/PyVCF3-1.0.0-cp39-cp39-linux_armv7l.whl#sha256=c288b5b3f724d0924a6d4977216943aee43c7bf5c08cbf71303013c1b55b1cb0 (from https://www.piwheels.org/simple/pyvcf3/) 2023-09-16T03:55:51,826 Skipping link: No binaries permitted for pyvcf3: https://www.piwheels.org/simple/pyvcf3/PyVCF3-1.0.0-cp39-cp39-linux_armv6l.whl#sha256=c288b5b3f724d0924a6d4977216943aee43c7bf5c08cbf71303013c1b55b1cb0 (from https://www.piwheels.org/simple/pyvcf3/) 2023-09-16T03:55:51,827 Skipping link: No binaries permitted for pyvcf3: https://www.piwheels.org/simple/pyvcf3/PyVCF3-1.0.0-cp37-cp37m-linux_armv7l.whl#sha256=197b00635133c0013e911b217a7bb40ea409deab499ca14890971576de63ecfe (from https://www.piwheels.org/simple/pyvcf3/) 2023-09-16T03:55:51,828 Skipping link: No binaries permitted for pyvcf3: https://www.piwheels.org/simple/pyvcf3/PyVCF3-1.0.0-cp37-cp37m-linux_armv6l.whl#sha256=197b00635133c0013e911b217a7bb40ea409deab499ca14890971576de63ecfe (from https://www.piwheels.org/simple/pyvcf3/) 2023-09-16T03:55:51,829 Skipping link: No binaries permitted for pyvcf3: https://www.piwheels.org/simple/pyvcf3/PyVCF3-1.0.0-cp35-cp35m-linux_armv7l.whl#sha256=804e89f835d7937364092d5d747f44095a51364a56661627f699c8a406722cfb (from https://www.piwheels.org/simple/pyvcf3/) 2023-09-16T03:55:51,829 Skipping link: No binaries permitted for pyvcf3: https://www.piwheels.org/simple/pyvcf3/PyVCF3-1.0.0-cp35-cp35m-linux_armv6l.whl#sha256=804e89f835d7937364092d5d747f44095a51364a56661627f699c8a406722cfb (from https://www.piwheels.org/simple/pyvcf3/) 2023-09-16T03:55:51,830 Skipping link: not a file: https://www.piwheels.org/simple/pyvcf3/ 2023-09-16T03:55:51,831 Skipping link: not a file: https://pypi.org/simple/pyvcf3/ 2023-09-16T03:55:51,870 Given no hashes to check 1 links for project 'pyvcf3': discarding no candidates 2023-09-16T03:55:51,906 Collecting pyvcf3==1.0.1 2023-09-16T03:55:51,908 Created temporary directory: /tmp/pip-unpack-u8ravwta 2023-09-16T03:55:52,134 Downloading PyVCF3-1.0.1.tar.gz (965 kB) 2023-09-16T03:55:52,428 Added pyvcf3==1.0.1 from https://files.pythonhosted.org/packages/9b/f3/79dd49b0c14edb1e6845fcfcbaebc059970466deadfced075037d1862147/PyVCF3-1.0.1.tar.gz to build tracker '/tmp/pip-build-tracker-dhg5fg8w' 2023-09-16T03:55:52,430 Running setup.py (path:/tmp/pip-wheel-s054bbmi/pyvcf3_2fd603e053e64c4aafcc4037962b4813/setup.py) egg_info for package pyvcf3 2023-09-16T03:55:52,431 Created temporary directory: /tmp/pip-pip-egg-info-ysj87myf 2023-09-16T03:55:52,432 Preparing metadata (setup.py): started 2023-09-16T03:55:52,433 Running command python setup.py egg_info 2023-09-16T03:55:52,994 running egg_info 2023-09-16T03:55:52,995 creating /tmp/pip-pip-egg-info-ysj87myf/PyVCF3.egg-info 2023-09-16T03:55:53,013 writing /tmp/pip-pip-egg-info-ysj87myf/PyVCF3.egg-info/PKG-INFO 2023-09-16T03:55:53,015 writing dependency_links to /tmp/pip-pip-egg-info-ysj87myf/PyVCF3.egg-info/dependency_links.txt 2023-09-16T03:55:53,017 writing entry points to /tmp/pip-pip-egg-info-ysj87myf/PyVCF3.egg-info/entry_points.txt 2023-09-16T03:55:53,018 writing requirements to /tmp/pip-pip-egg-info-ysj87myf/PyVCF3.egg-info/requires.txt 2023-09-16T03:55:53,019 writing top-level names to /tmp/pip-pip-egg-info-ysj87myf/PyVCF3.egg-info/top_level.txt 2023-09-16T03:55:53,020 writing manifest file '/tmp/pip-pip-egg-info-ysj87myf/PyVCF3.egg-info/SOURCES.txt' 2023-09-16T03:55:53,103 reading manifest file '/tmp/pip-pip-egg-info-ysj87myf/PyVCF3.egg-info/SOURCES.txt' 2023-09-16T03:55:53,104 reading manifest template 'MANIFEST.in' 2023-09-16T03:55:53,120 adding license file 'LICENSE' 2023-09-16T03:55:53,123 writing manifest file '/tmp/pip-pip-egg-info-ysj87myf/PyVCF3.egg-info/SOURCES.txt' 2023-09-16T03:55:53,197 Preparing metadata (setup.py): finished with status 'done' 2023-09-16T03:55:53,201 Source in /tmp/pip-wheel-s054bbmi/pyvcf3_2fd603e053e64c4aafcc4037962b4813 has version 1.0.1, which satisfies requirement pyvcf3==1.0.1 from https://files.pythonhosted.org/packages/9b/f3/79dd49b0c14edb1e6845fcfcbaebc059970466deadfced075037d1862147/PyVCF3-1.0.1.tar.gz 2023-09-16T03:55:53,202 Removed pyvcf3==1.0.1 from https://files.pythonhosted.org/packages/9b/f3/79dd49b0c14edb1e6845fcfcbaebc059970466deadfced075037d1862147/PyVCF3-1.0.1.tar.gz from build tracker '/tmp/pip-build-tracker-dhg5fg8w' 2023-09-16T03:55:53,207 Created temporary directory: /tmp/pip-unpack-d6qiap69 2023-09-16T03:55:53,208 Created temporary directory: /tmp/pip-unpack-4bkd4xpb 2023-09-16T03:55:53,212 Building wheels for collected packages: pyvcf3 2023-09-16T03:55:53,216 Created temporary directory: /tmp/pip-wheel-5hosa94s 2023-09-16T03:55:53,216 Building wheel for pyvcf3 (setup.py): started 2023-09-16T03:55:53,217 Destination directory: /tmp/pip-wheel-5hosa94s 2023-09-16T03:55:53,218 Running command python setup.py bdist_wheel 2023-09-16T03:55:53,969 running bdist_wheel 2023-09-16T03:55:54,054 running build 2023-09-16T03:55:54,054 running build_py 2023-09-16T03:55:54,076 creating build 2023-09-16T03:55:54,076 creating build/lib 2023-09-16T03:55:54,077 creating build/lib/vcf 2023-09-16T03:55:54,078 copying vcf/__init__.py -> build/lib/vcf 2023-09-16T03:55:54,080 copying vcf/sample_filter.py -> build/lib/vcf 2023-09-16T03:55:54,082 copying vcf/filters.py -> build/lib/vcf 2023-09-16T03:55:54,084 copying vcf/utils.py -> build/lib/vcf 2023-09-16T03:55:54,086 copying vcf/model.py -> build/lib/vcf 2023-09-16T03:55:54,088 copying vcf/parser.py -> build/lib/vcf 2023-09-16T03:55:54,091 creating build/lib/vcf/test 2023-09-16T03:55:54,092 copying vcf/test/test_vcf.py -> build/lib/vcf/test 2023-09-16T03:55:54,096 copying vcf/test/__init__.py -> build/lib/vcf/test 2023-09-16T03:55:54,097 copying vcf/test/prof.py -> build/lib/vcf/test 2023-09-16T03:55:54,098 running egg_info 2023-09-16T03:55:54,144 writing PyVCF3.egg-info/PKG-INFO 2023-09-16T03:55:54,146 writing dependency_links to PyVCF3.egg-info/dependency_links.txt 2023-09-16T03:55:54,147 writing entry points to PyVCF3.egg-info/entry_points.txt 2023-09-16T03:55:54,148 writing requirements to PyVCF3.egg-info/requires.txt 2023-09-16T03:55:54,150 writing top-level names to PyVCF3.egg-info/top_level.txt 2023-09-16T03:55:54,179 reading manifest file 'PyVCF3.egg-info/SOURCES.txt' 2023-09-16T03:55:54,182 reading manifest template 'MANIFEST.in' 2023-09-16T03:55:54,198 adding license file 'LICENSE' 2023-09-16T03:55:54,202 writing manifest file 'PyVCF3.egg-info/SOURCES.txt' 2023-09-16T03:55:54,208 copying vcf/cparse.pyx -> build/lib/vcf 2023-09-16T03:55:54,211 copying vcf/test/1kg.sites.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,214 copying vcf/test/1kg.vcf.gz -> build/lib/vcf/test 2023-09-16T03:55:54,229 copying vcf/test/FT.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,231 copying vcf/test/bad-info-character.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,233 copying vcf/test/bcftools.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,237 copying vcf/test/contig_idonly.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,239 copying vcf/test/example-4.0.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,241 copying vcf/test/example-4.1-bnd.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,243 copying vcf/test/example-4.1-info-multiple-values.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,245 copying vcf/test/example-4.1-ploidy.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,247 copying vcf/test/example-4.1-sv.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,249 copying vcf/test/example-4.1.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,251 copying vcf/test/example-4.2.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,254 copying vcf/test/freebayes.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,258 copying vcf/test/gatk.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,261 copying vcf/test/gatk_26_meta.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,263 copying vcf/test/gonl.chr20.release4.gtc.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,266 copying vcf/test/info-type-character.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,268 copying vcf/test/issue-140-file1.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,270 copying vcf/test/issue-140-file2.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,272 copying vcf/test/issue-140-file3.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,274 copying vcf/test/issue-16.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,276 copying vcf/test/issue-201.vcf.gz -> build/lib/vcf/test 2023-09-16T03:55:54,278 copying vcf/test/issue-201.vcf.gz.tbi -> build/lib/vcf/test 2023-09-16T03:55:54,280 copying vcf/test/issue-214.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,282 copying vcf/test/issue-254.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,284 copying vcf/test/issue_49.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,286 copying vcf/test/metadata-whitespace.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,289 copying vcf/test/mixed-filtering.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,291 copying vcf/test/null_genotype_mono.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,293 copying vcf/test/parse-meta-line.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,295 copying vcf/test/samples-space.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,297 copying vcf/test/samtools.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,299 copying vcf/test/strelka.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,301 copying vcf/test/string_as_flag.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,303 copying vcf/test/tb.vcf.gz -> build/lib/vcf/test 2023-09-16T03:55:54,305 copying vcf/test/tb.vcf.gz.tbi -> build/lib/vcf/test 2023-09-16T03:55:54,307 copying vcf/test/uncalled_genotypes.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,309 copying vcf/test/walk_left.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,311 copying vcf/test/walk_refcall.vcf -> build/lib/vcf/test 2023-09-16T03:55:54,314 running build_scripts 2023-09-16T03:55:54,314 creating build/scripts-3.11 2023-09-16T03:55:54,315 copying and adjusting scripts/vcf_melt -> build/scripts-3.11 2023-09-16T03:55:54,317 copying and adjusting scripts/vcf_filter.py -> build/scripts-3.11 2023-09-16T03:55:54,319 copying and adjusting scripts/vcf_sample_filter.py -> build/scripts-3.11 2023-09-16T03:55:54,320 changing mode of build/scripts-3.11/vcf_melt from 644 to 755 2023-09-16T03:55:54,320 changing mode of build/scripts-3.11/vcf_filter.py from 644 to 755 2023-09-16T03:55:54,321 changing mode of build/scripts-3.11/vcf_sample_filter.py from 644 to 755 2023-09-16T03:55:54,340 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-09-16T03:55:54,340 !! 2023-09-16T03:55:54,341 ******************************************************************************** 2023-09-16T03:55:54,342 Please avoid running ``setup.py`` directly. 2023-09-16T03:55:54,342 Instead, use pypa/build, pypa/installer or other 2023-09-16T03:55:54,343 standards-based tools. 2023-09-16T03:55:54,344 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-09-16T03:55:54,345 ******************************************************************************** 2023-09-16T03:55:54,346 !! 2023-09-16T03:55:54,346 self.initialize_options() 2023-09-16T03:55:54,360 installing to build/bdist.linux-armv7l/wheel 2023-09-16T03:55:54,361 running install 2023-09-16T03:55:54,385 running install_lib 2023-09-16T03:55:54,405 creating build/bdist.linux-armv7l 2023-09-16T03:55:54,406 creating build/bdist.linux-armv7l/wheel 2023-09-16T03:55:54,407 creating build/bdist.linux-armv7l/wheel/vcf 2023-09-16T03:55:54,408 copying build/lib/vcf/__init__.py -> build/bdist.linux-armv7l/wheel/vcf 2023-09-16T03:55:54,411 creating build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,412 copying build/lib/vcf/test/mixed-filtering.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,414 copying build/lib/vcf/test/walk_left.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,416 copying build/lib/vcf/test/issue-16.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,418 copying build/lib/vcf/test/walk_refcall.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,419 copying build/lib/vcf/test/gatk_26_meta.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,421 copying build/lib/vcf/test/metadata-whitespace.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,424 copying build/lib/vcf/test/issue-201.vcf.gz -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,426 copying build/lib/vcf/test/test_vcf.py -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,429 copying build/lib/vcf/test/example-4.0.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,430 copying build/lib/vcf/test/__init__.py -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,432 copying build/lib/vcf/test/null_genotype_mono.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,434 copying build/lib/vcf/test/gatk.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,436 copying build/lib/vcf/test/1kg.sites.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,439 copying build/lib/vcf/test/issue-140-file2.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,440 copying build/lib/vcf/test/bcftools.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,444 copying build/lib/vcf/test/issue-254.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,445 copying build/lib/vcf/test/tb.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,447 copying build/lib/vcf/test/example-4.1-ploidy.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,448 copying build/lib/vcf/test/issue-201.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,450 copying build/lib/vcf/test/string_as_flag.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,452 copying build/lib/vcf/test/1kg.vcf.gz -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,465 copying build/lib/vcf/test/bad-info-character.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,467 copying build/lib/vcf/test/FT.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,469 copying build/lib/vcf/test/prof.py -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,471 copying build/lib/vcf/test/strelka.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,473 copying build/lib/vcf/test/samples-space.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,475 copying build/lib/vcf/test/contig_idonly.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,477 copying build/lib/vcf/test/example-4.1-bnd.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,478 copying build/lib/vcf/test/samtools.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,480 copying build/lib/vcf/test/example-4.1-sv.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,482 copying build/lib/vcf/test/example-4.1-info-multiple-values.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,484 copying build/lib/vcf/test/example-4.1.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,486 copying build/lib/vcf/test/issue_49.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,488 copying build/lib/vcf/test/parse-meta-line.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,489 copying build/lib/vcf/test/uncalled_genotypes.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,491 copying build/lib/vcf/test/issue-214.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,493 copying build/lib/vcf/test/freebayes.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,497 copying build/lib/vcf/test/tb.vcf.gz -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,499 copying build/lib/vcf/test/info-type-character.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,501 copying build/lib/vcf/test/issue-140-file3.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,503 copying build/lib/vcf/test/gonl.chr20.release4.gtc.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,505 copying build/lib/vcf/test/issue-140-file1.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,507 copying build/lib/vcf/test/example-4.2.vcf -> build/bdist.linux-armv7l/wheel/vcf/test 2023-09-16T03:55:54,510 copying build/lib/vcf/sample_filter.py -> build/bdist.linux-armv7l/wheel/vcf 2023-09-16T03:55:54,511 copying build/lib/vcf/filters.py -> build/bdist.linux-armv7l/wheel/vcf 2023-09-16T03:55:54,513 copying build/lib/vcf/cparse.pyx -> build/bdist.linux-armv7l/wheel/vcf 2023-09-16T03:55:54,515 copying build/lib/vcf/utils.py -> build/bdist.linux-armv7l/wheel/vcf 2023-09-16T03:55:54,517 copying build/lib/vcf/model.py -> build/bdist.linux-armv7l/wheel/vcf 2023-09-16T03:55:54,520 copying build/lib/vcf/parser.py -> build/bdist.linux-armv7l/wheel/vcf 2023-09-16T03:55:54,522 running install_egg_info 2023-09-16T03:55:54,546 Copying PyVCF3.egg-info to build/bdist.linux-armv7l/wheel/PyVCF3-1.0.1-py3.11.egg-info 2023-09-16T03:55:54,557 running install_scripts 2023-09-16T03:55:54,558 creating build/bdist.linux-armv7l/wheel/PyVCF3-1.0.1.data 2023-09-16T03:55:54,559 creating build/bdist.linux-armv7l/wheel/PyVCF3-1.0.1.data/scripts 2023-09-16T03:55:54,560 copying build/scripts-3.11/vcf_melt -> build/bdist.linux-armv7l/wheel/PyVCF3-1.0.1.data/scripts 2023-09-16T03:55:54,562 copying build/scripts-3.11/vcf_sample_filter.py -> build/bdist.linux-armv7l/wheel/PyVCF3-1.0.1.data/scripts 2023-09-16T03:55:54,564 copying build/scripts-3.11/vcf_filter.py -> build/bdist.linux-armv7l/wheel/PyVCF3-1.0.1.data/scripts 2023-09-16T03:55:54,566 changing mode of build/bdist.linux-armv7l/wheel/PyVCF3-1.0.1.data/scripts/vcf_melt to 755 2023-09-16T03:55:54,566 changing mode of build/bdist.linux-armv7l/wheel/PyVCF3-1.0.1.data/scripts/vcf_sample_filter.py to 755 2023-09-16T03:55:54,567 changing mode of build/bdist.linux-armv7l/wheel/PyVCF3-1.0.1.data/scripts/vcf_filter.py to 755 2023-09-16T03:55:54,580 creating build/bdist.linux-armv7l/wheel/PyVCF3-1.0.1.dist-info/WHEEL 2023-09-16T03:55:54,582 creating '/tmp/pip-wheel-5hosa94s/PyVCF3-1.0.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-09-16T03:55:54,586 adding 'PyVCF3-1.0.1.data/scripts/vcf_filter.py' 2023-09-16T03:55:54,587 adding 'PyVCF3-1.0.1.data/scripts/vcf_melt' 2023-09-16T03:55:54,588 adding 'PyVCF3-1.0.1.data/scripts/vcf_sample_filter.py' 2023-09-16T03:55:54,591 adding 'vcf/__init__.py' 2023-09-16T03:55:54,593 adding 'vcf/cparse.pyx' 2023-09-16T03:55:54,594 adding 'vcf/filters.py' 2023-09-16T03:55:54,597 adding 'vcf/model.py' 2023-09-16T03:55:54,602 adding 'vcf/parser.py' 2023-09-16T03:55:54,603 adding 'vcf/sample_filter.py' 2023-09-16T03:55:54,605 adding 'vcf/utils.py' 2023-09-16T03:55:54,611 adding 'vcf/test/1kg.sites.vcf' 2023-09-16T03:55:54,709 adding 'vcf/test/1kg.vcf.gz' 2023-09-16T03:55:54,717 adding 'vcf/test/FT.vcf' 2023-09-16T03:55:54,719 adding 'vcf/test/__init__.py' 2023-09-16T03:55:54,720 adding 'vcf/test/bad-info-character.vcf' 2023-09-16T03:55:54,727 adding 'vcf/test/bcftools.vcf' 2023-09-16T03:55:54,728 adding 'vcf/test/contig_idonly.vcf' 2023-09-16T03:55:54,730 adding 'vcf/test/example-4.0.vcf' 2023-09-16T03:55:54,731 adding 'vcf/test/example-4.1-bnd.vcf' 2023-09-16T03:55:54,732 adding 'vcf/test/example-4.1-info-multiple-values.vcf' 2023-09-16T03:55:54,733 adding 'vcf/test/example-4.1-ploidy.vcf' 2023-09-16T03:55:54,735 adding 'vcf/test/example-4.1-sv.vcf' 2023-09-16T03:55:54,736 adding 'vcf/test/example-4.1.vcf' 2023-09-16T03:55:54,740 adding 'vcf/test/example-4.2.vcf' 2023-09-16T03:55:54,755 adding 'vcf/test/freebayes.vcf' 2023-09-16T03:55:54,759 adding 'vcf/test/gatk.vcf' 2023-09-16T03:55:54,760 adding 'vcf/test/gatk_26_meta.vcf' 2023-09-16T03:55:54,762 adding 'vcf/test/gonl.chr20.release4.gtc.vcf' 2023-09-16T03:55:54,763 adding 'vcf/test/info-type-character.vcf' 2023-09-16T03:55:54,765 adding 'vcf/test/issue-140-file1.vcf' 2023-09-16T03:55:54,766 adding 'vcf/test/issue-140-file2.vcf' 2023-09-16T03:55:54,768 adding 'vcf/test/issue-140-file3.vcf' 2023-09-16T03:55:54,769 adding 'vcf/test/issue-16.vcf' 2023-09-16T03:55:54,770 adding 'vcf/test/issue-201.vcf.gz' 2023-09-16T03:55:54,771 adding 'vcf/test/issue-201.vcf.gz.tbi' 2023-09-16T03:55:54,773 adding 'vcf/test/issue-214.vcf' 2023-09-16T03:55:54,774 adding 'vcf/test/issue-254.vcf' 2023-09-16T03:55:54,775 adding 'vcf/test/issue_49.vcf' 2023-09-16T03:55:54,779 adding 'vcf/test/metadata-whitespace.vcf' 2023-09-16T03:55:54,780 adding 'vcf/test/mixed-filtering.vcf' 2023-09-16T03:55:54,782 adding 'vcf/test/null_genotype_mono.vcf' 2023-09-16T03:55:54,783 adding 'vcf/test/parse-meta-line.vcf' 2023-09-16T03:55:54,784 adding 'vcf/test/prof.py' 2023-09-16T03:55:54,785 adding 'vcf/test/samples-space.vcf' 2023-09-16T03:55:54,787 adding 'vcf/test/samtools.vcf' 2023-09-16T03:55:54,788 adding 'vcf/test/strelka.vcf' 2023-09-16T03:55:54,789 adding 'vcf/test/string_as_flag.vcf' 2023-09-16T03:55:54,791 adding 'vcf/test/tb.vcf.gz' 2023-09-16T03:55:54,792 adding 'vcf/test/tb.vcf.gz.tbi' 2023-09-16T03:55:54,797 adding 'vcf/test/test_vcf.py' 2023-09-16T03:55:54,798 adding 'vcf/test/uncalled_genotypes.vcf' 2023-09-16T03:55:54,800 adding 'vcf/test/walk_left.vcf' 2023-09-16T03:55:54,801 adding 'vcf/test/walk_refcall.vcf' 2023-09-16T03:55:54,802 adding 'PyVCF3-1.0.1.dist-info/LICENSE' 2023-09-16T03:55:54,803 adding 'PyVCF3-1.0.1.dist-info/METADATA' 2023-09-16T03:55:54,804 adding 'PyVCF3-1.0.1.dist-info/WHEEL' 2023-09-16T03:55:54,805 adding 'PyVCF3-1.0.1.dist-info/entry_points.txt' 2023-09-16T03:55:54,806 adding 'PyVCF3-1.0.1.dist-info/top_level.txt' 2023-09-16T03:55:54,807 adding 'PyVCF3-1.0.1.dist-info/RECORD' 2023-09-16T03:55:54,819 removing build/bdist.linux-armv7l/wheel 2023-09-16T03:55:54,927 Building wheel for pyvcf3 (setup.py): finished with status 'done' 2023-09-16T03:55:54,941 Created wheel for pyvcf3: filename=PyVCF3-1.0.1-py3-none-any.whl size=977471 sha256=e8bf3e88ac7b88b6eccd3c91b52606b3c182cdaa49ac4d683f5c60817a46cd96 2023-09-16T03:55:54,943 Stored in directory: /tmp/pip-ephem-wheel-cache-un242ggq/wheels/7b/26/2d/bc6ee41b7698627007c8e32521a2c0719c9c69a9a1cabcf271 2023-09-16T03:55:54,954 Successfully built pyvcf3 2023-09-16T03:55:54,985 Removed build tracker: '/tmp/pip-build-tracker-dhg5fg8w'