2022-01-28T23:00:43,105 Created temporary directory: /tmp/pip-ephem-wheel-cache-yzf5kcxk
2022-01-28T23:00:43,110 Created temporary directory: /tmp/pip-req-tracker-clbjibk3
2022-01-28T23:00:43,111 Initialized build tracking at /tmp/pip-req-tracker-clbjibk3
2022-01-28T23:00:43,111 Created build tracker: /tmp/pip-req-tracker-clbjibk3
2022-01-28T23:00:43,112 Entered build tracker: /tmp/pip-req-tracker-clbjibk3
2022-01-28T23:00:43,113 Created temporary directory: /tmp/pip-wheel-u4176wk1
2022-01-28T23:00:43,178 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2022-01-28T23:00:43,184 2 location(s) to search for versions of pyvcf3:
2022-01-28T23:00:43,184 * https://pypi.org/simple/pyvcf3/
2022-01-28T23:00:43,184 * https://www.piwheels.org/simple/pyvcf3/
2022-01-28T23:00:43,185 Fetching project page and analyzing links: https://pypi.org/simple/pyvcf3/
2022-01-28T23:00:43,186 Getting page https://pypi.org/simple/pyvcf3/
2022-01-28T23:00:43,189 Found index url https://pypi.org/simple
2022-01-28T23:00:43,390   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/)
2022-01-28T23:00:43,391   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
2022-01-28T23:00:43,391   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
2022-01-28T23:00:43,392 Fetching project page and analyzing links: https://www.piwheels.org/simple/pyvcf3/
2022-01-28T23:00:43,393 Getting page https://www.piwheels.org/simple/pyvcf3/
2022-01-28T23:00:43,395 Found index url https://www.piwheels.org/simple
2022-01-28T23:00:43,619   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/)
2022-01-28T23:00:43,620   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/)
2022-01-28T23:00:43,620   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/)
2022-01-28T23:00:43,621   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/)
2022-01-28T23:00:43,621   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/)
2022-01-28T23:00:43,622   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/)
2022-01-28T23:00:43,622   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/)
2022-01-28T23:00:43,623   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/)
2022-01-28T23:00:43,623   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/)
2022-01-28T23:00:43,624   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/)
2022-01-28T23:00:43,624 Skipping link: not a file: https://www.piwheels.org/simple/pyvcf3/
2022-01-28T23:00:43,625 Skipping link: not a file: https://pypi.org/simple/pyvcf3/
2022-01-28T23:00:43,669 Given no hashes to check 1 links for project 'pyvcf3': discarding no candidates
2022-01-28T23:00:43,712 Collecting pyvcf3==1.0.1
2022-01-28T23:00:43,715   Created temporary directory: /tmp/pip-unpack-c0j4njmk
2022-01-28T23:00:43,809   Downloading PyVCF3-1.0.1.tar.gz (965 kB)
2022-01-28T23:00:44,418   Added pyvcf3==1.0.1 from https://files.pythonhosted.org/packages/9b/f3/79dd49b0c14edb1e6845fcfcbaebc059970466deadfced075037d1862147/PyVCF3-1.0.1.tar.gz#sha256=6c5da84692a61fa8ef7dcc66c4c702df489e17e0cb18773e4b1934cdc8d222b6 to build tracker '/tmp/pip-req-tracker-clbjibk3'
2022-01-28T23:00:44,420   Running setup.py (path:/tmp/pip-wheel-u4176wk1/pyvcf3_9eb12e7cd0af42d3b3faa58ef78f8e1a/setup.py) egg_info for package pyvcf3
2022-01-28T23:00:44,421   Created temporary directory: /tmp/pip-pip-egg-info-4_0jzp3e
2022-01-28T23:00:44,422   Preparing metadata (setup.py): started
2022-01-28T23:00:44,422   Running command python setup.py egg_info
2022-01-28T23:00:46,498   running egg_info
2022-01-28T23:00:46,502   creating /tmp/pip-pip-egg-info-4_0jzp3e/PyVCF3.egg-info
2022-01-28T23:00:46,516   writing manifest file '/tmp/pip-pip-egg-info-4_0jzp3e/PyVCF3.egg-info/SOURCES.txt'
2022-01-28T23:00:46,609   writing manifest file '/tmp/pip-pip-egg-info-4_0jzp3e/PyVCF3.egg-info/SOURCES.txt'
2022-01-28T23:00:46,732   Preparing metadata (setup.py): finished with status 'done'
2022-01-28T23:00:46,745   Source in /tmp/pip-wheel-u4176wk1/pyvcf3_9eb12e7cd0af42d3b3faa58ef78f8e1a 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#sha256=6c5da84692a61fa8ef7dcc66c4c702df489e17e0cb18773e4b1934cdc8d222b6
2022-01-28T23:00:46,748   Removed pyvcf3==1.0.1 from https://files.pythonhosted.org/packages/9b/f3/79dd49b0c14edb1e6845fcfcbaebc059970466deadfced075037d1862147/PyVCF3-1.0.1.tar.gz#sha256=6c5da84692a61fa8ef7dcc66c4c702df489e17e0cb18773e4b1934cdc8d222b6 from build tracker '/tmp/pip-req-tracker-clbjibk3'
2022-01-28T23:00:46,759 Created temporary directory: /tmp/pip-unpack-90yglsro
2022-01-28T23:00:46,760 Building wheels for collected packages: pyvcf3
2022-01-28T23:00:46,776   Created temporary directory: /tmp/pip-wheel-5eoz2e4w
2022-01-28T23:00:46,777   Building wheel for pyvcf3 (setup.py): started
2022-01-28T23:00:46,778   Destination directory: /tmp/pip-wheel-5eoz2e4w
2022-01-28T23:00:46,778   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-u4176wk1/pyvcf3_9eb12e7cd0af42d3b3faa58ef78f8e1a/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-u4176wk1/pyvcf3_9eb12e7cd0af42d3b3faa58ef78f8e1a/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-5eoz2e4w
2022-01-28T23:00:48,879   running bdist_wheel
2022-01-28T23:00:48,889   running build
2022-01-28T23:00:48,890   running build_py
2022-01-28T23:00:48,899   creating build
2022-01-28T23:00:48,900   creating build/lib.linux-armv7l-3.9
2022-01-28T23:00:48,902   creating build/lib.linux-armv7l-3.9/vcf
2022-01-28T23:00:48,905   copying vcf/model.py -> build/lib.linux-armv7l-3.9/vcf
2022-01-28T23:00:48,911   copying vcf/sample_filter.py -> build/lib.linux-armv7l-3.9/vcf
2022-01-28T23:00:48,915   copying vcf/utils.py -> build/lib.linux-armv7l-3.9/vcf
2022-01-28T23:00:48,918   copying vcf/filters.py -> build/lib.linux-armv7l-3.9/vcf
2022-01-28T23:00:48,923   copying vcf/__init__.py -> build/lib.linux-armv7l-3.9/vcf
2022-01-28T23:00:48,927   copying vcf/parser.py -> build/lib.linux-armv7l-3.9/vcf
2022-01-28T23:00:48,934   creating build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:48,935   copying vcf/test/test_vcf.py -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:48,942   copying vcf/test/__init__.py -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:48,945   copying vcf/test/prof.py -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:48,947   running egg_info
2022-01-28T23:00:49,069   writing manifest file 'PyVCF3.egg-info/SOURCES.txt'
2022-01-28T23:00:49,087   copying vcf/cparse.pyx -> build/lib.linux-armv7l-3.9/vcf
2022-01-28T23:00:49,091   copying vcf/test/1kg.sites.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,097   copying vcf/test/1kg.vcf.gz -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,141   copying vcf/test/FT.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,147   copying vcf/test/bad-info-character.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,151   copying vcf/test/bcftools.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,160   copying vcf/test/contig_idonly.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,165   copying vcf/test/example-4.0.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,169   copying vcf/test/example-4.1-bnd.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,174   copying vcf/test/example-4.1-info-multiple-values.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,178   copying vcf/test/example-4.1-ploidy.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,182   copying vcf/test/example-4.1-sv.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,187   copying vcf/test/example-4.1.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,191   copying vcf/test/example-4.2.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,197   copying vcf/test/freebayes.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,207   copying vcf/test/gatk.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,213   copying vcf/test/gatk_26_meta.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,218   copying vcf/test/gonl.chr20.release4.gtc.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,223   copying vcf/test/info-type-character.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,227   copying vcf/test/issue-140-file1.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,232   copying vcf/test/issue-140-file2.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,236   copying vcf/test/issue-140-file3.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,241   copying vcf/test/issue-16.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,245   copying vcf/test/issue-201.vcf.gz -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,249   copying vcf/test/issue-201.vcf.gz.tbi -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,254   copying vcf/test/issue-214.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,258   copying vcf/test/issue-254.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,262   copying vcf/test/issue_49.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,267   copying vcf/test/metadata-whitespace.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,274   copying vcf/test/mixed-filtering.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,278   copying vcf/test/null_genotype_mono.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,283   copying vcf/test/parse-meta-line.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,288   copying vcf/test/samples-space.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,292   copying vcf/test/samtools.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,296   copying vcf/test/strelka.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,301   copying vcf/test/string_as_flag.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,306   copying vcf/test/tb.vcf.gz -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,310   copying vcf/test/tb.vcf.gz.tbi -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,314   copying vcf/test/uncalled_genotypes.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,318   copying vcf/test/walk_left.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,322   copying vcf/test/walk_refcall.vcf -> build/lib.linux-armv7l-3.9/vcf/test
2022-01-28T23:00:49,329   running build_ext
2022-01-28T23:00:50,911   /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-u4176wk1/pyvcf3_9eb12e7cd0af42d3b3faa58ef78f8e1a/vcf/cparse.pyx
2022-01-28T23:00:50,911     tree = Parsing.p_module(s, pxd, full_module_name)
2022-01-28T23:00:51,826   creating build/temp.linux-armv7l-3.9
2022-01-28T23:00:51,827   creating build/temp.linux-armv7l-3.9/vcf
2022-01-28T23:00:51,828   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/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-3.9/vcf/cparse.o
2022-01-28T23:01:14,234   arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-3.9/vcf/cparse.o -L/usr/lib -o build/lib.linux-armv7l-3.9/vcf/cparse.cpython-39-arm-linux-gnueabihf.so
2022-01-28T23:01:14,529   running build_scripts
2022-01-28T23:01:14,530   creating build/scripts-3.9
2022-01-28T23:01:14,554   /usr/local/lib/python3.9/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
2022-01-28T23:01:14,555     warnings.warn(
2022-01-28T23:01:14,560   running install
2022-01-28T23:01:14,623   running install_lib
2022-01-28T23:01:14,631   creating build/bdist.linux-armv7l
2022-01-28T23:01:14,631   creating build/bdist.linux-armv7l/wheel
2022-01-28T23:01:14,634   creating build/bdist.linux-armv7l/wheel/vcf
2022-01-28T23:01:14,686   creating build/bdist.linux-armv7l/wheel/vcf/test
2022-01-28T23:01:14,895   running install_egg_info
2022-01-28T23:01:14,919   Copying PyVCF3.egg-info to build/bdist.linux-armv7l/wheel/PyVCF3-1.0.1-py3.9.egg-info
2022-01-28T23:01:14,944   running install_scripts
2022-01-28T23:01:14,995   creating build/bdist.linux-armv7l/wheel/PyVCF3-1.0.1.data
2022-01-28T23:01:14,997   creating build/bdist.linux-armv7l/wheel/PyVCF3-1.0.1.data/scripts
2022-01-28T23:01:16,225   Building wheel for pyvcf3 (setup.py): finished with status 'done'
2022-01-28T23:01:16,264   Created wheel for pyvcf3: filename=PyVCF3-1.0.1-cp39-cp39-linux_armv7l.whl size=1194384 sha256=b5c8fed57dd1f35872b4b6dbf824f7c9795cf7e0345ed0c7fa9014e6fb9b9b9e
2022-01-28T23:01:16,265   Stored in directory: /tmp/pip-ephem-wheel-cache-yzf5kcxk/wheels/04/50/e2/ab41a241bc5384b979e882987840dfbb938a4561308bbb9c70
2022-01-28T23:01:16,292 Successfully built pyvcf3
2022-01-28T23:01:16,384 Removed build tracker: '/tmp/pip-req-tracker-clbjibk3'