2021-07-14T21:39:24,108 Created temporary directory: /tmp/pip-ephem-wheel-cache-l8l99bst
2021-07-14T21:39:24,110 Created temporary directory: /tmp/pip-req-tracker-i5e04q6t
2021-07-14T21:39:24,111 Initialized build tracking at /tmp/pip-req-tracker-i5e04q6t
2021-07-14T21:39:24,111 Created build tracker: /tmp/pip-req-tracker-i5e04q6t
2021-07-14T21:39:24,111 Entered build tracker: /tmp/pip-req-tracker-i5e04q6t
2021-07-14T21:39:24,111 Created temporary directory: /tmp/pip-wheel-kizwjhrl
2021-07-14T21:39:24,142 1 location(s) to search for versions of py-popgen:
2021-07-14T21:39:24,142 * https://pypi.org/simple/py-popgen/
2021-07-14T21:39:24,142 Fetching project page and analyzing links: https://pypi.org/simple/py-popgen/
2021-07-14T21:39:24,143 Getting page https://pypi.org/simple/py-popgen/
2021-07-14T21:39:24,144 Found index url https://pypi.org/simple
2021-07-14T21:39:24,244   Found link https://files.pythonhosted.org/packages/ef/06/30919016d98c175fa7e978a21f5d9e6a51fb0732c9d816506704cb6ea805/py-popgen-0.0.1.tar.gz#sha256=c95c719e8e1536b59b32fd617118d8374e8b4438ec114d1fc48704ccf9ccaf9a (from https://pypi.org/simple/py-popgen/), version: 0.0.1
2021-07-14T21:39:24,245   Found link https://files.pythonhosted.org/packages/58/00/c1f0bde98f08d43f77941c57adf7d76ad7efb536bf7971a706f6cf65fc19/py-popgen-0.0.2.tar.gz#sha256=150557350080571d2db292b647478c80bfe7bfd81a3750db368276e613fae36d (from https://pypi.org/simple/py-popgen/), version: 0.0.2
2021-07-14T21:39:24,246   Found link https://files.pythonhosted.org/packages/6c/3c/38e142063e1bf93855d1f3230be131211f779f8b117d7d72d2350befdd46/py-popgen-0.1.tar.gz#sha256=e27fb4877027f544d95ae0c11406d08ea69239b5f67b563d2a17cc82d5fa0ea3 (from https://pypi.org/simple/py-popgen/) (requires-python:>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*), version: 0.1
2021-07-14T21:39:24,248   Found link https://files.pythonhosted.org/packages/fc/51/633c5a82433e33626559de8c18a3cbd4fa996c127e5ad6b4189e2b014432/py-popgen-0.1.1.tar.gz#sha256=f2808c99f4719d9e5a439cd4169a043dc77b53a8c3211a39623a48128a645c32 (from https://pypi.org/simple/py-popgen/) (requires-python:>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*), version: 0.1.1
2021-07-14T21:39:24,249   Found link https://files.pythonhosted.org/packages/5d/35/6c5a59236e0646c45b539d879678adb3d1ff418e33ccfbda03a9aef95420/py-popgen-0.1.2.tar.gz#sha256=29493332c6131f297c20575b30e7a15ee2782dd517cb6bd7c3e25bd06f38e37e (from https://pypi.org/simple/py-popgen/) (requires-python:>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*), version: 0.1.2
2021-07-14T21:39:24,250   Found link https://files.pythonhosted.org/packages/c3/80/281287a24b61a82d164b91b344c00fbc32fae7530ae8cb681352b4a62997/py-popgen-0.1.3.tar.gz#sha256=f96e091bdf05b28954c4f0550adb2dee824cde8881c00616498a6f3ada14ab0b (from https://pypi.org/simple/py-popgen/) (requires-python:>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*), version: 0.1.3
2021-07-14T21:39:24,252   Found link https://files.pythonhosted.org/packages/82/59/78398c3e81107c8b43ddb18d7957ba023ca534a96d3ec17ba05995cc7757/py-popgen-0.1.5.tar.gz#sha256=3d18d3360fdc4296a01f3c530757723b4ffe97bed9776e54f643b480e9439bcc (from https://pypi.org/simple/py-popgen/) (requires-python:>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*), version: 0.1.5
2021-07-14T21:39:24,253   Found link https://files.pythonhosted.org/packages/32/46/dc42908cc9e52642d9ea27938cd13f4d5cf7b06e0fe13680c0d2482d9cc5/py-popgen-0.1.6.tar.gz#sha256=160d2c545729a8ac81d7146baff2f48df6cc8728161ffd534462e7d93343fb21 (from https://pypi.org/simple/py-popgen/) (requires-python:>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*), version: 0.1.6
2021-07-14T21:39:24,254   Found link https://files.pythonhosted.org/packages/41/b1/4391bd0ceb7049a3adf3bb0b1f6e722a50153ef8002f441aba196d95b8d5/py-popgen-0.1.7.tar.gz#sha256=c6a4cb6f8f2064a6188888dc2e1804c9abdb338f23a23c057cdcf9ca2e410867 (from https://pypi.org/simple/py-popgen/) (requires-python:>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*), version: 0.1.7
2021-07-14T21:39:24,256   Found link https://files.pythonhosted.org/packages/b8/75/30ac9e5cffe406627a8cac665467910364be97808c17defcb42a1bf45c06/py-popgen-0.1.8.tar.gz#sha256=7278deed48de6eac28aaef32c6df010cdf81403dd86400ab5923da84d95ea1eb (from https://pypi.org/simple/py-popgen/) (requires-python:>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*), version: 0.1.8
2021-07-14T21:39:24,256   Found link https://files.pythonhosted.org/packages/88/3c/6b73834e1fa600547be5f512a468b05278988b42551f60dc0ea8b9a2f4e4/py-popgen-0.1.9.tar.gz#sha256=92ad36bf05549cf11b2d14ed11949c7ce54c40d2d626831117fec075dd169be2 (from https://pypi.org/simple/py-popgen/) (requires-python:>=3.6.*, !=3.8.*), version: 0.1.9
2021-07-14T21:39:24,257   Found link https://files.pythonhosted.org/packages/ab/81/50731960a816f3bcc8b702f08afc519b0ddf8e24c410407d1d6df077cdbf/py-popgen-0.1.10.tar.gz#sha256=59b548162f03fc77dd477985f74ac1d952b0c58a47ed42b4930fe392df0a2096 (from https://pypi.org/simple/py-popgen/) (requires-python:>=3.6.*, !=3.8.*), version: 0.1.10
2021-07-14T21:39:24,275   Found link https://files.pythonhosted.org/packages/67/60/fbff5462a4af1c54c37a10d333d2e44ee195b3f3ae78d402d41855b0ee45/py_popgen-0.1.10-py3-none-any.whl#sha256=dbca10ee0c0fea4b850cb8d571a408da3f8e8501a722852118c4e099ef2bc06d (from https://pypi.org/simple/py-popgen/) (requires-python:>=3.6.*, !=3.8.*), version: 0.1.10
2021-07-14T21:39:24,276   Found link https://files.pythonhosted.org/packages/e7/d0/6b98b77af174bd0426ba17172150f14c425f719afce215ed8fda20f38365/py-popgen-0.1.11.tar.gz#sha256=76233954accb51ce297bdb29314660d8151f7e6949a53752a79194d7f4f86b65 (from https://pypi.org/simple/py-popgen/) (requires-python:>=3.6.*, !=3.8.*), version: 0.1.11
2021-07-14T21:39:24,277   Found link https://files.pythonhosted.org/packages/65/2d/e6b28bebe9042fc9194bc2420af218acf7b7aa137b61666f7584cc6b68b8/py-popgen-0.1.12.tar.gz#sha256=4288c9594ed38c9db8764c3139f8a7b6292e6edfa6126344db2e985aadd9696e (from https://pypi.org/simple/py-popgen/) (requires-python:>=3.6.*, !=3.8.*), version: 0.1.12
2021-07-14T21:39:24,277 Skipping link: not a file: https://pypi.org/simple/py-popgen/
2021-07-14T21:39:24,280 Given no hashes to check 1 links for project 'py-popgen': discarding no candidates
2021-07-14T21:39:24,299 Collecting py-popgen==0.1.2
2021-07-14T21:39:24,301   Created temporary directory: /tmp/pip-unpack-_6ocgcfd
2021-07-14T21:39:29,659   Downloading py-popgen-0.1.2.tar.gz (27.2 MB)
2021-07-14T21:39:34,579   Added py-popgen==0.1.2 from https://files.pythonhosted.org/packages/5d/35/6c5a59236e0646c45b539d879678adb3d1ff418e33ccfbda03a9aef95420/py-popgen-0.1.2.tar.gz#sha256=29493332c6131f297c20575b30e7a15ee2782dd517cb6bd7c3e25bd06f38e37e to build tracker '/tmp/pip-req-tracker-i5e04q6t'
2021-07-14T21:39:34,580     Running setup.py (path:/tmp/pip-wheel-kizwjhrl/py-popgen_e0014fa4d7164bf6b540bade56f228a3/setup.py) egg_info for package py-popgen
2021-07-14T21:39:34,580     Created temporary directory: /tmp/pip-pip-egg-info-zkdtiw4h
2021-07-14T21:39:34,581     Running command python setup.py egg_info
2021-07-14T21:39:36,186     running egg_info
2021-07-14T21:39:36,188     creating /tmp/pip-pip-egg-info-zkdtiw4h/py_popgen.egg-info
2021-07-14T21:39:36,189     writing /tmp/pip-pip-egg-info-zkdtiw4h/py_popgen.egg-info/PKG-INFO
2021-07-14T21:39:36,191     writing dependency_links to /tmp/pip-pip-egg-info-zkdtiw4h/py_popgen.egg-info/dependency_links.txt
2021-07-14T21:39:36,193     writing requirements to /tmp/pip-pip-egg-info-zkdtiw4h/py_popgen.egg-info/requires.txt
2021-07-14T21:39:36,194     writing top-level names to /tmp/pip-pip-egg-info-zkdtiw4h/py_popgen.egg-info/top_level.txt
2021-07-14T21:39:36,196     writing manifest file '/tmp/pip-pip-egg-info-zkdtiw4h/py_popgen.egg-info/SOURCES.txt'
2021-07-14T21:39:36,396     reading manifest file '/tmp/pip-pip-egg-info-zkdtiw4h/py_popgen.egg-info/SOURCES.txt'
2021-07-14T21:39:36,397     reading manifest template 'MANIFEST.in'
2021-07-14T21:39:36,412     writing manifest file '/tmp/pip-pip-egg-info-zkdtiw4h/py_popgen.egg-info/SOURCES.txt'
2021-07-14T21:39:36,520   Source in /tmp/pip-wheel-kizwjhrl/py-popgen_e0014fa4d7164bf6b540bade56f228a3 has version 0.1.2, which satisfies requirement py-popgen==0.1.2 from https://files.pythonhosted.org/packages/5d/35/6c5a59236e0646c45b539d879678adb3d1ff418e33ccfbda03a9aef95420/py-popgen-0.1.2.tar.gz#sha256=29493332c6131f297c20575b30e7a15ee2782dd517cb6bd7c3e25bd06f38e37e
2021-07-14T21:39:36,521   Removed py-popgen==0.1.2 from https://files.pythonhosted.org/packages/5d/35/6c5a59236e0646c45b539d879678adb3d1ff418e33ccfbda03a9aef95420/py-popgen-0.1.2.tar.gz#sha256=29493332c6131f297c20575b30e7a15ee2782dd517cb6bd7c3e25bd06f38e37e from build tracker '/tmp/pip-req-tracker-i5e04q6t'
2021-07-14T21:39:36,530 Created temporary directory: /tmp/pip-unpack-wztxlod5
2021-07-14T21:39:36,530 Building wheels for collected packages: py-popgen
2021-07-14T21:39:36,534   Created temporary directory: /tmp/pip-wheel-eys2skf4
2021-07-14T21:39:36,535   Building wheel for py-popgen (setup.py): started
2021-07-14T21:39:36,535   Destination directory: /tmp/pip-wheel-eys2skf4
2021-07-14T21:39:36,535   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-kizwjhrl/py-popgen_e0014fa4d7164bf6b540bade56f228a3/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-kizwjhrl/py-popgen_e0014fa4d7164bf6b540bade56f228a3/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-eys2skf4
2021-07-14T21:39:38,143   running bdist_wheel
2021-07-14T21:39:38,148   running build
2021-07-14T21:39:38,149   running build_py
2021-07-14T21:39:38,315   creating build
2021-07-14T21:39:38,316   creating build/lib.linux-armv7l-3.9
2021-07-14T21:39:38,316   creating build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,317   copying pgpipe/plink_ld.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,320   copying pgpipe/informative_loci_filter.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,322   copying pgpipe/vcf_split_pysam.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,325   copying pgpipe/vcf_filter.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,328   copying pgpipe/logging_module.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,329   copying pgpipe/vcf_ref_to_seq.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,332   copying pgpipe/vcftools.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,334   copying pgpipe/stat_sampler.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,337   copying pgpipe/parse_functions.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,339   copying pgpipe/fasta.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,340   copying pgpipe/admixture.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,343   copying pgpipe/ima_to_treemix.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,344   copying pgpipe/four_gamete.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,347   copying pgpipe/vcf_filter_bcftools.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,350   copying pgpipe/convert.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,353   copying pgpipe/admixtools.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,355   copying pgpipe/vcf_to_treemix.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,357   copying pgpipe/ima_priors.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,359   copying pgpipe/argparse_sets.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,361   copying pgpipe/site_stats.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,363   copying pgpipe/model_sampler.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,365   copying pgpipe/plink.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,367   copying pgpipe/shapeit.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,369   copying pgpipe/get_nonmissing_chunks.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,372   copying pgpipe/vcf_filter_vcftools.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,374   copying pgpipe/model_creator.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,377   copying pgpipe/vcf_sampler.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,379   copying pgpipe/eigenstrat_fstats.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,382   copying pgpipe/extend_loci.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,383   copying pgpipe/vcf_utilities.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,386   copying pgpipe/__init__.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,387   copying pgpipe/vcf_split.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,391   copying pgpipe/vcf_liftover.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,393   copying pgpipe/bed_tasks.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,395   copying pgpipe/picard.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,397   copying pgpipe/bed_invert.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,399   copying pgpipe/genome_region.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,402   copying pgpipe/model.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,404   copying pgpipe/vcf_calc.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,407   copying pgpipe/ima3_wrapper.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,410   copying pgpipe/min_pop_filter.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,411   copying pgpipe/vcf_to_ima.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,414   copying pgpipe/graph_plotter.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,416   copying pgpipe/bedtools.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,418   copying pgpipe/filter_single_vcf.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,419   copying pgpipe/fasta_utilities.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,421   copying pgpipe/subtract_bed.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,422   copying pgpipe/vcf_reader_func.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,425   copying pgpipe/beagle.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,427   copying pgpipe/vcf_phase.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,430   copying pgpipe/bcftools.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,433   running egg_info
2021-07-14T21:39:38,446   writing py_popgen.egg-info/PKG-INFO
2021-07-14T21:39:38,447   writing dependency_links to py_popgen.egg-info/dependency_links.txt
2021-07-14T21:39:38,449   writing requirements to py_popgen.egg-info/requires.txt
2021-07-14T21:39:38,450   writing top-level names to py_popgen.egg-info/top_level.txt
2021-07-14T21:39:38,483   reading manifest file 'py_popgen.egg-info/SOURCES.txt'
2021-07-14T21:39:38,486   reading manifest template 'MANIFEST.in'
2021-07-14T21:39:38,510   writing manifest file 'py_popgen.egg-info/SOURCES.txt'
2021-07-14T21:39:38,512   copying pgpipe/test_cython.c -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,518   copying pgpipe/test_cython.pyx -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,522   running build_ext
2021-07-14T21:39:38,527   building 'pgpipe.test_cython' extension
2021-07-14T21:39:38,527   creating build/temp.linux-armv7l-3.9
2021-07-14T21:39:38,528   creating build/temp.linux-armv7l-3.9/pgpipe
2021-07-14T21:39:38,528   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.9 -c pgpipe/test_cython.c -o build/temp.linux-armv7l-3.9/pgpipe/test_cython.o
2021-07-14T21:39:38,898   pgpipe/test_cython.c: In function ‘__pyx_pf_6pgpipe_11test_cython_getAlleleCountArray’:
2021-07-14T21:39:38,899   pgpipe/test_cython.c:1426:17: warning: array subscript has type ‘char’ [-Wchar-subscripts]
2021-07-14T21:39:38,899    1426 |       (__pyx_v_d[__pyx_t_5]) = ((__pyx_v_d[__pyx_t_5]) + 1);
2021-07-14T21:39:38,899         |                 ^
2021-07-14T21:39:38,900   pgpipe/test_cython.c:1426:43: warning: array subscript has type ‘char’ [-Wchar-subscripts]
2021-07-14T21:39:38,900    1426 |       (__pyx_v_d[__pyx_t_5]) = ((__pyx_v_d[__pyx_t_5]) + 1);
2021-07-14T21:39:38,900         |                                           ^
2021-07-14T21:39:38,905   pgpipe/test_cython.c: In function ‘__pyx_pf_6pgpipe_11test_cython_2getAlleleCountArraySub’:
2021-07-14T21:39:38,906   pgpipe/test_cython.c:1842:17: warning: array subscript has type ‘char’ [-Wchar-subscripts]
2021-07-14T21:39:38,907    1842 |       (__pyx_v_d[__pyx_t_8]) = ((__pyx_v_d[__pyx_t_8]) + 1);
2021-07-14T21:39:38,907         |                 ^
2021-07-14T21:39:38,908   pgpipe/test_cython.c:1842:43: warning: array subscript has type ‘char’ [-Wchar-subscripts]
2021-07-14T21:39:38,908    1842 |       (__pyx_v_d[__pyx_t_8]) = ((__pyx_v_d[__pyx_t_8]) + 1);
2021-07-14T21:39:38,908         |                                           ^
2021-07-14T21:39:38,924   pgpipe/test_cython.c: In function ‘__Pyx_ParseOptionalKeywords’:
2021-07-14T21:39:38,925   pgpipe/test_cython.c:2686:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-14T21:39:38,925    2686 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-14T21:39:38,925         |                     ^
2021-07-14T21:39:38,926   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-14T21:39:38,926                    from /usr/include/python3.9/Python.h:97,
2021-07-14T21:39:38,926                    from pgpipe/test_cython.c:16:
2021-07-14T21:39:38,927   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-14T21:39:38,927     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-14T21:39:38,927         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-14T21:39:38,928   pgpipe/test_cython.c:2686:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-14T21:39:38,929    2686 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-14T21:39:38,929         |                     ^
2021-07-14T21:39:38,929   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-14T21:39:38,929                    from /usr/include/python3.9/Python.h:97,
2021-07-14T21:39:38,929                    from pgpipe/test_cython.c:16:
2021-07-14T21:39:38,929   /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
2021-07-14T21:39:38,929     580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
2021-07-14T21:39:38,929         |                                             ^~~~~~~~~~~~~~~~~~~
2021-07-14T21:39:38,930   pgpipe/test_cython.c:2686:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-14T21:39:38,930    2686 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-14T21:39:38,930         |                     ^
2021-07-14T21:39:38,930   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-14T21:39:38,930                    from /usr/include/python3.9/Python.h:97,
2021-07-14T21:39:38,930                    from pgpipe/test_cython.c:16:
2021-07-14T21:39:38,930   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-14T21:39:38,931     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-14T21:39:38,931         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-14T21:39:38,931   pgpipe/test_cython.c:2686:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-14T21:39:38,931    2686 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-14T21:39:38,931         |                     ^
2021-07-14T21:39:38,931   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-14T21:39:38,932                    from /usr/include/python3.9/Python.h:97,
2021-07-14T21:39:38,932                    from pgpipe/test_cython.c:16:
2021-07-14T21:39:38,932   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-14T21:39:38,932     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-14T21:39:38,932         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-14T21:39:38,932   pgpipe/test_cython.c:2686:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-14T21:39:38,933    2686 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-14T21:39:38,933         |                     ^
2021-07-14T21:39:38,933   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-14T21:39:38,933                    from /usr/include/python3.9/Python.h:97,
2021-07-14T21:39:38,933                    from pgpipe/test_cython.c:16:
2021-07-14T21:39:38,933   /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
2021-07-14T21:39:38,933     580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
2021-07-14T21:39:38,933         |                                             ^~~~~~~~~~~~~~~~~~~
2021-07-14T21:39:38,934   pgpipe/test_cython.c:2686:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-14T21:39:38,934    2686 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-14T21:39:38,934         |                     ^
2021-07-14T21:39:38,934   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-14T21:39:38,934                    from /usr/include/python3.9/Python.h:97,
2021-07-14T21:39:38,934                    from pgpipe/test_cython.c:16:
2021-07-14T21:39:38,935   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-14T21:39:38,935     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-14T21:39:38,935         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-14T21:39:38,936   pgpipe/test_cython.c:2702:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-14T21:39:38,936    2702 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-14T21:39:38,936         |                         ^
2021-07-14T21:39:38,936   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-14T21:39:38,936                    from /usr/include/python3.9/Python.h:97,
2021-07-14T21:39:38,936                    from pgpipe/test_cython.c:16:
2021-07-14T21:39:38,937   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-14T21:39:38,937     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-14T21:39:38,937         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-14T21:39:38,937   pgpipe/test_cython.c:2702:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-14T21:39:38,937    2702 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-14T21:39:38,937         |                         ^
2021-07-14T21:39:38,938   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-14T21:39:38,938                    from /usr/include/python3.9/Python.h:97,
2021-07-14T21:39:38,938                    from pgpipe/test_cython.c:16:
2021-07-14T21:39:38,938   /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
2021-07-14T21:39:38,938     580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
2021-07-14T21:39:38,938         |                                             ^~~~~~~~~~~~~~~~~~~
2021-07-14T21:39:38,939   pgpipe/test_cython.c:2702:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-14T21:39:38,939    2702 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-14T21:39:38,939         |                         ^
2021-07-14T21:39:38,939   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-14T21:39:38,939                    from /usr/include/python3.9/Python.h:97,
2021-07-14T21:39:38,939                    from pgpipe/test_cython.c:16:
2021-07-14T21:39:38,939   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-14T21:39:38,939     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-14T21:39:38,940         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-14T21:39:38,940   pgpipe/test_cython.c:2702:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-14T21:39:38,940    2702 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-14T21:39:38,940         |                         ^
2021-07-14T21:39:38,940   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-14T21:39:38,940                    from /usr/include/python3.9/Python.h:97,
2021-07-14T21:39:38,941                    from pgpipe/test_cython.c:16:
2021-07-14T21:39:38,941   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-14T21:39:38,941     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-14T21:39:38,941         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-14T21:39:38,941   pgpipe/test_cython.c:2702:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-14T21:39:38,941    2702 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-14T21:39:38,942         |                         ^
2021-07-14T21:39:38,942   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-14T21:39:38,942                    from /usr/include/python3.9/Python.h:97,
2021-07-14T21:39:38,942                    from pgpipe/test_cython.c:16:
2021-07-14T21:39:38,942   /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
2021-07-14T21:39:38,942     580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
2021-07-14T21:39:38,942         |                                             ^~~~~~~~~~~~~~~~~~~
2021-07-14T21:39:38,943   pgpipe/test_cython.c:2702:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-14T21:39:38,943    2702 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-14T21:39:38,943         |                         ^
2021-07-14T21:39:38,943   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-14T21:39:38,943                    from /usr/include/python3.9/Python.h:97,
2021-07-14T21:39:38,943                    from pgpipe/test_cython.c:16:
2021-07-14T21:39:38,943   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-14T21:39:38,944     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-14T21:39:38,944         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-14T21:39:40,204   arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/pgpipe/test_cython.o -o build/lib.linux-armv7l-3.9/pgpipe/test_cython.cpython-39-arm-linux-gnueabihf.so
2021-07-14T21:39:40,310   running build_scripts
2021-07-14T21:39:40,311   creating build/scripts-3.9
2021-07-14T21:39:40,312   copying and adjusting pgpipe/vcf_filter.py -> build/scripts-3.9
2021-07-14T21:39:40,315   copying and adjusting pgpipe/vcf_calc.py -> build/scripts-3.9
2021-07-14T21:39:40,318   copying and adjusting pgpipe/vcf_split.py -> build/scripts-3.9
2021-07-14T21:39:40,320   copying and adjusting pgpipe/vcf_phase.py -> build/scripts-3.9
2021-07-14T21:39:40,323   copying pgpipe/four_gamete.py -> build/scripts-3.9
2021-07-14T21:39:40,326   copying and adjusting pgpipe/stat_sampler.py -> build/scripts-3.9
2021-07-14T21:39:40,328   copying and adjusting pgpipe/bed_tasks.py -> build/scripts-3.9
2021-07-14T21:39:40,330   copying and adjusting pgpipe/informative_loci_filter.py -> build/scripts-3.9
2021-07-14T21:39:40,332   copying and adjusting pgpipe/convert.py -> build/scripts-3.9
2021-07-14T21:39:40,334   copying and adjusting pgpipe/vcf_to_ima.py -> build/scripts-3.9
2021-07-14T21:39:40,337   copying and adjusting pgpipe/admixture.py -> build/scripts-3.9
2021-07-14T21:39:40,339   copying and adjusting pgpipe/plink_ld.py -> build/scripts-3.9
2021-07-14T21:39:40,341   copying and adjusting pgpipe/ima3_wrapper.py -> build/scripts-3.9
2021-07-14T21:39:40,342   copying and adjusting pgpipe/eigenstrat_fstats.py -> build/scripts-3.9
2021-07-14T21:39:40,345   copying and adjusting pgpipe/vcf_liftover.py -> build/scripts-3.9
2021-07-14T21:39:40,347   copying and adjusting pgpipe/vcf_utilities.py -> build/scripts-3.9
2021-07-14T21:39:40,349   changing mode of build/scripts-3.9/vcf_filter.py from 644 to 755
2021-07-14T21:39:40,349   changing mode of build/scripts-3.9/vcf_calc.py from 644 to 755
2021-07-14T21:39:40,349   changing mode of build/scripts-3.9/vcf_split.py from 644 to 755
2021-07-14T21:39:40,349   changing mode of build/scripts-3.9/vcf_phase.py from 644 to 755
2021-07-14T21:39:40,350   changing mode of build/scripts-3.9/four_gamete.py from 644 to 755
2021-07-14T21:39:40,350   changing mode of build/scripts-3.9/stat_sampler.py from 644 to 755
2021-07-14T21:39:40,350   changing mode of build/scripts-3.9/bed_tasks.py from 644 to 755
2021-07-14T21:39:40,350   changing mode of build/scripts-3.9/informative_loci_filter.py from 644 to 755
2021-07-14T21:39:40,351   changing mode of build/scripts-3.9/convert.py from 644 to 755
2021-07-14T21:39:40,351   changing mode of build/scripts-3.9/vcf_to_ima.py from 644 to 755
2021-07-14T21:39:40,351   changing mode of build/scripts-3.9/admixture.py from 644 to 755
2021-07-14T21:39:40,351   changing mode of build/scripts-3.9/plink_ld.py from 644 to 755
2021-07-14T21:39:40,352   changing mode of build/scripts-3.9/ima3_wrapper.py from 644 to 755
2021-07-14T21:39:40,352   changing mode of build/scripts-3.9/eigenstrat_fstats.py from 644 to 755
2021-07-14T21:39:40,352   changing mode of build/scripts-3.9/vcf_liftover.py from 644 to 755
2021-07-14T21:39:40,352   changing mode of build/scripts-3.9/vcf_utilities.py from 644 to 755
2021-07-14T21:39:40,359   installing to build/bdist.linux-armv7l/wheel
2021-07-14T21:39:40,359   running install
2021-07-14T21:39:40,360   running install_lib
2021-07-14T21:39:40,363   creating build/bdist.linux-armv7l
2021-07-14T21:39:40,364   creating build/bdist.linux-armv7l/wheel
2021-07-14T21:39:40,366   creating build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,367   copying build/lib.linux-armv7l-3.9/pgpipe/plink_ld.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,370   copying build/lib.linux-armv7l-3.9/pgpipe/informative_loci_filter.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,372   copying build/lib.linux-armv7l-3.9/pgpipe/test_cython.pyx -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,373   copying build/lib.linux-armv7l-3.9/pgpipe/vcf_split_pysam.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,376   copying build/lib.linux-armv7l-3.9/pgpipe/test_cython.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,380   copying build/lib.linux-armv7l-3.9/pgpipe/vcf_filter.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,383   copying build/lib.linux-armv7l-3.9/pgpipe/logging_module.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,385   copying build/lib.linux-armv7l-3.9/pgpipe/vcf_ref_to_seq.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,387   copying build/lib.linux-armv7l-3.9/pgpipe/vcftools.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,390   copying build/lib.linux-armv7l-3.9/pgpipe/stat_sampler.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,392   copying build/lib.linux-armv7l-3.9/pgpipe/parse_functions.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,394   copying build/lib.linux-armv7l-3.9/pgpipe/fasta.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,396   copying build/lib.linux-armv7l-3.9/pgpipe/admixture.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,398   copying build/lib.linux-armv7l-3.9/pgpipe/ima_to_treemix.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,399   copying build/lib.linux-armv7l-3.9/pgpipe/four_gamete.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,402   copying build/lib.linux-armv7l-3.9/pgpipe/vcf_filter_bcftools.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,405   copying build/lib.linux-armv7l-3.9/pgpipe/convert.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,407   copying build/lib.linux-armv7l-3.9/pgpipe/admixtools.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,410   copying build/lib.linux-armv7l-3.9/pgpipe/vcf_to_treemix.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,411   copying build/lib.linux-armv7l-3.9/pgpipe/ima_priors.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,413   copying build/lib.linux-armv7l-3.9/pgpipe/test_cython.c -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,418   copying build/lib.linux-armv7l-3.9/pgpipe/argparse_sets.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,420   copying build/lib.linux-armv7l-3.9/pgpipe/site_stats.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,422   copying build/lib.linux-armv7l-3.9/pgpipe/model_sampler.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,424   copying build/lib.linux-armv7l-3.9/pgpipe/plink.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,427   copying build/lib.linux-armv7l-3.9/pgpipe/shapeit.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,429   copying build/lib.linux-armv7l-3.9/pgpipe/get_nonmissing_chunks.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,431   copying build/lib.linux-armv7l-3.9/pgpipe/vcf_filter_vcftools.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,433   copying build/lib.linux-armv7l-3.9/pgpipe/model_creator.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,436   copying build/lib.linux-armv7l-3.9/pgpipe/vcf_sampler.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,438   copying build/lib.linux-armv7l-3.9/pgpipe/eigenstrat_fstats.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,441   copying build/lib.linux-armv7l-3.9/pgpipe/extend_loci.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,443   copying build/lib.linux-armv7l-3.9/pgpipe/vcf_utilities.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,445   copying build/lib.linux-armv7l-3.9/pgpipe/__init__.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,446   copying build/lib.linux-armv7l-3.9/pgpipe/vcf_split.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,449   copying build/lib.linux-armv7l-3.9/pgpipe/vcf_liftover.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,451   copying build/lib.linux-armv7l-3.9/pgpipe/bed_tasks.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,454   copying build/lib.linux-armv7l-3.9/pgpipe/picard.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,456   copying build/lib.linux-armv7l-3.9/pgpipe/bed_invert.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,458   copying build/lib.linux-armv7l-3.9/pgpipe/genome_region.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,460   copying build/lib.linux-armv7l-3.9/pgpipe/model.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,463   copying build/lib.linux-armv7l-3.9/pgpipe/vcf_calc.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,465   copying build/lib.linux-armv7l-3.9/pgpipe/ima3_wrapper.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,467   copying build/lib.linux-armv7l-3.9/pgpipe/min_pop_filter.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,469   copying build/lib.linux-armv7l-3.9/pgpipe/vcf_to_ima.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,472   copying build/lib.linux-armv7l-3.9/pgpipe/graph_plotter.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,474   copying build/lib.linux-armv7l-3.9/pgpipe/bedtools.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,476   copying build/lib.linux-armv7l-3.9/pgpipe/filter_single_vcf.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,478   copying build/lib.linux-armv7l-3.9/pgpipe/fasta_utilities.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,479   copying build/lib.linux-armv7l-3.9/pgpipe/subtract_bed.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,481   copying build/lib.linux-armv7l-3.9/pgpipe/vcf_reader_func.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,483   copying build/lib.linux-armv7l-3.9/pgpipe/beagle.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,485   copying build/lib.linux-armv7l-3.9/pgpipe/vcf_phase.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,488   copying build/lib.linux-armv7l-3.9/pgpipe/bcftools.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:39:40,490   running install_egg_info
2021-07-14T21:39:40,495   Copying py_popgen.egg-info to build/bdist.linux-armv7l/wheel/py_popgen-0.1.2-py3.9.egg-info
2021-07-14T21:39:40,505   running install_scripts
2021-07-14T21:39:40,525   creating build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data
2021-07-14T21:39:40,526   creating build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts
2021-07-14T21:39:40,527   copying build/scripts-3.9/plink_ld.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts
2021-07-14T21:39:40,529   copying build/scripts-3.9/informative_loci_filter.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts
2021-07-14T21:39:40,531   copying build/scripts-3.9/vcf_filter.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts
2021-07-14T21:39:40,534   copying build/scripts-3.9/stat_sampler.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts
2021-07-14T21:39:40,537   copying build/scripts-3.9/admixture.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts
2021-07-14T21:39:40,539   copying build/scripts-3.9/four_gamete.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts
2021-07-14T21:39:40,542   copying build/scripts-3.9/convert.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts
2021-07-14T21:39:40,545   copying build/scripts-3.9/eigenstrat_fstats.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts
2021-07-14T21:39:40,547   copying build/scripts-3.9/vcf_utilities.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts
2021-07-14T21:39:40,550   copying build/scripts-3.9/vcf_split.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts
2021-07-14T21:39:40,552   copying build/scripts-3.9/vcf_liftover.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts
2021-07-14T21:39:40,555   copying build/scripts-3.9/bed_tasks.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts
2021-07-14T21:39:40,557   copying build/scripts-3.9/vcf_calc.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts
2021-07-14T21:39:40,560   copying build/scripts-3.9/ima3_wrapper.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts
2021-07-14T21:39:40,562   copying build/scripts-3.9/vcf_to_ima.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts
2021-07-14T21:39:40,565   copying build/scripts-3.9/vcf_phase.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts
2021-07-14T21:39:40,567   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/plink_ld.py to 755
2021-07-14T21:39:40,568   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/informative_loci_filter.py to 755
2021-07-14T21:39:40,568   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/vcf_filter.py to 755
2021-07-14T21:39:40,568   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/stat_sampler.py to 755
2021-07-14T21:39:40,569   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/admixture.py to 755
2021-07-14T21:39:40,569   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/four_gamete.py to 755
2021-07-14T21:39:40,569   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/convert.py to 755
2021-07-14T21:39:40,569   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/eigenstrat_fstats.py to 755
2021-07-14T21:39:40,570   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/vcf_utilities.py to 755
2021-07-14T21:39:40,570   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/vcf_split.py to 755
2021-07-14T21:39:40,570   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/vcf_liftover.py to 755
2021-07-14T21:39:40,570   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/bed_tasks.py to 755
2021-07-14T21:39:40,571   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/vcf_calc.py to 755
2021-07-14T21:39:40,571   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/ima3_wrapper.py to 755
2021-07-14T21:39:40,571   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/vcf_to_ima.py to 755
2021-07-14T21:39:40,571   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/vcf_phase.py to 755
2021-07-14T21:39:40,593   creating build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.dist-info/WHEEL
2021-07-14T21:39:40,596   creating '/tmp/pip-wheel-eys2skf4/py_popgen-0.1.2-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2021-07-14T21:39:40,599   adding 'pgpipe/__init__.py'
2021-07-14T21:39:40,601   adding 'pgpipe/admixtools.py'
2021-07-14T21:39:40,603   adding 'pgpipe/admixture.py'
2021-07-14T21:39:40,605   adding 'pgpipe/argparse_sets.py'
2021-07-14T21:39:40,608   adding 'pgpipe/bcftools.py'
2021-07-14T21:39:40,609   adding 'pgpipe/beagle.py'
2021-07-14T21:39:40,611   adding 'pgpipe/bed_invert.py'
2021-07-14T21:39:40,613   adding 'pgpipe/bed_tasks.py'
2021-07-14T21:39:40,614   adding 'pgpipe/bedtools.py'
2021-07-14T21:39:40,616   adding 'pgpipe/convert.py'
2021-07-14T21:39:40,619   adding 'pgpipe/eigenstrat_fstats.py'
2021-07-14T21:39:40,620   adding 'pgpipe/extend_loci.py'
2021-07-14T21:39:40,622   adding 'pgpipe/fasta.py'
2021-07-14T21:39:40,623   adding 'pgpipe/fasta_utilities.py'
2021-07-14T21:39:40,624   adding 'pgpipe/filter_single_vcf.py'
2021-07-14T21:39:40,629   adding 'pgpipe/four_gamete.py'
2021-07-14T21:39:40,632   adding 'pgpipe/genome_region.py'
2021-07-14T21:39:40,634   adding 'pgpipe/get_nonmissing_chunks.py'
2021-07-14T21:39:40,635   adding 'pgpipe/graph_plotter.py'
2021-07-14T21:39:40,636   adding 'pgpipe/ima3_wrapper.py'
2021-07-14T21:39:40,638   adding 'pgpipe/ima_priors.py'
2021-07-14T21:39:40,639   adding 'pgpipe/ima_to_treemix.py'
2021-07-14T21:39:40,641   adding 'pgpipe/informative_loci_filter.py'
2021-07-14T21:39:40,642   adding 'pgpipe/logging_module.py'
2021-07-14T21:39:40,643   adding 'pgpipe/min_pop_filter.py'
2021-07-14T21:39:40,645   adding 'pgpipe/model.py'
2021-07-14T21:39:40,648   adding 'pgpipe/model_creator.py'
2021-07-14T21:39:40,649   adding 'pgpipe/model_sampler.py'
2021-07-14T21:39:40,651   adding 'pgpipe/parse_functions.py'
2021-07-14T21:39:40,653   adding 'pgpipe/picard.py'
2021-07-14T21:39:40,655   adding 'pgpipe/plink.py'
2021-07-14T21:39:40,658   adding 'pgpipe/plink_ld.py'
2021-07-14T21:39:40,660   adding 'pgpipe/shapeit.py'
2021-07-14T21:39:40,661   adding 'pgpipe/site_stats.py'
2021-07-14T21:39:40,663   adding 'pgpipe/stat_sampler.py'
2021-07-14T21:39:40,665   adding 'pgpipe/subtract_bed.py'
2021-07-14T21:39:40,679   adding 'pgpipe/test_cython.c'
2021-07-14T21:39:40,699   adding 'pgpipe/test_cython.cpython-39-arm-linux-gnueabihf.so'
2021-07-14T21:39:40,701   adding 'pgpipe/test_cython.pyx'
2021-07-14T21:39:40,704   adding 'pgpipe/vcf_calc.py'
2021-07-14T21:39:40,709   adding 'pgpipe/vcf_filter.py'
2021-07-14T21:39:40,713   adding 'pgpipe/vcf_filter_bcftools.py'
2021-07-14T21:39:40,716   adding 'pgpipe/vcf_filter_vcftools.py'
2021-07-14T21:39:40,718   adding 'pgpipe/vcf_liftover.py'
2021-07-14T21:39:40,723   adding 'pgpipe/vcf_phase.py'
2021-07-14T21:39:40,726   adding 'pgpipe/vcf_reader_func.py'
2021-07-14T21:39:40,728   adding 'pgpipe/vcf_ref_to_seq.py'
2021-07-14T21:39:40,731   adding 'pgpipe/vcf_sampler.py'
2021-07-14T21:39:40,734   adding 'pgpipe/vcf_split.py'
2021-07-14T21:39:40,736   adding 'pgpipe/vcf_split_pysam.py'
2021-07-14T21:39:40,740   adding 'pgpipe/vcf_to_ima.py'
2021-07-14T21:39:40,741   adding 'pgpipe/vcf_to_treemix.py'
2021-07-14T21:39:40,744   adding 'pgpipe/vcf_utilities.py'
2021-07-14T21:39:40,747   adding 'pgpipe/vcftools.py'
2021-07-14T21:39:40,750   adding 'py_popgen-0.1.2.data/scripts/admixture.py'
2021-07-14T21:39:40,752   adding 'py_popgen-0.1.2.data/scripts/bed_tasks.py'
2021-07-14T21:39:40,754   adding 'py_popgen-0.1.2.data/scripts/convert.py'
2021-07-14T21:39:40,757   adding 'py_popgen-0.1.2.data/scripts/eigenstrat_fstats.py'
2021-07-14T21:39:40,762   adding 'py_popgen-0.1.2.data/scripts/four_gamete.py'
2021-07-14T21:39:40,764   adding 'py_popgen-0.1.2.data/scripts/ima3_wrapper.py'
2021-07-14T21:39:40,766   adding 'py_popgen-0.1.2.data/scripts/informative_loci_filter.py'
2021-07-14T21:39:40,769   adding 'py_popgen-0.1.2.data/scripts/plink_ld.py'
2021-07-14T21:39:40,771   adding 'py_popgen-0.1.2.data/scripts/stat_sampler.py'
2021-07-14T21:39:40,774   adding 'py_popgen-0.1.2.data/scripts/vcf_calc.py'
2021-07-14T21:39:40,779   adding 'py_popgen-0.1.2.data/scripts/vcf_filter.py'
2021-07-14T21:39:40,781   adding 'py_popgen-0.1.2.data/scripts/vcf_liftover.py'
2021-07-14T21:39:40,785   adding 'py_popgen-0.1.2.data/scripts/vcf_phase.py'
2021-07-14T21:39:40,788   adding 'py_popgen-0.1.2.data/scripts/vcf_split.py'
2021-07-14T21:39:40,792   adding 'py_popgen-0.1.2.data/scripts/vcf_to_ima.py'
2021-07-14T21:39:40,794   adding 'py_popgen-0.1.2.data/scripts/vcf_utilities.py'
2021-07-14T21:39:40,796   adding 'py_popgen-0.1.2.dist-info/METADATA'
2021-07-14T21:39:40,797   adding 'py_popgen-0.1.2.dist-info/WHEEL'
2021-07-14T21:39:40,798   adding 'py_popgen-0.1.2.dist-info/top_level.txt'
2021-07-14T21:39:40,800   adding 'py_popgen-0.1.2.dist-info/RECORD'
2021-07-14T21:39:40,807   removing build/bdist.linux-armv7l/wheel
2021-07-14T21:39:40,934   Building wheel for py-popgen (setup.py): finished with status 'done'
2021-07-14T21:39:40,940   Created wheel for py-popgen: filename=py_popgen-0.1.2-cp39-cp39-linux_armv7l.whl size=327208 sha256=48b48a8460c9daef39ece426ed317c744fd9fa5f0c83089ef971d7178bec21bc
2021-07-14T21:39:40,941   Stored in directory: /tmp/pip-ephem-wheel-cache-l8l99bst/wheels/52/62/07/37dac0d08026bb941ec3c6956db111bda82f37b7134dd8f399
2021-07-14T21:39:40,952 Successfully built py-popgen
2021-07-14T21:39:40,967 Removed build tracker: '/tmp/pip-req-tracker-i5e04q6t'