2021-07-14T21:04:36,456 Created temporary directory: /tmp/pip-ephem-wheel-cache-0c4uynvx
2021-07-14T21:04:36,459 Created temporary directory: /tmp/pip-req-tracker-510nzzlb
2021-07-14T21:04:36,460 Initialized build tracking at /tmp/pip-req-tracker-510nzzlb
2021-07-14T21:04:36,460 Created build tracker: /tmp/pip-req-tracker-510nzzlb
2021-07-14T21:04:36,460 Entered build tracker: /tmp/pip-req-tracker-510nzzlb
2021-07-14T21:04:36,461 Created temporary directory: /tmp/pip-wheel-5gp9_xzp
2021-07-14T21:04:36,491 1 location(s) to search for versions of py-popgen:
2021-07-14T21:04:36,491 * https://pypi.org/simple/py-popgen/
2021-07-14T21:04:36,491 Fetching project page and analyzing links: https://pypi.org/simple/py-popgen/
2021-07-14T21:04:36,492 Getting page https://pypi.org/simple/py-popgen/
2021-07-14T21:04:36,494 Found index url https://pypi.org/simple
2021-07-14T21:04:36,590   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
2021-07-14T21:04:36,590   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
2021-07-14T21:04:36,592   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
2021-07-14T21:04:36,594   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
2021-07-14T21:04:36,595   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
2021-07-14T21:04:36,597   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
2021-07-14T21:04:36,598   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
2021-07-14T21:04:36,599   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
2021-07-14T21:04:36,601   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
2021-07-14T21:04:36,602   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
2021-07-14T21:04:36,603   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
2021-07-14T21:04:36,603   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
2021-07-14T21:04:36,621   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
2021-07-14T21:04:36,622   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
2021-07-14T21:04:36,623   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
2021-07-14T21:04:36,623 Skipping link: not a file: https://pypi.org/simple/py-popgen/
2021-07-14T21:04:36,629 Given no hashes to check 1 links for project 'py-popgen': discarding no candidates
2021-07-14T21:04:36,649 Collecting py-popgen==0.1.1
2021-07-14T21:04:36,650   Created temporary directory: /tmp/pip-unpack-r_6w92ww
2021-07-14T21:04:39,845   Downloading py-popgen-0.1.1.tar.gz (27.2 MB)
2021-07-14T21:04:44,807   Added py-popgen==0.1.1 from https://files.pythonhosted.org/packages/fc/51/633c5a82433e33626559de8c18a3cbd4fa996c127e5ad6b4189e2b014432/py-popgen-0.1.1.tar.gz#sha256=f2808c99f4719d9e5a439cd4169a043dc77b53a8c3211a39623a48128a645c32 to build tracker '/tmp/pip-req-tracker-510nzzlb'
2021-07-14T21:04:44,808     Running setup.py (path:/tmp/pip-wheel-5gp9_xzp/py-popgen_7b02d3136c9c45aaa15532503877f3d0/setup.py) egg_info for package py-popgen
2021-07-14T21:04:44,809     Created temporary directory: /tmp/pip-pip-egg-info-jhvzcum_
2021-07-14T21:04:44,809     Running command python setup.py egg_info
2021-07-14T21:04:46,721     running egg_info
2021-07-14T21:04:46,724     creating /tmp/pip-pip-egg-info-jhvzcum_/py_popgen.egg-info
2021-07-14T21:04:46,725     writing /tmp/pip-pip-egg-info-jhvzcum_/py_popgen.egg-info/PKG-INFO
2021-07-14T21:04:46,728     writing dependency_links to /tmp/pip-pip-egg-info-jhvzcum_/py_popgen.egg-info/dependency_links.txt
2021-07-14T21:04:46,730     writing requirements to /tmp/pip-pip-egg-info-jhvzcum_/py_popgen.egg-info/requires.txt
2021-07-14T21:04:46,731     writing top-level names to /tmp/pip-pip-egg-info-jhvzcum_/py_popgen.egg-info/top_level.txt
2021-07-14T21:04:46,733     writing manifest file '/tmp/pip-pip-egg-info-jhvzcum_/py_popgen.egg-info/SOURCES.txt'
2021-07-14T21:04:46,940     reading manifest file '/tmp/pip-pip-egg-info-jhvzcum_/py_popgen.egg-info/SOURCES.txt'
2021-07-14T21:04:46,942     reading manifest template 'MANIFEST.in'
2021-07-14T21:04:46,962     writing manifest file '/tmp/pip-pip-egg-info-jhvzcum_/py_popgen.egg-info/SOURCES.txt'
2021-07-14T21:04:47,073   Source in /tmp/pip-wheel-5gp9_xzp/py-popgen_7b02d3136c9c45aaa15532503877f3d0 has version 0.1.1, which satisfies requirement py-popgen==0.1.1 from https://files.pythonhosted.org/packages/fc/51/633c5a82433e33626559de8c18a3cbd4fa996c127e5ad6b4189e2b014432/py-popgen-0.1.1.tar.gz#sha256=f2808c99f4719d9e5a439cd4169a043dc77b53a8c3211a39623a48128a645c32
2021-07-14T21:04:47,074   Removed py-popgen==0.1.1 from https://files.pythonhosted.org/packages/fc/51/633c5a82433e33626559de8c18a3cbd4fa996c127e5ad6b4189e2b014432/py-popgen-0.1.1.tar.gz#sha256=f2808c99f4719d9e5a439cd4169a043dc77b53a8c3211a39623a48128a645c32 from build tracker '/tmp/pip-req-tracker-510nzzlb'
2021-07-14T21:04:47,083 Created temporary directory: /tmp/pip-unpack-s21iguie
2021-07-14T21:04:47,083 Building wheels for collected packages: py-popgen
2021-07-14T21:04:47,088   Created temporary directory: /tmp/pip-wheel-nug41zs2
2021-07-14T21:04:47,088   Building wheel for py-popgen (setup.py): started
2021-07-14T21:04:47,089   Destination directory: /tmp/pip-wheel-nug41zs2
2021-07-14T21:04:47,089   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-5gp9_xzp/py-popgen_7b02d3136c9c45aaa15532503877f3d0/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-5gp9_xzp/py-popgen_7b02d3136c9c45aaa15532503877f3d0/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-nug41zs2
2021-07-14T21:04:49,012   running bdist_wheel
2021-07-14T21:04:49,018   running build
2021-07-14T21:04:49,018   running build_py
2021-07-14T21:04:49,182   creating build
2021-07-14T21:04:49,183   creating build/lib.linux-armv7l-3.9
2021-07-14T21:04:49,183   creating build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,185   copying pgpipe/vcf_to_ima.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,188   copying pgpipe/bed_invert.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,191   copying pgpipe/model_creator.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,193   copying pgpipe/stat_sampler.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,196   copying pgpipe/fasta.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,198   copying pgpipe/min_pop_filter.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,200   copying pgpipe/informative_loci_filter.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,203   copying pgpipe/ima3_wrapper.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,205   copying pgpipe/logging_module.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,207   copying pgpipe/vcf_reader_func.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,210   copying pgpipe/vcf_split_pysam.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,213   copying pgpipe/vcf_to_treemix.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,216   copying pgpipe/fasta_utilities.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,218   copying pgpipe/beagle.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,220   copying pgpipe/model_sampler.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,223   copying pgpipe/parse_functions.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,226   copying pgpipe/vcftools.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,229   copying pgpipe/vcf_sampler.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,231   copying pgpipe/vcf_split.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,235   copying pgpipe/plink_ld.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,238   copying pgpipe/extend_loci.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,240   copying pgpipe/model.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,243   copying pgpipe/eigenstrat_fstats.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,247   copying pgpipe/vcf_liftover.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,250   copying pgpipe/admixture.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,253   copying pgpipe/plink.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,256   copying pgpipe/ima_to_treemix.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,258   copying pgpipe/shapeit.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,261   copying pgpipe/subtract_bed.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,263   copying pgpipe/convert.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,266   copying pgpipe/get_nonmissing_chunks.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,269   copying pgpipe/vcf_utilities.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,272   copying pgpipe/vcf_calc.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,275   copying pgpipe/admixtools.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,278   copying pgpipe/__init__.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,280   copying pgpipe/bcftools.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,284   copying pgpipe/argparse_sets.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,286   copying pgpipe/vcf_phase.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,290   copying pgpipe/vcf_filter_bcftools.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,293   copying pgpipe/vcf_filter_vcftools.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,296   copying pgpipe/graph_plotter.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,298   copying pgpipe/filter_single_vcf.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,300   copying pgpipe/bed_tasks.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,303   copying pgpipe/genome_region.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,305   copying pgpipe/ima_priors.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,307   copying pgpipe/site_stats.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,309   copying pgpipe/picard.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,313   copying pgpipe/vcf_filter.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,316   copying pgpipe/vcf_ref_to_seq.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,319   copying pgpipe/bedtools.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,322   copying pgpipe/four_gamete.py -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,325   running egg_info
2021-07-14T21:04:49,340   writing py_popgen.egg-info/PKG-INFO
2021-07-14T21:04:49,342   writing dependency_links to py_popgen.egg-info/dependency_links.txt
2021-07-14T21:04:49,344   writing requirements to py_popgen.egg-info/requires.txt
2021-07-14T21:04:49,346   writing top-level names to py_popgen.egg-info/top_level.txt
2021-07-14T21:04:49,384   reading manifest file 'py_popgen.egg-info/SOURCES.txt'
2021-07-14T21:04:49,388   reading manifest template 'MANIFEST.in'
2021-07-14T21:04:49,414   writing manifest file 'py_popgen.egg-info/SOURCES.txt'
2021-07-14T21:04:49,417   copying pgpipe/test_cython.c -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,423   copying pgpipe/test_cython.pyx -> build/lib.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,428   running build_ext
2021-07-14T21:04:49,432   building 'pgpipe.test_cython' extension
2021-07-14T21:04:49,433   creating build/temp.linux-armv7l-3.9
2021-07-14T21:04:49,433   creating build/temp.linux-armv7l-3.9/pgpipe
2021-07-14T21:04:49,434   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
2021-07-14T21:04:49,824   pgpipe/test_cython.c: In function ‘__pyx_pf_6pgpipe_11test_cython_getAlleleCountArray’:
2021-07-14T21:04:49,825   pgpipe/test_cython.c:1426:17: warning: array subscript has type ‘char’ [-Wchar-subscripts]
2021-07-14T21:04:49,825    1426 |       (__pyx_v_d[__pyx_t_5]) = ((__pyx_v_d[__pyx_t_5]) + 1);
2021-07-14T21:04:49,825         |                 ^
2021-07-14T21:04:49,826   pgpipe/test_cython.c:1426:43: warning: array subscript has type ‘char’ [-Wchar-subscripts]
2021-07-14T21:04:49,826    1426 |       (__pyx_v_d[__pyx_t_5]) = ((__pyx_v_d[__pyx_t_5]) + 1);
2021-07-14T21:04:49,826         |                                           ^
2021-07-14T21:04:49,832   pgpipe/test_cython.c: In function ‘__pyx_pf_6pgpipe_11test_cython_2getAlleleCountArraySub’:
2021-07-14T21:04:49,833   pgpipe/test_cython.c:1842:17: warning: array subscript has type ‘char’ [-Wchar-subscripts]
2021-07-14T21:04:49,833    1842 |       (__pyx_v_d[__pyx_t_8]) = ((__pyx_v_d[__pyx_t_8]) + 1);
2021-07-14T21:04:49,834         |                 ^
2021-07-14T21:04:49,835   pgpipe/test_cython.c:1842:43: warning: array subscript has type ‘char’ [-Wchar-subscripts]
2021-07-14T21:04:49,835    1842 |       (__pyx_v_d[__pyx_t_8]) = ((__pyx_v_d[__pyx_t_8]) + 1);
2021-07-14T21:04:49,835         |                                           ^
2021-07-14T21:04:49,854   pgpipe/test_cython.c: In function ‘__Pyx_ParseOptionalKeywords’:
2021-07-14T21:04:49,855   pgpipe/test_cython.c:2686:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-14T21:04:49,855    2686 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-14T21:04:49,856         |                     ^
2021-07-14T21:04:49,857   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-14T21:04:49,857                    from /usr/include/python3.9/Python.h:97,
2021-07-14T21:04:49,857                    from pgpipe/test_cython.c:16:
2021-07-14T21:04:49,857   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-14T21:04:49,857     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-14T21:04:49,857         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-14T21:04:49,859   pgpipe/test_cython.c:2686:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-14T21:04:49,859    2686 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-14T21:04:49,859         |                     ^
2021-07-14T21:04:49,860   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-14T21:04:49,860                    from /usr/include/python3.9/Python.h:97,
2021-07-14T21:04:49,860                    from pgpipe/test_cython.c:16:
2021-07-14T21:04:49,860   /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
2021-07-14T21:04:49,860     580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
2021-07-14T21:04:49,860         |                                             ^~~~~~~~~~~~~~~~~~~
2021-07-14T21:04:49,862   pgpipe/test_cython.c:2686:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-14T21:04:49,862    2686 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-14T21:04:49,862         |                     ^
2021-07-14T21:04:49,863   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-14T21:04:49,863                    from /usr/include/python3.9/Python.h:97,
2021-07-14T21:04:49,863                    from pgpipe/test_cython.c:16:
2021-07-14T21:04:49,863   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-14T21:04:49,863     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-14T21:04:49,863         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-14T21:04:49,865   pgpipe/test_cython.c:2686:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-14T21:04:49,865    2686 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-14T21:04:49,865         |                     ^
2021-07-14T21:04:49,866   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-14T21:04:49,866                    from /usr/include/python3.9/Python.h:97,
2021-07-14T21:04:49,866                    from pgpipe/test_cython.c:16:
2021-07-14T21:04:49,866   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-14T21:04:49,866     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-14T21:04:49,866         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-14T21:04:49,867   pgpipe/test_cython.c:2686:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-14T21:04:49,867    2686 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-14T21:04:49,867         |                     ^
2021-07-14T21:04:49,867   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-14T21:04:49,867                    from /usr/include/python3.9/Python.h:97,
2021-07-14T21:04:49,868                    from pgpipe/test_cython.c:16:
2021-07-14T21:04:49,868   /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
2021-07-14T21:04:49,868     580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
2021-07-14T21:04:49,868         |                                             ^~~~~~~~~~~~~~~~~~~
2021-07-14T21:04:49,869   pgpipe/test_cython.c:2686:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-14T21:04:49,869    2686 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-14T21:04:49,869         |                     ^
2021-07-14T21:04:49,869   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-14T21:04:49,869                    from /usr/include/python3.9/Python.h:97,
2021-07-14T21:04:49,869                    from pgpipe/test_cython.c:16:
2021-07-14T21:04:49,869   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-14T21:04:49,870     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-14T21:04:49,870         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-14T21:04:49,871   pgpipe/test_cython.c:2702:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-14T21:04:49,871    2702 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-14T21:04:49,872         |                         ^
2021-07-14T21:04:49,872   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-14T21:04:49,872                    from /usr/include/python3.9/Python.h:97,
2021-07-14T21:04:49,872                    from pgpipe/test_cython.c:16:
2021-07-14T21:04:49,872   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-14T21:04:49,872     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-14T21:04:49,872         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-14T21:04:49,873   pgpipe/test_cython.c:2702:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-14T21:04:49,873    2702 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-14T21:04:49,873         |                         ^
2021-07-14T21:04:49,873   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-14T21:04:49,874                    from /usr/include/python3.9/Python.h:97,
2021-07-14T21:04:49,874                    from pgpipe/test_cython.c:16:
2021-07-14T21:04:49,874   /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
2021-07-14T21:04:49,874     580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
2021-07-14T21:04:49,874         |                                             ^~~~~~~~~~~~~~~~~~~
2021-07-14T21:04:49,875   pgpipe/test_cython.c:2702:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-14T21:04:49,875    2702 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-14T21:04:49,875         |                         ^
2021-07-14T21:04:49,875   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-14T21:04:49,875                    from /usr/include/python3.9/Python.h:97,
2021-07-14T21:04:49,875                    from pgpipe/test_cython.c:16:
2021-07-14T21:04:49,876   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-14T21:04:49,876     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-14T21:04:49,876         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-14T21:04:49,877   pgpipe/test_cython.c:2702:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-14T21:04:49,877    2702 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-14T21:04:49,877         |                         ^
2021-07-14T21:04:49,877   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-14T21:04:49,877                    from /usr/include/python3.9/Python.h:97,
2021-07-14T21:04:49,877                    from pgpipe/test_cython.c:16:
2021-07-14T21:04:49,877   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-14T21:04:49,878     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-14T21:04:49,878         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-14T21:04:49,878   pgpipe/test_cython.c:2702:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-14T21:04:49,879    2702 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-14T21:04:49,879         |                         ^
2021-07-14T21:04:49,879   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-14T21:04:49,879                    from /usr/include/python3.9/Python.h:97,
2021-07-14T21:04:49,879                    from pgpipe/test_cython.c:16:
2021-07-14T21:04:49,879   /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
2021-07-14T21:04:49,879     580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
2021-07-14T21:04:49,879         |                                             ^~~~~~~~~~~~~~~~~~~
2021-07-14T21:04:49,880   pgpipe/test_cython.c:2702:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-14T21:04:49,880    2702 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-14T21:04:49,881         |                         ^
2021-07-14T21:04:49,881   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-14T21:04:49,881                    from /usr/include/python3.9/Python.h:97,
2021-07-14T21:04:49,881                    from pgpipe/test_cython.c:16:
2021-07-14T21:04:49,881   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-14T21:04:49,881     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-14T21:04:49,881         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-14T21:04:51,155   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
2021-07-14T21:04:51,275   running build_scripts
2021-07-14T21:04:51,275   creating build/scripts-3.9
2021-07-14T21:04:51,276   copying and adjusting pgpipe/vcf_filter.py -> build/scripts-3.9
2021-07-14T21:04:51,281   copying and adjusting pgpipe/vcf_calc.py -> build/scripts-3.9
2021-07-14T21:04:51,284   copying and adjusting pgpipe/vcf_split.py -> build/scripts-3.9
2021-07-14T21:04:51,287   copying and adjusting pgpipe/vcf_phase.py -> build/scripts-3.9
2021-07-14T21:04:51,292   copying pgpipe/four_gamete.py -> build/scripts-3.9
2021-07-14T21:04:51,296   copying and adjusting pgpipe/stat_sampler.py -> build/scripts-3.9
2021-07-14T21:04:51,299   copying and adjusting pgpipe/bed_tasks.py -> build/scripts-3.9
2021-07-14T21:04:51,302   copying and adjusting pgpipe/informative_loci_filter.py -> build/scripts-3.9
2021-07-14T21:04:51,304   copying and adjusting pgpipe/convert.py -> build/scripts-3.9
2021-07-14T21:04:51,307   copying and adjusting pgpipe/vcf_to_ima.py -> build/scripts-3.9
2021-07-14T21:04:51,310   copying and adjusting pgpipe/admixture.py -> build/scripts-3.9
2021-07-14T21:04:51,312   copying and adjusting pgpipe/plink_ld.py -> build/scripts-3.9
2021-07-14T21:04:51,315   copying and adjusting pgpipe/ima3_wrapper.py -> build/scripts-3.9
2021-07-14T21:04:51,317   copying and adjusting pgpipe/eigenstrat_fstats.py -> build/scripts-3.9
2021-07-14T21:04:51,320   copying and adjusting pgpipe/vcf_liftover.py -> build/scripts-3.9
2021-07-14T21:04:51,322   copying and adjusting pgpipe/vcf_utilities.py -> build/scripts-3.9
2021-07-14T21:04:51,324   changing mode of build/scripts-3.9/vcf_filter.py from 644 to 755
2021-07-14T21:04:51,325   changing mode of build/scripts-3.9/vcf_calc.py from 644 to 755
2021-07-14T21:04:51,325   changing mode of build/scripts-3.9/vcf_split.py from 644 to 755
2021-07-14T21:04:51,325   changing mode of build/scripts-3.9/vcf_phase.py from 644 to 755
2021-07-14T21:04:51,326   changing mode of build/scripts-3.9/four_gamete.py from 644 to 755
2021-07-14T21:04:51,326   changing mode of build/scripts-3.9/stat_sampler.py from 644 to 755
2021-07-14T21:04:51,326   changing mode of build/scripts-3.9/bed_tasks.py from 644 to 755
2021-07-14T21:04:51,327   changing mode of build/scripts-3.9/informative_loci_filter.py from 644 to 755
2021-07-14T21:04:51,327   changing mode of build/scripts-3.9/convert.py from 644 to 755
2021-07-14T21:04:51,327   changing mode of build/scripts-3.9/vcf_to_ima.py from 644 to 755
2021-07-14T21:04:51,328   changing mode of build/scripts-3.9/admixture.py from 644 to 755
2021-07-14T21:04:51,328   changing mode of build/scripts-3.9/plink_ld.py from 644 to 755
2021-07-14T21:04:51,328   changing mode of build/scripts-3.9/ima3_wrapper.py from 644 to 755
2021-07-14T21:04:51,329   changing mode of build/scripts-3.9/eigenstrat_fstats.py from 644 to 755
2021-07-14T21:04:51,329   changing mode of build/scripts-3.9/vcf_liftover.py from 644 to 755
2021-07-14T21:04:51,329   changing mode of build/scripts-3.9/vcf_utilities.py from 644 to 755
2021-07-14T21:04:51,338   installing to build/bdist.linux-armv7l/wheel
2021-07-14T21:04:51,339   running install
2021-07-14T21:04:51,340   running install_lib
2021-07-14T21:04:51,345   creating build/bdist.linux-armv7l
2021-07-14T21:04:51,345   creating build/bdist.linux-armv7l/wheel
2021-07-14T21:04:51,349   creating build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,350   copying build/lib.linux-armv7l-3.9/pgpipe/vcf_to_ima.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,354   copying build/lib.linux-armv7l-3.9/pgpipe/bed_invert.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,356   copying build/lib.linux-armv7l-3.9/pgpipe/model_creator.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,359   copying build/lib.linux-armv7l-3.9/pgpipe/stat_sampler.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,362   copying build/lib.linux-armv7l-3.9/pgpipe/fasta.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,365   copying build/lib.linux-armv7l-3.9/pgpipe/min_pop_filter.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,367   copying build/lib.linux-armv7l-3.9/pgpipe/informative_loci_filter.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,370   copying build/lib.linux-armv7l-3.9/pgpipe/ima3_wrapper.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,373   copying build/lib.linux-armv7l-3.9/pgpipe/logging_module.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,375   copying build/lib.linux-armv7l-3.9/pgpipe/vcf_reader_func.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,378   copying build/lib.linux-armv7l-3.9/pgpipe/vcf_split_pysam.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,381   copying build/lib.linux-armv7l-3.9/pgpipe/vcf_to_treemix.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,384   copying build/lib.linux-armv7l-3.9/pgpipe/fasta_utilities.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,386   copying build/lib.linux-armv7l-3.9/pgpipe/beagle.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,388   copying build/lib.linux-armv7l-3.9/pgpipe/model_sampler.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,391   copying build/lib.linux-armv7l-3.9/pgpipe/parse_functions.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,394   copying build/lib.linux-armv7l-3.9/pgpipe/vcftools.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,398   copying build/lib.linux-armv7l-3.9/pgpipe/vcf_sampler.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,401   copying build/lib.linux-armv7l-3.9/pgpipe/vcf_split.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,404   copying build/lib.linux-armv7l-3.9/pgpipe/plink_ld.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,407   copying build/lib.linux-armv7l-3.9/pgpipe/extend_loci.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,409   copying build/lib.linux-armv7l-3.9/pgpipe/model.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,412   copying build/lib.linux-armv7l-3.9/pgpipe/eigenstrat_fstats.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,415   copying build/lib.linux-armv7l-3.9/pgpipe/vcf_liftover.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,418   copying build/lib.linux-armv7l-3.9/pgpipe/admixture.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,422   copying build/lib.linux-armv7l-3.9/pgpipe/plink.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,425   copying build/lib.linux-armv7l-3.9/pgpipe/ima_to_treemix.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,427   copying build/lib.linux-armv7l-3.9/pgpipe/shapeit.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,429   copying build/lib.linux-armv7l-3.9/pgpipe/subtract_bed.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,431   copying build/lib.linux-armv7l-3.9/pgpipe/convert.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,434   copying build/lib.linux-armv7l-3.9/pgpipe/get_nonmissing_chunks.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,437   copying build/lib.linux-armv7l-3.9/pgpipe/vcf_utilities.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,440   copying build/lib.linux-armv7l-3.9/pgpipe/vcf_calc.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,443   copying build/lib.linux-armv7l-3.9/pgpipe/admixtools.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,447   copying build/lib.linux-armv7l-3.9/pgpipe/test_cython.pyx -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,449   copying build/lib.linux-armv7l-3.9/pgpipe/__init__.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,451   copying build/lib.linux-armv7l-3.9/pgpipe/bcftools.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,454   copying build/lib.linux-armv7l-3.9/pgpipe/argparse_sets.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,456   copying build/lib.linux-armv7l-3.9/pgpipe/vcf_phase.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,460   copying build/lib.linux-armv7l-3.9/pgpipe/test_cython.c -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,467   copying build/lib.linux-armv7l-3.9/pgpipe/vcf_filter_bcftools.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,470   copying build/lib.linux-armv7l-3.9/pgpipe/vcf_filter_vcftools.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,473   copying build/lib.linux-armv7l-3.9/pgpipe/graph_plotter.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,476   copying build/lib.linux-armv7l-3.9/pgpipe/filter_single_vcf.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,478   copying build/lib.linux-armv7l-3.9/pgpipe/bed_tasks.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,480   copying build/lib.linux-armv7l-3.9/pgpipe/genome_region.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,483   copying build/lib.linux-armv7l-3.9/pgpipe/ima_priors.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,485   copying build/lib.linux-armv7l-3.9/pgpipe/test_cython.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,490   copying build/lib.linux-armv7l-3.9/pgpipe/site_stats.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,492   copying build/lib.linux-armv7l-3.9/pgpipe/picard.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,495   copying build/lib.linux-armv7l-3.9/pgpipe/vcf_filter.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,500   copying build/lib.linux-armv7l-3.9/pgpipe/vcf_ref_to_seq.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,503   copying build/lib.linux-armv7l-3.9/pgpipe/bedtools.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,505   copying build/lib.linux-armv7l-3.9/pgpipe/four_gamete.py -> build/bdist.linux-armv7l/wheel/pgpipe
2021-07-14T21:04:51,509   running install_egg_info
2021-07-14T21:04:51,514   Copying py_popgen.egg-info to build/bdist.linux-armv7l/wheel/py_popgen-0.1.1-py3.9.egg-info
2021-07-14T21:04:51,527   running install_scripts
2021-07-14T21:04:51,552   creating build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data
2021-07-14T21:04:51,552   creating build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts
2021-07-14T21:04:51,553   copying build/scripts-3.9/vcf_to_ima.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts
2021-07-14T21:04:51,556   copying build/scripts-3.9/stat_sampler.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts
2021-07-14T21:04:51,559   copying build/scripts-3.9/informative_loci_filter.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts
2021-07-14T21:04:51,561   copying build/scripts-3.9/ima3_wrapper.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts
2021-07-14T21:04:51,564   copying build/scripts-3.9/vcf_split.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts
2021-07-14T21:04:51,566   copying build/scripts-3.9/plink_ld.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts
2021-07-14T21:04:51,570   copying build/scripts-3.9/eigenstrat_fstats.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts
2021-07-14T21:04:51,573   copying build/scripts-3.9/vcf_liftover.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts
2021-07-14T21:04:51,575   copying build/scripts-3.9/admixture.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts
2021-07-14T21:04:51,578   copying build/scripts-3.9/convert.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts
2021-07-14T21:04:51,581   copying build/scripts-3.9/vcf_utilities.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts
2021-07-14T21:04:51,583   copying build/scripts-3.9/vcf_calc.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts
2021-07-14T21:04:51,586   copying build/scripts-3.9/vcf_phase.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts
2021-07-14T21:04:51,590   copying build/scripts-3.9/bed_tasks.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts
2021-07-14T21:04:51,592   copying build/scripts-3.9/vcf_filter.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts
2021-07-14T21:04:51,596   copying build/scripts-3.9/four_gamete.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts
2021-07-14T21:04:51,600   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts/vcf_to_ima.py to 755
2021-07-14T21:04:51,600   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts/stat_sampler.py to 755
2021-07-14T21:04:51,601   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts/informative_loci_filter.py to 755
2021-07-14T21:04:51,601   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts/ima3_wrapper.py to 755
2021-07-14T21:04:51,601   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts/vcf_split.py to 755
2021-07-14T21:04:51,602   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts/plink_ld.py to 755
2021-07-14T21:04:51,602   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts/eigenstrat_fstats.py to 755
2021-07-14T21:04:51,603   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts/vcf_liftover.py to 755
2021-07-14T21:04:51,603   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts/admixture.py to 755
2021-07-14T21:04:51,603   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts/convert.py to 755
2021-07-14T21:04:51,604   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts/vcf_utilities.py to 755
2021-07-14T21:04:51,604   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts/vcf_calc.py to 755
2021-07-14T21:04:51,605   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts/vcf_phase.py to 755
2021-07-14T21:04:51,605   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts/bed_tasks.py to 755
2021-07-14T21:04:51,606   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts/vcf_filter.py to 755
2021-07-14T21:04:51,606   changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.data/scripts/four_gamete.py to 755
2021-07-14T21:04:51,638   creating build/bdist.linux-armv7l/wheel/py_popgen-0.1.1.dist-info/WHEEL
2021-07-14T21:04:51,641   creating '/tmp/pip-wheel-nug41zs2/py_popgen-0.1.1-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2021-07-14T21:04:51,646   adding 'pgpipe/__init__.py'
2021-07-14T21:04:51,649   adding 'pgpipe/admixtools.py'
2021-07-14T21:04:51,651   adding 'pgpipe/admixture.py'
2021-07-14T21:04:51,653   adding 'pgpipe/argparse_sets.py'
2021-07-14T21:04:51,657   adding 'pgpipe/bcftools.py'
2021-07-14T21:04:51,660   adding 'pgpipe/beagle.py'
2021-07-14T21:04:51,662   adding 'pgpipe/bed_invert.py'
2021-07-14T21:04:51,665   adding 'pgpipe/bed_tasks.py'
2021-07-14T21:04:51,667   adding 'pgpipe/bedtools.py'
2021-07-14T21:04:51,670   adding 'pgpipe/convert.py'
2021-07-14T21:04:51,674   adding 'pgpipe/eigenstrat_fstats.py'
2021-07-14T21:04:51,676   adding 'pgpipe/extend_loci.py'
2021-07-14T21:04:51,677   adding 'pgpipe/fasta.py'
2021-07-14T21:04:51,679   adding 'pgpipe/fasta_utilities.py'
2021-07-14T21:04:51,680   adding 'pgpipe/filter_single_vcf.py'
2021-07-14T21:04:51,686   adding 'pgpipe/four_gamete.py'
2021-07-14T21:04:51,690   adding 'pgpipe/genome_region.py'
2021-07-14T21:04:51,692   adding 'pgpipe/get_nonmissing_chunks.py'
2021-07-14T21:04:51,694   adding 'pgpipe/graph_plotter.py'
2021-07-14T21:04:51,696   adding 'pgpipe/ima3_wrapper.py'
2021-07-14T21:04:51,698   adding 'pgpipe/ima_priors.py'
2021-07-14T21:04:51,699   adding 'pgpipe/ima_to_treemix.py'
2021-07-14T21:04:51,702   adding 'pgpipe/informative_loci_filter.py'
2021-07-14T21:04:51,703   adding 'pgpipe/logging_module.py'
2021-07-14T21:04:51,705   adding 'pgpipe/min_pop_filter.py'
2021-07-14T21:04:51,707   adding 'pgpipe/model.py'
2021-07-14T21:04:51,710   adding 'pgpipe/model_creator.py'
2021-07-14T21:04:51,712   adding 'pgpipe/model_sampler.py'
2021-07-14T21:04:51,714   adding 'pgpipe/parse_functions.py'
2021-07-14T21:04:51,716   adding 'pgpipe/picard.py'
2021-07-14T21:04:51,719   adding 'pgpipe/plink.py'
2021-07-14T21:04:51,723   adding 'pgpipe/plink_ld.py'
2021-07-14T21:04:51,725   adding 'pgpipe/shapeit.py'
2021-07-14T21:04:51,727   adding 'pgpipe/site_stats.py'
2021-07-14T21:04:51,730   adding 'pgpipe/stat_sampler.py'
2021-07-14T21:04:51,731   adding 'pgpipe/subtract_bed.py'
2021-07-14T21:04:51,747   adding 'pgpipe/test_cython.c'
2021-07-14T21:04:51,768   adding 'pgpipe/test_cython.cpython-39-arm-linux-gnueabihf.so'
2021-07-14T21:04:51,770   adding 'pgpipe/test_cython.pyx'
2021-07-14T21:04:51,774   adding 'pgpipe/vcf_calc.py'
2021-07-14T21:04:51,779   adding 'pgpipe/vcf_filter.py'
2021-07-14T21:04:51,783   adding 'pgpipe/vcf_filter_bcftools.py'
2021-07-14T21:04:51,787   adding 'pgpipe/vcf_filter_vcftools.py'
2021-07-14T21:04:51,790   adding 'pgpipe/vcf_liftover.py'
2021-07-14T21:04:51,794   adding 'pgpipe/vcf_phase.py'
2021-07-14T21:04:51,798   adding 'pgpipe/vcf_reader_func.py'
2021-07-14T21:04:51,801   adding 'pgpipe/vcf_ref_to_seq.py'
2021-07-14T21:04:51,805   adding 'pgpipe/vcf_sampler.py'
2021-07-14T21:04:51,808   adding 'pgpipe/vcf_split.py'
2021-07-14T21:04:51,811   adding 'pgpipe/vcf_split_pysam.py'
2021-07-14T21:04:51,815   adding 'pgpipe/vcf_to_ima.py'
2021-07-14T21:04:51,817   adding 'pgpipe/vcf_to_treemix.py'
2021-07-14T21:04:51,820   adding 'pgpipe/vcf_utilities.py'
2021-07-14T21:04:51,823   adding 'pgpipe/vcftools.py'
2021-07-14T21:04:51,827   adding 'py_popgen-0.1.1.data/scripts/admixture.py'
2021-07-14T21:04:51,830   adding 'py_popgen-0.1.1.data/scripts/bed_tasks.py'
2021-07-14T21:04:51,833   adding 'py_popgen-0.1.1.data/scripts/convert.py'
2021-07-14T21:04:51,836   adding 'py_popgen-0.1.1.data/scripts/eigenstrat_fstats.py'
2021-07-14T21:04:51,842   adding 'py_popgen-0.1.1.data/scripts/four_gamete.py'
2021-07-14T21:04:51,844   adding 'py_popgen-0.1.1.data/scripts/ima3_wrapper.py'
2021-07-14T21:04:51,847   adding 'py_popgen-0.1.1.data/scripts/informative_loci_filter.py'
2021-07-14T21:04:51,850   adding 'py_popgen-0.1.1.data/scripts/plink_ld.py'
2021-07-14T21:04:51,854   adding 'py_popgen-0.1.1.data/scripts/stat_sampler.py'
2021-07-14T21:04:51,857   adding 'py_popgen-0.1.1.data/scripts/vcf_calc.py'
2021-07-14T21:04:51,862   adding 'py_popgen-0.1.1.data/scripts/vcf_filter.py'
2021-07-14T21:04:51,865   adding 'py_popgen-0.1.1.data/scripts/vcf_liftover.py'
2021-07-14T21:04:51,870   adding 'py_popgen-0.1.1.data/scripts/vcf_phase.py'
2021-07-14T21:04:51,874   adding 'py_popgen-0.1.1.data/scripts/vcf_split.py'
2021-07-14T21:04:51,878   adding 'py_popgen-0.1.1.data/scripts/vcf_to_ima.py'
2021-07-14T21:04:51,881   adding 'py_popgen-0.1.1.data/scripts/vcf_utilities.py'
2021-07-14T21:04:51,884   adding 'py_popgen-0.1.1.dist-info/METADATA'
2021-07-14T21:04:51,885   adding 'py_popgen-0.1.1.dist-info/WHEEL'
2021-07-14T21:04:51,886   adding 'py_popgen-0.1.1.dist-info/top_level.txt'
2021-07-14T21:04:51,888   adding 'py_popgen-0.1.1.dist-info/RECORD'
2021-07-14T21:04:51,895   removing build/bdist.linux-armv7l/wheel
2021-07-14T21:04:52,032   Building wheel for py-popgen (setup.py): finished with status 'done'
2021-07-14T21:04:52,038   Created wheel for py-popgen: filename=py_popgen-0.1.1-cp39-cp39-linux_armv7l.whl size=327209 sha256=0138365f18eb8d38c39ff877395adee19bdfeb70457ee564d999e07be6024eab
2021-07-14T21:04:52,039   Stored in directory: /tmp/pip-ephem-wheel-cache-0c4uynvx/wheels/9b/00/ac/963a715971ae6ef875532fe43871aaf992c82caa2e0bd61495
2021-07-14T21:04:52,049 Successfully built py-popgen
2021-07-14T21:04:52,063 Removed build tracker: '/tmp/pip-req-tracker-510nzzlb'