2025-09-08T19:56:41,354 Created temporary directory: /tmp/pip-build-tracker-u7klqi5e 2025-09-08T19:56:41,355 Initialized build tracking at /tmp/pip-build-tracker-u7klqi5e 2025-09-08T19:56:41,355 Created build tracker: /tmp/pip-build-tracker-u7klqi5e 2025-09-08T19:56:41,355 Entered build tracker: /tmp/pip-build-tracker-u7klqi5e 2025-09-08T19:56:41,355 Created temporary directory: /tmp/pip-wheel-kmymmvxm 2025-09-08T19:56:41,358 Created temporary directory: /tmp/pip-ephem-wheel-cache-17dgu05t 2025-09-08T19:56:41,417 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T19:56:41,420 2 location(s) to search for versions of py-popgen: 2025-09-08T19:56:41,420 * https://pypi.org/simple/py-popgen/ 2025-09-08T19:56:41,420 * https://www.piwheels.org/simple/py-popgen/ 2025-09-08T19:56:41,420 Fetching project page and analyzing links: https://pypi.org/simple/py-popgen/ 2025-09-08T19:56:41,420 Getting page https://pypi.org/simple/py-popgen/ 2025-09-08T19:56:41,421 Found index url https://pypi.org/simple/ 2025-09-08T19:56:41,498 Fetched page https://pypi.org/simple/py-popgen/ as application/vnd.pypi.simple.v1+json 2025-09-08T19:56:41,500 Found link https://files.pythonhosted.org/packages/ef/06/30919016d98c175fa7e978a21f5d9e6a51fb0732c9d816506704cb6ea805/py-popgen-0.0.1.tar.gz (from https://pypi.org/simple/py-popgen/), version: 0.0.1 2025-09-08T19:56:41,500 Found link https://files.pythonhosted.org/packages/58/00/c1f0bde98f08d43f77941c57adf7d76ad7efb536bf7971a706f6cf65fc19/py-popgen-0.0.2.tar.gz (from https://pypi.org/simple/py-popgen/), version: 0.0.2 2025-09-08T19:56:41,502 Found link https://files.pythonhosted.org/packages/6c/3c/38e142063e1bf93855d1f3230be131211f779f8b117d7d72d2350befdd46/py-popgen-0.1.tar.gz (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 2025-09-08T19:56:41,502 Found link 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https://files.pythonhosted.org/packages/6a/86/1079aa710002cd905b80f2bc21c4ac2a954f0cc09e58dbe2f9088eeeec64/py-popgen-0.1.13.tar.gz (from https://pypi.org/simple/py-popgen/) (requires-python:>=3.6.*, !=3.8.*) 2025-09-08T19:56:41,506 Found link https://files.pythonhosted.org/packages/6a/86/1079aa710002cd905b80f2bc21c4ac2a954f0cc09e58dbe2f9088eeeec64/py-popgen-0.1.13.tar.gz (from https://pypi.org/simple/py-popgen/) (requires-python:>=3.6.*, !=3.8.*), version: 0.1.13 2025-09-08T19:56:41,506 Fetching project page and analyzing links: https://www.piwheels.org/simple/py-popgen/ 2025-09-08T19:56:41,506 Getting page https://www.piwheels.org/simple/py-popgen/ 2025-09-08T19:56:41,507 Found index url https://www.piwheels.org/simple/ 2025-09-08T19:56:41,643 Fetched page https://www.piwheels.org/simple/py-popgen/ as text/html 2025-09-08T19:56:41,655 Skipping link: No binaries permitted for py-popgen: 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2025-09-08T19:56:41,657 Skipping link: No binaries permitted for py-popgen: https://archive1.piwheels.org/simple/py-popgen/py_popgen-0.1.3-cp37-cp37m-linux_armv6l.whl#sha256=7fc03fbf75c64927a3dad988df065cba975cdb25477f40bb407b47bb29b94e8a (from https://www.piwheels.org/simple/py-popgen/) (requires-python:>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*) 2025-09-08T19:56:41,657 Skipping link: No binaries permitted for py-popgen: https://archive1.piwheels.org/simple/py-popgen/py_popgen-0.1.3-cp37-cp37m-linux_armv7l.whl#sha256=7fc03fbf75c64927a3dad988df065cba975cdb25477f40bb407b47bb29b94e8a (from https://www.piwheels.org/simple/py-popgen/) (requires-python:>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*) 2025-09-08T19:56:41,657 Skipping link: No binaries permitted for py-popgen: https://archive1.piwheels.org/simple/py-popgen/py_popgen-0.1.3-cp39-cp39-linux_armv6l.whl#sha256=1a6814c897aaaece70742d67a5f4c4060cbde2b995e187369eed2e13c2e1acdd (from 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https://archive1.piwheels.org/simple/py-popgen/py_popgen-0.1.1-cp39-cp39-linux_armv7l.whl#sha256=0138365f18eb8d38c39ff877395adee19bdfeb70457ee564d999e07be6024eab (from https://www.piwheels.org/simple/py-popgen/) (requires-python:>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*) 2025-09-08T19:56:41,660 Skipping link: No binaries permitted for py-popgen: https://archive1.piwheels.org/simple/py-popgen/py_popgen-0.1.1-cp37-cp37m-linux_armv6l.whl#sha256=8f8b0e808c5bb73e80eed3ffcb8d45b8bd327d24901ece83a055fe123ee8509b (from https://www.piwheels.org/simple/py-popgen/) (requires-python:>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*) 2025-09-08T19:56:41,660 Skipping link: No binaries permitted for py-popgen: https://archive1.piwheels.org/simple/py-popgen/py_popgen-0.1.1-cp37-cp37m-linux_armv7l.whl#sha256=8f8b0e808c5bb73e80eed3ffcb8d45b8bd327d24901ece83a055fe123ee8509b (from https://www.piwheels.org/simple/py-popgen/) (requires-python:>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*) 2025-09-08T19:56:41,660 Skipping link: No binaries permitted for py-popgen: https://archive1.piwheels.org/simple/py-popgen/py_popgen-0.1.1-cp311-cp311-linux_armv6l.whl#sha256=9f76e86dc83b9c84e76816419b2df52798630b229f660bcba935301d6904f1d8 (from https://www.piwheels.org/simple/py-popgen/) (requires-python:>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*) 2025-09-08T19:56:41,660 Skipping link: No binaries permitted for py-popgen: https://archive1.piwheels.org/simple/py-popgen/py_popgen-0.1.1-cp311-cp311-linux_armv7l.whl#sha256=9f76e86dc83b9c84e76816419b2df52798630b229f660bcba935301d6904f1d8 (from https://www.piwheels.org/simple/py-popgen/) (requires-python:>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*) 2025-09-08T19:56:41,660 Skipping link: No binaries permitted for py-popgen: https://www.piwheels.org/simple/py-popgen/py_popgen-0.1.1-cp313-cp313-linux_armv6l.whl#sha256=76d64310432fac534ea759f5852ee509473d94c551b8a694d330b0e7b47ea4ba (from https://www.piwheels.org/simple/py-popgen/) (requires-python:>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*) 2025-09-08T19:56:41,660 Skipping link: No binaries permitted for py-popgen: https://www.piwheels.org/simple/py-popgen/py_popgen-0.1.1-cp313-cp313-linux_armv7l.whl#sha256=76d64310432fac534ea759f5852ee509473d94c551b8a694d330b0e7b47ea4ba (from https://www.piwheels.org/simple/py-popgen/) (requires-python:>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*) 2025-09-08T19:56:41,661 Skipping link: No binaries permitted for py-popgen: https://archive1.piwheels.org/simple/py-popgen/py_popgen-0.1-cp39-cp39-linux_armv6l.whl#sha256=b0c087110c013e0d30e95ebc134ba7873a08eedd822d4346678ba0d828ba597d (from https://www.piwheels.org/simple/py-popgen/) (requires-python:>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*) 2025-09-08T19:56:41,661 Skipping link: No binaries permitted for py-popgen: https://archive1.piwheels.org/simple/py-popgen/py_popgen-0.1-cp39-cp39-linux_armv7l.whl#sha256=b0c087110c013e0d30e95ebc134ba7873a08eedd822d4346678ba0d828ba597d (from https://www.piwheels.org/simple/py-popgen/) (requires-python:>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*) 2025-09-08T19:56:41,661 Skipping link: No binaries permitted for py-popgen: https://archive1.piwheels.org/simple/py-popgen/py_popgen-0.1-cp37-cp37m-linux_armv7l.whl#sha256=92bf0666cb3a3f117b66f7260b69266203e795adef3b57e8f78b5f8973ad7319 (from https://www.piwheels.org/simple/py-popgen/) (requires-python:>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*) 2025-09-08T19:56:41,661 Skipping link: No binaries permitted for py-popgen: https://archive1.piwheels.org/simple/py-popgen/py_popgen-0.1-cp37-cp37m-linux_armv6l.whl#sha256=92bf0666cb3a3f117b66f7260b69266203e795adef3b57e8f78b5f8973ad7319 (from https://www.piwheels.org/simple/py-popgen/) (requires-python:>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*) 2025-09-08T19:56:41,661 Skipping link: No binaries permitted for py-popgen: https://archive1.piwheels.org/simple/py-popgen/py_popgen-0.1-cp311-cp311-linux_armv6l.whl#sha256=ebbc1403c57d9555dd0059a251f381f04fc20d2396adeb4785d6e3d9d531efc0 (from https://www.piwheels.org/simple/py-popgen/) (requires-python:>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*) 2025-09-08T19:56:41,661 Skipping link: No binaries permitted for py-popgen: https://archive1.piwheels.org/simple/py-popgen/py_popgen-0.1-cp311-cp311-linux_armv7l.whl#sha256=ebbc1403c57d9555dd0059a251f381f04fc20d2396adeb4785d6e3d9d531efc0 (from https://www.piwheels.org/simple/py-popgen/) (requires-python:>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*) 2025-09-08T19:56:41,662 Skipping link: No binaries permitted for py-popgen: https://www.piwheels.org/simple/py-popgen/py_popgen-0.1-cp313-cp313-linux_armv6l.whl#sha256=5661aad46507a933371a5106a1a3480a92ce95b4daa7eaac0edcb272ef39bcbf (from https://www.piwheels.org/simple/py-popgen/) (requires-python:>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*) 2025-09-08T19:56:41,662 Skipping link: No binaries permitted for py-popgen: https://www.piwheels.org/simple/py-popgen/py_popgen-0.1-cp313-cp313-linux_armv7l.whl#sha256=5661aad46507a933371a5106a1a3480a92ce95b4daa7eaac0edcb272ef39bcbf (from https://www.piwheels.org/simple/py-popgen/) (requires-python:>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*) 2025-09-08T19:56:41,662 Skipping link: No binaries permitted for py-popgen: https://archive1.piwheels.org/simple/py-popgen/py_popgen-0.0.2-py3-none-any.whl#sha256=3244180ece2de707e6b164aa7ab0613b2cebd85db12b846cc163fb6cf84e474e (from https://www.piwheels.org/simple/py-popgen/) 2025-09-08T19:56:41,662 Skipping link: No binaries permitted for py-popgen: https://archive1.piwheels.org/simple/py-popgen/py_popgen-0.0.1-py3-none-any.whl#sha256=6a14d66683002e85987826592b3378b6479fb1ebde0c837646dd0c2adbfa59a6 (from https://www.piwheels.org/simple/py-popgen/) 2025-09-08T19:56:41,662 Skipping link: not a file: https://www.piwheels.org/simple/py-popgen/ 2025-09-08T19:56:41,663 Skipping link: not a file: https://pypi.org/simple/py-popgen/ 2025-09-08T19:56:41,686 Given no hashes to check 1 links for project 'py-popgen': discarding no candidates 2025-09-08T19:56:41,687 Collecting py-popgen==0.1.2 2025-09-08T19:56:41,689 Created temporary directory: /tmp/pip-unpack-p7mut_v0 2025-09-08T19:56:41,845 Downloading py-popgen-0.1.2.tar.gz (27.2 MB) 2025-09-08T19:56:46,639 Added py-popgen==0.1.2 from https://files.pythonhosted.org/packages/5d/35/6c5a59236e0646c45b539d879678adb3d1ff418e33ccfbda03a9aef95420/py-popgen-0.1.2.tar.gz to build tracker '/tmp/pip-build-tracker-u7klqi5e' 2025-09-08T19:56:46,640 Running setup.py (path:/tmp/pip-wheel-kmymmvxm/py-popgen_26fe816838e34e61b8430183330160af/setup.py) egg_info for package py-popgen 2025-09-08T19:56:46,641 Created temporary directory: /tmp/pip-pip-egg-info-zx638ev9 2025-09-08T19:56:46,641 Preparing metadata (setup.py): started 2025-09-08T19:56:46,642 Running command python setup.py egg_info 2025-09-08T19:56:48,686 Compiling pgpipe/test_cython.pyx because it changed. 2025-09-08T19:56:48,686 [1/1] Cythonizing pgpipe/test_cython.pyx 2025-09-08T19:56:49,180 running egg_info 2025-09-08T19:56:49,255 creating /tmp/pip-pip-egg-info-zx638ev9/py_popgen.egg-info 2025-09-08T19:56:49,255 writing /tmp/pip-pip-egg-info-zx638ev9/py_popgen.egg-info/PKG-INFO 2025-09-08T19:56:49,256 writing dependency_links to /tmp/pip-pip-egg-info-zx638ev9/py_popgen.egg-info/dependency_links.txt 2025-09-08T19:56:49,257 writing requirements to /tmp/pip-pip-egg-info-zx638ev9/py_popgen.egg-info/requires.txt 2025-09-08T19:56:49,257 writing top-level names to /tmp/pip-pip-egg-info-zx638ev9/py_popgen.egg-info/top_level.txt 2025-09-08T19:56:49,258 writing manifest file '/tmp/pip-pip-egg-info-zx638ev9/py_popgen.egg-info/SOURCES.txt' 2025-09-08T19:56:49,636 reading manifest file '/tmp/pip-pip-egg-info-zx638ev9/py_popgen.egg-info/SOURCES.txt' 2025-09-08T19:56:49,636 reading manifest template 'MANIFEST.in' 2025-09-08T19:56:49,645 writing manifest file '/tmp/pip-pip-egg-info-zx638ev9/py_popgen.egg-info/SOURCES.txt' 2025-09-08T19:56:49,903 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T19:56:49,908 Source in /tmp/pip-wheel-kmymmvxm/py-popgen_26fe816838e34e61b8430183330160af 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 2025-09-08T19:56:49,908 Removed py-popgen==0.1.2 from https://files.pythonhosted.org/packages/5d/35/6c5a59236e0646c45b539d879678adb3d1ff418e33ccfbda03a9aef95420/py-popgen-0.1.2.tar.gz from build tracker '/tmp/pip-build-tracker-u7klqi5e' 2025-09-08T19:56:49,917 Created temporary directory: /tmp/pip-unpack-2wov_745 2025-09-08T19:56:49,917 Created temporary directory: /tmp/pip-unpack-7my08qmf 2025-09-08T19:56:49,917 Building wheels for collected packages: py-popgen 2025-09-08T19:56:49,918 Created temporary directory: /tmp/pip-wheel-v8464m_f 2025-09-08T19:56:49,919 DEPRECATION: Building 'py-popgen' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'py-popgen'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-08T19:56:49,920 Building wheel for py-popgen (setup.py): started 2025-09-08T19:56:49,921 Destination directory: /tmp/pip-wheel-v8464m_f 2025-09-08T19:56:49,921 Running command python setup.py bdist_wheel 2025-09-08T19:56:51,331 running bdist_wheel 2025-09-08T19:56:51,697 running build 2025-09-08T19:56:51,697 running build_py 2025-09-08T19:56:51,774 creating build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,774 copying pgpipe/vcftools.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,775 copying pgpipe/vcf_utilities.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,776 copying pgpipe/vcf_to_treemix.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,776 copying pgpipe/vcf_to_ima.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,777 copying pgpipe/vcf_split_pysam.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,777 copying pgpipe/vcf_split.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,778 copying pgpipe/vcf_sampler.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,779 copying pgpipe/vcf_ref_to_seq.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,779 copying pgpipe/vcf_reader_func.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,780 copying pgpipe/vcf_phase.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,780 copying pgpipe/vcf_liftover.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,781 copying pgpipe/vcf_filter_vcftools.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,782 copying pgpipe/vcf_filter_bcftools.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,782 copying pgpipe/vcf_filter.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,783 copying pgpipe/vcf_calc.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,783 copying pgpipe/subtract_bed.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,784 copying pgpipe/stat_sampler.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,785 copying pgpipe/site_stats.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,785 copying pgpipe/shapeit.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,786 copying pgpipe/plink_ld.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,786 copying pgpipe/plink.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,787 copying pgpipe/picard.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,787 copying pgpipe/parse_functions.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,788 copying pgpipe/model_sampler.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,789 copying pgpipe/model_creator.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,789 copying pgpipe/model.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,790 copying pgpipe/min_pop_filter.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,790 copying pgpipe/logging_module.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,791 copying pgpipe/informative_loci_filter.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,791 copying pgpipe/ima_to_treemix.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,792 copying pgpipe/ima_priors.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,792 copying pgpipe/ima3_wrapper.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,793 copying pgpipe/graph_plotter.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,793 copying pgpipe/get_nonmissing_chunks.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,794 copying pgpipe/genome_region.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,794 copying pgpipe/four_gamete.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,795 copying pgpipe/filter_single_vcf.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,795 copying pgpipe/fasta_utilities.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,796 copying pgpipe/fasta.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,797 copying pgpipe/extend_loci.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,797 copying pgpipe/eigenstrat_fstats.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,798 copying pgpipe/convert.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,798 copying pgpipe/bedtools.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,799 copying pgpipe/bed_tasks.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,799 copying pgpipe/bed_invert.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,800 copying pgpipe/beagle.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,800 copying pgpipe/bcftools.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,801 copying pgpipe/argparse_sets.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,802 copying pgpipe/admixture.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,802 copying pgpipe/admixtools.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,803 copying pgpipe/__init__.py -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,803 running egg_info 2025-09-08T19:56:51,876 writing py_popgen.egg-info/PKG-INFO 2025-09-08T19:56:51,877 writing dependency_links to py_popgen.egg-info/dependency_links.txt 2025-09-08T19:56:51,878 writing requirements to py_popgen.egg-info/requires.txt 2025-09-08T19:56:51,878 writing top-level names to py_popgen.egg-info/top_level.txt 2025-09-08T19:56:51,955 reading manifest file 'py_popgen.egg-info/SOURCES.txt' 2025-09-08T19:56:51,960 reading manifest template 'MANIFEST.in' 2025-09-08T19:56:51,972 writing manifest file 'py_popgen.egg-info/SOURCES.txt' 2025-09-08T19:56:51,973 copying pgpipe/test_cython.c -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,975 copying pgpipe/test_cython.pyx -> build/lib.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,977 running build_ext 2025-09-08T19:56:51,984 building 'pgpipe.test_cython' extension 2025-09-08T19:56:51,985 creating build/temp.linux-armv7l-cpython-313/pgpipe 2025-09-08T19:56:51,985 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/python3.13 -c pgpipe/test_cython.c -o build/temp.linux-armv7l-cpython-313/pgpipe/test_cython.o 2025-09-08T19:56:52,356 pgpipe/test_cython.c: In function ‘__pyx_pf_6pgpipe_11test_cython_getAlleleCountArray’: 2025-09-08T19:56:52,358 pgpipe/test_cython.c:2951:17: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2025-09-08T19:56:52,358 2951 | (__pyx_v_d[__pyx_t_5]) = ((__pyx_v_d[__pyx_t_5]) + 1); 2025-09-08T19:56:52,358 | ^ 2025-09-08T19:56:52,361 pgpipe/test_cython.c:2951:43: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2025-09-08T19:56:52,361 2951 | (__pyx_v_d[__pyx_t_5]) = ((__pyx_v_d[__pyx_t_5]) + 1); 2025-09-08T19:56:52,361 | ^ 2025-09-08T19:56:52,369 pgpipe/test_cython.c: In function ‘__pyx_pf_6pgpipe_11test_cython_2getAlleleCountArraySub’: 2025-09-08T19:56:52,371 pgpipe/test_cython.c:3399:17: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2025-09-08T19:56:52,372 3399 | (__pyx_v_d[__pyx_t_8]) = ((__pyx_v_d[__pyx_t_8]) + 1); 2025-09-08T19:56:52,372 | ^ 2025-09-08T19:56:52,375 pgpipe/test_cython.c:3399:43: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2025-09-08T19:56:52,375 3399 | (__pyx_v_d[__pyx_t_8]) = ((__pyx_v_d[__pyx_t_8]) + 1); 2025-09-08T19:56:52,375 | ^ 2025-09-08T19:56:55,559 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-313/pgpipe/test_cython.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-313/pgpipe/test_cython.cpython-313-arm-linux-gnueabihf.so 2025-09-08T19:56:55,677 running build_scripts 2025-09-08T19:56:55,678 creating build/scripts-3.13 2025-09-08T19:56:55,678 copying and adjusting pgpipe/vcf_filter.py -> build/scripts-3.13 2025-09-08T19:56:55,680 copying and adjusting pgpipe/vcf_calc.py -> build/scripts-3.13 2025-09-08T19:56:55,681 copying and adjusting pgpipe/vcf_split.py -> build/scripts-3.13 2025-09-08T19:56:55,682 copying and adjusting pgpipe/vcf_phase.py -> build/scripts-3.13 2025-09-08T19:56:55,683 copying and adjusting pgpipe/four_gamete.py -> build/scripts-3.13 2025-09-08T19:56:55,684 copying and adjusting pgpipe/stat_sampler.py -> build/scripts-3.13 2025-09-08T19:56:55,685 copying and adjusting pgpipe/bed_tasks.py -> build/scripts-3.13 2025-09-08T19:56:55,686 copying and adjusting pgpipe/informative_loci_filter.py -> build/scripts-3.13 2025-09-08T19:56:55,687 copying and adjusting pgpipe/convert.py -> build/scripts-3.13 2025-09-08T19:56:55,687 copying and adjusting pgpipe/vcf_to_ima.py -> build/scripts-3.13 2025-09-08T19:56:55,689 copying and adjusting pgpipe/admixture.py -> build/scripts-3.13 2025-09-08T19:56:55,690 copying and adjusting pgpipe/plink_ld.py -> build/scripts-3.13 2025-09-08T19:56:55,691 copying and adjusting pgpipe/ima3_wrapper.py -> build/scripts-3.13 2025-09-08T19:56:55,692 copying and adjusting pgpipe/eigenstrat_fstats.py -> build/scripts-3.13 2025-09-08T19:56:55,693 copying and adjusting pgpipe/vcf_liftover.py -> build/scripts-3.13 2025-09-08T19:56:55,694 copying and adjusting pgpipe/vcf_utilities.py -> build/scripts-3.13 2025-09-08T19:56:55,695 changing mode of build/scripts-3.13/vcf_filter.py from 644 to 755 2025-09-08T19:56:55,695 changing mode of build/scripts-3.13/vcf_calc.py from 644 to 755 2025-09-08T19:56:55,695 changing mode of build/scripts-3.13/vcf_split.py from 644 to 755 2025-09-08T19:56:55,696 changing mode of build/scripts-3.13/vcf_phase.py from 644 to 755 2025-09-08T19:56:55,696 changing mode of build/scripts-3.13/four_gamete.py from 644 to 755 2025-09-08T19:56:55,696 changing mode of build/scripts-3.13/stat_sampler.py from 644 to 755 2025-09-08T19:56:55,696 changing mode of build/scripts-3.13/bed_tasks.py from 644 to 755 2025-09-08T19:56:55,696 changing mode of build/scripts-3.13/informative_loci_filter.py from 644 to 755 2025-09-08T19:56:55,696 changing mode of build/scripts-3.13/convert.py from 644 to 755 2025-09-08T19:56:55,697 changing mode of build/scripts-3.13/vcf_to_ima.py from 644 to 755 2025-09-08T19:56:55,697 changing mode of build/scripts-3.13/admixture.py from 644 to 755 2025-09-08T19:56:55,697 changing mode of build/scripts-3.13/plink_ld.py from 644 to 755 2025-09-08T19:56:55,697 changing mode of build/scripts-3.13/ima3_wrapper.py from 644 to 755 2025-09-08T19:56:55,697 changing mode of build/scripts-3.13/eigenstrat_fstats.py from 644 to 755 2025-09-08T19:56:55,697 changing mode of build/scripts-3.13/vcf_liftover.py from 644 to 755 2025-09-08T19:56:55,697 changing mode of build/scripts-3.13/vcf_utilities.py from 644 to 755 2025-09-08T19:56:55,774 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-09-08T19:56:55,775 !! 2025-09-08T19:56:55,775 ******************************************************************************** 2025-09-08T19:56:55,775 Please avoid running ``setup.py`` directly. 2025-09-08T19:56:55,775 Instead, use pypa/build, pypa/installer or other 2025-09-08T19:56:55,775 standards-based tools. 2025-09-08T19:56:55,775 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-08T19:56:55,775 or your builds will no longer be supported. 2025-09-08T19:56:55,776 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-09-08T19:56:55,776 ******************************************************************************** 2025-09-08T19:56:55,776 !! 2025-09-08T19:56:55,776 self.initialize_options() 2025-09-08T19:56:55,848 installing to build/bdist.linux-armv7l/wheel 2025-09-08T19:56:55,849 running install 2025-09-08T19:56:55,871 running install_lib 2025-09-08T19:56:55,945 creating build/bdist.linux-armv7l/wheel 2025-09-08T19:56:55,945 creating build/bdist.linux-armv7l/wheel/pgpipe 2025-09-08T19:56:55,946 copying build/lib.linux-armv7l-cpython-313/pgpipe/test_cython.cpython-313-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,947 copying build/lib.linux-armv7l-cpython-313/pgpipe/test_cython.pyx -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,947 copying build/lib.linux-armv7l-cpython-313/pgpipe/test_cython.c -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,949 copying build/lib.linux-armv7l-cpython-313/pgpipe/__init__.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,949 copying build/lib.linux-armv7l-cpython-313/pgpipe/admixtools.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,950 copying build/lib.linux-armv7l-cpython-313/pgpipe/admixture.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,950 copying build/lib.linux-armv7l-cpython-313/pgpipe/argparse_sets.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,951 copying build/lib.linux-armv7l-cpython-313/pgpipe/bcftools.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,951 copying build/lib.linux-armv7l-cpython-313/pgpipe/beagle.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,951 copying build/lib.linux-armv7l-cpython-313/pgpipe/bed_invert.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,952 copying build/lib.linux-armv7l-cpython-313/pgpipe/bed_tasks.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,952 copying build/lib.linux-armv7l-cpython-313/pgpipe/bedtools.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,953 copying build/lib.linux-armv7l-cpython-313/pgpipe/convert.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,953 copying build/lib.linux-armv7l-cpython-313/pgpipe/eigenstrat_fstats.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,954 copying build/lib.linux-armv7l-cpython-313/pgpipe/extend_loci.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,954 copying build/lib.linux-armv7l-cpython-313/pgpipe/fasta.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,954 copying build/lib.linux-armv7l-cpython-313/pgpipe/fasta_utilities.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,955 copying build/lib.linux-armv7l-cpython-313/pgpipe/filter_single_vcf.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,955 copying build/lib.linux-armv7l-cpython-313/pgpipe/four_gamete.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,955 copying build/lib.linux-armv7l-cpython-313/pgpipe/genome_region.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,956 copying build/lib.linux-armv7l-cpython-313/pgpipe/get_nonmissing_chunks.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,956 copying build/lib.linux-armv7l-cpython-313/pgpipe/graph_plotter.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,957 copying build/lib.linux-armv7l-cpython-313/pgpipe/ima3_wrapper.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,957 copying build/lib.linux-armv7l-cpython-313/pgpipe/ima_priors.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,958 copying build/lib.linux-armv7l-cpython-313/pgpipe/ima_to_treemix.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,958 copying build/lib.linux-armv7l-cpython-313/pgpipe/informative_loci_filter.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,958 copying build/lib.linux-armv7l-cpython-313/pgpipe/logging_module.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,959 copying build/lib.linux-armv7l-cpython-313/pgpipe/min_pop_filter.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,959 copying build/lib.linux-armv7l-cpython-313/pgpipe/model.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,959 copying build/lib.linux-armv7l-cpython-313/pgpipe/model_creator.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,960 copying build/lib.linux-armv7l-cpython-313/pgpipe/model_sampler.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,960 copying build/lib.linux-armv7l-cpython-313/pgpipe/parse_functions.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,960 copying build/lib.linux-armv7l-cpython-313/pgpipe/picard.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,961 copying build/lib.linux-armv7l-cpython-313/pgpipe/plink.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,961 copying build/lib.linux-armv7l-cpython-313/pgpipe/plink_ld.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,962 copying build/lib.linux-armv7l-cpython-313/pgpipe/shapeit.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,962 copying build/lib.linux-armv7l-cpython-313/pgpipe/site_stats.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,962 copying build/lib.linux-armv7l-cpython-313/pgpipe/stat_sampler.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,963 copying build/lib.linux-armv7l-cpython-313/pgpipe/subtract_bed.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,963 copying build/lib.linux-armv7l-cpython-313/pgpipe/vcf_calc.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,964 copying build/lib.linux-armv7l-cpython-313/pgpipe/vcf_filter.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,964 copying build/lib.linux-armv7l-cpython-313/pgpipe/vcf_filter_bcftools.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,965 copying build/lib.linux-armv7l-cpython-313/pgpipe/vcf_filter_vcftools.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,965 copying build/lib.linux-armv7l-cpython-313/pgpipe/vcf_liftover.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,966 copying build/lib.linux-armv7l-cpython-313/pgpipe/vcf_phase.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,966 copying build/lib.linux-armv7l-cpython-313/pgpipe/vcf_reader_func.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,967 copying build/lib.linux-armv7l-cpython-313/pgpipe/vcf_ref_to_seq.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,967 copying build/lib.linux-armv7l-cpython-313/pgpipe/vcf_sampler.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,967 copying build/lib.linux-armv7l-cpython-313/pgpipe/vcf_split.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,968 copying build/lib.linux-armv7l-cpython-313/pgpipe/vcf_split_pysam.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,968 copying build/lib.linux-armv7l-cpython-313/pgpipe/vcf_to_ima.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,969 copying build/lib.linux-armv7l-cpython-313/pgpipe/vcf_to_treemix.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,969 copying build/lib.linux-armv7l-cpython-313/pgpipe/vcf_utilities.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,970 copying build/lib.linux-armv7l-cpython-313/pgpipe/vcftools.py -> build/bdist.linux-armv7l/wheel/./pgpipe 2025-09-08T19:56:55,970 running install_egg_info 2025-09-08T19:56:56,046 Copying py_popgen.egg-info to build/bdist.linux-armv7l/wheel/./py_popgen-0.1.2-py3.13.egg-info 2025-09-08T19:56:56,048 running install_scripts 2025-09-08T19:56:56,048 creating build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts 2025-09-08T19:56:56,049 copying build/scripts-3.13/vcf_utilities.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts 2025-09-08T19:56:56,049 copying build/scripts-3.13/vcf_liftover.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts 2025-09-08T19:56:56,050 copying build/scripts-3.13/eigenstrat_fstats.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts 2025-09-08T19:56:56,050 copying build/scripts-3.13/ima3_wrapper.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts 2025-09-08T19:56:56,050 copying build/scripts-3.13/plink_ld.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts 2025-09-08T19:56:56,051 copying build/scripts-3.13/admixture.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts 2025-09-08T19:56:56,051 copying build/scripts-3.13/vcf_to_ima.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts 2025-09-08T19:56:56,052 copying build/scripts-3.13/convert.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts 2025-09-08T19:56:56,052 copying build/scripts-3.13/informative_loci_filter.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts 2025-09-08T19:56:56,053 copying build/scripts-3.13/bed_tasks.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts 2025-09-08T19:56:56,053 copying build/scripts-3.13/stat_sampler.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts 2025-09-08T19:56:56,054 copying build/scripts-3.13/four_gamete.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts 2025-09-08T19:56:56,054 copying build/scripts-3.13/vcf_phase.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts 2025-09-08T19:56:56,055 copying build/scripts-3.13/vcf_split.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts 2025-09-08T19:56:56,055 copying build/scripts-3.13/vcf_calc.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts 2025-09-08T19:56:56,056 copying build/scripts-3.13/vcf_filter.py -> build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts 2025-09-08T19:56:56,056 changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/vcf_utilities.py to 755 2025-09-08T19:56:56,057 changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/vcf_liftover.py to 755 2025-09-08T19:56:56,057 changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/eigenstrat_fstats.py to 755 2025-09-08T19:56:56,057 changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/ima3_wrapper.py to 755 2025-09-08T19:56:56,057 changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/plink_ld.py to 755 2025-09-08T19:56:56,057 changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/admixture.py to 755 2025-09-08T19:56:56,057 changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/vcf_to_ima.py to 755 2025-09-08T19:56:56,057 changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/convert.py to 755 2025-09-08T19:56:56,057 changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/informative_loci_filter.py to 755 2025-09-08T19:56:56,058 changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/bed_tasks.py to 755 2025-09-08T19:56:56,058 changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/stat_sampler.py to 755 2025-09-08T19:56:56,058 changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/four_gamete.py to 755 2025-09-08T19:56:56,058 changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/vcf_phase.py to 755 2025-09-08T19:56:56,058 changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/vcf_split.py to 755 2025-09-08T19:56:56,058 changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/vcf_calc.py to 755 2025-09-08T19:56:56,058 changing mode of build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.data/scripts/vcf_filter.py to 755 2025-09-08T19:56:56,108 creating build/bdist.linux-armv7l/wheel/py_popgen-0.1.2.dist-info/WHEEL 2025-09-08T19:56:56,109 creating '/tmp/pip-wheel-v8464m_f/py_popgen-0.1.2-cp313-cp313-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-09-08T19:56:56,110 adding 'pgpipe/__init__.py' 2025-09-08T19:56:56,112 adding 'pgpipe/admixtools.py' 2025-09-08T19:56:56,113 adding 'pgpipe/admixture.py' 2025-09-08T19:56:56,114 adding 'pgpipe/argparse_sets.py' 2025-09-08T19:56:56,117 adding 'pgpipe/bcftools.py' 2025-09-08T19:56:56,118 adding 'pgpipe/beagle.py' 2025-09-08T19:56:56,119 adding 'pgpipe/bed_invert.py' 2025-09-08T19:56:56,120 adding 'pgpipe/bed_tasks.py' 2025-09-08T19:56:56,121 adding 'pgpipe/bedtools.py' 2025-09-08T19:56:56,123 adding 'pgpipe/convert.py' 2025-09-08T19:56:56,125 adding 'pgpipe/eigenstrat_fstats.py' 2025-09-08T19:56:56,126 adding 'pgpipe/extend_loci.py' 2025-09-08T19:56:56,126 adding 'pgpipe/fasta.py' 2025-09-08T19:56:56,127 adding 'pgpipe/fasta_utilities.py' 2025-09-08T19:56:56,128 adding 'pgpipe/filter_single_vcf.py' 2025-09-08T19:56:56,132 adding 'pgpipe/four_gamete.py' 2025-09-08T19:56:56,134 adding 'pgpipe/genome_region.py' 2025-09-08T19:56:56,136 adding 'pgpipe/get_nonmissing_chunks.py' 2025-09-08T19:56:56,137 adding 'pgpipe/graph_plotter.py' 2025-09-08T19:56:56,138 adding 'pgpipe/ima3_wrapper.py' 2025-09-08T19:56:56,139 adding 'pgpipe/ima_priors.py' 2025-09-08T19:56:56,139 adding 'pgpipe/ima_to_treemix.py' 2025-09-08T19:56:56,141 adding 'pgpipe/informative_loci_filter.py' 2025-09-08T19:56:56,142 adding 'pgpipe/logging_module.py' 2025-09-08T19:56:56,142 adding 'pgpipe/min_pop_filter.py' 2025-09-08T19:56:56,144 adding 'pgpipe/model.py' 2025-09-08T19:56:56,145 adding 'pgpipe/model_creator.py' 2025-09-08T19:56:56,147 adding 'pgpipe/model_sampler.py' 2025-09-08T19:56:56,148 adding 'pgpipe/parse_functions.py' 2025-09-08T19:56:56,149 adding 'pgpipe/picard.py' 2025-09-08T19:56:56,151 adding 'pgpipe/plink.py' 2025-09-08T19:56:56,153 adding 'pgpipe/plink_ld.py' 2025-09-08T19:56:56,154 adding 'pgpipe/shapeit.py' 2025-09-08T19:56:56,155 adding 'pgpipe/site_stats.py' 2025-09-08T19:56:56,157 adding 'pgpipe/stat_sampler.py' 2025-09-08T19:56:56,158 adding 'pgpipe/subtract_bed.py' 2025-09-08T19:56:56,189 adding 'pgpipe/test_cython.c' 2025-09-08T19:56:56,231 adding 'pgpipe/test_cython.cpython-313-arm-linux-gnueabihf.so' 2025-09-08T19:56:56,233 adding 'pgpipe/test_cython.pyx' 2025-09-08T19:56:56,236 adding 'pgpipe/vcf_calc.py' 2025-09-08T19:56:56,239 adding 'pgpipe/vcf_filter.py' 2025-09-08T19:56:56,243 adding 'pgpipe/vcf_filter_bcftools.py' 2025-09-08T19:56:56,246 adding 'pgpipe/vcf_filter_vcftools.py' 2025-09-08T19:56:56,247 adding 'pgpipe/vcf_liftover.py' 2025-09-08T19:56:56,251 adding 'pgpipe/vcf_phase.py' 2025-09-08T19:56:56,254 adding 'pgpipe/vcf_reader_func.py' 2025-09-08T19:56:56,256 adding 'pgpipe/vcf_ref_to_seq.py' 2025-09-08T19:56:56,258 adding 'pgpipe/vcf_sampler.py' 2025-09-08T19:56:56,260 adding 'pgpipe/vcf_split.py' 2025-09-08T19:56:56,262 adding 'pgpipe/vcf_split_pysam.py' 2025-09-08T19:56:56,265 adding 'pgpipe/vcf_to_ima.py' 2025-09-08T19:56:56,266 adding 'pgpipe/vcf_to_treemix.py' 2025-09-08T19:56:56,268 adding 'pgpipe/vcf_utilities.py' 2025-09-08T19:56:56,270 adding 'pgpipe/vcftools.py' 2025-09-08T19:56:56,272 adding 'py_popgen-0.1.2.data/scripts/admixture.py' 2025-09-08T19:56:56,274 adding 'py_popgen-0.1.2.data/scripts/bed_tasks.py' 2025-09-08T19:56:56,275 adding 'py_popgen-0.1.2.data/scripts/convert.py' 2025-09-08T19:56:56,277 adding 'py_popgen-0.1.2.data/scripts/eigenstrat_fstats.py' 2025-09-08T19:56:56,282 adding 'py_popgen-0.1.2.data/scripts/four_gamete.py' 2025-09-08T19:56:56,283 adding 'py_popgen-0.1.2.data/scripts/ima3_wrapper.py' 2025-09-08T19:56:56,284 adding 'py_popgen-0.1.2.data/scripts/informative_loci_filter.py' 2025-09-08T19:56:56,286 adding 'py_popgen-0.1.2.data/scripts/plink_ld.py' 2025-09-08T19:56:56,289 adding 'py_popgen-0.1.2.data/scripts/stat_sampler.py' 2025-09-08T19:56:56,291 adding 'py_popgen-0.1.2.data/scripts/vcf_calc.py' 2025-09-08T19:56:56,295 adding 'py_popgen-0.1.2.data/scripts/vcf_filter.py' 2025-09-08T19:56:56,296 adding 'py_popgen-0.1.2.data/scripts/vcf_liftover.py' 2025-09-08T19:56:56,300 adding 'py_popgen-0.1.2.data/scripts/vcf_phase.py' 2025-09-08T19:56:56,303 adding 'py_popgen-0.1.2.data/scripts/vcf_split.py' 2025-09-08T19:56:56,306 adding 'py_popgen-0.1.2.data/scripts/vcf_to_ima.py' 2025-09-08T19:56:56,308 adding 'py_popgen-0.1.2.data/scripts/vcf_utilities.py' 2025-09-08T19:56:56,309 adding 'py_popgen-0.1.2.dist-info/METADATA' 2025-09-08T19:56:56,309 adding 'py_popgen-0.1.2.dist-info/WHEEL' 2025-09-08T19:56:56,309 adding 'py_popgen-0.1.2.dist-info/top_level.txt' 2025-09-08T19:56:56,311 adding 'py_popgen-0.1.2.dist-info/RECORD' 2025-09-08T19:56:56,312 removing build/bdist.linux-armv7l/wheel 2025-09-08T19:56:56,460 Building wheel for py-popgen (setup.py): finished with status 'done' 2025-09-08T19:56:56,465 Created wheel for py-popgen: filename=py_popgen-0.1.2-cp313-cp313-linux_armv7l.whl size=401276 sha256=681b33a59c729e6e9a8d6628eb159f7e85d65e08b6ef87d5a6ff47f0fd2285fb 2025-09-08T19:56:56,466 Stored in directory: /tmp/pip-ephem-wheel-cache-17dgu05t/wheels/88/c6/9e/b77bee3052a4bba5308d5ad2289b304f54ce22e85d5b03b322 2025-09-08T19:56:56,475 Successfully built py-popgen 2025-09-08T19:56:56,477 Removed build tracker: '/tmp/pip-build-tracker-u7klqi5e'