2023-11-06T19:46:01,935 Created temporary directory: /tmp/pip-build-tracker-5a1so2_k 2023-11-06T19:46:01,936 Initialized build tracking at /tmp/pip-build-tracker-5a1so2_k 2023-11-06T19:46:01,937 Created build tracker: /tmp/pip-build-tracker-5a1so2_k 2023-11-06T19:46:01,937 Entered build tracker: /tmp/pip-build-tracker-5a1so2_k 2023-11-06T19:46:01,938 Created temporary directory: /tmp/pip-wheel-lw607g9z 2023-11-06T19:46:01,941 Created temporary directory: /tmp/pip-ephem-wheel-cache-si1hcr2t 2023-11-06T19:46:01,963 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-11-06T19:46:01,967 2 location(s) to search for versions of amptk: 2023-11-06T19:46:01,967 * https://pypi.org/simple/amptk/ 2023-11-06T19:46:01,967 * https://www.piwheels.org/simple/amptk/ 2023-11-06T19:46:01,968 Fetching project page and analyzing links: https://pypi.org/simple/amptk/ 2023-11-06T19:46:01,969 Getting page https://pypi.org/simple/amptk/ 2023-11-06T19:46:01,970 Found index url https://pypi.org/simple/ 2023-11-06T19:46:02,190 Fetched page https://pypi.org/simple/amptk/ as application/vnd.pypi.simple.v1+json 2023-11-06T19:46:02,195 Skipping link: No binaries permitted for amptk: https://files.pythonhosted.org/packages/6f/34/5ca4622b12ca9815635d87f325b9190fe542592142dc9f9c940ee797be1b/amptk-1.3.0-py2-none-any.whl (from https://pypi.org/simple/amptk/) (requires-python:>=2.7.0) 2023-11-06T19:46:02,195 Skipping link: No binaries permitted for amptk: https://files.pythonhosted.org/packages/c8/87/34c1a064653f16cc2ef7d687a7f1c35ebc5bf25afe6f906fa5463e5c54fa/amptk-1.3.0-py2.py3-none-any.whl (from https://pypi.org/simple/amptk/) (requires-python:>=2.7.0) 2023-11-06T19:46:02,196 Found link https://files.pythonhosted.org/packages/cf/56/2d5affae81bdf311d7d23faa4758ad387d5fd572ac503a5c90897b339796/amptk-1.3.0.tar.gz (from https://pypi.org/simple/amptk/) (requires-python:>=2.7.0), version: 1.3.0 2023-11-06T19:46:02,197 Skipping link: No binaries permitted for amptk: https://files.pythonhosted.org/packages/79/90/56fd4e5542392026e884ed2c47914fad850f7747e5632c1b6bbe4315e942/amptk-1.4.0-py2.py3-none-any.whl (from https://pypi.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*, <4) 2023-11-06T19:46:02,198 Found link https://files.pythonhosted.org/packages/d6/85/35dbea394dc7414c23e2eae6b05658b64705fe98e9126b311961108702c1/amptk-1.4.0.tar.gz (from https://pypi.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*, <4), version: 1.4.0 2023-11-06T19:46:02,199 Skipping link: No binaries permitted for amptk: https://files.pythonhosted.org/packages/03/51/4537d37e9f48889e17b7bc5e52dc369a785f2d97542c06ceafd808f76a1b/amptk-1.4.1-py2.py3-none-any.whl (from https://pypi.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*, <4) 2023-11-06T19:46:02,200 Found link https://files.pythonhosted.org/packages/57/06/2a7e9d73de4c33f1b3d2b09dc51b221da5c9efb77433c19c61b555040470/amptk-1.4.1.tar.gz (from https://pypi.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*, <4), version: 1.4.1 2023-11-06T19:46:02,201 Skipping link: No binaries permitted for amptk: https://files.pythonhosted.org/packages/91/79/4a6582435ef35f66de33becafaade0caef9af42be9bb241775b44a599c50/amptk-1.4.2-py2.py3-none-any.whl (from https://pypi.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*, <4) 2023-11-06T19:46:02,203 Found link https://files.pythonhosted.org/packages/d5/7b/b0e7232b8f180d83fc1f2d8e9c3639a43d7da52c84600a2bd70341ab1d7e/amptk-1.4.2.tar.gz (from https://pypi.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*, <4), version: 1.4.2 2023-11-06T19:46:02,203 Skipping link: No binaries permitted for amptk: https://files.pythonhosted.org/packages/cb/cc/bb79cd3ec020d571560a26b84975e414c2de200a3ba27dab9f1cf35990cc/amptk-1.5.0-py2.py3-none-any.whl (from https://pypi.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*, <4) 2023-11-06T19:46:02,205 Found link https://files.pythonhosted.org/packages/7a/de/454cf109ce14c3fd2435860231a87e157ccc2e59f237e052ae9869568880/amptk-1.5.0.tar.gz (from https://pypi.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*, <4), version: 1.5.0 2023-11-06T19:46:02,205 Skipping link: No binaries permitted for amptk: https://files.pythonhosted.org/packages/c8/b3/b1839528e3602062043ba88c91b6eb8a7f8713a3d1e80699677d90c38baa/amptk-1.5.1-py2.py3-none-any.whl (from https://pypi.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*, <3.8) 2023-11-06T19:46:02,207 Link requires a different Python (3.11.2 not in: '>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*, <3.8'): https://files.pythonhosted.org/packages/8d/cc/5b4adb595d64c5dfb6093e98a233a9dd9486ac0c9661dfd47e9f74c089e9/amptk-1.5.1.tar.gz (from https://pypi.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*, <3.8) 2023-11-06T19:46:02,207 Skipping link: 1.5.1 Requires-Python >=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*, <3.8: https://files.pythonhosted.org/packages/8d/cc/5b4adb595d64c5dfb6093e98a233a9dd9486ac0c9661dfd47e9f74c089e9/amptk-1.5.1.tar.gz (from https://pypi.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*, <3.8) 2023-11-06T19:46:02,208 Skipping link: No binaries permitted for amptk: https://files.pythonhosted.org/packages/f5/e0/a138b50ea63c83718fa62f51a5710fb03aea5fac478121d4fcb56c7660b7/amptk-1.5.2-py3-none-any.whl (from https://pypi.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*, <3.8) 2023-11-06T19:46:02,208 Link requires a different Python (3.11.2 not in: '>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*, <3.8'): https://files.pythonhosted.org/packages/64/32/bc98a54a9d75211351c1ccdf62d8b827866a43c6340ee921d5716ffbd572/amptk-1.5.2.tar.gz (from https://pypi.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*, <3.8) 2023-11-06T19:46:02,209 Skipping link: 1.5.2 Requires-Python >=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*, <3.8: https://files.pythonhosted.org/packages/64/32/bc98a54a9d75211351c1ccdf62d8b827866a43c6340ee921d5716ffbd572/amptk-1.5.2.tar.gz (from https://pypi.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*, <3.8) 2023-11-06T19:46:02,209 Skipping link: No binaries permitted for amptk: https://files.pythonhosted.org/packages/ea/00/d81c9bee0879366f5b3b47266608893062da2956cb48480985d1ff7ae522/amptk-1.5.3-py3-none-any.whl (from https://pypi.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*) 2023-11-06T19:46:02,211 Found link https://files.pythonhosted.org/packages/71/61/907c876d48777630aee0fa84ddab34a024fd59355c10f8a99cfab0c0e1dd/amptk-1.5.3.tar.gz (from https://pypi.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*), version: 1.5.3 2023-11-06T19:46:02,211 Skipping link: No binaries permitted for amptk: https://files.pythonhosted.org/packages/86/78/6d81364da40abd0a3e3c8d05b7926d725bb11f66a9a1fa85e253125e18fa/amptk-1.5.4-py3-none-any.whl (from https://pypi.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*) 2023-11-06T19:46:02,213 Found link https://files.pythonhosted.org/packages/57/ea/be2bde6a861e1fc7557b509e44ecae291f7bef60d72a26fe4e724161c584/amptk-1.5.4.tar.gz (from https://pypi.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*), version: 1.5.4 2023-11-06T19:46:02,213 Skipping link: No binaries permitted for amptk: https://files.pythonhosted.org/packages/05/cf/e22a910d9dc0182b83b71a00e7b67f8a6b3d2f1cdda63c06fbcc3c190dea/amptk-1.5.5-py3-none-any.whl (from https://pypi.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*) 2023-11-06T19:46:02,215 Found link https://files.pythonhosted.org/packages/35/c5/71fcf47afecda9dbb55c02d2753f26f43aca1d1fa3fe34eec2b3a55911a4/amptk-1.5.5.tar.gz (from https://pypi.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*), version: 1.5.5 2023-11-06T19:46:02,215 Skipping link: No binaries permitted for amptk: https://files.pythonhosted.org/packages/cb/9a/344a26e92830900ed2319d4263f93a9b2344fb751680da842def9bd8bc21/amptk-1.6.0-py3-none-any.whl (from https://pypi.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*) 2023-11-06T19:46:02,217 Found link https://files.pythonhosted.org/packages/46/ca/ecef4d474a439bf0f63335d3516adc82572484c1878d7c003e5add611e95/amptk-1.6.0.tar.gz (from https://pypi.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*), version: 1.6.0 2023-11-06T19:46:02,217 Fetching project page and analyzing links: https://www.piwheels.org/simple/amptk/ 2023-11-06T19:46:02,218 Getting page https://www.piwheels.org/simple/amptk/ 2023-11-06T19:46:02,219 Found index url https://www.piwheels.org/simple/ 2023-11-06T19:46:02,388 Fetched page https://www.piwheels.org/simple/amptk/ as text/html 2023-11-06T19:46:02,392 Skipping link: No binaries permitted for amptk: https://www.piwheels.org/simple/amptk/amptk-1.5.5-py3-none-any.whl#sha256=b2c92138f1dc935fa86eeae466478e2e4d499bd596e9a07a91c8efe55aa9abe3 (from https://www.piwheels.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*) 2023-11-06T19:46:02,393 Skipping link: No binaries permitted for amptk: https://www.piwheels.org/simple/amptk/amptk-1.5.4-py3-none-any.whl#sha256=30dea724e9e77667c7f0b80f3312f92af219a0090ab4035ddb839658abb897a4 (from https://www.piwheels.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*) 2023-11-06T19:46:02,394 Skipping link: No binaries permitted for amptk: https://www.piwheels.org/simple/amptk/amptk-1.5.3-py3-none-any.whl#sha256=c0ceab7c24b276ab3d24602c264b0e6821cdbb5501152543d914f4b6f19cffeb (from https://www.piwheels.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*) 2023-11-06T19:46:02,394 Skipping link: No binaries permitted for amptk: https://www.piwheels.org/simple/amptk/amptk-1.5.2-py3-none-any.whl#sha256=dbe2da7f1d918a5205c2d629da87d69c2e2dd59f8da1c02f0f1a81953617a910 (from https://www.piwheels.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*, <3.8) 2023-11-06T19:46:02,395 Skipping link: No binaries permitted for amptk: https://www.piwheels.org/simple/amptk/amptk-1.5.1-py2.py3-none-any.whl#sha256=3b78af6b110512d4aee660433a3abf41c5edfed2df26458dddba9684e1262e51 (from https://www.piwheels.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*, <3.8) 2023-11-06T19:46:02,395 Skipping link: No binaries permitted for amptk: https://www.piwheels.org/simple/amptk/amptk-1.5.0-py2.py3-none-any.whl#sha256=3de21ef89f2b5ef3820b3a60e623177ccf1e6d2036a0097245a6d58de4ce6f77 (from https://www.piwheels.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*, <4) 2023-11-06T19:46:02,396 Skipping link: No binaries permitted for amptk: https://www.piwheels.org/simple/amptk/amptk-1.4.2-py2.py3-none-any.whl#sha256=6269e5d4c32d93d0f99446afab777ded0ae4b4ce2a1eef628acb16b36e237209 (from https://www.piwheels.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*, <4) 2023-11-06T19:46:02,396 Skipping link: No binaries permitted for amptk: https://www.piwheels.org/simple/amptk/amptk-1.4.1-py2.py3-none-any.whl#sha256=1205d11db04015915cefe912d7f4caf0c0a62c30628c9864ac56ffb6335717f5 (from https://www.piwheels.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*, <4) 2023-11-06T19:46:02,397 Skipping link: No binaries permitted for amptk: https://www.piwheels.org/simple/amptk/amptk-1.4.0-py2.py3-none-any.whl#sha256=8266c953d249d11e5c2623795bc2b90e1326dabe5710673aadd421b8a0c047eb (from https://www.piwheels.org/simple/amptk/) (requires-python:>=2.7.0, !=3.0.*, !=3.1.*, !=3.2.*, <4) 2023-11-06T19:46:02,397 Skipping link: No binaries permitted for amptk: https://www.piwheels.org/simple/amptk/amptk-1.3.0-py3-none-any.whl#sha256=d4b626c7af06d0dfdb92e6f0ea0f04f31eb30e7268adaa467cb50de59415a6cd (from https://www.piwheels.org/simple/amptk/) (requires-python:>=2.7.0) 2023-11-06T19:46:02,398 Skipping link: not a file: https://www.piwheels.org/simple/amptk/ 2023-11-06T19:46:02,399 Skipping link: not a file: https://pypi.org/simple/amptk/ 2023-11-06T19:46:02,419 Given no hashes to check 1 links for project 'amptk': discarding no candidates 2023-11-06T19:46:02,439 Collecting amptk==1.6.0 2023-11-06T19:46:02,441 Created temporary directory: /tmp/pip-unpack-vlhq_qgi 2023-11-06T19:46:02,681 Downloading amptk-1.6.0.tar.gz (2.1 MB) 2023-11-06T19:46:03,584 Added amptk==1.6.0 from https://files.pythonhosted.org/packages/46/ca/ecef4d474a439bf0f63335d3516adc82572484c1878d7c003e5add611e95/amptk-1.6.0.tar.gz to build tracker '/tmp/pip-build-tracker-5a1so2_k' 2023-11-06T19:46:03,586 Running setup.py (path:/tmp/pip-wheel-lw607g9z/amptk_a0937fbc191c49829b82cc2eb4f280e6/setup.py) egg_info for package amptk 2023-11-06T19:46:03,587 Created temporary directory: /tmp/pip-pip-egg-info-80r8koov 2023-11-06T19:46:03,588 Preparing metadata (setup.py): started 2023-11-06T19:46:03,590 Running command python setup.py egg_info 2023-11-06T19:46:04,616 running egg_info 2023-11-06T19:46:04,617 creating /tmp/pip-pip-egg-info-80r8koov/amptk.egg-info 2023-11-06T19:46:04,641 writing /tmp/pip-pip-egg-info-80r8koov/amptk.egg-info/PKG-INFO 2023-11-06T19:46:04,645 writing dependency_links to /tmp/pip-pip-egg-info-80r8koov/amptk.egg-info/dependency_links.txt 2023-11-06T19:46:04,646 writing entry points to /tmp/pip-pip-egg-info-80r8koov/amptk.egg-info/entry_points.txt 2023-11-06T19:46:04,647 writing requirements to /tmp/pip-pip-egg-info-80r8koov/amptk.egg-info/requires.txt 2023-11-06T19:46:04,648 writing top-level names to /tmp/pip-pip-egg-info-80r8koov/amptk.egg-info/top_level.txt 2023-11-06T19:46:04,650 writing manifest file '/tmp/pip-pip-egg-info-80r8koov/amptk.egg-info/SOURCES.txt' 2023-11-06T19:46:04,751 reading manifest file '/tmp/pip-pip-egg-info-80r8koov/amptk.egg-info/SOURCES.txt' 2023-11-06T19:46:04,753 reading manifest template 'MANIFEST.in' 2023-11-06T19:46:04,758 adding license file 'LICENSE.md' 2023-11-06T19:46:04,762 writing manifest file '/tmp/pip-pip-egg-info-80r8koov/amptk.egg-info/SOURCES.txt' 2023-11-06T19:46:04,870 Preparing metadata (setup.py): finished with status 'done' 2023-11-06T19:46:04,874 Source in /tmp/pip-wheel-lw607g9z/amptk_a0937fbc191c49829b82cc2eb4f280e6 has version 1.6.0, which satisfies requirement amptk==1.6.0 from https://files.pythonhosted.org/packages/46/ca/ecef4d474a439bf0f63335d3516adc82572484c1878d7c003e5add611e95/amptk-1.6.0.tar.gz 2023-11-06T19:46:04,875 Removed amptk==1.6.0 from https://files.pythonhosted.org/packages/46/ca/ecef4d474a439bf0f63335d3516adc82572484c1878d7c003e5add611e95/amptk-1.6.0.tar.gz from build tracker '/tmp/pip-build-tracker-5a1so2_k' 2023-11-06T19:46:04,882 Created temporary directory: /tmp/pip-unpack-kfj1kh5d 2023-11-06T19:46:04,883 Created temporary directory: /tmp/pip-unpack-s6mbeiqf 2023-11-06T19:46:04,896 Building wheels for collected packages: amptk 2023-11-06T19:46:04,900 Created temporary directory: /tmp/pip-wheel-bg84svs2 2023-11-06T19:46:04,901 Building wheel for amptk (setup.py): started 2023-11-06T19:46:04,902 Destination directory: /tmp/pip-wheel-bg84svs2 2023-11-06T19:46:04,903 Running command python setup.py bdist_wheel 2023-11-06T19:46:05,890 running bdist_wheel 2023-11-06T19:46:05,984 running build 2023-11-06T19:46:05,985 running build_py 2023-11-06T19:46:06,012 creating build 2023-11-06T19:46:06,012 creating build/lib 2023-11-06T19:46:06,013 creating build/lib/amptk 2023-11-06T19:46:06,014 copying amptk/__init__.py -> build/lib/amptk 2023-11-06T19:46:06,016 copying amptk/process_illumina_folder.py -> build/lib/amptk 2023-11-06T19:46:06,018 copying amptk/pybam.py -> build/lib/amptk 2023-11-06T19:46:06,022 copying amptk/__version__.py -> build/lib/amptk 2023-11-06T19:46:06,023 copying amptk/process_illumina2.py -> build/lib/amptk 2023-11-06T19:46:06,026 copying amptk/unoise2.py -> build/lib/amptk 2023-11-06T19:46:06,028 copying amptk/keep_samples.py -> build/lib/amptk 2023-11-06T19:46:06,030 copying amptk/amptk.py -> build/lib/amptk 2023-11-06T19:46:06,033 copying amptk/process_ont.py -> build/lib/amptk 2023-11-06T19:46:06,036 copying amptk/remove_samples.py -> build/lib/amptk 2023-11-06T19:46:06,037 copying amptk/process_pacbio.py -> build/lib/amptk 2023-11-06T19:46:06,040 copying amptk/barcode_rarify.py -> build/lib/amptk 2023-11-06T19:46:06,041 copying amptk/lulu.py -> build/lib/amptk 2023-11-06T19:46:06,043 copying amptk/OTU_cluster.py -> build/lib/amptk 2023-11-06T19:46:06,046 copying amptk/OTU_cluster_ref.py -> build/lib/amptk 2023-11-06T19:46:06,048 copying amptk/dada2_pacbio.py -> build/lib/amptk 2023-11-06T19:46:06,051 copying amptk/fastq2sra.py -> build/lib/amptk 2023-11-06T19:46:06,054 copying amptk/process_illumina_raw.py -> build/lib/amptk 2023-11-06T19:46:06,056 copying amptk/get_barcode_counts.py -> build/lib/amptk 2023-11-06T19:46:06,059 copying amptk/dada2.py -> build/lib/amptk 2023-11-06T19:46:06,062 copying amptk/stackedBarGraph.py -> build/lib/amptk 2023-11-06T19:46:06,064 copying amptk/parse_adonis.py -> build/lib/amptk 2023-11-06T19:46:06,066 copying amptk/stats.py -> build/lib/amptk 2023-11-06T19:46:06,069 copying amptk/extract_region.py -> build/lib/amptk 2023-11-06T19:46:06,072 copying amptk/filter.py -> build/lib/amptk 2023-11-06T19:46:06,075 copying amptk/info.py -> build/lib/amptk 2023-11-06T19:46:06,078 copying amptk/csv2heatmap.py -> build/lib/amptk 2023-11-06T19:46:06,080 copying amptk/summarize_taxonomy.py -> build/lib/amptk 2023-11-06T19:46:06,082 copying amptk/collapse_taxonomy.py -> build/lib/amptk 2023-11-06T19:46:06,083 copying amptk/assign_taxonomy.py -> build/lib/amptk 2023-11-06T19:46:06,086 copying amptk/heatmap.py -> build/lib/amptk 2023-11-06T19:46:06,088 copying amptk/install.py -> build/lib/amptk 2023-11-06T19:46:06,090 copying amptk/drop.py -> build/lib/amptk 2023-11-06T19:46:06,092 copying amptk/unoise3.py -> build/lib/amptk 2023-11-06T19:46:06,094 copying amptk/ont_cluster.py -> build/lib/amptk 2023-11-06T19:46:06,096 copying amptk/process_ion.py -> build/lib/amptk 2023-11-06T19:46:06,098 copying amptk/merge_metadata.py -> build/lib/amptk 2023-11-06T19:46:06,101 copying amptk/funguild.py -> build/lib/amptk 2023-11-06T19:46:06,103 copying amptk/amptklib.py -> build/lib/amptk 2023-11-06T19:46:06,106 running egg_info 2023-11-06T19:46:06,162 writing amptk.egg-info/PKG-INFO 2023-11-06T19:46:06,165 writing dependency_links to amptk.egg-info/dependency_links.txt 2023-11-06T19:46:06,166 writing entry points to amptk.egg-info/entry_points.txt 2023-11-06T19:46:06,168 writing requirements to amptk.egg-info/requires.txt 2023-11-06T19:46:06,169 writing top-level names to amptk.egg-info/top_level.txt 2023-11-06T19:46:06,196 reading manifest file 'amptk.egg-info/SOURCES.txt' 2023-11-06T19:46:06,200 reading manifest template 'MANIFEST.in' 2023-11-06T19:46:06,204 adding license file 'LICENSE.md' 2023-11-06T19:46:06,208 writing manifest file 'amptk.egg-info/SOURCES.txt' 2023-11-06T19:46:06,211 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'amptk.DB' is absent from the `packages` configuration. 2023-11-06T19:46:06,212 !! 2023-11-06T19:46:06,213 ******************************************************************************** 2023-11-06T19:46:06,213 ############################ 2023-11-06T19:46:06,214 # Package would be ignored # 2023-11-06T19:46:06,214 ############################ 2023-11-06T19:46:06,215 Python recognizes 'amptk.DB' as an importable package[^1], 2023-11-06T19:46:06,215 but it is absent from setuptools' `packages` configuration. 2023-11-06T19:46:06,216 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-06T19:46:06,217 package, please make sure that 'amptk.DB' is explicitly added 2023-11-06T19:46:06,217 to the `packages` configuration field. 2023-11-06T19:46:06,218 Alternatively, you can also rely on setuptools' discovery methods 2023-11-06T19:46:06,219 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-06T19:46:06,219 instead of `find_packages(...)`/`find:`). 2023-11-06T19:46:06,220 You can read more about "package discovery" on setuptools documentation page: 2023-11-06T19:46:06,222 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-06T19:46:06,222 If you don't want 'amptk.DB' to be distributed and are 2023-11-06T19:46:06,223 already explicitly excluding 'amptk.DB' via 2023-11-06T19:46:06,223 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-06T19:46:06,223 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-06T19:46:06,224 combination with a more fine grained `package-data` configuration. 2023-11-06T19:46:06,225 You can read more about "package data files" on setuptools documentation page: 2023-11-06T19:46:06,226 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-06T19:46:06,228 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-06T19:46:06,228 even if it does not contain any `.py` files. 2023-11-06T19:46:06,229 On the other hand, currently there is no concept of package data 2023-11-06T19:46:06,229 directory, all directories are treated like packages. 2023-11-06T19:46:06,229 ******************************************************************************** 2023-11-06T19:46:06,230 !! 2023-11-06T19:46:06,231 check.warn(importable) 2023-11-06T19:46:06,231 copying amptk/check_version.R -> build/lib/amptk 2023-11-06T19:46:06,232 copying amptk/dada2_pipeline_nofilt.R -> build/lib/amptk 2023-11-06T19:46:06,232 copying amptk/downloads.json -> build/lib/amptk 2023-11-06T19:46:06,233 copying amptk/downloadsv1.6.0.json -> build/lib/amptk 2023-11-06T19:46:06,233 copying amptk/phyloseq_nmds.R -> build/lib/amptk 2023-11-06T19:46:06,234 copying amptk/phyloseq_nmds_indicator.R -> build/lib/amptk 2023-11-06T19:46:06,234 copying amptk/primers.json -> build/lib/amptk 2023-11-06T19:46:06,235 copying amptk/runLULU.R -> build/lib/amptk 2023-11-06T19:46:06,235 creating build/lib/amptk/DB 2023-11-06T19:46:06,236 copying amptk/DB/amptk_mock1.fa -> build/lib/amptk/DB 2023-11-06T19:46:06,236 copying amptk/DB/amptk_mock2.fa -> build/lib/amptk/DB 2023-11-06T19:46:06,239 copying amptk/DB/amptk_mock3.fa -> build/lib/amptk/DB 2023-11-06T19:46:06,241 copying amptk/DB/amptk_synmock.fa -> build/lib/amptk/DB 2023-11-06T19:46:06,243 copying amptk/DB/ioncode_barcodes.fa -> build/lib/amptk/DB 2023-11-06T19:46:06,245 copying amptk/DB/ionxpress_barcodes.fa -> build/lib/amptk/DB 2023-11-06T19:46:06,249 running build_scripts 2023-11-06T19:46:06,249 creating build/scripts-3.11 2023-11-06T19:46:06,250 copying and adjusting scripts/bold2utax.py -> build/scripts-3.11 2023-11-06T19:46:06,253 copying and adjusting scripts/amptk_synthetic_mock.py -> build/scripts-3.11 2023-11-06T19:46:06,255 changing mode of build/scripts-3.11/bold2utax.py from 644 to 755 2023-11-06T19:46:06,255 changing mode of build/scripts-3.11/amptk_synthetic_mock.py from 644 to 755 2023-11-06T19:46:06,279 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-11-06T19:46:06,280 !! 2023-11-06T19:46:06,281 ******************************************************************************** 2023-11-06T19:46:06,281 Please avoid running ``setup.py`` directly. 2023-11-06T19:46:06,282 Instead, use pypa/build, pypa/installer or other 2023-11-06T19:46:06,282 standards-based tools. 2023-11-06T19:46:06,284 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-11-06T19:46:06,284 ******************************************************************************** 2023-11-06T19:46:06,285 !! 2023-11-06T19:46:06,286 self.initialize_options() 2023-11-06T19:46:06,304 installing to build/bdist.linux-armv7l/wheel 2023-11-06T19:46:06,305 running install 2023-11-06T19:46:06,328 running install_lib 2023-11-06T19:46:06,353 creating build/bdist.linux-armv7l 2023-11-06T19:46:06,354 creating build/bdist.linux-armv7l/wheel 2023-11-06T19:46:06,356 creating build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,357 copying build/lib/amptk/__init__.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,359 copying build/lib/amptk/process_illumina_folder.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,362 copying build/lib/amptk/runLULU.R -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,363 copying build/lib/amptk/pybam.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,366 copying build/lib/amptk/__version__.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,368 copying build/lib/amptk/process_illumina2.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,370 copying build/lib/amptk/unoise2.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,372 copying build/lib/amptk/keep_samples.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,374 copying build/lib/amptk/amptk.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,377 copying build/lib/amptk/primers.json -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,379 copying build/lib/amptk/process_ont.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,381 copying build/lib/amptk/remove_samples.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,383 copying build/lib/amptk/process_pacbio.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,385 copying build/lib/amptk/barcode_rarify.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,387 copying build/lib/amptk/lulu.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,389 copying build/lib/amptk/OTU_cluster.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,391 copying build/lib/amptk/downloadsv1.6.0.json -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,393 copying build/lib/amptk/check_version.R -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,395 copying build/lib/amptk/OTU_cluster_ref.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,397 copying build/lib/amptk/dada2_pacbio.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,400 copying build/lib/amptk/fastq2sra.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,403 copying build/lib/amptk/dada2_pipeline_nofilt.R -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,405 copying build/lib/amptk/process_illumina_raw.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,407 copying build/lib/amptk/get_barcode_counts.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,409 copying build/lib/amptk/downloads.json -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,410 copying build/lib/amptk/dada2.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,413 copying build/lib/amptk/stackedBarGraph.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,415 copying build/lib/amptk/parse_adonis.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,417 copying build/lib/amptk/stats.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,419 copying build/lib/amptk/extract_region.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,422 copying build/lib/amptk/filter.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,425 copying build/lib/amptk/info.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,426 copying build/lib/amptk/phyloseq_nmds_indicator.R -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,429 copying build/lib/amptk/csv2heatmap.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,431 copying build/lib/amptk/summarize_taxonomy.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,433 copying build/lib/amptk/collapse_taxonomy.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,435 copying build/lib/amptk/assign_taxonomy.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,438 copying build/lib/amptk/heatmap.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,440 copying build/lib/amptk/install.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,443 copying build/lib/amptk/drop.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,445 creating build/bdist.linux-armv7l/wheel/amptk/DB 2023-11-06T19:46:06,446 copying build/lib/amptk/DB/amptk_synmock.fa -> build/bdist.linux-armv7l/wheel/amptk/DB 2023-11-06T19:46:06,448 copying build/lib/amptk/DB/amptk_mock3.fa -> build/bdist.linux-armv7l/wheel/amptk/DB 2023-11-06T19:46:06,450 copying build/lib/amptk/DB/ionxpress_barcodes.fa -> build/bdist.linux-armv7l/wheel/amptk/DB 2023-11-06T19:46:06,452 copying build/lib/amptk/DB/amptk_mock1.fa -> build/bdist.linux-armv7l/wheel/amptk/DB 2023-11-06T19:46:06,454 copying build/lib/amptk/DB/amptk_mock2.fa -> build/bdist.linux-armv7l/wheel/amptk/DB 2023-11-06T19:46:06,456 copying build/lib/amptk/DB/ioncode_barcodes.fa -> build/bdist.linux-armv7l/wheel/amptk/DB 2023-11-06T19:46:06,458 copying build/lib/amptk/unoise3.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,461 copying build/lib/amptk/ont_cluster.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,462 copying build/lib/amptk/process_ion.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,465 copying build/lib/amptk/merge_metadata.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,466 copying build/lib/amptk/phyloseq_nmds.R -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,469 copying build/lib/amptk/funguild.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,471 copying build/lib/amptk/amptklib.py -> build/bdist.linux-armv7l/wheel/amptk 2023-11-06T19:46:06,474 running install_egg_info 2023-11-06T19:46:06,505 Copying amptk.egg-info to build/bdist.linux-armv7l/wheel/amptk-1.6.0-py3.11.egg-info 2023-11-06T19:46:06,516 running install_scripts 2023-11-06T19:46:06,518 creating build/bdist.linux-armv7l/wheel/amptk-1.6.0.data 2023-11-06T19:46:06,518 creating build/bdist.linux-armv7l/wheel/amptk-1.6.0.data/scripts 2023-11-06T19:46:06,519 copying build/scripts-3.11/amptk_synthetic_mock.py -> build/bdist.linux-armv7l/wheel/amptk-1.6.0.data/scripts 2023-11-06T19:46:06,522 copying build/scripts-3.11/bold2utax.py -> build/bdist.linux-armv7l/wheel/amptk-1.6.0.data/scripts 2023-11-06T19:46:06,524 changing mode of build/bdist.linux-armv7l/wheel/amptk-1.6.0.data/scripts/amptk_synthetic_mock.py to 755 2023-11-06T19:46:06,524 changing mode of build/bdist.linux-armv7l/wheel/amptk-1.6.0.data/scripts/bold2utax.py to 755 2023-11-06T19:46:06,542 creating build/bdist.linux-armv7l/wheel/amptk-1.6.0.dist-info/WHEEL 2023-11-06T19:46:06,544 creating '/tmp/pip-wheel-bg84svs2/amptk-1.6.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-11-06T19:46:06,548 adding 'amptk/OTU_cluster.py' 2023-11-06T19:46:06,551 adding 'amptk/OTU_cluster_ref.py' 2023-11-06T19:46:06,553 adding 'amptk/__init__.py' 2023-11-06T19:46:06,554 adding 'amptk/__version__.py' 2023-11-06T19:46:06,559 adding 'amptk/amptk.py' 2023-11-06T19:46:06,568 adding 'amptk/amptklib.py' 2023-11-06T19:46:06,573 adding 'amptk/assign_taxonomy.py' 2023-11-06T19:46:06,575 adding 'amptk/barcode_rarify.py' 2023-11-06T19:46:06,576 adding 'amptk/check_version.R' 2023-11-06T19:46:06,578 adding 'amptk/collapse_taxonomy.py' 2023-11-06T19:46:06,579 adding 'amptk/csv2heatmap.py' 2023-11-06T19:46:06,582 adding 'amptk/dada2.py' 2023-11-06T19:46:06,584 adding 'amptk/dada2_pacbio.py' 2023-11-06T19:46:06,586 adding 'amptk/dada2_pipeline_nofilt.R' 2023-11-06T19:46:06,587 adding 'amptk/downloads.json' 2023-11-06T19:46:06,588 adding 'amptk/downloadsv1.6.0.json' 2023-11-06T19:46:06,590 adding 'amptk/drop.py' 2023-11-06T19:46:06,593 adding 'amptk/extract_region.py' 2023-11-06T19:46:06,596 adding 'amptk/fastq2sra.py' 2023-11-06T19:46:06,601 adding 'amptk/filter.py' 2023-11-06T19:46:06,603 adding 'amptk/funguild.py' 2023-11-06T19:46:06,604 adding 'amptk/get_barcode_counts.py' 2023-11-06T19:46:06,606 adding 'amptk/heatmap.py' 2023-11-06T19:46:06,608 adding 'amptk/info.py' 2023-11-06T19:46:06,609 adding 'amptk/install.py' 2023-11-06T19:46:06,610 adding 'amptk/keep_samples.py' 2023-11-06T19:46:06,612 adding 'amptk/lulu.py' 2023-11-06T19:46:06,613 adding 'amptk/merge_metadata.py' 2023-11-06T19:46:06,615 adding 'amptk/ont_cluster.py' 2023-11-06T19:46:06,616 adding 'amptk/parse_adonis.py' 2023-11-06T19:46:06,618 adding 'amptk/phyloseq_nmds.R' 2023-11-06T19:46:06,621 adding 'amptk/phyloseq_nmds_indicator.R' 2023-11-06T19:46:06,622 adding 'amptk/primers.json' 2023-11-06T19:46:06,624 adding 'amptk/process_illumina2.py' 2023-11-06T19:46:06,627 adding 'amptk/process_illumina_folder.py' 2023-11-06T19:46:06,630 adding 'amptk/process_illumina_raw.py' 2023-11-06T19:46:06,633 adding 'amptk/process_ion.py' 2023-11-06T19:46:06,635 adding 'amptk/process_ont.py' 2023-11-06T19:46:06,637 adding 'amptk/process_pacbio.py' 2023-11-06T19:46:06,642 adding 'amptk/pybam.py' 2023-11-06T19:46:06,644 adding 'amptk/remove_samples.py' 2023-11-06T19:46:06,645 adding 'amptk/runLULU.R' 2023-11-06T19:46:06,647 adding 'amptk/stackedBarGraph.py' 2023-11-06T19:46:06,649 adding 'amptk/stats.py' 2023-11-06T19:46:06,651 adding 'amptk/summarize_taxonomy.py' 2023-11-06T19:46:06,653 adding 'amptk/unoise2.py' 2023-11-06T19:46:06,655 adding 'amptk/unoise3.py' 2023-11-06T19:46:06,658 adding 'amptk/DB/amptk_mock1.fa' 2023-11-06T19:46:06,663 adding 'amptk/DB/amptk_mock2.fa' 2023-11-06T19:46:06,667 adding 'amptk/DB/amptk_mock3.fa' 2023-11-06T19:46:06,669 adding 'amptk/DB/amptk_synmock.fa' 2023-11-06T19:46:06,671 adding 'amptk/DB/ioncode_barcodes.fa' 2023-11-06T19:46:06,673 adding 'amptk/DB/ionxpress_barcodes.fa' 2023-11-06T19:46:06,675 adding 'amptk-1.6.0.data/scripts/amptk_synthetic_mock.py' 2023-11-06T19:46:06,677 adding 'amptk-1.6.0.data/scripts/bold2utax.py' 2023-11-06T19:46:06,679 adding 'amptk-1.6.0.dist-info/LICENSE.md' 2023-11-06T19:46:06,680 adding 'amptk-1.6.0.dist-info/METADATA' 2023-11-06T19:46:06,681 adding 'amptk-1.6.0.dist-info/WHEEL' 2023-11-06T19:46:06,682 adding 'amptk-1.6.0.dist-info/entry_points.txt' 2023-11-06T19:46:06,683 adding 'amptk-1.6.0.dist-info/top_level.txt' 2023-11-06T19:46:06,684 adding 'amptk-1.6.0.dist-info/RECORD' 2023-11-06T19:46:06,688 removing build/bdist.linux-armv7l/wheel 2023-11-06T19:46:06,814 Building wheel for amptk (setup.py): finished with status 'done' 2023-11-06T19:46:06,819 Created wheel for amptk: filename=amptk-1.6.0-py3-none-any.whl size=201016 sha256=8bf9a8438a2ab54a21b3a23d489586d913f9f9c831a9696e1e15eea6a83a5e11 2023-11-06T19:46:06,820 Stored in directory: /tmp/pip-ephem-wheel-cache-si1hcr2t/wheels/bf/29/c1/2c6786a74c2e0b6b13ab71e070571e11360e2e3daa445b3afd 2023-11-06T19:46:06,833 Successfully built amptk 2023-11-06T19:46:07,104 Removed build tracker: '/tmp/pip-build-tracker-5a1so2_k'