2023-09-26T17:28:50,390 Created temporary directory: /tmp/pip-build-tracker-4xpb7z4y
2023-09-26T17:28:50,391 Initialized build tracking at /tmp/pip-build-tracker-4xpb7z4y
2023-09-26T17:28:50,391 Created build tracker: /tmp/pip-build-tracker-4xpb7z4y
2023-09-26T17:28:50,392 Entered build tracker: /tmp/pip-build-tracker-4xpb7z4y
2023-09-26T17:28:50,393 Created temporary directory: /tmp/pip-wheel-es1sjpmp
2023-09-26T17:28:50,396 Created temporary directory: /tmp/pip-ephem-wheel-cache-hu2p_d9q
2023-09-26T17:28:50,417 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-09-26T17:28:50,421 2 location(s) to search for versions of capcruncher:
2023-09-26T17:28:50,421 * https://pypi.org/simple/capcruncher/
2023-09-26T17:28:50,421 * https://www.piwheels.org/simple/capcruncher/
2023-09-26T17:28:50,421 Fetching project page and analyzing links: https://pypi.org/simple/capcruncher/
2023-09-26T17:28:50,422 Getting page https://pypi.org/simple/capcruncher/
2023-09-26T17:28:50,424 Found index url https://pypi.org/simple/
2023-09-26T17:28:50,564 Fetched page https://pypi.org/simple/capcruncher/ as application/vnd.pypi.simple.v1+json
2023-09-26T17:28:50,569   Skipping link: No binaries permitted for capcruncher: https://files.pythonhosted.org/packages/34/0a/9e75866768f2f383fb94a19406fc1351c2752e365607839d6e2bb1d8d84b/capcruncher-0.1.0a1-py3-none-any.whl (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.8)
2023-09-26T17:28:50,570   Found link https://files.pythonhosted.org/packages/3c/f1/f89b867eec66701b2f41487ec19a3092f869cba76c6d15750220af30ab7b/capcruncher-0.1.0a1.tar.gz (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.8), version: 0.1.0a1
2023-09-26T17:28:50,571   Skipping link: No binaries permitted for capcruncher: https://files.pythonhosted.org/packages/1d/1b/b3083fd403c5ea09c7ac18edb1a69b795ab753e1dce96d3837c6777c090a/capcruncher-0.1.0a2-py3-none-any.whl (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.8)
2023-09-26T17:28:50,572   Found link https://files.pythonhosted.org/packages/78/43/1dbd9816f26f28c8ea8e41109f7b55f3c29216ae9ee9faf3132455ee5900/capcruncher-0.1.0a2.tar.gz (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.8), version: 0.1.0a2
2023-09-26T17:28:50,572   Skipping link: No binaries permitted for capcruncher: https://files.pythonhosted.org/packages/af/21/1bd19a95d650d782bd61f0617e2ade19b8ea9dfc2583d5188cf31fc9e2ac/capcruncher-0.1.1a0-py3-none-any.whl (from https://pypi.org/simple/capcruncher/)
2023-09-26T17:28:50,573   Found link https://files.pythonhosted.org/packages/4b/58/8c4c26cb67c97bc632d4fd7df6b754a3d7d52d9224a12b5ef30f1551e18a/capcruncher-0.1.1a0.tar.gz (from https://pypi.org/simple/capcruncher/), version: 0.1.1a0
2023-09-26T17:28:50,574   Skipping link: No binaries permitted for capcruncher: https://files.pythonhosted.org/packages/09/3a/0d4e2559f5fcd1ea08ba4a59a2174bfa9b4e362fb6fbbeff57652bc8b43b/capcruncher-0.1.1a1-py3-none-any.whl (from https://pypi.org/simple/capcruncher/)
2023-09-26T17:28:50,574   Found link https://files.pythonhosted.org/packages/fc/38/d9f3fbb589780a7116c60af23e14e0ffec82fa966bd6fac06494df1ff972/capcruncher-0.1.1a1.tar.gz (from https://pypi.org/simple/capcruncher/), version: 0.1.1a1
2023-09-26T17:28:50,575   Skipping link: No binaries permitted for capcruncher: https://files.pythonhosted.org/packages/d8/b8/f378ab302aba8e011a3548bc8e12ca018dd51bae5e175f2aeac9b7023dbe/capcruncher-0.2.0-py3-none-any.whl (from https://pypi.org/simple/capcruncher/)
2023-09-26T17:28:50,576   Found link https://files.pythonhosted.org/packages/ab/85/07383d62359c33bab143b6f85173a09852963625a5c6e23bbfd5c54d81d4/capcruncher-0.2.0.tar.gz (from https://pypi.org/simple/capcruncher/), version: 0.2.0
2023-09-26T17:28:50,576   Skipping link: No binaries permitted for capcruncher: https://files.pythonhosted.org/packages/20/fb/21512e9e9259664564498669e39be1c06854d7b9a4b2c088d640dbaed48b/capcruncher-0.2.2-py3-none-any.whl (from https://pypi.org/simple/capcruncher/)
2023-09-26T17:28:50,577   Found link https://files.pythonhosted.org/packages/d6/8a/d499689bfadfc8c5ad88d9403619ffd62fe9169a359c304a3ef25d368b1d/capcruncher-0.2.2.tar.gz (from https://pypi.org/simple/capcruncher/), version: 0.2.2
2023-09-26T17:28:50,578   Skipping link: No binaries permitted for capcruncher: https://files.pythonhosted.org/packages/37/32/8d0b33d160aeec619f8cc86611ac7771733f9a300176f3b7fbc5f94dc51a/capcruncher-0.2.3-py3-none-any.whl (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.8)
2023-09-26T17:28:50,579   Found link https://files.pythonhosted.org/packages/e7/da/78b7ae1ccdca4a9c2a0abdd16e308facc1909da2e159ce2d565c05fad639/capcruncher-0.2.3.tar.gz (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.8), version: 0.2.3
2023-09-26T17:28:50,580   Skipping link: No binaries permitted for capcruncher: https://files.pythonhosted.org/packages/26/e5/2b7ada507bb60d04dfafa0655d63edd3b82cdfb5476b8672acf0cb5477b9/capcruncher-0.3.1-py3-none-any.whl (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.10)
2023-09-26T17:28:50,580   Found link https://files.pythonhosted.org/packages/43/bd/2aabc1f9b8e2fae522852b4f3c8f27f42aadcf50016eb7bfcdfe83d499bb/capcruncher-0.3.1.tar.gz (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.10), version: 0.3.1
2023-09-26T17:28:50,581   Skipping link: No binaries permitted for capcruncher: https://files.pythonhosted.org/packages/23/34/26f733de022f420176a15aaccb50dc49d6eac08dcf68d147f08d3abb257b/capcruncher-0.3.2-py3-none-any.whl (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.10)
2023-09-26T17:28:50,582   Found link https://files.pythonhosted.org/packages/b4/c4/a3c7065d7c993db2680c1303d40862031cc6e8535aca5b023ded383d4520/capcruncher-0.3.2.tar.gz (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.10), version: 0.3.2
2023-09-26T17:28:50,582   Skipping link: No binaries permitted for capcruncher: https://files.pythonhosted.org/packages/80/d5/ae6f38bc4ec0724841406c0125296bad843a1ca2fe9e2dfce8bb73796ae5/capcruncher-0.3.3-py3-none-any.whl (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.10)
2023-09-26T17:28:50,583   Found link https://files.pythonhosted.org/packages/21/8f/8063b68decdfed76375774899994ce09bf6f2362453110d3a7e3091d0f47/capcruncher-0.3.3.tar.gz (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.10), version: 0.3.3
2023-09-26T17:28:50,584   Skipping link: No binaries permitted for capcruncher: https://files.pythonhosted.org/packages/61/55/adac692b940cca0f453b760ec8c3be9b325e22afb8e8693717fcebd202c0/capcruncher-0.3.4-py3-none-any.whl (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.10)
2023-09-26T17:28:50,585   Found link https://files.pythonhosted.org/packages/b1/78/c98a2a4a6e62b5bd169af128129633b9e06bce32b0284b79c68808a8f0e5/capcruncher-0.3.4.tar.gz (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.10), version: 0.3.4
2023-09-26T17:28:50,585   Skipping link: No binaries permitted for capcruncher: https://files.pythonhosted.org/packages/a7/b0/ed93710d654d62b661c227e5ab7cd4318633571b06cf746789710ca33465/capcruncher-0.3.5-py3-none-any.whl (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.10)
2023-09-26T17:28:50,586   Found link https://files.pythonhosted.org/packages/37/ea/966e9f14e18737107ed291ea6d3646f5a05e13a9566c2e70e0a7cd9ed172/capcruncher-0.3.5.tar.gz (from https://pypi.org/simple/capcruncher/) (requires-python:>=3.10), version: 0.3.5
2023-09-26T17:28:50,587 Fetching project page and analyzing links: https://www.piwheels.org/simple/capcruncher/
2023-09-26T17:28:50,588 Getting page https://www.piwheels.org/simple/capcruncher/
2023-09-26T17:28:50,589 Found index url https://www.piwheels.org/simple/
2023-09-26T17:28:50,755 Fetched page https://www.piwheels.org/simple/capcruncher/ as text/html
2023-09-26T17:28:50,758   Skipping link: No binaries permitted for capcruncher: https://www.piwheels.org/simple/capcruncher/capcruncher-0.3.2-py3-none-any.whl#sha256=cb9bbb6e602e5e11dcbac280be5520518f0110c58eb9bc7937644b956c455a02 (from https://www.piwheels.org/simple/capcruncher/) (requires-python:>=3.10)
2023-09-26T17:28:50,759   Skipping link: No binaries permitted for capcruncher: https://www.piwheels.org/simple/capcruncher/capcruncher-0.3.1-py3-none-any.whl#sha256=010cc17949484bec95ba588bf89f30d450d6476b8e7c612e14f32270db999b52 (from https://www.piwheels.org/simple/capcruncher/) (requires-python:>=3.10)
2023-09-26T17:28:50,760   Skipping link: No binaries permitted for capcruncher: https://www.piwheels.org/simple/capcruncher/capcruncher-0.2.3-py3-none-any.whl#sha256=3640a41566ec698430601c7ee8ff373d698ad995981fcb1564072cbdaadeaa70 (from https://www.piwheels.org/simple/capcruncher/) (requires-python:>=3.8)
2023-09-26T17:28:50,761   Skipping link: No binaries permitted for capcruncher: https://www.piwheels.org/simple/capcruncher/capcruncher-0.2.2-py3-none-any.whl#sha256=696271de6a0cfb479ebe5c059b46015c0b54a4883b28fac6d3f60d3f10360694 (from https://www.piwheels.org/simple/capcruncher/)
2023-09-26T17:28:50,761   Skipping link: No binaries permitted for capcruncher: https://www.piwheels.org/simple/capcruncher/capcruncher-0.2.0-py3-none-any.whl#sha256=a376e09af30f629484777d94d245a0a18cdee37e332344294623f74a218de161 (from https://www.piwheels.org/simple/capcruncher/)
2023-09-26T17:28:50,761   Skipping link: No binaries permitted for capcruncher: https://www.piwheels.org/simple/capcruncher/capcruncher-0.1.1a1-py3-none-any.whl#sha256=45ad47d1025882de7d3ae2436f95d9c690fb55f4ad3320a464754782dd2a9ce8 (from https://www.piwheels.org/simple/capcruncher/)
2023-09-26T17:28:50,762   Skipping link: No binaries permitted for capcruncher: https://www.piwheels.org/simple/capcruncher/capcruncher-0.1.1a0-py3-none-any.whl#sha256=33582eed6498ac35fff342bc97adfeec48d012dca74e99a13b6c8ed596465d0d (from https://www.piwheels.org/simple/capcruncher/)
2023-09-26T17:28:50,762   Skipping link: No binaries permitted for capcruncher: https://www.piwheels.org/simple/capcruncher/capcruncher-0.1.0a2-py3-none-any.whl#sha256=a9cad04a0fa53e9864f02ac8641b704ba78bd0da1a8d83c5e84199e7ae183222 (from https://www.piwheels.org/simple/capcruncher/) (requires-python:>=3.8)
2023-09-26T17:28:50,763   Skipping link: No binaries permitted for capcruncher: https://www.piwheels.org/simple/capcruncher/capcruncher-0.1.0a1-py3-none-any.whl#sha256=8d0852e344db844525d67d074e33a0880f102073b0bdc5d77c2c3bd498ffee5b (from https://www.piwheels.org/simple/capcruncher/) (requires-python:>=3.8)
2023-09-26T17:28:50,763 Skipping link: not a file: https://www.piwheels.org/simple/capcruncher/
2023-09-26T17:28:50,764 Skipping link: not a file: https://pypi.org/simple/capcruncher/
2023-09-26T17:28:50,784 Given no hashes to check 1 links for project 'capcruncher': discarding no candidates
2023-09-26T17:28:50,802 Collecting capcruncher==0.3.3
2023-09-26T17:28:50,804   Created temporary directory: /tmp/pip-unpack-rb2cb_gd
2023-09-26T17:28:51,043   Downloading capcruncher-0.3.3.tar.gz (84.9 MB)
2023-09-26T17:29:10,597   Added capcruncher==0.3.3 from https://files.pythonhosted.org/packages/21/8f/8063b68decdfed76375774899994ce09bf6f2362453110d3a7e3091d0f47/capcruncher-0.3.3.tar.gz to build tracker '/tmp/pip-build-tracker-4xpb7z4y'
2023-09-26T17:29:10,605   Created temporary directory: /tmp/pip-build-env-s936yx8k
2023-09-26T17:29:10,609   Installing build dependencies: started
2023-09-26T17:29:10,611   Running command pip subprocess to install build dependencies
2023-09-26T17:29:11,737   Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11)
2023-09-26T17:29:12,228   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-09-26T17:29:13,766   Collecting setuptools>=61.0
2023-09-26T17:29:13,767     Obtaining dependency information for setuptools>=61.0 from https://files.pythonhosted.org/packages/bb/26/7945080113158354380a12ce26873dd6c1ebd88d47f5bc24e2c5bb38c16a/setuptools-68.2.2-py3-none-any.whl.metadata
2023-09-26T17:29:13,773     Using cached setuptools-68.2.2-py3-none-any.whl.metadata (6.3 kB)
2023-09-26T17:29:13,983   Collecting wheel
2023-09-26T17:29:13,999     Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.2-py3-none-any.whl (64 kB)
2023-09-26T17:29:14,293   Collecting setuptools_scm[toml]>=6.2
2023-09-26T17:29:14,294     Obtaining dependency information for setuptools_scm[toml]>=6.2 from https://files.pythonhosted.org/packages/ca/04/4ea91c627355ae6d976bf7f1fc2815372a96b1b87bf290c8d726d10a08a1/setuptools_scm-8.0.3-py3-none-any.whl.metadata
2023-09-26T17:29:14,299     Using cached setuptools_scm-8.0.3-py3-none-any.whl.metadata (6.1 kB)
2023-09-26T17:29:14,648   Collecting packaging>=20 (from setuptools_scm[toml]>=6.2)
2023-09-26T17:29:14,662     Using cached https://www.piwheels.org/simple/packaging/packaging-23.1-py3-none-any.whl (48 kB)
2023-09-26T17:29:14,729   Using cached setuptools-68.2.2-py3-none-any.whl (807 kB)
2023-09-26T17:29:14,750   Using cached setuptools_scm-8.0.3-py3-none-any.whl (41 kB)
2023-09-26T17:29:17,229   Installing collected packages: wheel, setuptools, packaging, setuptools_scm
2023-09-26T17:29:17,451     Creating /tmp/pip-build-env-s936yx8k/overlay/local/bin
2023-09-26T17:29:17,453     changing mode of /tmp/pip-build-env-s936yx8k/overlay/local/bin/wheel to 755
2023-09-26T17:29:20,333   Successfully installed packaging-23.1 setuptools-68.2.2 setuptools_scm-8.0.3 wheel-0.41.2
2023-09-26T17:29:20,936   Installing build dependencies: finished with status 'done'
2023-09-26T17:29:20,940   Getting requirements to build wheel: started
2023-09-26T17:29:20,941   Running command Getting requirements to build wheel
2023-09-26T17:29:21,470   /tmp/pip-build-env-s936yx8k/overlay/local/lib/python3.11/dist-packages/setuptools/config/setupcfg.py:293: _DeprecatedConfig: Deprecated config in `setup.cfg`
2023-09-26T17:29:21,470   !!

2023-09-26T17:29:21,471           ********************************************************************************
2023-09-26T17:29:21,472           The license_file parameter is deprecated, use license_files instead.

2023-09-26T17:29:21,473           By 2023-Oct-30, you need to update your project and remove deprecated calls
2023-09-26T17:29:21,473           or your builds will no longer be supported.

2023-09-26T17:29:21,474           See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
2023-09-26T17:29:21,475           ********************************************************************************

2023-09-26T17:29:21,476   !!
2023-09-26T17:29:21,477     parsed = self.parsers.get(option_name, lambda x: x)(value)
2023-09-26T17:29:21,669   /tmp/pip-build-env-s936yx8k/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:73: _WouldIgnoreField: `classifiers` defined outside of `pyproject.toml` would be ignored.
2023-09-26T17:29:21,669   !!

2023-09-26T17:29:21,671           ********************************************************************************
2023-09-26T17:29:21,671           ##########################################################################
2023-09-26T17:29:21,672           # configuration would be ignored/result in error due to `pyproject.toml` #
2023-09-26T17:29:21,672           ##########################################################################

2023-09-26T17:29:21,674           The following seems to be defined outside of `pyproject.toml`:

2023-09-26T17:29:21,675           `classifiers = ['Environment :: Console', 'Intended Audience :: Science/Research', 'Operating System :: POSIX :: Linux', 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)', 'Topic :: Scientific/Engineering :: Bio-Informatics', 'Programming Language :: Python :: 3 :: Only', 'Programming Language :: Python :: Implementation :: CPython']`

2023-09-26T17:29:21,676           According to the spec (see the link below), however, setuptools CANNOT
2023-09-26T17:29:21,676           consider this value unless `classifiers` is listed as `dynamic`.

2023-09-26T17:29:21,677           https://packaging.python.org/en/latest/specifications/declaring-project-metadata/

2023-09-26T17:29:21,679           For the time being, `setuptools` will still consider the given value (as a
2023-09-26T17:29:21,679           **transitional** measure), but please note that future releases of setuptools will
2023-09-26T17:29:21,680           follow strictly the standard.

2023-09-26T17:29:21,681           To prevent this warning, you can list `classifiers` under `dynamic` or alternatively
2023-09-26T17:29:21,681           remove the `[project]` table from your file and rely entirely on other means of
2023-09-26T17:29:21,682           configuration.

2023-09-26T17:29:21,682           By 2023-Oct-30, you need to update your project and remove deprecated calls
2023-09-26T17:29:21,683           or your builds will no longer be supported.
2023-09-26T17:29:21,683           ********************************************************************************

2023-09-26T17:29:21,684   !!
2023-09-26T17:29:21,685     _handle_missing_dynamic(dist, project_table)
2023-09-26T17:29:21,685   /tmp/pip-build-env-s936yx8k/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:73: _WouldIgnoreField: `scripts` defined outside of `pyproject.toml` would be ignored.
2023-09-26T17:29:21,686   !!

2023-09-26T17:29:21,687           ********************************************************************************
2023-09-26T17:29:21,687           ##########################################################################
2023-09-26T17:29:21,688           # configuration would be ignored/result in error due to `pyproject.toml` #
2023-09-26T17:29:21,688           ##########################################################################

2023-09-26T17:29:21,689           The following seems to be defined outside of `pyproject.toml`:

2023-09-26T17:29:21,690           `scripts = ['capcruncher = capcruncher.cli:cli']`

2023-09-26T17:29:21,691           According to the spec (see the link below), however, setuptools CANNOT
2023-09-26T17:29:21,691           consider this value unless `scripts` is listed as `dynamic`.

2023-09-26T17:29:21,692           https://packaging.python.org/en/latest/specifications/declaring-project-metadata/

2023-09-26T17:29:21,694           For the time being, `setuptools` will still consider the given value (as a
2023-09-26T17:29:21,694           **transitional** measure), but please note that future releases of setuptools will
2023-09-26T17:29:21,695           follow strictly the standard.

2023-09-26T17:29:21,696           To prevent this warning, you can list `scripts` under `dynamic` or alternatively
2023-09-26T17:29:21,696           remove the `[project]` table from your file and rely entirely on other means of
2023-09-26T17:29:21,697           configuration.

2023-09-26T17:29:21,698           By 2023-Oct-30, you need to update your project and remove deprecated calls
2023-09-26T17:29:21,699           or your builds will no longer be supported.
2023-09-26T17:29:21,699           ********************************************************************************

2023-09-26T17:29:21,700   !!
2023-09-26T17:29:21,701     _handle_missing_dynamic(dist, project_table)
2023-09-26T17:29:21,971   running egg_info
2023-09-26T17:29:21,976   writing capcruncher.egg-info/PKG-INFO
2023-09-26T17:29:21,983   writing dependency_links to capcruncher.egg-info/dependency_links.txt
2023-09-26T17:29:21,985   writing entry points to capcruncher.egg-info/entry_points.txt
2023-09-26T17:29:21,987   writing requirements to capcruncher.egg-info/requires.txt
2023-09-26T17:29:21,988   writing top-level names to capcruncher.egg-info/top_level.txt
2023-09-26T17:29:22,039   ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any
2023-09-26T17:29:22,043   reading manifest file 'capcruncher.egg-info/SOURCES.txt'
2023-09-26T17:29:22,051   reading manifest template 'MANIFEST.in'
2023-09-26T17:29:22,082   adding license file 'LICENSE'
2023-09-26T17:29:22,092   writing manifest file 'capcruncher.egg-info/SOURCES.txt'
2023-09-26T17:29:22,214   Getting requirements to build wheel: finished with status 'done'
2023-09-26T17:29:22,229   Created temporary directory: /tmp/pip-modern-metadata-e3sm1wyh
2023-09-26T17:29:22,231   Preparing metadata (pyproject.toml): started
2023-09-26T17:29:22,232   Running command Preparing metadata (pyproject.toml)
2023-09-26T17:29:22,818   /tmp/pip-build-env-s936yx8k/overlay/local/lib/python3.11/dist-packages/setuptools/config/setupcfg.py:293: _DeprecatedConfig: Deprecated config in `setup.cfg`
2023-09-26T17:29:22,818   !!

2023-09-26T17:29:22,819           ********************************************************************************
2023-09-26T17:29:22,820           The license_file parameter is deprecated, use license_files instead.

2023-09-26T17:29:22,821           By 2023-Oct-30, you need to update your project and remove deprecated calls
2023-09-26T17:29:22,821           or your builds will no longer be supported.

2023-09-26T17:29:22,822           See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
2023-09-26T17:29:22,822           ********************************************************************************

2023-09-26T17:29:22,824   !!
2023-09-26T17:29:22,825     parsed = self.parsers.get(option_name, lambda x: x)(value)
2023-09-26T17:29:22,873   /tmp/pip-build-env-s936yx8k/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:73: _WouldIgnoreField: `classifiers` defined outside of `pyproject.toml` would be ignored.
2023-09-26T17:29:22,873   !!

2023-09-26T17:29:22,874           ********************************************************************************
2023-09-26T17:29:22,875           ##########################################################################
2023-09-26T17:29:22,875           # configuration would be ignored/result in error due to `pyproject.toml` #
2023-09-26T17:29:22,876           ##########################################################################

2023-09-26T17:29:22,877           The following seems to be defined outside of `pyproject.toml`:

2023-09-26T17:29:22,878           `classifiers = ['Environment :: Console', 'Intended Audience :: Science/Research', 'Operating System :: POSIX :: Linux', 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)', 'Topic :: Scientific/Engineering :: Bio-Informatics', 'Programming Language :: Python :: 3 :: Only', 'Programming Language :: Python :: Implementation :: CPython']`

2023-09-26T17:29:22,879           According to the spec (see the link below), however, setuptools CANNOT
2023-09-26T17:29:22,880           consider this value unless `classifiers` is listed as `dynamic`.

2023-09-26T17:29:22,881           https://packaging.python.org/en/latest/specifications/declaring-project-metadata/

2023-09-26T17:29:22,882           For the time being, `setuptools` will still consider the given value (as a
2023-09-26T17:29:22,883           **transitional** measure), but please note that future releases of setuptools will
2023-09-26T17:29:22,884           follow strictly the standard.

2023-09-26T17:29:22,885           To prevent this warning, you can list `classifiers` under `dynamic` or alternatively
2023-09-26T17:29:22,885           remove the `[project]` table from your file and rely entirely on other means of
2023-09-26T17:29:22,886           configuration.

2023-09-26T17:29:22,887           By 2023-Oct-30, you need to update your project and remove deprecated calls
2023-09-26T17:29:22,888           or your builds will no longer be supported.
2023-09-26T17:29:22,888           ********************************************************************************

2023-09-26T17:29:22,890   !!
2023-09-26T17:29:22,890     _handle_missing_dynamic(dist, project_table)
2023-09-26T17:29:22,891   /tmp/pip-build-env-s936yx8k/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:73: _WouldIgnoreField: `scripts` defined outside of `pyproject.toml` would be ignored.
2023-09-26T17:29:22,891   !!

2023-09-26T17:29:22,893           ********************************************************************************
2023-09-26T17:29:22,893           ##########################################################################
2023-09-26T17:29:22,894           # configuration would be ignored/result in error due to `pyproject.toml` #
2023-09-26T17:29:22,894           ##########################################################################

2023-09-26T17:29:22,896           The following seems to be defined outside of `pyproject.toml`:

2023-09-26T17:29:22,897           `scripts = ['capcruncher = capcruncher.cli:cli']`

2023-09-26T17:29:22,898           According to the spec (see the link below), however, setuptools CANNOT
2023-09-26T17:29:22,898           consider this value unless `scripts` is listed as `dynamic`.

2023-09-26T17:29:22,899           https://packaging.python.org/en/latest/specifications/declaring-project-metadata/

2023-09-26T17:29:22,900           For the time being, `setuptools` will still consider the given value (as a
2023-09-26T17:29:22,900           **transitional** measure), but please note that future releases of setuptools will
2023-09-26T17:29:22,901           follow strictly the standard.

2023-09-26T17:29:22,902           To prevent this warning, you can list `scripts` under `dynamic` or alternatively
2023-09-26T17:29:22,902           remove the `[project]` table from your file and rely entirely on other means of
2023-09-26T17:29:22,903           configuration.

2023-09-26T17:29:22,904           By 2023-Oct-30, you need to update your project and remove deprecated calls
2023-09-26T17:29:22,904           or your builds will no longer be supported.
2023-09-26T17:29:22,905           ********************************************************************************

2023-09-26T17:29:22,906   !!
2023-09-26T17:29:22,906     _handle_missing_dynamic(dist, project_table)
2023-09-26T17:29:23,161   running dist_info
2023-09-26T17:29:23,167   creating /tmp/pip-modern-metadata-e3sm1wyh/capcruncher.egg-info
2023-09-26T17:29:23,172   writing /tmp/pip-modern-metadata-e3sm1wyh/capcruncher.egg-info/PKG-INFO
2023-09-26T17:29:23,179   writing dependency_links to /tmp/pip-modern-metadata-e3sm1wyh/capcruncher.egg-info/dependency_links.txt
2023-09-26T17:29:23,181   writing entry points to /tmp/pip-modern-metadata-e3sm1wyh/capcruncher.egg-info/entry_points.txt
2023-09-26T17:29:23,183   writing requirements to /tmp/pip-modern-metadata-e3sm1wyh/capcruncher.egg-info/requires.txt
2023-09-26T17:29:23,184   writing top-level names to /tmp/pip-modern-metadata-e3sm1wyh/capcruncher.egg-info/top_level.txt
2023-09-26T17:29:23,185   writing manifest file '/tmp/pip-modern-metadata-e3sm1wyh/capcruncher.egg-info/SOURCES.txt'
2023-09-26T17:29:23,229   ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any
2023-09-26T17:29:23,232   reading manifest file '/tmp/pip-modern-metadata-e3sm1wyh/capcruncher.egg-info/SOURCES.txt'
2023-09-26T17:29:23,234   reading manifest template 'MANIFEST.in'
2023-09-26T17:29:23,263   adding license file 'LICENSE'
2023-09-26T17:29:23,267   writing manifest file '/tmp/pip-modern-metadata-e3sm1wyh/capcruncher.egg-info/SOURCES.txt'
2023-09-26T17:29:23,268   creating '/tmp/pip-modern-metadata-e3sm1wyh/capcruncher-0.3.3.dist-info'
2023-09-26T17:29:23,437   Preparing metadata (pyproject.toml): finished with status 'done'
2023-09-26T17:29:23,448   Source in /tmp/pip-wheel-es1sjpmp/capcruncher_501e5345788147c2b477c779a49e9693 has version 0.3.3, which satisfies requirement capcruncher==0.3.3 from https://files.pythonhosted.org/packages/21/8f/8063b68decdfed76375774899994ce09bf6f2362453110d3a7e3091d0f47/capcruncher-0.3.3.tar.gz
2023-09-26T17:29:23,449   Removed capcruncher==0.3.3 from https://files.pythonhosted.org/packages/21/8f/8063b68decdfed76375774899994ce09bf6f2362453110d3a7e3091d0f47/capcruncher-0.3.3.tar.gz from build tracker '/tmp/pip-build-tracker-4xpb7z4y'
2023-09-26T17:29:23,469 Created temporary directory: /tmp/pip-unpack-fbi_j7oo
2023-09-26T17:29:23,470 Created temporary directory: /tmp/pip-unpack-x87n4tcu
2023-09-26T17:29:23,519 Building wheels for collected packages: capcruncher
2023-09-26T17:29:23,523   Created temporary directory: /tmp/pip-wheel-5ltwhinx
2023-09-26T17:29:23,524   Destination directory: /tmp/pip-wheel-5ltwhinx
2023-09-26T17:29:23,526   Building wheel for capcruncher (pyproject.toml): started
2023-09-26T17:29:23,527   Running command Building wheel for capcruncher (pyproject.toml)
2023-09-26T17:29:24,077   /tmp/pip-build-env-s936yx8k/overlay/local/lib/python3.11/dist-packages/setuptools/config/setupcfg.py:293: _DeprecatedConfig: Deprecated config in `setup.cfg`
2023-09-26T17:29:24,077   !!

2023-09-26T17:29:24,078           ********************************************************************************
2023-09-26T17:29:24,079           The license_file parameter is deprecated, use license_files instead.

2023-09-26T17:29:24,080           By 2023-Oct-30, you need to update your project and remove deprecated calls
2023-09-26T17:29:24,080           or your builds will no longer be supported.

2023-09-26T17:29:24,081           See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
2023-09-26T17:29:24,082           ********************************************************************************

2023-09-26T17:29:24,083   !!
2023-09-26T17:29:24,084     parsed = self.parsers.get(option_name, lambda x: x)(value)
2023-09-26T17:29:24,130   /tmp/pip-build-env-s936yx8k/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:73: _WouldIgnoreField: `classifiers` defined outside of `pyproject.toml` would be ignored.
2023-09-26T17:29:24,131   !!

2023-09-26T17:29:24,132           ********************************************************************************
2023-09-26T17:29:24,132           ##########################################################################
2023-09-26T17:29:24,133           # configuration would be ignored/result in error due to `pyproject.toml` #
2023-09-26T17:29:24,133           ##########################################################################

2023-09-26T17:29:24,134           The following seems to be defined outside of `pyproject.toml`:

2023-09-26T17:29:24,136           `classifiers = ['Environment :: Console', 'Intended Audience :: Science/Research', 'Operating System :: POSIX :: Linux', 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)', 'Topic :: Scientific/Engineering :: Bio-Informatics', 'Programming Language :: Python :: 3 :: Only', 'Programming Language :: Python :: Implementation :: CPython']`

2023-09-26T17:29:24,137           According to the spec (see the link below), however, setuptools CANNOT
2023-09-26T17:29:24,137           consider this value unless `classifiers` is listed as `dynamic`.

2023-09-26T17:29:24,138           https://packaging.python.org/en/latest/specifications/declaring-project-metadata/

2023-09-26T17:29:24,139           For the time being, `setuptools` will still consider the given value (as a
2023-09-26T17:29:24,140           **transitional** measure), but please note that future releases of setuptools will
2023-09-26T17:29:24,141           follow strictly the standard.

2023-09-26T17:29:24,142           To prevent this warning, you can list `classifiers` under `dynamic` or alternatively
2023-09-26T17:29:24,143           remove the `[project]` table from your file and rely entirely on other means of
2023-09-26T17:29:24,143           configuration.

2023-09-26T17:29:24,145           By 2023-Oct-30, you need to update your project and remove deprecated calls
2023-09-26T17:29:24,145           or your builds will no longer be supported.
2023-09-26T17:29:24,146           ********************************************************************************

2023-09-26T17:29:24,147   !!
2023-09-26T17:29:24,148     _handle_missing_dynamic(dist, project_table)
2023-09-26T17:29:24,148   /tmp/pip-build-env-s936yx8k/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:73: _WouldIgnoreField: `scripts` defined outside of `pyproject.toml` would be ignored.
2023-09-26T17:29:24,149   !!

2023-09-26T17:29:24,150           ********************************************************************************
2023-09-26T17:29:24,151           ##########################################################################
2023-09-26T17:29:24,152           # configuration would be ignored/result in error due to `pyproject.toml` #
2023-09-26T17:29:24,152           ##########################################################################

2023-09-26T17:29:24,154           The following seems to be defined outside of `pyproject.toml`:

2023-09-26T17:29:24,155           `scripts = ['capcruncher = capcruncher.cli:cli']`

2023-09-26T17:29:24,156           According to the spec (see the link below), however, setuptools CANNOT
2023-09-26T17:29:24,156           consider this value unless `scripts` is listed as `dynamic`.

2023-09-26T17:29:24,157           https://packaging.python.org/en/latest/specifications/declaring-project-metadata/

2023-09-26T17:29:24,158           For the time being, `setuptools` will still consider the given value (as a
2023-09-26T17:29:24,159           **transitional** measure), but please note that future releases of setuptools will
2023-09-26T17:29:24,159           follow strictly the standard.

2023-09-26T17:29:24,160           To prevent this warning, you can list `scripts` under `dynamic` or alternatively
2023-09-26T17:29:24,161           remove the `[project]` table from your file and rely entirely on other means of
2023-09-26T17:29:24,161           configuration.

2023-09-26T17:29:24,162           By 2023-Oct-30, you need to update your project and remove deprecated calls
2023-09-26T17:29:24,163           or your builds will no longer be supported.
2023-09-26T17:29:24,163           ********************************************************************************

2023-09-26T17:29:24,164   !!
2023-09-26T17:29:24,165     _handle_missing_dynamic(dist, project_table)
2023-09-26T17:29:24,405   running bdist_wheel
2023-09-26T17:29:24,427   running build
2023-09-26T17:29:24,428   running build_py
2023-09-26T17:29:24,433   creating build
2023-09-26T17:29:24,434   creating build/lib
2023-09-26T17:29:24,435   creating build/lib/capcruncher
2023-09-26T17:29:24,436   copying capcruncher/__init__.py -> build/lib/capcruncher
2023-09-26T17:29:24,438   copying capcruncher/utils.py -> build/lib/capcruncher
2023-09-26T17:29:24,440   copying capcruncher/_version.py -> build/lib/capcruncher
2023-09-26T17:29:24,442   creating build/lib/capcruncher/pipeline
2023-09-26T17:29:24,443   copying capcruncher/pipeline/utils.py -> build/lib/capcruncher/pipeline
2023-09-26T17:29:24,447   creating build/lib/capcruncher/api
2023-09-26T17:29:24,448   copying capcruncher/api/count.py -> build/lib/capcruncher/api
2023-09-26T17:29:24,450   copying capcruncher/api/__init__.py -> build/lib/capcruncher/api
2023-09-26T17:29:24,451   copying capcruncher/api/statistics.py -> build/lib/capcruncher/api
2023-09-26T17:29:24,453   copying capcruncher/api/storage.py -> build/lib/capcruncher/api
2023-09-26T17:29:24,456   copying capcruncher/api/digest.py -> build/lib/capcruncher/api
2023-09-26T17:29:24,458   copying capcruncher/api/pileup.py -> build/lib/capcruncher/api
2023-09-26T17:29:24,460   copying capcruncher/api/deduplicate.py -> build/lib/capcruncher/api
2023-09-26T17:29:24,463   copying capcruncher/api/filter.py -> build/lib/capcruncher/api
2023-09-26T17:29:24,466   copying capcruncher/api/io.py -> build/lib/capcruncher/api
2023-09-26T17:29:24,469   copying capcruncher/api/annotate.py -> build/lib/capcruncher/api
2023-09-26T17:29:24,471   copying capcruncher/api/plotting.py -> build/lib/capcruncher/api
2023-09-26T17:29:24,474   creating build/lib/capcruncher/cli
2023-09-26T17:29:24,476   copying capcruncher/cli/fastq_deduplicate.py -> build/lib/capcruncher/cli
2023-09-26T17:29:24,478   copying capcruncher/cli/interactions_compare.py -> build/lib/capcruncher/cli
2023-09-26T17:29:24,480   copying capcruncher/cli/interactions_count.py -> build/lib/capcruncher/cli
2023-09-26T17:29:24,482   copying capcruncher/cli/__init__.py -> build/lib/capcruncher/cli
2023-09-26T17:29:24,484   copying capcruncher/cli/interactions_store.py -> build/lib/capcruncher/cli
2023-09-26T17:29:24,485   copying capcruncher/cli/alignments_filter.py -> build/lib/capcruncher/cli
2023-09-26T17:29:24,487   copying capcruncher/cli/interactions_deduplicate.py -> build/lib/capcruncher/cli
2023-09-26T17:29:24,489   copying capcruncher/cli/plot.py -> build/lib/capcruncher/cli
2023-09-26T17:29:24,491   copying capcruncher/cli/cli_plot.py -> build/lib/capcruncher/cli
2023-09-26T17:29:24,493   copying capcruncher/cli/cli_fastq.py -> build/lib/capcruncher/cli
2023-09-26T17:29:24,495   copying capcruncher/cli/cli_utilities.py -> build/lib/capcruncher/cli
2023-09-26T17:29:24,497   copying capcruncher/cli/alignments_annotate.py -> build/lib/capcruncher/cli
2023-09-26T17:29:24,499   copying capcruncher/cli/interactions_pileup.py -> build/lib/capcruncher/cli
2023-09-26T17:29:24,500   copying capcruncher/cli/interactions_differential.py -> build/lib/capcruncher/cli
2023-09-26T17:29:24,502   copying capcruncher/cli/genome_digest.py -> build/lib/capcruncher/cli
2023-09-26T17:29:24,504   copying capcruncher/cli/cli_genome.py -> build/lib/capcruncher/cli
2023-09-26T17:29:24,506   copying capcruncher/cli/fastq_split.py -> build/lib/capcruncher/cli
2023-09-26T17:29:24,508   copying capcruncher/cli/cli_pipeline.py -> build/lib/capcruncher/cli
2023-09-26T17:29:24,509   copying capcruncher/cli/cli_interactions.py -> build/lib/capcruncher/cli
2023-09-26T17:29:24,511   copying capcruncher/cli/cli_alignments.py -> build/lib/capcruncher/cli
2023-09-26T17:29:24,513   copying capcruncher/cli/fastq_digest.py -> build/lib/capcruncher/cli
2023-09-26T17:29:24,517   creating build/lib/capcruncher/pipeline/workflow
2023-09-26T17:29:24,518   creating build/lib/capcruncher/pipeline/workflow/report
2023-09-26T17:29:24,519   copying capcruncher/pipeline/workflow/report/make_report.py -> build/lib/capcruncher/pipeline/workflow/report
2023-09-26T17:29:24,522   creating build/lib/capcruncher/pipeline/workflow/scripts
2023-09-26T17:29:24,523   copying capcruncher/pipeline/workflow/scripts/count_identified_viewpoints.py -> build/lib/capcruncher/pipeline/workflow/scripts
2023-09-26T17:29:24,525   copying capcruncher/pipeline/workflow/scripts/combine_filtering_stats.py -> build/lib/capcruncher/pipeline/workflow/scripts
2023-09-26T17:29:24,526   copying capcruncher/pipeline/workflow/scripts/remove_duplicate_coordinates.py -> build/lib/capcruncher/pipeline/workflow/scripts
2023-09-26T17:29:24,528   copying capcruncher/pipeline/workflow/scripts/identify_viewpoints_with_interactions.py -> build/lib/capcruncher/pipeline/workflow/scripts
2023-09-26T17:29:24,529   copying capcruncher/pipeline/workflow/scripts/combine_digestion_stats.py -> build/lib/capcruncher/pipeline/workflow/scripts
2023-09-26T17:29:24,531   copying capcruncher/pipeline/workflow/scripts/combine_stats_read_level.py -> build/lib/capcruncher/pipeline/workflow/scripts
2023-09-26T17:29:24,533   copying capcruncher/pipeline/workflow/scripts/plot.py -> build/lib/capcruncher/pipeline/workflow/scripts
2023-09-26T17:29:24,534   copying capcruncher/pipeline/workflow/scripts/make_ucsc_hub.py -> build/lib/capcruncher/pipeline/workflow/scripts
2023-09-26T17:29:24,536   copying capcruncher/pipeline/workflow/scripts/combine_deduplication_stats.py -> build/lib/capcruncher/pipeline/workflow/scripts
2023-09-26T17:29:24,538   copying capcruncher/pipeline/workflow/scripts/combine_cis_and_trans_stats.py -> build/lib/capcruncher/pipeline/workflow/scripts
2023-09-26T17:29:24,539   copying capcruncher/pipeline/workflow/scripts/combine_alignment_deduplication_stats.py -> build/lib/capcruncher/pipeline/workflow/scripts
2023-09-26T17:29:24,542   running egg_info
2023-09-26T17:29:24,547   writing capcruncher.egg-info/PKG-INFO
2023-09-26T17:29:24,553   writing dependency_links to capcruncher.egg-info/dependency_links.txt
2023-09-26T17:29:24,555   writing entry points to capcruncher.egg-info/entry_points.txt
2023-09-26T17:29:24,557   writing requirements to capcruncher.egg-info/requires.txt
2023-09-26T17:29:24,558   writing top-level names to capcruncher.egg-info/top_level.txt
2023-09-26T17:29:24,593   ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any
2023-09-26T17:29:24,596   reading manifest file 'capcruncher.egg-info/SOURCES.txt'
2023-09-26T17:29:24,602   reading manifest template 'MANIFEST.in'
2023-09-26T17:29:24,639   adding license file 'LICENSE'
2023-09-26T17:29:24,648   writing manifest file 'capcruncher.egg-info/SOURCES.txt'
2023-09-26T17:29:24,660   creating build/lib/capcruncher/data
2023-09-26T17:29:24,661   copying capcruncher/data/logo.txt -> build/lib/capcruncher/data
2023-09-26T17:29:24,663   copying capcruncher/pipeline/workflow/Snakefile -> build/lib/capcruncher/pipeline/workflow
2023-09-26T17:29:24,666   creating build/lib/capcruncher/pipeline/config
2023-09-26T17:29:24,666   copying capcruncher/pipeline/config/cookiecutter.json -> build/lib/capcruncher/pipeline/config
2023-09-26T17:29:24,668   creating build/lib/capcruncher/pipeline/config/{{cookiecutter.date}}_{{cookiecutter.__project_id}}_{{cookiecutter.__assay}}
2023-09-26T17:29:24,669   copying capcruncher/pipeline/config/{{cookiecutter.date}}_{{cookiecutter.__project_id}}_{{cookiecutter.__assay}}/capcruncher_config.yml -> build/lib/capcruncher/pipeline/config/{{cookiecutter.date}}_{{cookiecutter.__project_id}}_{{cookiecutter.__assay}}
2023-09-26T17:29:24,671   creating build/lib/capcruncher/pipeline/workflow/envs
2023-09-26T17:29:24,672   copying capcruncher/pipeline/workflow/envs/environment.yml -> build/lib/capcruncher/pipeline/workflow/envs
2023-09-26T17:29:24,674   creating build/lib/capcruncher/pipeline/workflow/rules
2023-09-26T17:29:24,675   copying capcruncher/pipeline/workflow/rules/align.smk -> build/lib/capcruncher/pipeline/workflow/rules
2023-09-26T17:29:24,677   copying capcruncher/pipeline/workflow/rules/annotate.smk -> build/lib/capcruncher/pipeline/workflow/rules
2023-09-26T17:29:24,679   copying capcruncher/pipeline/workflow/rules/compare.smk -> build/lib/capcruncher/pipeline/workflow/rules
2023-09-26T17:29:24,681   copying capcruncher/pipeline/workflow/rules/digest.smk -> build/lib/capcruncher/pipeline/workflow/rules
2023-09-26T17:29:24,683   copying capcruncher/pipeline/workflow/rules/fastq.smk -> build/lib/capcruncher/pipeline/workflow/rules
2023-09-26T17:29:24,685   copying capcruncher/pipeline/workflow/rules/filter.smk -> build/lib/capcruncher/pipeline/workflow/rules
2023-09-26T17:29:24,688   copying capcruncher/pipeline/workflow/rules/pileup.smk -> build/lib/capcruncher/pipeline/workflow/rules
2023-09-26T17:29:24,690   copying capcruncher/pipeline/workflow/rules/qc.smk -> build/lib/capcruncher/pipeline/workflow/rules
2023-09-26T17:29:24,692   copying capcruncher/pipeline/workflow/rules/statistics.smk -> build/lib/capcruncher/pipeline/workflow/rules
2023-09-26T17:29:24,694   copying capcruncher/pipeline/workflow/rules/visualise.smk -> build/lib/capcruncher/pipeline/workflow/rules
2023-09-26T17:29:24,696   copying capcruncher/pipeline/workflow/report/capcruncher_report.qmd -> build/lib/capcruncher/pipeline/workflow/report
2023-09-26T17:29:24,699   copying capcruncher/pipeline/workflow/report/report_text.yml -> build/lib/capcruncher/pipeline/workflow/report
2023-09-26T17:29:24,701   creating build/lib/capcruncher/pipeline/workflow/data
2023-09-26T17:29:24,702   copying capcruncher/pipeline/workflow/data/annotation_defaults.json -> build/lib/capcruncher/pipeline/workflow/data
2023-09-26T17:29:24,704   creating build/lib/capcruncher/pipeline/workflow/envs/profiles
2023-09-26T17:29:24,705   creating build/lib/capcruncher/pipeline/workflow/envs/profiles/profile_singularity
2023-09-26T17:29:24,706   copying capcruncher/pipeline/workflow/envs/profiles/profile_singularity/config.yaml -> build/lib/capcruncher/pipeline/workflow/envs/profiles/profile_singularity
2023-09-26T17:29:24,708   creating build/lib/capcruncher/pipeline/workflow/envs/profiles/profile_drmaa_singularity
2023-09-26T17:29:24,709   copying capcruncher/pipeline/workflow/envs/profiles/profile_drmaa_singularity/config.yaml -> build/lib/capcruncher/pipeline/workflow/envs/profiles/profile_drmaa_singularity
2023-09-26T17:29:24,726   installing to build/bdist.linux-armv7l/wheel
2023-09-26T17:29:24,727   running install
2023-09-26T17:29:24,751   running install_lib
2023-09-26T17:29:24,756   creating build/bdist.linux-armv7l
2023-09-26T17:29:24,757   creating build/bdist.linux-armv7l/wheel
2023-09-26T17:29:24,758   creating build/bdist.linux-armv7l/wheel/capcruncher
2023-09-26T17:29:24,759   copying build/lib/capcruncher/__init__.py -> build/bdist.linux-armv7l/wheel/capcruncher
2023-09-26T17:29:24,761   copying build/lib/capcruncher/utils.py -> build/bdist.linux-armv7l/wheel/capcruncher
2023-09-26T17:29:24,764   creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline
2023-09-26T17:29:24,765   creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow
2023-09-26T17:29:24,767   creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/envs
2023-09-26T17:29:24,768   copying build/lib/capcruncher/pipeline/workflow/envs/environment.yml -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/envs
2023-09-26T17:29:24,770   creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/envs/profiles
2023-09-26T17:29:24,771   creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/envs/profiles/profile_singularity
2023-09-26T17:29:24,772   copying build/lib/capcruncher/pipeline/workflow/envs/profiles/profile_singularity/config.yaml -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/envs/profiles/profile_singularity
2023-09-26T17:29:24,774   creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/envs/profiles/profile_drmaa_singularity
2023-09-26T17:29:24,775   copying build/lib/capcruncher/pipeline/workflow/envs/profiles/profile_drmaa_singularity/config.yaml -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/envs/profiles/profile_drmaa_singularity
2023-09-26T17:29:24,777   creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules
2023-09-26T17:29:24,778   copying build/lib/capcruncher/pipeline/workflow/rules/align.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules
2023-09-26T17:29:24,780   copying build/lib/capcruncher/pipeline/workflow/rules/pileup.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules
2023-09-26T17:29:24,782   copying build/lib/capcruncher/pipeline/workflow/rules/filter.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules
2023-09-26T17:29:24,784   copying build/lib/capcruncher/pipeline/workflow/rules/fastq.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules
2023-09-26T17:29:24,787   copying build/lib/capcruncher/pipeline/workflow/rules/annotate.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules
2023-09-26T17:29:24,789   copying build/lib/capcruncher/pipeline/workflow/rules/statistics.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules
2023-09-26T17:29:24,792   copying build/lib/capcruncher/pipeline/workflow/rules/visualise.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules
2023-09-26T17:29:24,795   copying build/lib/capcruncher/pipeline/workflow/rules/qc.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules
2023-09-26T17:29:24,797   copying build/lib/capcruncher/pipeline/workflow/rules/compare.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules
2023-09-26T17:29:24,800   copying build/lib/capcruncher/pipeline/workflow/rules/digest.smk -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/rules
2023-09-26T17:29:24,802   copying build/lib/capcruncher/pipeline/workflow/Snakefile -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow
2023-09-26T17:29:24,805   creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/report
2023-09-26T17:29:24,806   copying build/lib/capcruncher/pipeline/workflow/report/capcruncher_report.qmd -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/report
2023-09-26T17:29:24,810   copying build/lib/capcruncher/pipeline/workflow/report/report_text.yml -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/report
2023-09-26T17:29:24,812   copying build/lib/capcruncher/pipeline/workflow/report/make_report.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/report
2023-09-26T17:29:24,816   creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/data
2023-09-26T17:29:24,817   copying build/lib/capcruncher/pipeline/workflow/data/annotation_defaults.json -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/data
2023-09-26T17:29:24,819   creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts
2023-09-26T17:29:24,820   copying build/lib/capcruncher/pipeline/workflow/scripts/count_identified_viewpoints.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts
2023-09-26T17:29:24,823   copying build/lib/capcruncher/pipeline/workflow/scripts/combine_filtering_stats.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts
2023-09-26T17:29:24,825   copying build/lib/capcruncher/pipeline/workflow/scripts/remove_duplicate_coordinates.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts
2023-09-26T17:29:24,827   copying build/lib/capcruncher/pipeline/workflow/scripts/identify_viewpoints_with_interactions.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts
2023-09-26T17:29:24,829   copying build/lib/capcruncher/pipeline/workflow/scripts/combine_digestion_stats.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts
2023-09-26T17:29:24,831   copying build/lib/capcruncher/pipeline/workflow/scripts/combine_stats_read_level.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts
2023-09-26T17:29:24,833   copying build/lib/capcruncher/pipeline/workflow/scripts/plot.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts
2023-09-26T17:29:24,835   copying build/lib/capcruncher/pipeline/workflow/scripts/make_ucsc_hub.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts
2023-09-26T17:29:24,837   copying build/lib/capcruncher/pipeline/workflow/scripts/combine_deduplication_stats.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts
2023-09-26T17:29:24,839   copying build/lib/capcruncher/pipeline/workflow/scripts/combine_cis_and_trans_stats.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts
2023-09-26T17:29:24,841   copying build/lib/capcruncher/pipeline/workflow/scripts/combine_alignment_deduplication_stats.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/workflow/scripts
2023-09-26T17:29:24,843   copying build/lib/capcruncher/pipeline/utils.py -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline
2023-09-26T17:29:24,846   creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/config
2023-09-26T17:29:24,848   creating build/bdist.linux-armv7l/wheel/capcruncher/pipeline/config/{{cookiecutter.date}}_{{cookiecutter.__project_id}}_{{cookiecutter.__assay}}
2023-09-26T17:29:24,849   copying build/lib/capcruncher/pipeline/config/{{cookiecutter.date}}_{{cookiecutter.__project_id}}_{{cookiecutter.__assay}}/capcruncher_config.yml -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/config/{{cookiecutter.date}}_{{cookiecutter.__project_id}}_{{cookiecutter.__assay}}
2023-09-26T17:29:24,852   copying build/lib/capcruncher/pipeline/config/cookiecutter.json -> build/bdist.linux-armv7l/wheel/capcruncher/pipeline/config
2023-09-26T17:29:24,855   creating build/bdist.linux-armv7l/wheel/capcruncher/data
2023-09-26T17:29:24,856   copying build/lib/capcruncher/data/logo.txt -> build/bdist.linux-armv7l/wheel/capcruncher/data
2023-09-26T17:29:24,858   copying build/lib/capcruncher/_version.py -> build/bdist.linux-armv7l/wheel/capcruncher
2023-09-26T17:29:24,861   creating build/bdist.linux-armv7l/wheel/capcruncher/api
2023-09-26T17:29:24,862   copying build/lib/capcruncher/api/count.py -> build/bdist.linux-armv7l/wheel/capcruncher/api
2023-09-26T17:29:24,864   copying build/lib/capcruncher/api/__init__.py -> build/bdist.linux-armv7l/wheel/capcruncher/api
2023-09-26T17:29:24,866   copying build/lib/capcruncher/api/statistics.py -> build/bdist.linux-armv7l/wheel/capcruncher/api
2023-09-26T17:29:24,868   copying build/lib/capcruncher/api/storage.py -> build/bdist.linux-armv7l/wheel/capcruncher/api
2023-09-26T17:29:24,871   copying build/lib/capcruncher/api/digest.py -> build/bdist.linux-armv7l/wheel/capcruncher/api
2023-09-26T17:29:24,874   copying build/lib/capcruncher/api/pileup.py -> build/bdist.linux-armv7l/wheel/capcruncher/api
2023-09-26T17:29:24,877   copying build/lib/capcruncher/api/deduplicate.py -> build/bdist.linux-armv7l/wheel/capcruncher/api
2023-09-26T17:29:24,879   copying build/lib/capcruncher/api/filter.py -> build/bdist.linux-armv7l/wheel/capcruncher/api
2023-09-26T17:29:24,882   copying build/lib/capcruncher/api/io.py -> build/bdist.linux-armv7l/wheel/capcruncher/api
2023-09-26T17:29:24,885   copying build/lib/capcruncher/api/annotate.py -> build/bdist.linux-armv7l/wheel/capcruncher/api
2023-09-26T17:29:24,887   copying build/lib/capcruncher/api/plotting.py -> build/bdist.linux-armv7l/wheel/capcruncher/api
2023-09-26T17:29:24,890   creating build/bdist.linux-armv7l/wheel/capcruncher/cli
2023-09-26T17:29:24,891   copying build/lib/capcruncher/cli/fastq_deduplicate.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli
2023-09-26T17:29:24,893   copying build/lib/capcruncher/cli/interactions_compare.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli
2023-09-26T17:29:24,895   copying build/lib/capcruncher/cli/interactions_count.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli
2023-09-26T17:29:24,897   copying build/lib/capcruncher/cli/__init__.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli
2023-09-26T17:29:24,899   copying build/lib/capcruncher/cli/interactions_store.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli
2023-09-26T17:29:24,901   copying build/lib/capcruncher/cli/alignments_filter.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli
2023-09-26T17:29:24,903   copying build/lib/capcruncher/cli/interactions_deduplicate.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli
2023-09-26T17:29:24,906   copying build/lib/capcruncher/cli/plot.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli
2023-09-26T17:29:24,907   copying build/lib/capcruncher/cli/cli_plot.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli
2023-09-26T17:29:24,909   copying build/lib/capcruncher/cli/cli_fastq.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli
2023-09-26T17:29:24,911   copying build/lib/capcruncher/cli/cli_utilities.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli
2023-09-26T17:29:24,914   copying build/lib/capcruncher/cli/alignments_annotate.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli
2023-09-26T17:29:24,916   copying build/lib/capcruncher/cli/interactions_pileup.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli
2023-09-26T17:29:24,918   copying build/lib/capcruncher/cli/interactions_differential.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli
2023-09-26T17:29:24,920   copying build/lib/capcruncher/cli/genome_digest.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli
2023-09-26T17:29:24,922   copying build/lib/capcruncher/cli/cli_genome.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli
2023-09-26T17:29:24,923   copying build/lib/capcruncher/cli/fastq_split.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli
2023-09-26T17:29:24,925   copying build/lib/capcruncher/cli/cli_pipeline.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli
2023-09-26T17:29:24,927   copying build/lib/capcruncher/cli/cli_interactions.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli
2023-09-26T17:29:24,929   copying build/lib/capcruncher/cli/cli_alignments.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli
2023-09-26T17:29:24,932   copying build/lib/capcruncher/cli/fastq_digest.py -> build/bdist.linux-armv7l/wheel/capcruncher/cli
2023-09-26T17:29:24,934   running install_egg_info
2023-09-26T17:29:24,939   Copying capcruncher.egg-info to build/bdist.linux-armv7l/wheel/capcruncher-0.3.3-py3.11.egg-info
2023-09-26T17:29:24,953   running install_scripts
2023-09-26T17:29:24,979   creating build/bdist.linux-armv7l/wheel/capcruncher-0.3.3.dist-info/WHEEL
2023-09-26T17:29:24,981   creating '/tmp/pip-wheel-5ltwhinx/.tmp-tdzz__7d/capcruncher-0.3.3-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2023-09-26T17:29:24,983   adding 'capcruncher/__init__.py'
2023-09-26T17:29:24,984   adding 'capcruncher/_version.py'
2023-09-26T17:29:24,987   adding 'capcruncher/utils.py'
2023-09-26T17:29:24,988   adding 'capcruncher/api/__init__.py'
2023-09-26T17:29:24,990   adding 'capcruncher/api/annotate.py'
2023-09-26T17:29:24,991   adding 'capcruncher/api/count.py'
2023-09-26T17:29:24,993   adding 'capcruncher/api/deduplicate.py'
2023-09-26T17:29:24,995   adding 'capcruncher/api/digest.py'
2023-09-26T17:29:24,999   adding 'capcruncher/api/filter.py'
2023-09-26T17:29:25,002   adding 'capcruncher/api/io.py'
2023-09-26T17:29:25,004   adding 'capcruncher/api/pileup.py'
2023-09-26T17:29:25,007   adding 'capcruncher/api/plotting.py'
2023-09-26T17:29:25,009   adding 'capcruncher/api/statistics.py'
2023-09-26T17:29:25,011   adding 'capcruncher/api/storage.py'
2023-09-26T17:29:25,013   adding 'capcruncher/cli/__init__.py'
2023-09-26T17:29:25,015   adding 'capcruncher/cli/alignments_annotate.py'
2023-09-26T17:29:25,017   adding 'capcruncher/cli/alignments_filter.py'
2023-09-26T17:29:25,018   adding 'capcruncher/cli/cli_alignments.py'
2023-09-26T17:29:25,020   adding 'capcruncher/cli/cli_fastq.py'
2023-09-26T17:29:25,021   adding 'capcruncher/cli/cli_genome.py'
2023-09-26T17:29:25,023   adding 'capcruncher/cli/cli_interactions.py'
2023-09-26T17:29:25,024   adding 'capcruncher/cli/cli_pipeline.py'
2023-09-26T17:29:25,026   adding 'capcruncher/cli/cli_plot.py'
2023-09-26T17:29:25,027   adding 'capcruncher/cli/cli_utilities.py'
2023-09-26T17:29:25,029   adding 'capcruncher/cli/fastq_deduplicate.py'
2023-09-26T17:29:25,030   adding 'capcruncher/cli/fastq_digest.py'
2023-09-26T17:29:25,032   adding 'capcruncher/cli/fastq_split.py'
2023-09-26T17:29:25,033   adding 'capcruncher/cli/genome_digest.py'
2023-09-26T17:29:25,035   adding 'capcruncher/cli/interactions_compare.py'
2023-09-26T17:29:25,036   adding 'capcruncher/cli/interactions_count.py'
2023-09-26T17:29:25,038   adding 'capcruncher/cli/interactions_deduplicate.py'
2023-09-26T17:29:25,040   adding 'capcruncher/cli/interactions_differential.py'
2023-09-26T17:29:25,041   adding 'capcruncher/cli/interactions_pileup.py'
2023-09-26T17:29:25,043   adding 'capcruncher/cli/interactions_store.py'
2023-09-26T17:29:25,044   adding 'capcruncher/cli/plot.py'
2023-09-26T17:29:25,046   adding 'capcruncher/data/logo.txt'
2023-09-26T17:29:25,049   adding 'capcruncher/pipeline/utils.py'
2023-09-26T17:29:25,051   adding 'capcruncher/pipeline/config/cookiecutter.json'
2023-09-26T17:29:25,053   adding 'capcruncher/pipeline/config/{{cookiecutter.date}}_{{cookiecutter.__project_id}}_{{cookiecutter.__assay}}/capcruncher_config.yml'
2023-09-26T17:29:25,055   adding 'capcruncher/pipeline/workflow/Snakefile'
2023-09-26T17:29:25,056   adding 'capcruncher/pipeline/workflow/data/annotation_defaults.json'
2023-09-26T17:29:25,058   adding 'capcruncher/pipeline/workflow/envs/environment.yml'
2023-09-26T17:29:25,060   adding 'capcruncher/pipeline/workflow/envs/profiles/profile_drmaa_singularity/config.yaml'
2023-09-26T17:29:25,062   adding 'capcruncher/pipeline/workflow/envs/profiles/profile_singularity/config.yaml'
2023-09-26T17:29:25,064   adding 'capcruncher/pipeline/workflow/report/capcruncher_report.qmd'
2023-09-26T17:29:25,067   adding 'capcruncher/pipeline/workflow/report/make_report.py'
2023-09-26T17:29:25,068   adding 'capcruncher/pipeline/workflow/report/report_text.yml'
2023-09-26T17:29:25,070   adding 'capcruncher/pipeline/workflow/rules/align.smk'
2023-09-26T17:29:25,072   adding 'capcruncher/pipeline/workflow/rules/annotate.smk'
2023-09-26T17:29:25,073   adding 'capcruncher/pipeline/workflow/rules/compare.smk'
2023-09-26T17:29:25,074   adding 'capcruncher/pipeline/workflow/rules/digest.smk'
2023-09-26T17:29:25,076   adding 'capcruncher/pipeline/workflow/rules/fastq.smk'
2023-09-26T17:29:25,078   adding 'capcruncher/pipeline/workflow/rules/filter.smk'
2023-09-26T17:29:25,079   adding 'capcruncher/pipeline/workflow/rules/pileup.smk'
2023-09-26T17:29:25,080   adding 'capcruncher/pipeline/workflow/rules/qc.smk'
2023-09-26T17:29:25,082   adding 'capcruncher/pipeline/workflow/rules/statistics.smk'
2023-09-26T17:29:25,083   adding 'capcruncher/pipeline/workflow/rules/visualise.smk'
2023-09-26T17:29:25,085   adding 'capcruncher/pipeline/workflow/scripts/combine_alignment_deduplication_stats.py'
2023-09-26T17:29:25,086   adding 'capcruncher/pipeline/workflow/scripts/combine_cis_and_trans_stats.py'
2023-09-26T17:29:25,087   adding 'capcruncher/pipeline/workflow/scripts/combine_deduplication_stats.py'
2023-09-26T17:29:25,088   adding 'capcruncher/pipeline/workflow/scripts/combine_digestion_stats.py'
2023-09-26T17:29:25,089   adding 'capcruncher/pipeline/workflow/scripts/combine_filtering_stats.py'
2023-09-26T17:29:25,090   adding 'capcruncher/pipeline/workflow/scripts/combine_stats_read_level.py'
2023-09-26T17:29:25,091   adding 'capcruncher/pipeline/workflow/scripts/count_identified_viewpoints.py'
2023-09-26T17:29:25,092   adding 'capcruncher/pipeline/workflow/scripts/identify_viewpoints_with_interactions.py'
2023-09-26T17:29:25,093   adding 'capcruncher/pipeline/workflow/scripts/make_ucsc_hub.py'
2023-09-26T17:29:25,095   adding 'capcruncher/pipeline/workflow/scripts/plot.py'
2023-09-26T17:29:25,096   adding 'capcruncher/pipeline/workflow/scripts/remove_duplicate_coordinates.py'
2023-09-26T17:29:25,103   adding 'capcruncher-0.3.3.dist-info/LICENSE'
2023-09-26T17:29:25,110   adding 'capcruncher-0.3.3.dist-info/METADATA'
2023-09-26T17:29:25,111   adding 'capcruncher-0.3.3.dist-info/WHEEL'
2023-09-26T17:29:25,112   adding 'capcruncher-0.3.3.dist-info/entry_points.txt'
2023-09-26T17:29:25,113   adding 'capcruncher-0.3.3.dist-info/top_level.txt'
2023-09-26T17:29:25,115   adding 'capcruncher-0.3.3.dist-info/RECORD'
2023-09-26T17:29:25,118   removing build/bdist.linux-armv7l/wheel
2023-09-26T17:29:25,263   Building wheel for capcruncher (pyproject.toml): finished with status 'done'
2023-09-26T17:29:25,271   Created wheel for capcruncher: filename=capcruncher-0.3.3-py3-none-any.whl size=160042 sha256=a622eec10ed86905ffdc0d9696093c93ede9ae0280eb0979727ed05b78c6aeed
2023-09-26T17:29:25,273   Stored in directory: /tmp/pip-ephem-wheel-cache-hu2p_d9q/wheels/f0/33/5c/16390f3bb731c21a79d8f28e5c3bd5d5e88daab8442fa7634d
2023-09-26T17:29:25,308 Successfully built capcruncher
2023-09-26T17:29:25,315 Removed build tracker: '/tmp/pip-build-tracker-4xpb7z4y'