2023-08-01T19:08:35,297 Created temporary directory: /tmp/pip-build-tracker-a3hrjfo9
2023-08-01T19:08:35,300 Initialized build tracking at /tmp/pip-build-tracker-a3hrjfo9
2023-08-01T19:08:35,300 Created build tracker: /tmp/pip-build-tracker-a3hrjfo9
2023-08-01T19:08:35,301 Entered build tracker: /tmp/pip-build-tracker-a3hrjfo9
2023-08-01T19:08:35,302 Created temporary directory: /tmp/pip-wheel-ykbr0_qk
2023-08-01T19:08:35,310 Created temporary directory: /tmp/pip-ephem-wheel-cache-jm4onnlo
2023-08-01T19:08:35,367 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-08-01T19:08:35,375 2 location(s) to search for versions of novartis-pisces:
2023-08-01T19:08:35,375 * https://pypi.org/simple/novartis-pisces/
2023-08-01T19:08:35,375 * https://www.piwheels.org/simple/novartis-pisces/
2023-08-01T19:08:35,376 Fetching project page and analyzing links: https://pypi.org/simple/novartis-pisces/
2023-08-01T19:08:35,377 Getting page https://pypi.org/simple/novartis-pisces/
2023-08-01T19:08:35,382 Found index url https://pypi.org/simple/
2023-08-01T19:08:35,569 Fetched page https://pypi.org/simple/novartis-pisces/ as application/vnd.pypi.simple.v1+json
2023-08-01T19:08:35,576   Found link https://files.pythonhosted.org/packages/7a/69/6e62653f167dfe6d2fa7f2f6527efa22825fecf80941f3190b20b8c0b972/novartis-pisces-0.1.1.tar.gz (from https://pypi.org/simple/novartis-pisces/), version: 0.1.1
2023-08-01T19:08:35,577   Found link https://files.pythonhosted.org/packages/88/19/cdb5149b3ea5580bafffd7f6b2b18807bdd1cf364154be052bfb17b7a392/novartis-pisces-0.1.2.tar.gz (from https://pypi.org/simple/novartis-pisces/), version: 0.1.2
2023-08-01T19:08:35,578   Found link https://files.pythonhosted.org/packages/b6/72/9686797df03a1087913e92f359e09d7f35458b06c9503d27cbfce69959d6/novartis-pisces-0.1.3.tar.gz (from https://pypi.org/simple/novartis-pisces/), version: 0.1.3
2023-08-01T19:08:35,579   Found link https://files.pythonhosted.org/packages/63/0c/bd21a99df2f38fc359ec3531b30c5439dbdd1d22e06cfeadf657af9be952/novartis-pisces-0.1.3.1.tar.gz (from https://pypi.org/simple/novartis-pisces/), version: 0.1.3.1
2023-08-01T19:08:35,579   Found link https://files.pythonhosted.org/packages/9b/25/e64baf962e42cecb02340a0221e24866dedd8c857121a69db18f86ed86a8/novartis-pisces-0.1.4.tar.gz (from https://pypi.org/simple/novartis-pisces/), version: 0.1.4
2023-08-01T19:08:35,580   Found link https://files.pythonhosted.org/packages/47/d7/f2333e006f03d2cb23636c41e665d0b6b5d1d4bd693e0c4328306fc581f2/novartis-pisces-0.1.4.2.tar.gz (from https://pypi.org/simple/novartis-pisces/), version: 0.1.4.2
2023-08-01T19:08:35,581   Found link https://files.pythonhosted.org/packages/0a/48/055cb93cbf103efb27a5299a5784324ad7e76fe666b9eea4ea529a6c784a/novartis-pisces-0.1.4.3.tar.gz (from https://pypi.org/simple/novartis-pisces/), version: 0.1.4.3
2023-08-01T19:08:35,582   Found link https://files.pythonhosted.org/packages/df/1b/609c197d769cf58999fef31ca73018158da30c34fee05041fa4b72131db8/novartis-pisces-0.1.4.4.tar.gz (from https://pypi.org/simple/novartis-pisces/), version: 0.1.4.4
2023-08-01T19:08:35,582   Found link https://files.pythonhosted.org/packages/f9/86/6109b1944321f01860299418d02854fa363d089bf41f2c88653bdd14cdc0/novartis-pisces-0.1.5.tar.gz (from https://pypi.org/simple/novartis-pisces/), version: 0.1.5
2023-08-01T19:08:35,583   Found link https://files.pythonhosted.org/packages/a3/e9/395d751e1b0d5b42d522459785f13d62837c39fbaf574a74dcbf43838982/novartis-pisces-0.1.5.1.tar.gz (from https://pypi.org/simple/novartis-pisces/), version: 0.1.5.1
2023-08-01T19:08:35,584   Found link https://files.pythonhosted.org/packages/5d/4f/545e40e9507a80647bfeb966da7da5271920101f1554d36fbc7306d0c0d6/novartis-pisces-0.1.5.2.tar.gz (from https://pypi.org/simple/novartis-pisces/), version: 0.1.5.2
2023-08-01T19:08:35,584   Found link https://files.pythonhosted.org/packages/49/5a/10d741c26a5aadf722151c257b4ace447289e332b20af2ac5e0004d91717/novartis-pisces-0.1.5.3.tar.gz (from https://pypi.org/simple/novartis-pisces/), version: 0.1.5.3
2023-08-01T19:08:35,585   Found link https://files.pythonhosted.org/packages/9d/c6/f5281428cd417282eaad9dc9f86285a2faf5439b385080706b933e75dbcc/novartis-pisces-0.1.5.4.tar.gz (from https://pypi.org/simple/novartis-pisces/), version: 0.1.5.4
2023-08-01T19:08:35,586 Fetching project page and analyzing links: https://www.piwheels.org/simple/novartis-pisces/
2023-08-01T19:08:35,587 Getting page https://www.piwheels.org/simple/novartis-pisces/
2023-08-01T19:08:35,589 Found index url https://www.piwheels.org/simple/
2023-08-01T19:08:38,743 Fetched page https://www.piwheels.org/simple/novartis-pisces/ as text/html
2023-08-01T19:08:38,754   Skipping link: No binaries permitted for novartis-pisces: https://www.piwheels.org/simple/novartis-pisces/novartis_pisces-0.1.5.3-py3-none-any.whl#sha256=0be70a0f10f544c510e42d56da47ae61656817a7a51943dbcaa0152b2f9d5b2e (from https://www.piwheels.org/simple/novartis-pisces/)
2023-08-01T19:08:38,754   Skipping link: No binaries permitted for novartis-pisces: https://www.piwheels.org/simple/novartis-pisces/novartis_pisces-0.1.5.2-py3-none-any.whl#sha256=ee8d2bce8468cf80bac576688fb20a9b147bedacf713b28a6331331038c5d297 (from https://www.piwheels.org/simple/novartis-pisces/)
2023-08-01T19:08:38,755   Skipping link: No binaries permitted for novartis-pisces: https://www.piwheels.org/simple/novartis-pisces/novartis_pisces-0.1.5.1-py3-none-any.whl#sha256=87da139877c1ef0c13f62f10cd4b8bb26d9b974802bbeaf78db3a35cc7d3db10 (from https://www.piwheels.org/simple/novartis-pisces/)
2023-08-01T19:08:38,756   Skipping link: No binaries permitted for novartis-pisces: https://www.piwheels.org/simple/novartis-pisces/novartis_pisces-0.1.5-py3-none-any.whl#sha256=7e39afffb0c219f2e37c2f7b017192cc9c5bb3792dd6af985d7939124a0103da (from https://www.piwheels.org/simple/novartis-pisces/)
2023-08-01T19:08:38,756   Skipping link: No binaries permitted for novartis-pisces: https://www.piwheels.org/simple/novartis-pisces/novartis_pisces-0.1.4.4-py3-none-any.whl#sha256=9a602e2da8188d15ac02b3692617eff25353f07156d354e90e113137fa3b61bd (from https://www.piwheels.org/simple/novartis-pisces/)
2023-08-01T19:08:38,757   Skipping link: No binaries permitted for novartis-pisces: https://www.piwheels.org/simple/novartis-pisces/novartis_pisces-0.1.4.3-py3-none-any.whl#sha256=0df67ceec82649982fda766535f4204513e9793b6cbf2249d232a8b3356a6612 (from https://www.piwheels.org/simple/novartis-pisces/)
2023-08-01T19:08:38,757   Skipping link: No binaries permitted for novartis-pisces: https://www.piwheels.org/simple/novartis-pisces/novartis_pisces-0.1.4.2-py3-none-any.whl#sha256=1f3afb64b4b21079a21a00759a77ab8d214e7fcb2e1828a43af80907f45fe8b1 (from https://www.piwheels.org/simple/novartis-pisces/)
2023-08-01T19:08:38,758   Skipping link: No binaries permitted for novartis-pisces: https://www.piwheels.org/simple/novartis-pisces/novartis_pisces-0.1.4-py3-none-any.whl#sha256=39a3055ebdc62506630a204a088cfa4f42615ade27909d36f06560f2ac8b75ba (from https://www.piwheels.org/simple/novartis-pisces/)
2023-08-01T19:08:38,758   Skipping link: No binaries permitted for novartis-pisces: https://www.piwheels.org/simple/novartis-pisces/novartis_pisces-0.1.3.1-py3-none-any.whl#sha256=01160ead2aa7f47bfe8a6b47b1989993ec6cc55701d98eb00b283a7dd2c005a0 (from https://www.piwheels.org/simple/novartis-pisces/)
2023-08-01T19:08:38,759   Skipping link: No binaries permitted for novartis-pisces: https://www.piwheels.org/simple/novartis-pisces/novartis_pisces-0.1.3-py3-none-any.whl#sha256=0022b6d3eb89c050d399a54f590cce7fd6b6ec8a6a2288d8d261e0e5cbefc8f4 (from https://www.piwheels.org/simple/novartis-pisces/)
2023-08-01T19:08:38,759   Skipping link: No binaries permitted for novartis-pisces: https://www.piwheels.org/simple/novartis-pisces/novartis_pisces-0.1.2-py3-none-any.whl#sha256=532b73754e880867474c1c9c9046f131bb6ac4a8f405bb90e268a409061f484b (from https://www.piwheels.org/simple/novartis-pisces/)
2023-08-01T19:08:38,760   Skipping link: No binaries permitted for novartis-pisces: https://www.piwheels.org/simple/novartis-pisces/novartis_pisces-0.1.1-py3-none-any.whl#sha256=7f340ebd9be1b1aef037720ffe1fc5123b123bf5952db113595023dc095cb0b4 (from https://www.piwheels.org/simple/novartis-pisces/)
2023-08-01T19:08:38,760 Skipping link: not a file: https://www.piwheels.org/simple/novartis-pisces/
2023-08-01T19:08:38,761 Skipping link: not a file: https://pypi.org/simple/novartis-pisces/
2023-08-01T19:08:38,798 Given no hashes to check 1 links for project 'novartis-pisces': discarding no candidates
2023-08-01T19:08:38,829 Collecting novartis-pisces==0.1.5.4
2023-08-01T19:08:38,833   Created temporary directory: /tmp/pip-unpack-x3gjqarp
2023-08-01T19:08:39,265   Downloading novartis-pisces-0.1.5.4.tar.gz (18.4 MB)
2023-08-01T19:08:47,196   Added novartis-pisces==0.1.5.4 from https://files.pythonhosted.org/packages/9d/c6/f5281428cd417282eaad9dc9f86285a2faf5439b385080706b933e75dbcc/novartis-pisces-0.1.5.4.tar.gz to build tracker '/tmp/pip-build-tracker-a3hrjfo9'
2023-08-01T19:08:47,201   Running setup.py (path:/tmp/pip-wheel-ykbr0_qk/novartis-pisces_969bd63926e04dcba47df953ff3afd65/setup.py) egg_info for package novartis-pisces
2023-08-01T19:08:47,202   Created temporary directory: /tmp/pip-pip-egg-info-fq8atbeb
2023-08-01T19:08:47,203   Preparing metadata (setup.py): started
2023-08-01T19:08:47,205   Running command python setup.py egg_info
2023-08-01T19:08:54,968   running egg_info
2023-08-01T19:08:54,972   creating /tmp/pip-pip-egg-info-fq8atbeb/novartis_pisces.egg-info
2023-08-01T19:08:55,048   writing /tmp/pip-pip-egg-info-fq8atbeb/novartis_pisces.egg-info/PKG-INFO
2023-08-01T19:08:55,053   writing dependency_links to /tmp/pip-pip-egg-info-fq8atbeb/novartis_pisces.egg-info/dependency_links.txt
2023-08-01T19:08:55,058   writing entry points to /tmp/pip-pip-egg-info-fq8atbeb/novartis_pisces.egg-info/entry_points.txt
2023-08-01T19:08:55,061   writing requirements to /tmp/pip-pip-egg-info-fq8atbeb/novartis_pisces.egg-info/requires.txt
2023-08-01T19:08:55,064   writing top-level names to /tmp/pip-pip-egg-info-fq8atbeb/novartis_pisces.egg-info/top_level.txt
2023-08-01T19:08:55,068   writing manifest file '/tmp/pip-pip-egg-info-fq8atbeb/novartis_pisces.egg-info/SOURCES.txt'
2023-08-01T19:08:55,494   /usr/local/lib/python3.7/dist-packages/setuptools/__init__.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
2023-08-01T19:08:55,494   !!

2023-08-01T19:08:55,495           ********************************************************************************
2023-08-01T19:08:55,495           Requirements should be satisfied by a PEP 517 installer.
2023-08-01T19:08:55,496           If you are using pip, you can try `pip install --use-pep517`.
2023-08-01T19:08:55,496           ********************************************************************************

2023-08-01T19:08:55,497   !!
2023-08-01T19:08:55,497     dist.fetch_build_eggs(dist.setup_requires)
2023-08-01T19:08:55,498   listing git files failed - pretending there aren't any
2023-08-01T19:08:55,520   reading manifest file '/tmp/pip-pip-egg-info-fq8atbeb/novartis_pisces.egg-info/SOURCES.txt'
2023-08-01T19:08:55,524   reading manifest template 'MANIFEST.in'
2023-08-01T19:08:55,537   adding license file 'LICENSE'
2023-08-01T19:08:55,544   writing manifest file '/tmp/pip-pip-egg-info-fq8atbeb/novartis_pisces.egg-info/SOURCES.txt'
2023-08-01T19:08:55,707   Preparing metadata (setup.py): finished with status 'done'
2023-08-01T19:08:55,720   Source in /tmp/pip-wheel-ykbr0_qk/novartis-pisces_969bd63926e04dcba47df953ff3afd65 has version 0.1.5.4, which satisfies requirement novartis-pisces==0.1.5.4 from https://files.pythonhosted.org/packages/9d/c6/f5281428cd417282eaad9dc9f86285a2faf5439b385080706b933e75dbcc/novartis-pisces-0.1.5.4.tar.gz
2023-08-01T19:08:55,722   Removed novartis-pisces==0.1.5.4 from https://files.pythonhosted.org/packages/9d/c6/f5281428cd417282eaad9dc9f86285a2faf5439b385080706b933e75dbcc/novartis-pisces-0.1.5.4.tar.gz from build tracker '/tmp/pip-build-tracker-a3hrjfo9'
2023-08-01T19:08:55,733 Created temporary directory: /tmp/pip-unpack-4075ft4c
2023-08-01T19:08:55,734 Building wheels for collected packages: novartis-pisces
2023-08-01T19:08:55,743   Created temporary directory: /tmp/pip-wheel-lby3o62p
2023-08-01T19:08:55,744   Building wheel for novartis-pisces (setup.py): started
2023-08-01T19:08:55,746   Destination directory: /tmp/pip-wheel-lby3o62p
2023-08-01T19:08:55,747   Running command python setup.py bdist_wheel
2023-08-01T19:08:57,461   /usr/local/lib/python3.7/dist-packages/setuptools/__init__.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
2023-08-01T19:08:57,462   !!

2023-08-01T19:08:57,463           ********************************************************************************
2023-08-01T19:08:57,463           Requirements should be satisfied by a PEP 517 installer.
2023-08-01T19:08:57,463           If you are using pip, you can try `pip install --use-pep517`.
2023-08-01T19:08:57,464           ********************************************************************************

2023-08-01T19:08:57,464   !!
2023-08-01T19:08:57,465     dist.fetch_build_eggs(dist.setup_requires)
2023-08-01T19:08:58,648   running bdist_wheel
2023-08-01T19:08:59,452   running build
2023-08-01T19:08:59,453   running build_py
2023-08-01T19:08:59,537   creating build
2023-08-01T19:08:59,539   creating build/lib
2023-08-01T19:08:59,541   creating build/lib/pisces
2023-08-01T19:08:59,544   copying pisces/index.py -> build/lib/pisces
2023-08-01T19:08:59,550   copying pisces/qc.py -> build/lib/pisces
2023-08-01T19:08:59,554   copying pisces/cli.py -> build/lib/pisces
2023-08-01T19:08:59,560   copying pisces/__init__.py -> build/lib/pisces
2023-08-01T19:08:59,565   copying pisces/fastq.py -> build/lib/pisces
2023-08-01T19:08:59,570   copying pisces/submit.py -> build/lib/pisces
2023-08-01T19:08:59,575   copying pisces/run.py -> build/lib/pisces
2023-08-01T19:08:59,578   running egg_info
2023-08-01T19:08:59,730   writing novartis_pisces.egg-info/PKG-INFO
2023-08-01T19:08:59,733   writing dependency_links to novartis_pisces.egg-info/dependency_links.txt
2023-08-01T19:08:59,737   writing entry points to novartis_pisces.egg-info/entry_points.txt
2023-08-01T19:08:59,740   writing requirements to novartis_pisces.egg-info/requires.txt
2023-08-01T19:08:59,742   writing top-level names to novartis_pisces.egg-info/top_level.txt
2023-08-01T19:08:59,998   listing git files failed - pretending there aren't any
2023-08-01T19:09:00,018   reading manifest file 'novartis_pisces.egg-info/SOURCES.txt'
2023-08-01T19:09:00,043   reading manifest template 'MANIFEST.in'
2023-08-01T19:09:00,055   adding license file 'LICENSE'
2023-08-01T19:09:00,067   writing manifest file 'novartis_pisces.egg-info/SOURCES.txt'
2023-08-01T19:09:00,079   /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'pisces.R' is absent from the `packages` configuration.
2023-08-01T19:09:00,079   !!

2023-08-01T19:09:00,080           ********************************************************************************
2023-08-01T19:09:00,080           ############################
2023-08-01T19:09:00,080           # Package would be ignored #
2023-08-01T19:09:00,081           ############################
2023-08-01T19:09:00,081           Python recognizes 'pisces.R' as an importable package[^1],
2023-08-01T19:09:00,081           but it is absent from setuptools' `packages` configuration.

2023-08-01T19:09:00,082           This leads to an ambiguous overall configuration. If you want to distribute this
2023-08-01T19:09:00,082           package, please make sure that 'pisces.R' is explicitly added
2023-08-01T19:09:00,083           to the `packages` configuration field.

2023-08-01T19:09:00,083           Alternatively, you can also rely on setuptools' discovery methods
2023-08-01T19:09:00,083           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-08-01T19:09:00,084           instead of `find_packages(...)`/`find:`).

2023-08-01T19:09:00,084           You can read more about "package discovery" on setuptools documentation page:

2023-08-01T19:09:00,085           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-08-01T19:09:00,086           If you don't want 'pisces.R' to be distributed and are
2023-08-01T19:09:00,086           already explicitly excluding 'pisces.R' via
2023-08-01T19:09:00,086           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-08-01T19:09:00,087           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-08-01T19:09:00,087           combination with a more fine grained `package-data` configuration.

2023-08-01T19:09:00,088           You can read more about "package data files" on setuptools documentation page:

2023-08-01T19:09:00,088           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-08-01T19:09:00,089           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-08-01T19:09:00,090                 even if it does not contain any `.py` files.
2023-08-01T19:09:00,090                 On the other hand, currently there is no concept of package data
2023-08-01T19:09:00,090                 directory, all directories are treated like packages.
2023-08-01T19:09:00,091           ********************************************************************************

2023-08-01T19:09:00,091   !!
2023-08-01T19:09:00,092     check.warn(importable)
2023-08-01T19:09:00,092   /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'pisces.R.renv' is absent from the `packages` configuration.
2023-08-01T19:09:00,093   !!

2023-08-01T19:09:00,093           ********************************************************************************
2023-08-01T19:09:00,094           ############################
2023-08-01T19:09:00,094           # Package would be ignored #
2023-08-01T19:09:00,094           ############################
2023-08-01T19:09:00,095           Python recognizes 'pisces.R.renv' as an importable package[^1],
2023-08-01T19:09:00,095           but it is absent from setuptools' `packages` configuration.

2023-08-01T19:09:00,096           This leads to an ambiguous overall configuration. If you want to distribute this
2023-08-01T19:09:00,096           package, please make sure that 'pisces.R.renv' is explicitly added
2023-08-01T19:09:00,096           to the `packages` configuration field.

2023-08-01T19:09:00,097           Alternatively, you can also rely on setuptools' discovery methods
2023-08-01T19:09:00,097           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-08-01T19:09:00,098           instead of `find_packages(...)`/`find:`).

2023-08-01T19:09:00,098           You can read more about "package discovery" on setuptools documentation page:

2023-08-01T19:09:00,099           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-08-01T19:09:00,100           If you don't want 'pisces.R.renv' to be distributed and are
2023-08-01T19:09:00,100           already explicitly excluding 'pisces.R.renv' via
2023-08-01T19:09:00,100           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-08-01T19:09:00,101           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-08-01T19:09:00,101           combination with a more fine grained `package-data` configuration.

2023-08-01T19:09:00,102           You can read more about "package data files" on setuptools documentation page:

2023-08-01T19:09:00,102           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-08-01T19:09:00,103           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-08-01T19:09:00,104                 even if it does not contain any `.py` files.
2023-08-01T19:09:00,104                 On the other hand, currently there is no concept of package data
2023-08-01T19:09:00,104                 directory, all directories are treated like packages.
2023-08-01T19:09:00,105           ********************************************************************************

2023-08-01T19:09:00,105   !!
2023-08-01T19:09:00,106     check.warn(importable)
2023-08-01T19:09:00,106   /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'pisces.data' is absent from the `packages` configuration.
2023-08-01T19:09:00,107   !!

2023-08-01T19:09:00,108           ********************************************************************************
2023-08-01T19:09:00,108           ############################
2023-08-01T19:09:00,108           # Package would be ignored #
2023-08-01T19:09:00,108           ############################
2023-08-01T19:09:00,109           Python recognizes 'pisces.data' as an importable package[^1],
2023-08-01T19:09:00,109           but it is absent from setuptools' `packages` configuration.

2023-08-01T19:09:00,110           This leads to an ambiguous overall configuration. If you want to distribute this
2023-08-01T19:09:00,110           package, please make sure that 'pisces.data' is explicitly added
2023-08-01T19:09:00,110           to the `packages` configuration field.

2023-08-01T19:09:00,111           Alternatively, you can also rely on setuptools' discovery methods
2023-08-01T19:09:00,111           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-08-01T19:09:00,112           instead of `find_packages(...)`/`find:`).

2023-08-01T19:09:00,112           You can read more about "package discovery" on setuptools documentation page:

2023-08-01T19:09:00,113           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-08-01T19:09:00,114           If you don't want 'pisces.data' to be distributed and are
2023-08-01T19:09:00,114           already explicitly excluding 'pisces.data' via
2023-08-01T19:09:00,114           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-08-01T19:09:00,115           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-08-01T19:09:00,115           combination with a more fine grained `package-data` configuration.

2023-08-01T19:09:00,116           You can read more about "package data files" on setuptools documentation page:

2023-08-01T19:09:00,116           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-08-01T19:09:00,117           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-08-01T19:09:00,117                 even if it does not contain any `.py` files.
2023-08-01T19:09:00,118                 On the other hand, currently there is no concept of package data
2023-08-01T19:09:00,118                 directory, all directories are treated like packages.
2023-08-01T19:09:00,119           ********************************************************************************

2023-08-01T19:09:00,119   !!
2023-08-01T19:09:00,119     check.warn(importable)
2023-08-01T19:09:00,120   /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'pisces.scripts' is absent from the `packages` configuration.
2023-08-01T19:09:00,120   !!

2023-08-01T19:09:00,121           ********************************************************************************
2023-08-01T19:09:00,121           ############################
2023-08-01T19:09:00,121           # Package would be ignored #
2023-08-01T19:09:00,122           ############################
2023-08-01T19:09:00,122           Python recognizes 'pisces.scripts' as an importable package[^1],
2023-08-01T19:09:00,122           but it is absent from setuptools' `packages` configuration.

2023-08-01T19:09:00,123           This leads to an ambiguous overall configuration. If you want to distribute this
2023-08-01T19:09:00,123           package, please make sure that 'pisces.scripts' is explicitly added
2023-08-01T19:09:00,124           to the `packages` configuration field.

2023-08-01T19:09:00,124           Alternatively, you can also rely on setuptools' discovery methods
2023-08-01T19:09:00,125           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-08-01T19:09:00,125           instead of `find_packages(...)`/`find:`).

2023-08-01T19:09:00,126           You can read more about "package discovery" on setuptools documentation page:

2023-08-01T19:09:00,127           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-08-01T19:09:00,127           If you don't want 'pisces.scripts' to be distributed and are
2023-08-01T19:09:00,128           already explicitly excluding 'pisces.scripts' via
2023-08-01T19:09:00,128           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-08-01T19:09:00,128           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-08-01T19:09:00,129           combination with a more fine grained `package-data` configuration.

2023-08-01T19:09:00,129           You can read more about "package data files" on setuptools documentation page:

2023-08-01T19:09:00,130           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-08-01T19:09:00,131           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-08-01T19:09:00,131                 even if it does not contain any `.py` files.
2023-08-01T19:09:00,132                 On the other hand, currently there is no concept of package data
2023-08-01T19:09:00,132                 directory, all directories are treated like packages.
2023-08-01T19:09:00,132           ********************************************************************************

2023-08-01T19:09:00,133   !!
2023-08-01T19:09:00,133     check.warn(importable)
2023-08-01T19:09:00,134   /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'pisces.tests' is absent from the `packages` configuration.
2023-08-01T19:09:00,134   !!

2023-08-01T19:09:00,134           ********************************************************************************
2023-08-01T19:09:00,135           ############################
2023-08-01T19:09:00,135           # Package would be ignored #
2023-08-01T19:09:00,135           ############################
2023-08-01T19:09:00,136           Python recognizes 'pisces.tests' as an importable package[^1],
2023-08-01T19:09:00,136           but it is absent from setuptools' `packages` configuration.

2023-08-01T19:09:00,137           This leads to an ambiguous overall configuration. If you want to distribute this
2023-08-01T19:09:00,137           package, please make sure that 'pisces.tests' is explicitly added
2023-08-01T19:09:00,137           to the `packages` configuration field.

2023-08-01T19:09:00,138           Alternatively, you can also rely on setuptools' discovery methods
2023-08-01T19:09:00,138           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-08-01T19:09:00,139           instead of `find_packages(...)`/`find:`).

2023-08-01T19:09:00,139           You can read more about "package discovery" on setuptools documentation page:

2023-08-01T19:09:00,140           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-08-01T19:09:00,141           If you don't want 'pisces.tests' to be distributed and are
2023-08-01T19:09:00,141           already explicitly excluding 'pisces.tests' via
2023-08-01T19:09:00,141           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-08-01T19:09:00,142           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-08-01T19:09:00,142           combination with a more fine grained `package-data` configuration.

2023-08-01T19:09:00,143           You can read more about "package data files" on setuptools documentation page:

2023-08-01T19:09:00,143           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-08-01T19:09:00,144           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-08-01T19:09:00,144                 even if it does not contain any `.py` files.
2023-08-01T19:09:00,145                 On the other hand, currently there is no concept of package data
2023-08-01T19:09:00,145                 directory, all directories are treated like packages.
2023-08-01T19:09:00,146           ********************************************************************************

2023-08-01T19:09:00,146   !!
2023-08-01T19:09:00,147     check.warn(importable)
2023-08-01T19:09:00,147   copying pisces/config.json -> build/lib/pisces
2023-08-01T19:09:00,147   creating build/lib/pisces/R
2023-08-01T19:09:00,148   copying pisces/R/.Rprofile -> build/lib/pisces/R
2023-08-01T19:09:00,148   copying pisces/R/.gitignore -> build/lib/pisces/R
2023-08-01T19:09:00,148   copying pisces/R/make_expression_matrix.R -> build/lib/pisces/R
2023-08-01T19:09:00,149   copying pisces/R/set_up_dependencies.R -> build/lib/pisces/R
2023-08-01T19:09:00,149   creating build/lib/pisces/R/renv
2023-08-01T19:09:00,149   copying pisces/R/renv/activate.R -> build/lib/pisces/R/renv
2023-08-01T19:09:00,149   creating build/lib/pisces/data
2023-08-01T19:09:00,150   copying pisces/data/fp_kmers.txt -> build/lib/pisces/data
2023-08-01T19:09:00,150   copying pisces/data/fp_kmers_col1.txt -> build/lib/pisces/data
2023-08-01T19:09:00,150   creating build/lib/pisces/scripts
2023-08-01T19:09:00,151   copying pisces/scripts/create_sample_sets_stripped.py -> build/lib/pisces/scripts
2023-08-01T19:09:00,151   copying pisces/scripts/kmer_counts_to_fingerprint_strand_and_pcthuman.py -> build/lib/pisces/scripts
2023-08-01T19:09:00,151   creating build/lib/pisces/tests
2023-08-01T19:09:00,152   copying pisces/tests/test_cli.py -> build/lib/pisces/tests
2023-08-01T19:09:00,244   /usr/local/lib/python3.7/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2023-08-01T19:09:00,245   !!

2023-08-01T19:09:00,245           ********************************************************************************
2023-08-01T19:09:00,246           Please avoid running ``setup.py`` directly.
2023-08-01T19:09:00,246           Instead, use pypa/build, pypa/installer, pypa/build or
2023-08-01T19:09:00,246           other standards-based tools.

2023-08-01T19:09:00,247           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2023-08-01T19:09:00,247           ********************************************************************************

2023-08-01T19:09:00,248   !!
2023-08-01T19:09:00,248     self.initialize_options()
2023-08-01T19:09:00,323   installing to build/bdist.linux-armv7l/wheel
2023-08-01T19:09:00,323   running install
2023-08-01T19:09:00,383   running install_lib
2023-08-01T19:09:00,463   creating build/bdist.linux-armv7l
2023-08-01T19:09:00,464   creating build/bdist.linux-armv7l/wheel
2023-08-01T19:09:00,468   creating build/bdist.linux-armv7l/wheel/pisces
2023-08-01T19:09:00,470   copying build/lib/pisces/index.py -> build/bdist.linux-armv7l/wheel/pisces
2023-08-01T19:09:00,476   copying build/lib/pisces/qc.py -> build/bdist.linux-armv7l/wheel/pisces
2023-08-01T19:09:00,481   creating build/bdist.linux-armv7l/wheel/pisces/tests
2023-08-01T19:09:00,483   copying build/lib/pisces/tests/test_cli.py -> build/bdist.linux-armv7l/wheel/pisces/tests
2023-08-01T19:09:00,487   copying build/lib/pisces/cli.py -> build/bdist.linux-armv7l/wheel/pisces
2023-08-01T19:09:00,491   copying build/lib/pisces/__init__.py -> build/bdist.linux-armv7l/wheel/pisces
2023-08-01T19:09:00,496   copying build/lib/pisces/fastq.py -> build/bdist.linux-armv7l/wheel/pisces
2023-08-01T19:09:00,502   creating build/bdist.linux-armv7l/wheel/pisces/scripts
2023-08-01T19:09:00,504   copying build/lib/pisces/scripts/kmer_counts_to_fingerprint_strand_and_pcthuman.py -> build/bdist.linux-armv7l/wheel/pisces/scripts
2023-08-01T19:09:00,509   copying build/lib/pisces/scripts/create_sample_sets_stripped.py -> build/bdist.linux-armv7l/wheel/pisces/scripts
2023-08-01T19:09:00,514   copying build/lib/pisces/submit.py -> build/bdist.linux-armv7l/wheel/pisces
2023-08-01T19:09:00,519   copying build/lib/pisces/run.py -> build/bdist.linux-armv7l/wheel/pisces
2023-08-01T19:09:00,524   creating build/bdist.linux-armv7l/wheel/pisces/data
2023-08-01T19:09:00,526   copying build/lib/pisces/data/fp_kmers.txt -> build/bdist.linux-armv7l/wheel/pisces/data
2023-08-01T19:09:00,533   copying build/lib/pisces/data/fp_kmers_col1.txt -> build/bdist.linux-armv7l/wheel/pisces/data
2023-08-01T19:09:00,539   creating build/bdist.linux-armv7l/wheel/pisces/R
2023-08-01T19:09:00,541   copying build/lib/pisces/R/set_up_dependencies.R -> build/bdist.linux-armv7l/wheel/pisces/R
2023-08-01T19:09:00,545   copying build/lib/pisces/R/.Rprofile -> build/bdist.linux-armv7l/wheel/pisces/R
2023-08-01T19:09:00,549   copying build/lib/pisces/R/make_expression_matrix.R -> build/bdist.linux-armv7l/wheel/pisces/R
2023-08-01T19:09:00,555   creating build/bdist.linux-armv7l/wheel/pisces/R/renv
2023-08-01T19:09:00,556   copying build/lib/pisces/R/renv/activate.R -> build/bdist.linux-armv7l/wheel/pisces/R/renv
2023-08-01T19:09:00,561   copying build/lib/pisces/R/.gitignore -> build/bdist.linux-armv7l/wheel/pisces/R
2023-08-01T19:09:00,564   copying build/lib/pisces/config.json -> build/bdist.linux-armv7l/wheel/pisces
2023-08-01T19:09:00,568   running install_egg_info
2023-08-01T19:09:00,645   Copying novartis_pisces.egg-info to build/bdist.linux-armv7l/wheel/novartis_pisces-0.1.5.4-py3.7.egg-info
2023-08-01T19:09:00,667   running install_scripts
2023-08-01T19:09:00,705   creating build/bdist.linux-armv7l/wheel/novartis_pisces-0.1.5.4.dist-info/WHEEL
2023-08-01T19:09:00,711   creating '/tmp/pip-wheel-lby3o62p/novartis_pisces-0.1.5.4-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2023-08-01T19:09:00,721   adding 'pisces/__init__.py'
2023-08-01T19:09:00,726   adding 'pisces/cli.py'
2023-08-01T19:09:00,728   adding 'pisces/config.json'
2023-08-01T19:09:00,732   adding 'pisces/fastq.py'
2023-08-01T19:09:00,738   adding 'pisces/index.py'
2023-08-01T19:09:00,742   adding 'pisces/qc.py'
2023-08-01T19:09:00,745   adding 'pisces/run.py'
2023-08-01T19:09:00,750   adding 'pisces/submit.py'
2023-08-01T19:09:00,753   adding 'pisces/R/.Rprofile'
2023-08-01T19:09:00,756   adding 'pisces/R/.gitignore'
2023-08-01T19:09:00,764   adding 'pisces/R/make_expression_matrix.R'
2023-08-01T19:09:00,767   adding 'pisces/R/set_up_dependencies.R'
2023-08-01T19:09:00,772   adding 'pisces/R/renv/activate.R'
2023-08-01T19:09:00,798   adding 'pisces/data/fp_kmers.txt'
2023-08-01T19:09:00,816   adding 'pisces/data/fp_kmers_col1.txt'
2023-08-01T19:09:00,825   adding 'pisces/scripts/create_sample_sets_stripped.py'
2023-08-01T19:09:00,829   adding 'pisces/scripts/kmer_counts_to_fingerprint_strand_and_pcthuman.py'
2023-08-01T19:09:00,833   adding 'pisces/tests/test_cli.py'
2023-08-01T19:09:00,838   adding 'novartis_pisces-0.1.5.4.dist-info/LICENSE'
2023-08-01T19:09:00,840   adding 'novartis_pisces-0.1.5.4.dist-info/METADATA'
2023-08-01T19:09:00,842   adding 'novartis_pisces-0.1.5.4.dist-info/WHEEL'
2023-08-01T19:09:00,844   adding 'novartis_pisces-0.1.5.4.dist-info/entry_points.txt'
2023-08-01T19:09:00,846   adding 'novartis_pisces-0.1.5.4.dist-info/top_level.txt'
2023-08-01T19:09:00,849   adding 'novartis_pisces-0.1.5.4.dist-info/RECORD'
2023-08-01T19:09:00,853   removing build/bdist.linux-armv7l/wheel
2023-08-01T19:09:01,065   Building wheel for novartis-pisces (setup.py): finished with status 'done'
2023-08-01T19:09:01,073   Created wheel for novartis-pisces: filename=novartis_pisces-0.1.5.4-py3-none-any.whl size=60819 sha256=79845ffb5ecc492427d9d248ddd78fe6a4ba1c7d907f9222c2f5ae290dff53f8
2023-08-01T19:09:01,076   Stored in directory: /tmp/pip-ephem-wheel-cache-jm4onnlo/wheels/59/1d/9f/e922e5d748c944e643a66cae21de4235a51237534b05e6f709
2023-08-01T19:09:01,104 Successfully built novartis-pisces
2023-08-01T19:09:01,116 Removed build tracker: '/tmp/pip-build-tracker-a3hrjfo9'