2023-09-12T12:18:56,277 Created temporary directory: /tmp/pip-build-tracker-p6r3raqa
2023-09-12T12:18:56,278 Initialized build tracking at /tmp/pip-build-tracker-p6r3raqa
2023-09-12T12:18:56,278 Created build tracker: /tmp/pip-build-tracker-p6r3raqa
2023-09-12T12:18:56,279 Entered build tracker: /tmp/pip-build-tracker-p6r3raqa
2023-09-12T12:18:56,280 Created temporary directory: /tmp/pip-wheel-5u_a0cqg
2023-09-12T12:18:56,283 Created temporary directory: /tmp/pip-ephem-wheel-cache-eamsv718
2023-09-12T12:18:56,304 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-09-12T12:18:56,308 2 location(s) to search for versions of pywes:
2023-09-12T12:18:56,308 * https://pypi.org/simple/pywes/
2023-09-12T12:18:56,308 * https://www.piwheels.org/simple/pywes/
2023-09-12T12:18:56,308 Fetching project page and analyzing links: https://pypi.org/simple/pywes/
2023-09-12T12:18:56,309 Getting page https://pypi.org/simple/pywes/
2023-09-12T12:18:56,311 Found index url https://pypi.org/simple/
2023-09-12T12:18:56,548 Fetched page https://pypi.org/simple/pywes/ as application/vnd.pypi.simple.v1+json
2023-09-12T12:18:56,549   Found link https://files.pythonhosted.org/packages/d2/58/c01d292d0076c070c219d7e557d5a20f126b0362fb4420fe9832e48f6c3c/pywes-0.0.2.tar.gz (from https://pypi.org/simple/pywes/), version: 0.0.2
2023-09-12T12:18:56,550 Fetching project page and analyzing links: https://www.piwheels.org/simple/pywes/
2023-09-12T12:18:56,550 Getting page https://www.piwheels.org/simple/pywes/
2023-09-12T12:18:56,552 Found index url https://www.piwheels.org/simple/
2023-09-12T12:18:56,830 Fetched page https://www.piwheels.org/simple/pywes/ as text/html
2023-09-12T12:18:56,831 Skipping link: not a file: https://www.piwheels.org/simple/pywes/
2023-09-12T12:18:56,831 Skipping link: not a file: https://pypi.org/simple/pywes/
2023-09-12T12:18:56,850 Given no hashes to check 1 links for project 'pywes': discarding no candidates
2023-09-12T12:18:56,867 Collecting pywes==0.0.2
2023-09-12T12:18:56,870   Created temporary directory: /tmp/pip-unpack-l2dg69ui
2023-09-12T12:18:57,524   Downloading pywes-0.0.2.tar.gz (9.6 MB)
2023-09-12T12:19:02,486   Added pywes==0.0.2 from https://files.pythonhosted.org/packages/d2/58/c01d292d0076c070c219d7e557d5a20f126b0362fb4420fe9832e48f6c3c/pywes-0.0.2.tar.gz to build tracker '/tmp/pip-build-tracker-p6r3raqa'
2023-09-12T12:19:02,488   Running setup.py (path:/tmp/pip-wheel-5u_a0cqg/pywes_c6d276dd6bae4a8eb49a22e3737709da/setup.py) egg_info for package pywes
2023-09-12T12:19:02,490   Created temporary directory: /tmp/pip-pip-egg-info-at3g3avb
2023-09-12T12:19:02,490   Preparing metadata (setup.py): started
2023-09-12T12:19:02,492   Running command python setup.py egg_info
2023-09-12T12:19:03,520   running egg_info
2023-09-12T12:19:03,522   creating /tmp/pip-pip-egg-info-at3g3avb/pywes.egg-info
2023-09-12T12:19:03,546   writing /tmp/pip-pip-egg-info-at3g3avb/pywes.egg-info/PKG-INFO
2023-09-12T12:19:03,548   writing dependency_links to /tmp/pip-pip-egg-info-at3g3avb/pywes.egg-info/dependency_links.txt
2023-09-12T12:19:03,551   writing top-level names to /tmp/pip-pip-egg-info-at3g3avb/pywes.egg-info/top_level.txt
2023-09-12T12:19:03,552   writing manifest file '/tmp/pip-pip-egg-info-at3g3avb/pywes.egg-info/SOURCES.txt'
2023-09-12T12:19:03,651   reading manifest file '/tmp/pip-pip-egg-info-at3g3avb/pywes.egg-info/SOURCES.txt'
2023-09-12T12:19:03,652   reading manifest template 'MANIFEST.in'
2023-09-12T12:19:03,663   writing manifest file '/tmp/pip-pip-egg-info-at3g3avb/pywes.egg-info/SOURCES.txt'
2023-09-12T12:19:03,770   Preparing metadata (setup.py): finished with status 'done'
2023-09-12T12:19:03,773   Source in /tmp/pip-wheel-5u_a0cqg/pywes_c6d276dd6bae4a8eb49a22e3737709da has version 0.0.2, which satisfies requirement pywes==0.0.2 from https://files.pythonhosted.org/packages/d2/58/c01d292d0076c070c219d7e557d5a20f126b0362fb4420fe9832e48f6c3c/pywes-0.0.2.tar.gz
2023-09-12T12:19:03,774   Removed pywes==0.0.2 from https://files.pythonhosted.org/packages/d2/58/c01d292d0076c070c219d7e557d5a20f126b0362fb4420fe9832e48f6c3c/pywes-0.0.2.tar.gz from build tracker '/tmp/pip-build-tracker-p6r3raqa'
2023-09-12T12:19:03,778 Created temporary directory: /tmp/pip-unpack-x_1p0_ud
2023-09-12T12:19:03,780 Created temporary directory: /tmp/pip-unpack-mqh8hths
2023-09-12T12:19:03,782 Building wheels for collected packages: pywes
2023-09-12T12:19:03,786   Created temporary directory: /tmp/pip-wheel-dx71zi_w
2023-09-12T12:19:03,786   Building wheel for pywes (setup.py): started
2023-09-12T12:19:03,787   Destination directory: /tmp/pip-wheel-dx71zi_w
2023-09-12T12:19:03,788   Running command python setup.py bdist_wheel
2023-09-12T12:19:04,766   running bdist_wheel
2023-09-12T12:19:04,858   running build
2023-09-12T12:19:04,859   running build_py
2023-09-12T12:19:04,885   creating build
2023-09-12T12:19:04,886   creating build/lib
2023-09-12T12:19:04,886   creating build/lib/bin
2023-09-12T12:19:04,887   copying bin/pedigree.py -> build/lib/bin
2023-09-12T12:19:04,889   copying bin/report.py -> build/lib/bin
2023-09-12T12:19:04,891   copying bin/acmg_rank.py -> build/lib/bin
2023-09-12T12:19:04,893   copying bin/pywes.py -> build/lib/bin
2023-09-12T12:19:04,894   copying bin/__init__.py -> build/lib/bin
2023-09-12T12:19:04,895   copying bin/annotation_filter.py -> build/lib/bin
2023-09-12T12:19:04,897   copying bin/omim_match.py -> build/lib/bin
2023-09-12T12:19:04,899   copying bin/hgvs.py -> build/lib/bin
2023-09-12T12:19:04,900   copying bin/infer_gender.py -> build/lib/bin
2023-09-12T12:19:04,902   copying bin/vcf_split.py -> build/lib/bin
2023-09-12T12:19:04,904   copying bin/trio.py -> build/lib/bin
2023-09-12T12:19:04,906   copying bin/database_format.py -> build/lib/bin
2023-09-12T12:19:04,908   copying bin/wes.py -> build/lib/bin
2023-09-12T12:19:04,910   copying bin/hg38Tohg19.py -> build/lib/bin
2023-09-12T12:19:04,911   copying bin/diff.py -> build/lib/bin
2023-09-12T12:19:04,913   running egg_info
2023-09-12T12:19:04,967   writing pywes.egg-info/PKG-INFO
2023-09-12T12:19:04,970   writing dependency_links to pywes.egg-info/dependency_links.txt
2023-09-12T12:19:04,972   writing top-level names to pywes.egg-info/top_level.txt
2023-09-12T12:19:04,998   reading manifest file 'pywes.egg-info/SOURCES.txt'
2023-09-12T12:19:05,001   reading manifest template 'MANIFEST.in'
2023-09-12T12:19:05,010   writing manifest file 'pywes.egg-info/SOURCES.txt'
2023-09-12T12:19:05,012   copying bin/.DS_Store -> build/lib/bin
2023-09-12T12:19:05,015   running build_scripts
2023-09-12T12:19:05,016   creating build/scripts-3.11
2023-09-12T12:19:05,017   copying and adjusting bin/pedigree.py -> build/scripts-3.11
2023-09-12T12:19:05,019   copying and adjusting bin/report.py -> build/scripts-3.11
2023-09-12T12:19:05,020   copying and adjusting bin/acmg_rank.py -> build/scripts-3.11
2023-09-12T12:19:05,021   copying and adjusting bin/pywes.py -> build/scripts-3.11
2023-09-12T12:19:05,023   copying and adjusting bin/annotation_filter.py -> build/scripts-3.11
2023-09-12T12:19:05,024   copying and adjusting bin/omim_match.py -> build/scripts-3.11
2023-09-12T12:19:05,026   copying and adjusting bin/hgvs.py -> build/scripts-3.11
2023-09-12T12:19:05,027   copying and adjusting bin/infer_gender.py -> build/scripts-3.11
2023-09-12T12:19:05,029   copying and adjusting bin/vcf_split.py -> build/scripts-3.11
2023-09-12T12:19:05,031   copying and adjusting bin/trio.py -> build/scripts-3.11
2023-09-12T12:19:05,032   copying and adjusting bin/database_format.py -> build/scripts-3.11
2023-09-12T12:19:05,034   Traceback (most recent call last):
2023-09-12T12:19:05,035     File "/usr/lib/python3.11/tokenize.py", line 334, in find_cookie
2023-09-12T12:19:05,036       line_string = line.decode('utf-8')
2023-09-12T12:19:05,036                     ^^^^^^^^^^^^^^^^^^^^
2023-09-12T12:19:05,037   UnicodeDecodeError: 'utf-8' codec can't decode byte 0x80 in position 3131: invalid start byte

2023-09-12T12:19:05,038   During handling of the above exception, another exception occurred:

2023-09-12T12:19:05,039   Traceback (most recent call last):
2023-09-12T12:19:05,040     File "<string>", line 2, in <module>
2023-09-12T12:19:05,041     File "<pip-setuptools-caller>", line 34, in <module>
2023-09-12T12:19:05,041     File "/tmp/pip-wheel-5u_a0cqg/pywes_c6d276dd6bae4a8eb49a22e3737709da/setup.py", line 13, in <module>
2023-09-12T12:19:05,042       setup(name='pywes',version='0.0.2',description='carrier and trio analysis',long_description=long_description, url='https://github.com/N-damo/exomreport',
2023-09-12T12:19:05,042     File "/usr/local/lib/python3.11/dist-packages/setuptools/__init__.py", line 103, in setup
2023-09-12T12:19:05,043       return distutils.core.setup(**attrs)
2023-09-12T12:19:05,043              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T12:19:05,044     File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/core.py", line 185, in setup
2023-09-12T12:19:05,044       return run_commands(dist)
2023-09-12T12:19:05,044              ^^^^^^^^^^^^^^^^^^
2023-09-12T12:19:05,045     File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/core.py", line 201, in run_commands
2023-09-12T12:19:05,045       dist.run_commands()
2023-09-12T12:19:05,046     File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py", line 969, in run_commands
2023-09-12T12:19:05,046       self.run_command(cmd)
2023-09-12T12:19:05,047     File "/usr/local/lib/python3.11/dist-packages/setuptools/dist.py", line 1001, in run_command
2023-09-12T12:19:05,047       super().run_command(command)
2023-09-12T12:19:05,048     File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py", line 988, in run_command
2023-09-12T12:19:05,048       cmd_obj.run()
2023-09-12T12:19:05,049     File "/usr/lib/python3/dist-packages/wheel/bdist_wheel.py", line 325, in run
2023-09-12T12:19:05,049       self.run_command("build")
2023-09-12T12:19:05,050     File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py", line 318, in run_command
2023-09-12T12:19:05,050       self.distribution.run_command(command)
2023-09-12T12:19:05,051     File "/usr/local/lib/python3.11/dist-packages/setuptools/dist.py", line 1001, in run_command
2023-09-12T12:19:05,051       super().run_command(command)
2023-09-12T12:19:05,052     File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py", line 988, in run_command
2023-09-12T12:19:05,053       cmd_obj.run()
2023-09-12T12:19:05,054     File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/command/build.py", line 131, in run
2023-09-12T12:19:05,055       self.run_command(cmd_name)
2023-09-12T12:19:05,056     File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py", line 318, in run_command
2023-09-12T12:19:05,057       self.distribution.run_command(command)
2023-09-12T12:19:05,058     File "/usr/local/lib/python3.11/dist-packages/setuptools/dist.py", line 1001, in run_command
2023-09-12T12:19:05,059       super().run_command(command)
2023-09-12T12:19:05,060     File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py", line 988, in run_command
2023-09-12T12:19:05,061       cmd_obj.run()
2023-09-12T12:19:05,062     File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/command/build_scripts.py", line 56, in run
2023-09-12T12:19:05,062       self.copy_scripts()
2023-09-12T12:19:05,063     File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/command/build_scripts.py", line 71, in copy_scripts
2023-09-12T12:19:05,064       self._copy_script(script, outfiles, updated_files)
2023-09-12T12:19:05,065     File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/command/build_scripts.py", line 90, in _copy_script
2023-09-12T12:19:05,065       f = tokenize.open(script)
2023-09-12T12:19:05,066           ^^^^^^^^^^^^^^^^^^^^^
2023-09-12T12:19:05,067     File "/usr/lib/python3.11/tokenize.py", line 398, in open
2023-09-12T12:19:05,068       encoding, lines = detect_encoding(buffer.readline)
2023-09-12T12:19:05,069                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T12:19:05,070     File "/usr/lib/python3.11/tokenize.py", line 375, in detect_encoding
2023-09-12T12:19:05,071       encoding = find_cookie(first)
2023-09-12T12:19:05,072                  ^^^^^^^^^^^^^^^^^^
2023-09-12T12:19:05,073     File "/usr/lib/python3.11/tokenize.py", line 339, in find_cookie
2023-09-12T12:19:05,073       raise SyntaxError(msg)
2023-09-12T12:19:05,074   SyntaxError: invalid or missing encoding declaration for 'bin/.DS_Store'
2023-09-12T12:19:05,162   ERROR: [present-rich] python setup.py bdist_wheel exited with 1
2023-09-12T12:19:05,175   [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c '
2023-09-12T12:19:05,175   exec(compile('"'"''"'"''"'"'
2023-09-12T12:19:05,175   # This is <pip-setuptools-caller> -- a caller that pip uses to run setup.py
2023-09-12T12:19:05,175   #
2023-09-12T12:19:05,175   # - It imports setuptools before invoking setup.py, to enable projects that directly
2023-09-12T12:19:05,175   #   import from `distutils.core` to work with newer packaging standards.
2023-09-12T12:19:05,175   # - It provides a clear error message when setuptools is not installed.
2023-09-12T12:19:05,175   # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so
2023-09-12T12:19:05,175   #   setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning:
2023-09-12T12:19:05,175   #     manifest_maker: standard file '"'"'-c'"'"' not found".
2023-09-12T12:19:05,175   # - It generates a shim setup.py, for handling setup.cfg-only projects.
2023-09-12T12:19:05,175   import os, sys, tokenize
2023-09-12T12:19:05,175   
2023-09-12T12:19:05,175   try:
2023-09-12T12:19:05,175       import setuptools
2023-09-12T12:19:05,175   except ImportError as error:
2023-09-12T12:19:05,175       print(
2023-09-12T12:19:05,175           "ERROR: Can not execute `setup.py` since setuptools is not available in "
2023-09-12T12:19:05,175           "the build environment.",
2023-09-12T12:19:05,175           file=sys.stderr,
2023-09-12T12:19:05,175       )
2023-09-12T12:19:05,175       sys.exit(1)
2023-09-12T12:19:05,175   
2023-09-12T12:19:05,175   __file__ = %r
2023-09-12T12:19:05,175   sys.argv[0] = __file__
2023-09-12T12:19:05,175   
2023-09-12T12:19:05,175   if os.path.exists(__file__):
2023-09-12T12:19:05,175       filename = __file__
2023-09-12T12:19:05,175       with tokenize.open(__file__) as f:
2023-09-12T12:19:05,175           setup_py_code = f.read()
2023-09-12T12:19:05,175   else:
2023-09-12T12:19:05,175       filename = "<auto-generated setuptools caller>"
2023-09-12T12:19:05,175       setup_py_code = "from setuptools import setup; setup()"
2023-09-12T12:19:05,175   
2023-09-12T12:19:05,175   exec(compile(setup_py_code, filename, "exec"))
2023-09-12T12:19:05,175   '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-5u_a0cqg/pywes_c6d276dd6bae4a8eb49a22e3737709da/setup.py'"'"',), "<pip-setuptools-caller>", "exec"))' bdist_wheel -d /tmp/pip-wheel-dx71zi_w[/]
2023-09-12T12:19:05,176   [bold magenta]cwd[/]: /tmp/pip-wheel-5u_a0cqg/pywes_c6d276dd6bae4a8eb49a22e3737709da/
2023-09-12T12:19:05,176   Building wheel for pywes (setup.py): finished with status 'error'
2023-09-12T12:19:05,178   ERROR: Failed building wheel for pywes
2023-09-12T12:19:05,179   Running setup.py clean for pywes
2023-09-12T12:19:05,180   Running command python setup.py clean
2023-09-12T12:19:06,188   running clean
2023-09-12T12:19:06,234   removing 'build/lib' (and everything under it)
2023-09-12T12:19:06,239   'build/bdist.linux-armv7l' does not exist -- can't clean it
2023-09-12T12:19:06,239   removing 'build/scripts-3.11' (and everything under it)
2023-09-12T12:19:06,242   removing 'build'
2023-09-12T12:19:06,347 Failed to build pywes
2023-09-12T12:19:06,348 ERROR: Failed to build one or more wheels
2023-09-12T12:19:06,350 Exception information:
2023-09-12T12:19:06,350 Traceback (most recent call last):
2023-09-12T12:19:06,350   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper
2023-09-12T12:19:06,350     status = run_func(*args)
2023-09-12T12:19:06,350              ^^^^^^^^^^^^^^^
2023-09-12T12:19:06,350   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper
2023-09-12T12:19:06,350     return func(self, options, args)
2023-09-12T12:19:06,350            ^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T12:19:06,350   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run
2023-09-12T12:19:06,350     raise CommandError("Failed to build one or more wheels")
2023-09-12T12:19:06,350 pip._internal.exceptions.CommandError: Failed to build one or more wheels
2023-09-12T12:19:06,353 Removed build tracker: '/tmp/pip-build-tracker-p6r3raqa'