2023-09-10T02:09:49,740 Created temporary directory: /tmp/pip-build-tracker-8yuz0md3
2023-09-10T02:09:49,741 Initialized build tracking at /tmp/pip-build-tracker-8yuz0md3
2023-09-10T02:09:49,742 Created build tracker: /tmp/pip-build-tracker-8yuz0md3
2023-09-10T02:09:49,742 Entered build tracker: /tmp/pip-build-tracker-8yuz0md3
2023-09-10T02:09:49,743 Created temporary directory: /tmp/pip-wheel-ath6jr31
2023-09-10T02:09:49,747 Created temporary directory: /tmp/pip-ephem-wheel-cache-9k_8i8gp
2023-09-10T02:09:49,770 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-09-10T02:09:49,774 2 location(s) to search for versions of tredparse:
2023-09-10T02:09:49,774 * https://pypi.org/simple/tredparse/
2023-09-10T02:09:49,774 * https://www.piwheels.org/simple/tredparse/
2023-09-10T02:09:49,774 Fetching project page and analyzing links: https://pypi.org/simple/tredparse/
2023-09-10T02:09:49,775 Getting page https://pypi.org/simple/tredparse/
2023-09-10T02:09:49,777 Found index url https://pypi.org/simple/
2023-09-10T02:09:49,916 Fetched page https://pypi.org/simple/tredparse/ as application/vnd.pypi.simple.v1+json
2023-09-10T02:09:49,918   Found link https://files.pythonhosted.org/packages/27/ce/05332b56a32fa249b226f606bca1b6ad4c0292a8a26541a10f23cea87234/tredparse-0.7.5.tar.gz (from https://pypi.org/simple/tredparse/), version: 0.7.5
2023-09-10T02:09:49,919   Found link https://files.pythonhosted.org/packages/1d/5d/560a1d2764bbb1ab47c1928ed611e130b3ac09ec97e47a35ddf33eb1fd95/tredparse-0.7.6.tar.gz (from https://pypi.org/simple/tredparse/), version: 0.7.6
2023-09-10T02:09:49,920   Found link https://files.pythonhosted.org/packages/76/1c/2729e46ac407eb52816cbbac94b06d0f3669dc8a7c2ef4cb8976ab071bdc/tredparse-0.7.7.tar.gz (from https://pypi.org/simple/tredparse/), version: 0.7.7
2023-09-10T02:09:49,921   Found link https://files.pythonhosted.org/packages/c0/37/e706aade86900143a0c6c83ad022a4feac9f1d8fa3573265806033d4395b/tredparse-0.7.8.tar.gz (from https://pypi.org/simple/tredparse/), version: 0.7.8
2023-09-10T02:09:49,921   Found link https://files.pythonhosted.org/packages/33/32/abbebafed6afbee2bb41e4e0f8be78a4ec2a391dcfef86121acee06b435e/tredparse-1.1.12.tar.gz (from https://pypi.org/simple/tredparse/), version: 1.1.12
2023-09-10T02:09:49,922 Fetching project page and analyzing links: https://www.piwheels.org/simple/tredparse/
2023-09-10T02:09:49,923 Getting page https://www.piwheels.org/simple/tredparse/
2023-09-10T02:09:49,924 Found index url https://www.piwheels.org/simple/
2023-09-10T02:09:50,205 Fetched page https://www.piwheels.org/simple/tredparse/ as text/html
2023-09-10T02:09:50,206 Skipping link: not a file: https://www.piwheels.org/simple/tredparse/
2023-09-10T02:09:50,207 Skipping link: not a file: https://pypi.org/simple/tredparse/
2023-09-10T02:09:50,226 Given no hashes to check 1 links for project 'tredparse': discarding no candidates
2023-09-10T02:09:50,245 Collecting tredparse==0.7.8
2023-09-10T02:09:50,249   Created temporary directory: /tmp/pip-unpack-s7zahl2c
2023-09-10T02:09:50,462   Downloading tredparse-0.7.8.tar.gz (247 kB)
2023-09-10T02:09:50,625   Added tredparse==0.7.8 from https://files.pythonhosted.org/packages/c0/37/e706aade86900143a0c6c83ad022a4feac9f1d8fa3573265806033d4395b/tredparse-0.7.8.tar.gz to build tracker '/tmp/pip-build-tracker-8yuz0md3'
2023-09-10T02:09:50,627   Running setup.py (path:/tmp/pip-wheel-ath6jr31/tredparse_c3fc5b32d33b45568719385ed3e3e909/setup.py) egg_info for package tredparse
2023-09-10T02:09:50,628   Created temporary directory: /tmp/pip-pip-egg-info-qxpt61nu
2023-09-10T02:09:50,629   Preparing metadata (setup.py): started
2023-09-10T02:09:50,630   Running command python setup.py egg_info
2023-09-10T02:09:51,994   running egg_info
2023-09-10T02:09:51,996   creating /tmp/pip-pip-egg-info-qxpt61nu/tredparse.egg-info
2023-09-10T02:09:52,021   writing /tmp/pip-pip-egg-info-qxpt61nu/tredparse.egg-info/PKG-INFO
2023-09-10T02:09:52,025   writing dependency_links to /tmp/pip-pip-egg-info-qxpt61nu/tredparse.egg-info/dependency_links.txt
2023-09-10T02:09:52,027   writing requirements to /tmp/pip-pip-egg-info-qxpt61nu/tredparse.egg-info/requires.txt
2023-09-10T02:09:52,028   writing top-level names to /tmp/pip-pip-egg-info-qxpt61nu/tredparse.egg-info/top_level.txt
2023-09-10T02:09:52,030   writing manifest file '/tmp/pip-pip-egg-info-qxpt61nu/tredparse.egg-info/SOURCES.txt'
2023-09-10T02:09:52,158   reading manifest file '/tmp/pip-pip-egg-info-qxpt61nu/tredparse.egg-info/SOURCES.txt'
2023-09-10T02:09:52,160   reading manifest template 'MANIFEST.in'
2023-09-10T02:09:52,163   adding license file 'LICENSE'
2023-09-10T02:09:52,166   writing manifest file '/tmp/pip-pip-egg-info-qxpt61nu/tredparse.egg-info/SOURCES.txt'
2023-09-10T02:09:52,282   Preparing metadata (setup.py): finished with status 'done'
2023-09-10T02:09:52,286   Source in /tmp/pip-wheel-ath6jr31/tredparse_c3fc5b32d33b45568719385ed3e3e909 has version 0.7.8, which satisfies requirement tredparse==0.7.8 from https://files.pythonhosted.org/packages/c0/37/e706aade86900143a0c6c83ad022a4feac9f1d8fa3573265806033d4395b/tredparse-0.7.8.tar.gz
2023-09-10T02:09:52,287   Removed tredparse==0.7.8 from https://files.pythonhosted.org/packages/c0/37/e706aade86900143a0c6c83ad022a4feac9f1d8fa3573265806033d4395b/tredparse-0.7.8.tar.gz from build tracker '/tmp/pip-build-tracker-8yuz0md3'
2023-09-10T02:09:52,293 Created temporary directory: /tmp/pip-unpack-po5y6xcl
2023-09-10T02:09:52,294 Created temporary directory: /tmp/pip-unpack-jkt7s_gg
2023-09-10T02:09:52,302 Building wheels for collected packages: tredparse
2023-09-10T02:09:52,307   Created temporary directory: /tmp/pip-wheel-pc11qhz7
2023-09-10T02:09:52,307   Building wheel for tredparse (setup.py): started
2023-09-10T02:09:52,309   Destination directory: /tmp/pip-wheel-pc11qhz7
2023-09-10T02:09:52,309   Running command python setup.py bdist_wheel
2023-09-10T02:09:53,630   running bdist_wheel
2023-09-10T02:09:53,722   running build
2023-09-10T02:09:53,723   running build_py
2023-09-10T02:09:53,749   creating build
2023-09-10T02:09:53,749   creating build/lib.linux-armv7l-cpython-311
2023-09-10T02:09:53,750   creating build/lib.linux-armv7l-cpython-311/ssw
2023-09-10T02:09:53,751   copying src/__init__.py -> build/lib.linux-armv7l-cpython-311/ssw
2023-09-10T02:09:53,753   copying src/ssw_wrap.py -> build/lib.linux-armv7l-cpython-311/ssw
2023-09-10T02:09:53,757   creating build/lib.linux-armv7l-cpython-311/tredparse
2023-09-10T02:09:53,758   copying tredparse/__init__.py -> build/lib.linux-armv7l-cpython-311/tredparse
2023-09-10T02:09:53,759   copying tredparse/meta.py -> build/lib.linux-armv7l-cpython-311/tredparse
2023-09-10T02:09:53,761   copying tredparse/jcvi.py -> build/lib.linux-armv7l-cpython-311/tredparse
2023-09-10T02:09:53,764   copying tredparse/tredplot.py -> build/lib.linux-armv7l-cpython-311/tredparse
2023-09-10T02:09:53,767   copying tredparse/utils.py -> build/lib.linux-armv7l-cpython-311/tredparse
2023-09-10T02:09:53,769   copying tredparse/tredreport.py -> build/lib.linux-armv7l-cpython-311/tredparse
2023-09-10T02:09:53,771   copying tredparse/bam_parser.py -> build/lib.linux-armv7l-cpython-311/tredparse
2023-09-10T02:09:53,773   copying tredparse/tred.py -> build/lib.linux-armv7l-cpython-311/tredparse
2023-09-10T02:09:53,776   copying tredparse/models.py -> build/lib.linux-armv7l-cpython-311/tredparse
2023-09-10T02:09:53,779   running egg_info
2023-09-10T02:09:53,833   writing tredparse.egg-info/PKG-INFO
2023-09-10T02:09:53,836   writing dependency_links to tredparse.egg-info/dependency_links.txt
2023-09-10T02:09:53,838   writing requirements to tredparse.egg-info/requires.txt
2023-09-10T02:09:53,839   writing top-level names to tredparse.egg-info/top_level.txt
2023-09-10T02:09:53,866   reading manifest file 'tredparse.egg-info/SOURCES.txt'
2023-09-10T02:09:53,869   reading manifest template 'MANIFEST.in'
2023-09-10T02:09:53,872   adding license file 'LICENSE'
2023-09-10T02:09:53,875   writing manifest file 'tredparse.egg-info/SOURCES.txt'
2023-09-10T02:09:53,878   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'tredparse.data' is absent from the `packages` configuration.
2023-09-10T02:09:53,878   !!

2023-09-10T02:09:53,879           ********************************************************************************
2023-09-10T02:09:53,880           ############################
2023-09-10T02:09:53,880           # Package would be ignored #
2023-09-10T02:09:53,881           ############################
2023-09-10T02:09:53,881           Python recognizes 'tredparse.data' as an importable package[^1],
2023-09-10T02:09:53,881           but it is absent from setuptools' `packages` configuration.

2023-09-10T02:09:53,882           This leads to an ambiguous overall configuration. If you want to distribute this
2023-09-10T02:09:53,884           package, please make sure that 'tredparse.data' is explicitly added
2023-09-10T02:09:53,885           to the `packages` configuration field.

2023-09-10T02:09:53,886           Alternatively, you can also rely on setuptools' discovery methods
2023-09-10T02:09:53,886           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-09-10T02:09:53,887           instead of `find_packages(...)`/`find:`).

2023-09-10T02:09:53,888           You can read more about "package discovery" on setuptools documentation page:

2023-09-10T02:09:53,890           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-09-10T02:09:53,891           If you don't want 'tredparse.data' to be distributed and are
2023-09-10T02:09:53,891           already explicitly excluding 'tredparse.data' via
2023-09-10T02:09:53,892           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-09-10T02:09:53,893           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-09-10T02:09:53,893           combination with a more fine grained `package-data` configuration.

2023-09-10T02:09:53,894           You can read more about "package data files" on setuptools documentation page:

2023-09-10T02:09:53,895           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-09-10T02:09:53,897           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-09-10T02:09:53,898                 even if it does not contain any `.py` files.
2023-09-10T02:09:53,898                 On the other hand, currently there is no concept of package data
2023-09-10T02:09:53,899                 directory, all directories are treated like packages.
2023-09-10T02:09:53,899           ********************************************************************************

2023-09-10T02:09:53,900   !!
2023-09-10T02:09:53,901     check.warn(importable)
2023-09-10T02:09:53,902   creating build/lib.linux-armv7l-cpython-311/tredparse/data
2023-09-10T02:09:53,902   copying tredparse/data/HLI_bams.csv.gz -> build/lib.linux-armv7l-cpython-311/tredparse/data
2023-09-10T02:09:53,903   copying tredparse/data/TREDs.alts.csv -> build/lib.linux-armv7l-cpython-311/tredparse/data
2023-09-10T02:09:53,903   copying tredparse/data/TREDs.meta.csv -> build/lib.linux-armv7l-cpython-311/tredparse/data
2023-09-10T02:09:53,904   copying tredparse/data/chrY.hg19.unique_ccn.gc -> build/lib.linux-armv7l-cpython-311/tredparse/data
2023-09-10T02:09:53,904   copying tredparse/data/chrY.hg38.unique_ccn.gc -> build/lib.linux-armv7l-cpython-311/tredparse/data
2023-09-10T02:09:53,905   copying tredparse/data/illumina_v3.pcrfree.stepmodel -> build/lib.linux-armv7l-cpython-311/tredparse/data
2023-09-10T02:09:53,905   copying tredparse/data/illumina_v3.pcrfree.stuttermodel -> build/lib.linux-armv7l-cpython-311/tredparse/data
2023-09-10T02:09:53,906   copying src/ssw.c -> build/lib.linux-armv7l-cpython-311/ssw
2023-09-10T02:09:53,909   copying src/ssw.h -> build/lib.linux-armv7l-cpython-311/ssw
2023-09-10T02:09:53,912   running build_ext
2023-09-10T02:09:54,385   building 'libssw' extension
2023-09-10T02:09:54,386   creating build/temp.linux-armv7l-cpython-311
2023-09-10T02:09:54,386   creating build/temp.linux-armv7l-cpython-311/src
2023-09-10T02:09:54,387   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc -I/usr/include/python3.11 -c src/ssw.c -o build/temp.linux-armv7l-cpython-311/src/ssw.o
2023-09-10T02:09:54,429   src/ssw.c:38:10: fatal error: emmintrin.h: No such file or directory
2023-09-10T02:09:54,430      38 | #include <emmintrin.h>
2023-09-10T02:09:54,430         |          ^~~~~~~~~~~~~
2023-09-10T02:09:54,431   compilation terminated.
2023-09-10T02:09:54,432   error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1
2023-09-10T02:09:54,573   ERROR: [present-rich] python setup.py bdist_wheel exited with 1
2023-09-10T02:09:54,586   [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c '
2023-09-10T02:09:54,586   exec(compile('"'"''"'"''"'"'
2023-09-10T02:09:54,586   # This is <pip-setuptools-caller> -- a caller that pip uses to run setup.py
2023-09-10T02:09:54,586   #
2023-09-10T02:09:54,586   # - It imports setuptools before invoking setup.py, to enable projects that directly
2023-09-10T02:09:54,586   #   import from `distutils.core` to work with newer packaging standards.
2023-09-10T02:09:54,586   # - It provides a clear error message when setuptools is not installed.
2023-09-10T02:09:54,586   # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so
2023-09-10T02:09:54,586   #   setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning:
2023-09-10T02:09:54,586   #     manifest_maker: standard file '"'"'-c'"'"' not found".
2023-09-10T02:09:54,586   # - It generates a shim setup.py, for handling setup.cfg-only projects.
2023-09-10T02:09:54,586   import os, sys, tokenize
2023-09-10T02:09:54,586   
2023-09-10T02:09:54,586   try:
2023-09-10T02:09:54,586       import setuptools
2023-09-10T02:09:54,586   except ImportError as error:
2023-09-10T02:09:54,586       print(
2023-09-10T02:09:54,586           "ERROR: Can not execute `setup.py` since setuptools is not available in "
2023-09-10T02:09:54,586           "the build environment.",
2023-09-10T02:09:54,586           file=sys.stderr,
2023-09-10T02:09:54,586       )
2023-09-10T02:09:54,586       sys.exit(1)
2023-09-10T02:09:54,586   
2023-09-10T02:09:54,586   __file__ = %r
2023-09-10T02:09:54,586   sys.argv[0] = __file__
2023-09-10T02:09:54,586   
2023-09-10T02:09:54,586   if os.path.exists(__file__):
2023-09-10T02:09:54,586       filename = __file__
2023-09-10T02:09:54,586       with tokenize.open(__file__) as f:
2023-09-10T02:09:54,586           setup_py_code = f.read()
2023-09-10T02:09:54,586   else:
2023-09-10T02:09:54,586       filename = "<auto-generated setuptools caller>"
2023-09-10T02:09:54,586       setup_py_code = "from setuptools import setup; setup()"
2023-09-10T02:09:54,586   
2023-09-10T02:09:54,586   exec(compile(setup_py_code, filename, "exec"))
2023-09-10T02:09:54,586   '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-ath6jr31/tredparse_c3fc5b32d33b45568719385ed3e3e909/setup.py'"'"',), "<pip-setuptools-caller>", "exec"))' bdist_wheel -d /tmp/pip-wheel-pc11qhz7[/]
2023-09-10T02:09:54,587   [bold magenta]cwd[/]: /tmp/pip-wheel-ath6jr31/tredparse_c3fc5b32d33b45568719385ed3e3e909/
2023-09-10T02:09:54,588   Building wheel for tredparse (setup.py): finished with status 'error'
2023-09-10T02:09:54,589   ERROR: Failed building wheel for tredparse
2023-09-10T02:09:54,590   Running setup.py clean for tredparse
2023-09-10T02:09:54,591   Running command python setup.py clean
2023-09-10T02:09:55,949   running clean
2023-09-10T02:09:55,994   removing 'build/temp.linux-armv7l-cpython-311' (and everything under it)
2023-09-10T02:09:55,996   removing 'build/lib.linux-armv7l-cpython-311' (and everything under it)
2023-09-10T02:09:56,003   'build/bdist.linux-armv7l' does not exist -- can't clean it
2023-09-10T02:09:56,004   'build/scripts-3.11' does not exist -- can't clean it
2023-09-10T02:09:56,005   removing 'build'
2023-09-10T02:09:56,120 Failed to build tredparse
2023-09-10T02:09:56,122 ERROR: Failed to build one or more wheels
2023-09-10T02:09:56,123 Exception information:
2023-09-10T02:09:56,123 Traceback (most recent call last):
2023-09-10T02:09:56,123   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper
2023-09-10T02:09:56,123     status = run_func(*args)
2023-09-10T02:09:56,123              ^^^^^^^^^^^^^^^
2023-09-10T02:09:56,123   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper
2023-09-10T02:09:56,123     return func(self, options, args)
2023-09-10T02:09:56,123            ^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-10T02:09:56,123   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run
2023-09-10T02:09:56,123     raise CommandError("Failed to build one or more wheels")
2023-09-10T02:09:56,123 pip._internal.exceptions.CommandError: Failed to build one or more wheels
2023-09-10T02:09:56,126 Removed build tracker: '/tmp/pip-build-tracker-8yuz0md3'