2023-09-10T00:29:18,512 Created temporary directory: /tmp/pip-build-tracker-e637z8yy
2023-09-10T00:29:18,513 Initialized build tracking at /tmp/pip-build-tracker-e637z8yy
2023-09-10T00:29:18,513 Created build tracker: /tmp/pip-build-tracker-e637z8yy
2023-09-10T00:29:18,514 Entered build tracker: /tmp/pip-build-tracker-e637z8yy
2023-09-10T00:29:18,515 Created temporary directory: /tmp/pip-wheel-karu1gei
2023-09-10T00:29:18,518 Created temporary directory: /tmp/pip-ephem-wheel-cache-gx3_o8_b
2023-09-10T00:29:18,542 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-09-10T00:29:18,546 2 location(s) to search for versions of tredparse:
2023-09-10T00:29:18,546 * https://pypi.org/simple/tredparse/
2023-09-10T00:29:18,546 * https://www.piwheels.org/simple/tredparse/
2023-09-10T00:29:18,546 Fetching project page and analyzing links: https://pypi.org/simple/tredparse/
2023-09-10T00:29:18,547 Getting page https://pypi.org/simple/tredparse/
2023-09-10T00:29:18,549 Found index url https://pypi.org/simple/
2023-09-10T00:29:18,688 Fetched page https://pypi.org/simple/tredparse/ as application/vnd.pypi.simple.v1+json
2023-09-10T00:29:18,690   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
2023-09-10T00:29:18,691   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
2023-09-10T00:29:18,692   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
2023-09-10T00:29:18,692   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
2023-09-10T00:29:18,693   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
2023-09-10T00:29:18,694 Fetching project page and analyzing links: https://www.piwheels.org/simple/tredparse/
2023-09-10T00:29:18,694 Getting page https://www.piwheels.org/simple/tredparse/
2023-09-10T00:29:18,696 Found index url https://www.piwheels.org/simple/
2023-09-10T00:29:18,979 Fetched page https://www.piwheels.org/simple/tredparse/ as text/html
2023-09-10T00:29:18,981 Skipping link: not a file: https://www.piwheels.org/simple/tredparse/
2023-09-10T00:29:18,981 Skipping link: not a file: https://pypi.org/simple/tredparse/
2023-09-10T00:29:19,000 Given no hashes to check 1 links for project 'tredparse': discarding no candidates
2023-09-10T00:29:19,018 Collecting tredparse==0.7.6
2023-09-10T00:29:19,021   Created temporary directory: /tmp/pip-unpack-l39vy8zl
2023-09-10T00:29:19,235   Downloading tredparse-0.7.6.tar.gz (245 kB)
2023-09-10T00:29:19,385   Added tredparse==0.7.6 from https://files.pythonhosted.org/packages/1d/5d/560a1d2764bbb1ab47c1928ed611e130b3ac09ec97e47a35ddf33eb1fd95/tredparse-0.7.6.tar.gz to build tracker '/tmp/pip-build-tracker-e637z8yy'
2023-09-10T00:29:19,387   Running setup.py (path:/tmp/pip-wheel-karu1gei/tredparse_ea468dbfe1b642afa845e0758aa42363/setup.py) egg_info for package tredparse
2023-09-10T00:29:19,388   Created temporary directory: /tmp/pip-pip-egg-info-dw2ew9bb
2023-09-10T00:29:19,389   Preparing metadata (setup.py): started
2023-09-10T00:29:19,390   Running command python setup.py egg_info
2023-09-10T00:29:20,638   running egg_info
2023-09-10T00:29:20,639   creating /tmp/pip-pip-egg-info-dw2ew9bb/tredparse.egg-info
2023-09-10T00:29:20,664   writing /tmp/pip-pip-egg-info-dw2ew9bb/tredparse.egg-info/PKG-INFO
2023-09-10T00:29:20,668   writing dependency_links to /tmp/pip-pip-egg-info-dw2ew9bb/tredparse.egg-info/dependency_links.txt
2023-09-10T00:29:20,670   writing requirements to /tmp/pip-pip-egg-info-dw2ew9bb/tredparse.egg-info/requires.txt
2023-09-10T00:29:20,671   writing top-level names to /tmp/pip-pip-egg-info-dw2ew9bb/tredparse.egg-info/top_level.txt
2023-09-10T00:29:20,673   writing manifest file '/tmp/pip-pip-egg-info-dw2ew9bb/tredparse.egg-info/SOURCES.txt'
2023-09-10T00:29:20,800   reading manifest file '/tmp/pip-pip-egg-info-dw2ew9bb/tredparse.egg-info/SOURCES.txt'
2023-09-10T00:29:20,801   reading manifest template 'MANIFEST.in'
2023-09-10T00:29:20,804   adding license file 'LICENSE'
2023-09-10T00:29:20,807   writing manifest file '/tmp/pip-pip-egg-info-dw2ew9bb/tredparse.egg-info/SOURCES.txt'
2023-09-10T00:29:20,914   Preparing metadata (setup.py): finished with status 'done'
2023-09-10T00:29:20,918   Source in /tmp/pip-wheel-karu1gei/tredparse_ea468dbfe1b642afa845e0758aa42363 has version 0.7.6, which satisfies requirement tredparse==0.7.6 from https://files.pythonhosted.org/packages/1d/5d/560a1d2764bbb1ab47c1928ed611e130b3ac09ec97e47a35ddf33eb1fd95/tredparse-0.7.6.tar.gz
2023-09-10T00:29:20,919   Removed tredparse==0.7.6 from https://files.pythonhosted.org/packages/1d/5d/560a1d2764bbb1ab47c1928ed611e130b3ac09ec97e47a35ddf33eb1fd95/tredparse-0.7.6.tar.gz from build tracker '/tmp/pip-build-tracker-e637z8yy'
2023-09-10T00:29:20,923 Created temporary directory: /tmp/pip-unpack-br_sy0td
2023-09-10T00:29:20,924 Created temporary directory: /tmp/pip-unpack-noha5ajf
2023-09-10T00:29:20,930 Building wheels for collected packages: tredparse
2023-09-10T00:29:20,934   Created temporary directory: /tmp/pip-wheel-8uh5bpss
2023-09-10T00:29:20,935   Building wheel for tredparse (setup.py): started
2023-09-10T00:29:20,936   Destination directory: /tmp/pip-wheel-8uh5bpss
2023-09-10T00:29:20,937   Running command python setup.py bdist_wheel
2023-09-10T00:29:21,966   running bdist_wheel
2023-09-10T00:29:22,061   running build
2023-09-10T00:29:22,061   running build_py
2023-09-10T00:29:22,087   creating build
2023-09-10T00:29:22,088   creating build/lib.linux-armv7l-cpython-311
2023-09-10T00:29:22,088   creating build/lib.linux-armv7l-cpython-311/ssw
2023-09-10T00:29:22,090   copying src/__init__.py -> build/lib.linux-armv7l-cpython-311/ssw
2023-09-10T00:29:22,092   copying src/ssw_wrap.py -> build/lib.linux-armv7l-cpython-311/ssw
2023-09-10T00:29:22,095   creating build/lib.linux-armv7l-cpython-311/tredparse
2023-09-10T00:29:22,096   copying tredparse/__init__.py -> build/lib.linux-armv7l-cpython-311/tredparse
2023-09-10T00:29:22,098   copying tredparse/meta.py -> build/lib.linux-armv7l-cpython-311/tredparse
2023-09-10T00:29:22,100   copying tredparse/jcvi.py -> build/lib.linux-armv7l-cpython-311/tredparse
2023-09-10T00:29:22,103   copying tredparse/utils.py -> build/lib.linux-armv7l-cpython-311/tredparse
2023-09-10T00:29:22,105   copying tredparse/models.py -> build/lib.linux-armv7l-cpython-311/tredparse
2023-09-10T00:29:22,108   copying tredparse/bam_parser.py -> build/lib.linux-armv7l-cpython-311/tredparse
2023-09-10T00:29:22,111   running egg_info
2023-09-10T00:29:22,168   writing tredparse.egg-info/PKG-INFO
2023-09-10T00:29:22,171   writing dependency_links to tredparse.egg-info/dependency_links.txt
2023-09-10T00:29:22,173   writing requirements to tredparse.egg-info/requires.txt
2023-09-10T00:29:22,174   writing top-level names to tredparse.egg-info/top_level.txt
2023-09-10T00:29:22,203   reading manifest file 'tredparse.egg-info/SOURCES.txt'
2023-09-10T00:29:22,206   reading manifest template 'MANIFEST.in'
2023-09-10T00:29:22,209   adding license file 'LICENSE'
2023-09-10T00:29:22,211   writing manifest file 'tredparse.egg-info/SOURCES.txt'
2023-09-10T00:29:22,214   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'tredparse.data' is absent from the `packages` configuration.
2023-09-10T00:29:22,214   !!

2023-09-10T00:29:22,215           ********************************************************************************
2023-09-10T00:29:22,216           ############################
2023-09-10T00:29:22,217           # Package would be ignored #
2023-09-10T00:29:22,217           ############################
2023-09-10T00:29:22,218           Python recognizes 'tredparse.data' as an importable package[^1],
2023-09-10T00:29:22,218           but it is absent from setuptools' `packages` configuration.

2023-09-10T00:29:22,219           This leads to an ambiguous overall configuration. If you want to distribute this
2023-09-10T00:29:22,220           package, please make sure that 'tredparse.data' is explicitly added
2023-09-10T00:29:22,220           to the `packages` configuration field.

2023-09-10T00:29:22,221           Alternatively, you can also rely on setuptools' discovery methods
2023-09-10T00:29:22,222           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-09-10T00:29:22,222           instead of `find_packages(...)`/`find:`).

2023-09-10T00:29:22,224           You can read more about "package discovery" on setuptools documentation page:

2023-09-10T00:29:22,225           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-09-10T00:29:22,225           If you don't want 'tredparse.data' to be distributed and are
2023-09-10T00:29:22,226           already explicitly excluding 'tredparse.data' via
2023-09-10T00:29:22,226           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-09-10T00:29:22,227           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-09-10T00:29:22,228           combination with a more fine grained `package-data` configuration.

2023-09-10T00:29:22,229           You can read more about "package data files" on setuptools documentation page:

2023-09-10T00:29:22,229           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-09-10T00:29:22,231           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-09-10T00:29:22,231                 even if it does not contain any `.py` files.
2023-09-10T00:29:22,232                 On the other hand, currently there is no concept of package data
2023-09-10T00:29:22,232                 directory, all directories are treated like packages.
2023-09-10T00:29:22,233           ********************************************************************************

2023-09-10T00:29:22,234   !!
2023-09-10T00:29:22,234     check.warn(importable)
2023-09-10T00:29:22,235   creating build/lib.linux-armv7l-cpython-311/tredparse/data
2023-09-10T00:29:22,235   copying tredparse/data/HLI_bams.csv.gz -> build/lib.linux-armv7l-cpython-311/tredparse/data
2023-09-10T00:29:22,236   copying tredparse/data/TREDs.alts.csv -> build/lib.linux-armv7l-cpython-311/tredparse/data
2023-09-10T00:29:22,236   copying tredparse/data/TREDs.meta.csv -> build/lib.linux-armv7l-cpython-311/tredparse/data
2023-09-10T00:29:22,237   copying tredparse/data/chrY.hg19.unique_ccn.gc -> build/lib.linux-armv7l-cpython-311/tredparse/data
2023-09-10T00:29:22,238   copying tredparse/data/chrY.hg38.unique_ccn.gc -> build/lib.linux-armv7l-cpython-311/tredparse/data
2023-09-10T00:29:22,240   copying tredparse/data/illumina_v3.pcrfree.stepmodel -> build/lib.linux-armv7l-cpython-311/tredparse/data
2023-09-10T00:29:22,242   copying tredparse/data/illumina_v3.pcrfree.stuttermodel -> build/lib.linux-armv7l-cpython-311/tredparse/data
2023-09-10T00:29:22,244   copying src/ssw.c -> build/lib.linux-armv7l-cpython-311/ssw
2023-09-10T00:29:22,247   copying src/ssw.h -> build/lib.linux-armv7l-cpython-311/ssw
2023-09-10T00:29:22,250   running build_ext
2023-09-10T00:29:22,751   building 'libssw' extension
2023-09-10T00:29:22,752   creating build/temp.linux-armv7l-cpython-311
2023-09-10T00:29:22,753   creating build/temp.linux-armv7l-cpython-311/src
2023-09-10T00:29:22,753   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
2023-09-10T00:29:22,796   src/ssw.c:38:10: fatal error: emmintrin.h: No such file or directory
2023-09-10T00:29:22,797      38 | #include <emmintrin.h>
2023-09-10T00:29:22,798         |          ^~~~~~~~~~~~~
2023-09-10T00:29:22,798   compilation terminated.
2023-09-10T00:29:22,801   error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1
2023-09-10T00:29:22,939   ERROR: [present-rich] python setup.py bdist_wheel exited with 1
2023-09-10T00:29:22,952   [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c '
2023-09-10T00:29:22,952   exec(compile('"'"''"'"''"'"'
2023-09-10T00:29:22,952   # This is <pip-setuptools-caller> -- a caller that pip uses to run setup.py
2023-09-10T00:29:22,952   #
2023-09-10T00:29:22,952   # - It imports setuptools before invoking setup.py, to enable projects that directly
2023-09-10T00:29:22,952   #   import from `distutils.core` to work with newer packaging standards.
2023-09-10T00:29:22,952   # - It provides a clear error message when setuptools is not installed.
2023-09-10T00:29:22,952   # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so
2023-09-10T00:29:22,952   #   setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning:
2023-09-10T00:29:22,952   #     manifest_maker: standard file '"'"'-c'"'"' not found".
2023-09-10T00:29:22,952   # - It generates a shim setup.py, for handling setup.cfg-only projects.
2023-09-10T00:29:22,952   import os, sys, tokenize
2023-09-10T00:29:22,952   
2023-09-10T00:29:22,952   try:
2023-09-10T00:29:22,952       import setuptools
2023-09-10T00:29:22,952   except ImportError as error:
2023-09-10T00:29:22,952       print(
2023-09-10T00:29:22,952           "ERROR: Can not execute `setup.py` since setuptools is not available in "
2023-09-10T00:29:22,952           "the build environment.",
2023-09-10T00:29:22,952           file=sys.stderr,
2023-09-10T00:29:22,952       )
2023-09-10T00:29:22,952       sys.exit(1)
2023-09-10T00:29:22,952   
2023-09-10T00:29:22,952   __file__ = %r
2023-09-10T00:29:22,952   sys.argv[0] = __file__
2023-09-10T00:29:22,952   
2023-09-10T00:29:22,952   if os.path.exists(__file__):
2023-09-10T00:29:22,952       filename = __file__
2023-09-10T00:29:22,952       with tokenize.open(__file__) as f:
2023-09-10T00:29:22,952           setup_py_code = f.read()
2023-09-10T00:29:22,952   else:
2023-09-10T00:29:22,952       filename = "<auto-generated setuptools caller>"
2023-09-10T00:29:22,952       setup_py_code = "from setuptools import setup; setup()"
2023-09-10T00:29:22,952   
2023-09-10T00:29:22,952   exec(compile(setup_py_code, filename, "exec"))
2023-09-10T00:29:22,952   '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-karu1gei/tredparse_ea468dbfe1b642afa845e0758aa42363/setup.py'"'"',), "<pip-setuptools-caller>", "exec"))' bdist_wheel -d /tmp/pip-wheel-8uh5bpss[/]
2023-09-10T00:29:22,953   [bold magenta]cwd[/]: /tmp/pip-wheel-karu1gei/tredparse_ea468dbfe1b642afa845e0758aa42363/
2023-09-10T00:29:22,953   Building wheel for tredparse (setup.py): finished with status 'error'
2023-09-10T00:29:22,955   ERROR: Failed building wheel for tredparse
2023-09-10T00:29:22,956   Running setup.py clean for tredparse
2023-09-10T00:29:22,957   Running command python setup.py clean
2023-09-10T00:29:23,958   running clean
2023-09-10T00:29:24,006   removing 'build/temp.linux-armv7l-cpython-311' (and everything under it)
2023-09-10T00:29:24,008   removing 'build/lib.linux-armv7l-cpython-311' (and everything under it)
2023-09-10T00:29:24,015   'build/bdist.linux-armv7l' does not exist -- can't clean it
2023-09-10T00:29:24,016   'build/scripts-3.11' does not exist -- can't clean it
2023-09-10T00:29:24,016   removing 'build'
2023-09-10T00:29:24,121 Failed to build tredparse
2023-09-10T00:29:24,122 ERROR: Failed to build one or more wheels
2023-09-10T00:29:24,124 Exception information:
2023-09-10T00:29:24,124 Traceback (most recent call last):
2023-09-10T00:29:24,124   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper
2023-09-10T00:29:24,124     status = run_func(*args)
2023-09-10T00:29:24,124              ^^^^^^^^^^^^^^^
2023-09-10T00:29:24,124   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper
2023-09-10T00:29:24,124     return func(self, options, args)
2023-09-10T00:29:24,124            ^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-10T00:29:24,124   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run
2023-09-10T00:29:24,124     raise CommandError("Failed to build one or more wheels")
2023-09-10T00:29:24,124 pip._internal.exceptions.CommandError: Failed to build one or more wheels
2023-09-10T00:29:24,127 Removed build tracker: '/tmp/pip-build-tracker-e637z8yy'