2025-09-08T09:44:30,526 Created temporary directory: /tmp/pip-build-tracker-9nyu7_3l 2025-09-08T09:44:30,527 Initialized build tracking at /tmp/pip-build-tracker-9nyu7_3l 2025-09-08T09:44:30,527 Created build tracker: /tmp/pip-build-tracker-9nyu7_3l 2025-09-08T09:44:30,527 Entered build tracker: /tmp/pip-build-tracker-9nyu7_3l 2025-09-08T09:44:30,527 Created temporary directory: /tmp/pip-wheel-0q9e2im8 2025-09-08T09:44:30,530 Created temporary directory: /tmp/pip-ephem-wheel-cache-grzsvx_b 2025-09-08T09:44:30,589 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T09:44:30,591 2 location(s) to search for versions of tredparse: 2025-09-08T09:44:30,591 * https://pypi.org/simple/tredparse/ 2025-09-08T09:44:30,591 * https://www.piwheels.org/simple/tredparse/ 2025-09-08T09:44:30,591 Fetching project page and analyzing links: https://pypi.org/simple/tredparse/ 2025-09-08T09:44:30,592 Getting page https://pypi.org/simple/tredparse/ 2025-09-08T09:44:30,593 Found index url https://pypi.org/simple/ 2025-09-08T09:44:30,663 Fetched page https://pypi.org/simple/tredparse/ as application/vnd.pypi.simple.v1+json 2025-09-08T09:44:30,664 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 2025-09-08T09:44:30,664 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 2025-09-08T09:44:30,664 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 2025-09-08T09:44:30,665 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 2025-09-08T09:44:30,665 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 2025-09-08T09:44:30,665 Fetching project page and analyzing links: https://www.piwheels.org/simple/tredparse/ 2025-09-08T09:44:30,665 Getting page https://www.piwheels.org/simple/tredparse/ 2025-09-08T09:44:30,666 Found index url https://www.piwheels.org/simple/ 2025-09-08T09:44:30,763 Fetched page https://www.piwheels.org/simple/tredparse/ as text/html 2025-09-08T09:44:30,764 Skipping link: not a file: https://www.piwheels.org/simple/tredparse/ 2025-09-08T09:44:30,764 Skipping link: not a file: https://pypi.org/simple/tredparse/ 2025-09-08T09:44:30,786 Given no hashes to check 1 links for project 'tredparse': discarding no candidates 2025-09-08T09:44:30,787 Collecting tredparse==0.7.6 2025-09-08T09:44:30,788 Created temporary directory: /tmp/pip-unpack-s7ejlm3q 2025-09-08T09:44:30,933 Downloading tredparse-0.7.6.tar.gz (245 kB) 2025-09-08T09:44:31,015 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-9nyu7_3l' 2025-09-08T09:44:31,016 Running setup.py (path:/tmp/pip-wheel-0q9e2im8/tredparse_2bf316397c9c4d04a1868eb9067f5d3d/setup.py) egg_info for package tredparse 2025-09-08T09:44:31,017 Created temporary directory: /tmp/pip-pip-egg-info-q5mpy88r 2025-09-08T09:44:31,017 Preparing metadata (setup.py): started 2025-09-08T09:44:31,018 Running command python setup.py egg_info 2025-09-08T09:44:32,183 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T09:44:32,183 !! 2025-09-08T09:44:32,183 ******************************************************************************** 2025-09-08T09:44:32,183 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T09:44:32,183 License :: OSI Approved :: BSD License 2025-09-08T09:44:32,184 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T09:44:32,184 ******************************************************************************** 2025-09-08T09:44:32,184 !! 2025-09-08T09:44:32,184 self._finalize_license_expression() 2025-09-08T09:44:32,258 running egg_info 2025-09-08T09:44:32,333 creating /tmp/pip-pip-egg-info-q5mpy88r/tredparse.egg-info 2025-09-08T09:44:32,333 writing /tmp/pip-pip-egg-info-q5mpy88r/tredparse.egg-info/PKG-INFO 2025-09-08T09:44:32,334 writing dependency_links to /tmp/pip-pip-egg-info-q5mpy88r/tredparse.egg-info/dependency_links.txt 2025-09-08T09:44:32,335 writing requirements to /tmp/pip-pip-egg-info-q5mpy88r/tredparse.egg-info/requires.txt 2025-09-08T09:44:32,335 writing top-level names to /tmp/pip-pip-egg-info-q5mpy88r/tredparse.egg-info/top_level.txt 2025-09-08T09:44:32,335 writing manifest file '/tmp/pip-pip-egg-info-q5mpy88r/tredparse.egg-info/SOURCES.txt' 2025-09-08T09:44:32,718 reading manifest file '/tmp/pip-pip-egg-info-q5mpy88r/tredparse.egg-info/SOURCES.txt' 2025-09-08T09:44:32,718 reading manifest template 'MANIFEST.in' 2025-09-08T09:44:32,720 adding license file 'LICENSE' 2025-09-08T09:44:32,723 writing manifest file '/tmp/pip-pip-egg-info-q5mpy88r/tredparse.egg-info/SOURCES.txt' 2025-09-08T09:44:32,835 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T09:44:32,840 Source in /tmp/pip-wheel-0q9e2im8/tredparse_2bf316397c9c4d04a1868eb9067f5d3d 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 2025-09-08T09:44:32,841 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-9nyu7_3l' 2025-09-08T09:44:32,845 Created temporary directory: /tmp/pip-unpack-s1l65dhg 2025-09-08T09:44:32,845 Created temporary directory: /tmp/pip-unpack-07r20g51 2025-09-08T09:44:32,845 Building wheels for collected packages: tredparse 2025-09-08T09:44:32,846 Created temporary directory: /tmp/pip-wheel-m0dtw810 2025-09-08T09:44:32,847 DEPRECATION: Building 'tredparse' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'tredparse'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-08T09:44:32,848 Building wheel for tredparse (setup.py): started 2025-09-08T09:44:32,848 Destination directory: /tmp/pip-wheel-m0dtw810 2025-09-08T09:44:32,848 Running command python setup.py bdist_wheel 2025-09-08T09:44:33,938 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T09:44:33,938 !! 2025-09-08T09:44:33,938 ******************************************************************************** 2025-09-08T09:44:33,938 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T09:44:33,939 License :: OSI Approved :: BSD License 2025-09-08T09:44:33,939 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T09:44:33,939 ******************************************************************************** 2025-09-08T09:44:33,939 !! 2025-09-08T09:44:33,939 self._finalize_license_expression() 2025-09-08T09:44:33,940 running bdist_wheel 2025-09-08T09:44:34,311 running build 2025-09-08T09:44:34,311 running build_py 2025-09-08T09:44:34,387 creating build/lib.linux-armv7l-cpython-313/ssw 2025-09-08T09:44:34,388 copying src/__init__.py -> build/lib.linux-armv7l-cpython-313/ssw 2025-09-08T09:44:34,389 copying src/ssw_wrap.py -> build/lib.linux-armv7l-cpython-313/ssw 2025-09-08T09:44:34,390 creating build/lib.linux-armv7l-cpython-313/tredparse 2025-09-08T09:44:34,390 copying tredparse/utils.py -> build/lib.linux-armv7l-cpython-313/tredparse 2025-09-08T09:44:34,391 copying tredparse/models.py -> build/lib.linux-armv7l-cpython-313/tredparse 2025-09-08T09:44:34,392 copying tredparse/meta.py -> build/lib.linux-armv7l-cpython-313/tredparse 2025-09-08T09:44:34,392 copying tredparse/jcvi.py -> build/lib.linux-armv7l-cpython-313/tredparse 2025-09-08T09:44:34,393 copying tredparse/bam_parser.py -> build/lib.linux-armv7l-cpython-313/tredparse 2025-09-08T09:44:34,393 copying tredparse/__init__.py -> build/lib.linux-armv7l-cpython-313/tredparse 2025-09-08T09:44:34,394 running egg_info 2025-09-08T09:44:34,469 writing tredparse.egg-info/PKG-INFO 2025-09-08T09:44:34,470 writing dependency_links to tredparse.egg-info/dependency_links.txt 2025-09-08T09:44:34,471 writing requirements to tredparse.egg-info/requires.txt 2025-09-08T09:44:34,471 writing top-level names to tredparse.egg-info/top_level.txt 2025-09-08T09:44:34,549 reading manifest file 'tredparse.egg-info/SOURCES.txt' 2025-09-08T09:44:34,551 reading manifest template 'MANIFEST.in' 2025-09-08T09:44:34,553 adding license file 'LICENSE' 2025-09-08T09:44:34,557 writing manifest file 'tredparse.egg-info/SOURCES.txt' 2025-09-08T09:44:34,558 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'tredparse.data' is absent from the `packages` configuration. 2025-09-08T09:44:34,558 !! 2025-09-08T09:44:34,558 ******************************************************************************** 2025-09-08T09:44:34,558 ############################ 2025-09-08T09:44:34,559 # Package would be ignored # 2025-09-08T09:44:34,559 ############################ 2025-09-08T09:44:34,559 Python recognizes 'tredparse.data' as an importable package[^1], 2025-09-08T09:44:34,559 but it is absent from setuptools' `packages` configuration. 2025-09-08T09:44:34,559 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T09:44:34,559 package, please make sure that 'tredparse.data' is explicitly added 2025-09-08T09:44:34,559 to the `packages` configuration field. 2025-09-08T09:44:34,559 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T09:44:34,559 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T09:44:34,560 instead of `find_packages(...)`/`find:`). 2025-09-08T09:44:34,560 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T09:44:34,560 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T09:44:34,560 If you don't want 'tredparse.data' to be distributed and are 2025-09-08T09:44:34,560 already explicitly excluding 'tredparse.data' via 2025-09-08T09:44:34,560 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T09:44:34,560 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T09:44:34,560 combination with a more fine grained `package-data` configuration. 2025-09-08T09:44:34,561 You can read more about "package data files" on setuptools documentation page: 2025-09-08T09:44:34,561 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T09:44:34,561 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T09:44:34,561 even if it does not contain any `.py` files. 2025-09-08T09:44:34,561 On the other hand, currently there is no concept of package data 2025-09-08T09:44:34,561 directory, all directories are treated like packages. 2025-09-08T09:44:34,561 ******************************************************************************** 2025-09-08T09:44:34,562 !! 2025-09-08T09:44:34,562 check.warn(importable) 2025-09-08T09:44:34,562 creating build/lib.linux-armv7l-cpython-313/tredparse/data 2025-09-08T09:44:34,562 copying tredparse/data/HLI_bams.csv.gz -> build/lib.linux-armv7l-cpython-313/tredparse/data 2025-09-08T09:44:34,562 copying tredparse/data/TREDs.alts.csv -> build/lib.linux-armv7l-cpython-313/tredparse/data 2025-09-08T09:44:34,563 copying tredparse/data/TREDs.meta.csv -> build/lib.linux-armv7l-cpython-313/tredparse/data 2025-09-08T09:44:34,563 copying tredparse/data/chrY.hg19.unique_ccn.gc -> build/lib.linux-armv7l-cpython-313/tredparse/data 2025-09-08T09:44:34,564 copying tredparse/data/chrY.hg38.unique_ccn.gc -> build/lib.linux-armv7l-cpython-313/tredparse/data 2025-09-08T09:44:34,565 copying tredparse/data/illumina_v3.pcrfree.stepmodel -> build/lib.linux-armv7l-cpython-313/tredparse/data 2025-09-08T09:44:34,565 copying tredparse/data/illumina_v3.pcrfree.stuttermodel -> build/lib.linux-armv7l-cpython-313/tredparse/data 2025-09-08T09:44:34,566 copying src/ssw.c -> build/lib.linux-armv7l-cpython-313/ssw 2025-09-08T09:44:34,566 copying src/ssw.h -> build/lib.linux-armv7l-cpython-313/ssw 2025-09-08T09:44:34,568 running build_ext 2025-09-08T09:44:34,928 building 'libssw' extension 2025-09-08T09:44:34,929 creating build/temp.linux-armv7l-cpython-313/src 2025-09-08T09:44:34,929 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -Isrc -I/usr/include/python3.13 -c src/ssw.c -o build/temp.linux-armv7l-cpython-313/src/ssw.o 2025-09-08T09:44:34,972 src/ssw.c:38:10: fatal error: emmintrin.h: No such file or directory 2025-09-08T09:44:34,972 38 | #include 2025-09-08T09:44:34,973 | ^~~~~~~~~~~~~ 2025-09-08T09:44:34,973 compilation terminated. 2025-09-08T09:44:34,975 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2025-09-08T09:44:35,123 ERROR: python setup.py bdist_wheel exited with 1 2025-09-08T09:44:35,135 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-08T09:44:35,135 exec(compile('"'"''"'"''"'"' 2025-09-08T09:44:35,135 # This is -- a caller that pip uses to run setup.py 2025-09-08T09:44:35,135 # 2025-09-08T09:44:35,135 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T09:44:35,135 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T09:44:35,135 # - It provides a clear error message when setuptools is not installed. 2025-09-08T09:44:35,135 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T09:44:35,135 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T09:44:35,135 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T09:44:35,135 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T09:44:35,135 import os, sys, tokenize, traceback 2025-09-08T09:44:35,135 2025-09-08T09:44:35,135 try: 2025-09-08T09:44:35,135 import setuptools 2025-09-08T09:44:35,135 except ImportError: 2025-09-08T09:44:35,135 print( 2025-09-08T09:44:35,135 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T09:44:35,135 "the build environment with exception:", 2025-09-08T09:44:35,135 file=sys.stderr, 2025-09-08T09:44:35,135 ) 2025-09-08T09:44:35,135 traceback.print_exc() 2025-09-08T09:44:35,135 sys.exit(1) 2025-09-08T09:44:35,135 2025-09-08T09:44:35,135 __file__ = %r 2025-09-08T09:44:35,135 sys.argv[0] = __file__ 2025-09-08T09:44:35,135 2025-09-08T09:44:35,135 if os.path.exists(__file__): 2025-09-08T09:44:35,135 filename = __file__ 2025-09-08T09:44:35,135 with tokenize.open(__file__) as f: 2025-09-08T09:44:35,135 setup_py_code = f.read() 2025-09-08T09:44:35,135 else: 2025-09-08T09:44:35,135 filename = "" 2025-09-08T09:44:35,135 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T09:44:35,135 2025-09-08T09:44:35,135 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T09:44:35,135 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-0q9e2im8/tredparse_2bf316397c9c4d04a1868eb9067f5d3d/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-m0dtw810[/] 2025-09-08T09:44:35,135 [bold magenta]cwd[/]: /tmp/pip-wheel-0q9e2im8/tredparse_2bf316397c9c4d04a1868eb9067f5d3d/ 2025-09-08T09:44:35,135 Building wheel for tredparse (setup.py): finished with status 'error' 2025-09-08T09:44:35,136 ERROR: Failed building wheel for tredparse 2025-09-08T09:44:35,137 Running setup.py clean for tredparse 2025-09-08T09:44:35,137 Running command python setup.py clean 2025-09-08T09:44:36,213 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T09:44:36,213 !! 2025-09-08T09:44:36,213 ******************************************************************************** 2025-09-08T09:44:36,213 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T09:44:36,214 License :: OSI Approved :: BSD License 2025-09-08T09:44:36,214 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T09:44:36,214 ******************************************************************************** 2025-09-08T09:44:36,214 !! 2025-09-08T09:44:36,214 self._finalize_license_expression() 2025-09-08T09:44:36,287 running clean 2025-09-08T09:44:36,435 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T09:44:36,435 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T09:44:36,436 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-08T09:44:36,436 'build/scripts-3.13' does not exist -- can't clean it 2025-09-08T09:44:36,436 removing 'build' 2025-09-08T09:44:36,548 Failed to build tredparse 2025-09-08T09:44:36,549 ERROR: Failed to build one or more wheels 2025-09-08T09:44:36,550 Exception information: 2025-09-08T09:44:36,550 Traceback (most recent call last): 2025-09-08T09:44:36,550 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T09:44:36,550 status = _inner_run() 2025-09-08T09:44:36,550 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T09:44:36,550 return self.run(options, args) 2025-09-08T09:44:36,550 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T09:44:36,550 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T09:44:36,550 return func(self, options, args) 2025-09-08T09:44:36,550 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T09:44:36,550 raise CommandError("Failed to build one or more wheels") 2025-09-08T09:44:36,550 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T09:44:36,554 Removed build tracker: '/tmp/pip-build-tracker-9nyu7_3l'