2025-09-08T10:04:34,496 Created temporary directory: /tmp/pip-build-tracker-_tmwlf0j 2025-09-08T10:04:34,497 Initialized build tracking at /tmp/pip-build-tracker-_tmwlf0j 2025-09-08T10:04:34,497 Created build tracker: /tmp/pip-build-tracker-_tmwlf0j 2025-09-08T10:04:34,497 Entered build tracker: /tmp/pip-build-tracker-_tmwlf0j 2025-09-08T10:04:34,497 Created temporary directory: /tmp/pip-wheel-ea7i81_4 2025-09-08T10:04:34,500 Created temporary directory: /tmp/pip-ephem-wheel-cache-mowih7rx 2025-09-08T10:04:34,556 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T10:04:34,559 2 location(s) to search for versions of tredparse: 2025-09-08T10:04:34,559 * https://pypi.org/simple/tredparse/ 2025-09-08T10:04:34,559 * https://www.piwheels.org/simple/tredparse/ 2025-09-08T10:04:34,559 Fetching project page and analyzing links: https://pypi.org/simple/tredparse/ 2025-09-08T10:04:34,559 Getting page https://pypi.org/simple/tredparse/ 2025-09-08T10:04:34,560 Found index url https://pypi.org/simple/ 2025-09-08T10:04:34,630 Fetched page https://pypi.org/simple/tredparse/ as application/vnd.pypi.simple.v1+json 2025-09-08T10:04:34,631 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 2025-09-08T10:04:34,632 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 2025-09-08T10:04:34,632 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 2025-09-08T10:04:34,632 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 2025-09-08T10:04:34,632 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 2025-09-08T10:04:34,633 Fetching project page and analyzing links: https://www.piwheels.org/simple/tredparse/ 2025-09-08T10:04:34,633 Getting page https://www.piwheels.org/simple/tredparse/ 2025-09-08T10:04:34,634 Found index url https://www.piwheels.org/simple/ 2025-09-08T10:04:34,752 Fetched page https://www.piwheels.org/simple/tredparse/ as text/html 2025-09-08T10:04:34,752 Skipping link: not a file: https://www.piwheels.org/simple/tredparse/ 2025-09-08T10:04:34,752 Skipping link: not a file: https://pypi.org/simple/tredparse/ 2025-09-08T10:04:34,779 Given no hashes to check 1 links for project 'tredparse': discarding no candidates 2025-09-08T10:04:34,780 Collecting tredparse==0.7.8 2025-09-08T10:04:34,782 Created temporary directory: /tmp/pip-unpack-ptd6e9xp 2025-09-08T10:04:34,921 Downloading tredparse-0.7.8.tar.gz (247 kB) 2025-09-08T10:04:34,994 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-_tmwlf0j' 2025-09-08T10:04:34,995 Running setup.py (path:/tmp/pip-wheel-ea7i81_4/tredparse_141319ca05064cf9b62a86f50df5bcad/setup.py) egg_info for package tredparse 2025-09-08T10:04:34,996 Created temporary directory: /tmp/pip-pip-egg-info-vwmmtk8d 2025-09-08T10:04:34,996 Preparing metadata (setup.py): started 2025-09-08T10:04:34,997 Running command python setup.py egg_info 2025-09-08T10:04:35,535 /tmp/pip-wheel-ea7i81_4/tredparse_141319ca05064cf9b62a86f50df5bcad/setup_helper.py:6: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81. 2025-09-08T10:04:35,535 import pkg_resources 2025-09-08T10:04:36,831 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T10:04:36,832 !! 2025-09-08T10:04:36,832 ******************************************************************************** 2025-09-08T10:04:36,832 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T10:04:36,832 License :: OSI Approved :: BSD License 2025-09-08T10:04:36,832 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T10:04:36,832 ******************************************************************************** 2025-09-08T10:04:36,833 !! 2025-09-08T10:04:36,833 self._finalize_license_expression() 2025-09-08T10:04:36,906 running egg_info 2025-09-08T10:04:36,978 creating /tmp/pip-pip-egg-info-vwmmtk8d/tredparse.egg-info 2025-09-08T10:04:36,978 writing /tmp/pip-pip-egg-info-vwmmtk8d/tredparse.egg-info/PKG-INFO 2025-09-08T10:04:36,980 writing dependency_links to /tmp/pip-pip-egg-info-vwmmtk8d/tredparse.egg-info/dependency_links.txt 2025-09-08T10:04:36,980 writing requirements to /tmp/pip-pip-egg-info-vwmmtk8d/tredparse.egg-info/requires.txt 2025-09-08T10:04:36,981 writing top-level names to /tmp/pip-pip-egg-info-vwmmtk8d/tredparse.egg-info/top_level.txt 2025-09-08T10:04:36,981 writing manifest file '/tmp/pip-pip-egg-info-vwmmtk8d/tredparse.egg-info/SOURCES.txt' 2025-09-08T10:04:37,353 reading manifest file '/tmp/pip-pip-egg-info-vwmmtk8d/tredparse.egg-info/SOURCES.txt' 2025-09-08T10:04:37,353 reading manifest template 'MANIFEST.in' 2025-09-08T10:04:37,356 adding license file 'LICENSE' 2025-09-08T10:04:37,359 writing manifest file '/tmp/pip-pip-egg-info-vwmmtk8d/tredparse.egg-info/SOURCES.txt' 2025-09-08T10:04:37,479 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T10:04:37,484 Source in /tmp/pip-wheel-ea7i81_4/tredparse_141319ca05064cf9b62a86f50df5bcad 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 2025-09-08T10:04:37,484 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-_tmwlf0j' 2025-09-08T10:04:37,489 Created temporary directory: /tmp/pip-unpack-jgpkoqfo 2025-09-08T10:04:37,490 Created temporary directory: /tmp/pip-unpack-6ijgu4tb 2025-09-08T10:04:37,490 Building wheels for collected packages: tredparse 2025-09-08T10:04:37,491 Created temporary directory: /tmp/pip-wheel-d77h21b1 2025-09-08T10:04:37,492 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 2025-09-08T10:04:37,493 Building wheel for tredparse (setup.py): started 2025-09-08T10:04:37,494 Destination directory: /tmp/pip-wheel-d77h21b1 2025-09-08T10:04:37,494 Running command python setup.py bdist_wheel 2025-09-08T10:04:38,022 /tmp/pip-wheel-ea7i81_4/tredparse_141319ca05064cf9b62a86f50df5bcad/setup_helper.py:6: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81. 2025-09-08T10:04:38,022 import pkg_resources 2025-09-08T10:04:39,271 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T10:04:39,272 !! 2025-09-08T10:04:39,272 ******************************************************************************** 2025-09-08T10:04:39,272 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T10:04:39,272 License :: OSI Approved :: BSD License 2025-09-08T10:04:39,272 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T10:04:39,272 ******************************************************************************** 2025-09-08T10:04:39,273 !! 2025-09-08T10:04:39,273 self._finalize_license_expression() 2025-09-08T10:04:39,273 running bdist_wheel 2025-09-08T10:04:39,645 running build 2025-09-08T10:04:39,645 running build_py 2025-09-08T10:04:39,723 creating build/lib.linux-armv7l-cpython-313/ssw 2025-09-08T10:04:39,724 copying src/__init__.py -> build/lib.linux-armv7l-cpython-313/ssw 2025-09-08T10:04:39,724 copying src/ssw_wrap.py -> build/lib.linux-armv7l-cpython-313/ssw 2025-09-08T10:04:39,726 creating build/lib.linux-armv7l-cpython-313/tredparse 2025-09-08T10:04:39,726 copying tredparse/meta.py -> build/lib.linux-armv7l-cpython-313/tredparse 2025-09-08T10:04:39,727 copying tredparse/tredreport.py -> build/lib.linux-armv7l-cpython-313/tredparse 2025-09-08T10:04:39,727 copying tredparse/utils.py -> build/lib.linux-armv7l-cpython-313/tredparse 2025-09-08T10:04:39,728 copying tredparse/bam_parser.py -> build/lib.linux-armv7l-cpython-313/tredparse 2025-09-08T10:04:39,728 copying tredparse/__init__.py -> build/lib.linux-armv7l-cpython-313/tredparse 2025-09-08T10:04:39,729 copying tredparse/jcvi.py -> build/lib.linux-armv7l-cpython-313/tredparse 2025-09-08T10:04:39,729 copying tredparse/models.py -> build/lib.linux-armv7l-cpython-313/tredparse 2025-09-08T10:04:39,730 copying tredparse/tred.py -> build/lib.linux-armv7l-cpython-313/tredparse 2025-09-08T10:04:39,731 copying tredparse/tredplot.py -> build/lib.linux-armv7l-cpython-313/tredparse 2025-09-08T10:04:39,732 running egg_info 2025-09-08T10:04:39,809 writing tredparse.egg-info/PKG-INFO 2025-09-08T10:04:39,810 writing dependency_links to tredparse.egg-info/dependency_links.txt 2025-09-08T10:04:39,811 writing requirements to tredparse.egg-info/requires.txt 2025-09-08T10:04:39,811 writing top-level names to tredparse.egg-info/top_level.txt 2025-09-08T10:04:39,889 reading manifest file 'tredparse.egg-info/SOURCES.txt' 2025-09-08T10:04:39,892 reading manifest template 'MANIFEST.in' 2025-09-08T10:04:39,894 adding license file 'LICENSE' 2025-09-08T10:04:39,897 writing manifest file 'tredparse.egg-info/SOURCES.txt' 2025-09-08T10:04:39,899 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'tredparse.data' is absent from the `packages` configuration. 2025-09-08T10:04:39,899 !! 2025-09-08T10:04:39,899 ******************************************************************************** 2025-09-08T10:04:39,899 ############################ 2025-09-08T10:04:39,899 # Package would be ignored # 2025-09-08T10:04:39,899 ############################ 2025-09-08T10:04:39,899 Python recognizes 'tredparse.data' as an importable package[^1], 2025-09-08T10:04:39,900 but it is absent from setuptools' `packages` configuration. 2025-09-08T10:04:39,900 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T10:04:39,900 package, please make sure that 'tredparse.data' is explicitly added 2025-09-08T10:04:39,900 to the `packages` configuration field. 2025-09-08T10:04:39,900 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T10:04:39,900 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T10:04:39,900 instead of `find_packages(...)`/`find:`). 2025-09-08T10:04:39,900 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T10:04:39,901 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T10:04:39,901 If you don't want 'tredparse.data' to be distributed and are 2025-09-08T10:04:39,901 already explicitly excluding 'tredparse.data' via 2025-09-08T10:04:39,901 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T10:04:39,901 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T10:04:39,901 combination with a more fine grained `package-data` configuration. 2025-09-08T10:04:39,901 You can read more about "package data files" on setuptools documentation page: 2025-09-08T10:04:39,902 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T10:04:39,902 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T10:04:39,902 even if it does not contain any `.py` files. 2025-09-08T10:04:39,902 On the other hand, currently there is no concept of package data 2025-09-08T10:04:39,902 directory, all directories are treated like packages. 2025-09-08T10:04:39,902 ******************************************************************************** 2025-09-08T10:04:39,902 !! 2025-09-08T10:04:39,902 check.warn(importable) 2025-09-08T10:04:39,903 creating build/lib.linux-armv7l-cpython-313/tredparse/data 2025-09-08T10:04:39,903 copying tredparse/data/HLI_bams.csv.gz -> build/lib.linux-armv7l-cpython-313/tredparse/data 2025-09-08T10:04:39,903 copying tredparse/data/TREDs.alts.csv -> build/lib.linux-armv7l-cpython-313/tredparse/data 2025-09-08T10:04:39,903 copying tredparse/data/TREDs.meta.csv -> build/lib.linux-armv7l-cpython-313/tredparse/data 2025-09-08T10:04:39,904 copying tredparse/data/chrY.hg19.unique_ccn.gc -> build/lib.linux-armv7l-cpython-313/tredparse/data 2025-09-08T10:04:39,905 copying tredparse/data/chrY.hg38.unique_ccn.gc -> build/lib.linux-armv7l-cpython-313/tredparse/data 2025-09-08T10:04:39,905 copying tredparse/data/illumina_v3.pcrfree.stepmodel -> build/lib.linux-armv7l-cpython-313/tredparse/data 2025-09-08T10:04:39,906 copying tredparse/data/illumina_v3.pcrfree.stuttermodel -> build/lib.linux-armv7l-cpython-313/tredparse/data 2025-09-08T10:04:39,906 copying src/ssw.c -> build/lib.linux-armv7l-cpython-313/ssw 2025-09-08T10:04:39,907 copying src/ssw.h -> build/lib.linux-armv7l-cpython-313/ssw 2025-09-08T10:04:39,908 running build_ext 2025-09-08T10:04:40,238 building 'libssw' extension 2025-09-08T10:04:40,239 creating build/temp.linux-armv7l-cpython-313/src 2025-09-08T10:04:40,239 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 2025-09-08T10:04:40,287 src/ssw.c:38:10: fatal error: emmintrin.h: No such file or directory 2025-09-08T10:04:40,287 38 | #include 2025-09-08T10:04:40,287 | ^~~~~~~~~~~~~ 2025-09-08T10:04:40,287 compilation terminated. 2025-09-08T10:04:40,289 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2025-09-08T10:04:40,444 ERROR: python setup.py bdist_wheel exited with 1 2025-09-08T10:04:40,456 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-08T10:04:40,456 exec(compile('"'"''"'"''"'"' 2025-09-08T10:04:40,456 # This is -- a caller that pip uses to run setup.py 2025-09-08T10:04:40,456 # 2025-09-08T10:04:40,456 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T10:04:40,456 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T10:04:40,456 # - It provides a clear error message when setuptools is not installed. 2025-09-08T10:04:40,456 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T10:04:40,456 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T10:04:40,456 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T10:04:40,456 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T10:04:40,456 import os, sys, tokenize, traceback 2025-09-08T10:04:40,456 2025-09-08T10:04:40,456 try: 2025-09-08T10:04:40,456 import setuptools 2025-09-08T10:04:40,456 except ImportError: 2025-09-08T10:04:40,456 print( 2025-09-08T10:04:40,456 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T10:04:40,456 "the build environment with exception:", 2025-09-08T10:04:40,456 file=sys.stderr, 2025-09-08T10:04:40,456 ) 2025-09-08T10:04:40,456 traceback.print_exc() 2025-09-08T10:04:40,456 sys.exit(1) 2025-09-08T10:04:40,456 2025-09-08T10:04:40,456 __file__ = %r 2025-09-08T10:04:40,456 sys.argv[0] = __file__ 2025-09-08T10:04:40,456 2025-09-08T10:04:40,456 if os.path.exists(__file__): 2025-09-08T10:04:40,456 filename = __file__ 2025-09-08T10:04:40,456 with tokenize.open(__file__) as f: 2025-09-08T10:04:40,456 setup_py_code = f.read() 2025-09-08T10:04:40,456 else: 2025-09-08T10:04:40,456 filename = "" 2025-09-08T10:04:40,456 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T10:04:40,456 2025-09-08T10:04:40,456 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T10:04:40,456 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-ea7i81_4/tredparse_141319ca05064cf9b62a86f50df5bcad/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-d77h21b1[/] 2025-09-08T10:04:40,457 [bold magenta]cwd[/]: /tmp/pip-wheel-ea7i81_4/tredparse_141319ca05064cf9b62a86f50df5bcad/ 2025-09-08T10:04:40,457 Building wheel for tredparse (setup.py): finished with status 'error' 2025-09-08T10:04:40,458 ERROR: Failed building wheel for tredparse 2025-09-08T10:04:40,459 Running setup.py clean for tredparse 2025-09-08T10:04:40,459 Running command python setup.py clean 2025-09-08T10:04:40,995 /tmp/pip-wheel-ea7i81_4/tredparse_141319ca05064cf9b62a86f50df5bcad/setup_helper.py:6: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81. 2025-09-08T10:04:40,995 import pkg_resources 2025-09-08T10:04:42,249 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T10:04:42,249 !! 2025-09-08T10:04:42,250 ******************************************************************************** 2025-09-08T10:04:42,250 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T10:04:42,250 License :: OSI Approved :: BSD License 2025-09-08T10:04:42,250 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T10:04:42,250 ******************************************************************************** 2025-09-08T10:04:42,250 !! 2025-09-08T10:04:42,250 self._finalize_license_expression() 2025-09-08T10:04:42,325 running clean 2025-09-08T10:04:42,468 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T10:04:42,469 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T10:04:42,470 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-08T10:04:42,470 'build/scripts-3.13' does not exist -- can't clean it 2025-09-08T10:04:42,470 removing 'build' 2025-09-08T10:04:42,589 Failed to build tredparse 2025-09-08T10:04:42,590 ERROR: Failed to build one or more wheels 2025-09-08T10:04:42,591 Exception information: 2025-09-08T10:04:42,591 Traceback (most recent call last): 2025-09-08T10:04:42,591 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T10:04:42,591 status = _inner_run() 2025-09-08T10:04:42,591 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T10:04:42,591 return self.run(options, args) 2025-09-08T10:04:42,591 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T10:04:42,591 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T10:04:42,591 return func(self, options, args) 2025-09-08T10:04:42,591 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T10:04:42,591 raise CommandError("Failed to build one or more wheels") 2025-09-08T10:04:42,591 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T10:04:42,595 Removed build tracker: '/tmp/pip-build-tracker-_tmwlf0j'