2025-09-08T09:22:30,981 Created temporary directory: /tmp/pip-build-tracker-mub3v_bn 2025-09-08T09:22:30,982 Initialized build tracking at /tmp/pip-build-tracker-mub3v_bn 2025-09-08T09:22:30,982 Created build tracker: /tmp/pip-build-tracker-mub3v_bn 2025-09-08T09:22:30,982 Entered build tracker: /tmp/pip-build-tracker-mub3v_bn 2025-09-08T09:22:30,982 Created temporary directory: /tmp/pip-wheel-_pagg9em 2025-09-08T09:22:30,985 Created temporary directory: /tmp/pip-ephem-wheel-cache-vo9chr94 2025-09-08T09:22:31,043 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T09:22:31,046 2 location(s) to search for versions of tredparse: 2025-09-08T09:22:31,046 * https://pypi.org/simple/tredparse/ 2025-09-08T09:22:31,046 * https://www.piwheels.org/simple/tredparse/ 2025-09-08T09:22:31,046 Fetching project page and analyzing links: https://pypi.org/simple/tredparse/ 2025-09-08T09:22:31,046 Getting page https://pypi.org/simple/tredparse/ 2025-09-08T09:22:31,047 Found index url https://pypi.org/simple/ 2025-09-08T09:22:31,194 Fetched page https://pypi.org/simple/tredparse/ as application/vnd.pypi.simple.v1+json 2025-09-08T09:22:31,195 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 2025-09-08T09:22:31,195 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 2025-09-08T09:22:31,196 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 2025-09-08T09:22:31,196 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 2025-09-08T09:22:31,196 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 2025-09-08T09:22:31,197 Fetching project page and analyzing links: https://www.piwheels.org/simple/tredparse/ 2025-09-08T09:22:31,197 Getting page https://www.piwheels.org/simple/tredparse/ 2025-09-08T09:22:31,198 Found index url https://www.piwheels.org/simple/ 2025-09-08T09:22:31,293 Fetched page https://www.piwheels.org/simple/tredparse/ as text/html 2025-09-08T09:22:31,294 Skipping link: not a file: https://www.piwheels.org/simple/tredparse/ 2025-09-08T09:22:31,294 Skipping link: not a file: https://pypi.org/simple/tredparse/ 2025-09-08T09:22:31,319 Given no hashes to check 1 links for project 'tredparse': discarding no candidates 2025-09-08T09:22:31,321 Collecting tredparse==0.7.5 2025-09-08T09:22:31,322 Created temporary directory: /tmp/pip-unpack-t52lfig_ 2025-09-08T09:22:31,488 Downloading tredparse-0.7.5.tar.gz (58 kB) 2025-09-08T09:22:31,535 Added tredparse==0.7.5 from https://files.pythonhosted.org/packages/27/ce/05332b56a32fa249b226f606bca1b6ad4c0292a8a26541a10f23cea87234/tredparse-0.7.5.tar.gz to build tracker '/tmp/pip-build-tracker-mub3v_bn' 2025-09-08T09:22:31,536 Running setup.py (path:/tmp/pip-wheel-_pagg9em/tredparse_a2b67644014746da8eb786804533abec/setup.py) egg_info for package tredparse 2025-09-08T09:22:31,536 Created temporary directory: /tmp/pip-pip-egg-info-6rn_8gig 2025-09-08T09:22:31,536 Preparing metadata (setup.py): started 2025-09-08T09:22:31,537 Running command python setup.py egg_info 2025-09-08T09:22:32,605 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T09:22:32,605 !! 2025-09-08T09:22:32,605 ******************************************************************************** 2025-09-08T09:22:32,606 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T09:22:32,606 License :: OSI Approved :: BSD License 2025-09-08T09:22:32,606 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T09:22:32,606 ******************************************************************************** 2025-09-08T09:22:32,606 !! 2025-09-08T09:22:32,606 self._finalize_license_expression() 2025-09-08T09:22:32,691 running egg_info 2025-09-08T09:22:32,765 creating /tmp/pip-pip-egg-info-6rn_8gig/tredparse.egg-info 2025-09-08T09:22:32,765 writing /tmp/pip-pip-egg-info-6rn_8gig/tredparse.egg-info/PKG-INFO 2025-09-08T09:22:32,766 writing dependency_links to /tmp/pip-pip-egg-info-6rn_8gig/tredparse.egg-info/dependency_links.txt 2025-09-08T09:22:32,767 writing requirements to /tmp/pip-pip-egg-info-6rn_8gig/tredparse.egg-info/requires.txt 2025-09-08T09:22:32,767 writing top-level names to /tmp/pip-pip-egg-info-6rn_8gig/tredparse.egg-info/top_level.txt 2025-09-08T09:22:32,768 writing manifest file '/tmp/pip-pip-egg-info-6rn_8gig/tredparse.egg-info/SOURCES.txt' 2025-09-08T09:22:33,143 reading manifest file '/tmp/pip-pip-egg-info-6rn_8gig/tredparse.egg-info/SOURCES.txt' 2025-09-08T09:22:33,144 reading manifest template 'MANIFEST.in' 2025-09-08T09:22:33,146 adding license file 'LICENSE' 2025-09-08T09:22:33,148 writing manifest file '/tmp/pip-pip-egg-info-6rn_8gig/tredparse.egg-info/SOURCES.txt' 2025-09-08T09:22:33,261 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T09:22:33,266 Source in /tmp/pip-wheel-_pagg9em/tredparse_a2b67644014746da8eb786804533abec has version 0.7.5, which satisfies requirement tredparse==0.7.5 from https://files.pythonhosted.org/packages/27/ce/05332b56a32fa249b226f606bca1b6ad4c0292a8a26541a10f23cea87234/tredparse-0.7.5.tar.gz 2025-09-08T09:22:33,267 Removed tredparse==0.7.5 from https://files.pythonhosted.org/packages/27/ce/05332b56a32fa249b226f606bca1b6ad4c0292a8a26541a10f23cea87234/tredparse-0.7.5.tar.gz from build tracker '/tmp/pip-build-tracker-mub3v_bn' 2025-09-08T09:22:33,271 Created temporary directory: /tmp/pip-unpack-a7x0cipq 2025-09-08T09:22:33,271 Created temporary directory: /tmp/pip-unpack-std8rxct 2025-09-08T09:22:33,271 Building wheels for collected packages: tredparse 2025-09-08T09:22:33,273 Created temporary directory: /tmp/pip-wheel-68kd2zbu 2025-09-08T09:22:33,273 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 2025-09-08T09:22:33,274 Building wheel for tredparse (setup.py): started 2025-09-08T09:22:33,275 Destination directory: /tmp/pip-wheel-68kd2zbu 2025-09-08T09:22:33,275 Running command python setup.py bdist_wheel 2025-09-08T09:22:34,352 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T09:22:34,352 !! 2025-09-08T09:22:34,352 ******************************************************************************** 2025-09-08T09:22:34,353 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T09:22:34,353 License :: OSI Approved :: BSD License 2025-09-08T09:22:34,353 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T09:22:34,353 ******************************************************************************** 2025-09-08T09:22:34,353 !! 2025-09-08T09:22:34,353 self._finalize_license_expression() 2025-09-08T09:22:34,354 running bdist_wheel 2025-09-08T09:22:34,720 running build 2025-09-08T09:22:34,721 running build_py 2025-09-08T09:22:34,797 creating build/lib.linux-armv7l-cpython-313/ssw 2025-09-08T09:22:34,797 copying src/__init__.py -> build/lib.linux-armv7l-cpython-313/ssw 2025-09-08T09:22:34,798 copying src/ssw_wrap.py -> build/lib.linux-armv7l-cpython-313/ssw 2025-09-08T09:22:34,799 creating build/lib.linux-armv7l-cpython-313/tredparse 2025-09-08T09:22:34,799 copying tredparse/utils.py -> build/lib.linux-armv7l-cpython-313/tredparse 2025-09-08T09:22:34,800 copying tredparse/models.py -> build/lib.linux-armv7l-cpython-313/tredparse 2025-09-08T09:22:34,801 copying tredparse/meta.py -> build/lib.linux-armv7l-cpython-313/tredparse 2025-09-08T09:22:34,801 copying tredparse/jcvi.py -> build/lib.linux-armv7l-cpython-313/tredparse 2025-09-08T09:22:34,802 copying tredparse/bam_parser.py -> build/lib.linux-armv7l-cpython-313/tredparse 2025-09-08T09:22:34,803 copying tredparse/__init__.py -> build/lib.linux-armv7l-cpython-313/tredparse 2025-09-08T09:22:34,804 running egg_info 2025-09-08T09:22:34,877 writing tredparse.egg-info/PKG-INFO 2025-09-08T09:22:34,878 writing dependency_links to tredparse.egg-info/dependency_links.txt 2025-09-08T09:22:34,879 writing requirements to tredparse.egg-info/requires.txt 2025-09-08T09:22:34,879 writing top-level names to tredparse.egg-info/top_level.txt 2025-09-08T09:22:34,955 reading manifest file 'tredparse.egg-info/SOURCES.txt' 2025-09-08T09:22:34,957 reading manifest template 'MANIFEST.in' 2025-09-08T09:22:34,959 adding license file 'LICENSE' 2025-09-08T09:22:34,961 writing manifest file 'tredparse.egg-info/SOURCES.txt' 2025-09-08T09:22:34,963 copying src/ssw.c -> build/lib.linux-armv7l-cpython-313/ssw 2025-09-08T09:22:34,964 copying src/ssw.h -> build/lib.linux-armv7l-cpython-313/ssw 2025-09-08T09:22:34,965 running build_ext 2025-09-08T09:22:35,298 building 'libssw' extension 2025-09-08T09:22:35,298 creating build/temp.linux-armv7l-cpython-313/src 2025-09-08T09:22:35,299 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 2025-09-08T09:22:35,343 src/ssw.c:38:10: fatal error: emmintrin.h: No such file or directory 2025-09-08T09:22:35,344 38 | #include 2025-09-08T09:22:35,344 | ^~~~~~~~~~~~~ 2025-09-08T09:22:35,344 compilation terminated. 2025-09-08T09:22:35,346 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2025-09-08T09:22:35,492 ERROR: python setup.py bdist_wheel exited with 1 2025-09-08T09:22:35,505 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-08T09:22:35,505 exec(compile('"'"''"'"''"'"' 2025-09-08T09:22:35,505 # This is -- a caller that pip uses to run setup.py 2025-09-08T09:22:35,505 # 2025-09-08T09:22:35,505 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T09:22:35,505 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T09:22:35,505 # - It provides a clear error message when setuptools is not installed. 2025-09-08T09:22:35,505 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T09:22:35,505 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T09:22:35,505 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T09:22:35,505 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T09:22:35,505 import os, sys, tokenize, traceback 2025-09-08T09:22:35,505 2025-09-08T09:22:35,505 try: 2025-09-08T09:22:35,505 import setuptools 2025-09-08T09:22:35,505 except ImportError: 2025-09-08T09:22:35,505 print( 2025-09-08T09:22:35,505 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T09:22:35,505 "the build environment with exception:", 2025-09-08T09:22:35,505 file=sys.stderr, 2025-09-08T09:22:35,505 ) 2025-09-08T09:22:35,505 traceback.print_exc() 2025-09-08T09:22:35,505 sys.exit(1) 2025-09-08T09:22:35,505 2025-09-08T09:22:35,505 __file__ = %r 2025-09-08T09:22:35,505 sys.argv[0] = __file__ 2025-09-08T09:22:35,505 2025-09-08T09:22:35,505 if os.path.exists(__file__): 2025-09-08T09:22:35,505 filename = __file__ 2025-09-08T09:22:35,505 with tokenize.open(__file__) as f: 2025-09-08T09:22:35,505 setup_py_code = f.read() 2025-09-08T09:22:35,505 else: 2025-09-08T09:22:35,505 filename = "" 2025-09-08T09:22:35,505 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T09:22:35,505 2025-09-08T09:22:35,505 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T09:22:35,505 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-_pagg9em/tredparse_a2b67644014746da8eb786804533abec/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-68kd2zbu[/] 2025-09-08T09:22:35,505 [bold magenta]cwd[/]: /tmp/pip-wheel-_pagg9em/tredparse_a2b67644014746da8eb786804533abec/ 2025-09-08T09:22:35,506 Building wheel for tredparse (setup.py): finished with status 'error' 2025-09-08T09:22:35,507 ERROR: Failed building wheel for tredparse 2025-09-08T09:22:35,508 Running setup.py clean for tredparse 2025-09-08T09:22:35,508 Running command python setup.py clean 2025-09-08T09:22:36,679 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T09:22:36,679 !! 2025-09-08T09:22:36,679 ******************************************************************************** 2025-09-08T09:22:36,679 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T09:22:36,680 License :: OSI Approved :: BSD License 2025-09-08T09:22:36,680 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T09:22:36,680 ******************************************************************************** 2025-09-08T09:22:36,680 !! 2025-09-08T09:22:36,680 self._finalize_license_expression() 2025-09-08T09:22:36,754 running clean 2025-09-08T09:22:36,899 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T09:22:36,899 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T09:22:36,900 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-08T09:22:36,900 'build/scripts-3.13' does not exist -- can't clean it 2025-09-08T09:22:36,900 removing 'build' 2025-09-08T09:22:37,012 Failed to build tredparse 2025-09-08T09:22:37,013 ERROR: Failed to build one or more wheels 2025-09-08T09:22:37,013 Exception information: 2025-09-08T09:22:37,013 Traceback (most recent call last): 2025-09-08T09:22:37,013 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T09:22:37,013 status = _inner_run() 2025-09-08T09:22:37,013 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T09:22:37,013 return self.run(options, args) 2025-09-08T09:22:37,013 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T09:22:37,013 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T09:22:37,013 return func(self, options, args) 2025-09-08T09:22:37,013 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T09:22:37,013 raise CommandError("Failed to build one or more wheels") 2025-09-08T09:22:37,013 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T09:22:37,018 Removed build tracker: '/tmp/pip-build-tracker-mub3v_bn'