2025-09-14T09:47:44,607 Created temporary directory: /tmp/pip-build-tracker-cbx2yxr6 2025-09-14T09:47:44,608 Initialized build tracking at /tmp/pip-build-tracker-cbx2yxr6 2025-09-14T09:47:44,608 Created build tracker: /tmp/pip-build-tracker-cbx2yxr6 2025-09-14T09:47:44,608 Entered build tracker: /tmp/pip-build-tracker-cbx2yxr6 2025-09-14T09:47:44,608 Created temporary directory: /tmp/pip-wheel-px06co6o 2025-09-14T09:47:44,612 Created temporary directory: /tmp/pip-ephem-wheel-cache-9vypite2 2025-09-14T09:47:44,671 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-14T09:47:44,673 2 location(s) to search for versions of bigphase: 2025-09-14T09:47:44,673 * https://pypi.org/simple/bigphase/ 2025-09-14T09:47:44,673 * https://www.piwheels.org/simple/bigphase/ 2025-09-14T09:47:44,674 Fetching project page and analyzing links: https://pypi.org/simple/bigphase/ 2025-09-14T09:47:44,674 Getting page https://pypi.org/simple/bigphase/ 2025-09-14T09:47:44,675 Found index url https://pypi.org/simple/ 2025-09-14T09:47:44,881 Fetched page https://pypi.org/simple/bigphase/ as application/vnd.pypi.simple.v1+json 2025-09-14T09:47:44,882 Found link https://files.pythonhosted.org/packages/a0/71/7839c0a22ba5cd0ac7768ac47b4cec82865f1fb0ef43b548cb79be88328b/bigphase-0.1.0.tar.gz (from https://pypi.org/simple/bigphase/), version: 0.1.0 2025-09-14T09:47:44,883 Found link https://files.pythonhosted.org/packages/50/8b/c53eaeb389ff9b6aa6eab1f861d875fd056f89443e6a029a0d6f2419d46c/bigphase-0.1.1.tar.gz (from https://pypi.org/simple/bigphase/), version: 0.1.1 2025-09-14T09:47:44,883 Found link https://files.pythonhosted.org/packages/2a/03/4c965f0d9e09ec76164ab6db236b98535a87595472baf194e218af849b9f/bigphase-0.1.2.tar.gz (from https://pypi.org/simple/bigphase/), version: 0.1.2 2025-09-14T09:47:44,883 Fetching project page and analyzing links: https://www.piwheels.org/simple/bigphase/ 2025-09-14T09:47:44,884 Getting page https://www.piwheels.org/simple/bigphase/ 2025-09-14T09:47:44,885 Found index url https://www.piwheels.org/simple/ 2025-09-14T09:47:44,974 Fetched page https://www.piwheels.org/simple/bigphase/ as text/html 2025-09-14T09:47:44,976 Skipping link: No binaries permitted for bigphase: https://archive1.piwheels.org/simple/bigphase/BigphASE-0.1.2-cp311-cp311-linux_armv6l.whl#sha256=69a303b5c201d99a6cca711d71a2560d9d81151dc0130dfb2ad6e67a328aa176 (from https://www.piwheels.org/simple/bigphase/) 2025-09-14T09:47:44,977 Skipping link: No binaries permitted for bigphase: https://archive1.piwheels.org/simple/bigphase/BigphASE-0.1.2-cp311-cp311-linux_armv7l.whl#sha256=69a303b5c201d99a6cca711d71a2560d9d81151dc0130dfb2ad6e67a328aa176 (from https://www.piwheels.org/simple/bigphase/) 2025-09-14T09:47:44,977 Skipping link: No binaries permitted for bigphase: https://archive1.piwheels.org/simple/bigphase/BigphASE-0.1.2-cp39-cp39-linux_armv6l.whl#sha256=2cfe64839d647121708fdf129cc0fc7c51eb591f04de3e64d058a728e10993fc (from https://www.piwheels.org/simple/bigphase/) 2025-09-14T09:47:44,977 Skipping link: No binaries permitted for bigphase: https://archive1.piwheels.org/simple/bigphase/BigphASE-0.1.2-cp39-cp39-linux_armv7l.whl#sha256=2cfe64839d647121708fdf129cc0fc7c51eb591f04de3e64d058a728e10993fc (from https://www.piwheels.org/simple/bigphase/) 2025-09-14T09:47:44,977 Skipping link: No binaries permitted for bigphase: https://archive1.piwheels.org/simple/bigphase/BigphASE-0.1.1-cp311-cp311-linux_armv6l.whl#sha256=a2ccfb0a324109f26c210cb3a9c63f82446370a03b6d184e03d2c81d61f67aa9 (from https://www.piwheels.org/simple/bigphase/) 2025-09-14T09:47:44,977 Skipping link: No binaries permitted for bigphase: https://archive1.piwheels.org/simple/bigphase/BigphASE-0.1.1-cp311-cp311-linux_armv7l.whl#sha256=a2ccfb0a324109f26c210cb3a9c63f82446370a03b6d184e03d2c81d61f67aa9 (from https://www.piwheels.org/simple/bigphase/) 2025-09-14T09:47:44,977 Skipping link: No binaries permitted for bigphase: https://archive1.piwheels.org/simple/bigphase/BigphASE-0.1.1-cp39-cp39-linux_armv6l.whl#sha256=0f5eb54473285f864553f122b9b3fbe9b5a87a9201ff26602ad211d162e06e4d (from https://www.piwheels.org/simple/bigphase/) 2025-09-14T09:47:44,977 Skipping link: No binaries permitted for bigphase: https://archive1.piwheels.org/simple/bigphase/BigphASE-0.1.1-cp39-cp39-linux_armv7l.whl#sha256=0f5eb54473285f864553f122b9b3fbe9b5a87a9201ff26602ad211d162e06e4d (from https://www.piwheels.org/simple/bigphase/) 2025-09-14T09:47:44,978 Skipping link: No binaries permitted for bigphase: https://archive1.piwheels.org/simple/bigphase/BigphASE-0.1.0-cp39-cp39-linux_armv6l.whl#sha256=0e6881ebbedd3f710e7e7ba01d62a9a975ba63d051f6a468a9c0f3503cafd156 (from https://www.piwheels.org/simple/bigphase/) 2025-09-14T09:47:44,978 Skipping link: No binaries permitted for bigphase: https://archive1.piwheels.org/simple/bigphase/BigphASE-0.1.0-cp39-cp39-linux_armv7l.whl#sha256=0e6881ebbedd3f710e7e7ba01d62a9a975ba63d051f6a468a9c0f3503cafd156 (from https://www.piwheels.org/simple/bigphase/) 2025-09-14T09:47:44,978 Skipping link: not a file: https://www.piwheels.org/simple/bigphase/ 2025-09-14T09:47:44,978 Skipping link: not a file: https://pypi.org/simple/bigphase/ 2025-09-14T09:47:45,003 Given no hashes to check 1 links for project 'bigphase': discarding no candidates 2025-09-14T09:47:45,004 Collecting bigphase==0.1.0 2025-09-14T09:47:45,006 Created temporary directory: /tmp/pip-unpack-5m35mx1n 2025-09-14T09:47:45,147 Downloading bigphase-0.1.0.tar.gz (125 kB) 2025-09-14T09:47:45,218 Added bigphase==0.1.0 from https://files.pythonhosted.org/packages/a0/71/7839c0a22ba5cd0ac7768ac47b4cec82865f1fb0ef43b548cb79be88328b/bigphase-0.1.0.tar.gz to build tracker '/tmp/pip-build-tracker-cbx2yxr6' 2025-09-14T09:47:45,219 Running setup.py (path:/tmp/pip-wheel-px06co6o/bigphase_49cf5563423043db9f1343a8de51233e/setup.py) egg_info for package bigphase 2025-09-14T09:47:45,219 Created temporary directory: /tmp/pip-pip-egg-info-mu08x4ho 2025-09-14T09:47:45,220 Preparing metadata (setup.py): started 2025-09-14T09:47:45,220 Running command python setup.py egg_info 2025-09-14T09:47:46,490 running egg_info 2025-09-14T09:47:46,578 creating /tmp/pip-pip-egg-info-mu08x4ho/BigphASE.egg-info 2025-09-14T09:47:46,578 writing /tmp/pip-pip-egg-info-mu08x4ho/BigphASE.egg-info/PKG-INFO 2025-09-14T09:47:46,579 writing dependency_links to /tmp/pip-pip-egg-info-mu08x4ho/BigphASE.egg-info/dependency_links.txt 2025-09-14T09:47:46,580 writing top-level names to /tmp/pip-pip-egg-info-mu08x4ho/BigphASE.egg-info/top_level.txt 2025-09-14T09:47:46,581 writing manifest file '/tmp/pip-pip-egg-info-mu08x4ho/BigphASE.egg-info/SOURCES.txt' 2025-09-14T09:47:46,843 reading manifest file '/tmp/pip-pip-egg-info-mu08x4ho/BigphASE.egg-info/SOURCES.txt' 2025-09-14T09:47:46,844 reading manifest template 'MANIFEST.in' 2025-09-14T09:47:46,846 adding license file 'LICENSE' 2025-09-14T09:47:46,849 writing manifest file '/tmp/pip-pip-egg-info-mu08x4ho/BigphASE.egg-info/SOURCES.txt' 2025-09-14T09:47:46,978 Preparing metadata (setup.py): finished with status 'done' 2025-09-14T09:47:46,983 Source in /tmp/pip-wheel-px06co6o/bigphase_49cf5563423043db9f1343a8de51233e has version 0.1.0, which satisfies requirement bigphase==0.1.0 from https://files.pythonhosted.org/packages/a0/71/7839c0a22ba5cd0ac7768ac47b4cec82865f1fb0ef43b548cb79be88328b/bigphase-0.1.0.tar.gz 2025-09-14T09:47:46,983 Removed bigphase==0.1.0 from https://files.pythonhosted.org/packages/a0/71/7839c0a22ba5cd0ac7768ac47b4cec82865f1fb0ef43b548cb79be88328b/bigphase-0.1.0.tar.gz from build tracker '/tmp/pip-build-tracker-cbx2yxr6' 2025-09-14T09:47:46,986 Created temporary directory: /tmp/pip-unpack-kp8xadl_ 2025-09-14T09:47:46,987 Created temporary directory: /tmp/pip-unpack-u989spga 2025-09-14T09:47:46,987 Building wheels for collected packages: bigphase 2025-09-14T09:47:46,988 Created temporary directory: /tmp/pip-wheel-6gft2o7s 2025-09-14T09:47:46,989 DEPRECATION: Building 'bigphase' 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 'bigphase'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-14T09:47:46,990 Building wheel for bigphase (setup.py): started 2025-09-14T09:47:46,991 Destination directory: /tmp/pip-wheel-6gft2o7s 2025-09-14T09:47:46,991 Running command python setup.py bdist_wheel 2025-09-14T09:47:48,172 running bdist_wheel 2025-09-14T09:47:48,519 running build 2025-09-14T09:47:48,519 running build_py 2025-09-14T09:47:48,609 creating build/lib.linux-armv7l-cpython-313/BigphASE 2025-09-14T09:47:48,610 copying src/BigphASE/utils.py -> build/lib.linux-armv7l-cpython-313/BigphASE 2025-09-14T09:47:48,610 copying src/BigphASE/options.py -> build/lib.linux-armv7l-cpython-313/BigphASE 2025-09-14T09:47:48,611 copying src/BigphASE/maker.py -> build/lib.linux-armv7l-cpython-313/BigphASE 2025-09-14T09:47:48,612 copying src/BigphASE/__init__.py -> build/lib.linux-armv7l-cpython-313/BigphASE 2025-09-14T09:47:48,612 running egg_info 2025-09-14T09:47:48,697 writing src/BigphASE.egg-info/PKG-INFO 2025-09-14T09:47:48,698 writing dependency_links to src/BigphASE.egg-info/dependency_links.txt 2025-09-14T09:47:48,699 writing top-level names to src/BigphASE.egg-info/top_level.txt 2025-09-14T09:47:48,793 reading manifest file 'src/BigphASE.egg-info/SOURCES.txt' 2025-09-14T09:47:48,796 reading manifest template 'MANIFEST.in' 2025-09-14T09:47:48,798 adding license file 'LICENSE' 2025-09-14T09:47:48,802 writing manifest file 'src/BigphASE.egg-info/SOURCES.txt' 2025-09-14T09:47:48,803 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'BigphASE.delta2hap' is absent from the `packages` configuration. 2025-09-14T09:47:48,804 !! 2025-09-14T09:47:48,804 ******************************************************************************** 2025-09-14T09:47:48,804 ############################ 2025-09-14T09:47:48,804 # Package would be ignored # 2025-09-14T09:47:48,804 ############################ 2025-09-14T09:47:48,804 Python recognizes 'BigphASE.delta2hap' as an importable package[^1], 2025-09-14T09:47:48,804 but it is absent from setuptools' `packages` configuration. 2025-09-14T09:47:48,804 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-14T09:47:48,805 package, please make sure that 'BigphASE.delta2hap' is explicitly added 2025-09-14T09:47:48,805 to the `packages` configuration field. 2025-09-14T09:47:48,805 Alternatively, you can also rely on setuptools' discovery methods 2025-09-14T09:47:48,805 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-14T09:47:48,805 instead of `find_packages(...)`/`find:`). 2025-09-14T09:47:48,805 You can read more about "package discovery" on setuptools documentation page: 2025-09-14T09:47:48,805 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-14T09:47:48,806 If you don't want 'BigphASE.delta2hap' to be distributed and are 2025-09-14T09:47:48,806 already explicitly excluding 'BigphASE.delta2hap' via 2025-09-14T09:47:48,806 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-14T09:47:48,806 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-14T09:47:48,806 combination with a more fine grained `package-data` configuration. 2025-09-14T09:47:48,806 You can read more about "package data files" on setuptools documentation page: 2025-09-14T09:47:48,806 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-14T09:47:48,807 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-14T09:47:48,807 even if it does not contain any `.py` files. 2025-09-14T09:47:48,807 On the other hand, currently there is no concept of package data 2025-09-14T09:47:48,807 directory, all directories are treated like packages. 2025-09-14T09:47:48,807 ******************************************************************************** 2025-09-14T09:47:48,807 !! 2025-09-14T09:47:48,807 check.warn(importable) 2025-09-14T09:47:48,808 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'BigphASE.delta2hap.bin' is absent from the `packages` configuration. 2025-09-14T09:47:48,808 !! 2025-09-14T09:47:48,808 ******************************************************************************** 2025-09-14T09:47:48,808 ############################ 2025-09-14T09:47:48,808 # Package would be ignored # 2025-09-14T09:47:48,808 ############################ 2025-09-14T09:47:48,808 Python recognizes 'BigphASE.delta2hap.bin' as an importable package[^1], 2025-09-14T09:47:48,809 but it is absent from setuptools' `packages` configuration. 2025-09-14T09:47:48,809 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-14T09:47:48,809 package, please make sure that 'BigphASE.delta2hap.bin' is explicitly added 2025-09-14T09:47:48,809 to the `packages` configuration field. 2025-09-14T09:47:48,809 Alternatively, you can also rely on setuptools' discovery methods 2025-09-14T09:47:48,809 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-14T09:47:48,809 instead of `find_packages(...)`/`find:`). 2025-09-14T09:47:48,810 You can read more about "package discovery" on setuptools documentation page: 2025-09-14T09:47:48,810 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-14T09:47:48,810 If you don't want 'BigphASE.delta2hap.bin' to be distributed and are 2025-09-14T09:47:48,810 already explicitly excluding 'BigphASE.delta2hap.bin' via 2025-09-14T09:47:48,810 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-14T09:47:48,810 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-14T09:47:48,810 combination with a more fine grained `package-data` configuration. 2025-09-14T09:47:48,811 You can read more about "package data files" on setuptools documentation page: 2025-09-14T09:47:48,811 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-14T09:47:48,811 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-14T09:47:48,811 even if it does not contain any `.py` files. 2025-09-14T09:47:48,811 On the other hand, currently there is no concept of package data 2025-09-14T09:47:48,812 directory, all directories are treated like packages. 2025-09-14T09:47:48,812 ******************************************************************************** 2025-09-14T09:47:48,812 !! 2025-09-14T09:47:48,812 check.warn(importable) 2025-09-14T09:47:48,812 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'BigphASE.delta2hap.include' is absent from the `packages` configuration. 2025-09-14T09:47:48,812 !! 2025-09-14T09:47:48,812 ******************************************************************************** 2025-09-14T09:47:48,812 ############################ 2025-09-14T09:47:48,813 # Package would be ignored # 2025-09-14T09:47:48,813 ############################ 2025-09-14T09:47:48,813 Python recognizes 'BigphASE.delta2hap.include' as an importable package[^1], 2025-09-14T09:47:48,813 but it is absent from setuptools' `packages` configuration. 2025-09-14T09:47:48,813 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-14T09:47:48,813 package, please make sure that 'BigphASE.delta2hap.include' is explicitly added 2025-09-14T09:47:48,813 to the `packages` configuration field. 2025-09-14T09:47:48,814 Alternatively, you can also rely on setuptools' discovery methods 2025-09-14T09:47:48,814 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-14T09:47:48,814 instead of `find_packages(...)`/`find:`). 2025-09-14T09:47:48,814 You can read more about "package discovery" on setuptools documentation page: 2025-09-14T09:47:48,814 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-14T09:47:48,814 If you don't want 'BigphASE.delta2hap.include' to be distributed and are 2025-09-14T09:47:48,814 already explicitly excluding 'BigphASE.delta2hap.include' via 2025-09-14T09:47:48,815 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-14T09:47:48,815 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-14T09:47:48,815 combination with a more fine grained `package-data` configuration. 2025-09-14T09:47:48,815 You can read more about "package data files" on setuptools documentation page: 2025-09-14T09:47:48,815 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-14T09:47:48,815 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-14T09:47:48,816 even if it does not contain any `.py` files. 2025-09-14T09:47:48,816 On the other hand, currently there is no concept of package data 2025-09-14T09:47:48,816 directory, all directories are treated like packages. 2025-09-14T09:47:48,816 ******************************************************************************** 2025-09-14T09:47:48,816 !! 2025-09-14T09:47:48,816 check.warn(importable) 2025-09-14T09:47:48,816 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'BigphASE.delta2hap.src' is absent from the `packages` configuration. 2025-09-14T09:47:48,816 !! 2025-09-14T09:47:48,817 ******************************************************************************** 2025-09-14T09:47:48,817 ############################ 2025-09-14T09:47:48,817 # Package would be ignored # 2025-09-14T09:47:48,817 ############################ 2025-09-14T09:47:48,817 Python recognizes 'BigphASE.delta2hap.src' as an importable package[^1], 2025-09-14T09:47:48,817 but it is absent from setuptools' `packages` configuration. 2025-09-14T09:47:48,817 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-14T09:47:48,818 package, please make sure that 'BigphASE.delta2hap.src' is explicitly added 2025-09-14T09:47:48,818 to the `packages` configuration field. 2025-09-14T09:47:48,818 Alternatively, you can also rely on setuptools' discovery methods 2025-09-14T09:47:48,818 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-14T09:47:48,818 instead of `find_packages(...)`/`find:`). 2025-09-14T09:47:48,818 You can read more about "package discovery" on setuptools documentation page: 2025-09-14T09:47:48,818 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-14T09:47:48,819 If you don't want 'BigphASE.delta2hap.src' to be distributed and are 2025-09-14T09:47:48,819 already explicitly excluding 'BigphASE.delta2hap.src' via 2025-09-14T09:47:48,819 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-14T09:47:48,819 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-14T09:47:48,819 combination with a more fine grained `package-data` configuration. 2025-09-14T09:47:48,819 You can read more about "package data files" on setuptools documentation page: 2025-09-14T09:47:48,820 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-14T09:47:48,820 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-14T09:47:48,820 even if it does not contain any `.py` files. 2025-09-14T09:47:48,820 On the other hand, currently there is no concept of package data 2025-09-14T09:47:48,820 directory, all directories are treated like packages. 2025-09-14T09:47:48,820 ******************************************************************************** 2025-09-14T09:47:48,820 !! 2025-09-14T09:47:48,821 check.warn(importable) 2025-09-14T09:47:48,821 creating build/lib.linux-armv7l-cpython-313/BigphASE/delta2hap 2025-09-14T09:47:48,821 copying src/BigphASE/delta2hap/CMakeLists.txt -> build/lib.linux-armv7l-cpython-313/BigphASE/delta2hap 2025-09-14T09:47:48,821 creating build/lib.linux-armv7l-cpython-313/BigphASE/delta2hap/bin 2025-09-14T09:47:48,821 copying src/BigphASE/delta2hap/bin/delta2hap -> build/lib.linux-armv7l-cpython-313/BigphASE/delta2hap/bin 2025-09-14T09:47:48,821 creating build/lib.linux-armv7l-cpython-313/BigphASE/delta2hap/include 2025-09-14T09:47:48,821 copying src/BigphASE/delta2hap/include/delta.h -> build/lib.linux-armv7l-cpython-313/BigphASE/delta2hap/include 2025-09-14T09:47:48,821 copying src/BigphASE/delta2hap/include/redirect_to_pager.h -> build/lib.linux-armv7l-cpython-313/BigphASE/delta2hap/include 2025-09-14T09:47:48,822 copying src/BigphASE/delta2hap/include/show-vcf.h -> build/lib.linux-armv7l-cpython-313/BigphASE/delta2hap/include 2025-09-14T09:47:48,822 copying src/BigphASE/delta2hap/include/sw_alignscore.h -> build/lib.linux-armv7l-cpython-313/BigphASE/delta2hap/include 2025-09-14T09:47:48,822 copying src/BigphASE/delta2hap/include/tigrinc.h -> build/lib.linux-armv7l-cpython-313/BigphASE/delta2hap/include 2025-09-14T09:47:48,822 copying src/BigphASE/delta2hap/include/translate.h -> build/lib.linux-armv7l-cpython-313/BigphASE/delta2hap/include 2025-09-14T09:47:48,822 creating build/lib.linux-armv7l-cpython-313/BigphASE/delta2hap/src 2025-09-14T09:47:48,822 copying src/BigphASE/delta2hap/src/delta.cpp -> build/lib.linux-armv7l-cpython-313/BigphASE/delta2hap/src 2025-09-14T09:47:48,822 copying src/BigphASE/delta2hap/src/delta2hap.cpp -> build/lib.linux-armv7l-cpython-313/BigphASE/delta2hap/src 2025-09-14T09:47:48,822 copying src/BigphASE/delta2hap/src/tigrinc.cpp -> build/lib.linux-armv7l-cpython-313/BigphASE/delta2hap/src 2025-09-14T09:47:48,822 copying src/BigphASE/delta2hap/src/translate.cpp -> build/lib.linux-armv7l-cpython-313/BigphASE/delta2hap/src 2025-09-14T09:47:48,823 running build_ext 2025-09-14T09:47:48,828 Compiling src/BigphASE/delta2hap/src/delta2hap.cpp... 2025-09-14T09:47:52,568 Compiling src/BigphASE/delta2hap/src/delta.cpp... 2025-09-14T09:47:56,392 Compiling src/BigphASE/delta2hap/src/tigrinc.cpp... 2025-09-14T09:47:56,772 Compiling src/BigphASE/delta2hap/src/translate.cpp... 2025-09-14T09:47:56,921 Linking src/BigphASE/delta2hap/bin/delta2hap... 2025-09-14T09:47:57,330 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-09-14T09:47:57,330 !! 2025-09-14T09:47:57,330 ******************************************************************************** 2025-09-14T09:47:57,330 Please avoid running ``setup.py`` directly. 2025-09-14T09:47:57,331 Instead, use pypa/build, pypa/installer or other 2025-09-14T09:47:57,331 standards-based tools. 2025-09-14T09:47:57,331 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-14T09:47:57,331 or your builds will no longer be supported. 2025-09-14T09:47:57,331 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-09-14T09:47:57,331 ******************************************************************************** 2025-09-14T09:47:57,332 !! 2025-09-14T09:47:57,332 self.initialize_options() 2025-09-14T09:47:57,418 installing to build/bdist.linux-armv7l/wheel 2025-09-14T09:47:57,419 running install 2025-09-14T09:47:57,443 running install_lib 2025-09-14T09:47:57,528 creating build/bdist.linux-armv7l/wheel 2025-09-14T09:47:57,529 creating build/bdist.linux-armv7l/wheel/BigphASE 2025-09-14T09:47:57,529 creating build/bdist.linux-armv7l/wheel/BigphASE/delta2hap 2025-09-14T09:47:57,530 creating build/bdist.linux-armv7l/wheel/BigphASE/delta2hap/src 2025-09-14T09:47:57,530 copying build/lib.linux-armv7l-cpython-313/BigphASE/delta2hap/src/translate.cpp -> build/bdist.linux-armv7l/wheel/./BigphASE/delta2hap/src 2025-09-14T09:47:57,531 copying build/lib.linux-armv7l-cpython-313/BigphASE/delta2hap/src/tigrinc.cpp -> build/bdist.linux-armv7l/wheel/./BigphASE/delta2hap/src 2025-09-14T09:47:57,531 copying build/lib.linux-armv7l-cpython-313/BigphASE/delta2hap/src/delta2hap.cpp -> build/bdist.linux-armv7l/wheel/./BigphASE/delta2hap/src 2025-09-14T09:47:57,532 copying build/lib.linux-armv7l-cpython-313/BigphASE/delta2hap/src/delta.cpp -> build/bdist.linux-armv7l/wheel/./BigphASE/delta2hap/src 2025-09-14T09:47:57,533 creating build/bdist.linux-armv7l/wheel/BigphASE/delta2hap/include 2025-09-14T09:47:57,533 copying build/lib.linux-armv7l-cpython-313/BigphASE/delta2hap/include/translate.h -> build/bdist.linux-armv7l/wheel/./BigphASE/delta2hap/include 2025-09-14T09:47:57,533 copying build/lib.linux-armv7l-cpython-313/BigphASE/delta2hap/include/tigrinc.h -> build/bdist.linux-armv7l/wheel/./BigphASE/delta2hap/include 2025-09-14T09:47:57,534 copying build/lib.linux-armv7l-cpython-313/BigphASE/delta2hap/include/sw_alignscore.h -> build/bdist.linux-armv7l/wheel/./BigphASE/delta2hap/include 2025-09-14T09:47:57,534 copying build/lib.linux-armv7l-cpython-313/BigphASE/delta2hap/include/show-vcf.h -> build/bdist.linux-armv7l/wheel/./BigphASE/delta2hap/include 2025-09-14T09:47:57,535 copying build/lib.linux-armv7l-cpython-313/BigphASE/delta2hap/include/redirect_to_pager.h -> build/bdist.linux-armv7l/wheel/./BigphASE/delta2hap/include 2025-09-14T09:47:57,535 copying build/lib.linux-armv7l-cpython-313/BigphASE/delta2hap/include/delta.h -> build/bdist.linux-armv7l/wheel/./BigphASE/delta2hap/include 2025-09-14T09:47:57,536 creating build/bdist.linux-armv7l/wheel/BigphASE/delta2hap/bin 2025-09-14T09:47:57,536 copying build/lib.linux-armv7l-cpython-313/BigphASE/delta2hap/bin/delta2hap -> build/bdist.linux-armv7l/wheel/./BigphASE/delta2hap/bin 2025-09-14T09:47:57,538 copying build/lib.linux-armv7l-cpython-313/BigphASE/delta2hap/CMakeLists.txt -> build/bdist.linux-armv7l/wheel/./BigphASE/delta2hap 2025-09-14T09:47:57,539 copying build/lib.linux-armv7l-cpython-313/BigphASE/__init__.py -> build/bdist.linux-armv7l/wheel/./BigphASE 2025-09-14T09:47:57,539 copying build/lib.linux-armv7l-cpython-313/BigphASE/maker.py -> build/bdist.linux-armv7l/wheel/./BigphASE 2025-09-14T09:47:57,540 copying build/lib.linux-armv7l-cpython-313/BigphASE/options.py -> build/bdist.linux-armv7l/wheel/./BigphASE 2025-09-14T09:47:57,540 copying build/lib.linux-armv7l-cpython-313/BigphASE/utils.py -> build/bdist.linux-armv7l/wheel/./BigphASE 2025-09-14T09:47:57,541 running install_egg_info 2025-09-14T09:47:57,630 Copying src/BigphASE.egg-info to build/bdist.linux-armv7l/wheel/./BigphASE-0.1.0-py3.13.egg-info 2025-09-14T09:47:57,632 running install_scripts 2025-09-14T09:47:57,633 Removed directory /tmp/pip-wheel-px06co6o/bigphase_49cf5563423043db9f1343a8de51233e/src/BigphASE/delta2hap/include 2025-09-14T09:47:57,633 Removed directory /tmp/pip-wheel-px06co6o/bigphase_49cf5563423043db9f1343a8de51233e/src/BigphASE/delta2hap/src 2025-09-14T09:47:57,634 Removed file /tmp/pip-wheel-px06co6o/bigphase_49cf5563423043db9f1343a8de51233e/src/BigphASE/delta2hap/CMakeLists.txt 2025-09-14T09:47:57,688 creating build/bdist.linux-armv7l/wheel/bigphase-0.1.0.dist-info/WHEEL 2025-09-14T09:47:57,689 creating '/tmp/pip-wheel-6gft2o7s/bigphase-0.1.0-cp313-cp313-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-09-14T09:47:57,690 adding 'BigphASE/__init__.py' 2025-09-14T09:47:57,692 adding 'BigphASE/maker.py' 2025-09-14T09:47:57,693 adding 'BigphASE/options.py' 2025-09-14T09:47:57,695 adding 'BigphASE/utils.py' 2025-09-14T09:47:57,695 adding 'BigphASE/delta2hap/CMakeLists.txt' 2025-09-14T09:47:57,741 adding 'BigphASE/delta2hap/bin/delta2hap' 2025-09-14T09:47:57,745 adding 'BigphASE/delta2hap/include/delta.h' 2025-09-14T09:47:57,746 adding 'BigphASE/delta2hap/include/redirect_to_pager.h' 2025-09-14T09:47:57,747 adding 'BigphASE/delta2hap/include/show-vcf.h' 2025-09-14T09:47:57,748 adding 'BigphASE/delta2hap/include/sw_alignscore.h' 2025-09-14T09:47:57,749 adding 'BigphASE/delta2hap/include/tigrinc.h' 2025-09-14T09:47:57,751 adding 'BigphASE/delta2hap/include/translate.h' 2025-09-14T09:47:57,754 adding 'BigphASE/delta2hap/src/delta.cpp' 2025-09-14T09:47:57,757 adding 'BigphASE/delta2hap/src/delta2hap.cpp' 2025-09-14T09:47:57,759 adding 'BigphASE/delta2hap/src/tigrinc.cpp' 2025-09-14T09:47:57,760 adding 'BigphASE/delta2hap/src/translate.cpp' 2025-09-14T09:47:57,766 adding 'bigphase-0.1.0.dist-info/licenses/LICENSE' 2025-09-14T09:47:57,767 adding 'bigphase-0.1.0.dist-info/METADATA' 2025-09-14T09:47:57,767 adding 'bigphase-0.1.0.dist-info/WHEEL' 2025-09-14T09:47:57,768 adding 'bigphase-0.1.0.dist-info/top_level.txt' 2025-09-14T09:47:57,769 adding 'bigphase-0.1.0.dist-info/RECORD' 2025-09-14T09:47:57,769 removing build/bdist.linux-armv7l/wheel 2025-09-14T09:47:57,902 Building wheel for bigphase (setup.py): finished with status 'done' 2025-09-14T09:47:57,905 Created wheel for bigphase: filename=bigphase-0.1.0-cp313-cp313-linux_armv7l.whl size=127392 sha256=b00896a1095049585c088d2f4d2517f5fbf59e92bb259408cdf58db0d8b12317 2025-09-14T09:47:57,906 Stored in directory: /tmp/pip-ephem-wheel-cache-9vypite2/wheels/0c/e1/49/c269ce26ffdb939a21464571eb376785d7203c16a64ab01026 2025-09-14T09:47:57,915 Successfully built bigphase 2025-09-14T09:47:57,917 Removed build tracker: '/tmp/pip-build-tracker-cbx2yxr6'