2025-09-12T18:46:50,984 Created temporary directory: /tmp/pip-build-tracker-l349_xcu 2025-09-12T18:46:50,985 Initialized build tracking at /tmp/pip-build-tracker-l349_xcu 2025-09-12T18:46:50,985 Created build tracker: /tmp/pip-build-tracker-l349_xcu 2025-09-12T18:46:50,985 Entered build tracker: /tmp/pip-build-tracker-l349_xcu 2025-09-12T18:46:50,986 Created temporary directory: /tmp/pip-wheel-dq6f1bka 2025-09-12T18:46:50,989 Created temporary directory: /tmp/pip-ephem-wheel-cache-qfz28cbm 2025-09-12T18:46:51,051 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-12T18:46:51,053 2 location(s) to search for versions of cpdb-protein: 2025-09-12T18:46:51,053 * https://pypi.org/simple/cpdb-protein/ 2025-09-12T18:46:51,053 * https://www.piwheels.org/simple/cpdb-protein/ 2025-09-12T18:46:51,054 Fetching project page and analyzing links: https://pypi.org/simple/cpdb-protein/ 2025-09-12T18:46:51,054 Getting page https://pypi.org/simple/cpdb-protein/ 2025-09-12T18:46:51,055 Found index url https://pypi.org/simple/ 2025-09-12T18:46:51,218 Fetched page https://pypi.org/simple/cpdb-protein/ as application/vnd.pypi.simple.v1+json 2025-09-12T18:46:51,219 Found link https://files.pythonhosted.org/packages/ed/58/a6f6d0924c7e4be968b8703eec99179403a13ce5e143660abef310a7717b/cpdb-protein-0.0.2.tar.gz (from https://pypi.org/simple/cpdb-protein/), version: 0.0.2 2025-09-12T18:46:51,219 Found link https://files.pythonhosted.org/packages/e6/25/653305959ded3d2da61b6c6d859fb1250c891728f1f821b329b4a808433c/cpdb-protein-0.1.0.tar.gz (from https://pypi.org/simple/cpdb-protein/), version: 0.1.0 2025-09-12T18:46:51,220 Found link https://files.pythonhosted.org/packages/bc/7d/207dd68c474541c4000f61ce823a1c1d2f0a431a63d4f4679b77aab6048f/cpdb-protein-0.2.0.tar.gz (from https://pypi.org/simple/cpdb-protein/), version: 0.2.0 2025-09-12T18:46:51,220 Fetching project page and analyzing links: https://www.piwheels.org/simple/cpdb-protein/ 2025-09-12T18:46:51,221 Getting page https://www.piwheels.org/simple/cpdb-protein/ 2025-09-12T18:46:51,222 Found index url https://www.piwheels.org/simple/ 2025-09-12T18:46:51,313 Fetched page https://www.piwheels.org/simple/cpdb-protein/ as text/html 2025-09-12T18:46:51,316 Skipping link: No binaries permitted for cpdb-protein: https://archive1.piwheels.org/simple/cpdb-protein/cpdb_protein-0.2.0-cp37-cp37m-linux_armv6l.whl#sha256=11318001e946ad005126a5189bc2779bdb4dd3939ae064d075a268bb798b96f2 (from https://www.piwheels.org/simple/cpdb-protein/) 2025-09-12T18:46:51,317 Skipping link: No binaries permitted for cpdb-protein: https://archive1.piwheels.org/simple/cpdb-protein/cpdb_protein-0.2.0-cp37-cp37m-linux_armv7l.whl#sha256=11318001e946ad005126a5189bc2779bdb4dd3939ae064d075a268bb798b96f2 (from https://www.piwheels.org/simple/cpdb-protein/) 2025-09-12T18:46:51,317 Skipping link: No binaries permitted for cpdb-protein: https://archive1.piwheels.org/simple/cpdb-protein/cpdb_protein-0.2.0-cp39-cp39-linux_armv6l.whl#sha256=acdf396dae9feafe2225637cec59b62895fe71c39b795ca9d182e43b4a20d529 (from https://www.piwheels.org/simple/cpdb-protein/) 2025-09-12T18:46:51,317 Skipping link: No binaries permitted for cpdb-protein: https://archive1.piwheels.org/simple/cpdb-protein/cpdb_protein-0.2.0-cp39-cp39-linux_armv7l.whl#sha256=acdf396dae9feafe2225637cec59b62895fe71c39b795ca9d182e43b4a20d529 (from https://www.piwheels.org/simple/cpdb-protein/) 2025-09-12T18:46:51,317 Skipping link: No binaries permitted for cpdb-protein: https://archive1.piwheels.org/simple/cpdb-protein/cpdb_protein-0.2.0-cp311-cp311-linux_armv6l.whl#sha256=f35a9c3c3f89a9b63f4fb139aceef6669a8e8e733b84e7674fbd8dac61b8e238 (from https://www.piwheels.org/simple/cpdb-protein/) 2025-09-12T18:46:51,317 Skipping link: No binaries permitted for cpdb-protein: https://archive1.piwheels.org/simple/cpdb-protein/cpdb_protein-0.2.0-cp311-cp311-linux_armv7l.whl#sha256=f35a9c3c3f89a9b63f4fb139aceef6669a8e8e733b84e7674fbd8dac61b8e238 (from https://www.piwheels.org/simple/cpdb-protein/) 2025-09-12T18:46:51,317 Skipping link: No binaries permitted for cpdb-protein: https://archive1.piwheels.org/simple/cpdb-protein/cpdb_protein-0.1.0-cp37-cp37m-linux_armv6l.whl#sha256=3687d224de19ddc0ac28fd68b69e64b178ac18fc406680daa254e74302d9d286 (from https://www.piwheels.org/simple/cpdb-protein/) 2025-09-12T18:46:51,317 Skipping link: No binaries permitted for cpdb-protein: https://archive1.piwheels.org/simple/cpdb-protein/cpdb_protein-0.1.0-cp37-cp37m-linux_armv7l.whl#sha256=3687d224de19ddc0ac28fd68b69e64b178ac18fc406680daa254e74302d9d286 (from https://www.piwheels.org/simple/cpdb-protein/) 2025-09-12T18:46:51,318 Skipping link: No binaries permitted for cpdb-protein: https://archive1.piwheels.org/simple/cpdb-protein/cpdb_protein-0.1.0-cp39-cp39-linux_armv6l.whl#sha256=b63d4d4b0f6f896667bc095a4452c0f770b56197f24b95fbb4ee73d95b0429b2 (from https://www.piwheels.org/simple/cpdb-protein/) 2025-09-12T18:46:51,318 Skipping link: No binaries permitted for cpdb-protein: https://archive1.piwheels.org/simple/cpdb-protein/cpdb_protein-0.1.0-cp39-cp39-linux_armv7l.whl#sha256=b63d4d4b0f6f896667bc095a4452c0f770b56197f24b95fbb4ee73d95b0429b2 (from https://www.piwheels.org/simple/cpdb-protein/) 2025-09-12T18:46:51,318 Skipping link: No binaries permitted for cpdb-protein: https://archive1.piwheels.org/simple/cpdb-protein/cpdb_protein-0.0.2-cp37-cp37m-linux_armv6l.whl#sha256=1bb3a8682dcca32281b7e6f610373ebf0e762ad6e260460f0c7036cfb7263c8a (from https://www.piwheels.org/simple/cpdb-protein/) 2025-09-12T18:46:51,318 Skipping link: No binaries permitted for cpdb-protein: https://archive1.piwheels.org/simple/cpdb-protein/cpdb_protein-0.0.2-cp37-cp37m-linux_armv7l.whl#sha256=1bb3a8682dcca32281b7e6f610373ebf0e762ad6e260460f0c7036cfb7263c8a (from https://www.piwheels.org/simple/cpdb-protein/) 2025-09-12T18:46:51,318 Skipping link: No binaries permitted for cpdb-protein: https://archive1.piwheels.org/simple/cpdb-protein/cpdb_protein-0.0.2-cp39-cp39-linux_armv6l.whl#sha256=20b2a381b6c48b7d95899055fcaedad232305b5e3e72404912e427110ca2af51 (from https://www.piwheels.org/simple/cpdb-protein/) 2025-09-12T18:46:51,318 Skipping link: No binaries permitted for cpdb-protein: https://archive1.piwheels.org/simple/cpdb-protein/cpdb_protein-0.0.2-cp39-cp39-linux_armv7l.whl#sha256=20b2a381b6c48b7d95899055fcaedad232305b5e3e72404912e427110ca2af51 (from https://www.piwheels.org/simple/cpdb-protein/) 2025-09-12T18:46:51,319 Skipping link: not a file: https://www.piwheels.org/simple/cpdb-protein/ 2025-09-12T18:46:51,319 Skipping link: not a file: https://pypi.org/simple/cpdb-protein/ 2025-09-12T18:46:51,343 Given no hashes to check 1 links for project 'cpdb-protein': discarding no candidates 2025-09-12T18:46:51,345 Collecting cpdb-protein==0.0.2 2025-09-12T18:46:51,346 Created temporary directory: /tmp/pip-unpack-h2r2sgyd 2025-09-12T18:46:51,485 Downloading cpdb-protein-0.0.2.tar.gz (58 kB) 2025-09-12T18:46:51,529 Added cpdb-protein==0.0.2 from https://files.pythonhosted.org/packages/ed/58/a6f6d0924c7e4be968b8703eec99179403a13ce5e143660abef310a7717b/cpdb-protein-0.0.2.tar.gz to build tracker '/tmp/pip-build-tracker-l349_xcu' 2025-09-12T18:46:51,531 Running setup.py (path:/tmp/pip-wheel-dq6f1bka/cpdb-protein_6d6d85a27b0445d0976d54f208fa006a/setup.py) egg_info for package cpdb-protein 2025-09-12T18:46:51,531 Created temporary directory: /tmp/pip-pip-egg-info-esbcoj_z 2025-09-12T18:46:51,531 Preparing metadata (setup.py): started 2025-09-12T18:46:51,532 Running command python setup.py egg_info 2025-09-12T18:46:55,271 Compiling ./cpdb/parser.pyx because it changed. 2025-09-12T18:46:55,271 [1/1] Cythonizing ./cpdb/parser.pyx 2025-09-12T18:46:55,826 running egg_info 2025-09-12T18:46:55,913 creating /tmp/pip-pip-egg-info-esbcoj_z/cpdb_protein.egg-info 2025-09-12T18:46:55,913 writing /tmp/pip-pip-egg-info-esbcoj_z/cpdb_protein.egg-info/PKG-INFO 2025-09-12T18:46:55,915 writing dependency_links to /tmp/pip-pip-egg-info-esbcoj_z/cpdb_protein.egg-info/dependency_links.txt 2025-09-12T18:46:55,915 writing requirements to /tmp/pip-pip-egg-info-esbcoj_z/cpdb_protein.egg-info/requires.txt 2025-09-12T18:46:55,916 writing top-level names to /tmp/pip-pip-egg-info-esbcoj_z/cpdb_protein.egg-info/top_level.txt 2025-09-12T18:46:55,916 writing manifest file '/tmp/pip-pip-egg-info-esbcoj_z/cpdb_protein.egg-info/SOURCES.txt' 2025-09-12T18:46:56,176 reading manifest file '/tmp/pip-pip-egg-info-esbcoj_z/cpdb_protein.egg-info/SOURCES.txt' 2025-09-12T18:46:56,177 reading manifest template 'MANIFEST.in' 2025-09-12T18:46:56,178 adding license file 'LICENSE' 2025-09-12T18:46:56,181 writing manifest file '/tmp/pip-pip-egg-info-esbcoj_z/cpdb_protein.egg-info/SOURCES.txt' 2025-09-12T18:46:56,587 Preparing metadata (setup.py): finished with status 'done' 2025-09-12T18:46:56,591 Source in /tmp/pip-wheel-dq6f1bka/cpdb-protein_6d6d85a27b0445d0976d54f208fa006a has version 0.0.2, which satisfies requirement cpdb-protein==0.0.2 from https://files.pythonhosted.org/packages/ed/58/a6f6d0924c7e4be968b8703eec99179403a13ce5e143660abef310a7717b/cpdb-protein-0.0.2.tar.gz 2025-09-12T18:46:56,592 Removed cpdb-protein==0.0.2 from https://files.pythonhosted.org/packages/ed/58/a6f6d0924c7e4be968b8703eec99179403a13ce5e143660abef310a7717b/cpdb-protein-0.0.2.tar.gz from build tracker '/tmp/pip-build-tracker-l349_xcu' 2025-09-12T18:46:56,595 Created temporary directory: /tmp/pip-unpack-_6a6z8hf 2025-09-12T18:46:56,595 Created temporary directory: /tmp/pip-unpack-6oz76p2_ 2025-09-12T18:46:56,595 Building wheels for collected packages: cpdb-protein 2025-09-12T18:46:56,596 Created temporary directory: /tmp/pip-wheel-czuamz90 2025-09-12T18:46:56,597 DEPRECATION: Building 'cpdb-protein' 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 'cpdb-protein'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-12T18:46:56,598 Building wheel for cpdb-protein (setup.py): started 2025-09-12T18:46:56,598 Destination directory: /tmp/pip-wheel-czuamz90 2025-09-12T18:46:56,599 Running command python setup.py bdist_wheel 2025-09-12T18:46:58,788 running bdist_wheel 2025-09-12T18:46:59,279 running build 2025-09-12T18:46:59,280 running build_ext 2025-09-12T18:46:59,288 building 'parser' extension 2025-09-12T18:46:59,290 creating build/temp.linux-armv7l-cpython-313/cpdb 2025-09-12T18:46:59,291 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/local/lib/python3.13/dist-packages/numpy/_core/include -I/usr/include/python3.13 -c ./cpdb/parser.c -o build/temp.linux-armv7l-cpython-313/cpdb/parser.o 2025-09-12T18:47:11,050 creating build/lib.linux-armv7l-cpython-313 2025-09-12T18:47:11,050 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-313/cpdb/parser.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-313/parser.cpython-313-arm-linux-gnueabihf.so 2025-09-12T18:47:11,289 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-09-12T18:47:11,289 !! 2025-09-12T18:47:11,289 ******************************************************************************** 2025-09-12T18:47:11,289 Please avoid running ``setup.py`` directly. 2025-09-12T18:47:11,290 Instead, use pypa/build, pypa/installer or other 2025-09-12T18:47:11,290 standards-based tools. 2025-09-12T18:47:11,290 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-12T18:47:11,290 or your builds will no longer be supported. 2025-09-12T18:47:11,290 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-09-12T18:47:11,290 ******************************************************************************** 2025-09-12T18:47:11,291 !! 2025-09-12T18:47:11,291 self.initialize_options() 2025-09-12T18:47:11,387 installing to build/bdist.linux-armv7l/wheel 2025-09-12T18:47:11,387 running install 2025-09-12T18:47:11,413 running install_lib 2025-09-12T18:47:11,507 creating build/bdist.linux-armv7l/wheel 2025-09-12T18:47:11,508 copying build/lib.linux-armv7l-cpython-313/parser.cpython-313-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2025-09-12T18:47:11,510 running install_egg_info 2025-09-12T18:47:11,610 running egg_info 2025-09-12T18:47:11,704 writing cpdb_protein.egg-info/PKG-INFO 2025-09-12T18:47:11,705 writing dependency_links to cpdb_protein.egg-info/dependency_links.txt 2025-09-12T18:47:11,706 writing requirements to cpdb_protein.egg-info/requires.txt 2025-09-12T18:47:11,707 writing top-level names to cpdb_protein.egg-info/top_level.txt 2025-09-12T18:47:11,804 reading manifest file 'cpdb_protein.egg-info/SOURCES.txt' 2025-09-12T18:47:11,806 reading manifest template 'MANIFEST.in' 2025-09-12T18:47:11,807 adding license file 'LICENSE' 2025-09-12T18:47:11,810 writing manifest file 'cpdb_protein.egg-info/SOURCES.txt' 2025-09-12T18:47:11,811 Copying cpdb_protein.egg-info to build/bdist.linux-armv7l/wheel/./cpdb_protein-0.0.2-py3.13.egg-info 2025-09-12T18:47:11,813 running install_scripts 2025-09-12T18:47:11,884 creating build/bdist.linux-armv7l/wheel/cpdb_protein-0.0.2.dist-info/WHEEL 2025-09-12T18:47:11,885 creating '/tmp/pip-wheel-czuamz90/cpdb_protein-0.0.2-cp313-cp313-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-09-12T18:47:11,985 adding 'parser.cpython-313-arm-linux-gnueabihf.so' 2025-09-12T18:47:11,990 adding 'cpdb_protein-0.0.2.dist-info/licenses/LICENSE' 2025-09-12T18:47:11,991 adding 'cpdb_protein-0.0.2.dist-info/METADATA' 2025-09-12T18:47:11,991 adding 'cpdb_protein-0.0.2.dist-info/WHEEL' 2025-09-12T18:47:11,992 adding 'cpdb_protein-0.0.2.dist-info/top_level.txt' 2025-09-12T18:47:11,993 adding 'cpdb_protein-0.0.2.dist-info/RECORD' 2025-09-12T18:47:11,993 removing build/bdist.linux-armv7l/wheel 2025-09-12T18:47:12,207 Building wheel for cpdb-protein (setup.py): finished with status 'done' 2025-09-12T18:47:12,210 Created wheel for cpdb-protein: filename=cpdb_protein-0.0.2-cp313-cp313-linux_armv7l.whl size=178411 sha256=08a1c29831f32dd7ed8090a15a4abf7ce65d1d459bdc34cf1fbb8c7b3fb85f61 2025-09-12T18:47:12,211 Stored in directory: /tmp/pip-ephem-wheel-cache-qfz28cbm/wheels/f0/fe/c4/e6648518e972dbfe63c37da3b161cd6e593e6a1ce0da2ee333 2025-09-12T18:47:12,220 Successfully built cpdb-protein 2025-09-12T18:47:12,222 Removed build tracker: '/tmp/pip-build-tracker-l349_xcu'