2025-10-15T09:49:00,598 Created temporary directory: /tmp/pip-build-tracker-kycxlx0k 2025-10-15T09:49:00,598 Initialized build tracking at /tmp/pip-build-tracker-kycxlx0k 2025-10-15T09:49:00,598 Created build tracker: /tmp/pip-build-tracker-kycxlx0k 2025-10-15T09:49:00,599 Entered build tracker: /tmp/pip-build-tracker-kycxlx0k 2025-10-15T09:49:00,599 Created temporary directory: /tmp/pip-wheel-ky1oo_1q 2025-10-15T09:49:00,602 Created temporary directory: /tmp/pip-ephem-wheel-cache-j03tum69 2025-10-15T09:49:00,665 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-10-15T09:49:00,667 2 location(s) to search for versions of gff3tool: 2025-10-15T09:49:00,667 * https://pypi.org/simple/gff3tool/ 2025-10-15T09:49:00,667 * https://www.piwheels.org/simple/gff3tool/ 2025-10-15T09:49:00,668 Fetching project page and analyzing links: https://pypi.org/simple/gff3tool/ 2025-10-15T09:49:00,668 Getting page https://pypi.org/simple/gff3tool/ 2025-10-15T09:49:00,669 Found index url https://pypi.org/simple/ 2025-10-15T09:49:00,816 Fetched page https://pypi.org/simple/gff3tool/ as application/vnd.pypi.simple.v1+json 2025-10-15T09:49:00,820 Found link https://files.pythonhosted.org/packages/71/33/dac2be6f38dd40d4f914814e7afe2cc5391f1bfecc77439612284de537a1/gff3tool-1.1.0.tar.gz (from https://pypi.org/simple/gff3tool/), version: 1.1.0 2025-10-15T09:49:00,821 Found link https://files.pythonhosted.org/packages/a1/f1/6630128adac220623c28a5f5ed4e6cfa070589143a0b2151237c20923149/gff3tool-1.3.0.tar.gz (from https://pypi.org/simple/gff3tool/), version: 1.3.0 2025-10-15T09:49:00,821 Found link https://files.pythonhosted.org/packages/71/cb/9b9d73fd7171571b9ad063fa3a6aac684aeebc7e958a37e2423c690d5110/gff3tool-1.4.1.tar.gz (from https://pypi.org/simple/gff3tool/), version: 1.4.1 2025-10-15T09:49:00,822 Found link https://files.pythonhosted.org/packages/23/bb/0b7952dfc7fb8992e6d7349eb55cbbe51e6c0750d57e33c01de5be39da46/gff3tool-1.4.2.tar.gz (from https://pypi.org/simple/gff3tool/), version: 1.4.2 2025-10-15T09:49:00,822 Found link https://files.pythonhosted.org/packages/7c/79/b59b3e47735edfe2ac2a9334c8e2836d63c0899b51f9badc416ae07e8353/gff3tool-1.4.3.tar.gz (from https://pypi.org/simple/gff3tool/), version: 1.4.3 2025-10-15T09:49:00,823 Found link https://files.pythonhosted.org/packages/cf/33/8cd85764a601bf3a5e0116f8b457c308294ec9c25139aacade6e21860335/gff3tool-1.4.4.tar.gz (from https://pypi.org/simple/gff3tool/), version: 1.4.4 2025-10-15T09:49:00,823 Skipping link: No binaries permitted for gff3tool: https://files.pythonhosted.org/packages/2a/4c/a16d0aae5fa870fc7630eb0536042fd3e0494467efd9f27cea6090cdbbe0/gff3tool-1.4.5-cp27-cp27m-win_amd64.whl (from https://pypi.org/simple/gff3tool/) 2025-10-15T09:49:00,824 Found link https://files.pythonhosted.org/packages/f8/78/330f714b6e771d69079128a44f61830c9ce22969eaa3b176dafb94c48809/gff3tool-1.4.5.tar.gz (from https://pypi.org/simple/gff3tool/), version: 1.4.5 2025-10-15T09:49:00,824 Found link https://files.pythonhosted.org/packages/8a/82/0f528dc498d7fdfbd6b8a968ed1cfee43ffa55461e77830a22f606aea3bb/gff3tool-2.0.0.tar.gz (from https://pypi.org/simple/gff3tool/), version: 2.0.0 2025-10-15T09:49:00,825 Found link https://files.pythonhosted.org/packages/aa/b3/cecb768a048bf2e661f0e77bf3208ed8ef203acbd93107b1f00d7b57da1e/gff3tool-2.0.1.tar.gz (from https://pypi.org/simple/gff3tool/), version: 2.0.1 2025-10-15T09:49:00,825 Found link https://files.pythonhosted.org/packages/21/2e/7e77d34adec82b4d896c8959c7993534810f8bc43cc374e984e5635bbf94/gff3tool-2.0.3.tar.gz (from https://pypi.org/simple/gff3tool/), version: 2.0.3 2025-10-15T09:49:00,826 Found link https://files.pythonhosted.org/packages/7f/12/d177f42f6e3a73dae82fd5cc89e7404de121ab381e5454ca8da11110d88a/gff3tool-2.1.0.tar.gz (from https://pypi.org/simple/gff3tool/), version: 2.1.0 2025-10-15T09:49:00,826 Fetching project page and analyzing links: https://www.piwheels.org/simple/gff3tool/ 2025-10-15T09:49:00,827 Getting page https://www.piwheels.org/simple/gff3tool/ 2025-10-15T09:49:00,829 Found index url https://www.piwheels.org/simple/ 2025-10-15T09:49:00,924 Fetched page https://www.piwheels.org/simple/gff3tool/ as text/html 2025-10-15T09:49:00,931 Skipping link: No binaries permitted for gff3tool: https://archive1.piwheels.org/simple/gff3tool/gff3tool-2.1.0-cp311-cp311-linux_armv6l.whl#sha256=866502237ec1e32fd2caee5c04df61c4464dc7db901009e864c3f53ff3f43d94 (from https://www.piwheels.org/simple/gff3tool/) 2025-10-15T09:49:00,931 Skipping link: No binaries permitted for gff3tool: https://archive1.piwheels.org/simple/gff3tool/gff3tool-2.1.0-cp311-cp311-linux_armv7l.whl#sha256=866502237ec1e32fd2caee5c04df61c4464dc7db901009e864c3f53ff3f43d94 (from https://www.piwheels.org/simple/gff3tool/) 2025-10-15T09:49:00,932 Skipping link: No binaries permitted for gff3tool: https://archive1.piwheels.org/simple/gff3tool/gff3tool-2.1.0-cp35-cp35m-linux_armv6l.whl#sha256=5eef1c37d908cd2d30f368726348cf85a26dc4d95abc8131735de5c720d7975b (from https://www.piwheels.org/simple/gff3tool/) 2025-10-15T09:49:00,932 Skipping link: No binaries permitted for gff3tool: https://archive1.piwheels.org/simple/gff3tool/gff3tool-2.1.0-cp35-cp35m-linux_armv7l.whl#sha256=5eef1c37d908cd2d30f368726348cf85a26dc4d95abc8131735de5c720d7975b (from https://www.piwheels.org/simple/gff3tool/) 2025-10-15T09:49:00,932 Skipping link: No binaries permitted for gff3tool: https://archive1.piwheels.org/simple/gff3tool/gff3tool-2.1.0-cp37-cp37m-linux_armv6l.whl#sha256=cfe6edebe5cd63bcd5cd38e34377d8c34eb8fdc675d148da65e75d4399db5ff6 (from https://www.piwheels.org/simple/gff3tool/) 2025-10-15T09:49:00,932 Skipping link: No binaries permitted for gff3tool: 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https://archive1.piwheels.org/simple/gff3tool/gff3tool-2.0.3-cp39-cp39-linux_armv6l.whl#sha256=66d9164d8245e216f080754a89df8cda4192f034e99a32532198ccf3c38f6faa (from https://www.piwheels.org/simple/gff3tool/) 2025-10-15T09:49:00,933 Skipping link: No binaries permitted for gff3tool: https://archive1.piwheels.org/simple/gff3tool/gff3tool-2.0.3-cp39-cp39-linux_armv7l.whl#sha256=66d9164d8245e216f080754a89df8cda4192f034e99a32532198ccf3c38f6faa (from https://www.piwheels.org/simple/gff3tool/) 2025-10-15T09:49:00,933 Skipping link: No binaries permitted for gff3tool: https://archive1.piwheels.org/simple/gff3tool/gff3tool-2.0.1-cp35-cp35m-linux_armv6l.whl#sha256=baa47b3147a931daf4958a447f96979e4448707996cc9d60ac45ad3ebb8e9c1f (from https://www.piwheels.org/simple/gff3tool/) 2025-10-15T09:49:00,933 Skipping link: No binaries permitted for gff3tool: 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(from https://www.piwheels.org/simple/gff3tool/) 2025-10-15T09:49:00,936 Skipping link: No binaries permitted for gff3tool: https://archive1.piwheels.org/simple/gff3tool/gff3tool-1.1.0-py3-none-any.whl#sha256=f5eefabf7e1b27382cef033e939fd956121ebf02ae4e7085b83ade5f98c69d90 (from https://www.piwheels.org/simple/gff3tool/) 2025-10-15T09:49:00,936 Skipping link: not a file: https://www.piwheels.org/simple/gff3tool/ 2025-10-15T09:49:00,936 Skipping link: not a file: https://pypi.org/simple/gff3tool/ 2025-10-15T09:49:00,963 Given no hashes to check 1 links for project 'gff3tool': discarding no candidates 2025-10-15T09:49:00,965 Collecting gff3tool==2.0.1 2025-10-15T09:49:00,966 Created temporary directory: /tmp/pip-unpack-4l5jzuvx 2025-10-15T09:49:01,104 Downloading gff3tool-2.0.1.tar.gz (79 kB) 2025-10-15T09:49:01,173 Added gff3tool==2.0.1 from https://files.pythonhosted.org/packages/aa/b3/cecb768a048bf2e661f0e77bf3208ed8ef203acbd93107b1f00d7b57da1e/gff3tool-2.0.1.tar.gz to build tracker '/tmp/pip-build-tracker-kycxlx0k' 2025-10-15T09:49:01,174 Running setup.py (path:/tmp/pip-wheel-ky1oo_1q/gff3tool_627a7c9166be4b5dab2e746cac8a507f/setup.py) egg_info for package gff3tool 2025-10-15T09:49:01,174 Created temporary directory: /tmp/pip-pip-egg-info-n9l1y2sr 2025-10-15T09:49:01,174 Preparing metadata (setup.py): started 2025-10-15T09:49:01,175 Running command python setup.py egg_info 2025-10-15T09:49:02,282 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'dist-dir' in 'sdist' (setup.cfg), please use the underscore name 'dist_dir' instead. 2025-10-15T09:49:02,282 !! 2025-10-15T09:49:02,282 ******************************************************************************** 2025-10-15T09:49:02,282 Usage of dash-separated 'dist-dir' will not be supported in future 2025-10-15T09:49:02,282 versions. Please use the underscore name 'dist_dir' instead. 2025-10-15T09:49:02,283 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-10-15T09:49:02,283 or your builds will no longer be supported. 2025-10-15T09:49:02,283 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-10-15T09:49:02,283 ******************************************************************************** 2025-10-15T09:49:02,283 !! 2025-10-15T09:49:02,283 opt = self._enforce_underscore(opt, section) 2025-10-15T09:49:02,706 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'dist-dir' in 'sdist' (setup.cfg), please use the underscore name 'dist_dir' instead. 2025-10-15T09:49:02,706 !! 2025-10-15T09:49:02,706 ******************************************************************************** 2025-10-15T09:49:02,706 Usage of dash-separated 'dist-dir' will not be supported in future 2025-10-15T09:49:02,706 versions. Please use the underscore name 'dist_dir' instead. 2025-10-15T09:49:02,706 (Affected: gff3tool). 2025-10-15T09:49:02,706 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-10-15T09:49:02,706 or your builds will no longer be supported. 2025-10-15T09:49:02,707 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-10-15T09:49:02,707 ******************************************************************************** 2025-10-15T09:49:02,707 !! 2025-10-15T09:49:02,707 opt = self._enforce_underscore(opt, section) 2025-10-15T09:49:02,707 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-10-15T09:49:02,707 !! 2025-10-15T09:49:02,707 ******************************************************************************** 2025-10-15T09:49:02,708 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-10-15T09:49:02,708 License :: Public Domain 2025-10-15T09:49:02,708 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-10-15T09:49:02,708 ******************************************************************************** 2025-10-15T09:49:02,708 !! 2025-10-15T09:49:02,708 self._finalize_license_expression() 2025-10-15T09:49:02,781 running egg_info 2025-10-15T09:49:02,856 creating /tmp/pip-pip-egg-info-n9l1y2sr/gff3tool.egg-info 2025-10-15T09:49:02,856 writing /tmp/pip-pip-egg-info-n9l1y2sr/gff3tool.egg-info/PKG-INFO 2025-10-15T09:49:02,857 writing dependency_links to /tmp/pip-pip-egg-info-n9l1y2sr/gff3tool.egg-info/dependency_links.txt 2025-10-15T09:49:02,858 writing entry points to /tmp/pip-pip-egg-info-n9l1y2sr/gff3tool.egg-info/entry_points.txt 2025-10-15T09:49:02,859 writing top-level names to /tmp/pip-pip-egg-info-n9l1y2sr/gff3tool.egg-info/top_level.txt 2025-10-15T09:49:02,859 writing manifest file '/tmp/pip-pip-egg-info-n9l1y2sr/gff3tool.egg-info/SOURCES.txt' 2025-10-15T09:49:03,013 reading manifest file '/tmp/pip-pip-egg-info-n9l1y2sr/gff3tool.egg-info/SOURCES.txt' 2025-10-15T09:49:03,014 reading manifest template 'MANIFEST.in' 2025-10-15T09:49:03,020 writing manifest file '/tmp/pip-pip-egg-info-n9l1y2sr/gff3tool.egg-info/SOURCES.txt' 2025-10-15T09:49:03,132 Preparing metadata (setup.py): finished with status 'done' 2025-10-15T09:49:03,137 Source in /tmp/pip-wheel-ky1oo_1q/gff3tool_627a7c9166be4b5dab2e746cac8a507f has version 2.0.1, which satisfies requirement gff3tool==2.0.1 from https://files.pythonhosted.org/packages/aa/b3/cecb768a048bf2e661f0e77bf3208ed8ef203acbd93107b1f00d7b57da1e/gff3tool-2.0.1.tar.gz 2025-10-15T09:49:03,137 Removed gff3tool==2.0.1 from https://files.pythonhosted.org/packages/aa/b3/cecb768a048bf2e661f0e77bf3208ed8ef203acbd93107b1f00d7b57da1e/gff3tool-2.0.1.tar.gz from build tracker '/tmp/pip-build-tracker-kycxlx0k' 2025-10-15T09:49:03,141 Created temporary directory: /tmp/pip-unpack-c9q7vbqo 2025-10-15T09:49:03,142 Created temporary directory: /tmp/pip-unpack-eahgq49a 2025-10-15T09:49:03,142 Building wheels for collected packages: gff3tool 2025-10-15T09:49:03,143 Created temporary directory: /tmp/pip-wheel-lvbugztg 2025-10-15T09:49:03,144 DEPRECATION: Building 'gff3tool' 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 'gff3tool'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-10-15T09:49:03,145 Building wheel for gff3tool (setup.py): started 2025-10-15T09:49:03,146 Destination directory: /tmp/pip-wheel-lvbugztg 2025-10-15T09:49:03,146 Running command python setup.py bdist_wheel 2025-10-15T09:49:04,400 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'dist-dir' in 'sdist' (setup.cfg), please use the underscore name 'dist_dir' instead. 2025-10-15T09:49:04,400 !! 2025-10-15T09:49:04,400 ******************************************************************************** 2025-10-15T09:49:04,400 Usage of dash-separated 'dist-dir' will not be supported in future 2025-10-15T09:49:04,401 versions. Please use the underscore name 'dist_dir' instead. 2025-10-15T09:49:04,401 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-10-15T09:49:04,401 or your builds will no longer be supported. 2025-10-15T09:49:04,401 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-10-15T09:49:04,401 ******************************************************************************** 2025-10-15T09:49:04,401 !! 2025-10-15T09:49:04,401 opt = self._enforce_underscore(opt, section) 2025-10-15T09:49:04,827 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'dist-dir' in 'sdist' (setup.cfg), please use the underscore name 'dist_dir' instead. 2025-10-15T09:49:04,827 !! 2025-10-15T09:49:04,828 ******************************************************************************** 2025-10-15T09:49:04,828 Usage of dash-separated 'dist-dir' will not be supported in future 2025-10-15T09:49:04,828 versions. Please use the underscore name 'dist_dir' instead. 2025-10-15T09:49:04,828 (Affected: gff3tool). 2025-10-15T09:49:04,828 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-10-15T09:49:04,828 or your builds will no longer be supported. 2025-10-15T09:49:04,828 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-10-15T09:49:04,828 ******************************************************************************** 2025-10-15T09:49:04,829 !! 2025-10-15T09:49:04,829 opt = self._enforce_underscore(opt, section) 2025-10-15T09:49:04,829 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-10-15T09:49:04,829 !! 2025-10-15T09:49:04,829 ******************************************************************************** 2025-10-15T09:49:04,829 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-10-15T09:49:04,829 License :: Public Domain 2025-10-15T09:49:04,830 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-10-15T09:49:04,830 ******************************************************************************** 2025-10-15T09:49:04,830 !! 2025-10-15T09:49:04,830 self._finalize_license_expression() 2025-10-15T09:49:04,830 running bdist_wheel 2025-10-15T09:49:05,122 running build 2025-10-15T09:49:20,221 /tmp/pip-wheel-ky1oo_1q/gff3tool_627a7c9166be4b5dab2e746cac8a507f/setup.py:62: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior. 2025-10-15T09:49:20,221 tar.extractall(blast_path) 2025-10-15T09:49:29,029 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-10-15T09:49:29,029 !! 2025-10-15T09:49:29,030 ******************************************************************************** 2025-10-15T09:49:29,030 Please avoid running ``setup.py`` directly. 2025-10-15T09:49:29,030 Instead, use pypa/build, pypa/installer or other 2025-10-15T09:49:29,030 standards-based tools. 2025-10-15T09:49:29,030 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-10-15T09:49:29,030 or your builds will no longer be supported. 2025-10-15T09:49:29,030 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-10-15T09:49:29,030 ******************************************************************************** 2025-10-15T09:49:29,031 !! 2025-10-15T09:49:29,031 self.initialize_options() 2025-10-15T09:49:29,104 installing to build/bdist.linux-armv7l/wheel 2025-10-15T09:49:29,104 running install 2025-10-15T09:49:29,126 running install_lib 2025-10-15T09:49:29,436 running build_py 2025-10-15T09:49:29,514 creating build/lib/gff3tool 2025-10-15T09:49:29,514 copying gff3tool/__init__.py -> build/lib/gff3tool 2025-10-15T09:49:29,515 creating build/lib/gff3tool/lib 2025-10-15T09:49:29,515 copying gff3tool/lib/__init__.py -> build/lib/gff3tool/lib 2025-10-15T09:49:29,516 copying gff3tool/lib/utils.py -> build/lib/gff3tool/lib 2025-10-15T09:49:29,516 copying gff3tool/lib/replace_OGS.py -> build/lib/gff3tool/lib 2025-10-15T09:49:29,517 copying gff3tool/lib/id_processor.py -> build/lib/gff3tool/lib 2025-10-15T09:49:29,518 copying gff3tool/lib/gff3_ID_generator.py -> build/lib/gff3tool/lib 2025-10-15T09:49:29,518 creating build/lib/gff3tool/bin 2025-10-15T09:49:29,519 copying gff3tool/bin/__init__.py -> build/lib/gff3tool/bin 2025-10-15T09:49:29,519 copying gff3tool/bin/version.py -> build/lib/gff3tool/bin 2025-10-15T09:49:29,520 copying gff3tool/bin/gff3_to_fasta.py -> build/lib/gff3tool/bin 2025-10-15T09:49:29,520 copying gff3tool/bin/gff3_sort.py -> build/lib/gff3tool/bin 2025-10-15T09:49:29,521 copying gff3tool/bin/gff3_QC.py -> build/lib/gff3tool/bin 2025-10-15T09:49:29,522 copying gff3tool/bin/gff3_merge.py -> build/lib/gff3tool/bin 2025-10-15T09:49:29,522 copying gff3tool/bin/gff3_fix.py -> build/lib/gff3tool/bin 2025-10-15T09:49:29,523 creating build/lib/gff3tool/lib/single_feature 2025-10-15T09:49:29,523 copying gff3tool/lib/single_feature/__init__.py -> build/lib/gff3tool/lib/single_feature 2025-10-15T09:49:29,524 copying gff3tool/lib/single_feature/single_feature.py -> build/lib/gff3tool/lib/single_feature 2025-10-15T09:49:29,524 creating build/lib/gff3tool/lib/intra_model 2025-10-15T09:49:29,525 copying gff3tool/lib/intra_model/__init__.py -> build/lib/gff3tool/lib/intra_model 2025-10-15T09:49:29,525 copying gff3tool/lib/intra_model/intra_model.py -> build/lib/gff3tool/lib/intra_model 2025-10-15T09:49:29,526 creating build/lib/gff3tool/lib/inter_model 2025-10-15T09:49:29,526 copying gff3tool/lib/inter_model/__init__.py -> build/lib/gff3tool/lib/inter_model 2025-10-15T09:49:29,527 copying gff3tool/lib/inter_model/inter_model.py -> build/lib/gff3tool/lib/inter_model 2025-10-15T09:49:29,528 creating build/lib/gff3tool/lib/gff3_merge 2025-10-15T09:49:29,528 copying gff3tool/lib/gff3_merge/__init__.py -> build/lib/gff3tool/lib/gff3_merge 2025-10-15T09:49:29,528 copying gff3tool/lib/gff3_merge/revision.py -> build/lib/gff3tool/lib/gff3_merge 2025-10-15T09:49:29,529 copying gff3tool/lib/gff3_merge/merge.py -> build/lib/gff3tool/lib/gff3_merge 2025-10-15T09:49:29,529 copying gff3tool/lib/gff3_merge/auto_replace_tag.py -> build/lib/gff3tool/lib/gff3_merge 2025-10-15T09:49:29,530 creating build/lib/gff3tool/lib/gff3_fix 2025-10-15T09:49:29,530 copying gff3tool/lib/gff3_fix/__init__.py -> build/lib/gff3tool/lib/gff3_fix 2025-10-15T09:49:29,531 copying gff3tool/lib/gff3_fix/fix.py -> build/lib/gff3tool/lib/gff3_fix 2025-10-15T09:49:29,532 creating build/lib/gff3tool/lib/gff3 2025-10-15T09:49:29,532 copying gff3tool/lib/gff3/__init__.py -> build/lib/gff3tool/lib/gff3 2025-10-15T09:49:29,533 copying gff3tool/lib/gff3/gff3.py -> build/lib/gff3tool/lib/gff3 2025-10-15T09:49:29,534 creating build/lib/gff3tool/lib/function4gff 2025-10-15T09:49:29,534 copying gff3tool/lib/function4gff/__init__.py -> build/lib/gff3tool/lib/function4gff 2025-10-15T09:49:29,534 copying gff3tool/lib/function4gff/function4gff.py -> build/lib/gff3tool/lib/function4gff 2025-10-15T09:49:29,535 creating build/lib/gff3tool/lib/ERROR 2025-10-15T09:49:29,535 copying gff3tool/lib/ERROR/__init__.py -> build/lib/gff3tool/lib/ERROR 2025-10-15T09:49:29,536 copying gff3tool/lib/ERROR/ERROR.py -> build/lib/gff3tool/lib/ERROR 2025-10-15T09:49:29,536 running egg_info 2025-10-15T09:49:29,610 writing gff3tool.egg-info/PKG-INFO 2025-10-15T09:49:29,611 writing dependency_links to gff3tool.egg-info/dependency_links.txt 2025-10-15T09:49:29,612 writing entry points to gff3tool.egg-info/entry_points.txt 2025-10-15T09:49:29,612 writing top-level names to gff3tool.egg-info/top_level.txt 2025-10-15T09:49:29,690 reading manifest file 'gff3tool.egg-info/SOURCES.txt' 2025-10-15T09:49:29,693 reading manifest template 'MANIFEST.in' 2025-10-15T09:49:29,700 writing manifest file 'gff3tool.egg-info/SOURCES.txt' 2025-10-15T09:49:29,702 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'gff3tool.lib.auto_assignment' is absent from the `packages` configuration. 2025-10-15T09:49:29,702 !! 2025-10-15T09:49:29,702 ******************************************************************************** 2025-10-15T09:49:29,702 ############################ 2025-10-15T09:49:29,702 # Package would be ignored # 2025-10-15T09:49:29,702 ############################ 2025-10-15T09:49:29,702 Python recognizes 'gff3tool.lib.auto_assignment' as an importable package[^1], 2025-10-15T09:49:29,703 but it is absent from setuptools' `packages` configuration. 2025-10-15T09:49:29,703 This leads to an ambiguous overall configuration. If you want to distribute this 2025-10-15T09:49:29,703 package, please make sure that 'gff3tool.lib.auto_assignment' is explicitly added 2025-10-15T09:49:29,703 to the `packages` configuration field. 2025-10-15T09:49:29,703 Alternatively, you can also rely on setuptools' discovery methods 2025-10-15T09:49:29,703 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-10-15T09:49:29,703 instead of `find_packages(...)`/`find:`). 2025-10-15T09:49:29,703 You can read more about "package discovery" on setuptools documentation page: 2025-10-15T09:49:29,704 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-10-15T09:49:29,704 If you don't want 'gff3tool.lib.auto_assignment' to be distributed and are 2025-10-15T09:49:29,704 already explicitly excluding 'gff3tool.lib.auto_assignment' via 2025-10-15T09:49:29,704 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-10-15T09:49:29,704 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-10-15T09:49:29,704 combination with a more fine grained `package-data` configuration. 2025-10-15T09:49:29,704 You can read more about "package data files" on setuptools documentation page: 2025-10-15T09:49:29,705 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-10-15T09:49:29,705 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-10-15T09:49:29,705 even if it does not contain any `.py` files. 2025-10-15T09:49:29,705 On the other hand, currently there is no concept of package data 2025-10-15T09:49:29,705 directory, all directories are treated like packages. 2025-10-15T09:49:29,705 ******************************************************************************** 2025-10-15T09:49:29,705 !! 2025-10-15T09:49:29,705 check.warn(importable) 2025-10-15T09:49:29,706 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'gff3tool.lib.check_gene_parent' is absent from the `packages` configuration. 2025-10-15T09:49:29,706 !! 2025-10-15T09:49:29,706 ******************************************************************************** 2025-10-15T09:49:29,706 ############################ 2025-10-15T09:49:29,706 # Package would be ignored # 2025-10-15T09:49:29,706 ############################ 2025-10-15T09:49:29,706 Python recognizes 'gff3tool.lib.check_gene_parent' as an importable package[^1], 2025-10-15T09:49:29,706 but it is absent from setuptools' `packages` configuration. 2025-10-15T09:49:29,706 This leads to an ambiguous overall configuration. If you want to distribute this 2025-10-15T09:49:29,707 package, please make sure that 'gff3tool.lib.check_gene_parent' is explicitly added 2025-10-15T09:49:29,707 to the `packages` configuration field. 2025-10-15T09:49:29,707 Alternatively, you can also rely on setuptools' discovery methods 2025-10-15T09:49:29,707 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-10-15T09:49:29,707 instead of `find_packages(...)`/`find:`). 2025-10-15T09:49:29,707 You can read more about "package discovery" on setuptools documentation page: 2025-10-15T09:49:29,707 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-10-15T09:49:29,708 If you don't want 'gff3tool.lib.check_gene_parent' to be distributed and are 2025-10-15T09:49:29,708 already explicitly excluding 'gff3tool.lib.check_gene_parent' via 2025-10-15T09:49:29,708 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-10-15T09:49:29,708 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-10-15T09:49:29,708 combination with a more fine grained `package-data` configuration. 2025-10-15T09:49:29,708 You can read more about "package data files" on setuptools documentation page: 2025-10-15T09:49:29,708 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-10-15T09:49:29,708 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-10-15T09:49:29,709 even if it does not contain any `.py` files. 2025-10-15T09:49:29,709 On the other hand, currently there is no concept of package data 2025-10-15T09:49:29,709 directory, all directories are treated like packages. 2025-10-15T09:49:29,709 ******************************************************************************** 2025-10-15T09:49:29,709 !! 2025-10-15T09:49:29,709 check.warn(importable) 2025-10-15T09:49:29,709 copying gff3tool/lib.md -> build/lib/gff3tool 2025-10-15T09:49:29,709 creating build/lib/gff3tool/lib/auto_assignment 2025-10-15T09:49:29,709 copying gff3tool/lib/auto_assignment/create_annotation_summaries_nov21-7.pl -> build/lib/gff3tool/lib/auto_assignment 2025-10-15T09:49:29,710 copying gff3tool/lib/auto_assignment/find_match.pl -> build/lib/gff3tool/lib/auto_assignment 2025-10-15T09:49:29,710 copying gff3tool/lib/auto_assignment/gen_spreadsheet.pl -> build/lib/gff3tool/lib/auto_assignment 2025-10-15T09:49:29,711 creating build/lib/gff3tool/lib/check_gene_parent 2025-10-15T09:49:29,711 copying gff3tool/lib/check_gene_parent/find_wrongly_split_gene_parent.pl -> build/lib/gff3tool/lib/check_gene_parent 2025-10-15T09:49:29,712 creating build/lib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:29,712 copying gff3tool/lib/ncbi-blast+/bin/blast_formatter -> build/lib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:29,831 copying gff3tool/lib/ncbi-blast+/bin/blastdb_aliastool -> build/lib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:29,907 copying gff3tool/lib/ncbi-blast+/bin/blastdbcheck -> build/lib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:29,991 copying gff3tool/lib/ncbi-blast+/bin/blastdbcmd -> build/lib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:30,098 copying gff3tool/lib/ncbi-blast+/bin/blastn -> build/lib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:30,216 copying gff3tool/lib/ncbi-blast+/bin/blastp -> build/lib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:30,334 copying gff3tool/lib/ncbi-blast+/bin/blastx -> build/lib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:30,453 copying gff3tool/lib/ncbi-blast+/bin/convert2blastmask -> build/lib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:30,529 copying gff3tool/lib/ncbi-blast+/bin/deltablast -> build/lib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:30,648 copying gff3tool/lib/ncbi-blast+/bin/dustmasker -> build/lib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:30,725 copying gff3tool/lib/ncbi-blast+/bin/legacy_blast.pl -> build/lib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:30,726 copying gff3tool/lib/ncbi-blast+/bin/makeblastdb -> build/lib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:30,809 copying gff3tool/lib/ncbi-blast+/bin/makembindex -> build/lib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:30,889 copying gff3tool/lib/ncbi-blast+/bin/makeprofiledb -> build/lib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:30,968 copying gff3tool/lib/ncbi-blast+/bin/psiblast -> build/lib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:31,086 copying gff3tool/lib/ncbi-blast+/bin/rpsblast -> build/lib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:31,203 copying gff3tool/lib/ncbi-blast+/bin/rpstblastn -> build/lib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:31,321 copying gff3tool/lib/ncbi-blast+/bin/segmasker -> build/lib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:31,399 copying gff3tool/lib/ncbi-blast+/bin/tblastn -> build/lib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:31,517 copying gff3tool/lib/ncbi-blast+/bin/tblastx -> build/lib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:31,633 copying gff3tool/lib/ncbi-blast+/bin/update_blastdb.pl -> build/lib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:31,633 copying gff3tool/lib/ncbi-blast+/bin/windowmasker -> build/lib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:31,728 creating build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib 2025-10-15T09:49:31,728 creating build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool 2025-10-15T09:49:31,728 copying build/lib/gff3tool/lib.md -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool 2025-10-15T09:49:31,729 creating build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/bin 2025-10-15T09:49:31,729 copying build/lib/gff3tool/bin/gff3_fix.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/bin 2025-10-15T09:49:31,730 copying build/lib/gff3tool/bin/gff3_merge.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/bin 2025-10-15T09:49:31,730 copying build/lib/gff3tool/bin/gff3_QC.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/bin 2025-10-15T09:49:31,730 copying build/lib/gff3tool/bin/gff3_sort.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/bin 2025-10-15T09:49:31,731 copying build/lib/gff3tool/bin/gff3_to_fasta.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/bin 2025-10-15T09:49:31,731 copying build/lib/gff3tool/bin/version.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/bin 2025-10-15T09:49:31,732 copying build/lib/gff3tool/bin/__init__.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/bin 2025-10-15T09:49:31,732 creating build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib 2025-10-15T09:49:31,733 creating build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+ 2025-10-15T09:49:31,733 creating build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:31,733 copying build/lib/gff3tool/lib/ncbi-blast+/bin/windowmasker -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:31,825 copying build/lib/gff3tool/lib/ncbi-blast+/bin/update_blastdb.pl -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:31,825 copying build/lib/gff3tool/lib/ncbi-blast+/bin/tblastx -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:31,941 copying build/lib/gff3tool/lib/ncbi-blast+/bin/tblastn -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:32,058 copying build/lib/gff3tool/lib/ncbi-blast+/bin/segmasker -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:32,136 copying build/lib/gff3tool/lib/ncbi-blast+/bin/rpstblastn -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:32,252 copying build/lib/gff3tool/lib/ncbi-blast+/bin/rpsblast -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:32,370 copying build/lib/gff3tool/lib/ncbi-blast+/bin/psiblast -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:32,485 copying build/lib/gff3tool/lib/ncbi-blast+/bin/makeprofiledb -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:32,564 copying build/lib/gff3tool/lib/ncbi-blast+/bin/makembindex -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:32,642 copying build/lib/gff3tool/lib/ncbi-blast+/bin/makeblastdb -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:32,726 copying build/lib/gff3tool/lib/ncbi-blast+/bin/legacy_blast.pl -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:32,727 copying build/lib/gff3tool/lib/ncbi-blast+/bin/dustmasker -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:32,803 copying build/lib/gff3tool/lib/ncbi-blast+/bin/deltablast -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:32,921 copying build/lib/gff3tool/lib/ncbi-blast+/bin/convert2blastmask -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:32,998 copying build/lib/gff3tool/lib/ncbi-blast+/bin/blastx -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:33,115 copying build/lib/gff3tool/lib/ncbi-blast+/bin/blastp -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:33,232 copying build/lib/gff3tool/lib/ncbi-blast+/bin/blastn -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:33,350 copying build/lib/gff3tool/lib/ncbi-blast+/bin/blastdbcmd -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:33,455 copying build/lib/gff3tool/lib/ncbi-blast+/bin/blastdbcheck -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:33,538 copying build/lib/gff3tool/lib/ncbi-blast+/bin/blastdb_aliastool -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:33,613 copying build/lib/gff3tool/lib/ncbi-blast+/bin/blast_formatter -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin 2025-10-15T09:49:33,731 creating build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/check_gene_parent 2025-10-15T09:49:33,731 copying build/lib/gff3tool/lib/check_gene_parent/find_wrongly_split_gene_parent.pl -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/check_gene_parent 2025-10-15T09:49:33,731 creating build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/auto_assignment 2025-10-15T09:49:33,732 copying build/lib/gff3tool/lib/auto_assignment/gen_spreadsheet.pl -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/auto_assignment 2025-10-15T09:49:33,732 copying build/lib/gff3tool/lib/auto_assignment/find_match.pl -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/auto_assignment 2025-10-15T09:49:33,733 copying build/lib/gff3tool/lib/auto_assignment/create_annotation_summaries_nov21-7.pl -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/auto_assignment 2025-10-15T09:49:33,733 creating build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/ERROR 2025-10-15T09:49:33,733 copying build/lib/gff3tool/lib/ERROR/ERROR.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/ERROR 2025-10-15T09:49:33,734 copying build/lib/gff3tool/lib/ERROR/__init__.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/ERROR 2025-10-15T09:49:33,734 creating build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/function4gff 2025-10-15T09:49:33,735 copying build/lib/gff3tool/lib/function4gff/function4gff.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/function4gff 2025-10-15T09:49:33,735 copying build/lib/gff3tool/lib/function4gff/__init__.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/function4gff 2025-10-15T09:49:33,736 creating build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/gff3 2025-10-15T09:49:33,736 copying build/lib/gff3tool/lib/gff3/gff3.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/gff3 2025-10-15T09:49:33,737 copying build/lib/gff3tool/lib/gff3/__init__.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/gff3 2025-10-15T09:49:33,737 creating build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/gff3_fix 2025-10-15T09:49:33,738 copying build/lib/gff3tool/lib/gff3_fix/fix.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/gff3_fix 2025-10-15T09:49:33,738 copying build/lib/gff3tool/lib/gff3_fix/__init__.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/gff3_fix 2025-10-15T09:49:33,739 creating build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/gff3_merge 2025-10-15T09:49:33,739 copying build/lib/gff3tool/lib/gff3_merge/auto_replace_tag.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/gff3_merge 2025-10-15T09:49:33,739 copying build/lib/gff3tool/lib/gff3_merge/merge.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/gff3_merge 2025-10-15T09:49:33,740 copying build/lib/gff3tool/lib/gff3_merge/revision.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/gff3_merge 2025-10-15T09:49:33,740 copying build/lib/gff3tool/lib/gff3_merge/__init__.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/gff3_merge 2025-10-15T09:49:33,741 creating build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/inter_model 2025-10-15T09:49:33,741 copying build/lib/gff3tool/lib/inter_model/inter_model.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/inter_model 2025-10-15T09:49:33,741 copying build/lib/gff3tool/lib/inter_model/__init__.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/inter_model 2025-10-15T09:49:33,742 creating build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/intra_model 2025-10-15T09:49:33,742 copying build/lib/gff3tool/lib/intra_model/intra_model.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/intra_model 2025-10-15T09:49:33,743 copying build/lib/gff3tool/lib/intra_model/__init__.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/intra_model 2025-10-15T09:49:33,743 creating build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/single_feature 2025-10-15T09:49:33,743 copying build/lib/gff3tool/lib/single_feature/single_feature.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/single_feature 2025-10-15T09:49:33,744 copying build/lib/gff3tool/lib/single_feature/__init__.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib/single_feature 2025-10-15T09:49:33,744 copying build/lib/gff3tool/lib/gff3_ID_generator.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib 2025-10-15T09:49:33,745 copying build/lib/gff3tool/lib/id_processor.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib 2025-10-15T09:49:33,745 copying build/lib/gff3tool/lib/replace_OGS.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib 2025-10-15T09:49:33,746 copying build/lib/gff3tool/lib/utils.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib 2025-10-15T09:49:33,746 copying build/lib/gff3tool/lib/__init__.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool/lib 2025-10-15T09:49:33,746 copying build/lib/gff3tool/__init__.py -> build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool 2025-10-15T09:49:33,747 running install_egg_info 2025-10-15T09:49:33,840 Copying gff3tool.egg-info to build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.data/purelib/gff3tool-2.0.1-py3.13.egg-info 2025-10-15T09:49:33,842 running install_scripts 2025-10-15T09:49:33,893 creating build/bdist.linux-armv7l/wheel/gff3tool-2.0.1.dist-info/WHEEL 2025-10-15T09:49:33,894 creating '/tmp/pip-wheel-lvbugztg/gff3tool-2.0.1-cp313-cp313-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-10-15T09:49:33,895 adding 'gff3tool-2.0.1.data/purelib/gff3tool/__init__.py' 2025-10-15T09:49:33,896 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib.md' 2025-10-15T09:49:33,897 adding 'gff3tool-2.0.1.data/purelib/gff3tool/bin/__init__.py' 2025-10-15T09:49:33,898 adding 'gff3tool-2.0.1.data/purelib/gff3tool/bin/gff3_QC.py' 2025-10-15T09:49:33,899 adding 'gff3tool-2.0.1.data/purelib/gff3tool/bin/gff3_fix.py' 2025-10-15T09:49:33,900 adding 'gff3tool-2.0.1.data/purelib/gff3tool/bin/gff3_merge.py' 2025-10-15T09:49:33,902 adding 'gff3tool-2.0.1.data/purelib/gff3tool/bin/gff3_sort.py' 2025-10-15T09:49:33,905 adding 'gff3tool-2.0.1.data/purelib/gff3tool/bin/gff3_to_fasta.py' 2025-10-15T09:49:33,906 adding 'gff3tool-2.0.1.data/purelib/gff3tool/bin/version.py' 2025-10-15T09:49:33,907 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/__init__.py' 2025-10-15T09:49:33,909 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/gff3_ID_generator.py' 2025-10-15T09:49:33,910 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/id_processor.py' 2025-10-15T09:49:33,914 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/replace_OGS.py' 2025-10-15T09:49:33,915 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/utils.py' 2025-10-15T09:49:33,916 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/ERROR/ERROR.py' 2025-10-15T09:49:33,917 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/ERROR/__init__.py' 2025-10-15T09:49:33,918 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/auto_assignment/create_annotation_summaries_nov21-7.pl' 2025-10-15T09:49:33,919 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/auto_assignment/find_match.pl' 2025-10-15T09:49:33,920 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/auto_assignment/gen_spreadsheet.pl' 2025-10-15T09:49:33,921 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/check_gene_parent/find_wrongly_split_gene_parent.pl' 2025-10-15T09:49:33,922 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/function4gff/__init__.py' 2025-10-15T09:49:33,923 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/function4gff/function4gff.py' 2025-10-15T09:49:33,924 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/gff3/__init__.py' 2025-10-15T09:49:33,931 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/gff3/gff3.py' 2025-10-15T09:49:33,933 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/gff3_fix/__init__.py' 2025-10-15T09:49:33,936 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/gff3_fix/fix.py' 2025-10-15T09:49:33,937 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/gff3_merge/__init__.py' 2025-10-15T09:49:33,938 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/gff3_merge/auto_replace_tag.py' 2025-10-15T09:49:33,939 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/gff3_merge/merge.py' 2025-10-15T09:49:33,941 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/gff3_merge/revision.py' 2025-10-15T09:49:33,942 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/inter_model/__init__.py' 2025-10-15T09:49:33,943 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/inter_model/inter_model.py' 2025-10-15T09:49:33,943 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/intra_model/__init__.py' 2025-10-15T09:49:33,945 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/intra_model/intra_model.py' 2025-10-15T09:49:38,850 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin/blast_formatter' 2025-10-15T09:49:42,109 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin/blastdb_aliastool' 2025-10-15T09:49:45,690 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin/blastdbcheck' 2025-10-15T09:49:50,183 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin/blastdbcmd' 2025-10-15T09:49:55,263 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin/blastn' 2025-10-15T09:50:00,367 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin/blastp' 2025-10-15T09:50:05,469 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin/blastx' 2025-10-15T09:50:08,875 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin/convert2blastmask' 2025-10-15T09:50:13,943 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin/deltablast' 2025-10-15T09:50:17,384 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin/dustmasker' 2025-10-15T09:50:17,518 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin/legacy_blast.pl' 2025-10-15T09:50:21,019 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin/makeblastdb' 2025-10-15T09:50:24,487 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin/makembindex' 2025-10-15T09:50:27,873 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin/makeprofiledb' 2025-10-15T09:50:32,925 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin/psiblast' 2025-10-15T09:50:38,040 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin/rpsblast' 2025-10-15T09:50:43,152 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin/rpstblastn' 2025-10-15T09:50:46,642 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin/segmasker' 2025-10-15T09:50:51,688 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin/tblastn' 2025-10-15T09:50:56,792 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin/tblastx' 2025-10-15T09:50:56,992 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin/update_blastdb.pl' 2025-10-15T09:51:00,818 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/ncbi-blast+/bin/windowmasker' 2025-10-15T09:51:00,974 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/single_feature/__init__.py' 2025-10-15T09:51:00,975 adding 'gff3tool-2.0.1.data/purelib/gff3tool/lib/single_feature/single_feature.py' 2025-10-15T09:51:00,977 adding 'gff3tool-2.0.1.dist-info/METADATA' 2025-10-15T09:51:00,977 adding 'gff3tool-2.0.1.dist-info/WHEEL' 2025-10-15T09:51:00,978 adding 'gff3tool-2.0.1.dist-info/entry_points.txt' 2025-10-15T09:51:00,978 adding 'gff3tool-2.0.1.dist-info/top_level.txt' 2025-10-15T09:51:00,980 adding 'gff3tool-2.0.1.dist-info/RECORD' 2025-10-15T09:51:00,980 removing build/bdist.linux-armv7l/wheel 2025-10-15T09:51:01,276 Building wheel for gff3tool (setup.py): finished with status 'done' 2025-10-15T09:51:03,052 Created wheel for gff3tool: filename=gff3tool-2.0.1-cp313-cp313-linux_armv7l.whl size=177059868 sha256=8ccb0023797e7a3b97eefc0af2ba5b4b6a46ba6d93e94d33185ae9aa3d8d14e6 2025-10-15T09:51:03,053 Stored in directory: /tmp/pip-ephem-wheel-cache-j03tum69/wheels/55/87/93/e107494838163a1d0c5668f02d344e84b048526e6b6a84b7bb 2025-10-15T09:51:03,064 Successfully built gff3tool 2025-10-15T09:51:03,407 Removed build tracker: '/tmp/pip-build-tracker-kycxlx0k'