2023-09-10T18:41:25,773 Created temporary directory: /tmp/pip-build-tracker-z6r4pugo 2023-09-10T18:41:25,774 Initialized build tracking at /tmp/pip-build-tracker-z6r4pugo 2023-09-10T18:41:25,774 Created build tracker: /tmp/pip-build-tracker-z6r4pugo 2023-09-10T18:41:25,775 Entered build tracker: /tmp/pip-build-tracker-z6r4pugo 2023-09-10T18:41:25,776 Created temporary directory: /tmp/pip-wheel-j_156mpb 2023-09-10T18:41:25,779 Created temporary directory: /tmp/pip-ephem-wheel-cache-s3n4r3d9 2023-09-10T18:41:25,804 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-10T18:41:25,808 2 location(s) to search for versions of gff3tool: 2023-09-10T18:41:25,808 * https://pypi.org/simple/gff3tool/ 2023-09-10T18:41:25,808 * https://www.piwheels.org/simple/gff3tool/ 2023-09-10T18:41:25,808 Fetching project page and analyzing links: https://pypi.org/simple/gff3tool/ 2023-09-10T18:41:25,810 Getting page https://pypi.org/simple/gff3tool/ 2023-09-10T18:41:25,812 Found index url https://pypi.org/simple/ 2023-09-10T18:41:26,066 Fetched page https://pypi.org/simple/gff3tool/ as application/vnd.pypi.simple.v1+json 2023-09-10T18:41:26,069 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 2023-09-10T18:41:26,070 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 2023-09-10T18:41:26,070 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 2023-09-10T18:41:26,071 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 2023-09-10T18:41:26,072 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 2023-09-10T18:41:26,072 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 2023-09-10T18:41:26,073 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/) 2023-09-10T18:41:26,074 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 2023-09-10T18:41:26,074 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 2023-09-10T18:41:26,075 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 2023-09-10T18:41:26,076 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 2023-09-10T18:41:26,077 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 2023-09-10T18:41:26,077 Fetching project page and analyzing links: https://www.piwheels.org/simple/gff3tool/ 2023-09-10T18:41:26,078 Getting page https://www.piwheels.org/simple/gff3tool/ 2023-09-10T18:41:26,079 Found index url https://www.piwheels.org/simple/ 2023-09-10T18:41:26,387 Fetched page https://www.piwheels.org/simple/gff3tool/ as text/html 2023-09-10T18:41:26,396 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-1.1.0-py3-none-any.whl#sha256=f5eefabf7e1b27382cef033e939fd956121ebf02ae4e7085b83ade5f98c69d90 (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,397 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-1.3.0-py3-none-any.whl#sha256=f993f46b60c812a88426ea96ad2c23aa521aee04c8bdad4016e21d03d6186291 (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,397 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-2.0.0-cp34-cp34m-linux_armv6l.whl#sha256=a6197f7982794de21eb411313c8591f643ea19667efba72907a0fbafd47ca4e7 (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,398 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-2.0.0-cp34-cp34m-linux_armv7l.whl#sha256=a6197f7982794de21eb411313c8591f643ea19667efba72907a0fbafd47ca4e7 (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,398 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-2.0.0-cp35-cp35m-linux_armv6l.whl#sha256=a6d1a1bf91d08ad305f7476e9a3439e57749b4091c112cbf4f73569a4f711a68 (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,399 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-2.0.0-cp35-cp35m-linux_armv7l.whl#sha256=a6d1a1bf91d08ad305f7476e9a3439e57749b4091c112cbf4f73569a4f711a68 (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,399 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-2.0.0-cp37-cp37m-linux_armv6l.whl#sha256=0be9d0d0079481fcbd19198c4fba52c6703b11b043e14bc17cd9b7863857efde (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,400 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-2.0.0-cp37-cp37m-linux_armv7l.whl#sha256=0be9d0d0079481fcbd19198c4fba52c6703b11b043e14bc17cd9b7863857efde (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,400 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-2.0.0-cp39-cp39-linux_armv6l.whl#sha256=7dbbba3501c691ddb06f2ace77ee9897d1e51e32f6e05430923d4a5e53b86174 (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,401 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-2.0.0-cp39-cp39-linux_armv7l.whl#sha256=7dbbba3501c691ddb06f2ace77ee9897d1e51e32f6e05430923d4a5e53b86174 (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,401 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-2.0.1-cp34-cp34m-linux_armv6l.whl#sha256=fa519097d18d8d8239808e305f0bb0549b3dd93a72ed8d5ea6f45d785e6bef11 (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,402 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-2.0.1-cp34-cp34m-linux_armv7l.whl#sha256=fa519097d18d8d8239808e305f0bb0549b3dd93a72ed8d5ea6f45d785e6bef11 (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,402 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-2.0.1-cp35-cp35m-linux_armv6l.whl#sha256=baa47b3147a931daf4958a447f96979e4448707996cc9d60ac45ad3ebb8e9c1f (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,403 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-2.0.1-cp35-cp35m-linux_armv7l.whl#sha256=baa47b3147a931daf4958a447f96979e4448707996cc9d60ac45ad3ebb8e9c1f (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,404 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-2.0.1-cp37-cp37m-linux_armv6l.whl#sha256=88be7d8c71c322212fdc989a672f6e0f10ed299cb5615d7d34f70058a0d6f928 (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,404 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-2.0.1-cp37-cp37m-linux_armv7l.whl#sha256=88be7d8c71c322212fdc989a672f6e0f10ed299cb5615d7d34f70058a0d6f928 (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,405 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-2.0.1-cp39-cp39-linux_armv6l.whl#sha256=a89f1ece9e20b3183b0eba298b269f1c4b0109af60b409f5d3f7bc0be4914bfd (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,405 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-2.0.1-cp39-cp39-linux_armv7l.whl#sha256=a89f1ece9e20b3183b0eba298b269f1c4b0109af60b409f5d3f7bc0be4914bfd (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,406 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-2.0.3-cp35-cp35m-linux_armv6l.whl#sha256=ce80154080e74e3fb30b340e7a76661a4b8f3d78c6104490aa6da9c40fdc91d6 (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,406 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-2.0.3-cp35-cp35m-linux_armv7l.whl#sha256=ce80154080e74e3fb30b340e7a76661a4b8f3d78c6104490aa6da9c40fdc91d6 (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,407 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-2.0.3-cp37-cp37m-linux_armv6l.whl#sha256=79c3e33604c37bc449a60874dbc1520dde9140874fb47948d3a087eeec48f52f (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,407 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-2.0.3-cp37-cp37m-linux_armv7l.whl#sha256=79c3e33604c37bc449a60874dbc1520dde9140874fb47948d3a087eeec48f52f (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,408 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-2.0.3-cp39-cp39-linux_armv6l.whl#sha256=66d9164d8245e216f080754a89df8cda4192f034e99a32532198ccf3c38f6faa (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,408 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-2.0.3-cp39-cp39-linux_armv7l.whl#sha256=66d9164d8245e216f080754a89df8cda4192f034e99a32532198ccf3c38f6faa (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,409 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-2.1.0-cp35-cp35m-linux_armv6l.whl#sha256=5eef1c37d908cd2d30f368726348cf85a26dc4d95abc8131735de5c720d7975b (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,410 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-2.1.0-cp35-cp35m-linux_armv7l.whl#sha256=5eef1c37d908cd2d30f368726348cf85a26dc4d95abc8131735de5c720d7975b (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,410 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-2.1.0-cp37-cp37m-linux_armv6l.whl#sha256=cfe6edebe5cd63bcd5cd38e34377d8c34eb8fdc675d148da65e75d4399db5ff6 (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,411 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-2.1.0-cp37-cp37m-linux_armv7l.whl#sha256=cfe6edebe5cd63bcd5cd38e34377d8c34eb8fdc675d148da65e75d4399db5ff6 (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,411 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-2.1.0-cp39-cp39-linux_armv6l.whl#sha256=acb5d3cb45afefe5eab3c74db7b776dda5cf59ce38bb15cbde8edddd6079c343 (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,412 Skipping link: No binaries permitted for gff3tool: https://www.piwheels.org/simple/gff3tool/gff3tool-2.1.0-cp39-cp39-linux_armv7l.whl#sha256=acb5d3cb45afefe5eab3c74db7b776dda5cf59ce38bb15cbde8edddd6079c343 (from https://www.piwheels.org/simple/gff3tool/) 2023-09-10T18:41:26,413 Skipping link: not a file: https://www.piwheels.org/simple/gff3tool/ 2023-09-10T18:41:26,413 Skipping link: not a file: https://pypi.org/simple/gff3tool/ 2023-09-10T18:41:26,432 Given no hashes to check 1 links for project 'gff3tool': discarding no candidates 2023-09-10T18:41:26,450 Collecting gff3tool==1.4.1 2023-09-10T18:41:26,453 Created temporary directory: /tmp/pip-unpack-q2tzybqp 2023-09-10T18:41:26,702 Downloading gff3tool-1.4.1.tar.gz (82 kB) 2023-09-10T18:41:26,862 Added gff3tool==1.4.1 from https://files.pythonhosted.org/packages/71/cb/9b9d73fd7171571b9ad063fa3a6aac684aeebc7e958a37e2423c690d5110/gff3tool-1.4.1.tar.gz to build tracker '/tmp/pip-build-tracker-z6r4pugo' 2023-09-10T18:41:26,864 Running setup.py (path:/tmp/pip-wheel-j_156mpb/gff3tool_e3a027749b0c423d9054f2f0cf5d8c95/setup.py) egg_info for package gff3tool 2023-09-10T18:41:26,865 Created temporary directory: /tmp/pip-pip-egg-info-2qzh_4zt 2023-09-10T18:41:26,866 Preparing metadata (setup.py): started 2023-09-10T18:41:26,867 Running command python setup.py egg_info 2023-09-10T18:41:27,324 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:744: SetuptoolsDeprecationWarning: Invalid dash-separated options 2023-09-10T18:41:27,324 !! 2023-09-10T18:41:27,325 ******************************************************************************** 2023-09-10T18:41:27,326 Usage of dash-separated 'dist-dir' will not be supported in future 2023-09-10T18:41:27,326 versions. Please use the underscore name 'dist_dir' instead. 2023-09-10T18:41:27,327 By 2023-Sep-26, you need to update your project and remove deprecated calls 2023-09-10T18:41:27,328 or your builds will no longer be supported. 2023-09-10T18:41:27,329 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-10T18:41:27,330 ******************************************************************************** 2023-09-10T18:41:27,331 !! 2023-09-10T18:41:27,331 opt = self.warn_dash_deprecation(opt, section) 2023-09-10T18:41:27,434 running egg_info 2023-09-10T18:41:27,437 creating /tmp/pip-pip-egg-info-2qzh_4zt/gff3tool.egg-info 2023-09-10T18:41:27,456 writing /tmp/pip-pip-egg-info-2qzh_4zt/gff3tool.egg-info/PKG-INFO 2023-09-10T18:41:27,459 writing dependency_links to /tmp/pip-pip-egg-info-2qzh_4zt/gff3tool.egg-info/dependency_links.txt 2023-09-10T18:41:27,460 writing entry points to /tmp/pip-pip-egg-info-2qzh_4zt/gff3tool.egg-info/entry_points.txt 2023-09-10T18:41:27,462 writing top-level names to /tmp/pip-pip-egg-info-2qzh_4zt/gff3tool.egg-info/top_level.txt 2023-09-10T18:41:27,463 writing manifest file '/tmp/pip-pip-egg-info-2qzh_4zt/gff3tool.egg-info/SOURCES.txt' 2023-09-10T18:41:27,529 reading manifest file '/tmp/pip-pip-egg-info-2qzh_4zt/gff3tool.egg-info/SOURCES.txt' 2023-09-10T18:41:27,531 reading manifest template 'MANIFEST.in' 2023-09-10T18:41:27,539 writing manifest file '/tmp/pip-pip-egg-info-2qzh_4zt/gff3tool.egg-info/SOURCES.txt' 2023-09-10T18:41:27,615 Preparing metadata (setup.py): finished with status 'done' 2023-09-10T18:41:27,619 Source in /tmp/pip-wheel-j_156mpb/gff3tool_e3a027749b0c423d9054f2f0cf5d8c95 has version 1.4.1, which satisfies requirement gff3tool==1.4.1 from https://files.pythonhosted.org/packages/71/cb/9b9d73fd7171571b9ad063fa3a6aac684aeebc7e958a37e2423c690d5110/gff3tool-1.4.1.tar.gz 2023-09-10T18:41:27,620 Removed gff3tool==1.4.1 from https://files.pythonhosted.org/packages/71/cb/9b9d73fd7171571b9ad063fa3a6aac684aeebc7e958a37e2423c690d5110/gff3tool-1.4.1.tar.gz from build tracker '/tmp/pip-build-tracker-z6r4pugo' 2023-09-10T18:41:27,624 Created temporary directory: /tmp/pip-unpack-ihwiyjaa 2023-09-10T18:41:27,625 Created temporary directory: /tmp/pip-unpack-jwhqkug4 2023-09-10T18:41:27,629 Building wheels for collected packages: gff3tool 2023-09-10T18:41:27,633 Created temporary directory: /tmp/pip-wheel-2rx1okil 2023-09-10T18:41:27,633 Building wheel for gff3tool (setup.py): started 2023-09-10T18:41:27,634 Destination directory: /tmp/pip-wheel-2rx1okil 2023-09-10T18:41:27,635 Running command python setup.py bdist_wheel 2023-09-10T18:41:28,095 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:744: SetuptoolsDeprecationWarning: Invalid dash-separated options 2023-09-10T18:41:28,095 !! 2023-09-10T18:41:28,097 ******************************************************************************** 2023-09-10T18:41:28,097 Usage of dash-separated 'dist-dir' will not be supported in future 2023-09-10T18:41:28,098 versions. Please use the underscore name 'dist_dir' instead. 2023-09-10T18:41:28,099 By 2023-Sep-26, you need to update your project and remove deprecated calls 2023-09-10T18:41:28,099 or your builds will no longer be supported. 2023-09-10T18:41:28,101 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-10T18:41:28,101 ******************************************************************************** 2023-09-10T18:41:28,103 !! 2023-09-10T18:41:28,103 opt = self.warn_dash_deprecation(opt, section) 2023-09-10T18:41:28,432 running bdist_wheel 2023-09-10T18:41:28,515 running build 2023-09-10T18:41:28,516 running build_py 2023-09-10T18:41:28,537 creating build 2023-09-10T18:41:28,538 creating build/lib 2023-09-10T18:41:28,539 creating build/lib/gff3tool 2023-09-10T18:41:28,540 copying gff3tool/__init__.py -> build/lib/gff3tool 2023-09-10T18:41:28,542 creating build/lib/gff3tool/lib 2023-09-10T18:41:28,543 copying gff3tool/lib/id_processor.py -> build/lib/gff3tool/lib 2023-09-10T18:41:28,545 copying gff3tool/lib/__init__.py -> build/lib/gff3tool/lib 2023-09-10T18:41:28,547 copying gff3tool/lib/replace_OGS.py -> build/lib/gff3tool/lib 2023-09-10T18:41:28,550 copying gff3tool/lib/utils.py -> build/lib/gff3tool/lib 2023-09-10T18:41:28,552 copying gff3tool/lib/fix.py -> build/lib/gff3tool/lib 2023-09-10T18:41:28,555 creating build/lib/gff3tool/bin 2023-09-10T18:41:28,556 copying gff3tool/bin/gff3_fix.py -> build/lib/gff3tool/bin 2023-09-10T18:41:28,558 copying gff3tool/bin/gff3_QC.py -> build/lib/gff3tool/bin 2023-09-10T18:41:28,560 copying gff3tool/bin/__init__.py -> build/lib/gff3tool/bin 2023-09-10T18:41:28,561 copying gff3tool/bin/gff3_to_fasta.py -> build/lib/gff3tool/bin 2023-09-10T18:41:28,563 copying gff3tool/bin/gff3_sort.py -> build/lib/gff3tool/bin 2023-09-10T18:41:28,566 copying gff3tool/bin/version.py -> build/lib/gff3tool/bin 2023-09-10T18:41:28,567 copying gff3tool/bin/gff3_merge.py -> build/lib/gff3tool/bin 2023-09-10T18:41:28,570 creating build/lib/gff3tool/lib/gff3_merge 2023-09-10T18:41:28,571 copying gff3tool/lib/gff3_merge/auto_replace_tag.py -> build/lib/gff3tool/lib/gff3_merge 2023-09-10T18:41:28,573 copying gff3tool/lib/gff3_merge/__init__.py -> build/lib/gff3tool/lib/gff3_merge 2023-09-10T18:41:28,575 copying gff3tool/lib/gff3_merge/merge.py -> build/lib/gff3tool/lib/gff3_merge 2023-09-10T18:41:28,577 copying gff3tool/lib/gff3_merge/revision.py -> build/lib/gff3tool/lib/gff3_merge 2023-09-10T18:41:28,580 creating build/lib/gff3tool/lib/gff3_fix 2023-09-10T18:41:28,581 copying gff3tool/lib/gff3_fix/__init__.py -> build/lib/gff3tool/lib/gff3_fix 2023-09-10T18:41:28,583 copying gff3tool/lib/gff3_fix/fix.py -> build/lib/gff3tool/lib/gff3_fix 2023-09-10T18:41:28,586 creating build/lib/gff3tool/lib/single_feature 2023-09-10T18:41:28,587 copying gff3tool/lib/single_feature/__init__.py -> build/lib/gff3tool/lib/single_feature 2023-09-10T18:41:28,588 copying gff3tool/lib/single_feature/single_feature.py -> build/lib/gff3tool/lib/single_feature 2023-09-10T18:41:28,591 creating build/lib/gff3tool/lib/inter_model 2023-09-10T18:41:28,592 copying gff3tool/lib/inter_model/__init__.py -> build/lib/gff3tool/lib/inter_model 2023-09-10T18:41:28,594 copying gff3tool/lib/inter_model/inter_model.py -> build/lib/gff3tool/lib/inter_model 2023-09-10T18:41:28,596 creating build/lib/gff3tool/lib/intra_model 2023-09-10T18:41:28,597 copying gff3tool/lib/intra_model/__init__.py -> build/lib/gff3tool/lib/intra_model 2023-09-10T18:41:28,598 copying gff3tool/lib/intra_model/intra_model.py -> build/lib/gff3tool/lib/intra_model 2023-09-10T18:41:28,601 creating build/lib/gff3tool/lib/ERROR 2023-09-10T18:41:28,602 copying gff3tool/lib/ERROR/__init__.py -> build/lib/gff3tool/lib/ERROR 2023-09-10T18:41:28,603 copying gff3tool/lib/ERROR/ERROR.py -> build/lib/gff3tool/lib/ERROR 2023-09-10T18:41:28,605 creating build/lib/gff3tool/lib/gff3 2023-09-10T18:41:28,606 copying gff3tool/lib/gff3/__init__.py -> build/lib/gff3tool/lib/gff3 2023-09-10T18:41:28,608 copying gff3tool/lib/gff3/gff3.py -> build/lib/gff3tool/lib/gff3 2023-09-10T18:41:28,612 creating build/lib/gff3tool/lib/function4gff 2023-09-10T18:41:28,612 copying gff3tool/lib/function4gff/__init__.py -> build/lib/gff3tool/lib/function4gff 2023-09-10T18:41:28,614 copying gff3tool/lib/function4gff/function4gff.py -> build/lib/gff3tool/lib/function4gff 2023-09-10T18:41:28,616 running egg_info 2023-09-10T18:41:28,663 writing gff3tool.egg-info/PKG-INFO 2023-09-10T18:41:28,665 writing dependency_links to gff3tool.egg-info/dependency_links.txt 2023-09-10T18:41:28,667 writing entry points to gff3tool.egg-info/entry_points.txt 2023-09-10T18:41:28,668 writing top-level names to gff3tool.egg-info/top_level.txt 2023-09-10T18:41:28,692 reading manifest file 'gff3tool.egg-info/SOURCES.txt' 2023-09-10T18:41:28,694 reading manifest template 'MANIFEST.in' 2023-09-10T18:41:28,702 writing manifest file 'gff3tool.egg-info/SOURCES.txt' 2023-09-10T18:41:28,704 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'gff3tool.lib.auto_assignment' is absent from the `packages` configuration. 2023-09-10T18:41:28,705 !! 2023-09-10T18:41:28,706 ******************************************************************************** 2023-09-10T18:41:28,706 ############################ 2023-09-10T18:41:28,707 # Package would be ignored # 2023-09-10T18:41:28,707 ############################ 2023-09-10T18:41:28,708 Python recognizes 'gff3tool.lib.auto_assignment' as an importable package[^1], 2023-09-10T18:41:28,708 but it is absent from setuptools' `packages` configuration. 2023-09-10T18:41:28,709 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-10T18:41:28,709 package, please make sure that 'gff3tool.lib.auto_assignment' is explicitly added 2023-09-10T18:41:28,710 to the `packages` configuration field. 2023-09-10T18:41:28,711 Alternatively, you can also rely on setuptools' discovery methods 2023-09-10T18:41:28,712 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-10T18:41:28,712 instead of `find_packages(...)`/`find:`). 2023-09-10T18:41:28,713 You can read more about "package discovery" on setuptools documentation page: 2023-09-10T18:41:28,714 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-10T18:41:28,715 If you don't want 'gff3tool.lib.auto_assignment' to be distributed and are 2023-09-10T18:41:28,715 already explicitly excluding 'gff3tool.lib.auto_assignment' via 2023-09-10T18:41:28,716 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-10T18:41:28,717 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-10T18:41:28,717 combination with a more fine grained `package-data` configuration. 2023-09-10T18:41:28,718 You can read more about "package data files" on setuptools documentation page: 2023-09-10T18:41:28,719 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-10T18:41:28,720 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-10T18:41:28,721 even if it does not contain any `.py` files. 2023-09-10T18:41:28,721 On the other hand, currently there is no concept of package data 2023-09-10T18:41:28,722 directory, all directories are treated like packages. 2023-09-10T18:41:28,722 ******************************************************************************** 2023-09-10T18:41:28,723 !! 2023-09-10T18:41:28,723 check.warn(importable) 2023-09-10T18:41:28,724 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'gff3tool.lib.check_gene_parent' is absent from the `packages` configuration. 2023-09-10T18:41:28,724 !! 2023-09-10T18:41:28,725 ******************************************************************************** 2023-09-10T18:41:28,726 ############################ 2023-09-10T18:41:28,726 # Package would be ignored # 2023-09-10T18:41:28,727 ############################ 2023-09-10T18:41:28,727 Python recognizes 'gff3tool.lib.check_gene_parent' as an importable package[^1], 2023-09-10T18:41:28,728 but it is absent from setuptools' `packages` configuration. 2023-09-10T18:41:28,728 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-10T18:41:28,729 package, please make sure that 'gff3tool.lib.check_gene_parent' is explicitly added 2023-09-10T18:41:28,729 to the `packages` configuration field. 2023-09-10T18:41:28,731 Alternatively, you can also rely on setuptools' discovery methods 2023-09-10T18:41:28,731 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-10T18:41:28,732 instead of `find_packages(...)`/`find:`). 2023-09-10T18:41:28,733 You can read more about "package discovery" on setuptools documentation page: 2023-09-10T18:41:28,734 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-10T18:41:28,735 If you don't want 'gff3tool.lib.check_gene_parent' to be distributed and are 2023-09-10T18:41:28,735 already explicitly excluding 'gff3tool.lib.check_gene_parent' via 2023-09-10T18:41:28,736 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-10T18:41:28,736 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-10T18:41:28,737 combination with a more fine grained `package-data` configuration. 2023-09-10T18:41:28,738 You can read more about "package data files" on setuptools documentation page: 2023-09-10T18:41:28,739 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-10T18:41:28,740 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-10T18:41:28,741 even if it does not contain any `.py` files. 2023-09-10T18:41:28,741 On the other hand, currently there is no concept of package data 2023-09-10T18:41:28,742 directory, all directories are treated like packages. 2023-09-10T18:41:28,744 ******************************************************************************** 2023-09-10T18:41:28,745 !! 2023-09-10T18:41:28,746 check.warn(importable) 2023-09-10T18:41:28,748 copying gff3tool/lib.md -> build/lib/gff3tool 2023-09-10T18:41:28,748 creating build/lib/gff3tool/lib/auto_assignment 2023-09-10T18:41:28,749 copying gff3tool/lib/auto_assignment/create_annotation_summaries_nov21-7.pl -> build/lib/gff3tool/lib/auto_assignment 2023-09-10T18:41:28,749 copying gff3tool/lib/auto_assignment/find_match.pl -> build/lib/gff3tool/lib/auto_assignment 2023-09-10T18:41:28,750 copying gff3tool/lib/auto_assignment/gen_spreadsheet.pl -> build/lib/gff3tool/lib/auto_assignment 2023-09-10T18:41:28,750 creating build/lib/gff3tool/lib/check_gene_parent 2023-09-10T18:41:28,751 copying gff3tool/lib/check_gene_parent/find_wrongly_split_gene_parent.pl -> build/lib/gff3tool/lib/check_gene_parent 2023-09-10T18:41:28,752 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-09-10T18:41:28,752 !! 2023-09-10T18:41:28,753 ******************************************************************************** 2023-09-10T18:41:28,754 Please avoid running ``setup.py`` directly. 2023-09-10T18:41:28,754 Instead, use pypa/build, pypa/installer or other 2023-09-10T18:41:28,755 standards-based tools. 2023-09-10T18:41:28,756 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-09-10T18:41:28,757 ******************************************************************************** 2023-09-10T18:41:28,758 !! 2023-09-10T18:41:28,758 self.initialize_options() 2023-09-10T18:41:28,762 installing to build/bdist.linux-armv7l/wheel 2023-09-10T18:41:28,762 running install 2023-09-10T18:41:28,787 Traceback (most recent call last): 2023-09-10T18:41:28,787 File "", line 2, in 2023-09-10T18:41:28,788 File "", line 34, in 2023-09-10T18:41:28,788 File "/tmp/pip-wheel-j_156mpb/gff3tool_e3a027749b0c423d9054f2f0cf5d8c95/setup.py", line 60, in 2023-09-10T18:41:28,789 setup( 2023-09-10T18:41:28,789 File "/usr/local/lib/python3.11/dist-packages/setuptools/__init__.py", line 107, in setup 2023-09-10T18:41:28,789 return distutils.core.setup(**attrs) 2023-09-10T18:41:28,790 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-10T18:41:28,790 File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/core.py", line 185, in setup 2023-09-10T18:41:28,791 return run_commands(dist) 2023-09-10T18:41:28,792 ^^^^^^^^^^^^^^^^^^ 2023-09-10T18:41:28,792 File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/core.py", line 201, in run_commands 2023-09-10T18:41:28,793 dist.run_commands() 2023-09-10T18:41:28,793 File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py", line 969, in run_commands 2023-09-10T18:41:28,794 self.run_command(cmd) 2023-09-10T18:41:28,794 File "/usr/local/lib/python3.11/dist-packages/setuptools/dist.py", line 1233, in run_command 2023-09-10T18:41:28,795 super().run_command(command) 2023-09-10T18:41:28,795 File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py", line 988, in run_command 2023-09-10T18:41:28,796 cmd_obj.run() 2023-09-10T18:41:28,797 File "/usr/lib/python3/dist-packages/wheel/bdist_wheel.py", line 360, in run 2023-09-10T18:41:28,797 self.run_command("install") 2023-09-10T18:41:28,797 File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py", line 318, in run_command 2023-09-10T18:41:28,798 self.distribution.run_command(command) 2023-09-10T18:41:28,799 File "/usr/local/lib/python3.11/dist-packages/setuptools/dist.py", line 1233, in run_command 2023-09-10T18:41:28,799 super().run_command(command) 2023-09-10T18:41:28,800 File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py", line 988, in run_command 2023-09-10T18:41:28,800 cmd_obj.run() 2023-09-10T18:41:28,801 File "/tmp/pip-wheel-j_156mpb/gff3tool_e3a027749b0c423d9054f2f0cf5d8c95/setup.py", line 32, in run 2023-09-10T18:41:28,802 urllib.urlretrieve('https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.31/ncbi-blast-2.2.31+-x64-linux.tar.gz', blast_file) 2023-09-10T18:41:28,803 ^^^^^^^^^^^^^^^^^^ 2023-09-10T18:41:28,803 AttributeError: module 'urllib' has no attribute 'urlretrieve' 2023-09-10T18:41:28,898 ERROR: [present-rich] python setup.py bdist_wheel exited with 1 2023-09-10T18:41:28,911 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2023-09-10T18:41:28,911 exec(compile('"'"''"'"''"'"' 2023-09-10T18:41:28,911 # This is -- a caller that pip uses to run setup.py 2023-09-10T18:41:28,911 # 2023-09-10T18:41:28,911 # - It imports setuptools before invoking setup.py, to enable projects that directly 2023-09-10T18:41:28,911 # import from `distutils.core` to work with newer packaging standards. 2023-09-10T18:41:28,911 # - It provides a clear error message when setuptools is not installed. 2023-09-10T18:41:28,911 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2023-09-10T18:41:28,911 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2023-09-10T18:41:28,911 # manifest_maker: standard file '"'"'-c'"'"' not found". 2023-09-10T18:41:28,911 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2023-09-10T18:41:28,911 import os, sys, tokenize 2023-09-10T18:41:28,911 2023-09-10T18:41:28,911 try: 2023-09-10T18:41:28,911 import setuptools 2023-09-10T18:41:28,911 except ImportError as error: 2023-09-10T18:41:28,911 print( 2023-09-10T18:41:28,911 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2023-09-10T18:41:28,911 "the build environment.", 2023-09-10T18:41:28,911 file=sys.stderr, 2023-09-10T18:41:28,911 ) 2023-09-10T18:41:28,911 sys.exit(1) 2023-09-10T18:41:28,911 2023-09-10T18:41:28,911 __file__ = %r 2023-09-10T18:41:28,911 sys.argv[0] = __file__ 2023-09-10T18:41:28,911 2023-09-10T18:41:28,911 if os.path.exists(__file__): 2023-09-10T18:41:28,911 filename = __file__ 2023-09-10T18:41:28,911 with tokenize.open(__file__) as f: 2023-09-10T18:41:28,911 setup_py_code = f.read() 2023-09-10T18:41:28,911 else: 2023-09-10T18:41:28,911 filename = "" 2023-09-10T18:41:28,911 setup_py_code = "from setuptools import setup; setup()" 2023-09-10T18:41:28,911 2023-09-10T18:41:28,911 exec(compile(setup_py_code, filename, "exec")) 2023-09-10T18:41:28,911 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-j_156mpb/gff3tool_e3a027749b0c423d9054f2f0cf5d8c95/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-2rx1okil[/] 2023-09-10T18:41:28,912 [bold magenta]cwd[/]: /tmp/pip-wheel-j_156mpb/gff3tool_e3a027749b0c423d9054f2f0cf5d8c95/ 2023-09-10T18:41:28,912 Building wheel for gff3tool (setup.py): finished with status 'error' 2023-09-10T18:41:28,913 ERROR: Failed building wheel for gff3tool 2023-09-10T18:41:28,915 Running setup.py clean for gff3tool 2023-09-10T18:41:28,916 Running command python setup.py clean 2023-09-10T18:41:29,356 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:744: SetuptoolsDeprecationWarning: Invalid dash-separated options 2023-09-10T18:41:29,357 !! 2023-09-10T18:41:29,358 ******************************************************************************** 2023-09-10T18:41:29,358 Usage of dash-separated 'dist-dir' will not be supported in future 2023-09-10T18:41:29,359 versions. Please use the underscore name 'dist_dir' instead. 2023-09-10T18:41:29,360 By 2023-Sep-26, you need to update your project and remove deprecated calls 2023-09-10T18:41:29,361 or your builds will no longer be supported. 2023-09-10T18:41:29,362 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-10T18:41:29,362 ******************************************************************************** 2023-09-10T18:41:29,363 !! 2023-09-10T18:41:29,364 opt = self.warn_dash_deprecation(opt, section) 2023-09-10T18:41:29,457 running clean 2023-09-10T18:41:29,497 removing 'build/lib' (and everything under it) 2023-09-10T18:41:29,513 'build/bdist.linux-armv7l' does not exist -- can't clean it 2023-09-10T18:41:29,514 'build/scripts-3.11' does not exist -- can't clean it 2023-09-10T18:41:29,515 removing 'build' 2023-09-10T18:41:29,590 Failed to build gff3tool 2023-09-10T18:41:29,592 ERROR: Failed to build one or more wheels 2023-09-10T18:41:29,593 Exception information: 2023-09-10T18:41:29,593 Traceback (most recent call last): 2023-09-10T18:41:29,593 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2023-09-10T18:41:29,593 status = run_func(*args) 2023-09-10T18:41:29,593 ^^^^^^^^^^^^^^^ 2023-09-10T18:41:29,593 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper 2023-09-10T18:41:29,593 return func(self, options, args) 2023-09-10T18:41:29,593 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-10T18:41:29,593 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run 2023-09-10T18:41:29,593 raise CommandError("Failed to build one or more wheels") 2023-09-10T18:41:29,593 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2023-09-10T18:41:29,596 Removed build tracker: '/tmp/pip-build-tracker-z6r4pugo'