2023-09-16T02:00:31,851 Created temporary directory: /tmp/pip-build-tracker-hka_0w5o 2023-09-16T02:00:31,853 Initialized build tracking at /tmp/pip-build-tracker-hka_0w5o 2023-09-16T02:00:31,853 Created build tracker: /tmp/pip-build-tracker-hka_0w5o 2023-09-16T02:00:31,854 Entered build tracker: /tmp/pip-build-tracker-hka_0w5o 2023-09-16T02:00:31,854 Created temporary directory: /tmp/pip-wheel-kw_gg2ub 2023-09-16T02:00:31,857 Created temporary directory: /tmp/pip-ephem-wheel-cache-b7e8nxay 2023-09-16T02:00:31,882 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-16T02:00:31,886 2 location(s) to search for versions of pybedtools: 2023-09-16T02:00:31,886 * https://pypi.org/simple/pybedtools/ 2023-09-16T02:00:31,886 * https://www.piwheels.org/simple/pybedtools/ 2023-09-16T02:00:31,887 Fetching project page and analyzing links: https://pypi.org/simple/pybedtools/ 2023-09-16T02:00:31,888 Getting page https://pypi.org/simple/pybedtools/ 2023-09-16T02:00:31,889 Found index url https://pypi.org/simple/ 2023-09-16T02:00:32,109 Fetched page https://pypi.org/simple/pybedtools/ as application/vnd.pypi.simple.v1+json 2023-09-16T02:00:32,116 Found link https://files.pythonhosted.org/packages/00/d9/aca9636b3e5b29f232fd6f60859f07f3420ec3c0712b50cb25c734a02a1f/pybedtools-0.2.2dev.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.2.2dev 2023-09-16T02:00:32,117 Found link https://files.pythonhosted.org/packages/44/19/a9bebb9eccd8d64d58202d5b3a151de81ffc7703a47503161b7615554703/pybedtools-0.5dev.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.5dev 2023-09-16T02:00:32,117 Found link https://files.pythonhosted.org/packages/e4/2f/e842c6b1165d706ebc62c931c11d4dfffe60e6b045ecf80eef7ea78d7afc/pybedtools-0.5rc1.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.5rc1 2023-09-16T02:00:32,118 Found link https://files.pythonhosted.org/packages/85/17/c89028c00537638629ca21be7f1b84e963fc8b63c1e9a5fda9884f86fb90/pybedtools-0.5.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.5 2023-09-16T02:00:32,118 Found link https://files.pythonhosted.org/packages/e7/9b/f082d2db470a0c9ba777a0d661fd5a7292c367840880040940de4a705e1f/pybedtools-0.5.5.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.5.5 2023-09-16T02:00:32,119 Found link https://files.pythonhosted.org/packages/3c/e7/365015ec8104195329635cb75ef745bff45d905271cd165f5048efaf48e3/pybedtools-0.6rc1.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6rc1 2023-09-16T02:00:32,120 Found link https://files.pythonhosted.org/packages/04/ce/0e1480725fe80eb9a401f59e1bcc28fce721f6c2c5d7be233894d0154551/pybedtools-0.6.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6 2023-09-16T02:00:32,121 Found link https://files.pythonhosted.org/packages/ac/25/c971ba83c6df08cbd17626339ec637df57a0aa409ba3042408ff349dd710/pybedtools-0.6.1.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6.1 2023-09-16T02:00:32,121 Found link https://files.pythonhosted.org/packages/3e/71/cb09c7b874a87803f9fb9a9b679d02a82879b9cadca4c93756e05e65a439/pybedtools-0.6.2.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6.2 2023-09-16T02:00:32,122 Found link https://files.pythonhosted.org/packages/28/0b/15291a1aac0a2a1eb814a0c883ccebf2eebaebbef9923bfa0444df0cb3a8/pybedtools-0.6.3.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6.3 2023-09-16T02:00:32,123 Found link https://files.pythonhosted.org/packages/7a/12/73027be04fc57dd3340e2120f0148c0aca569b16e62333f32a40b2b06ee0/pybedtools-0.6.4.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6.4 2023-09-16T02:00:32,123 Found link https://files.pythonhosted.org/packages/a4/98/dab963ff44ddd40849a01b145b6d769158d9794b979fdbfd173728e06e5b/pybedtools-0.6.5.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6.5 2023-09-16T02:00:32,124 Found link https://files.pythonhosted.org/packages/a3/91/02e900caea18ee909665440727222a9f37c9a532170c52684123f07d6e21/pybedtools-0.6.6.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6.6 2023-09-16T02:00:32,125 Found link https://files.pythonhosted.org/packages/af/ff/7d488b19b8e4109bbaf7b7e4c5dc53207f2c4354d7729cf73f17a79fa104/pybedtools-0.6.7.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6.7 2023-09-16T02:00:32,126 Found link https://files.pythonhosted.org/packages/aa/e9/c92a7e58326bf76534af1fbd4074def6999130b1838b4dcc51e9f3ba5e17/pybedtools-0.6.8.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6.8 2023-09-16T02:00:32,126 Found link https://files.pythonhosted.org/packages/79/20/2a0861cc9ffc41043efd814cdf860828f4b2213573c82ea6138eb6cb221b/pybedtools-0.6.9.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6.9 2023-09-16T02:00:32,127 Found link https://files.pythonhosted.org/packages/e6/8d/06beb4e8a9e9a4ce042af337a5b855a789da586072d0c418ed9cb9398628/pybedtools-0.7.0.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.7.0 2023-09-16T02:00:32,127 Found link https://files.pythonhosted.org/packages/b5/1c/1b7e66668105e5b84cc6224a54ce552c6a6113e9b34c980fc436140e6be1/pybedtools-0.7.1.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.7.1 2023-09-16T02:00:32,128 Found link https://files.pythonhosted.org/packages/a2/43/d80dbf32da421c78ea84a386402e1840dd06f3aba7e5fe73e8134e1ce50a/pybedtools-0.7.4.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.7.4 2023-09-16T02:00:32,129 Found link https://files.pythonhosted.org/packages/ed/f1/2caa4dc57b62707f0df147c0820d1fc8565e439c5f5c86778df7a2fec59f/pybedtools-0.7.5.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.7.5 2023-09-16T02:00:32,129 Found link https://files.pythonhosted.org/packages/f4/49/ce7ccc0ad79189eb8b8eec170c350643e7a209f98e34dae239a954d6fdb0/pybedtools-0.7.6.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.7.6 2023-09-16T02:00:32,130 Found link https://files.pythonhosted.org/packages/c2/a6/29fd41e86b38e7ca39eb7818c422e927534f2bd324c34cfd411cfca203b0/pybedtools-0.7.7.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.7.7 2023-09-16T02:00:32,130 Found link https://files.pythonhosted.org/packages/2d/ee/aa19e50e03e06c817d00eadf8b56824b9e473da8c3e8ca3b33a11717ee6f/pybedtools-0.7.8.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.7.8 2023-09-16T02:00:32,131 Found link https://files.pythonhosted.org/packages/7c/66/8aecffd830eddbd05c1c3e737f87220cef9f2a8358f1d692f85b30269520/pybedtools-0.7.9.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.7.9 2023-09-16T02:00:32,132 Found link https://files.pythonhosted.org/packages/09/57/e7668e8644c60413be05b8cc9c23aaea3a0717b4025843d8c26b7c4822af/pybedtools-0.7.10.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.7.10 2023-09-16T02:00:32,132 Found link https://files.pythonhosted.org/packages/ca/b6/af143d5247cfe331e32c96ca92056293140eb8ce788d37842f6dcea734b4/pybedtools-0.8.0.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.8.0 2023-09-16T02:00:32,133 Found link https://files.pythonhosted.org/packages/bf/14/152220f39cda6b9b72810eeed103c6ec78422429adabe3aafc3eaf6feb40/pybedtools-0.8.1.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.8.1 2023-09-16T02:00:32,134 Found link https://files.pythonhosted.org/packages/5b/57/46e9c8135954550d1d3a05db5b0462a264239f7f71c78af304bb47c5c900/pybedtools-0.8.2.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.8.2 2023-09-16T02:00:32,135 Found link https://files.pythonhosted.org/packages/58/e2/410bb188b47582e2fd2f7176173b7b7bf46e122bb17fb4422552f4a6c604/pybedtools-0.9.0.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.9.0 2023-09-16T02:00:32,135 Found link https://files.pythonhosted.org/packages/38/00/f07c17e25f9cc8e2d22b30aace73733e275b1804196f744f0178012a0d16/pybedtools-0.9.1.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.9.1 2023-09-16T02:00:32,136 Fetching project page and analyzing links: https://www.piwheels.org/simple/pybedtools/ 2023-09-16T02:00:32,137 Getting page https://www.piwheels.org/simple/pybedtools/ 2023-09-16T02:00:32,138 Found index url https://www.piwheels.org/simple/ 2023-09-16T02:00:37,992 Fetched page https://www.piwheels.org/simple/pybedtools/ as text/html 2023-09-16T02:00:38,028 Skipping link: No binaries permitted for pybedtools: https://www.piwheels.org/simple/pybedtools/pybedtools-0.9.1-cp39-cp39-linux_armv7l.whl#sha256=aac4ce2ebe92db07c21f083906878a68f16480f350569fd0e6765abad7cc0212 (from https://www.piwheels.org/simple/pybedtools/) 2023-09-16T02:00:38,029 Skipping link: No binaries permitted for pybedtools: https://www.piwheels.org/simple/pybedtools/pybedtools-0.9.1-cp39-cp39-linux_armv6l.whl#sha256=aac4ce2ebe92db07c21f083906878a68f16480f350569fd0e6765abad7cc0212 (from https://www.piwheels.org/simple/pybedtools/) 2023-09-16T02:00:38,030 Skipping link: No binaries permitted for pybedtools: https://www.piwheels.org/simple/pybedtools/pybedtools-0.9.1-cp37-cp37m-linux_armv7l.whl#sha256=c7f6b104f90209f3bba532c14d050fd36cf6dcb6a25866f1c57d2eb933853fd1 (from https://www.piwheels.org/simple/pybedtools/) 2023-09-16T02:00:38,031 Skipping link: No binaries permitted for pybedtools: 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https://www.piwheels.org/simple/pybedtools/pybedtools-0.2.2.dev0-py3-none-any.whl#sha256=37efef7ea02a872e8d60cd34e5a36bd3e480eaccf7121bd8ac67647dd4550efc (from https://www.piwheels.org/simple/pybedtools/) 2023-09-16T02:00:38,084 Skipping link: not a file: https://www.piwheels.org/simple/pybedtools/ 2023-09-16T02:00:38,085 Skipping link: not a file: https://pypi.org/simple/pybedtools/ 2023-09-16T02:00:38,106 Given no hashes to check 1 links for project 'pybedtools': discarding no candidates 2023-09-16T02:00:38,124 Collecting pybedtools==0.9.0 2023-09-16T02:00:38,127 Created temporary directory: /tmp/pip-unpack-t0r79pid 2023-09-16T02:00:38,352 Downloading pybedtools-0.9.0.tar.gz (12.5 MB) 2023-09-16T02:00:40,680 Added pybedtools==0.9.0 from https://files.pythonhosted.org/packages/58/e2/410bb188b47582e2fd2f7176173b7b7bf46e122bb17fb4422552f4a6c604/pybedtools-0.9.0.tar.gz to build tracker '/tmp/pip-build-tracker-hka_0w5o' 2023-09-16T02:00:40,682 Running setup.py (path:/tmp/pip-wheel-kw_gg2ub/pybedtools_96045f1d4476408083eb6ca92a34358e/setup.py) egg_info for package pybedtools 2023-09-16T02:00:40,683 Created temporary directory: /tmp/pip-pip-egg-info-gt1bycq9 2023-09-16T02:00:40,684 Preparing metadata (setup.py): started 2023-09-16T02:00:40,685 Running command python setup.py egg_info 2023-09-16T02:00:41,325 /tmp/pip-wheel-kw_gg2ub/pybedtools_96045f1d4476408083eb6ca92a34358e/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 2023-09-16T02:00:41,325 import pkg_resources 2023-09-16T02:00:41,755 running egg_info 2023-09-16T02:00:41,756 creating /tmp/pip-pip-egg-info-gt1bycq9/pybedtools.egg-info 2023-09-16T02:00:41,780 writing /tmp/pip-pip-egg-info-gt1bycq9/pybedtools.egg-info/PKG-INFO 2023-09-16T02:00:41,783 writing dependency_links to /tmp/pip-pip-egg-info-gt1bycq9/pybedtools.egg-info/dependency_links.txt 2023-09-16T02:00:41,785 writing requirements to /tmp/pip-pip-egg-info-gt1bycq9/pybedtools.egg-info/requires.txt 2023-09-16T02:00:41,786 writing top-level names to /tmp/pip-pip-egg-info-gt1bycq9/pybedtools.egg-info/top_level.txt 2023-09-16T02:00:41,787 writing manifest file '/tmp/pip-pip-egg-info-gt1bycq9/pybedtools.egg-info/SOURCES.txt' 2023-09-16T02:00:41,854 reading manifest file '/tmp/pip-pip-egg-info-gt1bycq9/pybedtools.egg-info/SOURCES.txt' 2023-09-16T02:00:41,856 adding license file 'LICENSE.txt' 2023-09-16T02:00:41,861 writing manifest file '/tmp/pip-pip-egg-info-gt1bycq9/pybedtools.egg-info/SOURCES.txt' 2023-09-16T02:00:41,976 Preparing metadata (setup.py): finished with status 'done' 2023-09-16T02:00:41,980 Source in /tmp/pip-wheel-kw_gg2ub/pybedtools_96045f1d4476408083eb6ca92a34358e has version 0.9.0, which satisfies requirement pybedtools==0.9.0 from https://files.pythonhosted.org/packages/58/e2/410bb188b47582e2fd2f7176173b7b7bf46e122bb17fb4422552f4a6c604/pybedtools-0.9.0.tar.gz 2023-09-16T02:00:41,981 Removed pybedtools==0.9.0 from https://files.pythonhosted.org/packages/58/e2/410bb188b47582e2fd2f7176173b7b7bf46e122bb17fb4422552f4a6c604/pybedtools-0.9.0.tar.gz from build tracker '/tmp/pip-build-tracker-hka_0w5o' 2023-09-16T02:00:41,986 Created temporary directory: /tmp/pip-unpack-ie51g0_0 2023-09-16T02:00:41,987 Created temporary directory: /tmp/pip-unpack-biey56ou 2023-09-16T02:00:41,992 Building wheels for collected packages: pybedtools 2023-09-16T02:00:41,996 Created temporary directory: /tmp/pip-wheel-7m5lick2 2023-09-16T02:00:41,996 Building wheel for pybedtools (setup.py): started 2023-09-16T02:00:41,998 Destination directory: /tmp/pip-wheel-7m5lick2 2023-09-16T02:00:41,998 Running command python setup.py bdist_wheel 2023-09-16T02:00:42,615 /tmp/pip-wheel-kw_gg2ub/pybedtools_96045f1d4476408083eb6ca92a34358e/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 2023-09-16T02:00:42,615 import pkg_resources 2023-09-16T02:00:43,025 running bdist_wheel 2023-09-16T02:00:43,048 The [wheel] section is deprecated. Use [bdist_wheel] instead. 2023-09-16T02:00:43,072 running build 2023-09-16T02:00:43,073 running build_py 2023-09-16T02:00:43,100 creating build 2023-09-16T02:00:43,101 creating build/lib.linux-armv7l-cpython-311 2023-09-16T02:00:43,102 creating build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-16T02:00:43,104 copying pybedtools/stats.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-16T02:00:43,106 copying pybedtools/settings.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-16T02:00:43,108 copying pybedtools/bedtool.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-16T02:00:43,113 copying pybedtools/parallel.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-16T02:00:43,115 copying pybedtools/__init__.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-16T02:00:43,117 copying pybedtools/genome_registry.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-16T02:00:43,122 copying pybedtools/logger.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-16T02:00:43,124 copying pybedtools/filenames.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-16T02:00:43,126 copying pybedtools/paths.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-16T02:00:43,128 copying pybedtools/version.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-16T02:00:43,130 copying pybedtools/helpers.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-16T02:00:43,133 creating build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-16T02:00:43,134 copying pybedtools/test/test_1.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-16T02:00:43,138 copying pybedtools/test/test_contrib.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-16T02:00:43,140 copying pybedtools/test/test_helpers.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-16T02:00:43,142 copying pybedtools/test/regression_tests.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-16T02:00:43,144 copying pybedtools/test/genomepy_integration.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-16T02:00:43,146 copying pybedtools/test/test_pathlib.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-16T02:00:43,148 copying pybedtools/test/__init__.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-16T02:00:43,150 copying pybedtools/test/test_issues.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-16T02:00:43,153 copying pybedtools/test/test_iter.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-16T02:00:43,155 copying pybedtools/test/test_len_leak.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-16T02:00:43,157 copying pybedtools/test/tfuncs.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-16T02:00:43,159 copying pybedtools/test/test_cbedtools.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-16T02:00:43,161 copying pybedtools/test/test_gzip_support.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-16T02:00:43,164 creating build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2023-09-16T02:00:43,165 copying pybedtools/contrib/long_range_interaction.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2023-09-16T02:00:43,168 copying pybedtools/contrib/venn_maker.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2023-09-16T02:00:43,170 copying pybedtools/contrib/plotting.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2023-09-16T02:00:43,173 copying pybedtools/contrib/intersection_matrix.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2023-09-16T02:00:43,175 copying pybedtools/contrib/__init__.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2023-09-16T02:00:43,177 copying pybedtools/contrib/bigbed.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2023-09-16T02:00:43,179 copying pybedtools/contrib/bigwig.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2023-09-16T02:00:43,182 creating build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,183 copying pybedtools/test/data/__init__.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,185 running egg_info 2023-09-16T02:00:43,215 creating pybedtools.egg-info 2023-09-16T02:00:43,242 writing pybedtools.egg-info/PKG-INFO 2023-09-16T02:00:43,246 writing dependency_links to pybedtools.egg-info/dependency_links.txt 2023-09-16T02:00:43,248 writing requirements to pybedtools.egg-info/requires.txt 2023-09-16T02:00:43,249 writing top-level names to pybedtools.egg-info/top_level.txt 2023-09-16T02:00:43,251 writing manifest file 'pybedtools.egg-info/SOURCES.txt' 2023-09-16T02:00:43,288 reading manifest file 'pybedtools.egg-info/SOURCES.txt' 2023-09-16T02:00:43,290 adding license file 'LICENSE.txt' 2023-09-16T02:00:43,295 writing manifest file 'pybedtools.egg-info/SOURCES.txt' 2023-09-16T02:00:43,298 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'pybedtools.include' is absent from the `packages` configuration. 2023-09-16T02:00:43,299 !! 2023-09-16T02:00:43,300 ******************************************************************************** 2023-09-16T02:00:43,300 ############################ 2023-09-16T02:00:43,300 # Package would be ignored # 2023-09-16T02:00:43,301 ############################ 2023-09-16T02:00:43,301 Python recognizes 'pybedtools.include' as an importable package[^1], 2023-09-16T02:00:43,302 but it is absent from setuptools' `packages` configuration. 2023-09-16T02:00:43,302 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-16T02:00:43,303 package, please make sure that 'pybedtools.include' is explicitly added 2023-09-16T02:00:43,303 to the `packages` configuration field. 2023-09-16T02:00:43,304 Alternatively, you can also rely on setuptools' discovery methods 2023-09-16T02:00:43,304 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-16T02:00:43,305 instead of `find_packages(...)`/`find:`). 2023-09-16T02:00:43,305 You can read more about "package discovery" on setuptools documentation page: 2023-09-16T02:00:43,306 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-16T02:00:43,307 If you don't want 'pybedtools.include' to be distributed and are 2023-09-16T02:00:43,308 already explicitly excluding 'pybedtools.include' via 2023-09-16T02:00:43,308 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-16T02:00:43,308 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-16T02:00:43,309 combination with a more fine grained `package-data` configuration. 2023-09-16T02:00:43,310 You can read more about "package data files" on setuptools documentation page: 2023-09-16T02:00:43,311 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-16T02:00:43,312 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-16T02:00:43,313 even if it does not contain any `.py` files. 2023-09-16T02:00:43,313 On the other hand, currently there is no concept of package data 2023-09-16T02:00:43,314 directory, all directories are treated like packages. 2023-09-16T02:00:43,314 ******************************************************************************** 2023-09-16T02:00:43,315 !! 2023-09-16T02:00:43,315 check.warn(importable) 2023-09-16T02:00:43,320 copying pybedtools/_Window.pyx -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-16T02:00:43,322 copying pybedtools/cbedtools.cpp -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-16T02:00:43,338 copying pybedtools/cbedtools.pxd -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-16T02:00:43,341 copying pybedtools/cbedtools.pyx -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-16T02:00:43,344 copying pybedtools/featurefuncs.cpp -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-16T02:00:43,353 copying pybedtools/featurefuncs.pyx -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-16T02:00:43,355 creating build/lib.linux-armv7l-cpython-311/pybedtools/include 2023-09-16T02:00:43,356 copying pybedtools/include/bedFile.cpp -> build/lib.linux-armv7l-cpython-311/pybedtools/include 2023-09-16T02:00:43,359 copying pybedtools/include/fileType.cpp -> build/lib.linux-armv7l-cpython-311/pybedtools/include 2023-09-16T02:00:43,361 copying pybedtools/include/gzstream.cpp -> build/lib.linux-armv7l-cpython-311/pybedtools/include 2023-09-16T02:00:43,363 copying pybedtools/test/data/genome.fa -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,365 copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,368 copying pybedtools/test/data/gdc.1.100.bam.bai -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,370 copying pybedtools/test/data/x.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,410 copying pybedtools/test/data/bedpe.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,412 copying pybedtools/test/data/democonfig.yaml -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,414 copying pybedtools/test/data/gdc.gff.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,416 copying pybedtools/test/data/gdc.gff -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,418 copying pybedtools/test/data/expand_test.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,420 copying pybedtools/test/data/gdc.50.200.bam.bai -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,422 copying pybedtools/test/data/x.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,464 copying pybedtools/test/data/gdc.sorted.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,466 copying pybedtools/test/data/a.links.html -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,468 copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,473 copying pybedtools/test/data/test_peaks.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,475 copying pybedtools/test/data/tag_test1.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,477 copying pybedtools/test/data/issue319.vcf.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,480 copying pybedtools/test/data/b.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,482 copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,485 copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,490 copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,499 copying pybedtools/test/data/1000genomes-example.vcf -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,501 copying pybedtools/test/data/snps.bed.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,632 copying pybedtools/test/data/hg38-base.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,634 copying pybedtools/test/data/gdc.50.200.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,636 copying pybedtools/test/data/c.gff -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,638 copying pybedtools/test/data/gdc.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,640 copying pybedtools/test/data/test_bedpe.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,642 copying pybedtools/test/data/a.igv_script -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,644 copying pybedtools/test/data/issue_121.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,646 copying pybedtools/test/data/reads.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,648 copying pybedtools/test/data/test.fa.fai -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,650 copying pybedtools/test/data/issue319.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,652 copying pybedtools/test/data/vcf-stderr-test.vcf -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,654 copying pybedtools/test/data/y.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,657 copying pybedtools/test/data/hg19.gff -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,663 copying pybedtools/test/data/a.bed.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,665 copying pybedtools/test/data/test_tsses.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,666 copying pybedtools/test/data/bedpe2.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,668 copying pybedtools/test/data/issue319.out.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,675 copying pybedtools/test/data/gdc.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,677 copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,680 copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,684 copying pybedtools/test/data/exons.gff -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,686 copying pybedtools/test/data/gdc.sorted.bam.bai -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,688 copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,692 copying pybedtools/test/data/vcf-stderr-test.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,694 copying pybedtools/test/data/164.gtf -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,696 copying pybedtools/test/data/gdc.1.100.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,698 copying pybedtools/test/data/mm9.bed12 -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,700 copying pybedtools/test/data/test.fa -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,702 copying pybedtools/test/data/small.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,705 copying pybedtools/test/data/multibamcov_test.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,707 copying pybedtools/test/data/d.gff -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,709 copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,718 copying pybedtools/test/data/small.fastq -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,720 copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,724 copying pybedtools/test/data/venn.c.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,726 copying pybedtools/test/data/gdc.cram -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,729 copying pybedtools/test/data/a.bed.gz.tbi -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,731 copying pybedtools/test/data/gdc.othersort.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,733 copying pybedtools/test/data/hg38-problem.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,735 copying pybedtools/test/data/tag_test2.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,737 copying pybedtools/test/data/venn.b.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,739 copying pybedtools/test/data/m1.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,741 copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,745 copying pybedtools/test/data/v.vcf -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,747 copying pybedtools/test/data/a.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,750 copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-16T02:00:43,779 running build_ext 2023-09-16T02:00:43,785 building 'pybedtools.cbedtools' extension 2023-09-16T02:00:43,785 creating build/temp.linux-armv7l-cpython-311 2023-09-16T02:00:43,786 creating build/temp.linux-armv7l-cpython-311/pybedtools 2023-09-16T02:00:43,787 creating build/temp.linux-armv7l-cpython-311/pybedtools/include 2023-09-16T02:00:43,788 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/cbedtools.cpp -o build/temp.linux-armv7l-cpython-311/pybedtools/cbedtools.o 2023-09-16T02:00:46,250 In file included from pybedtools/cbedtools.cpp:731: 2023-09-16T02:00:46,251 pybedtools/include/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: 2023-09-16T02:00:46,251 pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 2023-09-16T02:00:46,252 92 | for (register short i = 0; i < _binLevels; ++i) { 2023-09-16T02:00:46,253 | ^ 2023-09-16T02:00:47,210 pybedtools/cbedtools.cpp: In function ‘int __Pyx_PyBytes_Equals(PyObject*, PyObject*, int)’: 2023-09-16T02:00:47,210 pybedtools/cbedtools.cpp:18681:43: warning: ‘PyBytesObject::ob_shash’ is deprecated [-Wdeprecated-declarations] 2023-09-16T02:00:47,211 18681 | hash1 = ((PyBytesObject*)s1)->ob_shash; 2023-09-16T02:00:47,211 | ^~~~~~~~ 2023-09-16T02:00:47,212 In file included from /usr/include/python3.11/bytesobject.h:62, 2023-09-16T02:00:47,212 from /usr/include/python3.11/Python.h:50, 2023-09-16T02:00:47,213 from pybedtools/cbedtools.cpp:35: 2023-09-16T02:00:47,214 /usr/include/python3.11/cpython/bytesobject.h:7:35: note: declared here 2023-09-16T02:00:47,214 7 | Py_DEPRECATED(3.11) Py_hash_t ob_shash; 2023-09-16T02:00:47,215 | ^~~~~~~~ 2023-09-16T02:00:47,215 pybedtools/cbedtools.cpp:18681:43: warning: ‘PyBytesObject::ob_shash’ is deprecated [-Wdeprecated-declarations] 2023-09-16T02:00:47,216 18681 | hash1 = ((PyBytesObject*)s1)->ob_shash; 2023-09-16T02:00:47,217 | ^~~~~~~~ 2023-09-16T02:00:47,217 /usr/include/python3.11/cpython/bytesobject.h:7:35: note: declared here 2023-09-16T02:00:47,218 7 | Py_DEPRECATED(3.11) Py_hash_t ob_shash; 2023-09-16T02:00:47,218 | ^~~~~~~~ 2023-09-16T02:00:47,219 pybedtools/cbedtools.cpp:18681:43: warning: ‘PyBytesObject::ob_shash’ is deprecated [-Wdeprecated-declarations] 2023-09-16T02:00:47,220 18681 | hash1 = ((PyBytesObject*)s1)->ob_shash; 2023-09-16T02:00:47,220 | ^~~~~~~~ 2023-09-16T02:00:47,221 /usr/include/python3.11/cpython/bytesobject.h:7:35: note: declared here 2023-09-16T02:00:47,221 7 | Py_DEPRECATED(3.11) Py_hash_t ob_shash; 2023-09-16T02:00:47,222 | ^~~~~~~~ 2023-09-16T02:00:47,223 pybedtools/cbedtools.cpp:18682:43: warning: ‘PyBytesObject::ob_shash’ is deprecated [-Wdeprecated-declarations] 2023-09-16T02:00:47,223 18682 | hash2 = ((PyBytesObject*)s2)->ob_shash; 2023-09-16T02:00:47,224 | ^~~~~~~~ 2023-09-16T02:00:47,224 /usr/include/python3.11/cpython/bytesobject.h:7:35: note: declared here 2023-09-16T02:00:47,225 7 | Py_DEPRECATED(3.11) Py_hash_t ob_shash; 2023-09-16T02:00:47,226 | ^~~~~~~~ 2023-09-16T02:00:47,226 pybedtools/cbedtools.cpp:18682:43: warning: ‘PyBytesObject::ob_shash’ is deprecated [-Wdeprecated-declarations] 2023-09-16T02:00:47,227 18682 | hash2 = ((PyBytesObject*)s2)->ob_shash; 2023-09-16T02:00:47,228 | ^~~~~~~~ 2023-09-16T02:00:47,228 /usr/include/python3.11/cpython/bytesobject.h:7:35: note: declared here 2023-09-16T02:00:47,229 7 | Py_DEPRECATED(3.11) Py_hash_t ob_shash; 2023-09-16T02:00:47,230 | ^~~~~~~~ 2023-09-16T02:00:47,230 pybedtools/cbedtools.cpp:18682:43: warning: ‘PyBytesObject::ob_shash’ is deprecated [-Wdeprecated-declarations] 2023-09-16T02:00:47,231 18682 | hash2 = ((PyBytesObject*)s2)->ob_shash; 2023-09-16T02:00:47,231 | ^~~~~~~~ 2023-09-16T02:00:47,232 /usr/include/python3.11/cpython/bytesobject.h:7:35: note: declared here 2023-09-16T02:00:47,232 7 | Py_DEPRECATED(3.11) Py_hash_t ob_shash; 2023-09-16T02:00:47,233 | ^~~~~~~~ 2023-09-16T02:00:47,251 pybedtools/cbedtools.cpp: In function ‘_PyErr_StackItem* __Pyx_PyErr_GetTopmostException(PyThreadState*)’: 2023-09-16T02:00:47,252 pybedtools/cbedtools.cpp:19126:23: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_type’ 2023-09-16T02:00:47,252 19126 | while ((exc_info->exc_type == NULL || exc_info->exc_type == Py_None) && 2023-09-16T02:00:47,253 | ^~~~~~~~ 2023-09-16T02:00:47,253 pybedtools/cbedtools.cpp:19126:53: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_type’ 2023-09-16T02:00:47,254 19126 | while ((exc_info->exc_type == NULL || exc_info->exc_type == Py_None) && 2023-09-16T02:00:47,254 | ^~~~~~~~ 2023-09-16T02:00:47,255 pybedtools/cbedtools.cpp: In function ‘void __Pyx__ExceptionSave(PyThreadState*, PyObject**, PyObject**, PyObject**)’: 2023-09-16T02:00:47,255 pybedtools/cbedtools.cpp:19140:23: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_type’ 2023-09-16T02:00:47,256 19140 | *type = exc_info->exc_type; 2023-09-16T02:00:47,257 | ^~~~~~~~ 2023-09-16T02:00:47,257 pybedtools/cbedtools.cpp:19142:21: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_traceback’ 2023-09-16T02:00:47,258 19142 | *tb = exc_info->exc_traceback; 2023-09-16T02:00:47,258 | ^~~~~~~~~~~~~ 2023-09-16T02:00:47,259 pybedtools/cbedtools.cpp: In function ‘void __Pyx__ExceptionReset(PyThreadState*, PyObject*, PyObject*, PyObject*)’: 2023-09-16T02:00:47,260 pybedtools/cbedtools.cpp:19156:26: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_type’ 2023-09-16T02:00:47,261 19156 | tmp_type = exc_info->exc_type; 2023-09-16T02:00:47,261 | ^~~~~~~~ 2023-09-16T02:00:47,262 pybedtools/cbedtools.cpp:19158:24: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_traceback’ 2023-09-16T02:00:47,263 19158 | tmp_tb = exc_info->exc_traceback; 2023-09-16T02:00:47,263 | ^~~~~~~~~~~~~ 2023-09-16T02:00:47,264 pybedtools/cbedtools.cpp:19159:15: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_type’ 2023-09-16T02:00:47,265 19159 | exc_info->exc_type = type; 2023-09-16T02:00:47,266 | ^~~~~~~~ 2023-09-16T02:00:47,266 pybedtools/cbedtools.cpp:19161:15: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_traceback’ 2023-09-16T02:00:47,267 19161 | exc_info->exc_traceback = tb; 2023-09-16T02:00:47,268 | ^~~~~~~~~~~~~ 2023-09-16T02:00:47,310 pybedtools/cbedtools.cpp: In function ‘int __Pyx__GetException(PyThreadState*, PyObject**, PyObject**, PyObject**)’: 2023-09-16T02:00:47,310 pybedtools/cbedtools.cpp:20178:30: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_type’ 2023-09-16T02:00:47,311 20178 | tmp_type = exc_info->exc_type; 2023-09-16T02:00:47,312 | ^~~~~~~~ 2023-09-16T02:00:47,312 pybedtools/cbedtools.cpp:20180:28: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_traceback’ 2023-09-16T02:00:47,313 20180 | tmp_tb = exc_info->exc_traceback; 2023-09-16T02:00:47,314 | ^~~~~~~~~~~~~ 2023-09-16T02:00:47,314 pybedtools/cbedtools.cpp:20181:19: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_type’ 2023-09-16T02:00:47,315 20181 | exc_info->exc_type = local_type; 2023-09-16T02:00:47,316 | ^~~~~~~~ 2023-09-16T02:00:47,316 pybedtools/cbedtools.cpp:20183:19: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_traceback’ 2023-09-16T02:00:47,317 20183 | exc_info->exc_traceback = local_tb; 2023-09-16T02:00:47,317 | ^~~~~~~~~~~~~ 2023-09-16T02:00:47,349 pybedtools/cbedtools.cpp: In function ‘void __Pyx__ExceptionSwap(PyThreadState*, PyObject**, PyObject**, PyObject**)’: 2023-09-16T02:00:47,350 pybedtools/cbedtools.cpp:20828:26: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_type’ 2023-09-16T02:00:47,350 20828 | tmp_type = exc_info->exc_type; 2023-09-16T02:00:47,351 | ^~~~~~~~ 2023-09-16T02:00:47,352 pybedtools/cbedtools.cpp:20830:24: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_traceback’ 2023-09-16T02:00:47,352 20830 | tmp_tb = exc_info->exc_traceback; 2023-09-16T02:00:47,353 | ^~~~~~~~~~~~~ 2023-09-16T02:00:47,354 pybedtools/cbedtools.cpp:20831:15: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_type’ 2023-09-16T02:00:47,354 20831 | exc_info->exc_type = *type; 2023-09-16T02:00:47,355 | ^~~~~~~~ 2023-09-16T02:00:47,356 pybedtools/cbedtools.cpp:20833:15: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_traceback’ 2023-09-16T02:00:47,357 20833 | exc_info->exc_traceback = *tb; 2023-09-16T02:00:47,358 | ^~~~~~~~~~~~~ 2023-09-16T02:00:47,386 pybedtools/cbedtools.cpp: In function ‘void __Pyx_AddTraceback(const char*, int, int, const char*)’: 2023-09-16T02:00:47,387 pybedtools/cbedtools.cpp:475:62: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2023-09-16T02:00:47,387 475 | #define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno) 2023-09-16T02:00:47,388 | ^~ 2023-09-16T02:00:47,389 pybedtools/cbedtools.cpp:21511:5: note: in expansion of macro ‘__Pyx_PyFrame_SetLineNumber’ 2023-09-16T02:00:47,389 21511 | __Pyx_PyFrame_SetLineNumber(py_frame, py_line); 2023-09-16T02:00:47,390 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-16T02:00:47,391 In file included from /usr/include/python3.11/Python.h:42: 2023-09-16T02:00:47,391 /usr/include/python3.11/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2023-09-16T02:00:47,392 22 | typedef struct _frame PyFrameObject; 2023-09-16T02:00:47,393 | ^~~~~~ 2023-09-16T02:00:48,337 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2023-09-16T02:00:48,454 ERROR: [present-rich] python setup.py bdist_wheel exited with 1 2023-09-16T02:00:48,468 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2023-09-16T02:00:48,468 exec(compile('"'"''"'"''"'"' 2023-09-16T02:00:48,468 # This is -- a caller that pip uses to run setup.py 2023-09-16T02:00:48,468 # 2023-09-16T02:00:48,468 # - It imports setuptools before invoking setup.py, to enable projects that directly 2023-09-16T02:00:48,468 # import from `distutils.core` to work with newer packaging standards. 2023-09-16T02:00:48,468 # - It provides a clear error message when setuptools is not installed. 2023-09-16T02:00:48,468 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2023-09-16T02:00:48,468 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2023-09-16T02:00:48,468 # manifest_maker: standard file '"'"'-c'"'"' not found". 2023-09-16T02:00:48,468 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2023-09-16T02:00:48,468 import os, sys, tokenize 2023-09-16T02:00:48,468 2023-09-16T02:00:48,468 try: 2023-09-16T02:00:48,468 import setuptools 2023-09-16T02:00:48,468 except ImportError as error: 2023-09-16T02:00:48,468 print( 2023-09-16T02:00:48,468 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2023-09-16T02:00:48,468 "the build environment.", 2023-09-16T02:00:48,468 file=sys.stderr, 2023-09-16T02:00:48,468 ) 2023-09-16T02:00:48,468 sys.exit(1) 2023-09-16T02:00:48,468 2023-09-16T02:00:48,468 __file__ = %r 2023-09-16T02:00:48,468 sys.argv[0] = __file__ 2023-09-16T02:00:48,468 2023-09-16T02:00:48,468 if os.path.exists(__file__): 2023-09-16T02:00:48,468 filename = __file__ 2023-09-16T02:00:48,468 with tokenize.open(__file__) as f: 2023-09-16T02:00:48,468 setup_py_code = f.read() 2023-09-16T02:00:48,468 else: 2023-09-16T02:00:48,468 filename = "" 2023-09-16T02:00:48,468 setup_py_code = "from setuptools import setup; setup()" 2023-09-16T02:00:48,468 2023-09-16T02:00:48,468 exec(compile(setup_py_code, filename, "exec")) 2023-09-16T02:00:48,468 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-kw_gg2ub/pybedtools_96045f1d4476408083eb6ca92a34358e/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-7m5lick2[/] 2023-09-16T02:00:48,469 [bold magenta]cwd[/]: /tmp/pip-wheel-kw_gg2ub/pybedtools_96045f1d4476408083eb6ca92a34358e/ 2023-09-16T02:00:48,470 Building wheel for pybedtools (setup.py): finished with status 'error' 2023-09-16T02:00:48,471 ERROR: Failed building wheel for pybedtools 2023-09-16T02:00:48,473 Running setup.py clean for pybedtools 2023-09-16T02:00:48,474 Running command python setup.py clean 2023-09-16T02:00:49,119 /tmp/pip-wheel-kw_gg2ub/pybedtools_96045f1d4476408083eb6ca92a34358e/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 2023-09-16T02:00:49,119 import pkg_resources 2023-09-16T02:00:49,518 usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...] 2023-09-16T02:00:49,519 or: setup.py --help [cmd1 cmd2 ...] 2023-09-16T02:00:49,520 or: setup.py --help-commands 2023-09-16T02:00:49,521 or: setup.py cmd --help 2023-09-16T02:00:49,523 error: option --all not recognized 2023-09-16T02:00:49,631 ERROR: [present-rich] python setup.py clean exited with 1 2023-09-16T02:00:49,636 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2023-09-16T02:00:49,636 exec(compile('"'"''"'"''"'"' 2023-09-16T02:00:49,636 # This is -- a caller that pip uses to run setup.py 2023-09-16T02:00:49,636 # 2023-09-16T02:00:49,636 # - It imports setuptools before invoking setup.py, to enable projects that directly 2023-09-16T02:00:49,636 # import from `distutils.core` to work with newer packaging standards. 2023-09-16T02:00:49,636 # - It provides a clear error message when setuptools is not installed. 2023-09-16T02:00:49,636 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2023-09-16T02:00:49,636 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2023-09-16T02:00:49,636 # manifest_maker: standard file '"'"'-c'"'"' not found". 2023-09-16T02:00:49,636 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2023-09-16T02:00:49,636 import os, sys, tokenize 2023-09-16T02:00:49,636 2023-09-16T02:00:49,636 try: 2023-09-16T02:00:49,636 import setuptools 2023-09-16T02:00:49,636 except ImportError as error: 2023-09-16T02:00:49,636 print( 2023-09-16T02:00:49,636 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2023-09-16T02:00:49,636 "the build environment.", 2023-09-16T02:00:49,636 file=sys.stderr, 2023-09-16T02:00:49,636 ) 2023-09-16T02:00:49,636 sys.exit(1) 2023-09-16T02:00:49,636 2023-09-16T02:00:49,636 __file__ = %r 2023-09-16T02:00:49,636 sys.argv[0] = __file__ 2023-09-16T02:00:49,636 2023-09-16T02:00:49,636 if os.path.exists(__file__): 2023-09-16T02:00:49,636 filename = __file__ 2023-09-16T02:00:49,636 with tokenize.open(__file__) as f: 2023-09-16T02:00:49,636 setup_py_code = f.read() 2023-09-16T02:00:49,636 else: 2023-09-16T02:00:49,636 filename = "" 2023-09-16T02:00:49,636 setup_py_code = "from setuptools import setup; setup()" 2023-09-16T02:00:49,636 2023-09-16T02:00:49,636 exec(compile(setup_py_code, filename, "exec")) 2023-09-16T02:00:49,636 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-kw_gg2ub/pybedtools_96045f1d4476408083eb6ca92a34358e/setup.py'"'"',), "", "exec"))' clean --all[/] 2023-09-16T02:00:49,637 [bold magenta]cwd[/]: /tmp/pip-wheel-kw_gg2ub/pybedtools_96045f1d4476408083eb6ca92a34358e 2023-09-16T02:00:49,637 ERROR: Failed cleaning build dir for pybedtools 2023-09-16T02:00:49,640 Failed to build pybedtools 2023-09-16T02:00:49,641 ERROR: Failed to build one or more wheels 2023-09-16T02:00:49,642 Exception information: 2023-09-16T02:00:49,642 Traceback (most recent call last): 2023-09-16T02:00:49,642 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2023-09-16T02:00:49,642 status = run_func(*args) 2023-09-16T02:00:49,642 ^^^^^^^^^^^^^^^ 2023-09-16T02:00:49,642 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper 2023-09-16T02:00:49,642 return func(self, options, args) 2023-09-16T02:00:49,642 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-16T02:00:49,642 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run 2023-09-16T02:00:49,642 raise CommandError("Failed to build one or more wheels") 2023-09-16T02:00:49,642 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2023-09-16T02:00:49,646 Removed build tracker: '/tmp/pip-build-tracker-hka_0w5o'