2023-09-08T18:58:42,630 Created temporary directory: /tmp/pip-build-tracker-8o41593l 2023-09-08T18:58:42,631 Initialized build tracking at /tmp/pip-build-tracker-8o41593l 2023-09-08T18:58:42,631 Created build tracker: /tmp/pip-build-tracker-8o41593l 2023-09-08T18:58:42,632 Entered build tracker: /tmp/pip-build-tracker-8o41593l 2023-09-08T18:58:42,632 Created temporary directory: /tmp/pip-wheel-1pxmev40 2023-09-08T18:58:42,636 Created temporary directory: /tmp/pip-ephem-wheel-cache-69aua39y 2023-09-08T18:58:42,657 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-08T18:58:42,661 2 location(s) to search for versions of pybedtools: 2023-09-08T18:58:42,661 * https://pypi.org/simple/pybedtools/ 2023-09-08T18:58:42,661 * https://www.piwheels.org/simple/pybedtools/ 2023-09-08T18:58:42,661 Fetching project page and analyzing links: https://pypi.org/simple/pybedtools/ 2023-09-08T18:58:42,662 Getting page https://pypi.org/simple/pybedtools/ 2023-09-08T18:58:42,664 Found index url https://pypi.org/simple/ 2023-09-08T18:58:42,805 Fetched page https://pypi.org/simple/pybedtools/ as application/vnd.pypi.simple.v1+json 2023-09-08T18:58:42,811 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 2023-09-08T18:58:42,812 Found link https://files.pythonhosted.org/packages/44/19/a9bebb9eccd8d64d58202d5b3a151de81ffc7703a47503161b7615554703/pybedtools-0.5dev.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.5dev 2023-09-08T18:58:42,812 Found link https://files.pythonhosted.org/packages/e4/2f/e842c6b1165d706ebc62c931c11d4dfffe60e6b045ecf80eef7ea78d7afc/pybedtools-0.5rc1.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.5rc1 2023-09-08T18:58:42,813 Found link https://files.pythonhosted.org/packages/85/17/c89028c00537638629ca21be7f1b84e963fc8b63c1e9a5fda9884f86fb90/pybedtools-0.5.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.5 2023-09-08T18:58:42,814 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 2023-09-08T18:58:42,814 Found link https://files.pythonhosted.org/packages/3c/e7/365015ec8104195329635cb75ef745bff45d905271cd165f5048efaf48e3/pybedtools-0.6rc1.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6rc1 2023-09-08T18:58:42,815 Found link https://files.pythonhosted.org/packages/04/ce/0e1480725fe80eb9a401f59e1bcc28fce721f6c2c5d7be233894d0154551/pybedtools-0.6.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6 2023-09-08T18:58:42,815 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 2023-09-08T18:58:42,816 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 2023-09-08T18:58:42,817 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 2023-09-08T18:58:42,817 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 2023-09-08T18:58:42,818 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 2023-09-08T18:58:42,819 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 2023-09-08T18:58:42,819 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 2023-09-08T18:58:42,820 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 2023-09-08T18:58:42,821 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 2023-09-08T18:58:42,821 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 2023-09-08T18:58:42,822 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 2023-09-08T18:58:42,822 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 2023-09-08T18:58:42,823 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 2023-09-08T18:58:42,824 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 2023-09-08T18:58:42,824 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 2023-09-08T18:58:42,825 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 2023-09-08T18:58:42,825 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 2023-09-08T18:58:42,826 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 2023-09-08T18:58:42,827 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 2023-09-08T18:58:42,828 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 2023-09-08T18:58:42,828 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 2023-09-08T18:58:42,829 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 2023-09-08T18:58:42,830 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 2023-09-08T18:58:42,830 Fetching project page and analyzing links: https://www.piwheels.org/simple/pybedtools/ 2023-09-08T18:58:42,831 Getting page https://www.piwheels.org/simple/pybedtools/ 2023-09-08T18:58:42,832 Found index url https://www.piwheels.org/simple/ 2023-09-08T18:58:43,126 Fetched page https://www.piwheels.org/simple/pybedtools/ as text/html 2023-09-08T18:58:43,144 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/) 2023-09-08T18:58:43,145 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/) 2023-09-08T18:58:43,145 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/) 2023-09-08T18:58:43,146 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/) 2023-09-08T18:58:43,182 Skipping link: not a file: https://www.piwheels.org/simple/pybedtools/ 2023-09-08T18:58:43,183 Skipping link: not a file: https://pypi.org/simple/pybedtools/ 2023-09-08T18:58:43,204 Given no hashes to check 1 links for project 'pybedtools': discarding no candidates 2023-09-08T18:58:43,222 Collecting pybedtools==0.7.1 2023-09-08T18:58:43,225 Created temporary directory: /tmp/pip-unpack-a4c349rr 2023-09-08T18:58:44,022 Downloading pybedtools-0.7.1.tar.gz (12.6 MB) 2023-09-08T18:58:47,712 Added pybedtools==0.7.1 from https://files.pythonhosted.org/packages/b5/1c/1b7e66668105e5b84cc6224a54ce552c6a6113e9b34c980fc436140e6be1/pybedtools-0.7.1.tar.gz to build tracker '/tmp/pip-build-tracker-8o41593l' 2023-09-08T18:58:47,714 Running setup.py (path:/tmp/pip-wheel-1pxmev40/pybedtools_0930855ae9ad42f7a8b8b6f37d00a391/setup.py) egg_info for package pybedtools 2023-09-08T18:58:47,715 Created temporary directory: /tmp/pip-pip-egg-info-w3l0wise 2023-09-08T18:58:47,715 Preparing metadata (setup.py): started 2023-09-08T18:58:47,717 Running command python setup.py egg_info 2023-09-08T18:58:48,183 /tmp/pip-wheel-1pxmev40/pybedtools_0930855ae9ad42f7a8b8b6f37d00a391/setup.py:25: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 2023-09-08T18:58:48,183 import pkg_resources 2023-09-08T18:58:48,814 running egg_info 2023-09-08T18:58:48,815 creating /tmp/pip-pip-egg-info-w3l0wise/pybedtools.egg-info 2023-09-08T18:58:48,842 writing /tmp/pip-pip-egg-info-w3l0wise/pybedtools.egg-info/PKG-INFO 2023-09-08T18:58:48,845 writing dependency_links to /tmp/pip-pip-egg-info-w3l0wise/pybedtools.egg-info/dependency_links.txt 2023-09-08T18:58:48,847 writing requirements to /tmp/pip-pip-egg-info-w3l0wise/pybedtools.egg-info/requires.txt 2023-09-08T18:58:48,848 writing top-level names to /tmp/pip-pip-egg-info-w3l0wise/pybedtools.egg-info/top_level.txt 2023-09-08T18:58:48,850 writing manifest file '/tmp/pip-pip-egg-info-w3l0wise/pybedtools.egg-info/SOURCES.txt' 2023-09-08T18:58:48,944 reading manifest file '/tmp/pip-pip-egg-info-w3l0wise/pybedtools.egg-info/SOURCES.txt' 2023-09-08T18:58:48,946 reading manifest template 'MANIFEST.in' 2023-09-08T18:58:49,193 warning: no previously-included files matching '__pycache__' found under directory '*' 2023-09-08T18:58:49,194 warning: no previously-included files matching '*.py[co]' found under directory '*' 2023-09-08T18:58:49,195 adding license file 'LICENSE.txt' 2023-09-08T18:58:49,206 writing manifest file '/tmp/pip-pip-egg-info-w3l0wise/pybedtools.egg-info/SOURCES.txt' 2023-09-08T18:58:49,321 Preparing metadata (setup.py): finished with status 'done' 2023-09-08T18:58:49,326 Source in /tmp/pip-wheel-1pxmev40/pybedtools_0930855ae9ad42f7a8b8b6f37d00a391 has version 0.7.1, which satisfies requirement pybedtools==0.7.1 from https://files.pythonhosted.org/packages/b5/1c/1b7e66668105e5b84cc6224a54ce552c6a6113e9b34c980fc436140e6be1/pybedtools-0.7.1.tar.gz 2023-09-08T18:58:49,327 Removed pybedtools==0.7.1 from https://files.pythonhosted.org/packages/b5/1c/1b7e66668105e5b84cc6224a54ce552c6a6113e9b34c980fc436140e6be1/pybedtools-0.7.1.tar.gz from build tracker '/tmp/pip-build-tracker-8o41593l' 2023-09-08T18:58:49,331 Created temporary directory: /tmp/pip-unpack-tzt8n2ez 2023-09-08T18:58:49,332 Created temporary directory: /tmp/pip-unpack-5okj1nz7 2023-09-08T18:58:49,337 Building wheels for collected packages: pybedtools 2023-09-08T18:58:49,341 Created temporary directory: /tmp/pip-wheel-dm7rg7z_ 2023-09-08T18:58:49,342 Building wheel for pybedtools (setup.py): started 2023-09-08T18:58:49,343 Destination directory: /tmp/pip-wheel-dm7rg7z_ 2023-09-08T18:58:49,343 Running command python setup.py bdist_wheel 2023-09-08T18:58:49,812 /tmp/pip-wheel-1pxmev40/pybedtools_0930855ae9ad42f7a8b8b6f37d00a391/setup.py:25: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 2023-09-08T18:58:49,812 import pkg_resources 2023-09-08T18:58:50,426 running bdist_wheel 2023-09-08T18:58:50,450 The [wheel] section is deprecated. Use [bdist_wheel] instead. 2023-09-08T18:58:50,474 running build 2023-09-08T18:58:50,475 running build_py 2023-09-08T18:58:50,501 creating build 2023-09-08T18:58:50,502 creating build/lib.linux-armv7l-cpython-311 2023-09-08T18:58:50,503 creating build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T18:58:50,504 copying pybedtools/filenames.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T18:58:50,506 copying pybedtools/__init__.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T18:58:50,508 copying pybedtools/helpers.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T18:58:50,510 copying pybedtools/stats.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T18:58:50,513 copying pybedtools/version.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T18:58:50,514 copying pybedtools/genome_registry.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T18:58:50,517 copying pybedtools/parallel.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T18:58:50,519 copying pybedtools/__main__.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T18:58:50,521 copying pybedtools/settings.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T18:58:50,523 copying pybedtools/logger.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T18:58:50,524 copying pybedtools/bedtool.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T18:58:50,530 creating build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-08T18:58:50,530 copying pybedtools/test/__init__.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-08T18:58:50,532 copying pybedtools/test/test_len_leak.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-08T18:58:50,534 copying pybedtools/test/regression_tests.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-08T18:58:50,536 copying pybedtools/test/test1.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-08T18:58:50,539 copying pybedtools/test/tfuncs.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-08T18:58:50,541 copying pybedtools/test/test_helpers.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-08T18:58:50,544 copying pybedtools/test/test_gzip_support.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-08T18:58:50,546 copying pybedtools/test/test_contrib.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-08T18:58:50,549 copying pybedtools/test/test_iter.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-08T18:58:50,552 copying pybedtools/test/test_scripts.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-08T18:58:50,556 copying pybedtools/test/test_cbedtools.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-08T18:58:50,561 creating build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2023-09-08T18:58:50,562 copying pybedtools/contrib/__init__.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2023-09-08T18:58:50,564 copying pybedtools/contrib/bigbed.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2023-09-08T18:58:50,566 copying pybedtools/contrib/classifier.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2023-09-08T18:58:50,569 copying pybedtools/contrib/plotting.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2023-09-08T18:58:50,789 copying pybedtools/contrib/intersection_matrix.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2023-09-08T18:58:50,791 copying pybedtools/contrib/bigwig.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2023-09-08T18:58:50,793 copying pybedtools/contrib/venn_maker.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2023-09-08T18:58:50,796 creating build/lib.linux-armv7l-cpython-311/pybedtools/scripts 2023-09-08T18:58:50,796 copying pybedtools/scripts/venn_gchart.py -> build/lib.linux-armv7l-cpython-311/pybedtools/scripts 2023-09-08T18:58:50,799 copying pybedtools/scripts/intron_exon_reads.py -> build/lib.linux-armv7l-cpython-311/pybedtools/scripts 2023-09-08T18:58:50,800 copying pybedtools/scripts/annotate.py -> build/lib.linux-armv7l-cpython-311/pybedtools/scripts 2023-09-08T18:58:50,803 copying pybedtools/scripts/__init__.py -> build/lib.linux-armv7l-cpython-311/pybedtools/scripts 2023-09-08T18:58:50,804 copying pybedtools/scripts/peak_pie.py -> build/lib.linux-armv7l-cpython-311/pybedtools/scripts 2023-09-08T18:58:50,806 copying pybedtools/scripts/py_ms_example.py -> build/lib.linux-armv7l-cpython-311/pybedtools/scripts 2023-09-08T18:58:50,808 copying pybedtools/scripts/intersection_matrix.py -> build/lib.linux-armv7l-cpython-311/pybedtools/scripts 2023-09-08T18:58:50,810 copying pybedtools/scripts/venn_mpl.py -> build/lib.linux-armv7l-cpython-311/pybedtools/scripts 2023-09-08T18:58:50,813 creating build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:50,814 copying pybedtools/test/data/__init__.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:50,824 copying pybedtools/test/data/gdc.1.100.bam.bai -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:50,826 copying pybedtools/test/data/venn.c.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:50,828 copying pybedtools/test/data/bedpe.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:50,830 copying pybedtools/test/data/gdc.sorted.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:50,832 copying pybedtools/test/data/mm9.bed12 -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:50,834 copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:50,836 copying pybedtools/test/data/expand_test.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:50,838 copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:50,843 copying pybedtools/test/data/x.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:50,889 copying pybedtools/test/data/multibamcov_test.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:50,890 copying pybedtools/test/data/x.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:50,922 copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:50,926 copying pybedtools/test/data/snps.bed.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,061 copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,065 copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,069 copying pybedtools/test/data/gdc.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,071 copying pybedtools/test/data/democonfig.yaml -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,073 copying pybedtools/test/data/gdc.sorted.bam.bai -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,075 copying pybedtools/test/data/gdc.gff.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,077 copying pybedtools/test/data/hg38-base.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,079 copying pybedtools/test/data/small.fastq -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,081 copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,090 copying pybedtools/test/data/gdc.1.100.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,092 copying pybedtools/test/data/c.gff -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,094 copying pybedtools/test/data/gdc.gff -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,096 copying pybedtools/test/data/gdc.50.200.bam.bai -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,098 copying pybedtools/test/data/venn.b.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,101 copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,104 copying pybedtools/test/data/tag_test1.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,106 copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,110 copying pybedtools/test/data/a.igv_script -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,112 copying pybedtools/test/data/tag_test2.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,114 copying pybedtools/test/data/hg19.gff -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,120 copying pybedtools/test/data/test.fa -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,122 copying pybedtools/test/data/y.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,124 copying pybedtools/test/data/gdc.50.200.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,126 copying pybedtools/test/data/d.gff -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,127 copying pybedtools/test/data/b.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,130 copying pybedtools/test/data/v.vcf -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,132 copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,135 copying pybedtools/test/data/reads.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,137 copying pybedtools/test/data/gdc.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,139 copying pybedtools/test/data/a.links.html -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,141 copying pybedtools/test/data/test.fa.fai -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,143 copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,148 copying pybedtools/test/data/small.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,150 copying pybedtools/test/data/exons.gff -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,152 copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,157 copying pybedtools/test/data/bedpe2.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,159 copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,172 copying pybedtools/test/data/a.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,174 copying pybedtools/test/data/m1.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,176 copying pybedtools/test/data/hg38-problem.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T18:58:51,178 copying pybedtools/cbedtools.pyx -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T18:58:51,181 copying pybedtools/featurefuncs.pyx -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T18:58:51,183 copying pybedtools/_Window.pyx -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T18:58:51,186 copying pybedtools/cbedtools.pxd -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T18:58:51,188 copying pybedtools/featurefuncs.cxx -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T18:58:51,198 copying pybedtools/cbedtools.cxx -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T18:58:51,212 copying pybedtools/_Window.c -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T18:58:51,221 running build_ext 2023-09-08T18:58:51,230 building 'pybedtools.cbedtools' extension 2023-09-08T18:58:51,231 creating build/temp.linux-armv7l-cpython-311 2023-09-08T18:58:51,231 creating build/temp.linux-armv7l-cpython-311/pybedtools 2023-09-08T18:58:51,233 creating build/temp.linux-armv7l-cpython-311/src 2023-09-08T18:58:51,234 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/ -I/usr/include/python3.11 -c pybedtools/cbedtools.cxx -o build/temp.linux-armv7l-cpython-311/pybedtools/cbedtools.o 2023-09-08T18:58:53,712 In file included from pybedtools/cbedtools.cxx:256: 2023-09-08T18:58:53,713 src/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: 2023-09-08T18:58:53,714 src/bedFile.h:92:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 2023-09-08T18:58:53,715 92 | for (register short i = 0; i < _binLevels; ++i) { 2023-09-08T18:58:53,715 | ^ 2023-09-08T18:58:53,786 In file included from /usr/include/python3.11/Python.h:44, 2023-09-08T18:58:53,787 from pybedtools/cbedtools.cxx:16: 2023-09-08T18:58:53,787 pybedtools/cbedtools.cxx: In function ‘int __Pyx_ListComp_Append(PyObject*, PyObject*)’: 2023-09-08T18:58:53,788 /usr/include/python3.11/object.h:145:30: error: lvalue required as left operand of assignment 2023-09-08T18:58:53,789 145 | # define Py_SIZE(ob) Py_SIZE(_PyObject_CAST(ob)) 2023-09-08T18:58:53,789 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ 2023-09-08T18:58:53,790 pybedtools/cbedtools.cxx:669:9: note: in expansion of macro ‘Py_SIZE’ 2023-09-08T18:58:53,790 669 | Py_SIZE(list) = len+1; 2023-09-08T18:58:53,791 | ^~~~~~~ 2023-09-08T18:58:53,791 pybedtools/cbedtools.cxx: In function ‘int __Pyx_PyList_Append(PyObject*, PyObject*)’: 2023-09-08T18:58:53,792 /usr/include/python3.11/object.h:145:30: error: lvalue required as left operand of assignment 2023-09-08T18:58:53,793 145 | # define Py_SIZE(ob) Py_SIZE(_PyObject_CAST(ob)) 2023-09-08T18:58:53,793 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ 2023-09-08T18:58:53,794 pybedtools/cbedtools.cxx:700:9: note: in expansion of macro ‘Py_SIZE’ 2023-09-08T18:58:53,794 700 | Py_SIZE(list) = len+1; 2023-09-08T18:58:53,795 | ^~~~~~~ 2023-09-08T18:58:54,403 pybedtools/cbedtools.cxx: In function ‘void __pyx_tp_dealloc_10pybedtools_9cbedtools_Interval(PyObject*)’: 2023-09-08T18:58:54,404 /usr/include/python3.11/object.h:127:34: error: lvalue required as increment operand 2023-09-08T18:58:54,405 127 | # define Py_REFCNT(ob) Py_REFCNT(_PyObject_CAST(ob)) 2023-09-08T18:58:54,405 | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,406 pybedtools/cbedtools.cxx:12953:7: note: in expansion of macro ‘Py_REFCNT’ 2023-09-08T18:58:54,406 12953 | ++Py_REFCNT(o); 2023-09-08T18:58:54,407 | ^~~~~~~~~ 2023-09-08T18:58:54,408 /usr/include/python3.11/object.h:127:34: error: lvalue required as decrement operand 2023-09-08T18:58:54,409 127 | # define Py_REFCNT(ob) Py_REFCNT(_PyObject_CAST(ob)) 2023-09-08T18:58:54,409 | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,410 pybedtools/cbedtools.cxx:12955:7: note: in expansion of macro ‘Py_REFCNT’ 2023-09-08T18:58:54,411 12955 | --Py_REFCNT(o); 2023-09-08T18:58:54,412 | ^~~~~~~~~ 2023-09-08T18:58:54,426 pybedtools/cbedtools.cxx: In function ‘void __pyx_tp_dealloc_10pybedtools_9cbedtools_IntervalFile(PyObject*)’: 2023-09-08T18:58:54,427 /usr/include/python3.11/object.h:127:34: error: lvalue required as increment operand 2023-09-08T18:58:54,427 127 | # define Py_REFCNT(ob) Py_REFCNT(_PyObject_CAST(ob)) 2023-09-08T18:58:54,428 | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,429 pybedtools/cbedtools.cxx:13426:7: note: in expansion of macro ‘Py_REFCNT’ 2023-09-08T18:58:54,429 13426 | ++Py_REFCNT(o); 2023-09-08T18:58:54,430 | ^~~~~~~~~ 2023-09-08T18:58:54,431 /usr/include/python3.11/object.h:127:34: error: lvalue required as decrement operand 2023-09-08T18:58:54,431 127 | # define Py_REFCNT(ob) Py_REFCNT(_PyObject_CAST(ob)) 2023-09-08T18:58:54,432 | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,433 pybedtools/cbedtools.cxx:13428:7: note: in expansion of macro ‘Py_REFCNT’ 2023-09-08T18:58:54,434 13428 | --Py_REFCNT(o); 2023-09-08T18:58:54,434 | ^~~~~~~~~ 2023-09-08T18:58:54,453 pybedtools/cbedtools.cxx: In function ‘int __Pyx_InitCachedConstants()’: 2023-09-08T18:58:54,454 pybedtools/cbedtools.cxx:13782:237: error: invalid conversion from ‘int’ to ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2023-09-08T18:58:54,454 13782 | __pyx_codeobj__15 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__14, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_cmp, 280, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 280; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2023-09-08T18:58:54,455 | ^~~ 2023-09-08T18:58:54,455 | | 2023-09-08T18:58:54,456 | int 2023-09-08T18:58:54,457 pybedtools/cbedtools.cxx:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2023-09-08T18:58:54,457 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2023-09-08T18:58:54,458 | ^~~~~ 2023-09-08T18:58:54,458 pybedtools/cbedtools.cxx:13782:242: error: invalid conversion from ‘PyObject*’ {aka ‘_object*’} to ‘int’ [-fpermissive] 2023-09-08T18:58:54,459 13782 | __pyx_codeobj__15 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__14, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_cmp, 280, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 280; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2023-09-08T18:58:54,460 | ^~~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,461 | | 2023-09-08T18:58:54,461 | PyObject* {aka _object*} 2023-09-08T18:58:54,462 pybedtools/cbedtools.cxx:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2023-09-08T18:58:54,462 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2023-09-08T18:58:54,463 | ^~~~ 2023-09-08T18:58:54,464 pybedtools/cbedtools.cxx:70:21: error: too few arguments to function ‘PyCodeObject* PyCode_New(int, int, int, int, int, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*)’ 2023-09-08T18:58:54,465 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2023-09-08T18:58:54,466 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,466 pybedtools/cbedtools.cxx:13782:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2023-09-08T18:58:54,467 13782 | __pyx_codeobj__15 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__14, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_cmp, 280, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 280; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2023-09-08T18:58:54,467 | ^~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,468 In file included from /usr/include/python3.11/Python.h:71: 2023-09-08T18:58:54,468 /usr/include/python3.11/cpython/code.h:148:28: note: declared here 2023-09-08T18:58:54,469 148 | PyAPI_FUNC(PyCodeObject *) PyCode_New( 2023-09-08T18:58:54,469 | ^~~~~~~~~~ 2023-09-08T18:58:54,479 pybedtools/cbedtools.cxx:14183:238: error: invalid conversion from ‘int’ to ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2023-09-08T18:58:54,479 14183 | __pyx_codeobj__70 = (PyObject*)__Pyx_PyCode_New(2, 0, 9, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__69, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_init, 145, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__70)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2023-09-08T18:58:54,480 | ^~~ 2023-09-08T18:58:54,480 | | 2023-09-08T18:58:54,481 | int 2023-09-08T18:58:54,481 pybedtools/cbedtools.cxx:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2023-09-08T18:58:54,482 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2023-09-08T18:58:54,482 | ^~~~~ 2023-09-08T18:58:54,483 pybedtools/cbedtools.cxx:14183:243: error: invalid conversion from ‘PyObject*’ {aka ‘_object*’} to ‘int’ [-fpermissive] 2023-09-08T18:58:54,484 14183 | __pyx_codeobj__70 = (PyObject*)__Pyx_PyCode_New(2, 0, 9, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__69, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_init, 145, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__70)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2023-09-08T18:58:54,484 | ^~~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,485 | | 2023-09-08T18:58:54,485 | PyObject* {aka _object*} 2023-09-08T18:58:54,486 pybedtools/cbedtools.cxx:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2023-09-08T18:58:54,487 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2023-09-08T18:58:54,487 | ^~~~ 2023-09-08T18:58:54,488 pybedtools/cbedtools.cxx:70:21: error: too few arguments to function ‘PyCodeObject* PyCode_New(int, int, int, int, int, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*)’ 2023-09-08T18:58:54,488 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2023-09-08T18:58:54,489 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,489 pybedtools/cbedtools.cxx:14183:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2023-09-08T18:58:54,490 14183 | __pyx_codeobj__70 = (PyObject*)__Pyx_PyCode_New(2, 0, 9, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__69, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_init, 145, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__70)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2023-09-08T18:58:54,490 | ^~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,491 /usr/include/python3.11/cpython/code.h:148:28: note: declared here 2023-09-08T18:58:54,491 148 | PyAPI_FUNC(PyCodeObject *) PyCode_New( 2023-09-08T18:58:54,492 | ^~~~~~~~~~ 2023-09-08T18:58:54,492 pybedtools/cbedtools.cxx:14198:237: error: invalid conversion from ‘int’ to ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2023-09-08T18:58:54,493 14198 | __pyx_codeobj__73 = (PyObject*)__Pyx_PyCode_New(1, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__72, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_str, 181, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2023-09-08T18:58:54,494 | ^~~ 2023-09-08T18:58:54,494 | | 2023-09-08T18:58:54,495 | int 2023-09-08T18:58:54,495 pybedtools/cbedtools.cxx:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2023-09-08T18:58:54,496 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2023-09-08T18:58:54,497 | ^~~~~ 2023-09-08T18:58:54,497 pybedtools/cbedtools.cxx:14198:242: error: invalid conversion from ‘PyObject*’ {aka ‘_object*’} to ‘int’ [-fpermissive] 2023-09-08T18:58:54,498 14198 | __pyx_codeobj__73 = (PyObject*)__Pyx_PyCode_New(1, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__72, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_str, 181, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2023-09-08T18:58:54,499 | ^~~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,500 | | 2023-09-08T18:58:54,500 | PyObject* {aka _object*} 2023-09-08T18:58:54,501 pybedtools/cbedtools.cxx:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2023-09-08T18:58:54,501 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2023-09-08T18:58:54,502 | ^~~~ 2023-09-08T18:58:54,502 pybedtools/cbedtools.cxx:70:21: error: too few arguments to function ‘PyCodeObject* PyCode_New(int, int, int, int, int, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*)’ 2023-09-08T18:58:54,503 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2023-09-08T18:58:54,503 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,504 pybedtools/cbedtools.cxx:14198:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2023-09-08T18:58:54,504 14198 | __pyx_codeobj__73 = (PyObject*)__Pyx_PyCode_New(1, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__72, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_str, 181, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2023-09-08T18:58:54,505 | ^~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,506 /usr/include/python3.11/cpython/code.h:148:28: note: declared here 2023-09-08T18:58:54,507 148 | PyAPI_FUNC(PyCodeObject *) PyCode_New( 2023-09-08T18:58:54,507 | ^~~~~~~~~~ 2023-09-08T18:58:54,508 pybedtools/cbedtools.cxx:14210:241: error: invalid conversion from ‘int’ to ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2023-09-08T18:58:54,509 14210 | __pyx_codeobj__75 = (PyObject*)__Pyx_PyCode_New(4, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__74, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_overlap, 708, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2023-09-08T18:58:54,509 | ^~~ 2023-09-08T18:58:54,510 | | 2023-09-08T18:58:54,511 | int 2023-09-08T18:58:54,511 pybedtools/cbedtools.cxx:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2023-09-08T18:58:54,512 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2023-09-08T18:58:54,513 | ^~~~~ 2023-09-08T18:58:54,514 pybedtools/cbedtools.cxx:14210:246: error: invalid conversion from ‘PyObject*’ {aka ‘_object*’} to ‘int’ [-fpermissive] 2023-09-08T18:58:54,514 14210 | __pyx_codeobj__75 = (PyObject*)__Pyx_PyCode_New(4, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__74, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_overlap, 708, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2023-09-08T18:58:54,515 | ^~~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,515 | | 2023-09-08T18:58:54,516 | PyObject* {aka _object*} 2023-09-08T18:58:54,516 pybedtools/cbedtools.cxx:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2023-09-08T18:58:54,517 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2023-09-08T18:58:54,517 | ^~~~ 2023-09-08T18:58:54,518 pybedtools/cbedtools.cxx:70:21: error: too few arguments to function ‘PyCodeObject* PyCode_New(int, int, int, int, int, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*)’ 2023-09-08T18:58:54,519 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2023-09-08T18:58:54,520 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,520 pybedtools/cbedtools.cxx:14210:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2023-09-08T18:58:54,521 14210 | __pyx_codeobj__75 = (PyObject*)__Pyx_PyCode_New(4, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__74, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_overlap, 708, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2023-09-08T18:58:54,522 | ^~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,522 /usr/include/python3.11/cpython/code.h:148:28: note: declared here 2023-09-08T18:58:54,523 148 | PyAPI_FUNC(PyCodeObject *) PyCode_New( 2023-09-08T18:58:54,523 | ^~~~~~~~~~ 2023-09-08T18:58:54,524 pybedtools/cbedtools.cxx: In function ‘PyObject* PyInit_cbedtools()’: 2023-09-08T18:58:54,525 pybedtools/cbedtools.cxx:14327:47: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2023-09-08T18:58:54,525 14327 | __pyx_type_10pybedtools_9cbedtools_Interval.tp_print = 0; 2023-09-08T18:58:54,526 | ^~~~~~~~ 2023-09-08T18:58:54,527 pybedtools/cbedtools.cxx:14342:55: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2023-09-08T18:58:54,528 14342 | __pyx_type_10pybedtools_9cbedtools_IntervalIterator.tp_print = 0; 2023-09-08T18:58:54,528 | ^~~~~~~~ 2023-09-08T18:58:54,529 pybedtools/cbedtools.cxx:14346:51: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2023-09-08T18:58:54,530 14346 | __pyx_type_10pybedtools_9cbedtools_IntervalFile.tp_print = 0; 2023-09-08T18:58:54,530 | ^~~~~~~~ 2023-09-08T18:58:54,580 pybedtools/cbedtools.cxx: In function ‘PyObject* __Pyx_decode_c_bytes(const char*, Py_ssize_t, Py_ssize_t, Py_ssize_t, const char*, const char*, PyObject* (*)(const char*, Py_ssize_t, const char*))’: 2023-09-08T18:58:54,581 pybedtools/cbedtools.cxx:15279:37: warning: ‘PyObject* PyUnicode_FromUnicode(const Py_UNICODE*, Py_ssize_t)’ is deprecated [-Wdeprecated-declarations] 2023-09-08T18:58:54,582 15279 | return PyUnicode_FromUnicode(NULL, 0); 2023-09-08T18:58:54,583 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2023-09-08T18:58:54,583 In file included from /usr/include/python3.11/unicodeobject.h:1042, 2023-09-08T18:58:54,584 from /usr/include/python3.11/Python.h:51: 2023-09-08T18:58:54,585 /usr/include/python3.11/cpython/unicodeobject.h:600:42: note: declared here 2023-09-08T18:58:54,586 600 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode( 2023-09-08T18:58:54,586 | ^~~~~~~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,587 pybedtools/cbedtools.cxx: In function ‘int __Pyx_ParseOptionalKeywords(PyObject*, PyObject***, PyObject*, PyObject**, Py_ssize_t, const char*)’: 2023-09-08T18:58:54,588 /usr/include/python3.11/cpython/unicodeobject.h:664:52: warning: ‘Py_ssize_t PyUnicode_GET_SIZE(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2023-09-08T18:58:54,588 664 | # define PyUnicode_GET_SIZE(op) PyUnicode_GET_SIZE(_PyObject_CAST(op)) 2023-09-08T18:58:54,589 | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,590 pybedtools/cbedtools.cxx:15349:22: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2023-09-08T18:58:54,590 15349 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2023-09-08T18:58:54,591 | ^~~~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,592 /usr/include/python3.11/cpython/unicodeobject.h:652:26: note: declared here 2023-09-08T18:58:54,593 652 | static inline Py_ssize_t PyUnicode_GET_SIZE(PyObject *op) 2023-09-08T18:58:54,593 | ^~~~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,594 /usr/include/python3.11/cpython/unicodeobject.h:664:52: warning: ‘Py_ssize_t PyUnicode_GET_SIZE(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2023-09-08T18:58:54,594 664 | # define PyUnicode_GET_SIZE(op) PyUnicode_GET_SIZE(_PyObject_CAST(op)) 2023-09-08T18:58:54,595 | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,596 pybedtools/cbedtools.cxx:15349:52: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2023-09-08T18:58:54,596 15349 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2023-09-08T18:58:54,597 | ^~~~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,598 /usr/include/python3.11/cpython/unicodeobject.h:652:26: note: declared here 2023-09-08T18:58:54,599 652 | static inline Py_ssize_t PyUnicode_GET_SIZE(PyObject *op) 2023-09-08T18:58:54,599 | ^~~~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,600 /usr/include/python3.11/cpython/unicodeobject.h:664:52: warning: ‘Py_ssize_t PyUnicode_GET_SIZE(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2023-09-08T18:58:54,601 664 | # define PyUnicode_GET_SIZE(op) PyUnicode_GET_SIZE(_PyObject_CAST(op)) 2023-09-08T18:58:54,602 | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,602 pybedtools/cbedtools.cxx:15365:26: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2023-09-08T18:58:54,603 15365 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2023-09-08T18:58:54,603 | ^~~~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,604 /usr/include/python3.11/cpython/unicodeobject.h:652:26: note: declared here 2023-09-08T18:58:54,605 652 | static inline Py_ssize_t PyUnicode_GET_SIZE(PyObject *op) 2023-09-08T18:58:54,605 | ^~~~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,606 /usr/include/python3.11/cpython/unicodeobject.h:664:52: warning: ‘Py_ssize_t PyUnicode_GET_SIZE(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2023-09-08T18:58:54,607 664 | # define PyUnicode_GET_SIZE(op) PyUnicode_GET_SIZE(_PyObject_CAST(op)) 2023-09-08T18:58:54,607 | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,608 pybedtools/cbedtools.cxx:15365:59: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2023-09-08T18:58:54,608 15365 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2023-09-08T18:58:54,609 | ^~~~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,610 /usr/include/python3.11/cpython/unicodeobject.h:652:26: note: declared here 2023-09-08T18:58:54,610 652 | static inline Py_ssize_t PyUnicode_GET_SIZE(PyObject *op) 2023-09-08T18:58:54,611 | ^~~~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,615 pybedtools/cbedtools.cxx: In function ‘void __Pyx_ExceptionSave(PyObject**, PyObject**, PyObject**)’: 2023-09-08T18:58:54,615 pybedtools/cbedtools.cxx:15695:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2023-09-08T18:58:54,616 15695 | *type = tstate->exc_type; 2023-09-08T18:58:54,616 | ^~~~~~~~ 2023-09-08T18:58:54,617 | curexc_type 2023-09-08T18:58:54,618 pybedtools/cbedtools.cxx:15696:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2023-09-08T18:58:54,618 15696 | *value = tstate->exc_value; 2023-09-08T18:58:54,619 | ^~~~~~~~~ 2023-09-08T18:58:54,620 | curexc_value 2023-09-08T18:58:54,621 pybedtools/cbedtools.cxx:15697:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2023-09-08T18:58:54,621 15697 | *tb = tstate->exc_traceback; 2023-09-08T18:58:54,622 | ^~~~~~~~~~~~~ 2023-09-08T18:58:54,623 | curexc_traceback 2023-09-08T18:58:54,623 pybedtools/cbedtools.cxx: In function ‘void __Pyx_ExceptionReset(PyObject*, PyObject*, PyObject*)’: 2023-09-08T18:58:54,624 pybedtools/cbedtools.cxx:15709:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2023-09-08T18:58:54,625 15709 | tmp_type = tstate->exc_type; 2023-09-08T18:58:54,625 | ^~~~~~~~ 2023-09-08T18:58:54,626 | curexc_type 2023-09-08T18:58:54,627 pybedtools/cbedtools.cxx:15710:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2023-09-08T18:58:54,627 15710 | tmp_value = tstate->exc_value; 2023-09-08T18:58:54,628 | ^~~~~~~~~ 2023-09-08T18:58:54,629 | curexc_value 2023-09-08T18:58:54,630 pybedtools/cbedtools.cxx:15711:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2023-09-08T18:58:54,630 15711 | tmp_tb = tstate->exc_traceback; 2023-09-08T18:58:54,631 | ^~~~~~~~~~~~~ 2023-09-08T18:58:54,632 | curexc_traceback 2023-09-08T18:58:54,632 pybedtools/cbedtools.cxx:15712:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2023-09-08T18:58:54,633 15712 | tstate->exc_type = type; 2023-09-08T18:58:54,633 | ^~~~~~~~ 2023-09-08T18:58:54,634 | curexc_type 2023-09-08T18:58:54,634 pybedtools/cbedtools.cxx:15713:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2023-09-08T18:58:54,635 15713 | tstate->exc_value = value; 2023-09-08T18:58:54,635 | ^~~~~~~~~ 2023-09-08T18:58:54,636 | curexc_value 2023-09-08T18:58:54,637 pybedtools/cbedtools.cxx:15714:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2023-09-08T18:58:54,637 15714 | tstate->exc_traceback = tb; 2023-09-08T18:58:54,638 | ^~~~~~~~~~~~~ 2023-09-08T18:58:54,638 | curexc_traceback 2023-09-08T18:58:54,655 pybedtools/cbedtools.cxx: In function ‘PyObject* __Pyx_CyFunction_Call(PyObject*, PyObject*, PyObject*)’: 2023-09-08T18:58:54,656 pybedtools/cbedtools.cxx:16220:32: warning: ‘PyObject* PyCFunction_Call(PyObject*, PyObject*, PyObject*)’ is deprecated [-Wdeprecated-declarations] 2023-09-08T18:58:54,656 16220 | return PyCFunction_Call(func, arg, kw); 2023-09-08T18:58:54,657 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2023-09-08T18:58:54,657 In file included from /usr/include/python3.11/Python.h:65: 2023-09-08T18:58:54,658 /usr/include/python3.11/methodobject.h:52:43: note: declared here 2023-09-08T18:58:54,658 52 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyCFunction_Call(PyObject *, PyObject *, PyObject *); 2023-09-08T18:58:54,659 | ^~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,660 pybedtools/cbedtools.cxx: In function ‘int __Pyx_CyFunction_init()’: 2023-09-08T18:58:54,661 pybedtools/cbedtools.cxx:16285:41: warning: ‘PyObject* PyCFunction_Call(PyObject*, PyObject*, PyObject*)’ is deprecated [-Wdeprecated-declarations] 2023-09-08T18:58:54,661 16285 | __pyx_CyFunctionType_type.tp_call = PyCFunction_Call; 2023-09-08T18:58:54,662 | ^~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,662 /usr/include/python3.11/methodobject.h:52:43: note: declared here 2023-09-08T18:58:54,663 52 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyCFunction_Call(PyObject *, PyObject *, PyObject *); 2023-09-08T18:58:54,664 | ^~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,671 pybedtools/cbedtools.cxx: In function ‘int __Pyx_GetException(PyObject**, PyObject**, PyObject**)’: 2023-09-08T18:58:54,671 pybedtools/cbedtools.cxx:16557:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2023-09-08T18:58:54,672 16557 | tmp_type = tstate->exc_type; 2023-09-08T18:58:54,673 | ^~~~~~~~ 2023-09-08T18:58:54,673 | curexc_type 2023-09-08T18:58:54,674 pybedtools/cbedtools.cxx:16558:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2023-09-08T18:58:54,675 16558 | tmp_value = tstate->exc_value; 2023-09-08T18:58:54,675 | ^~~~~~~~~ 2023-09-08T18:58:54,676 | curexc_value 2023-09-08T18:58:54,677 pybedtools/cbedtools.cxx:16559:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2023-09-08T18:58:54,677 16559 | tmp_tb = tstate->exc_traceback; 2023-09-08T18:58:54,678 | ^~~~~~~~~~~~~ 2023-09-08T18:58:54,679 | curexc_traceback 2023-09-08T18:58:54,679 pybedtools/cbedtools.cxx:16560:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2023-09-08T18:58:54,680 16560 | tstate->exc_type = local_type; 2023-09-08T18:58:54,680 | ^~~~~~~~ 2023-09-08T18:58:54,681 | curexc_type 2023-09-08T18:58:54,682 pybedtools/cbedtools.cxx:16561:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2023-09-08T18:58:54,682 16561 | tstate->exc_value = local_value; 2023-09-08T18:58:54,683 | ^~~~~~~~~ 2023-09-08T18:58:54,683 | curexc_value 2023-09-08T18:58:54,684 pybedtools/cbedtools.cxx:16562:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2023-09-08T18:58:54,684 16562 | tstate->exc_traceback = local_tb; 2023-09-08T18:58:54,685 | ^~~~~~~~~~~~~ 2023-09-08T18:58:54,685 | curexc_traceback 2023-09-08T18:58:54,700 pybedtools/cbedtools.cxx: In function ‘void __Pyx_ExceptionSwap(PyObject**, PyObject**, PyObject**)’: 2023-09-08T18:58:54,701 pybedtools/cbedtools.cxx:16886:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2023-09-08T18:58:54,702 16886 | tmp_type = tstate->exc_type; 2023-09-08T18:58:54,702 | ^~~~~~~~ 2023-09-08T18:58:54,703 | curexc_type 2023-09-08T18:58:54,703 pybedtools/cbedtools.cxx:16887:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2023-09-08T18:58:54,704 16887 | tmp_value = tstate->exc_value; 2023-09-08T18:58:54,705 | ^~~~~~~~~ 2023-09-08T18:58:54,705 | curexc_value 2023-09-08T18:58:54,706 pybedtools/cbedtools.cxx:16888:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2023-09-08T18:58:54,707 16888 | tmp_tb = tstate->exc_traceback; 2023-09-08T18:58:54,708 | ^~~~~~~~~~~~~ 2023-09-08T18:58:54,708 | curexc_traceback 2023-09-08T18:58:54,709 pybedtools/cbedtools.cxx:16889:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2023-09-08T18:58:54,710 16889 | tstate->exc_type = *type; 2023-09-08T18:58:54,711 | ^~~~~~~~ 2023-09-08T18:58:54,711 | curexc_type 2023-09-08T18:58:54,712 pybedtools/cbedtools.cxx:16890:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2023-09-08T18:58:54,713 16890 | tstate->exc_value = *value; 2023-09-08T18:58:54,713 | ^~~~~~~~~ 2023-09-08T18:58:54,714 | curexc_value 2023-09-08T18:58:54,714 pybedtools/cbedtools.cxx:16891:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2023-09-08T18:58:54,715 16891 | tstate->exc_traceback = *tb; 2023-09-08T18:58:54,716 | ^~~~~~~~~~~~~ 2023-09-08T18:58:54,716 | curexc_traceback 2023-09-08T18:58:54,726 pybedtools/cbedtools.cxx: In function ‘PyCodeObject* __Pyx_CreateCodeObjectForTraceback(const char*, int, int, const char*)’: 2023-09-08T18:58:54,726 pybedtools/cbedtools.cxx:17204:9: error: invalid conversion from ‘int’ to ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2023-09-08T18:58:54,727 17204 | py_line, 2023-09-08T18:58:54,728 | ^~~~~~~ 2023-09-08T18:58:54,728 | | 2023-09-08T18:58:54,729 | int 2023-09-08T18:58:54,729 pybedtools/cbedtools.cxx:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2023-09-08T18:58:54,729 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2023-09-08T18:58:54,730 | ^~~~~ 2023-09-08T18:58:54,730 pybedtools/cbedtools.cxx:17205:9: error: invalid conversion from ‘PyObject*’ {aka ‘_object*’} to ‘int’ [-fpermissive] 2023-09-08T18:58:54,731 17205 | __pyx_empty_bytes /*PyObject *lnotab*/ 2023-09-08T18:58:54,731 | ^~~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,731 | | 2023-09-08T18:58:54,732 | PyObject* {aka _object*} 2023-09-08T18:58:54,732 pybedtools/cbedtools.cxx:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2023-09-08T18:58:54,733 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2023-09-08T18:58:54,733 | ^~~~ 2023-09-08T18:58:54,734 pybedtools/cbedtools.cxx:70:21: error: too few arguments to function ‘PyCodeObject* PyCode_New(int, int, int, int, int, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*)’ 2023-09-08T18:58:54,735 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2023-09-08T18:58:54,735 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,736 pybedtools/cbedtools.cxx:17190:15: note: in expansion of macro ‘__Pyx_PyCode_New’ 2023-09-08T18:58:54,736 17190 | py_code = __Pyx_PyCode_New( 2023-09-08T18:58:54,737 | ^~~~~~~~~~~~~~~~ 2023-09-08T18:58:54,738 /usr/include/python3.11/cpython/code.h:148:28: note: declared here 2023-09-08T18:58:54,739 148 | PyAPI_FUNC(PyCodeObject *) PyCode_New( 2023-09-08T18:58:54,739 | ^~~~~~~~~~ 2023-09-08T18:58:54,740 pybedtools/cbedtools.cxx: In function ‘void __Pyx_AddTraceback(const char*, int, int, const char*)’: 2023-09-08T18:58:54,741 pybedtools/cbedtools.cxx:17233:13: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2023-09-08T18:58:54,742 17233 | py_frame->f_lineno = py_line; 2023-09-08T18:58:54,742 | ^~ 2023-09-08T18:58:54,743 In file included from /usr/include/python3.11/Python.h:42: 2023-09-08T18:58:54,744 /usr/include/python3.11/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2023-09-08T18:58:54,745 22 | typedef struct _frame PyFrameObject; 2023-09-08T18:58:54,745 | ^~~~~~ 2023-09-08T18:58:55,469 pybedtools/cbedtools.cxx: At global scope: 2023-09-08T18:58:55,470 pybedtools/cbedtools.cxx:7940:12: warning: ‘int __pyx_pw_10pybedtools_9cbedtools_8Interval_33__nonzero__(PyObject*)’ defined but not used [-Wunused-function] 2023-09-08T18:58:55,471 7940 | static int __pyx_pw_10pybedtools_9cbedtools_8Interval_33__nonzero__(PyObject *__pyx_v_self) { 2023-09-08T18:58:55,472 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T18:58:55,484 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2023-09-08T18:58:55,597 ERROR: [present-rich] python setup.py bdist_wheel exited with 1 2023-09-08T18:58:55,610 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2023-09-08T18:58:55,610 exec(compile('"'"''"'"''"'"' 2023-09-08T18:58:55,610 # This is -- a caller that pip uses to run setup.py 2023-09-08T18:58:55,610 # 2023-09-08T18:58:55,610 # - It imports setuptools before invoking setup.py, to enable projects that directly 2023-09-08T18:58:55,610 # import from `distutils.core` to work with newer packaging standards. 2023-09-08T18:58:55,610 # - It provides a clear error message when setuptools is not installed. 2023-09-08T18:58:55,610 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2023-09-08T18:58:55,610 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2023-09-08T18:58:55,610 # manifest_maker: standard file '"'"'-c'"'"' not found". 2023-09-08T18:58:55,610 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2023-09-08T18:58:55,610 import os, sys, tokenize 2023-09-08T18:58:55,610 2023-09-08T18:58:55,610 try: 2023-09-08T18:58:55,610 import setuptools 2023-09-08T18:58:55,610 except ImportError as error: 2023-09-08T18:58:55,610 print( 2023-09-08T18:58:55,610 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2023-09-08T18:58:55,610 "the build environment.", 2023-09-08T18:58:55,610 file=sys.stderr, 2023-09-08T18:58:55,610 ) 2023-09-08T18:58:55,610 sys.exit(1) 2023-09-08T18:58:55,610 2023-09-08T18:58:55,610 __file__ = %r 2023-09-08T18:58:55,610 sys.argv[0] = __file__ 2023-09-08T18:58:55,610 2023-09-08T18:58:55,610 if os.path.exists(__file__): 2023-09-08T18:58:55,610 filename = __file__ 2023-09-08T18:58:55,610 with tokenize.open(__file__) as f: 2023-09-08T18:58:55,610 setup_py_code = f.read() 2023-09-08T18:58:55,610 else: 2023-09-08T18:58:55,610 filename = "" 2023-09-08T18:58:55,610 setup_py_code = "from setuptools import setup; setup()" 2023-09-08T18:58:55,610 2023-09-08T18:58:55,610 exec(compile(setup_py_code, filename, "exec")) 2023-09-08T18:58:55,610 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-1pxmev40/pybedtools_0930855ae9ad42f7a8b8b6f37d00a391/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-dm7rg7z_[/] 2023-09-08T18:58:55,611 [bold magenta]cwd[/]: /tmp/pip-wheel-1pxmev40/pybedtools_0930855ae9ad42f7a8b8b6f37d00a391/ 2023-09-08T18:58:55,612 Building wheel for pybedtools (setup.py): finished with status 'error' 2023-09-08T18:58:55,613 ERROR: Failed building wheel for pybedtools 2023-09-08T18:58:55,615 Running setup.py clean for pybedtools 2023-09-08T18:58:55,616 Running command python setup.py clean 2023-09-08T18:58:56,081 /tmp/pip-wheel-1pxmev40/pybedtools_0930855ae9ad42f7a8b8b6f37d00a391/setup.py:25: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 2023-09-08T18:58:56,082 import pkg_resources 2023-09-08T18:58:56,673 running clean 2023-09-08T18:58:56,826 Failed to build pybedtools 2023-09-08T18:58:56,828 ERROR: Failed to build one or more wheels 2023-09-08T18:58:56,829 Exception information: 2023-09-08T18:58:56,829 Traceback (most recent call last): 2023-09-08T18:58:56,829 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2023-09-08T18:58:56,829 status = run_func(*args) 2023-09-08T18:58:56,829 ^^^^^^^^^^^^^^^ 2023-09-08T18:58:56,829 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper 2023-09-08T18:58:56,829 return func(self, options, args) 2023-09-08T18:58:56,829 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-08T18:58:56,829 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run 2023-09-08T18:58:56,829 raise CommandError("Failed to build one or more wheels") 2023-09-08T18:58:56,829 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2023-09-08T18:58:56,832 Removed build tracker: '/tmp/pip-build-tracker-8o41593l'