2023-09-08T19:41:34,893 Created temporary directory: /tmp/pip-build-tracker-5f9zdumj 2023-09-08T19:41:34,894 Initialized build tracking at /tmp/pip-build-tracker-5f9zdumj 2023-09-08T19:41:34,894 Created build tracker: /tmp/pip-build-tracker-5f9zdumj 2023-09-08T19:41:34,895 Entered build tracker: /tmp/pip-build-tracker-5f9zdumj 2023-09-08T19:41:34,896 Created temporary directory: /tmp/pip-wheel-1l5kyt6z 2023-09-08T19:41:34,899 Created temporary directory: /tmp/pip-ephem-wheel-cache-paapactw 2023-09-08T19:41:34,922 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-08T19:41:34,926 2 location(s) to search for versions of pybedtools: 2023-09-08T19:41:34,926 * https://pypi.org/simple/pybedtools/ 2023-09-08T19:41:34,926 * https://www.piwheels.org/simple/pybedtools/ 2023-09-08T19:41:34,927 Fetching project page and analyzing links: https://pypi.org/simple/pybedtools/ 2023-09-08T19:41:34,927 Getting page https://pypi.org/simple/pybedtools/ 2023-09-08T19:41:34,929 Found index url https://pypi.org/simple/ 2023-09-08T19:41:35,146 Fetched page https://pypi.org/simple/pybedtools/ as application/vnd.pypi.simple.v1+json 2023-09-08T19:41:35,153 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 2023-09-08T19:41:35,153 Found link https://files.pythonhosted.org/packages/44/19/a9bebb9eccd8d64d58202d5b3a151de81ffc7703a47503161b7615554703/pybedtools-0.5dev.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.5dev 2023-09-08T19:41:35,154 Found link https://files.pythonhosted.org/packages/e4/2f/e842c6b1165d706ebc62c931c11d4dfffe60e6b045ecf80eef7ea78d7afc/pybedtools-0.5rc1.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.5rc1 2023-09-08T19:41:35,155 Found link https://files.pythonhosted.org/packages/85/17/c89028c00537638629ca21be7f1b84e963fc8b63c1e9a5fda9884f86fb90/pybedtools-0.5.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.5 2023-09-08T19:41:35,155 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 2023-09-08T19:41:35,156 Found link https://files.pythonhosted.org/packages/3c/e7/365015ec8104195329635cb75ef745bff45d905271cd165f5048efaf48e3/pybedtools-0.6rc1.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6rc1 2023-09-08T19:41:35,157 Found link https://files.pythonhosted.org/packages/04/ce/0e1480725fe80eb9a401f59e1bcc28fce721f6c2c5d7be233894d0154551/pybedtools-0.6.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6 2023-09-08T19:41:35,158 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 2023-09-08T19:41:35,159 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 2023-09-08T19:41:35,159 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 2023-09-08T19:41:35,160 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 2023-09-08T19:41:35,161 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 2023-09-08T19:41:35,162 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 2023-09-08T19:41:35,162 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 2023-09-08T19:41:35,163 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 2023-09-08T19:41:35,164 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 2023-09-08T19:41:35,165 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 2023-09-08T19:41:35,165 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 2023-09-08T19:41:35,166 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 2023-09-08T19:41:35,166 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 2023-09-08T19:41:35,167 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 2023-09-08T19:41:35,168 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 2023-09-08T19:41:35,168 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 2023-09-08T19:41:35,169 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 2023-09-08T19:41:35,169 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 2023-09-08T19:41:35,170 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 2023-09-08T19:41:35,171 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 2023-09-08T19:41:35,171 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 2023-09-08T19:41:35,172 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 2023-09-08T19:41:35,173 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 2023-09-08T19:41:35,173 Fetching project page and analyzing links: https://www.piwheels.org/simple/pybedtools/ 2023-09-08T19:41:35,174 Getting page https://www.piwheels.org/simple/pybedtools/ 2023-09-08T19:41:35,176 Found index url https://www.piwheels.org/simple/ 2023-09-08T19:41:35,532 Fetched page https://www.piwheels.org/simple/pybedtools/ as text/html 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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/) 2023-09-08T19:41:35,623 Skipping link: not a file: https://www.piwheels.org/simple/pybedtools/ 2023-09-08T19:41:35,623 Skipping link: not a file: https://pypi.org/simple/pybedtools/ 2023-09-08T19:41:35,655 Given no hashes to check 1 links for project 'pybedtools': discarding no candidates 2023-09-08T19:41:35,681 Collecting pybedtools==0.7.4 2023-09-08T19:41:35,684 Created temporary directory: /tmp/pip-unpack-jkw06tbk 2023-09-08T19:41:36,587 Downloading pybedtools-0.7.4.tar.gz (12.6 MB) 2023-09-08T19:41:40,340 Added pybedtools==0.7.4 from https://files.pythonhosted.org/packages/a2/43/d80dbf32da421c78ea84a386402e1840dd06f3aba7e5fe73e8134e1ce50a/pybedtools-0.7.4.tar.gz to build tracker '/tmp/pip-build-tracker-5f9zdumj' 2023-09-08T19:41:40,342 Running setup.py (path:/tmp/pip-wheel-1l5kyt6z/pybedtools_388b853b015c45dbb33a2d15209aed96/setup.py) egg_info for package pybedtools 2023-09-08T19:41:40,343 Created temporary directory: /tmp/pip-pip-egg-info-55glhfvr 2023-09-08T19:41:40,344 Preparing metadata (setup.py): started 2023-09-08T19:41:40,345 Running command python setup.py egg_info 2023-09-08T19:41:40,824 /tmp/pip-wheel-1l5kyt6z/pybedtools_388b853b015c45dbb33a2d15209aed96/setup.py:25: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 2023-09-08T19:41:40,824 import pkg_resources 2023-09-08T19:41:41,445 running egg_info 2023-09-08T19:41:41,447 creating /tmp/pip-pip-egg-info-55glhfvr/pybedtools.egg-info 2023-09-08T19:41:41,471 writing /tmp/pip-pip-egg-info-55glhfvr/pybedtools.egg-info/PKG-INFO 2023-09-08T19:41:41,475 writing dependency_links to /tmp/pip-pip-egg-info-55glhfvr/pybedtools.egg-info/dependency_links.txt 2023-09-08T19:41:41,477 writing requirements to /tmp/pip-pip-egg-info-55glhfvr/pybedtools.egg-info/requires.txt 2023-09-08T19:41:41,478 writing top-level names to /tmp/pip-pip-egg-info-55glhfvr/pybedtools.egg-info/top_level.txt 2023-09-08T19:41:41,479 writing manifest file '/tmp/pip-pip-egg-info-55glhfvr/pybedtools.egg-info/SOURCES.txt' 2023-09-08T19:41:41,573 reading manifest file '/tmp/pip-pip-egg-info-55glhfvr/pybedtools.egg-info/SOURCES.txt' 2023-09-08T19:41:41,574 reading manifest template 'MANIFEST.in' 2023-09-08T19:41:41,741 warning: no previously-included files matching '__pycache__' found under directory '*' 2023-09-08T19:41:41,742 warning: no previously-included files matching '*.py[co]' found under directory '*' 2023-09-08T19:41:41,743 adding license file 'LICENSE.txt' 2023-09-08T19:41:41,750 writing manifest file '/tmp/pip-pip-egg-info-55glhfvr/pybedtools.egg-info/SOURCES.txt' 2023-09-08T19:41:41,862 Preparing metadata (setup.py): finished with status 'done' 2023-09-08T19:41:41,866 Source in /tmp/pip-wheel-1l5kyt6z/pybedtools_388b853b015c45dbb33a2d15209aed96 has version 0.7.4, which satisfies requirement pybedtools==0.7.4 from https://files.pythonhosted.org/packages/a2/43/d80dbf32da421c78ea84a386402e1840dd06f3aba7e5fe73e8134e1ce50a/pybedtools-0.7.4.tar.gz 2023-09-08T19:41:41,868 Removed pybedtools==0.7.4 from https://files.pythonhosted.org/packages/a2/43/d80dbf32da421c78ea84a386402e1840dd06f3aba7e5fe73e8134e1ce50a/pybedtools-0.7.4.tar.gz from build tracker '/tmp/pip-build-tracker-5f9zdumj' 2023-09-08T19:41:41,872 Created temporary directory: /tmp/pip-unpack-k_zni75r 2023-09-08T19:41:41,873 Created temporary directory: /tmp/pip-unpack-sn_52d6j 2023-09-08T19:41:41,878 Building wheels for collected packages: pybedtools 2023-09-08T19:41:41,883 Created temporary directory: /tmp/pip-wheel-l206sizy 2023-09-08T19:41:41,883 Building wheel for pybedtools (setup.py): started 2023-09-08T19:41:41,885 Destination directory: /tmp/pip-wheel-l206sizy 2023-09-08T19:41:41,885 Running command python setup.py bdist_wheel 2023-09-08T19:41:42,348 /tmp/pip-wheel-1l5kyt6z/pybedtools_388b853b015c45dbb33a2d15209aed96/setup.py:25: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 2023-09-08T19:41:42,349 import pkg_resources 2023-09-08T19:41:42,954 running bdist_wheel 2023-09-08T19:41:42,979 The [wheel] section is deprecated. Use [bdist_wheel] instead. 2023-09-08T19:41:43,004 running build 2023-09-08T19:41:43,004 running build_py 2023-09-08T19:41:43,031 creating build 2023-09-08T19:41:43,032 creating build/lib.linux-armv7l-cpython-311 2023-09-08T19:41:43,032 creating build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T19:41:43,034 copying pybedtools/logger.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T19:41:43,036 copying pybedtools/genome_registry.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T19:41:43,039 copying pybedtools/parallel.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T19:41:43,041 copying pybedtools/__init__.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T19:41:43,043 copying pybedtools/version.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T19:41:43,045 copying pybedtools/stats.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T19:41:43,046 copying pybedtools/helpers.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T19:41:43,049 copying pybedtools/__main__.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T19:41:43,050 copying pybedtools/settings.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T19:41:43,052 copying pybedtools/bedtool.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T19:41:43,056 copying pybedtools/filenames.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T19:41:43,058 creating build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-08T19:41:43,059 copying pybedtools/test/tfuncs.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-08T19:41:43,061 copying pybedtools/test/test1.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-08T19:41:43,064 copying pybedtools/test/test_scripts.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-08T19:41:43,067 copying pybedtools/test/test_gzip_support.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-08T19:41:43,069 copying pybedtools/test/test_cbedtools.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-08T19:41:43,071 copying pybedtools/test/test_len_leak.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-08T19:41:43,073 copying pybedtools/test/regression_tests.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-08T19:41:43,074 copying pybedtools/test/__init__.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-08T19:41:43,076 copying pybedtools/test/test_contrib.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-08T19:41:43,078 copying pybedtools/test/test_helpers.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-08T19:41:43,080 copying pybedtools/test/test_iter.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2023-09-08T19:41:43,083 creating build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2023-09-08T19:41:43,084 copying pybedtools/contrib/intersection_matrix.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2023-09-08T19:41:43,086 copying pybedtools/contrib/classifier.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2023-09-08T19:41:43,089 copying pybedtools/contrib/venn_maker.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2023-09-08T19:41:43,091 copying pybedtools/contrib/plotting.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2023-09-08T19:41:43,094 copying pybedtools/contrib/__init__.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2023-09-08T19:41:43,095 copying pybedtools/contrib/bigbed.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2023-09-08T19:41:43,097 copying pybedtools/contrib/bigwig.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2023-09-08T19:41:43,100 creating build/lib.linux-armv7l-cpython-311/pybedtools/scripts 2023-09-08T19:41:43,101 copying pybedtools/scripts/intersection_matrix.py -> build/lib.linux-armv7l-cpython-311/pybedtools/scripts 2023-09-08T19:41:43,103 copying pybedtools/scripts/py_ms_example.py -> build/lib.linux-armv7l-cpython-311/pybedtools/scripts 2023-09-08T19:41:43,105 copying pybedtools/scripts/venn_gchart.py -> build/lib.linux-armv7l-cpython-311/pybedtools/scripts 2023-09-08T19:41:43,107 copying pybedtools/scripts/intron_exon_reads.py -> build/lib.linux-armv7l-cpython-311/pybedtools/scripts 2023-09-08T19:41:43,109 copying pybedtools/scripts/__init__.py -> build/lib.linux-armv7l-cpython-311/pybedtools/scripts 2023-09-08T19:41:43,111 copying pybedtools/scripts/peak_pie.py -> build/lib.linux-armv7l-cpython-311/pybedtools/scripts 2023-09-08T19:41:43,113 copying pybedtools/scripts/venn_mpl.py -> build/lib.linux-armv7l-cpython-311/pybedtools/scripts 2023-09-08T19:41:43,115 copying pybedtools/scripts/annotate.py -> build/lib.linux-armv7l-cpython-311/pybedtools/scripts 2023-09-08T19:41:43,118 creating build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,119 copying pybedtools/test/data/__init__.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,129 copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,133 copying pybedtools/test/data/test.fa.fai -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,135 copying pybedtools/test/data/small.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,137 copying pybedtools/test/data/x.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,166 copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,174 copying pybedtools/test/data/a.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,176 copying pybedtools/test/data/gdc.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,178 copying pybedtools/test/data/gdc.gff -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,180 copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,182 copying pybedtools/test/data/snps.bed.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,308 copying pybedtools/test/data/gdc.1.100.bam.bai -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,310 copying pybedtools/test/data/vcf-stderr-test.vcf -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,312 copying pybedtools/test/data/expand_test.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,314 copying pybedtools/test/data/a.links.html -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,316 copying pybedtools/test/data/multibamcov_test.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,318 copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,321 copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,324 copying pybedtools/test/data/b.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,326 copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,331 copying pybedtools/test/data/reads.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,333 copying pybedtools/test/data/d.gff -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,335 copying pybedtools/test/data/hg19.gff -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,341 copying pybedtools/test/data/venn.b.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,343 copying pybedtools/test/data/x.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,383 copying pybedtools/test/data/hg38-problem.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,385 copying pybedtools/test/data/test.fa -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,387 copying pybedtools/test/data/gdc.50.200.bam.bai -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,389 copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,393 copying pybedtools/test/data/venn.c.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,396 copying pybedtools/test/data/mm9.bed12 -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,398 copying pybedtools/test/data/gdc.1.100.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,400 copying pybedtools/test/data/bedpe.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,402 copying pybedtools/test/data/hg38-base.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,404 copying pybedtools/test/data/gdc.sorted.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,406 copying pybedtools/test/data/vcf-stderr-test.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,408 copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,411 copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,420 copying pybedtools/test/data/tag_test2.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,422 copying pybedtools/test/data/c.gff -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,424 copying pybedtools/test/data/m1.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,426 copying pybedtools/test/data/gdc.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,428 copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,431 copying pybedtools/test/data/gdc.sorted.bam.bai -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,432 copying pybedtools/test/data/small.fastq -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,434 copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,438 copying pybedtools/test/data/exons.gff -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,439 copying pybedtools/test/data/y.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,441 copying pybedtools/test/data/gdc.50.200.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,443 copying pybedtools/test/data/a.igv_script -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,445 copying pybedtools/test/data/v.vcf -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,447 copying pybedtools/test/data/democonfig.yaml -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,449 copying pybedtools/test/data/bedpe2.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,451 copying pybedtools/test/data/gdc.gff.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,453 copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,458 copying pybedtools/test/data/tag_test1.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2023-09-08T19:41:43,460 copying pybedtools/_Window.pyx -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T19:41:43,463 copying pybedtools/featurefuncs.pyx -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T19:41:43,465 copying pybedtools/cbedtools.pyx -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T19:41:43,468 copying pybedtools/cbedtools.pxd -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T19:41:43,470 copying pybedtools/cbedtools.cxx -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T19:41:43,485 copying pybedtools/featurefuncs.cxx -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T19:41:43,493 copying pybedtools/_Window.c -> build/lib.linux-armv7l-cpython-311/pybedtools 2023-09-08T19:41:43,502 running build_ext 2023-09-08T19:41:43,508 building 'pybedtools.cbedtools' extension 2023-09-08T19:41:43,508 creating build/temp.linux-armv7l-cpython-311 2023-09-08T19:41:43,509 creating build/temp.linux-armv7l-cpython-311/pybedtools 2023-09-08T19:41:43,510 creating build/temp.linux-armv7l-cpython-311/src 2023-09-08T19:41:43,510 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 2023-09-08T19:41:44,071 pybedtools/cbedtools.cxx:16110:12: fatal error: longintrepr.h: No such file or directory 2023-09-08T19:41:44,072 16110 | #include "longintrepr.h" 2023-09-08T19:41:44,072 | ^~~~~~~~~~~~~~~ 2023-09-08T19:41:44,073 compilation terminated. 2023-09-08T19:41:44,077 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2023-09-08T19:41:44,188 ERROR: [present-rich] python setup.py bdist_wheel exited with 1 2023-09-08T19:41:44,201 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2023-09-08T19:41:44,201 exec(compile('"'"''"'"''"'"' 2023-09-08T19:41:44,201 # This is -- a caller that pip uses to run setup.py 2023-09-08T19:41:44,201 # 2023-09-08T19:41:44,201 # - It imports setuptools before invoking setup.py, to enable projects that directly 2023-09-08T19:41:44,201 # import from `distutils.core` to work with newer packaging standards. 2023-09-08T19:41:44,201 # - It provides a clear error message when setuptools is not installed. 2023-09-08T19:41:44,201 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2023-09-08T19:41:44,201 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2023-09-08T19:41:44,201 # manifest_maker: standard file '"'"'-c'"'"' not found". 2023-09-08T19:41:44,201 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2023-09-08T19:41:44,201 import os, sys, tokenize 2023-09-08T19:41:44,201 2023-09-08T19:41:44,201 try: 2023-09-08T19:41:44,201 import setuptools 2023-09-08T19:41:44,201 except ImportError as error: 2023-09-08T19:41:44,201 print( 2023-09-08T19:41:44,201 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2023-09-08T19:41:44,201 "the build environment.", 2023-09-08T19:41:44,201 file=sys.stderr, 2023-09-08T19:41:44,201 ) 2023-09-08T19:41:44,201 sys.exit(1) 2023-09-08T19:41:44,201 2023-09-08T19:41:44,201 __file__ = %r 2023-09-08T19:41:44,201 sys.argv[0] = __file__ 2023-09-08T19:41:44,201 2023-09-08T19:41:44,201 if os.path.exists(__file__): 2023-09-08T19:41:44,201 filename = __file__ 2023-09-08T19:41:44,201 with tokenize.open(__file__) as f: 2023-09-08T19:41:44,201 setup_py_code = f.read() 2023-09-08T19:41:44,201 else: 2023-09-08T19:41:44,201 filename = "" 2023-09-08T19:41:44,201 setup_py_code = "from setuptools import setup; setup()" 2023-09-08T19:41:44,201 2023-09-08T19:41:44,201 exec(compile(setup_py_code, filename, "exec")) 2023-09-08T19:41:44,201 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-1l5kyt6z/pybedtools_388b853b015c45dbb33a2d15209aed96/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-l206sizy[/] 2023-09-08T19:41:44,201 [bold magenta]cwd[/]: /tmp/pip-wheel-1l5kyt6z/pybedtools_388b853b015c45dbb33a2d15209aed96/ 2023-09-08T19:41:44,202 Building wheel for pybedtools (setup.py): finished with status 'error' 2023-09-08T19:41:44,203 ERROR: Failed building wheel for pybedtools 2023-09-08T19:41:44,204 Running setup.py clean for pybedtools 2023-09-08T19:41:44,206 Running command python setup.py clean 2023-09-08T19:41:44,698 /tmp/pip-wheel-1l5kyt6z/pybedtools_388b853b015c45dbb33a2d15209aed96/setup.py:25: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 2023-09-08T19:41:44,698 import pkg_resources 2023-09-08T19:41:45,309 running clean 2023-09-08T19:41:45,461 Failed to build pybedtools 2023-09-08T19:41:45,463 ERROR: Failed to build one or more wheels 2023-09-08T19:41:45,464 Exception information: 2023-09-08T19:41:45,464 Traceback (most recent call last): 2023-09-08T19:41:45,464 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2023-09-08T19:41:45,464 status = run_func(*args) 2023-09-08T19:41:45,464 ^^^^^^^^^^^^^^^ 2023-09-08T19:41:45,464 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper 2023-09-08T19:41:45,464 return func(self, options, args) 2023-09-08T19:41:45,464 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-08T19:41:45,464 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run 2023-09-08T19:41:45,464 raise CommandError("Failed to build one or more wheels") 2023-09-08T19:41:45,464 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2023-09-08T19:41:45,467 Removed build tracker: '/tmp/pip-build-tracker-5f9zdumj'