2023-09-09T08:58:23,965 Created temporary directory: /tmp/pip-build-tracker-hg9s1ew0 2023-09-09T08:58:23,966 Initialized build tracking at /tmp/pip-build-tracker-hg9s1ew0 2023-09-09T08:58:23,967 Created build tracker: /tmp/pip-build-tracker-hg9s1ew0 2023-09-09T08:58:23,967 Entered build tracker: /tmp/pip-build-tracker-hg9s1ew0 2023-09-09T08:58:23,968 Created temporary directory: /tmp/pip-wheel-pnm1gdzw 2023-09-09T08:58:23,971 Created temporary directory: /tmp/pip-ephem-wheel-cache-_9twsfqb 2023-09-09T08:58:23,993 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-09T08:58:23,996 2 location(s) to search for versions of transvar: 2023-09-09T08:58:23,996 * https://pypi.org/simple/transvar/ 2023-09-09T08:58:23,996 * https://www.piwheels.org/simple/transvar/ 2023-09-09T08:58:23,997 Fetching project page and analyzing links: https://pypi.org/simple/transvar/ 2023-09-09T08:58:23,998 Getting page https://pypi.org/simple/transvar/ 2023-09-09T08:58:23,999 Found index url https://pypi.org/simple/ 2023-09-09T08:58:24,141 Fetched page https://pypi.org/simple/transvar/ as application/vnd.pypi.simple.v1+json 2023-09-09T08:58:24,149 Found link https://files.pythonhosted.org/packages/08/6c/f47d5c1b30408e08f19c5fbe42e03f57a234057fe1dd4c82a2e908a38a73/TransVar-2.2.3.20160407.tar.gz (from https://pypi.org/simple/transvar/), version: 2.2.3.20160407 2023-09-09T08:58:24,150 Found link https://files.pythonhosted.org/packages/2c/44/b95ffb8f13d8bb611c15adacdcf61cf24e51685cd193b2a1769270183e14/TransVar-2.2.4.20160407.tar.gz (from https://pypi.org/simple/transvar/), version: 2.2.4.20160407 2023-09-09T08:58:24,150 Found link https://files.pythonhosted.org/packages/d2/5c/083e2ec87dbae164c1ba791cd88f7a14473859980e3f5775a88cb9f18c8d/TransVar-2.2.5.20160408.tar.gz (from https://pypi.org/simple/transvar/), version: 2.2.5.20160408 2023-09-09T08:58:24,151 Found link https://files.pythonhosted.org/packages/2b/7b/f71bd04791a21d7c6c51ed2801b53cfde506c57fcaaa90eff0c0b96cc4bc/TransVar-2.2.6.20160427.tar.gz (from https://pypi.org/simple/transvar/), version: 2.2.6.20160427 2023-09-09T08:58:24,151 Found link https://files.pythonhosted.org/packages/bb/a1/1dd7275f4a930448d1e66a40cc720e505b7cce8dae450dfbc0b73b6fe391/TransVar-2.2.7.20160427.tar.gz (from https://pypi.org/simple/transvar/), version: 2.2.7.20160427 2023-09-09T08:58:24,152 Found link https://files.pythonhosted.org/packages/d3/df/680fb4f9e32967ef2beb3fdc548eea6f6496eeb25f673f5c4e4c5ed22ef8/TransVar-2.2.8.20160502.tar.gz (from https://pypi.org/simple/transvar/), version: 2.2.8.20160502 2023-09-09T08:58:24,153 Found link https://files.pythonhosted.org/packages/87/4c/00f096288e5b2636dc7cf2a49ea6465649734cfddde6698ee315d2fc5b4a/TransVar-2.2.9.20160503.tar.gz (from https://pypi.org/simple/transvar/), version: 2.2.9.20160503 2023-09-09T08:58:24,153 Found link https://files.pythonhosted.org/packages/ee/0f/b340f49b44ef2d0fe305c4e4f44b393a44af7d64e5d6ccc9dc9464887e32/TransVar-2.2.10.20160512.tar.gz (from https://pypi.org/simple/transvar/), version: 2.2.10.20160512 2023-09-09T08:58:24,154 Found link https://files.pythonhosted.org/packages/57/b1/34e879cdcc60d291102d0634efbc6bcc588f8af5052009c8943a8755c968/TransVar-2.2.11.20160531.tar.gz (from https://pypi.org/simple/transvar/), version: 2.2.11.20160531 2023-09-09T08:58:24,155 Found link https://files.pythonhosted.org/packages/0e/e2/86c1e324c0af3086c36628c7b94caf19547b18560ea667d28825f8f57ae3/TransVar-2.2.12.20160723.tar.gz (from https://pypi.org/simple/transvar/), version: 2.2.12.20160723 2023-09-09T08:58:24,155 Found link https://files.pythonhosted.org/packages/d1/fe/a13f91f948c3e89d08e0a8acb2eadf0759cbc816a57456196736218b46ce/TransVar-2.2.13.20160723.tar.gz (from https://pypi.org/simple/transvar/), version: 2.2.13.20160723 2023-09-09T08:58:24,156 Found link https://files.pythonhosted.org/packages/fb/f4/02b249106131830b0bb00c0b10b15a10ded8f03077da8bccd72d2c8a7366/TransVar-2.2.14.20161002.tar.gz (from https://pypi.org/simple/transvar/), version: 2.2.14.20161002 2023-09-09T08:58:24,157 Found link https://files.pythonhosted.org/packages/9b/02/2d7ef5f0bbf746e2f4781ccb3d24822af377b188b9dbbee30cec829fa487/TransVar-2.2.15.20161002.tar.gz (from https://pypi.org/simple/transvar/), version: 2.2.15.20161002 2023-09-09T08:58:24,157 Found link https://files.pythonhosted.org/packages/19/d8/a0c36f428d8acca26cc8bce1f8aa79a7597db4f05c79c8d2943fe9b153fc/TransVar-2.3.0.20161007.tar.gz (from https://pypi.org/simple/transvar/), version: 2.3.0.20161007 2023-09-09T08:58:24,158 Found link https://files.pythonhosted.org/packages/5a/06/25e17459a69dfe3545ec60e9bcb25352c8b7507b69dcd7d91231b347362e/TransVar-2.3.1.20161012.tar.gz (from https://pypi.org/simple/transvar/), version: 2.3.1.20161012 2023-09-09T08:58:24,159 Found link https://files.pythonhosted.org/packages/ec/a4/7f39c4bdd55034793debeb843b84bb3a4a1772af2ad4853e233aa3bfae7b/TransVar-2.3.2.20161106.tar.gz (from https://pypi.org/simple/transvar/), version: 2.3.2.20161106 2023-09-09T08:58:24,159 Found link https://files.pythonhosted.org/packages/f0/28/2bd84a4700ef07a998e80e9ad09f7180f4758f68077d854a8541b6b31143/TransVar-2.3.3.20161203.tar.gz (from https://pypi.org/simple/transvar/), version: 2.3.3.20161203 2023-09-09T08:58:24,160 Found link https://files.pythonhosted.org/packages/bc/b3/a0c9a2edf84c397fbf5a6624ddec2f9f961c2b79e070589c361781257111/TransVar-2.3.4.20161215.tar.gz (from https://pypi.org/simple/transvar/), version: 2.3.4.20161215 2023-09-09T08:58:24,160 Found link https://files.pythonhosted.org/packages/5c/34/222a51489e07dcad5f29f78cee8e0f8e74b1b8b21cd7bb6d12dd2573129d/TransVar-2.4.0.20180701.tar.gz (from https://pypi.org/simple/transvar/), version: 2.4.0.20180701 2023-09-09T08:58:24,161 Found link https://files.pythonhosted.org/packages/06/41/dfa097486b76d3d8351d5fe4599e0b69ad71cfda1d739d8cd98faa4efaf6/TransVar-2.4.1.20180815.tar.gz (from https://pypi.org/simple/transvar/), version: 2.4.1.20180815 2023-09-09T08:58:24,161 Found link https://files.pythonhosted.org/packages/4b/a2/9a02c155404499b4baac5d5bc7fa994ca77101238e544967a6a612bebefb/TransVar-2.4.2.20181231.linux-x86_64.tar.gz (from https://pypi.org/simple/transvar/), version: 2.4.2.20181231.linux-x86_64 2023-09-09T08:58:24,162 Found link https://files.pythonhosted.org/packages/e3/2c/24dd2011bdbbae662607eaf3bb98dc4671d2ca97863adfbe1a0979e44b7c/TransVar-2.4.3.20181231.macosx-10.7-x86_64.tar.gz (from https://pypi.org/simple/transvar/), version: 2.4.3.20181231.macosx-10.7-x86_64 2023-09-09T08:58:24,163 Found link https://files.pythonhosted.org/packages/a8/00/d435ffe1c3ef6122be1c0b159b09844ea00e26c283a200ffeabd86b1b9e5/TransVar-2.4.5.20190121.linux-x86_64.tar.gz (from https://pypi.org/simple/transvar/), version: 2.4.5.20190121.linux-x86_64 2023-09-09T08:58:24,164 Found link https://files.pythonhosted.org/packages/e5/bb/05b86cb6a1785fefad9c6fa49647c2fca8a5af25622285bc9a7858d313fe/TransVar-2.4.6.20190121.tar.gz (from https://pypi.org/simple/transvar/), version: 2.4.6.20190121 2023-09-09T08:58:24,165 Found link https://files.pythonhosted.org/packages/b4/2a/981908e0b8034e128753a08697d1693342e35c262ac9801384db7c3f67dc/TransVar-2.4.7.20190122.tar.gz (from https://pypi.org/simple/transvar/), version: 2.4.7.20190122 2023-09-09T08:58:24,165 Found link https://files.pythonhosted.org/packages/59/c0/9367847eb7367bec582f0878a199f102667c7d16bd2a8fc74d1e750d2b28/TransVar-2.4.8.20190122.tar.gz (from https://pypi.org/simple/transvar/), version: 2.4.8.20190122 2023-09-09T08:58:24,166 Found link https://files.pythonhosted.org/packages/b4/07/5354a402238297ebc687a5a64df3acced1e8c7a550cb8366f0cc597728bd/TransVar-2.5.0.20190314.tar.gz (from https://pypi.org/simple/transvar/), version: 2.5.0.20190314 2023-09-09T08:58:24,167 Found link https://files.pythonhosted.org/packages/59/d6/2905c05c60e0d50545825a2cc6affafddb5d22ceea996c7d89c9cbad82de/TransVar-2.5.1.20190326.tar.gz (from https://pypi.org/simple/transvar/), version: 2.5.1.20190326 2023-09-09T08:58:24,167 Found link https://files.pythonhosted.org/packages/aa/ee/db5408c9dd1f8fda18cc47d4a59f8b6452a0b423036c11fb8094d3b8c4b1/TransVar-2.5.2.20190401.tar.gz (from https://pypi.org/simple/transvar/), version: 2.5.2.20190401 2023-09-09T08:58:24,168 Found link https://files.pythonhosted.org/packages/0f/d1/23d5e5144a7827d866608e83f2a50708a81fc0adf035399fbe2e3f27f269/TransVar-2.5.3.20190424.tar.gz (from https://pypi.org/simple/transvar/), version: 2.5.3.20190424 2023-09-09T08:58:24,169 Found link https://files.pythonhosted.org/packages/6b/0d/54c1aedb8dc212405906f0de57c59dc3b4886648f0778453ffc419fcb3ae/TransVar-2.5.4.20190424.tar.gz (from https://pypi.org/simple/transvar/), version: 2.5.4.20190424 2023-09-09T08:58:24,170 Found link https://files.pythonhosted.org/packages/00/53/c95a1a2ceb64819124d248268e47bb49f3083e7b7303579dc82fe7e8b63f/TransVar-2.5.5.20190430.tar.gz (from https://pypi.org/simple/transvar/), version: 2.5.5.20190430 2023-09-09T08:58:24,170 Found link https://files.pythonhosted.org/packages/98/75/2a931b2024578b9e983478b8e5dc9c8a97d17abd853d61764eebc8899c6a/TransVar-2.5.6.20190605.tar.gz (from https://pypi.org/simple/transvar/), version: 2.5.6.20190605 2023-09-09T08:58:24,171 Found link https://files.pythonhosted.org/packages/69/3b/ace0d9d8535fecba01f3ad0889616325acac49a14f48e88ad4f0fcae867b/TransVar-2.5.7.20190617.tar.gz (from https://pypi.org/simple/transvar/), version: 2.5.7.20190617 2023-09-09T08:58:24,171 Found link https://files.pythonhosted.org/packages/90/2a/c79f2efcef9d5d4ef7be668b76359baa7342ace17e5f864f5e3800c6b288/TransVar-2.5.8.20190813.tar.gz (from https://pypi.org/simple/transvar/), version: 2.5.8.20190813 2023-09-09T08:58:24,172 Found link https://files.pythonhosted.org/packages/99/89/e759694b24f6a9d74049e8dd66bd9194e54e4bb97effbca4c69dff9f9046/TransVar-2.5.9.20190830.tar.gz (from https://pypi.org/simple/transvar/), version: 2.5.9.20190830 2023-09-09T08:58:24,172 Found link https://files.pythonhosted.org/packages/b5/8d/7016d6a3488c2cfdfa5669c1f11ed6970d32eb2e3bbe9efad980d0a0b7e8/TransVar-2.5.10.20211024.tar.gz (from https://pypi.org/simple/transvar/), version: 2.5.10.20211024 2023-09-09T08:58:24,173 Fetching project page and analyzing links: https://www.piwheels.org/simple/transvar/ 2023-09-09T08:58:24,174 Getting page https://www.piwheels.org/simple/transvar/ 2023-09-09T08:58:24,175 Found index url https://www.piwheels.org/simple/ 2023-09-09T08:58:24,441 Fetched page https://www.piwheels.org/simple/transvar/ as text/html 2023-09-09T08:58:24,443 Skipping link: not a file: https://www.piwheels.org/simple/transvar/ 2023-09-09T08:58:24,443 Skipping link: not a file: https://pypi.org/simple/transvar/ 2023-09-09T08:58:24,466 Given no hashes to check 1 links for project 'transvar': discarding no candidates 2023-09-09T08:58:24,485 Collecting transvar==2.3.4.20161215 2023-09-09T08:58:24,487 Created temporary directory: /tmp/pip-unpack-k9dm5qm9 2023-09-09T08:58:24,720 Downloading TransVar-2.3.4.20161215.tar.gz (640 kB) 2023-09-09T08:58:25,258 Added transvar==2.3.4.20161215 from https://files.pythonhosted.org/packages/bc/b3/a0c9a2edf84c397fbf5a6624ddec2f9f961c2b79e070589c361781257111/TransVar-2.3.4.20161215.tar.gz to build tracker '/tmp/pip-build-tracker-hg9s1ew0' 2023-09-09T08:58:25,260 Running setup.py (path:/tmp/pip-wheel-pnm1gdzw/transvar_052467e4c2ed41dc8b7500cd68d6fd4a/setup.py) egg_info for package transvar 2023-09-09T08:58:25,261 Created temporary directory: /tmp/pip-pip-egg-info-ajy3x_cp 2023-09-09T08:58:25,261 Preparing metadata (setup.py): started 2023-09-09T08:58:25,263 Running command python setup.py egg_info 2023-09-09T08:58:26,049 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:510: SetuptoolsDeprecationWarning: Invalid dash-separated options 2023-09-09T08:58:26,049 !! 2023-09-09T08:58:26,050 ******************************************************************************** 2023-09-09T08:58:26,051 Usage of dash-separated 'description-file' will not be supported in future 2023-09-09T08:58:26,051 versions. Please use the underscore name 'description_file' instead. 2023-09-09T08:58:26,053 By 2023-Sep-26, you need to update your project and remove deprecated calls 2023-09-09T08:58:26,053 or your builds will no longer be supported. 2023-09-09T08:58:26,055 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-09T08:58:26,055 ******************************************************************************** 2023-09-09T08:58:26,056 !! 2023-09-09T08:58:26,057 opt = self.warn_dash_deprecation(opt, section) 2023-09-09T08:58:26,376 running egg_info 2023-09-09T08:58:26,378 creating /tmp/pip-pip-egg-info-ajy3x_cp/TransVar.egg-info 2023-09-09T08:58:26,401 writing /tmp/pip-pip-egg-info-ajy3x_cp/TransVar.egg-info/PKG-INFO 2023-09-09T08:58:26,404 writing dependency_links to /tmp/pip-pip-egg-info-ajy3x_cp/TransVar.egg-info/dependency_links.txt 2023-09-09T08:58:26,406 writing requirements to /tmp/pip-pip-egg-info-ajy3x_cp/TransVar.egg-info/requires.txt 2023-09-09T08:58:26,407 writing top-level names to /tmp/pip-pip-egg-info-ajy3x_cp/TransVar.egg-info/top_level.txt 2023-09-09T08:58:26,408 writing manifest file '/tmp/pip-pip-egg-info-ajy3x_cp/TransVar.egg-info/SOURCES.txt' 2023-09-09T08:58:26,509 reading manifest file '/tmp/pip-pip-egg-info-ajy3x_cp/TransVar.egg-info/SOURCES.txt' 2023-09-09T08:58:26,511 reading manifest template 'MANIFEST.in' 2023-09-09T08:58:26,771 writing manifest file '/tmp/pip-pip-egg-info-ajy3x_cp/TransVar.egg-info/SOURCES.txt' 2023-09-09T08:58:26,899 Preparing metadata (setup.py): finished with status 'done' 2023-09-09T08:58:26,903 Source in /tmp/pip-wheel-pnm1gdzw/transvar_052467e4c2ed41dc8b7500cd68d6fd4a has version 2.3.4.20161215, which satisfies requirement transvar==2.3.4.20161215 from https://files.pythonhosted.org/packages/bc/b3/a0c9a2edf84c397fbf5a6624ddec2f9f961c2b79e070589c361781257111/TransVar-2.3.4.20161215.tar.gz 2023-09-09T08:58:26,904 Removed transvar==2.3.4.20161215 from https://files.pythonhosted.org/packages/bc/b3/a0c9a2edf84c397fbf5a6624ddec2f9f961c2b79e070589c361781257111/TransVar-2.3.4.20161215.tar.gz from build tracker '/tmp/pip-build-tracker-hg9s1ew0' 2023-09-09T08:58:26,908 Created temporary directory: /tmp/pip-unpack-3oje_5w7 2023-09-09T08:58:26,909 Created temporary directory: /tmp/pip-unpack-uqh0pg8z 2023-09-09T08:58:26,913 Building wheels for collected packages: transvar 2023-09-09T08:58:26,917 Created temporary directory: /tmp/pip-wheel-wql8id6r 2023-09-09T08:58:26,918 Building wheel for transvar (setup.py): started 2023-09-09T08:58:26,919 Destination directory: /tmp/pip-wheel-wql8id6r 2023-09-09T08:58:26,920 Running command python setup.py bdist_wheel 2023-09-09T08:58:27,667 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:510: SetuptoolsDeprecationWarning: Invalid dash-separated options 2023-09-09T08:58:27,667 !! 2023-09-09T08:58:27,668 ******************************************************************************** 2023-09-09T08:58:27,669 Usage of dash-separated 'description-file' will not be supported in future 2023-09-09T08:58:27,670 versions. Please use the underscore name 'description_file' instead. 2023-09-09T08:58:27,671 By 2023-Sep-26, you need to update your project and remove deprecated calls 2023-09-09T08:58:27,671 or your builds will no longer be supported. 2023-09-09T08:58:27,672 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-09T08:58:27,673 ******************************************************************************** 2023-09-09T08:58:27,674 !! 2023-09-09T08:58:27,675 opt = self.warn_dash_deprecation(opt, section) 2023-09-09T08:58:28,000 running bdist_wheel 2023-09-09T08:58:28,071 running build 2023-09-09T08:58:28,071 running build_py 2023-09-09T08:58:28,098 creating build 2023-09-09T08:58:28,099 creating build/lib.linux-armv7l-cpython-311 2023-09-09T08:58:28,100 creating build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:58:28,101 copying transvar/annodb.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:58:28,103 copying transvar/parser.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:58:28,106 copying transvar/faidx.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:58:28,108 copying transvar/argparse.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:58:28,113 copying transvar/codonsearch.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:58:28,117 copying transvar/frameshift.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:58:28,120 copying transvar/anno.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:58:28,122 copying transvar/err.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:58:28,124 copying transvar/mnv.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:58:28,126 copying transvar/localdb.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:58:28,128 copying transvar/config.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:58:28,131 copying transvar/mutation.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:58:28,133 copying transvar/utils.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:58:28,135 copying transvar/insertion.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:58:28,137 copying transvar/transcripts.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:58:28,140 copying transvar/snv.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:58:28,143 copying transvar/deletion.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:58:28,145 copying transvar/describe.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:58:28,147 copying transvar/region.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:58:28,150 copying transvar/record.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:58:28,152 copying transvar/__init__.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:58:28,154 copying transvar/version.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:58:28,155 copying transvar/proteinseqs.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:58:28,157 creating build/lib.linux-armv7l-cpython-311/transvar/ssw 2023-09-09T08:58:28,158 copying transvar/ssw/__init__.py -> build/lib.linux-armv7l-cpython-311/transvar/ssw 2023-09-09T08:58:28,162 running build_ext 2023-09-09T08:58:28,640 building 'transvar.tabix' extension 2023-09-09T08:58:28,641 creating build/temp.linux-armv7l-cpython-311 2023-09-09T08:58:28,641 creating build/temp.linux-armv7l-cpython-311/external 2023-09-09T08:58:28,642 creating build/temp.linux-armv7l-cpython-311/external/pytabix 2023-09-09T08:58:28,643 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Iexternal/pytabix -I/usr/include/python3.11 -c external/pytabix/bgzf.c -o build/temp.linux-armv7l-cpython-311/external/pytabix/bgzf.o -w 2023-09-09T08:58:29,310 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Iexternal/pytabix -I/usr/include/python3.11 -c external/pytabix/bgzip.c -o build/temp.linux-armv7l-cpython-311/external/pytabix/bgzip.o -w 2023-09-09T08:58:29,705 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Iexternal/pytabix -I/usr/include/python3.11 -c external/pytabix/index.c -o build/temp.linux-armv7l-cpython-311/external/pytabix/index.o -w 2023-09-09T08:58:32,507 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Iexternal/pytabix -I/usr/include/python3.11 -c external/pytabix/knetfile.c -o build/temp.linux-armv7l-cpython-311/external/pytabix/knetfile.o -w 2023-09-09T08:58:33,281 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Iexternal/pytabix -I/usr/include/python3.11 -c external/pytabix/kstring.c -o build/temp.linux-armv7l-cpython-311/external/pytabix/kstring.o -w 2023-09-09T08:58:33,695 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Iexternal/pytabix -I/usr/include/python3.11 -c external/pytabix/tabixmodule.c -o build/temp.linux-armv7l-cpython-311/external/pytabix/tabixmodule.o -w 2023-09-09T08:58:34,298 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/external/pytabix/bgzf.o build/temp.linux-armv7l-cpython-311/external/pytabix/bgzip.o build/temp.linux-armv7l-cpython-311/external/pytabix/index.o build/temp.linux-armv7l-cpython-311/external/pytabix/knetfile.o build/temp.linux-armv7l-cpython-311/external/pytabix/kstring.o build/temp.linux-armv7l-cpython-311/external/pytabix/tabixmodule.o -L/usr/lib/arm-linux-gnueabihf -lz -o build/lib.linux-armv7l-cpython-311/transvar/tabix.cpython-311-arm-linux-gnueabihf.so 2023-09-09T08:58:34,409 building 'transvar.ssw._sswlib' extension 2023-09-09T08:58:34,409 creating build/temp.linux-armv7l-cpython-311/external/ssw 2023-09-09T08:58:34,410 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Iexternal/ssw -I/usr/include/python3.11 -c external/ssw/encode.c -o build/temp.linux-armv7l-cpython-311/external/ssw/encode.o -W -Wall -O2 -finline-functions -fPIC -shared -Wl,-soname,sswlib 2023-09-09T08:58:34,551 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Iexternal/ssw -I/usr/include/python3.11 -c external/ssw/ssw.c -o build/temp.linux-armv7l-cpython-311/external/ssw/ssw.o -W -Wall -O2 -finline-functions -fPIC -shared -Wl,-soname,sswlib 2023-09-09T08:58:34,593 external/ssw/ssw.c:38:10: fatal error: emmintrin.h: No such file or directory 2023-09-09T08:58:34,594 38 | #include 2023-09-09T08:58:34,594 | ^~~~~~~~~~~~~ 2023-09-09T08:58:34,595 compilation terminated. 2023-09-09T08:58:34,598 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2023-09-09T08:58:34,749 ERROR: [present-rich] python setup.py bdist_wheel exited with 1 2023-09-09T08:58:34,762 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2023-09-09T08:58:34,762 exec(compile('"'"''"'"''"'"' 2023-09-09T08:58:34,762 # This is -- a caller that pip uses to run setup.py 2023-09-09T08:58:34,762 # 2023-09-09T08:58:34,762 # - It imports setuptools before invoking setup.py, to enable projects that directly 2023-09-09T08:58:34,762 # import from `distutils.core` to work with newer packaging standards. 2023-09-09T08:58:34,762 # - It provides a clear error message when setuptools is not installed. 2023-09-09T08:58:34,762 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2023-09-09T08:58:34,762 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2023-09-09T08:58:34,762 # manifest_maker: standard file '"'"'-c'"'"' not found". 2023-09-09T08:58:34,762 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2023-09-09T08:58:34,762 import os, sys, tokenize 2023-09-09T08:58:34,762 2023-09-09T08:58:34,762 try: 2023-09-09T08:58:34,762 import setuptools 2023-09-09T08:58:34,762 except ImportError as error: 2023-09-09T08:58:34,762 print( 2023-09-09T08:58:34,762 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2023-09-09T08:58:34,762 "the build environment.", 2023-09-09T08:58:34,762 file=sys.stderr, 2023-09-09T08:58:34,762 ) 2023-09-09T08:58:34,762 sys.exit(1) 2023-09-09T08:58:34,762 2023-09-09T08:58:34,762 __file__ = %r 2023-09-09T08:58:34,762 sys.argv[0] = __file__ 2023-09-09T08:58:34,762 2023-09-09T08:58:34,762 if os.path.exists(__file__): 2023-09-09T08:58:34,762 filename = __file__ 2023-09-09T08:58:34,762 with tokenize.open(__file__) as f: 2023-09-09T08:58:34,762 setup_py_code = f.read() 2023-09-09T08:58:34,762 else: 2023-09-09T08:58:34,762 filename = "" 2023-09-09T08:58:34,762 setup_py_code = "from setuptools import setup; setup()" 2023-09-09T08:58:34,762 2023-09-09T08:58:34,762 exec(compile(setup_py_code, filename, "exec")) 2023-09-09T08:58:34,762 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-pnm1gdzw/transvar_052467e4c2ed41dc8b7500cd68d6fd4a/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-wql8id6r[/] 2023-09-09T08:58:34,763 [bold magenta]cwd[/]: /tmp/pip-wheel-pnm1gdzw/transvar_052467e4c2ed41dc8b7500cd68d6fd4a/ 2023-09-09T08:58:34,764 Building wheel for transvar (setup.py): finished with status 'error' 2023-09-09T08:58:34,766 ERROR: Failed building wheel for transvar 2023-09-09T08:58:34,767 Running setup.py clean for transvar 2023-09-09T08:58:34,768 Running command python setup.py clean 2023-09-09T08:58:35,558 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:510: SetuptoolsDeprecationWarning: Invalid dash-separated options 2023-09-09T08:58:35,559 !! 2023-09-09T08:58:35,560 ******************************************************************************** 2023-09-09T08:58:35,560 Usage of dash-separated 'description-file' will not be supported in future 2023-09-09T08:58:35,561 versions. Please use the underscore name 'description_file' instead. 2023-09-09T08:58:35,562 By 2023-Sep-26, you need to update your project and remove deprecated calls 2023-09-09T08:58:35,562 or your builds will no longer be supported. 2023-09-09T08:58:35,563 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-09T08:58:35,564 ******************************************************************************** 2023-09-09T08:58:35,565 !! 2023-09-09T08:58:35,566 opt = self.warn_dash_deprecation(opt, section) 2023-09-09T08:58:35,892 running clean 2023-09-09T08:58:35,915 removing 'build/temp.linux-armv7l-cpython-311' (and everything under it) 2023-09-09T08:58:35,920 removing 'build/lib.linux-armv7l-cpython-311' (and everything under it) 2023-09-09T08:58:35,929 'build/bdist.linux-armv7l' does not exist -- can't clean it 2023-09-09T08:58:35,929 'build/scripts-3.11' does not exist -- can't clean it 2023-09-09T08:58:35,930 removing 'build' 2023-09-09T08:58:36,056 Failed to build transvar 2023-09-09T08:58:36,057 ERROR: Failed to build one or more wheels 2023-09-09T08:58:36,059 Exception information: 2023-09-09T08:58:36,059 Traceback (most recent call last): 2023-09-09T08:58:36,059 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2023-09-09T08:58:36,059 status = run_func(*args) 2023-09-09T08:58:36,059 ^^^^^^^^^^^^^^^ 2023-09-09T08:58:36,059 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper 2023-09-09T08:58:36,059 return func(self, options, args) 2023-09-09T08:58:36,059 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-09T08:58:36,059 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run 2023-09-09T08:58:36,059 raise CommandError("Failed to build one or more wheels") 2023-09-09T08:58:36,059 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2023-09-09T08:58:36,062 Removed build tracker: '/tmp/pip-build-tracker-hg9s1ew0'