2023-09-09T08:48:47,038 Created temporary directory: /tmp/pip-build-tracker-p5wuc0s9 2023-09-09T08:48:47,039 Initialized build tracking at /tmp/pip-build-tracker-p5wuc0s9 2023-09-09T08:48:47,040 Created build tracker: /tmp/pip-build-tracker-p5wuc0s9 2023-09-09T08:48:47,040 Entered build tracker: /tmp/pip-build-tracker-p5wuc0s9 2023-09-09T08:48:47,041 Created temporary directory: /tmp/pip-wheel-5vyoky2z 2023-09-09T08:48:47,044 Created temporary directory: /tmp/pip-ephem-wheel-cache-ak7cui1k 2023-09-09T08:48:47,066 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-09T08:48:47,070 2 location(s) to search for versions of transvar: 2023-09-09T08:48:47,070 * https://pypi.org/simple/transvar/ 2023-09-09T08:48:47,070 * https://www.piwheels.org/simple/transvar/ 2023-09-09T08:48:47,071 Fetching project page and analyzing links: https://pypi.org/simple/transvar/ 2023-09-09T08:48:47,071 Getting page https://pypi.org/simple/transvar/ 2023-09-09T08:48:47,073 Found index url https://pypi.org/simple/ 2023-09-09T08:48:47,212 Fetched page https://pypi.org/simple/transvar/ as application/vnd.pypi.simple.v1+json 2023-09-09T08:48:47,219 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 2023-09-09T08:48:47,220 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 2023-09-09T08:48:47,221 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 2023-09-09T08:48:47,221 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 2023-09-09T08:48:47,222 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 2023-09-09T08:48:47,222 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 2023-09-09T08:48:47,223 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 2023-09-09T08:48:47,224 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 2023-09-09T08:48:47,225 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 2023-09-09T08:48:47,225 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 2023-09-09T08:48:47,226 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 2023-09-09T08:48:47,227 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 2023-09-09T08:48:47,227 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 2023-09-09T08:48:47,228 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 2023-09-09T08:48:47,229 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 2023-09-09T08:48:47,229 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 2023-09-09T08:48:47,230 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 2023-09-09T08:48:47,231 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 2023-09-09T08:48:47,231 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 2023-09-09T08:48:47,232 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 2023-09-09T08:48:47,232 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 2023-09-09T08:48:47,233 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 2023-09-09T08:48:47,234 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 2023-09-09T08:48:47,235 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 2023-09-09T08:48:47,235 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 2023-09-09T08:48:47,236 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 2023-09-09T08:48:47,237 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 2023-09-09T08:48:47,237 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 2023-09-09T08:48:47,238 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 2023-09-09T08:48:47,239 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 2023-09-09T08:48:47,240 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 2023-09-09T08:48:47,240 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 2023-09-09T08:48:47,241 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 2023-09-09T08:48:47,241 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 2023-09-09T08:48:47,242 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 2023-09-09T08:48:47,242 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 2023-09-09T08:48:47,243 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 2023-09-09T08:48:47,244 Fetching project page and analyzing links: https://www.piwheels.org/simple/transvar/ 2023-09-09T08:48:47,245 Getting page https://www.piwheels.org/simple/transvar/ 2023-09-09T08:48:47,246 Found index url https://www.piwheels.org/simple/ 2023-09-09T08:48:47,518 Fetched page https://www.piwheels.org/simple/transvar/ as text/html 2023-09-09T08:48:47,519 Skipping link: not a file: https://www.piwheels.org/simple/transvar/ 2023-09-09T08:48:47,520 Skipping link: not a file: https://pypi.org/simple/transvar/ 2023-09-09T08:48:47,542 Given no hashes to check 1 links for project 'transvar': discarding no candidates 2023-09-09T08:48:47,560 Collecting transvar==2.3.3.20161203 2023-09-09T08:48:47,563 Created temporary directory: /tmp/pip-unpack-qgx6k5ul 2023-09-09T08:48:47,787 Downloading TransVar-2.3.3.20161203.tar.gz (640 kB) 2023-09-09T08:48:49,211 Added transvar==2.3.3.20161203 from https://files.pythonhosted.org/packages/f0/28/2bd84a4700ef07a998e80e9ad09f7180f4758f68077d854a8541b6b31143/TransVar-2.3.3.20161203.tar.gz to build tracker '/tmp/pip-build-tracker-p5wuc0s9' 2023-09-09T08:48:49,213 Running setup.py (path:/tmp/pip-wheel-5vyoky2z/transvar_702d3e036a0e45ada6addae3d31436d7/setup.py) egg_info for package transvar 2023-09-09T08:48:49,214 Created temporary directory: /tmp/pip-pip-egg-info-18bol09a 2023-09-09T08:48:49,215 Preparing metadata (setup.py): started 2023-09-09T08:48:49,216 Running command python setup.py egg_info 2023-09-09T08:48:50,960 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:510: SetuptoolsDeprecationWarning: Invalid dash-separated options 2023-09-09T08:48:50,960 !! 2023-09-09T08:48:50,962 ******************************************************************************** 2023-09-09T08:48:50,963 Usage of dash-separated 'description-file' will not be supported in future 2023-09-09T08:48:50,963 versions. Please use the underscore name 'description_file' instead. 2023-09-09T08:48:50,965 By 2023-Sep-26, you need to update your project and remove deprecated calls 2023-09-09T08:48:50,966 or your builds will no longer be supported. 2023-09-09T08:48:50,968 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-09T08:48:50,968 ******************************************************************************** 2023-09-09T08:48:50,969 !! 2023-09-09T08:48:50,970 opt = self.warn_dash_deprecation(opt, section) 2023-09-09T08:48:51,328 running egg_info 2023-09-09T08:48:51,331 creating /tmp/pip-pip-egg-info-18bol09a/TransVar.egg-info 2023-09-09T08:48:51,361 writing /tmp/pip-pip-egg-info-18bol09a/TransVar.egg-info/PKG-INFO 2023-09-09T08:48:51,366 writing dependency_links to /tmp/pip-pip-egg-info-18bol09a/TransVar.egg-info/dependency_links.txt 2023-09-09T08:48:51,370 writing requirements to /tmp/pip-pip-egg-info-18bol09a/TransVar.egg-info/requires.txt 2023-09-09T08:48:51,372 writing top-level names to /tmp/pip-pip-egg-info-18bol09a/TransVar.egg-info/top_level.txt 2023-09-09T08:48:51,375 writing manifest file '/tmp/pip-pip-egg-info-18bol09a/TransVar.egg-info/SOURCES.txt' 2023-09-09T08:48:51,513 reading manifest file '/tmp/pip-pip-egg-info-18bol09a/TransVar.egg-info/SOURCES.txt' 2023-09-09T08:48:51,515 reading manifest template 'MANIFEST.in' 2023-09-09T08:48:51,897 writing manifest file '/tmp/pip-pip-egg-info-18bol09a/TransVar.egg-info/SOURCES.txt' 2023-09-09T08:48:52,042 Preparing metadata (setup.py): finished with status 'done' 2023-09-09T08:48:52,046 Source in /tmp/pip-wheel-5vyoky2z/transvar_702d3e036a0e45ada6addae3d31436d7 has version 2.3.3.20161203, which satisfies requirement transvar==2.3.3.20161203 from https://files.pythonhosted.org/packages/f0/28/2bd84a4700ef07a998e80e9ad09f7180f4758f68077d854a8541b6b31143/TransVar-2.3.3.20161203.tar.gz 2023-09-09T08:48:52,047 Removed transvar==2.3.3.20161203 from https://files.pythonhosted.org/packages/f0/28/2bd84a4700ef07a998e80e9ad09f7180f4758f68077d854a8541b6b31143/TransVar-2.3.3.20161203.tar.gz from build tracker '/tmp/pip-build-tracker-p5wuc0s9' 2023-09-09T08:48:52,051 Created temporary directory: /tmp/pip-unpack-y46p81jk 2023-09-09T08:48:52,052 Created temporary directory: /tmp/pip-unpack-nq74uzu2 2023-09-09T08:48:52,056 Building wheels for collected packages: transvar 2023-09-09T08:48:52,060 Created temporary directory: /tmp/pip-wheel-fy3vhcsk 2023-09-09T08:48:52,060 Building wheel for transvar (setup.py): started 2023-09-09T08:48:52,061 Destination directory: /tmp/pip-wheel-fy3vhcsk 2023-09-09T08:48:52,062 Running command python setup.py bdist_wheel 2023-09-09T08:48:52,803 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:510: SetuptoolsDeprecationWarning: Invalid dash-separated options 2023-09-09T08:48:52,803 !! 2023-09-09T08:48:52,804 ******************************************************************************** 2023-09-09T08:48:52,805 Usage of dash-separated 'description-file' will not be supported in future 2023-09-09T08:48:52,805 versions. Please use the underscore name 'description_file' instead. 2023-09-09T08:48:52,806 By 2023-Sep-26, you need to update your project and remove deprecated calls 2023-09-09T08:48:52,807 or your builds will no longer be supported. 2023-09-09T08:48:52,808 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-09T08:48:52,809 ******************************************************************************** 2023-09-09T08:48:52,810 !! 2023-09-09T08:48:52,810 opt = self.warn_dash_deprecation(opt, section) 2023-09-09T08:48:53,128 running bdist_wheel 2023-09-09T08:48:53,197 running build 2023-09-09T08:48:53,198 running build_py 2023-09-09T08:48:53,225 creating build 2023-09-09T08:48:53,225 creating build/lib.linux-armv7l-cpython-311 2023-09-09T08:48:53,226 creating build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:48:53,227 copying transvar/mutation.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:48:53,230 copying transvar/anno.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:48:53,233 copying transvar/record.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:48:53,237 copying transvar/proteinseqs.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:48:53,239 copying transvar/__init__.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:48:53,241 copying transvar/snv.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:48:53,247 copying transvar/utils.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:48:53,255 copying transvar/argparse.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:48:53,272 copying transvar/parser.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:48:53,278 copying transvar/transcripts.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:48:53,284 copying transvar/deletion.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:48:53,291 copying transvar/config.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:48:53,298 copying transvar/insertion.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:48:53,300 copying transvar/codonsearch.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:48:53,302 copying transvar/err.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:48:53,303 copying transvar/version.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:48:53,305 copying transvar/annodb.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:48:53,306 copying transvar/describe.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:48:53,309 copying transvar/mnv.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:48:53,311 copying transvar/faidx.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:48:53,313 copying transvar/region.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:48:53,315 copying transvar/localdb.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:48:53,318 copying transvar/frameshift.py -> build/lib.linux-armv7l-cpython-311/transvar 2023-09-09T08:48:53,320 creating build/lib.linux-armv7l-cpython-311/transvar/ssw 2023-09-09T08:48:53,321 copying transvar/ssw/__init__.py -> build/lib.linux-armv7l-cpython-311/transvar/ssw 2023-09-09T08:48:53,324 running build_ext 2023-09-09T08:48:53,797 building 'transvar.tabix' extension 2023-09-09T08:48:53,797 creating build/temp.linux-armv7l-cpython-311 2023-09-09T08:48:53,798 creating build/temp.linux-armv7l-cpython-311/external 2023-09-09T08:48:53,799 creating build/temp.linux-armv7l-cpython-311/external/pytabix 2023-09-09T08:48:53,800 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 2023-09-09T08:48:54,491 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 2023-09-09T08:48:54,883 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 2023-09-09T08:48:57,716 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 2023-09-09T08:48:58,485 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 2023-09-09T08:48:58,901 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 2023-09-09T08:48:59,507 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 2023-09-09T08:48:59,617 building 'transvar.ssw._sswlib' extension 2023-09-09T08:48:59,618 creating build/temp.linux-armv7l-cpython-311/external/ssw 2023-09-09T08:48:59,619 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 2023-09-09T08:48:59,757 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 2023-09-09T08:48:59,800 external/ssw/ssw.c:38:10: fatal error: emmintrin.h: No such file or directory 2023-09-09T08:48:59,800 38 | #include 2023-09-09T08:48:59,801 | ^~~~~~~~~~~~~ 2023-09-09T08:48:59,802 compilation terminated. 2023-09-09T08:48:59,804 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2023-09-09T08:48:59,955 ERROR: [present-rich] python setup.py bdist_wheel exited with 1 2023-09-09T08:48:59,968 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2023-09-09T08:48:59,968 exec(compile('"'"''"'"''"'"' 2023-09-09T08:48:59,968 # This is -- a caller that pip uses to run setup.py 2023-09-09T08:48:59,968 # 2023-09-09T08:48:59,968 # - It imports setuptools before invoking setup.py, to enable projects that directly 2023-09-09T08:48:59,968 # import from `distutils.core` to work with newer packaging standards. 2023-09-09T08:48:59,968 # - It provides a clear error message when setuptools is not installed. 2023-09-09T08:48:59,968 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2023-09-09T08:48:59,968 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2023-09-09T08:48:59,968 # manifest_maker: standard file '"'"'-c'"'"' not found". 2023-09-09T08:48:59,968 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2023-09-09T08:48:59,968 import os, sys, tokenize 2023-09-09T08:48:59,968 2023-09-09T08:48:59,968 try: 2023-09-09T08:48:59,968 import setuptools 2023-09-09T08:48:59,968 except ImportError as error: 2023-09-09T08:48:59,968 print( 2023-09-09T08:48:59,968 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2023-09-09T08:48:59,968 "the build environment.", 2023-09-09T08:48:59,968 file=sys.stderr, 2023-09-09T08:48:59,968 ) 2023-09-09T08:48:59,968 sys.exit(1) 2023-09-09T08:48:59,968 2023-09-09T08:48:59,968 __file__ = %r 2023-09-09T08:48:59,968 sys.argv[0] = __file__ 2023-09-09T08:48:59,968 2023-09-09T08:48:59,968 if os.path.exists(__file__): 2023-09-09T08:48:59,968 filename = __file__ 2023-09-09T08:48:59,968 with tokenize.open(__file__) as f: 2023-09-09T08:48:59,968 setup_py_code = f.read() 2023-09-09T08:48:59,968 else: 2023-09-09T08:48:59,968 filename = "" 2023-09-09T08:48:59,968 setup_py_code = "from setuptools import setup; setup()" 2023-09-09T08:48:59,968 2023-09-09T08:48:59,968 exec(compile(setup_py_code, filename, "exec")) 2023-09-09T08:48:59,968 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-5vyoky2z/transvar_702d3e036a0e45ada6addae3d31436d7/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-fy3vhcsk[/] 2023-09-09T08:48:59,969 [bold magenta]cwd[/]: /tmp/pip-wheel-5vyoky2z/transvar_702d3e036a0e45ada6addae3d31436d7/ 2023-09-09T08:48:59,970 Building wheel for transvar (setup.py): finished with status 'error' 2023-09-09T08:48:59,971 ERROR: Failed building wheel for transvar 2023-09-09T08:48:59,972 Running setup.py clean for transvar 2023-09-09T08:48:59,973 Running command python setup.py clean 2023-09-09T08:49:00,708 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:510: SetuptoolsDeprecationWarning: Invalid dash-separated options 2023-09-09T08:49:00,708 !! 2023-09-09T08:49:00,709 ******************************************************************************** 2023-09-09T08:49:00,710 Usage of dash-separated 'description-file' will not be supported in future 2023-09-09T08:49:00,710 versions. Please use the underscore name 'description_file' instead. 2023-09-09T08:49:00,711 By 2023-Sep-26, you need to update your project and remove deprecated calls 2023-09-09T08:49:00,712 or your builds will no longer be supported. 2023-09-09T08:49:00,713 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-09T08:49:00,714 ******************************************************************************** 2023-09-09T08:49:00,715 !! 2023-09-09T08:49:00,715 opt = self.warn_dash_deprecation(opt, section) 2023-09-09T08:49:01,035 running clean 2023-09-09T08:49:01,058 removing 'build/temp.linux-armv7l-cpython-311' (and everything under it) 2023-09-09T08:49:01,063 removing 'build/lib.linux-armv7l-cpython-311' (and everything under it) 2023-09-09T08:49:01,070 'build/bdist.linux-armv7l' does not exist -- can't clean it 2023-09-09T08:49:01,071 'build/scripts-3.11' does not exist -- can't clean it 2023-09-09T08:49:01,071 removing 'build' 2023-09-09T08:49:01,197 Failed to build transvar 2023-09-09T08:49:01,199 ERROR: Failed to build one or more wheels 2023-09-09T08:49:01,200 Exception information: 2023-09-09T08:49:01,200 Traceback (most recent call last): 2023-09-09T08:49:01,200 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2023-09-09T08:49:01,200 status = run_func(*args) 2023-09-09T08:49:01,200 ^^^^^^^^^^^^^^^ 2023-09-09T08:49:01,200 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper 2023-09-09T08:49:01,200 return func(self, options, args) 2023-09-09T08:49:01,200 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-09T08:49:01,200 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run 2023-09-09T08:49:01,200 raise CommandError("Failed to build one or more wheels") 2023-09-09T08:49:01,200 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2023-09-09T08:49:01,204 Removed build tracker: '/tmp/pip-build-tracker-p5wuc0s9'