2022-10-26T01:43:41,095 Created temporary directory: /tmp/pip-ephem-wheel-cache-2onoxusj 2022-10-26T01:43:41,097 Created temporary directory: /tmp/pip-build-tracker-xt0ek6r5 2022-10-26T01:43:41,097 Initialized build tracking at /tmp/pip-build-tracker-xt0ek6r5 2022-10-26T01:43:41,098 Created build tracker: /tmp/pip-build-tracker-xt0ek6r5 2022-10-26T01:43:41,098 Entered build tracker: /tmp/pip-build-tracker-xt0ek6r5 2022-10-26T01:43:41,098 Created temporary directory: /tmp/pip-wheel-sbx0xzwc 2022-10-26T01:43:41,101 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2022-10-26T01:43:41,104 Created temporary directory: /tmp/pip-ephem-wheel-cache-drg22o20 2022-10-26T01:43:41,131 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-10-26T01:43:41,134 2 location(s) to search for versions of whatshap: 2022-10-26T01:43:41,134 * https://pypi.org/simple/whatshap/ 2022-10-26T01:43:41,134 * https://www.piwheels.org/simple/whatshap/ 2022-10-26T01:43:41,134 Fetching project page and analyzing links: https://pypi.org/simple/whatshap/ 2022-10-26T01:43:41,135 Getting page https://pypi.org/simple/whatshap/ 2022-10-26T01:43:41,136 Found index url https://pypi.org/simple 2022-10-26T01:43:41,189 Fetched page https://pypi.org/simple/whatshap/ as application/vnd.pypi.simple.v1+json 2022-10-26T01:43:41,199 Found link https://files.pythonhosted.org/packages/35/95/43ff2304cd59ade39e64aadaeaec48e8c12bbe6262bcbbbd7b7d89487757/whatshap-0.9.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.9 2022-10-26T01:43:41,200 Found link https://files.pythonhosted.org/packages/f0/4b/f2b882803ac66b969414d8427ee8b4ca2c29b17cfead0fd85f349dc66983/whatshap-0.10.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.10 2022-10-26T01:43:41,200 Found link https://files.pythonhosted.org/packages/fc/dc/30559c28fb54985773fb242f5768fc206e054e44e45962a32cf4fd29a794/whatshap-0.11.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.11 2022-10-26T01:43:41,200 Found link https://files.pythonhosted.org/packages/01/84/31a5ea338647d0256a4a5c57e98d7a563f387e6a47f1e26299b89e3f2da1/whatshap-0.12.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.12 2022-10-26T01:43:41,201 Found link https://files.pythonhosted.org/packages/e2/f3/c71cb4bc3ba3b1234ee0c5fe729c60440164e07437695ca09c61750e0e11/whatshap-0.13.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.13 2022-10-26T01:43:41,201 Found link https://files.pythonhosted.org/packages/cd/d3/a63285d15b0da196a259197e46d9f61a852d1b3c94800f4a82ca4e31e307/whatshap-0.14.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.14 2022-10-26T01:43:41,201 Found link https://files.pythonhosted.org/packages/ec/d4/d6c19b716926895ee3def919ab23194212172ed5cf89ccb91c2949fb258d/whatshap-0.14.1.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.14.1 2022-10-26T01:43:41,201 Found link https://files.pythonhosted.org/packages/ca/13/6454e5e8f6c858a203378b3e22f13518f092ba85aa6d7a9a9796d22c28e0/whatshap-0.15.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.15 2022-10-26T01:43:41,202 Found link https://files.pythonhosted.org/packages/3d/cb/55730a8713ecba10f6d987dbd935ba31ded92f9af1ddd250896f3c1cfc3b/whatshap-0.16.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.16 2022-10-26T01:43:41,202 Found link 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https://files.pythonhosted.org/packages/94/69/20b124a032b37c73ac56708744cbf2542cbc3e31390f261853ca5a6f62fe/whatshap-1.1.tar.gz (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6), version: 1.1 2022-10-26T01:43:41,207 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/ce/5e/0c32569323ea5e7c036cd9344aa669d92e4a30bbcd4a00dda5483dad67a4/whatshap-1.2-cp36-cp36m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6) 2022-10-26T01:43:41,207 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/c0/b0/0055bf0099361e24f02851b3df68d75e1165a7e13d8b6c4a5bbf1215f924/whatshap-1.2-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6) 2022-10-26T01:43:41,207 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/43/09/3fe5c7130f5356b2b7b911539b52c090e2ee6532c14fc3f29fdbf6c2b569/whatshap-1.2-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6) 2022-10-26T01:43:41,207 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/d1/af/55a5fe140b3a0491c7a19b961b8b6275573194827fb52c17908b2e2699b5/whatshap-1.2-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6) 2022-10-26T01:43:41,208 Found link https://files.pythonhosted.org/packages/24/ba/a6b7ded0e342f0cdeb268e0e92b1c0812ca9c0804e11efc8c4e7e5cb6be9/whatshap-1.2.tar.gz (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6), version: 1.2 2022-10-26T01:43:41,208 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/19/36/1423d4adb6f4d7e58f5fdf8c59aaa8b5cec9d73bb5b2450f17f4089e8438/whatshap-1.2.1-cp36-cp36m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6) 2022-10-26T01:43:41,208 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/3f/9c/52ce1b726a9b98f628c468b30877edc720c6c8022ae0d13fee6088f894b6/whatshap-1.2.1-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6) 2022-10-26T01:43:41,209 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/22/c1/d7295d4b3732dc286990b85348401b3bf932bdcb196162f14100472683f3/whatshap-1.2.1-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6) 2022-10-26T01:43:41,209 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/ff/36/181d416f2c1557879d2647e73964bd0d5d2fd3b79376ec3463435d2363ba/whatshap-1.2.1-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6) 2022-10-26T01:43:41,209 Found link https://files.pythonhosted.org/packages/e1/e3/84376a94a15622efc336fe72ffb37d448b91abfe5fa21421684495e30eb9/whatshap-1.2.1.tar.gz (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6), version: 1.2.1 2022-10-26T01:43:41,210 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/34/c8/7365412dc082fc9b1a0415cde547086f44e0196148ec60ffdd49afc8ecf5/whatshap-1.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6) 2022-10-26T01:43:41,210 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/76/52/dca5eac4abe3642ccf23b7dbbf4283589e4065c13f5bd9240e84c3227b4e/whatshap-1.3-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6) 2022-10-26T01:43:41,210 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/08/df/825622346a1833f3b1fc5b89f613b711eb1003cb2a04986ad3016b22bae3/whatshap-1.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6) 2022-10-26T01:43:41,210 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/36/4a/c1dc0eb7ebde0b5e5ad75d202f1c994399ca25bab7a31fe56da18185865f/whatshap-1.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6) 2022-10-26T01:43:41,211 Found link 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https://files.pythonhosted.org/packages/3f/86/778bbef5c06bdf48c738fdcd64c0a947398d78a168d1dfc949fc7665afa2/whatshap-1.6-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7) 2022-10-26T01:43:41,214 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/9d/60/749fe7dcbb28f21abc3190a171443c8f78d7a20a1a1dfac592966fb55dc4/whatshap-1.6-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7) 2022-10-26T01:43:41,214 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/cd/76/28f1ce30b1cf0a26eae2a508d057b78425595104780955b36e938ac7fcbe/whatshap-1.6-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7) 2022-10-26T01:43:41,215 Found link https://files.pythonhosted.org/packages/e8/90/09feab715cafd8ca8bb664dc9dee9058a4db861adf50e0c1a4ebc86b07cc/whatshap-1.6.tar.gz (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7), version: 1.6 2022-10-26T01:43:41,215 Fetching project page and analyzing links: https://www.piwheels.org/simple/whatshap/ 2022-10-26T01:43:41,216 Getting page https://www.piwheels.org/simple/whatshap/ 2022-10-26T01:43:41,217 Found index url https://www.piwheels.org/simple 2022-10-26T01:43:41,384 Fetched page https://www.piwheels.org/simple/whatshap/ as text/html 2022-10-26T01:43:41,397 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.18-cp37-cp37m-linux_armv7l.whl#sha256=b81040280694883d7079a4b3e449bba14fc4d30f293e9a1d76a1e0578ac01cba (from https://www.piwheels.org/simple/whatshap/) (requires-python:>=3.4) 2022-10-26T01:43:41,398 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.18-cp37-cp37m-linux_armv6l.whl#sha256=b81040280694883d7079a4b3e449bba14fc4d30f293e9a1d76a1e0578ac01cba (from https://www.piwheels.org/simple/whatshap/) (requires-python:>=3.4) 2022-10-26T01:43:41,398 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.18-cp34-cp34m-linux_armv6l.whl#sha256=226c2159db0239fcad3b0d9731ae11ad7f161e18a0f51b5d76fbb7aa02bc5b12 (from https://www.piwheels.org/simple/whatshap/) (requires-python:>=3.4) 2022-10-26T01:43:41,398 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.18-cp34-cp34m-linux_armv7l.whl#sha256=226c2159db0239fcad3b0d9731ae11ad7f161e18a0f51b5d76fbb7aa02bc5b12 (from https://www.piwheels.org/simple/whatshap/) (requires-python:>=3.4) 2022-10-26T01:43:41,398 Skipping link: No binaries permitted for whatshap: 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https://www.piwheels.org/simple/whatshap/) 2022-10-26T01:43:41,400 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.17-cp34-cp34m-linux_armv6l.whl#sha256=57ed4c07b260ca5103118fe34d7875af69bcda84b3267f3c8a96147f5475b355 (from https://www.piwheels.org/simple/whatshap/) 2022-10-26T01:43:41,400 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.16-cp34-cp34m-linux_armv7l.whl#sha256=f220db8040faaacd90867ade6d504314e1412588bf15490cd43486b80012a5cb (from https://www.piwheels.org/simple/whatshap/) 2022-10-26T01:43:41,400 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.16-cp34-cp34m-linux_armv6l.whl#sha256=f220db8040faaacd90867ade6d504314e1412588bf15490cd43486b80012a5cb (from https://www.piwheels.org/simple/whatshap/) 2022-10-26T01:43:41,400 Skipping link: No binaries permitted for whatshap: 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https://www.piwheels.org/simple/whatshap/) 2022-10-26T01:43:41,401 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.15-cp35-cp35m-linux_armv6l.whl#sha256=11a60ad9e4b9824b86108d6157dbb52400aaa31d739e08a8ccefaac8f79e4d3c (from https://www.piwheels.org/simple/whatshap/) 2022-10-26T01:43:41,401 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.15-cp35-cp35m-linux_armv7l.whl#sha256=11a60ad9e4b9824b86108d6157dbb52400aaa31d739e08a8ccefaac8f79e4d3c (from https://www.piwheels.org/simple/whatshap/) 2022-10-26T01:43:41,402 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.15-cp34-cp34m-linux_armv7l.whl#sha256=8a603d7a9a636e78f0f8297e9ad41b9b829dc8bb2bed01428406d595852b7bb8 (from https://www.piwheels.org/simple/whatshap/) 2022-10-26T01:43:41,402 Skipping link: No binaries permitted for whatshap: 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(from https://www.piwheels.org/simple/whatshap/) 2022-10-26T01:43:41,403 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.14.1-cp35-cp35m-linux_armv7l.whl#sha256=d814d13967bc9b15f994573546cdeed83bac50694e44fb4105c3ae83bbfd97b7 (from https://www.piwheels.org/simple/whatshap/) 2022-10-26T01:43:41,403 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.14-cp35-cp35m-linux_armv6l.whl#sha256=e0ac1dca2abae0b88b1fa764b4d4ca853bb6bc4b02de20b09e8d51448b20aafc (from https://www.piwheels.org/simple/whatshap/) 2022-10-26T01:43:41,403 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.14-cp35-cp35m-linux_armv7l.whl#sha256=e0ac1dca2abae0b88b1fa764b4d4ca853bb6bc4b02de20b09e8d51448b20aafc (from https://www.piwheels.org/simple/whatshap/) 2022-10-26T01:43:41,403 Skipping link: No binaries permitted for whatshap: 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https://www.piwheels.org/simple/whatshap/) 2022-10-26T01:43:41,406 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.11-cp34-cp34m-linux_armv7l.whl#sha256=528f0411be5d1bd6559dd1531b52beb67ca918a09fd418fd2921199f88ff71ef (from https://www.piwheels.org/simple/whatshap/) 2022-10-26T01:43:41,406 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.11-cp35-cp35m-linux_armv6l.whl#sha256=48a0027e08f6762e26e61673a253a95ecda25e8f32a31a8cbd3655365c25c051 (from https://www.piwheels.org/simple/whatshap/) 2022-10-26T01:43:41,406 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.11-cp35-cp35m-linux_armv7l.whl#sha256=48a0027e08f6762e26e61673a253a95ecda25e8f32a31a8cbd3655365c25c051 (from https://www.piwheels.org/simple/whatshap/) 2022-10-26T01:43:41,406 Skipping link: No binaries permitted for whatshap: 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https://www.piwheels.org/simple/whatshap/) 2022-10-26T01:43:41,407 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.9-cp35-cp35m-linux_armv7l.whl#sha256=d3ebf8ce2fc15a5397ece9beb236c6e54c2653d414d727f48aae8e025b674a14 (from https://www.piwheels.org/simple/whatshap/) 2022-10-26T01:43:41,407 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.9-cp35-cp35m-linux_armv6l.whl#sha256=d3ebf8ce2fc15a5397ece9beb236c6e54c2653d414d727f48aae8e025b674a14 (from https://www.piwheels.org/simple/whatshap/) 2022-10-26T01:43:41,407 Skipping link: not a file: https://www.piwheels.org/simple/whatshap/ 2022-10-26T01:43:41,408 Skipping link: not a file: https://pypi.org/simple/whatshap/ 2022-10-26T01:43:41,428 Given no hashes to check 1 links for project 'whatshap': discarding no candidates 2022-10-26T01:43:41,445 Collecting whatshap==1.5 2022-10-26T01:43:41,447 Created temporary directory: /tmp/pip-unpack-khijwoxw 2022-10-26T01:43:41,496 Downloading whatshap-1.5.tar.gz (5.1 MB) 2022-10-26T01:43:42,909 Added whatshap==1.5 from https://files.pythonhosted.org/packages/2a/0a/71c5db75b44c886e492294328b41f970bfcfdef1c409e8ed3981a0ff519e/whatshap-1.5.tar.gz to build tracker '/tmp/pip-build-tracker-xt0ek6r5' 2022-10-26T01:43:42,914 Created temporary directory: /tmp/pip-build-env-nrs6m5xq 2022-10-26T01:43:42,922 Installing build dependencies: started 2022-10-26T01:43:42,922 Running command pip subprocess to install build dependencies 2022-10-26T01:43:44,113 Using pip 22.3 from /usr/local/lib/python3.9/dist-packages/pip (python 3.9) 2022-10-26T01:43:44,477 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2022-10-26T01:43:44,501 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-10-26T01:43:46,110 Collecting setuptools>=43 2022-10-26T01:43:46,280 Using cached https://www.piwheels.org/simple/setuptools/setuptools-65.5.0-py3-none-any.whl (1.2 MB) 2022-10-26T01:43:46,725 Collecting setuptools_scm 2022-10-26T01:43:46,745 Using cached https://www.piwheels.org/simple/setuptools-scm/setuptools_scm-7.0.5-py3-none-any.whl (42 kB) 2022-10-26T01:43:48,146 Collecting cython~=0.29.20 2022-10-26T01:43:48,632 Using cached https://www.piwheels.org/simple/cython/Cython-0.29.32-cp39-cp39-linux_armv7l.whl (5.0 MB) 2022-10-26T01:43:49,038 Collecting packaging>=20.0 2022-10-26T01:43:49,056 Using cached https://www.piwheels.org/simple/packaging/packaging-21.3-py3-none-any.whl (40 kB) 2022-10-26T01:43:49,187 Collecting tomli>=1.0.0 2022-10-26T01:43:49,204 Using cached https://www.piwheels.org/simple/tomli/tomli-2.0.1-py3-none-any.whl (12 kB) 2022-10-26T01:43:49,325 Collecting typing-extensions 2022-10-26T01:43:49,344 Using cached https://www.piwheels.org/simple/typing-extensions/typing_extensions-4.4.0-py3-none-any.whl (26 kB) 2022-10-26T01:43:49,612 Collecting pyparsing!=3.0.5,>=2.0.2 2022-10-26T01:43:49,653 Using cached https://www.piwheels.org/simple/pyparsing/pyparsing-3.0.9-py3-none-any.whl (98 kB) 2022-10-26T01:43:51,462 Installing collected packages: typing-extensions, tomli, setuptools, pyparsing, cython, packaging, setuptools_scm 2022-10-26T01:43:57,569 Creating /tmp/pip-build-env-nrs6m5xq/overlay/bin 2022-10-26T01:43:57,571 changing mode of /tmp/pip-build-env-nrs6m5xq/overlay/bin/cygdb to 755 2022-10-26T01:43:57,573 changing mode of /tmp/pip-build-env-nrs6m5xq/overlay/bin/cython to 755 2022-10-26T01:43:57,575 changing mode of /tmp/pip-build-env-nrs6m5xq/overlay/bin/cythonize to 755 2022-10-26T01:43:57,902 Successfully installed cython-0.29.32 packaging-21.3 pyparsing-3.0.9 setuptools-65.5.0 setuptools_scm-7.0.5 tomli-2.0.1 typing-extensions-4.4.0 2022-10-26T01:43:58,253 Installing build dependencies: finished with status 'done' 2022-10-26T01:43:58,259 Getting requirements to build wheel: started 2022-10-26T01:43:58,260 Running command Getting requirements to build wheel 2022-10-26T01:44:05,827 warning: whatshap/priorityqueue.pyx:201:7: Unreachable code 2022-10-26T01:44:06,058 Compiling whatshap/core.pyx because it depends on /tmp/pip-build-env-nrs6m5xq/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2022-10-26T01:44:06,058 Compiling whatshap/priorityqueue.pyx because it depends on /tmp/pip-build-env-nrs6m5xq/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2022-10-26T01:44:06,058 Compiling whatshap/align.pyx because it depends on /tmp/pip-build-env-nrs6m5xq/overlay/lib/python3.9/site-packages/Cython/Includes/libc/__init__.pxd. 2022-10-26T01:44:06,058 [1/3] Cythonizing whatshap/align.pyx 2022-10-26T01:44:06,058 [2/3] Cythonizing whatshap/core.pyx 2022-10-26T01:44:06,059 [3/3] Cythonizing whatshap/priorityqueue.pyx 2022-10-26T01:44:06,297 running egg_info 2022-10-26T01:44:06,304 writing whatshap.egg-info/PKG-INFO 2022-10-26T01:44:06,306 writing dependency_links to whatshap.egg-info/dependency_links.txt 2022-10-26T01:44:06,309 writing entry points to whatshap.egg-info/entry_points.txt 2022-10-26T01:44:06,311 writing requirements to whatshap.egg-info/requires.txt 2022-10-26T01:44:06,313 writing top-level names to whatshap.egg-info/top_level.txt 2022-10-26T01:44:06,373 listing git files failed - pretending there aren't any 2022-10-26T01:44:06,386 reading manifest file 'whatshap.egg-info/SOURCES.txt' 2022-10-26T01:44:06,441 reading manifest template 'MANIFEST.in' 2022-10-26T01:44:06,455 adding license file 'LICENSE' 2022-10-26T01:44:06,472 writing manifest file 'whatshap.egg-info/SOURCES.txt' 2022-10-26T01:44:07,080 Getting requirements to build wheel: finished with status 'done' 2022-10-26T01:44:07,099 Installing backend dependencies: started 2022-10-26T01:44:07,100 Running command pip subprocess to install backend dependencies 2022-10-26T01:44:08,293 Using pip 22.3 from /usr/local/lib/python3.9/dist-packages/pip (python 3.9) 2022-10-26T01:44:08,660 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2022-10-26T01:44:08,685 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-10-26T01:44:09,141 Collecting wheel 2022-10-26T01:44:09,160 Using cached https://www.piwheels.org/simple/wheel/wheel-0.37.1-py2.py3-none-any.whl (35 kB) 2022-10-26T01:44:10,543 Installing collected packages: wheel 2022-10-26T01:44:10,684 Creating /tmp/pip-build-env-nrs6m5xq/normal/bin 2022-10-26T01:44:10,686 changing mode of /tmp/pip-build-env-nrs6m5xq/normal/bin/wheel to 755 2022-10-26T01:44:10,699 Successfully installed wheel-0.37.1 2022-10-26T01:44:10,921 Installing backend dependencies: finished with status 'done' 2022-10-26T01:44:10,924 Created temporary directory: /tmp/pip-modern-metadata-o49i7ugy 2022-10-26T01:44:10,927 Preparing metadata (pyproject.toml): started 2022-10-26T01:44:10,928 Running command Preparing metadata (pyproject.toml) 2022-10-26T01:44:12,657 running dist_info 2022-10-26T01:44:12,678 creating /tmp/pip-modern-metadata-o49i7ugy/whatshap.egg-info 2022-10-26T01:44:12,685 writing /tmp/pip-modern-metadata-o49i7ugy/whatshap.egg-info/PKG-INFO 2022-10-26T01:44:12,687 writing dependency_links to /tmp/pip-modern-metadata-o49i7ugy/whatshap.egg-info/dependency_links.txt 2022-10-26T01:44:12,689 writing entry points to /tmp/pip-modern-metadata-o49i7ugy/whatshap.egg-info/entry_points.txt 2022-10-26T01:44:12,691 writing requirements to /tmp/pip-modern-metadata-o49i7ugy/whatshap.egg-info/requires.txt 2022-10-26T01:44:12,692 writing top-level names to /tmp/pip-modern-metadata-o49i7ugy/whatshap.egg-info/top_level.txt 2022-10-26T01:44:12,693 writing manifest file '/tmp/pip-modern-metadata-o49i7ugy/whatshap.egg-info/SOURCES.txt' 2022-10-26T01:44:12,753 listing git files failed - pretending there aren't any 2022-10-26T01:44:12,762 reading manifest file '/tmp/pip-modern-metadata-o49i7ugy/whatshap.egg-info/SOURCES.txt' 2022-10-26T01:44:12,768 reading manifest template 'MANIFEST.in' 2022-10-26T01:44:12,790 adding license file 'LICENSE' 2022-10-26T01:44:12,798 writing manifest file '/tmp/pip-modern-metadata-o49i7ugy/whatshap.egg-info/SOURCES.txt' 2022-10-26T01:44:12,799 creating '/tmp/pip-modern-metadata-o49i7ugy/whatshap-1.5.dist-info' 2022-10-26T01:44:12,890 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2022-10-26T01:44:13,085 Preparing metadata (pyproject.toml): finished with status 'done' 2022-10-26T01:44:13,092 Source in /tmp/pip-wheel-sbx0xzwc/whatshap_57cc939431e34aa28170d7016512d06d has version 1.5, which satisfies requirement whatshap==1.5 from https://files.pythonhosted.org/packages/2a/0a/71c5db75b44c886e492294328b41f970bfcfdef1c409e8ed3981a0ff519e/whatshap-1.5.tar.gz 2022-10-26T01:44:13,093 Removed whatshap==1.5 from https://files.pythonhosted.org/packages/2a/0a/71c5db75b44c886e492294328b41f970bfcfdef1c409e8ed3981a0ff519e/whatshap-1.5.tar.gz from build tracker '/tmp/pip-build-tracker-xt0ek6r5' 2022-10-26T01:44:13,100 Created temporary directory: /tmp/pip-unpack-lkcl7ut5 2022-10-26T01:44:13,100 Building wheels for collected packages: whatshap 2022-10-26T01:44:13,105 Created temporary directory: /tmp/pip-wheel-vt4jtfpy 2022-10-26T01:44:13,106 Destination directory: /tmp/pip-wheel-vt4jtfpy 2022-10-26T01:44:13,108 Building wheel for whatshap (pyproject.toml): started 2022-10-26T01:44:13,109 Running command Building wheel for whatshap (pyproject.toml) 2022-10-26T01:44:14,759 running bdist_wheel 2022-10-26T01:44:14,780 running build 2022-10-26T01:44:14,781 running build_py 2022-10-26T01:44:14,791 creating build 2022-10-26T01:44:14,792 creating build/lib.linux-armv7l-cpython-39 2022-10-26T01:44:14,792 creating build/lib.linux-armv7l-cpython-39/whatshap 2022-10-26T01:44:14,794 copying whatshap/__init__.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-10-26T01:44:14,796 copying whatshap/timer.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-10-26T01:44:14,798 copying whatshap/verification.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-10-26T01:44:14,800 copying whatshap/variant.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-10-26T01:44:14,802 copying whatshap/utils.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-10-26T01:44:14,804 copying whatshap/variants.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-10-26T01:44:14,807 copying whatshap/pedigree.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-10-26T01:44:14,809 copying whatshap/threading.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-10-26T01:44:14,812 copying whatshap/reorder.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-10-26T01:44:14,815 copying whatshap/polyphaseutil.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-10-26T01:44:14,817 copying whatshap/coverage.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-10-26T01:44:14,819 copying whatshap/graph.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-10-26T01:44:14,821 copying whatshap/polyphaseplots.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-10-26T01:44:14,824 copying whatshap/testhelpers.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-10-26T01:44:14,826 copying whatshap/args.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-10-26T01:44:14,828 copying whatshap/merge.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-10-26T01:44:14,831 copying whatshap/__main__.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-10-26T01:44:14,833 copying whatshap/_version.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-10-26T01:44:14,835 copying whatshap/vcf.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-10-26T01:44:14,838 copying whatshap/bam.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-10-26T01:44:14,842 creating build/lib.linux-armv7l-cpython-39/whatshap/cli 2022-10-26T01:44:14,843 copying whatshap/cli/__init__.py -> build/lib.linux-armv7l-cpython-39/whatshap/cli 2022-10-26T01:44:14,856 copying whatshap/cli/phase.py -> build/lib.linux-armv7l-cpython-39/whatshap/cli 2022-10-26T01:44:14,860 copying whatshap/cli/hapcut2vcf.py -> build/lib.linux-armv7l-cpython-39/whatshap/cli 2022-10-26T01:44:14,862 copying whatshap/cli/polyphase.py -> build/lib.linux-armv7l-cpython-39/whatshap/cli 2022-10-26T01:44:14,865 copying whatshap/cli/find_snv_candidates.py -> build/lib.linux-armv7l-cpython-39/whatshap/cli 2022-10-26T01:44:14,868 copying whatshap/cli/genotype.py -> build/lib.linux-armv7l-cpython-39/whatshap/cli 2022-10-26T01:44:14,871 copying whatshap/cli/compare.py -> build/lib.linux-armv7l-cpython-39/whatshap/cli 2022-10-26T01:44:14,874 copying whatshap/cli/split.py -> build/lib.linux-armv7l-cpython-39/whatshap/cli 2022-10-26T01:44:14,877 copying whatshap/cli/haplotag.py -> build/lib.linux-armv7l-cpython-39/whatshap/cli 2022-10-26T01:44:14,880 copying whatshap/cli/unphase.py -> build/lib.linux-armv7l-cpython-39/whatshap/cli 2022-10-26T01:44:14,882 copying whatshap/cli/stats.py -> build/lib.linux-armv7l-cpython-39/whatshap/cli 2022-10-26T01:44:14,887 running build_ext 2022-10-26T01:44:14,893 building 'whatshap.core' extension 2022-10-26T01:44:14,894 creating build/temp.linux-armv7l-cpython-39 2022-10-26T01:44:14,895 creating build/temp.linux-armv7l-cpython-39/src 2022-10-26T01:44:14,897 creating build/temp.linux-armv7l-cpython-39/src/hapchat 2022-10-26T01:44:14,898 creating build/temp.linux-armv7l-cpython-39/src/polyphase 2022-10-26T01:44:14,900 creating build/temp.linux-armv7l-cpython-39/whatshap 2022-10-26T01:44:14,901 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.9 -c src/backwardcolumniterator.cpp -o build/temp.linux-armv7l-cpython-39/src/backwardcolumniterator.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-10-26T01:44:16,553 In file included from /usr/include/c++/10/cassert:44, 2022-10-26T01:44:16,553 from src/backwardcolumniterator.cpp:1: 2022-10-26T01:44:16,553 src/backwardcolumniterator.cpp: In member function ‘void BackwardColumnIterator::jump_to_column(int)’: 2022-10-26T01:44:16,554 src/backwardcolumniterator.cpp:121:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-10-26T01:44:16,554 121 | assert(k < positions->size()); 2022-10-26T01:44:16,554 | ~~^~~~~~~~~~~~~~~~~~~ 2022-10-26T01:44:16,554 src/backwardcolumniterator.cpp:140:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2022-10-26T01:44:16,554 140 | assert(active_entry < read->getVariantCount()); 2022-10-26T01:44:16,555 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2022-10-26T01:44:18,125 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.9 -c src/binomial.cpp -o build/temp.linux-armv7l-cpython-39/src/binomial.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-10-26T01:44:18,400 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.9 -c src/columnindexingiterator.cpp -o build/temp.linux-armv7l-cpython-39/src/columnindexingiterator.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-10-26T01:44:19,474 src/columnindexingiterator.cpp: In member function ‘unsigned int ColumnIndexingIterator::index_forward_projection(unsigned int)’: 2022-10-26T01:44:19,474 src/columnindexingiterator.cpp:90:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-10-26T01:44:19,474 90 | for(int j=0; j< parent->read_ids.size(); ++j) { 2022-10-26T01:44:19,474 | ~^~~~~~~~~~~~~~~~~~~~~~~~~ 2022-10-26T01:44:19,475 src/columnindexingiterator.cpp:92:8: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-10-26T01:44:19,475 92 | if(m != -1) { 2022-10-26T01:44:19,475 | ~~^~~~~ 2022-10-26T01:44:19,475 src/columnindexingiterator.cpp:89:15: warning: unused variable ‘s’ [-Wunused-variable] 2022-10-26T01:44:19,475 89 | unsigned int s = 1; 2022-10-26T01:44:19,476 | ^ 2022-10-26T01:44:19,762 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.9 -c src/columnindexingscheme.cpp -o build/temp.linux-armv7l-cpython-39/src/columnindexingscheme.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-10-26T01:44:20,825 src/columnindexingscheme.cpp: In constructor ‘ColumnIndexingScheme::ColumnIndexingScheme(const ColumnIndexingScheme*, const std::vector&)’: 2022-10-26T01:44:20,825 src/columnindexingscheme.cpp:22:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-10-26T01:44:20,825 22 | while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-10-26T01:44:20,826 22 | while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-10-26T01:44:20,828 71 | while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-10-26T01:44:20,829 71 | while ((iread_ids.size()) && (j > ColumnIterator::get_next()’: 2022-10-26T01:44:22,885 src/columniterator.cpp:105:33: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2022-10-26T01:44:22,885 105 | assert(list_it->active_entry < read->getVariantCount()); 2022-10-26T01:44:22,885 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2022-10-26T01:44:22,903 src/columniterator.cpp: In member function ‘void ColumnIterator::jump_to_column(size_t)’: 2022-10-26T01:44:22,904 src/columniterator.cpp:161:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2022-10-26T01:44:22,904 161 | assert(active_entry < read->getVariantCount()); 2022-10-26T01:44:22,904 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2022-10-26T01:44:24,523 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.9 -c src/entry.cpp -o build/temp.linux-armv7l-cpython-39/src/entry.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-10-26T01:44:25,495 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.9 -c src/genotype.cpp -o build/temp.linux-armv7l-cpython-39/src/genotype.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-10-26T01:44:27,845 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.9 -c src/genotypecolumncostcomputer.cpp -o build/temp.linux-armv7l-cpython-39/src/genotypecolumncostcomputer.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-10-26T01:44:30,590 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.9 -c src/genotypedistribution.cpp -o build/temp.linux-armv7l-cpython-39/src/genotypedistribution.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-10-26T01:44:31,757 src/genotypedistribution.cpp: In member function ‘double GenotypeDistribution::errorProbability() const’: 2022-10-26T01:44:31,757 src/genotypedistribution.cpp:55:9: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2022-10-26T01:44:31,757 55 | if (i == best_index) continue; 2022-10-26T01:44:31,757 | ~~^~~~~~~~~~~~~ 2022-10-26T01:44:32,218 In file included from /usr/include/c++/10/vector:72, 2022-10-26T01:44:32,218 from src/genotypedistribution.h:4, 2022-10-26T01:44:32,218 from src/genotypedistribution.cpp:5: 2022-10-26T01:44:32,218 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2022-10-26T01:44:32,218 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-10-26T01:44:32,219 426 | vector<_Tp, _Alloc>:: 2022-10-26T01:44:32,219 | ^~~~~~~~~~~~~~~~~~~ 2022-10-26T01:44:32,252 In file included from /usr/include/c++/10/vector:67, 2022-10-26T01:44:32,252 from src/genotypedistribution.h:4, 2022-10-26T01:44:32,253 from src/genotypedistribution.cpp:5: 2022-10-26T01:44:32,253 /usr/include/c++/10/bits/stl_vector.h: In constructor ‘GenotypeDistribution::GenotypeDistribution(double, double, double)’: 2022-10-26T01:44:32,253 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-10-26T01:44:32,253 1198 | _M_realloc_insert(end(), __x); 2022-10-26T01:44:32,253 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-10-26T01:44:32,253 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-10-26T01:44:32,253 1198 | _M_realloc_insert(end(), __x); 2022-10-26T01:44:32,254 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-10-26T01:44:32,254 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-10-26T01:44:32,254 1198 | _M_realloc_insert(end(), __x); 2022-10-26T01:44:32,254 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-10-26T01:44:32,436 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.9 -c src/genotypedptable.cpp -o build/temp.linux-armv7l-cpython-39/src/genotypedptable.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-10-26T01:44:34,531 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::clear_forward_table()’: 2022-10-26T01:44:34,532 src/genotypedptable.cpp:61:12: warning: unused variable ‘column_count’ [-Wunused-variable] 2022-10-26T01:44:34,532 61 | size_t column_count = input_column_iterator.get_column_count(); 2022-10-26T01:44:34,532 | ^~~~~~~~~~~~ 2022-10-26T01:44:34,586 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_index()’: 2022-10-26T01:44:34,587 src/genotypedptable.cpp:91:18: warning: unused variable ‘transmission_configurations’ [-Wunused-variable] 2022-10-26T01:44:34,587 91 | unsigned int transmission_configurations = pow(4, pedigree->triple_count()); 2022-10-26T01:44:34,587 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-10-26T01:44:34,590 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_backward_prob()’: 2022-10-26T01:44:34,591 src/genotypedptable.cpp:152:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2022-10-26T01:44:34,591 152 | if ((k>1) && (column_index < column_count-1) && (((column_index+1)%k) != 0)) { 2022-10-26T01:44:34,591 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2022-10-26T01:44:34,594 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_forward_prob()’: 2022-10-26T01:44:34,594 src/genotypedptable.cpp:178:12: warning: unused variable ‘k’ [-Wunused-variable] 2022-10-26T01:44:34,594 178 | size_t k = (size_t)sqrt(input_column_iterator.get_column_count()); 2022-10-26T01:44:34,594 | ^ 2022-10-26T01:44:38,315 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.9 -c src/genotyper.cpp -o build/temp.linux-armv7l-cpython-39/src/genotyper.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-10-26T01:44:40,627 In file included from /usr/include/c++/10/vector:72, 2022-10-26T01:44:40,627 from src/columniterator.h:4, 2022-10-26T01:44:40,627 from src/genotyper.cpp:6: 2022-10-26T01:44:40,627 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Genotype&}; _Tp = Genotype; _Alloc = std::allocator]’: 2022-10-26T01:44:40,628 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-10-26T01:44:40,628 426 | vector<_Tp, _Alloc>:: 2022-10-26T01:44:40,628 | ^~~~~~~~~~~~~~~~~~~ 2022-10-26T01:44:40,817 In file included from /usr/include/c++/10/vector:67, 2022-10-26T01:44:40,818 from src/columniterator.h:4, 2022-10-26T01:44:40,818 from src/genotyper.cpp:6: 2022-10-26T01:44:40,818 /usr/include/c++/10/bits/stl_vector.h: In function ‘void compute_genotypes(const ReadSet&, std::vector*, std::vector*, std::vector*)’: 2022-10-26T01:44:40,818 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-10-26T01:44:40,818 1198 | _M_realloc_insert(end(), __x); 2022-10-26T01:44:40,819 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-10-26T01:44:40,987 In file included from /usr/include/c++/10/vector:72, 2022-10-26T01:44:40,987 from src/columniterator.h:4, 2022-10-26T01:44:40,987 from src/genotyper.cpp:6: 2022-10-26T01:44:40,987 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Genotype}; _Tp = Genotype; _Alloc = std::allocator]’: 2022-10-26T01:44:40,987 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-10-26T01:44:40,988 426 | vector<_Tp, _Alloc>:: 2022-10-26T01:44:40,988 | ^~~~~~~~~~~~~~~~~~~ 2022-10-26T01:44:41,099 /usr/include/c++/10/bits/vector.tcc: In function ‘void compute_polyploid_genotypes(const ReadSet&, size_t, std::vector*, std::vector*)’: 2022-10-26T01:44:41,099 /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-10-26T01:44:41,100 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2022-10-26T01:44:41,100 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-10-26T01:44:41,100 In file included from /usr/include/c++/10/vector:67, 2022-10-26T01:44:41,101 from src/columniterator.h:4, 2022-10-26T01:44:41,101 from src/genotyper.cpp:6: 2022-10-26T01:44:41,101 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-10-26T01:44:41,101 1198 | _M_realloc_insert(end(), __x); 2022-10-26T01:44:41,101 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-10-26T01:44:41,510 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.9 -c src/graycodes.cpp -o build/temp.linux-armv7l-cpython-39/src/graycodes.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-10-26T01:44:42,525 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.9 -c src/hapchat/balancedcombinations.cpp -o build/temp.linux-armv7l-cpython-39/src/hapchat/balancedcombinations.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-10-26T01:44:46,142 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.9 -c src/hapchat/basictypes.cpp -o build/temp.linux-armv7l-cpython-39/src/hapchat/basictypes.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-10-26T01:44:47,740 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.9 -c src/hapchat/binomialcoefficient.cpp -o build/temp.linux-armv7l-cpython-39/src/hapchat/binomialcoefficient.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-10-26T01:44:50,305 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.9 -c src/hapchat/hapchatcolumniterator.cpp -o build/temp.linux-armv7l-cpython-39/src/hapchat/hapchatcolumniterator.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-10-26T01:44:52,545 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.9 -c src/hapchat/hapchatcore.cpp -o build/temp.linux-armv7l-cpython-39/src/hapchat/hapchatcore.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-10-26T01:44:54,711 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::run_core()’: 2022-10-26T01:44:54,711 src/hapchat/hapchatcore.cpp:145:11: warning: variable ‘counter_columns’ set but not used [-Wunused-but-set-variable] 2022-10-26T01:44:54,711 145 | Counter counter_columns; 2022-10-26T01:44:54,712 | ^~~~~~~~~~~~~~~ 2022-10-26T01:44:54,721 src/hapchat/hapchatcore.cpp: In member function ‘bool HapChatCore::check_end(HapChatColumnIterator, const std::vector >&, const Pointer&, const bool&)’: 2022-10-26T01:44:54,721 src/hapchat/hapchatcore.cpp:208:74: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-10-26T01:44:54,722 208 | return (!re_run && (hap.is_ended() && (input[pointer][0].get_read_id() == -1))); 2022-10-26T01:44:54,722 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2022-10-26T01:44:54,861 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::dp(const constants_t&, std::vector&, std::vector&, Counter&, Cost&, Counter&, Counter&, Counter&, Counter&, HapChatColumnIterator)’: 2022-10-26T01:44:54,861 src/hapchat/hapchatcore.cpp:939:8: warning: unused variable ‘old_k’ [-Wunused-variable] 2022-10-26T01:44:54,861 939 | int old_k = k_j[input_pointer]; 2022-10-26T01:44:54,861 | ^~~~~ 2022-10-26T01:44:54,879 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::intersect(const Column&, const Column&, const Pointer&, std::vector >&, std::vector >&, std::vector >&, std::vector&, const bool&)’: 2022-10-26T01:44:54,879 src/hapchat/hapchatcore.cpp:1114:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-10-26T01:44:54,879 1114 | (colJ[j].get_read_id() != -1) && 2022-10-26T01:44:54,879 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2022-10-26T01:44:54,879 src/hapchat/hapchatcore.cpp:1115:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-10-26T01:44:54,880 1115 | (colQ[i].get_read_id() != -1)) { 2022-10-26T01:44:54,880 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2022-10-26T01:44:54,881 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::represent_column(const Column&, BitColumn&, Counter&, BitColumn&, Counter&)’: 2022-10-26T01:44:54,882 src/hapchat/hapchatcore.cpp:1159:58: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-10-26T01:44:54,882 1159 | while(cov < column.size() && column[cov].get_read_id() != -1) { 2022-10-26T01:44:54,882 | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2022-10-26T01:44:54,886 src/hapchat/hapchatcore.cpp: In member function ‘int HapChatCore::compute_active_common(const Column&, const Column&, unsigned int&)’: 2022-10-26T01:44:54,886 src/hapchat/hapchatcore.cpp:1294:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-10-26T01:44:54,887 1294 | (colJ[j].get_read_id() != -1) && 2022-10-26T01:44:54,887 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2022-10-26T01:44:54,887 src/hapchat/hapchatcore.cpp:1295:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-10-26T01:44:54,887 1295 | (colQ[i].get_read_id() != -1)) { 2022-10-26T01:44:54,887 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2022-10-26T01:44:54,889 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::insert_col_and_update(std::vector >&, std::vector&, std::vector&, std::vector&, const Pointer&, const Column&, std::vector&, const Counter&)’: 2022-10-26T01:44:54,890 src/hapchat/hapchatcore.cpp:1350:67: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-10-26T01:44:54,890 1350 | if(i < input[pointer].size() && input[pointer][i].get_read_id() != -1) 2022-10-26T01:44:54,890 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2022-10-26T01:44:55,902 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.9 -c src/indexset.cpp -o build/temp.linux-armv7l-cpython-39/src/indexset.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-10-26T01:44:57,465 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.9 -c src/pedigree.cpp -o build/temp.linux-armv7l-cpython-39/src/pedigree.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-10-26T01:44:58,839 In file included from /usr/include/c++/10/cassert:44, 2022-10-26T01:44:58,839 from src/pedigree.cpp:4: 2022-10-26T01:44:58,839 src/pedigree.cpp: In member function ‘void Pedigree::addIndividual(unsigned int, std::vector, std::vector)’: 2022-10-26T01:44:58,839 src/pedigree.cpp:32:26: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2022-10-26T01:44:58,839 32 | assert(genotypes.size() == variant_count); 2022-10-26T01:44:58,840 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2022-10-26T01:44:58,840 src/pedigree.cpp:33:37: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2022-10-26T01:44:58,840 33 | assert(genotype_likelihoods.size() == variant_count); 2022-10-26T01:44:58,840 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2022-10-26T01:44:58,849 src/pedigree.cpp: In member function ‘const Genotype* Pedigree::get_genotype_by_id(unsigned int, unsigned int) const’: 2022-10-26T01:44:58,849 src/pedigree.cpp:70:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] 2022-10-26T01:44:58,849 70 | assert(variant_index < variant_count); 2022-10-26T01:44:58,849 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2022-10-26T01:44:58,850 src/pedigree.cpp: In member function ‘const PhredGenotypeLikelihoods* Pedigree::get_genotype_likelihoods_by_id(unsigned int, unsigned int) const’: 2022-10-26T01:44:58,850 src/pedigree.cpp:81:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] 2022-10-26T01:44:58,850 81 | assert(variant_index < variant_count); 2022-10-26T01:44:58,850 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2022-10-26T01:44:58,862 src/pedigree.cpp: In member function ‘std::string Pedigree::toString() const’: 2022-10-26T01:44:58,862 src/pedigree.cpp:112:21: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘const int’ [-Wsign-compare] 2022-10-26T01:44:58,862 112 | for (size_t j=0; j&, size_t, const std::vector&, const Pedigree*, const PedigreePartitions&, bool)’: 2022-10-26T01:45:02,775 src/pedigreecolumncostcomputer.cpp:25:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-10-26T01:45:02,775 25 | for (unsigned int i = 0; i < (1< PedigreeColumnCostComputer::get_alleles()’: 2022-10-26T01:45:02,812 src/pedigreecolumncostcomputer.cpp:119:15: warning: unused variable ‘second_best_cost’ [-Wunused-variable] 2022-10-26T01:45:02,812 119 | unsigned int second_best_cost = numeric_limits < unsigned int >::max(); 2022-10-26T01:45:02,812 | ^~~~~~~~~~~~~~~~ 2022-10-26T01:45:03,930 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.9 -c src/pedigreedptable.cpp -o build/temp.linux-armv7l-cpython-39/src/pedigreedptable.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-10-26T01:45:10,135 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.9 -c src/pedigreepartitions.cpp -o build/temp.linux-armv7l-cpython-39/src/pedigreepartitions.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-10-26T01:45:12,015 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.9 -c src/phredgenotypelikelihoods.cpp -o build/temp.linux-armv7l-cpython-39/src/phredgenotypelikelihoods.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-10-26T01:45:13,573 In file included from /usr/include/c++/10/vector:72, 2022-10-26T01:45:13,574 from src/genotype.h:4, 2022-10-26T01:45:13,574 from src/phredgenotypelikelihoods.h:5, 2022-10-26T01:45:13,574 from src/phredgenotypelikelihoods.cpp:4: 2022-10-26T01:45:13,574 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Genotype}; _Tp = Genotype; _Alloc = std::allocator]’: 2022-10-26T01:45:13,574 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-10-26T01:45:13,574 426 | vector<_Tp, _Alloc>:: 2022-10-26T01:45:13,575 | ^~~~~~~~~~~~~~~~~~~ 2022-10-26T01:45:13,606 /usr/include/c++/10/bits/vector.tcc: In member function ‘void PhredGenotypeLikelihoods::get_genotypes(std::vector&) const’: 2022-10-26T01:45:13,606 /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-10-26T01:45:13,607 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2022-10-26T01:45:13,607 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-10-26T01:45:13,744 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.9 -c src/polyphase/clustereditingsolution.cpp -o build/temp.linux-armv7l-cpython-39/src/polyphase/clustereditingsolution.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-10-26T01:45:15,574 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.9 -c src/polyphase/clustereditingsolver.cpp -o build/temp.linux-armv7l-cpython-39/src/polyphase/clustereditingsolver.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-10-26T01:45:17,693 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.9 -c src/polyphase/edgeheap.cpp -o build/temp.linux-armv7l-cpython-39/src/polyphase/edgeheap.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-10-26T01:45:21,849 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.9 -c src/polyphase/haplothreader.cpp -o build/temp.linux-armv7l-cpython-39/src/polyphase/haplothreader.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-10-26T01:45:22,982 In file included from src/polyphase/haplothreader.h:4, 2022-10-26T01:45:22,983 from src/polyphase/haplothreader.cpp:1: 2022-10-26T01:45:22,983 src/polyphase/tuple.h:26:50: warning: left shift count >= width of type [-Wshift-count-overflow] 2022-10-26T01:45:22,983 26 | 31UL << 20, 31UL << 25, 31UL << 30, 31UL << 35, 2022-10-26T01:45:22,983 | ~~~~~^~~~~ 2022-10-26T01:45:22,983 src/polyphase/tuple.h:27:14: warning: left shift count >= width of type [-Wshift-count-overflow] 2022-10-26T01:45:22,983 27 | 31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55}; 2022-10-26T01:45:22,984 | ~~~~~^~~~~ 2022-10-26T01:45:22,984 src/polyphase/tuple.h:27:26: warning: left shift count >= width of type [-Wshift-count-overflow] 2022-10-26T01:45:22,984 27 | 31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55}; 2022-10-26T01:45:22,984 | ~~~~~^~~~~ 2022-10-26T01:45:22,984 src/polyphase/tuple.h:27:38: warning: left shift count >= width of type [-Wshift-count-overflow] 2022-10-26T01:45:22,984 27 | 31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55}; 2022-10-26T01:45:22,984 | ~~~~~^~~~~ 2022-10-26T01:45:22,985 src/polyphase/tuple.h:27:50: warning: left shift count >= width of type [-Wshift-count-overflow] 2022-10-26T01:45:22,985 27 | 31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55}; 2022-10-26T01:45:22,985 | ~~~~~^~~~~ 2022-10-26T01:45:22,985 src/polyphase/tuple.h:26:50: error: right operand of shift expression ‘(31 << 35)’ is greater than or equal to the precision 32 of the left operand [-fpermissive] 2022-10-26T01:45:22,985 26 | 31UL << 20, 31UL << 25, 31UL << 30, 31UL << 35, 2022-10-26T01:45:22,985 | ~~~~~^~~~~ 2022-10-26T01:45:24,605 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2022-10-26T01:45:24,795 ERROR: [present-rich] Building wheel for whatshap (pyproject.toml) exited with 1 2022-10-26T01:45:24,813 [bold magenta]full command[/]: [blue]/usr/bin/python3 /usr/local/lib/python3.9/dist-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /tmp/tmp2ugfm972[/] 2022-10-26T01:45:24,813 [bold magenta]cwd[/]: /tmp/pip-wheel-sbx0xzwc/whatshap_57cc939431e34aa28170d7016512d06d 2022-10-26T01:45:24,814 Building wheel for whatshap (pyproject.toml): finished with status 'error' 2022-10-26T01:45:24,816 ERROR: Failed building wheel for whatshap 2022-10-26T01:45:24,819 Failed to build whatshap 2022-10-26T01:45:24,820 ERROR: Failed to build one or more wheels 2022-10-26T01:45:24,821 Exception information: 2022-10-26T01:45:24,821 Traceback (most recent call last): 2022-10-26T01:45:24,821 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 160, in exc_logging_wrapper 2022-10-26T01:45:24,821 status = run_func(*args) 2022-10-26T01:45:24,821 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 247, in wrapper 2022-10-26T01:45:24,821 return func(self, options, args) 2022-10-26T01:45:24,821 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 201, in run 2022-10-26T01:45:24,821 raise CommandError("Failed to build one or more wheels") 2022-10-26T01:45:24,821 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2022-10-26T01:45:24,825 Removed build tracker: '/tmp/pip-build-tracker-xt0ek6r5'