2024-01-26T16:02:37,595 Created temporary directory: /tmp/pip-build-tracker-nthd336h 2024-01-26T16:02:37,596 Initialized build tracking at /tmp/pip-build-tracker-nthd336h 2024-01-26T16:02:37,597 Created build tracker: /tmp/pip-build-tracker-nthd336h 2024-01-26T16:02:37,597 Entered build tracker: /tmp/pip-build-tracker-nthd336h 2024-01-26T16:02:37,598 Created temporary directory: /tmp/pip-wheel-exo_lejj 2024-01-26T16:02:37,601 Created temporary directory: /tmp/pip-ephem-wheel-cache-x80mzp19 2024-01-26T16:02:37,627 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-01-26T16:02:37,630 2 location(s) to search for versions of whatshap: 2024-01-26T16:02:37,630 * https://pypi.org/simple/whatshap/ 2024-01-26T16:02:37,630 * https://www.piwheels.org/simple/whatshap/ 2024-01-26T16:02:37,631 Fetching project page and analyzing links: https://pypi.org/simple/whatshap/ 2024-01-26T16:02:37,632 Getting page https://pypi.org/simple/whatshap/ 2024-01-26T16:02:37,634 Found index url https://pypi.org/simple/ 2024-01-26T16:02:37,855 Fetched page https://pypi.org/simple/whatshap/ as application/vnd.pypi.simple.v1+json 2024-01-26T16:02:37,870 Found link https://files.pythonhosted.org/packages/35/95/43ff2304cd59ade39e64aadaeaec48e8c12bbe6262bcbbbd7b7d89487757/whatshap-0.9.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.9 2024-01-26T16:02:37,870 Found link https://files.pythonhosted.org/packages/f0/4b/f2b882803ac66b969414d8427ee8b4ca2c29b17cfead0fd85f349dc66983/whatshap-0.10.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.10 2024-01-26T16:02:37,871 Found link https://files.pythonhosted.org/packages/fc/dc/30559c28fb54985773fb242f5768fc206e054e44e45962a32cf4fd29a794/whatshap-0.11.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.11 2024-01-26T16:02:37,872 Found link https://files.pythonhosted.org/packages/01/84/31a5ea338647d0256a4a5c57e98d7a563f387e6a47f1e26299b89e3f2da1/whatshap-0.12.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.12 2024-01-26T16:02:37,872 Found link https://files.pythonhosted.org/packages/e2/f3/c71cb4bc3ba3b1234ee0c5fe729c60440164e07437695ca09c61750e0e11/whatshap-0.13.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.13 2024-01-26T16:02:37,873 Found link https://files.pythonhosted.org/packages/cd/d3/a63285d15b0da196a259197e46d9f61a852d1b3c94800f4a82ca4e31e307/whatshap-0.14.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.14 2024-01-26T16:02:37,874 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 2024-01-26T16:02:37,874 Found link https://files.pythonhosted.org/packages/ca/13/6454e5e8f6c858a203378b3e22f13518f092ba85aa6d7a9a9796d22c28e0/whatshap-0.15.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.15 2024-01-26T16:02:37,875 Found link https://files.pythonhosted.org/packages/3d/cb/55730a8713ecba10f6d987dbd935ba31ded92f9af1ddd250896f3c1cfc3b/whatshap-0.16.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.16 2024-01-26T16:02:37,876 Found link https://files.pythonhosted.org/packages/79/11/79da12b8c23f43b00fab8a6206f75cc1cc8c1902ff30eca53c17abe2f633/whatshap-0.17.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.17 2024-01-26T16:02:37,876 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/97/19/5758de9357d2639e81f774dffd5227278df2df7f56e81f080098f00c8d5a/whatshap-0.18-cp34-cp34m-manylinux1_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.4) 2024-01-26T16:02:37,877 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/d0/72/94dc654f66164a351a1a9540e28b4bdf34a81046fbf26b5955725bea2f64/whatshap-0.18-cp35-cp35m-manylinux1_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.4) 2024-01-26T16:02:37,878 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/0a/50/c9c89e7f3a59251a91e618165ccc2586b626643a4c59dfd8d1b32f9b6bbb/whatshap-0.18-cp36-cp36m-manylinux1_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.4) 2024-01-26T16:02:37,878 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/32/77/e9e6f3e15a89ea87b0a3ed50e99af2a375a897707eb8b4c81209af918ff0/whatshap-0.18-cp37-cp37m-manylinux1_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.4) 2024-01-26T16:02:37,879 Found link https://files.pythonhosted.org/packages/f0/e4/4392c2f1320ea8d4b79a76e3a6dcb9bd7bf6ed70e11499c9acf2db2d42ef/whatshap-0.18.tar.gz (from https://pypi.org/simple/whatshap/) (requires-python:>=3.4), version: 0.18 2024-01-26T16:02:37,880 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/0f/f5/78e5fa758144941f08b1de923889c7123e4d20368837904fc004592b6ec9/whatshap-1.0-cp36-cp36m-manylinux2010_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6) 2024-01-26T16:02:37,880 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/42/cb/53a1a2a160846a225c6184da26e8f6d6577f5af378e3a90aab728bb5b504/whatshap-1.0-cp37-cp37m-manylinux2010_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6) 2024-01-26T16:02:37,881 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/63/91/5aaa2ec02a362e784d7be43f43b1e243fa9153ef5d9ab3ada91759638444/whatshap-1.0-cp38-cp38-manylinux2010_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6) 2024-01-26T16:02:37,882 Found link https://files.pythonhosted.org/packages/c0/c8/98036e04fb95249128d6b49ca61691e1d8eea484dd94611f90efb5857174/whatshap-1.0.tar.gz (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6), version: 1.0 2024-01-26T16:02:37,882 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/8a/fb/dfaa97a9ec1fe333dcd730498376d33bc21de017760b633d8dd84f9cd9f6/whatshap-1.1-cp36-cp36m-manylinux2010_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6) 2024-01-26T16:02:37,883 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/37/4e/a06bd339ea7179e750d49fec27caba7a6b364f608b5126105770333a6dfa/whatshap-1.1-cp37-cp37m-manylinux2010_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6) 2024-01-26T16:02:37,884 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/2b/61/3000e39650a20faf011d74e41c3a6e3eea11195b1dad6cc8398665539363/whatshap-1.1-cp38-cp38-manylinux2010_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6) 2024-01-26T16:02:37,884 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/37/1a/f9708037de73715099098762c13e8e0681129041d41fb0ab508004ed2aa7/whatshap-1.1-cp39-cp39-manylinux2010_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6) 2024-01-26T16:02:37,885 Found link 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 2024-01-26T16:02:37,886 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) 2024-01-26T16:02:37,887 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) 2024-01-26T16:02:37,887 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) 2024-01-26T16:02:37,888 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) 2024-01-26T16:02:37,889 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 2024-01-26T16:02:37,890 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) 2024-01-26T16:02:37,890 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) 2024-01-26T16:02:37,891 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) 2024-01-26T16:02:37,891 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) 2024-01-26T16:02:37,892 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 2024-01-26T16:02:37,893 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) 2024-01-26T16:02:37,894 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) 2024-01-26T16:02:37,894 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) 2024-01-26T16:02:37,895 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) 2024-01-26T16:02:37,896 Found link https://files.pythonhosted.org/packages/14/ad/1e00006ef2a451b8487b267a6e6261472c3730ee9fbf9bf88ab3e33cdb3e/whatshap-1.3.tar.gz (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6), version: 1.3 2024-01-26T16:02:37,897 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/60/13/79e33b73a1b737584ad7e23c662a1b621c417813d0d8d81936fe0fe6608f/whatshap-1.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7) 2024-01-26T16:02:37,897 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/5c/c5/96fe2f18f74aee649db37a25a583d01219c01dfae7b33af7df36f5eee414/whatshap-1.4-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7) 2024-01-26T16:02:37,898 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/16/12/069f3e690d0af16ee52c63dcad13bfb35b8fbd9b03f56ea8682a8ed47bf6/whatshap-1.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7) 2024-01-26T16:02:37,899 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/25/cf/3c12968b3e30141df2e518fe234bf38341db7474df5f890bd1c67664541f/whatshap-1.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7) 2024-01-26T16:02:37,900 Found link https://files.pythonhosted.org/packages/15/1e/1b29e356fc0b8a1fbbffe808c02a67eae8ebd922a78567aa5eb867b47070/whatshap-1.4.tar.gz (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7), version: 1.4 2024-01-26T16:02:37,901 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/b6/5b/6e5b19bbab49bf45651cdf2eac3fe33a06d7959f65cfeba15dd08bae35e9/whatshap-1.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7) 2024-01-26T16:02:37,901 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/14/cf/91e8519226ffc8d3459582832b7d0cdf4fda7b4c324deecfadce3f55be55/whatshap-1.5-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7) 2024-01-26T16:02:37,902 Skipping link: No binaries permitted for whatshap: 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https://files.pythonhosted.org/packages/f8/76/4a671a933194f2ccbf2fc70513516312fae6054fbdbe69b250919082fa4c/whatshap-1.6-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7) 2024-01-26T16:02:37,905 Skipping link: No binaries permitted for whatshap: 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) 2024-01-26T16:02:37,905 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) 2024-01-26T16:02:37,906 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) 2024-01-26T16:02:37,907 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 2024-01-26T16:02:37,908 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/63/0a/21389d1b959cd489c4a0abf1343e9bcff61d45af7de9470ffa350d2eeb4d/whatshap-1.7-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7) 2024-01-26T16:02:37,909 Skipping link: No binaries permitted for whatshap: 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https://files.pythonhosted.org/packages/1f/44/d11315edea202d6399af062186a30ba12a17c489115f56ed417e25921453/whatshap-1.7.tar.gz (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7), version: 1.7 2024-01-26T16:02:37,911 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/e2/4e/b4bf39415abe9944df3062b4e9c1c8ce901cae6ba1b3780d0a3c23c3e146/whatshap-2.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7) 2024-01-26T16:02:37,911 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/28/4c/c2a9597d07eadbcf8427ec843cc784f572603292ee9bbb339fd79cea5075/whatshap-2.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7) 2024-01-26T16:02:37,912 Skipping link: No binaries permitted for whatshap: 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https://files.pythonhosted.org/packages/c3/10/b53674fa02c1d5b23887f5a6b0fbf6936ce35dcd08f65e994c18601b20cb/whatshap-2.0.tar.gz (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7), version: 2.0 2024-01-26T16:02:37,915 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/0d/b6/8e7ffd69dbe910122ab4823ab5c399e80bb1474249206a40845eaebdeb85/whatshap-2.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7) 2024-01-26T16:02:37,916 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/67/e4/e8c62a755fb9f20ae55a1639128794f9e3ca161484bce2455344028282c2/whatshap-2.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7) 2024-01-26T16:02:37,916 Skipping link: No binaries permitted for whatshap: 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https://files.pythonhosted.org/packages/35/1a/d6fedb787eac8d616ec598f6a42cf2289bcc11dbbfdeae65afdf1dcb7bfc/whatshap-2.1.tar.gz (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7), version: 2.1 2024-01-26T16:02:37,919 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/d8/a4/52140707bffcd2065aace3fc2afba37af7a13724634d8901430a25f299e0/whatshap-2.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7) 2024-01-26T16:02:37,919 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/89/fb/cfd6df89637e64a02fcc7f5bd575c9203b737641f53128127b704c6c9cf7/whatshap-2.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7) 2024-01-26T16:02:37,920 Skipping link: No binaries permitted for whatshap: 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https://files.pythonhosted.org/packages/00/f3/2e2c850755629a151c2027b636f253745bbbfeee052870f03e99f94a4996/whatshap-2.2.tar.gz (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7), version: 2.2 2024-01-26T16:02:37,923 Fetching project page and analyzing links: https://www.piwheels.org/simple/whatshap/ 2024-01-26T16:02:37,923 Getting page https://www.piwheels.org/simple/whatshap/ 2024-01-26T16:02:37,925 Found index url https://www.piwheels.org/simple/ 2024-01-26T16:02:38,091 Fetched page https://www.piwheels.org/simple/whatshap/ as text/html 2024-01-26T16:02:38,104 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) 2024-01-26T16:02:38,105 Skipping link: No binaries permitted for whatshap: 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https://www.piwheels.org/simple/whatshap/whatshap-0.14-cp34-cp34m-linux_armv7l.whl#sha256=3ddde88fb4fed1664ec3d46039aca72142fa5dcde177a40f49c2cec09b407f9f (from https://www.piwheels.org/simple/whatshap/) 2024-01-26T16:02:38,121 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.14-cp34-cp34m-linux_armv6l.whl#sha256=3ddde88fb4fed1664ec3d46039aca72142fa5dcde177a40f49c2cec09b407f9f (from https://www.piwheels.org/simple/whatshap/) 2024-01-26T16:02:38,121 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.13-cp35-cp35m-linux_armv6l.whl#sha256=7989e2894821071f43ee744ecc59f1abfa98748cf39719c28c881e6098c74037 (from https://www.piwheels.org/simple/whatshap/) 2024-01-26T16:02:38,122 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.13-cp35-cp35m-linux_armv7l.whl#sha256=7989e2894821071f43ee744ecc59f1abfa98748cf39719c28c881e6098c74037 (from https://www.piwheels.org/simple/whatshap/) 2024-01-26T16:02:38,122 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.13-cp34-cp34m-linux_armv7l.whl#sha256=856ee3772161445e2245334076268dca61b504968b90dab43b07943ed6ddeebd (from https://www.piwheels.org/simple/whatshap/) 2024-01-26T16:02:38,123 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.13-cp34-cp34m-linux_armv6l.whl#sha256=856ee3772161445e2245334076268dca61b504968b90dab43b07943ed6ddeebd (from https://www.piwheels.org/simple/whatshap/) 2024-01-26T16:02:38,124 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.12-cp35-cp35m-linux_armv7l.whl#sha256=77398db6e7b93ab468c1a87e64d128696987ae7573bf6bb87d6d4ad6853c68cd (from https://www.piwheels.org/simple/whatshap/) 2024-01-26T16:02:38,124 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.12-cp35-cp35m-linux_armv6l.whl#sha256=77398db6e7b93ab468c1a87e64d128696987ae7573bf6bb87d6d4ad6853c68cd (from https://www.piwheels.org/simple/whatshap/) 2024-01-26T16:02:38,124 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.12-cp34-cp34m-linux_armv6l.whl#sha256=61ca54a67abc75d161b394f41a6a10efa1b7e25ce94a20fb5e17bf768fbcc153 (from https://www.piwheels.org/simple/whatshap/) 2024-01-26T16:02:38,125 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.12-cp34-cp34m-linux_armv7l.whl#sha256=61ca54a67abc75d161b394f41a6a10efa1b7e25ce94a20fb5e17bf768fbcc153 (from https://www.piwheels.org/simple/whatshap/) 2024-01-26T16:02:38,126 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/) 2024-01-26T16:02:38,126 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.11-cp34-cp34m-linux_armv6l.whl#sha256=528f0411be5d1bd6559dd1531b52beb67ca918a09fd418fd2921199f88ff71ef (from https://www.piwheels.org/simple/whatshap/) 2024-01-26T16:02:38,127 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/) 2024-01-26T16:02:38,127 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/) 2024-01-26T16:02:38,128 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.10-cp34-cp34m-linux_armv7l.whl#sha256=4833edfe84ef3c9eeb5c68262dad5be3a637379d59eae98ed10774ee66a5a925 (from https://www.piwheels.org/simple/whatshap/) 2024-01-26T16:02:38,129 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.10-cp34-cp34m-linux_armv6l.whl#sha256=4833edfe84ef3c9eeb5c68262dad5be3a637379d59eae98ed10774ee66a5a925 (from https://www.piwheels.org/simple/whatshap/) 2024-01-26T16:02:38,129 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.9-cp34-cp34m-linux_armv7l.whl#sha256=78adbda77e2ec4fe0f66ea86826ad8d025f743ba6bbf39d050783ec1cb07c83a (from https://www.piwheels.org/simple/whatshap/) 2024-01-26T16:02:38,130 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.9-cp34-cp34m-linux_armv6l.whl#sha256=78adbda77e2ec4fe0f66ea86826ad8d025f743ba6bbf39d050783ec1cb07c83a (from https://www.piwheels.org/simple/whatshap/) 2024-01-26T16:02:38,130 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/) 2024-01-26T16:02:38,131 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/) 2024-01-26T16:02:38,132 Skipping link: not a file: https://www.piwheels.org/simple/whatshap/ 2024-01-26T16:02:38,132 Skipping link: not a file: https://pypi.org/simple/whatshap/ 2024-01-26T16:02:38,155 Given no hashes to check 1 links for project 'whatshap': discarding no candidates 2024-01-26T16:02:38,174 Collecting whatshap==2.2 2024-01-26T16:02:38,395 Created temporary directory: /tmp/pip-unpack-1nuwyiid 2024-01-26T16:02:38,807 Downloading whatshap-2.2.tar.gz (5.4 MB) 2024-01-26T16:02:40,861 Added whatshap==2.2 from https://files.pythonhosted.org/packages/00/f3/2e2c850755629a151c2027b636f253745bbbfeee052870f03e99f94a4996/whatshap-2.2.tar.gz to build tracker '/tmp/pip-build-tracker-nthd336h' 2024-01-26T16:02:40,869 Created temporary directory: /tmp/pip-build-env-_y9yk18z 2024-01-26T16:02:40,873 Installing build dependencies: started 2024-01-26T16:02:40,874 Running command pip subprocess to install build dependencies 2024-01-26T16:02:42,041 Using pip 23.3.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2024-01-26T16:02:42,651 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-01-26T16:02:44,060 Collecting setuptools>=63 2024-01-26T16:02:44,076 Using cached https://www.piwheels.org/simple/setuptools/setuptools-69.0.3-py3-none-any.whl (819 kB) 2024-01-26T16:02:45,476 Collecting cython~=0.29.20 2024-01-26T16:02:45,493 Using cached https://www.piwheels.org/simple/cython/Cython-0.29.37-cp311-cp311-linux_armv7l.whl (5.0 MB) 2024-01-26T16:02:45,979 Collecting setuptools_scm[toml] 2024-01-26T16:02:45,993 Using cached https://www.piwheels.org/simple/setuptools-scm/setuptools_scm-8.0.4-py3-none-any.whl (42 kB) 2024-01-26T16:02:46,382 Collecting packaging>=20 (from setuptools_scm[toml]) 2024-01-26T16:02:46,396 Using cached https://www.piwheels.org/simple/packaging/packaging-23.2-py3-none-any.whl (53 kB) 2024-01-26T16:02:46,506 Collecting typing-extensions (from setuptools_scm[toml]) 2024-01-26T16:02:46,521 Using cached https://www.piwheels.org/simple/typing-extensions/typing_extensions-4.9.0-py3-none-any.whl (32 kB) 2024-01-26T16:02:49,947 Installing collected packages: typing-extensions, setuptools, packaging, cython, setuptools_scm 2024-01-26T16:02:55,698 Creating /tmp/pip-build-env-_y9yk18z/overlay/local/bin 2024-01-26T16:02:55,700 changing mode of /tmp/pip-build-env-_y9yk18z/overlay/local/bin/cygdb to 755 2024-01-26T16:02:55,702 changing mode of /tmp/pip-build-env-_y9yk18z/overlay/local/bin/cython to 755 2024-01-26T16:02:55,705 changing mode of /tmp/pip-build-env-_y9yk18z/overlay/local/bin/cythonize to 755 2024-01-26T16:02:55,930 Successfully installed cython-0.29.37 packaging-23.2 setuptools-69.0.3 setuptools_scm-8.0.4 typing-extensions-4.9.0 2024-01-26T16:02:56,404 [notice] A new release of pip is available: 23.3.1 -> 23.3.2 2024-01-26T16:02:56,405 [notice] To update, run: python3 -m pip install --upgrade pip 2024-01-26T16:02:56,772 Installing build dependencies: finished with status 'done' 2024-01-26T16:02:56,775 Getting requirements to build wheel: started 2024-01-26T16:02:56,776 Running command Getting requirements to build wheel 2024-01-26T16:03:04,940 warning: whatshap/priorityqueue.pyx:201:7: Unreachable code 2024-01-26T16:03:06,704 Compiling whatshap/core.pyx because it depends on /tmp/pip-build-env-_y9yk18z/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd. 2024-01-26T16:03:06,705 Compiling whatshap/polyphase/solver.pyx because it depends on /tmp/pip-build-env-_y9yk18z/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd. 2024-01-26T16:03:06,706 Compiling whatshap/readselect.pyx because it depends on /tmp/pip-build-env-_y9yk18z/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd. 2024-01-26T16:03:06,707 Compiling whatshap/priorityqueue.pyx because it depends on /tmp/pip-build-env-_y9yk18z/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd. 2024-01-26T16:03:06,707 Compiling whatshap/align.pyx because it depends on /tmp/pip-build-env-_y9yk18z/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/string.pxd. 2024-01-26T16:03:06,708 [1/5] Cythonizing whatshap/align.pyx 2024-01-26T16:03:06,709 [2/5] Cythonizing whatshap/core.pyx 2024-01-26T16:03:06,709 [3/5] Cythonizing whatshap/polyphase/solver.pyx 2024-01-26T16:03:06,710 [4/5] Cythonizing whatshap/priorityqueue.pyx 2024-01-26T16:03:06,710 [5/5] Cythonizing whatshap/readselect.pyx 2024-01-26T16:03:07,298 running egg_info 2024-01-26T16:03:07,305 writing whatshap.egg-info/PKG-INFO 2024-01-26T16:03:07,312 writing dependency_links to whatshap.egg-info/dependency_links.txt 2024-01-26T16:03:07,315 writing entry points to whatshap.egg-info/entry_points.txt 2024-01-26T16:03:07,319 writing requirements to whatshap.egg-info/requires.txt 2024-01-26T16:03:07,320 writing top-level names to whatshap.egg-info/top_level.txt 2024-01-26T16:03:07,389 ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any 2024-01-26T16:03:07,395 reading manifest file 'whatshap.egg-info/SOURCES.txt' 2024-01-26T16:03:07,410 reading manifest template 'MANIFEST.in' 2024-01-26T16:03:07,419 adding license file 'LICENSE' 2024-01-26T16:03:07,435 writing manifest file 'whatshap.egg-info/SOURCES.txt' 2024-01-26T16:03:08,424 Getting requirements to build wheel: finished with status 'done' 2024-01-26T16:03:10,023 Installing backend dependencies: started 2024-01-26T16:03:10,025 Running command pip subprocess to install backend dependencies 2024-01-26T16:03:12,469 Using pip 23.3.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2024-01-26T16:03:13,201 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-01-26T16:03:13,696 Collecting wheel 2024-01-26T16:03:13,712 Using cached https://www.piwheels.org/simple/wheel/wheel-0.42.0-py3-none-any.whl (65 kB) 2024-01-26T16:03:17,150 Installing collected packages: wheel 2024-01-26T16:03:17,385 Creating /tmp/pip-build-env-_y9yk18z/normal/local/bin 2024-01-26T16:03:17,388 changing mode of /tmp/pip-build-env-_y9yk18z/normal/local/bin/wheel to 755 2024-01-26T16:03:17,399 Successfully installed wheel-0.42.0 2024-01-26T16:03:18,356 [notice] A new release of pip is available: 23.3.1 -> 23.3.2 2024-01-26T16:03:18,356 [notice] To update, run: python3 -m pip install --upgrade pip 2024-01-26T16:03:18,839 Installing backend dependencies: finished with status 'done' 2024-01-26T16:03:18,841 Created temporary directory: /tmp/pip-modern-metadata-y2cca1nz 2024-01-26T16:03:18,845 Preparing metadata (pyproject.toml): started 2024-01-26T16:03:18,846 Running command Preparing metadata (pyproject.toml) 2024-01-26T16:03:21,005 running dist_info 2024-01-26T16:03:21,011 creating /tmp/pip-modern-metadata-y2cca1nz/whatshap.egg-info 2024-01-26T16:03:21,017 writing /tmp/pip-modern-metadata-y2cca1nz/whatshap.egg-info/PKG-INFO 2024-01-26T16:03:21,023 writing dependency_links to /tmp/pip-modern-metadata-y2cca1nz/whatshap.egg-info/dependency_links.txt 2024-01-26T16:03:21,025 writing entry points to /tmp/pip-modern-metadata-y2cca1nz/whatshap.egg-info/entry_points.txt 2024-01-26T16:03:21,028 writing requirements to /tmp/pip-modern-metadata-y2cca1nz/whatshap.egg-info/requires.txt 2024-01-26T16:03:21,030 writing top-level names to /tmp/pip-modern-metadata-y2cca1nz/whatshap.egg-info/top_level.txt 2024-01-26T16:03:21,031 writing manifest file '/tmp/pip-modern-metadata-y2cca1nz/whatshap.egg-info/SOURCES.txt' 2024-01-26T16:03:21,095 ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any 2024-01-26T16:03:21,098 reading manifest file '/tmp/pip-modern-metadata-y2cca1nz/whatshap.egg-info/SOURCES.txt' 2024-01-26T16:03:21,100 reading manifest template 'MANIFEST.in' 2024-01-26T16:03:21,115 adding license file 'LICENSE' 2024-01-26T16:03:21,123 writing manifest file '/tmp/pip-modern-metadata-y2cca1nz/whatshap.egg-info/SOURCES.txt' 2024-01-26T16:03:21,124 creating '/tmp/pip-modern-metadata-y2cca1nz/whatshap-2.2.dist-info' 2024-01-26T16:03:21,341 Preparing metadata (pyproject.toml): finished with status 'done' 2024-01-26T16:03:21,345 Source in /tmp/pip-wheel-exo_lejj/whatshap_a3a1471e65fa4b668e7b70dad19ffc8a has version 2.2, which satisfies requirement whatshap==2.2 from https://files.pythonhosted.org/packages/00/f3/2e2c850755629a151c2027b636f253745bbbfeee052870f03e99f94a4996/whatshap-2.2.tar.gz 2024-01-26T16:03:21,346 Removed whatshap==2.2 from https://files.pythonhosted.org/packages/00/f3/2e2c850755629a151c2027b636f253745bbbfeee052870f03e99f94a4996/whatshap-2.2.tar.gz from build tracker '/tmp/pip-build-tracker-nthd336h' 2024-01-26T16:03:21,352 Created temporary directory: /tmp/pip-unpack-con_tcll 2024-01-26T16:03:21,353 Created temporary directory: /tmp/pip-unpack-6furer7g 2024-01-26T16:03:21,387 Building wheels for collected packages: whatshap 2024-01-26T16:03:21,391 Created temporary directory: /tmp/pip-wheel-bdhz8w8s 2024-01-26T16:03:21,392 Destination directory: /tmp/pip-wheel-bdhz8w8s 2024-01-26T16:03:21,394 Building wheel for whatshap (pyproject.toml): started 2024-01-26T16:03:21,395 Running command Building wheel for whatshap (pyproject.toml) 2024-01-26T16:03:22,845 running bdist_wheel 2024-01-26T16:03:22,866 running build 2024-01-26T16:03:22,866 running build_py 2024-01-26T16:03:22,873 creating build 2024-01-26T16:03:22,874 creating build/lib.linux-armv7l-cpython-311 2024-01-26T16:03:22,874 creating build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:22,876 copying whatshap/variants.py -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:22,879 copying whatshap/bam.py -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:22,881 copying whatshap/timer.py -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:22,883 copying whatshap/verification.py -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:22,885 copying whatshap/coverage.py -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:22,887 copying whatshap/__main__.py -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:22,889 copying whatshap/pedigree.py -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:22,891 copying whatshap/vcf.py -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:22,895 copying whatshap/__init__.py -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:22,897 copying whatshap/graph.py -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:22,899 copying whatshap/variant.py -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:22,901 copying whatshap/utils.py -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:22,902 copying whatshap/phred_scores.py -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:22,904 copying whatshap/merge.py -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:22,906 copying whatshap/args.py -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:22,908 copying whatshap/_version.py -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:22,910 copying whatshap/testhelpers.py -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:22,913 creating build/lib.linux-armv7l-cpython-311/whatshap/polyphase 2024-01-26T16:03:22,914 copying whatshap/polyphase/reorder.py -> build/lib.linux-armv7l-cpython-311/whatshap/polyphase 2024-01-26T16:03:22,917 copying whatshap/polyphase/offspringscoring.py -> build/lib.linux-armv7l-cpython-311/whatshap/polyphase 2024-01-26T16:03:22,919 copying whatshap/polyphase/clusterarrangement.py -> build/lib.linux-armv7l-cpython-311/whatshap/polyphase 2024-01-26T16:03:22,920 copying whatshap/polyphase/variantselection.py -> build/lib.linux-armv7l-cpython-311/whatshap/polyphase 2024-01-26T16:03:22,922 copying whatshap/polyphase/__init__.py -> build/lib.linux-armv7l-cpython-311/whatshap/polyphase 2024-01-26T16:03:22,924 copying whatshap/polyphase/algorithm.py -> build/lib.linux-armv7l-cpython-311/whatshap/polyphase 2024-01-26T16:03:22,926 copying whatshap/polyphase/threading.py -> build/lib.linux-armv7l-cpython-311/whatshap/polyphase 2024-01-26T16:03:22,929 copying whatshap/polyphase/plots.py -> build/lib.linux-armv7l-cpython-311/whatshap/polyphase 2024-01-26T16:03:22,932 creating build/lib.linux-armv7l-cpython-311/whatshap/cli 2024-01-26T16:03:22,933 copying whatshap/cli/stats.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli 2024-01-26T16:03:22,935 copying whatshap/cli/find_snv_candidates.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli 2024-01-26T16:03:22,937 copying whatshap/cli/learn.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli 2024-01-26T16:03:22,939 copying whatshap/cli/phase.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli 2024-01-26T16:03:22,942 copying whatshap/cli/polyphasegenetic.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli 2024-01-26T16:03:22,944 copying whatshap/cli/haplotag.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli 2024-01-26T16:03:22,947 copying whatshap/cli/genotype.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli 2024-01-26T16:03:22,950 copying whatshap/cli/polyphase.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli 2024-01-26T16:03:22,952 copying whatshap/cli/compare.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli 2024-01-26T16:03:22,955 copying whatshap/cli/split.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli 2024-01-26T16:03:22,958 copying whatshap/cli/__init__.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli 2024-01-26T16:03:22,959 copying whatshap/cli/unphase.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli 2024-01-26T16:03:22,961 copying whatshap/cli/hapcut2vcf.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli 2024-01-26T16:03:22,963 running egg_info 2024-01-26T16:03:22,968 writing whatshap.egg-info/PKG-INFO 2024-01-26T16:03:22,974 writing dependency_links to whatshap.egg-info/dependency_links.txt 2024-01-26T16:03:22,976 writing entry points to whatshap.egg-info/entry_points.txt 2024-01-26T16:03:22,978 writing requirements to whatshap.egg-info/requires.txt 2024-01-26T16:03:22,980 writing top-level names to whatshap.egg-info/top_level.txt 2024-01-26T16:03:23,012 ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any 2024-01-26T16:03:23,015 reading manifest file 'whatshap.egg-info/SOURCES.txt' 2024-01-26T16:03:23,053 reading manifest template 'MANIFEST.in' 2024-01-26T16:03:23,061 adding license file 'LICENSE' 2024-01-26T16:03:23,076 writing manifest file 'whatshap.egg-info/SOURCES.txt' 2024-01-26T16:03:23,089 copying whatshap/.gitignore -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:23,091 copying whatshap/_variants.pyi -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:23,093 copying whatshap/_variants.pyx -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:23,095 copying whatshap/align.pyi -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:23,097 copying whatshap/align.pyx -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:23,100 copying whatshap/core.pxd -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:23,101 copying whatshap/core.pyi -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:23,104 copying whatshap/core.pyx -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:23,106 copying whatshap/cpp.pxd -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:23,109 copying whatshap/priorityqueue.pxd -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:23,110 copying whatshap/priorityqueue.pyi -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:23,112 copying whatshap/priorityqueue.pyx -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:23,115 copying whatshap/readselect.pyi -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:23,117 copying whatshap/readselect.pyx -> build/lib.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:23,119 copying whatshap/polyphase/solver.cpp -> build/lib.linux-armv7l-cpython-311/whatshap/polyphase 2024-01-26T16:03:23,131 copying whatshap/polyphase/solver.pxd -> build/lib.linux-armv7l-cpython-311/whatshap/polyphase 2024-01-26T16:03:23,133 copying whatshap/polyphase/solver.pyi -> build/lib.linux-armv7l-cpython-311/whatshap/polyphase 2024-01-26T16:03:23,135 copying whatshap/polyphase/solver.pyx -> build/lib.linux-armv7l-cpython-311/whatshap/polyphase 2024-01-26T16:03:23,139 running build_ext 2024-01-26T16:03:23,144 building 'whatshap.core' extension 2024-01-26T16:03:23,145 creating build/temp.linux-armv7l-cpython-311 2024-01-26T16:03:23,146 creating build/temp.linux-armv7l-cpython-311/src 2024-01-26T16:03:23,147 creating build/temp.linux-armv7l-cpython-311/src/hapchat 2024-01-26T16:03:23,148 creating build/temp.linux-armv7l-cpython-311/whatshap 2024-01-26T16:03:23,149 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.11 -c src/backwardcolumniterator.cpp -o build/temp.linux-armv7l-cpython-311/src/backwardcolumniterator.o -std=c++11 -Werror=return-type -Werror=narrowing 2024-01-26T16:03:25,000 In file included from /usr/include/c++/12/cassert:44, 2024-01-26T16:03:25,001 from src/backwardcolumniterator.cpp:1: 2024-01-26T16:03:25,001 src/backwardcolumniterator.cpp: In member function ‘void BackwardColumnIterator::jump_to_column(int)’: 2024-01-26T16:03:25,002 src/backwardcolumniterator.cpp:121:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2024-01-26T16:03:25,003 121 | assert(k < positions->size()); 2024-01-26T16:03:25,004 | ~~^~~~~~~~~~~~~~~~~~~ 2024-01-26T16:03:25,004 src/backwardcolumniterator.cpp:140:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-01-26T16:03:25,005 140 | assert(active_entry < read->getVariantCount()); 2024-01-26T16:03:25,006 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2024-01-26T16:03:26,789 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.11 -c src/binomial.cpp -o build/temp.linux-armv7l-cpython-311/src/binomial.o -std=c++11 -Werror=return-type -Werror=narrowing 2024-01-26T16:03:27,178 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.11 -c src/caller.cpp -o build/temp.linux-armv7l-cpython-311/src/caller.o -std=c++11 -Werror=return-type -Werror=narrowing 2024-01-26T16:03:29,188 src/caller.cpp: In member function ‘void Caller::enumerate_kmers(int, std::string&, int, std::vector >&)’: 2024-01-26T16:03:29,189 src/caller.cpp:258:13: warning: unused variable ‘BAM_CPAD’ [-Wunused-variable] 2024-01-26T16:03:29,190 258 | int BAM_CPAD = 6 ; // P 2024-01-26T16:03:29,191 | ^~~~~~~~ 2024-01-26T16:03:29,191 src/caller.cpp:261:13: warning: unused variable ‘BAM_CBACK’ [-Wunused-variable] 2024-01-26T16:03:29,192 261 | int BAM_CBACK = 9 ; // B 2024-01-26T16:03:29,193 | ^~~~~~~~~ 2024-01-26T16:03:35,236 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.11 -c src/columnindexingiterator.cpp -o build/temp.linux-armv7l-cpython-311/src/columnindexingiterator.o -std=c++11 -Werror=return-type -Werror=narrowing 2024-01-26T16:03:36,505 src/columnindexingiterator.cpp: In member function ‘unsigned int ColumnIndexingIterator::index_forward_projection(unsigned int)’: 2024-01-26T16:03:36,506 src/columnindexingiterator.cpp:90:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2024-01-26T16:03:36,506 90 | for(int j=0; j< parent->read_ids.size(); ++j) { 2024-01-26T16:03:36,507 | ~^~~~~~~~~~~~~~~~~~~~~~~~~ 2024-01-26T16:03:36,508 src/columnindexingiterator.cpp:92:22: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-01-26T16:03:36,508 92 | if(m != -1) { 2024-01-26T16:03:36,509 | ~~^~~~~ 2024-01-26T16:03:36,509 src/columnindexingiterator.cpp:89:22: warning: unused variable ‘s’ [-Wunused-variable] 2024-01-26T16:03:36,510 89 | unsigned int s = 1; 2024-01-26T16:03:36,511 | ^ 2024-01-26T16:03:36,819 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.11 -c src/columnindexingscheme.cpp -o build/temp.linux-armv7l-cpython-311/src/columnindexingscheme.o -std=c++11 -Werror=return-type -Werror=narrowing 2024-01-26T16:03:38,077 src/columnindexingscheme.cpp: In constructor ‘ColumnIndexingScheme::ColumnIndexingScheme(const ColumnIndexingScheme*, const std::vector&)’: 2024-01-26T16:03:38,078 src/columnindexingscheme.cpp:22:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2024-01-26T16:03:38,079 22 | while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2024-01-26T16:03:38,081 22 | while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2024-01-26T16:03:38,084 71 | while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2024-01-26T16:03:38,086 71 | while ((iread_ids.size()) && (j > ColumnIterator::get_next()’: 2024-01-26T16:03:40,463 src/columniterator.cpp:105:54: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-01-26T16:03:40,464 105 | assert(list_it->active_entry < read->getVariantCount()); 2024-01-26T16:03:40,464 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2024-01-26T16:03:40,480 src/columniterator.cpp: In member function ‘void ColumnIterator::jump_to_column(size_t)’: 2024-01-26T16:03:40,481 src/columniterator.cpp:161:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-01-26T16:03:40,482 161 | assert(active_entry < read->getVariantCount()); 2024-01-26T16:03:40,482 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2024-01-26T16:03:42,319 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.11 -c src/entry.cpp -o build/temp.linux-armv7l-cpython-311/src/entry.o -std=c++11 -Werror=return-type -Werror=narrowing 2024-01-26T16:03:43,470 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.11 -c src/genotype.cpp -o build/temp.linux-armv7l-cpython-311/src/genotype.o -std=c++11 -Werror=return-type -Werror=narrowing 2024-01-26T16:03:46,083 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.11 -c src/genotypecolumncostcomputer.cpp -o build/temp.linux-armv7l-cpython-311/src/genotypecolumncostcomputer.o -std=c++11 -Werror=return-type -Werror=narrowing 2024-01-26T16:03:49,321 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.11 -c src/genotypedistribution.cpp -o build/temp.linux-armv7l-cpython-311/src/genotypedistribution.o -std=c++11 -Werror=return-type -Werror=narrowing 2024-01-26T16:03:50,711 src/genotypedistribution.cpp: In member function ‘double GenotypeDistribution::errorProbability() const’: 2024-01-26T16:03:50,712 src/genotypedistribution.cpp:55:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-01-26T16:03:50,713 55 | if (i == best_index) continue; 2024-01-26T16:03:50,713 | ~~^~~~~~~~~~~~~ 2024-01-26T16:03:51,267 In file included from /usr/include/c++/12/vector:70, 2024-01-26T16:03:51,268 from src/genotypedistribution.h:4, 2024-01-26T16:03:51,269 from src/genotypedistribution.cpp:5: 2024-01-26T16:03:51,269 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2024-01-26T16:03:51,270 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2024-01-26T16:03:51,271 439 | vector<_Tp, _Alloc>:: 2024-01-26T16:03:51,272 | ^~~~~~~~~~~~~~~~~~~ 2024-01-26T16:03:51,307 In file included from /usr/include/c++/12/vector:64: 2024-01-26T16:03:51,307 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2024-01-26T16:03:51,308 inlined from ‘GenotypeDistribution::GenotypeDistribution(double, double, double)’ at src/genotypedistribution.cpp:10:24: 2024-01-26T16:03:51,308 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2024-01-26T16:03:51,309 1287 | _M_realloc_insert(end(), __x); 2024-01-26T16:03:51,309 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-01-26T16:03:51,310 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2024-01-26T16:03:51,310 inlined from ‘GenotypeDistribution::GenotypeDistribution(double, double, double)’ at src/genotypedistribution.cpp:11:24: 2024-01-26T16:03:51,311 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2024-01-26T16:03:51,311 1287 | _M_realloc_insert(end(), __x); 2024-01-26T16:03:51,312 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-01-26T16:03:51,312 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2024-01-26T16:03:51,313 inlined from ‘GenotypeDistribution::GenotypeDistribution(double, double, double)’ at src/genotypedistribution.cpp:12:24: 2024-01-26T16:03:51,314 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2024-01-26T16:03:51,314 1287 | _M_realloc_insert(end(), __x); 2024-01-26T16:03:51,315 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-01-26T16:03:51,480 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.11 -c src/genotypedptable.cpp -o build/temp.linux-armv7l-cpython-311/src/genotypedptable.o -std=c++11 -Werror=return-type -Werror=narrowing 2024-01-26T16:03:53,960 In file included from src/genotypedptable.cpp:11: 2024-01-26T16:03:53,961 src/genotypedptable.h: In member function ‘void GenotypeDPTable::genotype_likelihood_t::divide_likelihoods_by(long double&)’: 2024-01-26T16:03:53,962 src/genotypedptable.h:38:95: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = divides; _Tp = long double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 2024-01-26T16:03:53,962 38 | std::transform(likelihoods.begin(), likelihoods.end(), likelihoods.begin(), std::bind2nd(std::divides(), val)); 2024-01-26T16:03:53,963 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-01-26T16:03:53,964 In file included from /usr/include/c++/12/bits/stl_function.h:1438, 2024-01-26T16:03:53,965 from /usr/include/c++/12/string:48, 2024-01-26T16:03:53,965 from /usr/include/c++/12/stdexcept:39, 2024-01-26T16:03:53,966 from src/genotypedptable.cpp:1: 2024-01-26T16:03:53,967 /usr/include/c++/12/backward/binders.h:172:5: note: declared here 2024-01-26T16:03:53,968 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2024-01-26T16:03:53,968 | ^~~~~~~ 2024-01-26T16:03:53,988 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::clear_forward_table()’: 2024-01-26T16:03:53,988 src/genotypedptable.cpp:61:12: warning: unused variable ‘column_count’ [-Wunused-variable] 2024-01-26T16:03:53,989 61 | size_t column_count = input_column_iterator.get_column_count(); 2024-01-26T16:03:53,990 | ^~~~~~~~~~~~ 2024-01-26T16:03:54,036 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_index()’: 2024-01-26T16:03:54,037 src/genotypedptable.cpp:91:18: warning: unused variable ‘transmission_configurations’ [-Wunused-variable] 2024-01-26T16:03:54,038 91 | unsigned int transmission_configurations = pow(4, pedigree->triple_count()); 2024-01-26T16:03:54,038 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-01-26T16:03:54,041 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_backward_prob()’: 2024-01-26T16:03:54,042 src/genotypedptable.cpp:152:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-01-26T16:03:54,042 152 | if ((k>1) && (column_index < column_count-1) && (((column_index+1)%k) != 0)) { 2024-01-26T16:03:54,043 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2024-01-26T16:03:54,046 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_forward_prob()’: 2024-01-26T16:03:54,046 src/genotypedptable.cpp:178:12: warning: unused variable ‘k’ [-Wunused-variable] 2024-01-26T16:03:54,047 178 | size_t k = (size_t)sqrt(input_column_iterator.get_column_count()); 2024-01-26T16:03:54,048 | ^ 2024-01-26T16:03:54,218 In file included from src/genotypedptable.h:15: 2024-01-26T16:03:54,219 src/vector2d.h: In instantiation of ‘void Vector2D::divide_entries_by(T) [with T = long double]’: 2024-01-26T16:03:54,219 src/genotypedptable.cpp:290:53: required from here 2024-01-26T16:03:54,220 src/vector2d.h:40:28: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = divides; _Tp = long double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 2024-01-26T16:03:54,221 40 | std::bind2nd(std::divides(),val)); 2024-01-26T16:03:54,221 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 2024-01-26T16:03:54,222 /usr/include/c++/12/backward/binders.h:172:5: note: declared here 2024-01-26T16:03:54,223 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2024-01-26T16:03:54,224 | ^~~~~~~ 2024-01-26T16:03:58,021 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.11 -c src/genotyper.cpp -o build/temp.linux-armv7l-cpython-311/src/genotyper.o -std=c++11 -Werror=return-type -Werror=narrowing 2024-01-26T16:04:00,566 In file included from /usr/include/c++/12/vector:70, 2024-01-26T16:04:00,567 from src/columniterator.h:4, 2024-01-26T16:04:00,567 from src/genotyper.cpp:6: 2024-01-26T16:04:00,568 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Genotype&}; _Tp = Genotype; _Alloc = std::allocator]’: 2024-01-26T16:04:00,568 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2024-01-26T16:04:00,569 439 | vector<_Tp, _Alloc>:: 2024-01-26T16:04:00,570 | ^~~~~~~~~~~~~~~~~~~ 2024-01-26T16:04:00,796 In file included from /usr/include/c++/12/vector:64: 2024-01-26T16:04:00,797 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Genotype; _Alloc = std::allocator]’, 2024-01-26T16:04:00,797 inlined from ‘void compute_genotypes(const ReadSet&, std::vector*, std::vector*, std::vector*)’ at src/genotyper.cpp:48:23: 2024-01-26T16:04:00,798 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2024-01-26T16:04:00,799 1287 | _M_realloc_insert(end(), __x); 2024-01-26T16:04:00,799 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-01-26T16:04:01,138 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.11 -c src/graycodes.cpp -o build/temp.linux-armv7l-cpython-311/src/graycodes.o -std=c++11 -Werror=return-type -Werror=narrowing 2024-01-26T16:04:02,317 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.11 -c src/hapchat/balancedcombinations.cpp -o build/temp.linux-armv7l-cpython-311/src/hapchat/balancedcombinations.o -std=c++11 -Werror=return-type -Werror=narrowing 2024-01-26T16:04:06,651 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.11 -c src/hapchat/basictypes.cpp -o build/temp.linux-armv7l-cpython-311/src/hapchat/basictypes.o -std=c++11 -Werror=return-type -Werror=narrowing 2024-01-26T16:04:08,531 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.11 -c src/hapchat/binomialcoefficient.cpp -o build/temp.linux-armv7l-cpython-311/src/hapchat/binomialcoefficient.o -std=c++11 -Werror=return-type -Werror=narrowing 2024-01-26T16:04:11,415 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.11 -c src/hapchat/hapchatcolumniterator.cpp -o build/temp.linux-armv7l-cpython-311/src/hapchat/hapchatcolumniterator.o -std=c++11 -Werror=return-type -Werror=narrowing 2024-01-26T16:04:14,017 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.11 -c src/hapchat/hapchatcore.cpp -o build/temp.linux-armv7l-cpython-311/src/hapchat/hapchatcore.o -std=c++11 -Werror=return-type -Werror=narrowing 2024-01-26T16:04:16,521 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::run_core()’: 2024-01-26T16:04:16,522 src/hapchat/hapchatcore.cpp:145:11: warning: variable ‘counter_columns’ set but not used [-Wunused-but-set-variable] 2024-01-26T16:04:16,523 145 | Counter counter_columns; 2024-01-26T16:04:16,523 | ^~~~~~~~~~~~~~~ 2024-01-26T16:04:16,540 src/hapchat/hapchatcore.cpp: In member function ‘bool HapChatCore::check_end(HapChatColumnIterator, const std::vector >&, const Pointer&, const bool&)’: 2024-01-26T16:04:16,541 src/hapchat/hapchatcore.cpp:208:74: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-01-26T16:04:16,541 208 | return (!re_run && (hap.is_ended() && (input[pointer][0].get_read_id() == -1))); 2024-01-26T16:04:16,542 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2024-01-26T16:04:16,696 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::dp(const constants_t&, std::vector&, std::vector&, Counter&, Cost&, Counter&, Counter&, Counter&, Counter&, HapChatColumnIterator)’: 2024-01-26T16:04:16,696 src/hapchat/hapchatcore.cpp:939:15: warning: unused variable ‘old_k’ [-Wunused-variable] 2024-01-26T16:04:16,697 939 | int old_k = k_j[input_pointer]; 2024-01-26T16:04:16,698 | ^~~~~ 2024-01-26T16:04:16,719 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&)’: 2024-01-26T16:04:16,720 src/hapchat/hapchatcore.cpp:1114:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-01-26T16:04:16,720 1114 | (colJ[j].get_read_id() != -1) && 2024-01-26T16:04:16,721 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2024-01-26T16:04:16,721 src/hapchat/hapchatcore.cpp:1115:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-01-26T16:04:16,722 1115 | (colQ[i].get_read_id() != -1)) { 2024-01-26T16:04:16,722 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2024-01-26T16:04:16,726 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::represent_column(const Column&, BitColumn&, Counter&, BitColumn&, Counter&)’: 2024-01-26T16:04:16,727 src/hapchat/hapchatcore.cpp:1159:58: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-01-26T16:04:16,727 1159 | while(cov < column.size() && column[cov].get_read_id() != -1) { 2024-01-26T16:04:16,728 | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2024-01-26T16:04:16,734 src/hapchat/hapchatcore.cpp: In member function ‘int HapChatCore::compute_active_common(const Column&, const Column&, unsigned int&)’: 2024-01-26T16:04:16,734 src/hapchat/hapchatcore.cpp:1294:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-01-26T16:04:16,735 1294 | (colJ[j].get_read_id() != -1) && 2024-01-26T16:04:16,736 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2024-01-26T16:04:16,737 src/hapchat/hapchatcore.cpp:1295:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-01-26T16:04:16,737 1295 | (colQ[i].get_read_id() != -1)) { 2024-01-26T16:04:16,738 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2024-01-26T16:04:16,742 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&)’: 2024-01-26T16:04:16,742 src/hapchat/hapchatcore.cpp:1350:67: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-01-26T16:04:16,743 1350 | if(i < input[pointer].size() && input[pointer][i].get_read_id() != -1) 2024-01-26T16:04:16,744 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2024-01-26T16:04:17,853 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.11 -c src/indexset.cpp -o build/temp.linux-armv7l-cpython-311/src/indexset.o -std=c++11 -Werror=return-type -Werror=narrowing 2024-01-26T16:04:19,717 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.11 -c src/multinomial.cpp -o build/temp.linux-armv7l-cpython-311/src/multinomial.o -std=c++11 -Werror=return-type -Werror=narrowing 2024-01-26T16:04:21,177 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.11 -c src/pedigree.cpp -o build/temp.linux-armv7l-cpython-311/src/pedigree.o -std=c++11 -Werror=return-type -Werror=narrowing 2024-01-26T16:04:22,767 In file included from /usr/include/c++/12/cassert:44, 2024-01-26T16:04:22,769 from src/pedigree.cpp:4: 2024-01-26T16:04:22,769 src/pedigree.cpp: In member function ‘void Pedigree::addIndividual(unsigned int, std::vector, std::vector)’: 2024-01-26T16:04:22,770 src/pedigree.cpp:32:33: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-01-26T16:04:22,770 32 | assert(genotypes.size() == variant_count); 2024-01-26T16:04:22,771 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2024-01-26T16:04:22,771 src/pedigree.cpp:33:44: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-01-26T16:04:22,772 33 | assert(genotype_likelihoods.size() == variant_count); 2024-01-26T16:04:22,772 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2024-01-26T16:04:22,790 src/pedigree.cpp: In member function ‘const Genotype* Pedigree::get_genotype_by_id(unsigned int, unsigned int) const’: 2024-01-26T16:04:22,790 src/pedigree.cpp:70:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] 2024-01-26T16:04:22,791 70 | assert(variant_index < variant_count); 2024-01-26T16:04:22,792 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2024-01-26T16:04:22,792 src/pedigree.cpp: In member function ‘const PhredGenotypeLikelihoods* Pedigree::get_genotype_likelihoods_by_id(unsigned int, unsigned int) const’: 2024-01-26T16:04:22,793 src/pedigree.cpp:81:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] 2024-01-26T16:04:22,794 81 | assert(variant_index < variant_count); 2024-01-26T16:04:22,794 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2024-01-26T16:04:22,803 src/pedigree.cpp: In member function ‘std::string Pedigree::toString() const’: 2024-01-26T16:04:22,804 src/pedigree.cpp:112:35: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘const int’ [-Wsign-compare] 2024-01-26T16:04:22,805 112 | for (size_t j=0; j&, size_t, const std::vector&, const Pedigree*, const PedigreePartitions&, bool)’: 2024-01-26T16:04:27,322 src/pedigreecolumncostcomputer.cpp:25:36: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-01-26T16:04:27,322 25 | for (unsigned int i = 0; i < (1< PedigreeColumnCostComputer::get_alleles()’: 2024-01-26T16:04:27,363 src/pedigreecolumncostcomputer.cpp:119:22: warning: unused variable ‘second_best_cost’ [-Wunused-variable] 2024-01-26T16:04:27,364 119 | unsigned int second_best_cost = numeric_limits < unsigned int >::max(); 2024-01-26T16:04:27,365 | ^~~~~~~~~~~~~~~~ 2024-01-26T16:04:28,597 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.11 -c src/pedigreedptable.cpp -o build/temp.linux-armv7l-cpython-311/src/pedigreedptable.o -std=c++11 -Werror=return-type -Werror=narrowing 2024-01-26T16:04:35,603 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.11 -c src/pedigreepartitions.cpp -o build/temp.linux-armv7l-cpython-311/src/pedigreepartitions.o -std=c++11 -Werror=return-type -Werror=narrowing 2024-01-26T16:04:37,745 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.11 -c src/pedmecheuristic.cpp -o build/temp.linux-armv7l-cpython-311/src/pedmecheuristic.o -std=c++11 -Werror=return-type -Werror=narrowing 2024-01-26T16:04:39,947 src/pedmecheuristic.cpp: In member function ‘void PedMecHeuristic::solve()’: 2024-01-26T16:04:39,947 src/pedmecheuristic.cpp:396:18: warning: unused variable ‘s’ [-Wunused-variable] 2024-01-26T16:04:39,948 396 | MecScore s = getOptPhasing(balances[p], optTrans[p], p, posPhasing, mut); 2024-01-26T16:04:39,948 | ^ 2024-01-26T16:04:57,082 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.11 -c src/phredgenotypelikelihoods.cpp -o build/temp.linux-armv7l-cpython-311/src/phredgenotypelikelihoods.o -std=c++11 -Werror=return-type -Werror=narrowing 2024-01-26T16:04:58,935 In file included from /usr/include/c++/12/vector:70, 2024-01-26T16:04:58,935 from src/genotype.h:5, 2024-01-26T16:04:58,936 from src/phredgenotypelikelihoods.h:5, 2024-01-26T16:04:58,937 from src/phredgenotypelikelihoods.cpp:4: 2024-01-26T16:04:58,937 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {Genotype}; _Tp = Genotype; _Alloc = std::allocator]’: 2024-01-26T16:04:58,938 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2024-01-26T16:04:58,939 439 | vector<_Tp, _Alloc>:: 2024-01-26T16:04:58,939 | ^~~~~~~~~~~~~~~~~~~ 2024-01-26T16:04:58,971 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Genotype}; _Tp = Genotype; _Alloc = std::allocator]’, 2024-01-26T16:04:58,972 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = Genotype; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2024-01-26T16:04:58,973 inlined from ‘void PhredGenotypeLikelihoods::get_genotypes(std::vector&) const’ at src/phredgenotypelikelihoods.cpp:53:22: 2024-01-26T16:04:58,973 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2024-01-26T16:04:58,974 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2024-01-26T16:04:58,974 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-01-26T16:04:59,096 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.11 -c src/read.cpp -o build/temp.linux-armv7l-cpython-311/src/read.o -std=c++11 -Werror=return-type -Werror=narrowing 2024-01-26T16:05:02,510 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.11 -c src/readset.cpp -o build/temp.linux-armv7l-cpython-311/src/readset.o -std=c++11 -Werror=return-type -Werror=narrowing 2024-01-26T16:05:07,578 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.11 -c src/transitionprobabilitycomputer.cpp -o build/temp.linux-armv7l-cpython-311/src/transitionprobabilitycomputer.o -std=c++11 -Werror=return-type -Werror=narrowing 2024-01-26T16:05:10,492 In file included from /usr/include/c++/12/vector:70, 2024-01-26T16:05:10,493 from src/vector2d.h:5, 2024-01-26T16:05:10,494 from src/transitionprobabilitycomputer.h:5, 2024-01-26T16:05:10,495 from src/transitionprobabilitycomputer.cpp:1: 2024-01-26T16:05:10,495 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator]’: 2024-01-26T16:05:10,496 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 2024-01-26T16:05:10,496 439 | vector<_Tp, _Alloc>:: 2024-01-26T16:05:10,497 | ^~~~~~~~~~~~~~~~~~~ 2024-01-26T16:05:11,091 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator]’, 2024-01-26T16:05:11,092 inlined from ‘TransitionProbabilityComputer::TransitionProbabilityComputer(size_t, unsigned int, const Pedigree*, const std::vector&)’ at src/transitionprobabilitycomputer.cpp:25:29: 2024-01-26T16:05:11,093 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 2024-01-26T16:05:11,093 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2024-01-26T16:05:11,094 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-01-26T16:05:11,824 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.11 -c whatshap/core.cpp -o build/temp.linux-armv7l-cpython-311/whatshap/core.o -std=c++11 -Werror=return-type -Werror=narrowing 2024-01-26T16:05:14,756 In file included from whatshap/core.cpp:848: 2024-01-26T16:05:14,757 src/genotypedptable.h: In member function ‘void GenotypeDPTable::genotype_likelihood_t::divide_likelihoods_by(long double&)’: 2024-01-26T16:05:14,758 src/genotypedptable.h:38:95: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = divides; _Tp = long double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 2024-01-26T16:05:14,758 38 | std::transform(likelihoods.begin(), likelihoods.end(), likelihoods.begin(), std::bind2nd(std::divides(), val)); 2024-01-26T16:05:14,759 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-01-26T16:05:14,760 In file included from /usr/include/c++/12/bits/stl_function.h:1438, 2024-01-26T16:05:14,760 from /usr/include/c++/12/string:48, 2024-01-26T16:05:14,761 from whatshap/core.cpp:820: 2024-01-26T16:05:14,762 /usr/include/c++/12/backward/binders.h:172:5: note: declared here 2024-01-26T16:05:14,762 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2024-01-26T16:05:14,763 | ^~~~~~~ 2024-01-26T16:05:15,119 In file included from whatshap/core.cpp:852: 2024-01-26T16:05:15,120 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::run_core()’: 2024-01-26T16:05:15,120 src/hapchat/hapchatcore.cpp:145:11: warning: variable ‘counter_columns’ set but not used [-Wunused-but-set-variable] 2024-01-26T16:05:15,121 145 | Counter counter_columns; 2024-01-26T16:05:15,121 | ^~~~~~~~~~~~~~~ 2024-01-26T16:05:15,132 src/hapchat/hapchatcore.cpp: In member function ‘bool HapChatCore::check_end(HapChatColumnIterator, const std::vector >&, const Pointer&, const bool&)’: 2024-01-26T16:05:15,133 src/hapchat/hapchatcore.cpp:208:74: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-01-26T16:05:15,133 208 | return (!re_run && (hap.is_ended() && (input[pointer][0].get_read_id() == -1))); 2024-01-26T16:05:15,134 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2024-01-26T16:05:15,292 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::dp(const constants_t&, std::vector&, std::vector&, Counter&, Cost&, Counter&, Counter&, Counter&, Counter&, HapChatColumnIterator)’: 2024-01-26T16:05:15,293 src/hapchat/hapchatcore.cpp:939:15: warning: unused variable ‘old_k’ [-Wunused-variable] 2024-01-26T16:05:15,293 939 | int old_k = k_j[input_pointer]; 2024-01-26T16:05:15,294 | ^~~~~ 2024-01-26T16:05:15,315 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&)’: 2024-01-26T16:05:15,315 src/hapchat/hapchatcore.cpp:1114:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-01-26T16:05:15,316 1114 | (colJ[j].get_read_id() != -1) && 2024-01-26T16:05:15,317 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2024-01-26T16:05:15,317 src/hapchat/hapchatcore.cpp:1115:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-01-26T16:05:15,318 1115 | (colQ[i].get_read_id() != -1)) { 2024-01-26T16:05:15,319 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2024-01-26T16:05:15,321 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::represent_column(const Column&, BitColumn&, Counter&, BitColumn&, Counter&)’: 2024-01-26T16:05:15,322 src/hapchat/hapchatcore.cpp:1159:58: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-01-26T16:05:15,323 1159 | while(cov < column.size() && column[cov].get_read_id() != -1) { 2024-01-26T16:05:15,323 | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2024-01-26T16:05:15,329 src/hapchat/hapchatcore.cpp: In member function ‘int HapChatCore::compute_active_common(const Column&, const Column&, unsigned int&)’: 2024-01-26T16:05:15,330 src/hapchat/hapchatcore.cpp:1294:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-01-26T16:05:15,331 1294 | (colJ[j].get_read_id() != -1) && 2024-01-26T16:05:15,331 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2024-01-26T16:05:15,332 src/hapchat/hapchatcore.cpp:1295:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-01-26T16:05:15,332 1295 | (colQ[i].get_read_id() != -1)) { 2024-01-26T16:05:15,333 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2024-01-26T16:05:15,337 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&)’: 2024-01-26T16:05:15,338 src/hapchat/hapchatcore.cpp:1350:67: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-01-26T16:05:15,339 1350 | if(i < input[pointer].size() && input[pointer][i].get_read_id() != -1) 2024-01-26T16:05:15,339 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2024-01-26T16:05:15,492 In file included from src/polyphase/haplothreader.h:5, 2024-01-26T16:05:15,493 from whatshap/core.cpp:858: 2024-01-26T16:05:15,493 src/polyphase/tuple.h: At global scope: 2024-01-26T16:05:15,494 src/polyphase/tuple.h:27:50: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-01-26T16:05:15,494 27 | 31UL << 20, 31UL << 25, 31UL << 30, 31UL << 35, 2024-01-26T16:05:15,495 | ~~~~~^~~~~ 2024-01-26T16:05:15,495 src/polyphase/tuple.h:28:14: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-01-26T16:05:15,496 28 | 31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55}; 2024-01-26T16:05:15,496 | ~~~~~^~~~~ 2024-01-26T16:05:15,496 src/polyphase/tuple.h:28:26: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-01-26T16:05:15,497 28 | 31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55}; 2024-01-26T16:05:15,497 | ~~~~~^~~~~ 2024-01-26T16:05:15,498 src/polyphase/tuple.h:28:38: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-01-26T16:05:15,498 28 | 31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55}; 2024-01-26T16:05:15,499 | ~~~~~^~~~~ 2024-01-26T16:05:15,499 src/polyphase/tuple.h:28:50: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-01-26T16:05:15,500 28 | 31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55}; 2024-01-26T16:05:15,501 | ~~~~~^~~~~ 2024-01-26T16:05:15,501 src/polyphase/tuple.h:27:50: error: right operand of shift expression ‘(31 << 35)’ is greater than or equal to the precision 32 of the left operand [-fpermissive] 2024-01-26T16:05:15,502 27 | 31UL << 20, 31UL << 25, 31UL << 30, 31UL << 35, 2024-01-26T16:05:15,503 | ~~~~~^~~~~ 2024-01-26T16:05:15,542 In file included from whatshap/core.cpp:859: 2024-01-26T16:05:15,543 src/polyphase/switchflipcalculator.h:32:14: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-01-26T16:05:15,543 32 | 15UL << 32, 15UL << 36, 15UL << 40, 15UL << 44, 2024-01-26T16:05:15,544 | ~~~~~^~~~~ 2024-01-26T16:05:15,544 src/polyphase/switchflipcalculator.h:32:26: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-01-26T16:05:15,545 32 | 15UL << 32, 15UL << 36, 15UL << 40, 15UL << 44, 2024-01-26T16:05:15,546 | ~~~~~^~~~~ 2024-01-26T16:05:15,546 src/polyphase/switchflipcalculator.h:32:38: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-01-26T16:05:15,547 32 | 15UL << 32, 15UL << 36, 15UL << 40, 15UL << 44, 2024-01-26T16:05:15,547 | ~~~~~^~~~~ 2024-01-26T16:05:15,548 src/polyphase/switchflipcalculator.h:32:50: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-01-26T16:05:15,549 32 | 15UL << 32, 15UL << 36, 15UL << 40, 15UL << 44, 2024-01-26T16:05:15,549 | ~~~~~^~~~~ 2024-01-26T16:05:15,550 src/polyphase/switchflipcalculator.h:33:14: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-01-26T16:05:15,551 33 | 15UL << 48, 15UL << 52, 15UL << 56, 15UL << 60 2024-01-26T16:05:15,551 | ~~~~~^~~~~ 2024-01-26T16:05:15,552 src/polyphase/switchflipcalculator.h:33:26: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-01-26T16:05:15,553 33 | 15UL << 48, 15UL << 52, 15UL << 56, 15UL << 60 2024-01-26T16:05:15,554 | ~~~~~^~~~~ 2024-01-26T16:05:15,554 src/polyphase/switchflipcalculator.h:33:38: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-01-26T16:05:15,555 33 | 15UL << 48, 15UL << 52, 15UL << 56, 15UL << 60 2024-01-26T16:05:15,555 | ~~~~~^~~~~ 2024-01-26T16:05:15,555 src/polyphase/switchflipcalculator.h:33:50: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-01-26T16:05:15,556 33 | 15UL << 48, 15UL << 52, 15UL << 56, 15UL << 60 2024-01-26T16:05:15,556 | ~~~~~^~~~~ 2024-01-26T16:05:15,557 src/polyphase/switchflipcalculator.h:32:14: error: right operand of shift expression ‘(15 << 32)’ is greater than or equal to the precision 32 of the left operand [-fpermissive] 2024-01-26T16:05:15,557 32 | 15UL << 32, 15UL << 36, 15UL << 40, 15UL << 44, 2024-01-26T16:05:15,558 | ~~~~~^~~~~ 2024-01-26T16:05:16,159 whatshap/core.cpp: In function ‘PyObject* __pyx_pf_8whatshap_4core_15PedigreeDPTable_4get_super_reads(__pyx_obj_8whatshap_4core_PedigreeDPTable*)’: 2024-01-26T16:05:16,159 whatshap/core.cpp:9069:33: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2024-01-26T16:05:16,160 9069 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { 2024-01-26T16:05:16,160 | ~~~~~~~~~~^~~~~~~~~~~ 2024-01-26T16:05:16,474 whatshap/core.cpp: In function ‘PyObject* __pyx_pf_8whatshap_4core_11HapChatCore_6get_super_reads(__pyx_obj_8whatshap_4core_HapChatCore*)’: 2024-01-26T16:05:16,475 whatshap/core.cpp:15302:33: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-01-26T16:05:16,476 15302 | for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { 2024-01-26T16:05:16,476 | ~~~~~~~~~~^~~~~~~~~~~ 2024-01-26T16:05:19,244 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2024-01-26T16:05:19,411 ERROR: Building wheel for whatshap (pyproject.toml) exited with 1 2024-01-26T16:05:19,425 [bold magenta]full command[/]: [blue]/usr/bin/python3 /usr/local/lib/python3.11/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py build_wheel /tmp/tmpoqh_bg6g[/] 2024-01-26T16:05:19,425 [bold magenta]cwd[/]: /tmp/pip-wheel-exo_lejj/whatshap_a3a1471e65fa4b668e7b70dad19ffc8a 2024-01-26T16:05:19,426 Building wheel for whatshap (pyproject.toml): finished with status 'error' 2024-01-26T16:05:19,428 ERROR: Failed building wheel for whatshap 2024-01-26T16:05:19,430 Failed to build whatshap 2024-01-26T16:05:19,432 ERROR: Failed to build one or more wheels 2024-01-26T16:05:19,433 Exception information: 2024-01-26T16:05:19,433 Traceback (most recent call last): 2024-01-26T16:05:19,433 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2024-01-26T16:05:19,433 status = run_func(*args) 2024-01-26T16:05:19,433 ^^^^^^^^^^^^^^^ 2024-01-26T16:05:19,433 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 245, in wrapper 2024-01-26T16:05:19,433 return func(self, options, args) 2024-01-26T16:05:19,433 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2024-01-26T16:05:19,433 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run 2024-01-26T16:05:19,433 raise CommandError("Failed to build one or more wheels") 2024-01-26T16:05:19,433 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2024-01-26T16:05:19,437 Removed build tracker: '/tmp/pip-build-tracker-nthd336h'