2023-09-12T16:59:27,681 Created temporary directory: /tmp/pip-build-tracker-70xvopas 2023-09-12T16:59:27,683 Initialized build tracking at /tmp/pip-build-tracker-70xvopas 2023-09-12T16:59:27,683 Created build tracker: /tmp/pip-build-tracker-70xvopas 2023-09-12T16:59:27,684 Entered build tracker: /tmp/pip-build-tracker-70xvopas 2023-09-12T16:59:27,684 Created temporary directory: /tmp/pip-wheel-5xn3kqpp 2023-09-12T16:59:27,688 Created temporary directory: /tmp/pip-ephem-wheel-cache-cwe5b5gj 2023-09-12T16:59:27,709 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-12T16:59:27,713 2 location(s) to search for versions of whatshap: 2023-09-12T16:59:27,713 * https://pypi.org/simple/whatshap/ 2023-09-12T16:59:27,713 * https://www.piwheels.org/simple/whatshap/ 2023-09-12T16:59:27,713 Fetching project page and analyzing links: https://pypi.org/simple/whatshap/ 2023-09-12T16:59:27,714 Getting page https://pypi.org/simple/whatshap/ 2023-09-12T16:59:27,716 Found index url https://pypi.org/simple/ 2023-09-12T16:59:27,930 Fetched page https://pypi.org/simple/whatshap/ as application/vnd.pypi.simple.v1+json 2023-09-12T16:59:27,942 Found link https://files.pythonhosted.org/packages/35/95/43ff2304cd59ade39e64aadaeaec48e8c12bbe6262bcbbbd7b7d89487757/whatshap-0.9.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.9 2023-09-12T16:59:27,943 Found link https://files.pythonhosted.org/packages/f0/4b/f2b882803ac66b969414d8427ee8b4ca2c29b17cfead0fd85f349dc66983/whatshap-0.10.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.10 2023-09-12T16:59:27,944 Found link https://files.pythonhosted.org/packages/fc/dc/30559c28fb54985773fb242f5768fc206e054e44e45962a32cf4fd29a794/whatshap-0.11.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.11 2023-09-12T16:59:27,944 Found link https://files.pythonhosted.org/packages/01/84/31a5ea338647d0256a4a5c57e98d7a563f387e6a47f1e26299b89e3f2da1/whatshap-0.12.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.12 2023-09-12T16:59:27,945 Found link https://files.pythonhosted.org/packages/e2/f3/c71cb4bc3ba3b1234ee0c5fe729c60440164e07437695ca09c61750e0e11/whatshap-0.13.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.13 2023-09-12T16:59:27,946 Found link https://files.pythonhosted.org/packages/cd/d3/a63285d15b0da196a259197e46d9f61a852d1b3c94800f4a82ca4e31e307/whatshap-0.14.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.14 2023-09-12T16:59:27,946 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 2023-09-12T16:59:27,947 Found link https://files.pythonhosted.org/packages/ca/13/6454e5e8f6c858a203378b3e22f13518f092ba85aa6d7a9a9796d22c28e0/whatshap-0.15.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.15 2023-09-12T16:59:27,948 Found link https://files.pythonhosted.org/packages/3d/cb/55730a8713ecba10f6d987dbd935ba31ded92f9af1ddd250896f3c1cfc3b/whatshap-0.16.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.16 2023-09-12T16:59:27,949 Found link https://files.pythonhosted.org/packages/79/11/79da12b8c23f43b00fab8a6206f75cc1cc8c1902ff30eca53c17abe2f633/whatshap-0.17.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.17 2023-09-12T16:59:27,949 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) 2023-09-12T16:59:27,950 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) 2023-09-12T16:59:27,951 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) 2023-09-12T16:59:27,951 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) 2023-09-12T16:59:27,953 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 2023-09-12T16:59:27,953 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) 2023-09-12T16:59:27,954 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) 2023-09-12T16:59:27,954 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) 2023-09-12T16:59:27,955 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 2023-09-12T16:59:27,955 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) 2023-09-12T16:59:27,956 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) 2023-09-12T16:59:27,957 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) 2023-09-12T16:59:27,957 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) 2023-09-12T16:59:27,958 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 2023-09-12T16:59:27,959 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) 2023-09-12T16:59:27,960 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) 2023-09-12T16:59:27,960 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) 2023-09-12T16:59:27,961 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) 2023-09-12T16:59:27,962 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 2023-09-12T16:59:27,963 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) 2023-09-12T16:59:27,963 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) 2023-09-12T16:59:27,964 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) 2023-09-12T16:59:27,964 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) 2023-09-12T16:59:27,965 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 2023-09-12T16:59:27,965 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) 2023-09-12T16:59:27,966 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) 2023-09-12T16:59:27,967 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) 2023-09-12T16:59:27,967 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) 2023-09-12T16:59:27,968 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 2023-09-12T16:59:27,969 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) 2023-09-12T16:59:27,969 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) 2023-09-12T16:59:27,970 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) 2023-09-12T16:59:27,971 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) 2023-09-12T16:59:27,972 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 2023-09-12T16:59:27,972 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) 2023-09-12T16:59:27,973 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) 2023-09-12T16:59:27,973 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) 2023-09-12T16:59:27,976 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) 2023-09-12T16:59:27,977 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) 2023-09-12T16:59:27,977 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) 2023-09-12T16:59:27,978 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 2023-09-12T16:59:27,979 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) 2023-09-12T16:59:27,980 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/e0/a3/dff518edaec7aa8efd2c7f1df8a494b7c4a0b49f7e6350c13228dee97351/whatshap-1.7-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7) 2023-09-12T16:59:27,980 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/c1/34/785976fd423c187d90e2be419af906a366c038a57503e2e4fb6599aca868/whatshap-1.7-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7) 2023-09-12T16:59:27,980 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/e1/81/8eaf7be1255b732643ce82307a72b015230b14842a15fc83b17bd264282d/whatshap-1.7-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7) 2023-09-12T16:59:27,981 Found link 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 2023-09-12T16:59:27,982 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) 2023-09-12T16:59:27,982 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) 2023-09-12T16:59:27,983 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/fa/f1/45172b5e64640fa04cdc3af57fc9848cf5d94d163dee6646a9aae67dfccb/whatshap-2.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7) 2023-09-12T16:59:27,983 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/48/aa/31e1727bb7f7f770df8192d2aa096d988d0a4345e3842c89c32badedd7a9/whatshap-2.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7) 2023-09-12T16:59:27,984 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/8e/5d/9af0551ffaa026d33b612a1bdfccdeabc4b93fd0af6313b57671aea0648a/whatshap-2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7) 2023-09-12T16:59:27,985 Found link 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 2023-09-12T16:59:27,986 Fetching project page and analyzing links: https://www.piwheels.org/simple/whatshap/ 2023-09-12T16:59:27,986 Getting page https://www.piwheels.org/simple/whatshap/ 2023-09-12T16:59:27,988 Found index url https://www.piwheels.org/simple/ 2023-09-12T16:59:28,254 Fetched page https://www.piwheels.org/simple/whatshap/ as text/html 2023-09-12T16:59:28,267 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) 2023-09-12T16:59:28,268 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) 2023-09-12T16:59:28,269 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) 2023-09-12T16:59:28,269 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) 2023-09-12T16:59:28,270 Skipping link: No binaries permitted for whatshap: 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https://www.piwheels.org/simple/whatshap/) 2023-09-12T16:59:28,274 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/) 2023-09-12T16:59:28,275 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/) 2023-09-12T16:59:28,275 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/) 2023-09-12T16:59:28,276 Skipping link: No binaries permitted for whatshap: 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https://www.piwheels.org/simple/whatshap/) 2023-09-12T16:59:28,278 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/) 2023-09-12T16:59:28,278 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/) 2023-09-12T16:59:28,279 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/) 2023-09-12T16:59:28,279 Skipping link: No binaries permitted for whatshap: 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(from https://www.piwheels.org/simple/whatshap/) 2023-09-12T16:59:28,281 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/) 2023-09-12T16:59:28,282 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/) 2023-09-12T16:59:28,282 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/) 2023-09-12T16:59:28,283 Skipping link: No binaries permitted for whatshap: 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https://www.piwheels.org/simple/whatshap/) 2023-09-12T16:59:28,285 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/) 2023-09-12T16:59:28,286 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/) 2023-09-12T16:59:28,286 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/) 2023-09-12T16:59:28,287 Skipping link: No binaries permitted for whatshap: 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https://www.piwheels.org/simple/whatshap/) 2023-09-12T16:59:28,289 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/) 2023-09-12T16:59:28,289 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/) 2023-09-12T16:59:28,290 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/) 2023-09-12T16:59:28,290 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/) 2023-09-12T16:59:28,291 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/) 2023-09-12T16:59:28,292 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/) 2023-09-12T16:59:28,292 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/) 2023-09-12T16:59:28,293 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/) 2023-09-12T16:59:28,293 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/) 2023-09-12T16:59:28,294 Skipping link: not a file: https://www.piwheels.org/simple/whatshap/ 2023-09-12T16:59:28,294 Skipping link: not a file: https://pypi.org/simple/whatshap/ 2023-09-12T16:59:28,315 Given no hashes to check 1 links for project 'whatshap': discarding no candidates 2023-09-12T16:59:28,333 Collecting whatshap==1.0 2023-09-12T16:59:28,336 Created temporary directory: /tmp/pip-unpack-p5n2cdvn 2023-09-12T16:59:28,558 Downloading whatshap-1.0.tar.gz (579 kB) 2023-09-12T16:59:29,079 Added whatshap==1.0 from https://files.pythonhosted.org/packages/c0/c8/98036e04fb95249128d6b49ca61691e1d8eea484dd94611f90efb5857174/whatshap-1.0.tar.gz to build tracker '/tmp/pip-build-tracker-70xvopas' 2023-09-12T16:59:29,081 Running setup.py (path:/tmp/pip-wheel-5xn3kqpp/whatshap_c3a872ebe6cc43faa57522cdc0478878/setup.py) egg_info for package whatshap 2023-09-12T16:59:29,082 Created temporary directory: /tmp/pip-pip-egg-info-ci1rk5_0 2023-09-12T16:59:29,082 Preparing metadata (setup.py): started 2023-09-12T16:59:29,084 Running command python setup.py egg_info 2023-09-12T16:59:30,036 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2023-09-12T16:59:30,037 !! 2023-09-12T16:59:30,038 ******************************************************************************** 2023-09-12T16:59:30,039 Requirements should be satisfied by a PEP 517 installer. 2023-09-12T16:59:30,039 If you are using pip, you can try `pip install --use-pep517`. 2023-09-12T16:59:30,040 ******************************************************************************** 2023-09-12T16:59:30,041 !! 2023-09-12T16:59:30,042 dist.fetch_build_eggs(dist.setup_requires) 2023-09-12T16:59:33,217 running egg_info 2023-09-12T16:59:33,219 creating /tmp/pip-pip-egg-info-ci1rk5_0/whatshap.egg-info 2023-09-12T16:59:33,249 writing /tmp/pip-pip-egg-info-ci1rk5_0/whatshap.egg-info/PKG-INFO 2023-09-12T16:59:33,255 writing dependency_links to /tmp/pip-pip-egg-info-ci1rk5_0/whatshap.egg-info/dependency_links.txt 2023-09-12T16:59:33,257 writing entry points to /tmp/pip-pip-egg-info-ci1rk5_0/whatshap.egg-info/entry_points.txt 2023-09-12T16:59:33,260 writing requirements to /tmp/pip-pip-egg-info-ci1rk5_0/whatshap.egg-info/requires.txt 2023-09-12T16:59:33,262 writing top-level names to /tmp/pip-pip-egg-info-ci1rk5_0/whatshap.egg-info/top_level.txt 2023-09-12T16:59:33,264 writing manifest file '/tmp/pip-pip-egg-info-ci1rk5_0/whatshap.egg-info/SOURCES.txt' 2023-09-12T16:59:33,438 listing git files failed - pretending there aren't any 2023-09-12T16:59:33,444 reading manifest file '/tmp/pip-pip-egg-info-ci1rk5_0/whatshap.egg-info/SOURCES.txt' 2023-09-12T16:59:33,449 writing manifest file '/tmp/pip-pip-egg-info-ci1rk5_0/whatshap.egg-info/SOURCES.txt' 2023-09-12T16:59:33,564 Preparing metadata (setup.py): finished with status 'done' 2023-09-12T16:59:33,567 Source in /tmp/pip-wheel-5xn3kqpp/whatshap_c3a872ebe6cc43faa57522cdc0478878 has version 1.0, which satisfies requirement whatshap==1.0 from https://files.pythonhosted.org/packages/c0/c8/98036e04fb95249128d6b49ca61691e1d8eea484dd94611f90efb5857174/whatshap-1.0.tar.gz 2023-09-12T16:59:33,568 Removed whatshap==1.0 from https://files.pythonhosted.org/packages/c0/c8/98036e04fb95249128d6b49ca61691e1d8eea484dd94611f90efb5857174/whatshap-1.0.tar.gz from build tracker '/tmp/pip-build-tracker-70xvopas' 2023-09-12T16:59:33,574 Created temporary directory: /tmp/pip-unpack-h51_jonz 2023-09-12T16:59:33,575 Created temporary directory: /tmp/pip-unpack-54yaxs5y 2023-09-12T16:59:33,594 Building wheels for collected packages: whatshap 2023-09-12T16:59:33,598 Created temporary directory: /tmp/pip-wheel-m3fbg6he 2023-09-12T16:59:33,599 Building wheel for whatshap (setup.py): started 2023-09-12T16:59:33,600 Destination directory: /tmp/pip-wheel-m3fbg6he 2023-09-12T16:59:33,600 Running command python setup.py bdist_wheel 2023-09-12T16:59:34,283 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2023-09-12T16:59:34,283 !! 2023-09-12T16:59:34,284 ******************************************************************************** 2023-09-12T16:59:34,285 Requirements should be satisfied by a PEP 517 installer. 2023-09-12T16:59:34,285 If you are using pip, you can try `pip install --use-pep517`. 2023-09-12T16:59:34,286 ******************************************************************************** 2023-09-12T16:59:34,287 !! 2023-09-12T16:59:34,288 dist.fetch_build_eggs(dist.setup_requires) 2023-09-12T16:59:34,919 running bdist_wheel 2023-09-12T16:59:35,003 running build 2023-09-12T16:59:35,004 running build_py 2023-09-12T16:59:35,037 creating build 2023-09-12T16:59:35,037 creating build/lib.linux-armv7l-cpython-311 2023-09-12T16:59:35,038 creating build/lib.linux-armv7l-cpython-311/whatshap 2023-09-12T16:59:35,040 copying whatshap/__main__.py -> build/lib.linux-armv7l-cpython-311/whatshap 2023-09-12T16:59:35,042 copying whatshap/math.py -> build/lib.linux-armv7l-cpython-311/whatshap 2023-09-12T16:59:35,043 copying whatshap/pedigree.py -> build/lib.linux-armv7l-cpython-311/whatshap 2023-09-12T16:59:35,046 copying whatshap/variants.py -> build/lib.linux-armv7l-cpython-311/whatshap 2023-09-12T16:59:35,048 copying whatshap/testhelpers.py -> build/lib.linux-armv7l-cpython-311/whatshap 2023-09-12T16:59:35,051 copying whatshap/graph.py -> build/lib.linux-armv7l-cpython-311/whatshap 2023-09-12T16:59:35,053 copying whatshap/coverage.py -> build/lib.linux-armv7l-cpython-311/whatshap 2023-09-12T16:59:35,055 copying whatshap/utils.py -> build/lib.linux-armv7l-cpython-311/whatshap 2023-09-12T16:59:35,057 copying whatshap/threading.py -> build/lib.linux-armv7l-cpython-311/whatshap 2023-09-12T16:59:35,060 copying whatshap/polyphaseplots.py -> build/lib.linux-armv7l-cpython-311/whatshap 2023-09-12T16:59:35,064 copying whatshap/args.py -> build/lib.linux-armv7l-cpython-311/whatshap 2023-09-12T16:59:35,067 copying whatshap/merge.py -> build/lib.linux-armv7l-cpython-311/whatshap 2023-09-12T16:59:35,069 copying whatshap/bam.py -> build/lib.linux-armv7l-cpython-311/whatshap 2023-09-12T16:59:35,072 copying whatshap/timer.py -> build/lib.linux-armv7l-cpython-311/whatshap 2023-09-12T16:59:35,074 copying whatshap/_version.py -> build/lib.linux-armv7l-cpython-311/whatshap 2023-09-12T16:59:35,076 copying whatshap/verification.py -> build/lib.linux-armv7l-cpython-311/whatshap 2023-09-12T16:59:35,078 copying whatshap/__init__.py -> build/lib.linux-armv7l-cpython-311/whatshap 2023-09-12T16:59:35,080 copying whatshap/vcf.py -> build/lib.linux-armv7l-cpython-311/whatshap 2023-09-12T16:59:35,084 creating build/lib.linux-armv7l-cpython-311/whatshap/cli 2023-09-12T16:59:35,085 copying whatshap/cli/genotype.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli 2023-09-12T16:59:35,088 copying whatshap/cli/polyphase.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli 2023-09-12T16:59:35,091 copying whatshap/cli/stats.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli 2023-09-12T16:59:35,093 copying whatshap/cli/find_snv_candidates.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli 2023-09-12T16:59:35,095 copying whatshap/cli/haplotag.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli 2023-09-12T16:59:35,098 copying whatshap/cli/hapcut2vcf.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli 2023-09-12T16:59:35,100 copying whatshap/cli/compare.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli 2023-09-12T16:59:35,102 copying whatshap/cli/unphase.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli 2023-09-12T16:59:35,104 copying whatshap/cli/split.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli 2023-09-12T16:59:35,106 copying whatshap/cli/__init__.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli 2023-09-12T16:59:35,108 copying whatshap/cli/phase.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli 2023-09-12T16:59:35,113 running build_ext 2023-09-12T16:59:35,118 building 'whatshap.core' extension 2023-09-12T16:59:35,119 creating build/temp.linux-armv7l-cpython-311 2023-09-12T16:59:35,120 creating build/temp.linux-armv7l-cpython-311/src 2023-09-12T16:59:35,121 creating build/temp.linux-armv7l-cpython-311/src/hapchat 2023-09-12T16:59:35,123 creating build/temp.linux-armv7l-cpython-311/src/polyphase 2023-09-12T16:59:35,124 creating build/temp.linux-armv7l-cpython-311/whatshap 2023-09-12T16:59:35,124 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -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 2023-09-12T16:59:36,956 In file included from /usr/include/c++/12/cassert:44, 2023-09-12T16:59:36,957 from src/backwardcolumniterator.cpp:1: 2023-09-12T16:59:36,957 src/backwardcolumniterator.cpp: In member function ‘void BackwardColumnIterator::jump_to_column(int)’: 2023-09-12T16:59:36,958 src/backwardcolumniterator.cpp:121:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T16:59:36,959 121 | assert(k < positions->size()); 2023-09-12T16:59:36,960 | ~~^~~~~~~~~~~~~~~~~~~ 2023-09-12T16:59:36,960 src/backwardcolumniterator.cpp:140:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2023-09-12T16:59:36,961 140 | assert(active_entry < read->getVariantCount()); 2023-09-12T16:59:36,962 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T16:59:38,731 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -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 2023-09-12T16:59:38,827 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -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 2023-09-12T16:59:40,090 src/columnindexingiterator.cpp: In member function ‘unsigned int ColumnIndexingIterator::index_forward_projection(unsigned int)’: 2023-09-12T16:59:40,090 src/columnindexingiterator.cpp:90:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T16:59:40,091 90 | for(int j=0; j< parent->read_ids.size(); ++j) { 2023-09-12T16:59:40,092 | ~^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T16:59:40,093 src/columnindexingiterator.cpp:92:22: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T16:59:40,093 92 | if(m != -1) { 2023-09-12T16:59:40,094 | ~~^~~~~ 2023-09-12T16:59:40,094 src/columnindexingiterator.cpp:89:22: warning: unused variable ‘s’ [-Wunused-variable] 2023-09-12T16:59:40,095 89 | unsigned int s = 1; 2023-09-12T16:59:40,095 | ^ 2023-09-12T16:59:40,401 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -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 2023-09-12T16:59:41,652 src/columnindexingscheme.cpp: In constructor ‘ColumnIndexingScheme::ColumnIndexingScheme(const ColumnIndexingScheme*, const std::vector&)’: 2023-09-12T16:59:41,653 src/columnindexingscheme.cpp:22:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T16:59:41,654 22 | while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T16:59:41,655 22 | while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T16:59:41,661 71 | while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-12T16:59:41,663 71 | while ((iread_ids.size()) && (j > ColumnIterator::get_next()’: 2023-09-12T16:59:44,028 src/columniterator.cpp:105:54: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2023-09-12T16:59:44,029 105 | assert(list_it->active_entry < read->getVariantCount()); 2023-09-12T16:59:44,030 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T16:59:44,047 src/columniterator.cpp: In member function ‘void ColumnIterator::jump_to_column(size_t)’: 2023-09-12T16:59:44,048 src/columniterator.cpp:161:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2023-09-12T16:59:44,048 161 | assert(active_entry < read->getVariantCount()); 2023-09-12T16:59:44,049 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T16:59:45,873 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -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 2023-09-12T16:59:47,004 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -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 2023-09-12T16:59:49,664 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -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 2023-09-12T16:59:52,863 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -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 2023-09-12T16:59:54,245 src/genotypedistribution.cpp: In member function ‘double GenotypeDistribution::errorProbability() const’: 2023-09-12T16:59:54,245 src/genotypedistribution.cpp:55:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2023-09-12T16:59:54,246 55 | if (i == best_index) continue; 2023-09-12T16:59:54,247 | ~~^~~~~~~~~~~~~ 2023-09-12T16:59:54,799 In file included from /usr/include/c++/12/vector:70, 2023-09-12T16:59:54,800 from src/genotypedistribution.h:4, 2023-09-12T16:59:54,801 from src/genotypedistribution.cpp:5: 2023-09-12T16:59:54,801 /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]’: 2023-09-12T16:59:54,802 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T16:59:54,802 439 | vector<_Tp, _Alloc>:: 2023-09-12T16:59:54,803 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T16:59:54,839 In file included from /usr/include/c++/12/vector:64: 2023-09-12T16:59:54,840 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T16:59:54,840 inlined from ‘GenotypeDistribution::GenotypeDistribution(double, double, double)’ at src/genotypedistribution.cpp:10:24: 2023-09-12T16:59:54,841 /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 2023-09-12T16:59:54,842 1287 | _M_realloc_insert(end(), __x); 2023-09-12T16:59:54,842 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T16:59:54,843 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T16:59:54,844 inlined from ‘GenotypeDistribution::GenotypeDistribution(double, double, double)’ at src/genotypedistribution.cpp:11:24: 2023-09-12T16:59:54,844 /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 2023-09-12T16:59:54,845 1287 | _M_realloc_insert(end(), __x); 2023-09-12T16:59:54,845 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T16:59:54,846 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-12T16:59:54,846 inlined from ‘GenotypeDistribution::GenotypeDistribution(double, double, double)’ at src/genotypedistribution.cpp:12:24: 2023-09-12T16:59:54,847 /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 2023-09-12T16:59:54,847 1287 | _M_realloc_insert(end(), __x); 2023-09-12T16:59:54,848 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T16:59:55,007 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -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 2023-09-12T16:59:57,461 In file included from src/genotypedptable.cpp:11: 2023-09-12T16:59:57,461 src/genotypedptable.h: In member function ‘void GenotypeDPTable::genotype_likelihood_t::divide_likelihoods_by(long double&)’: 2023-09-12T16:59:57,462 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] 2023-09-12T16:59:57,462 38 | std::transform(likelihoods.begin(), likelihoods.end(), likelihoods.begin(), std::bind2nd(std::divides(), val)); 2023-09-12T16:59:57,463 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T16:59:57,464 In file included from /usr/include/c++/12/bits/stl_function.h:1438, 2023-09-12T16:59:57,464 from /usr/include/c++/12/string:48, 2023-09-12T16:59:57,465 from /usr/include/c++/12/stdexcept:39, 2023-09-12T16:59:57,466 from src/genotypedptable.cpp:1: 2023-09-12T16:59:57,467 /usr/include/c++/12/backward/binders.h:172:5: note: declared here 2023-09-12T16:59:57,467 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2023-09-12T16:59:57,468 | ^~~~~~~ 2023-09-12T16:59:57,491 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::clear_forward_table()’: 2023-09-12T16:59:57,492 src/genotypedptable.cpp:61:12: warning: unused variable ‘column_count’ [-Wunused-variable] 2023-09-12T16:59:57,492 61 | size_t column_count = input_column_iterator.get_column_count(); 2023-09-12T16:59:57,493 | ^~~~~~~~~~~~ 2023-09-12T16:59:57,540 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_index()’: 2023-09-12T16:59:57,541 src/genotypedptable.cpp:91:18: warning: unused variable ‘transmission_configurations’ [-Wunused-variable] 2023-09-12T16:59:57,542 91 | unsigned int transmission_configurations = pow(4, pedigree->triple_count()); 2023-09-12T16:59:57,543 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T16:59:57,547 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_backward_prob()’: 2023-09-12T16:59:57,547 src/genotypedptable.cpp:152:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-12T16:59:57,548 152 | if ((k>1) && (column_index < column_count-1) && (((column_index+1)%k) != 0)) { 2023-09-12T16:59:57,549 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2023-09-12T16:59:57,553 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_forward_prob()’: 2023-09-12T16:59:57,553 src/genotypedptable.cpp:178:12: warning: unused variable ‘k’ [-Wunused-variable] 2023-09-12T16:59:57,554 178 | size_t k = (size_t)sqrt(input_column_iterator.get_column_count()); 2023-09-12T16:59:57,554 | ^ 2023-09-12T16:59:57,725 In file included from src/genotypedptable.h:15: 2023-09-12T16:59:57,725 src/vector2d.h: In instantiation of ‘void Vector2D::divide_entries_by(T) [with T = long double]’: 2023-09-12T16:59:57,726 src/genotypedptable.cpp:290:53: required from here 2023-09-12T16:59:57,726 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] 2023-09-12T16:59:57,727 40 | std::bind2nd(std::divides(),val)); 2023-09-12T16:59:57,727 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T16:59:57,728 /usr/include/c++/12/backward/binders.h:172:5: note: declared here 2023-09-12T16:59:57,728 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2023-09-12T16:59:57,729 | ^~~~~~~ 2023-09-12T17:00:01,507 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -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 2023-09-12T17:00:04,218 In file included from /usr/include/c++/12/vector:70, 2023-09-12T17:00:04,219 from src/columniterator.h:4, 2023-09-12T17:00:04,220 from src/genotyper.cpp:6: 2023-09-12T17:00:04,220 /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]’: 2023-09-12T17:00:04,221 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T17:00:04,222 439 | vector<_Tp, _Alloc>:: 2023-09-12T17:00:04,222 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T17:00:04,442 In file included from /usr/include/c++/12/vector:64: 2023-09-12T17:00:04,443 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Genotype; _Alloc = std::allocator]’, 2023-09-12T17:00:04,444 inlined from ‘void compute_genotypes(const ReadSet&, std::vector*, std::vector*, std::vector*)’ at src/genotyper.cpp:48:23: 2023-09-12T17:00:04,444 /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 2023-09-12T17:00:04,445 1287 | _M_realloc_insert(end(), __x); 2023-09-12T17:00:04,445 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T17:00:04,617 /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]’: 2023-09-12T17:00:04,618 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T17:00:04,618 439 | vector<_Tp, _Alloc>:: 2023-09-12T17:00:04,619 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T17:00:04,757 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Genotype}; _Tp = Genotype; _Alloc = std::allocator]’, 2023-09-12T17:00:04,758 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, 2023-09-12T17:00:04,759 inlined from ‘void compute_polyploid_genotypes(const ReadSet&, size_t, std::vector*, std::vector*)’ at src/genotyper.cpp:88:24: 2023-09-12T17:00:04,759 /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 2023-09-12T17:00:04,760 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T17:00:04,760 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T17:00:04,761 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Genotype; _Alloc = std::allocator]’, 2023-09-12T17:00:04,761 inlined from ‘void compute_polyploid_genotypes(const ReadSet&, size_t, std::vector*, std::vector*)’ at src/genotyper.cpp:103:24: 2023-09-12T17:00:04,762 /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 2023-09-12T17:00:04,763 1287 | _M_realloc_insert(end(), __x); 2023-09-12T17:00:04,763 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-12T17:00:05,118 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -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 2023-09-12T17:00:06,363 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -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 2023-09-12T17:00:10,654 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -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 2023-09-12T17:00:12,505 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -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 2023-09-12T17:00:15,382 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -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 2023-09-12T17:00:17,974 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -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 2023-09-12T17:00:20,485 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::run_core()’: 2023-09-12T17:00:20,486 src/hapchat/hapchatcore.cpp:145:11: warning: variable ‘counter_columns’ set but not used [-Wunused-but-set-variable] 2023-09-12T17:00:20,487 145 | Counter counter_columns; 2023-09-12T17:00:20,488 | ^~~~~~~~~~~~~~~ 2023-09-12T17:00:20,502 src/hapchat/hapchatcore.cpp: In member function ‘bool HapChatCore::check_end(HapChatColumnIterator, const std::vector >&, const Pointer&, const bool&)’: 2023-09-12T17:00:20,503 src/hapchat/hapchatcore.cpp:208:74: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T17:00:20,504 208 | return (!re_run && (hap.is_ended() && (input[pointer][0].get_read_id() == -1))); 2023-09-12T17:00:20,504 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2023-09-12T17:00:20,655 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::dp(const constants_t&, std::vector&, std::vector&, Counter&, Cost&, Counter&, Counter&, Counter&, Counter&, HapChatColumnIterator)’: 2023-09-12T17:00:20,656 src/hapchat/hapchatcore.cpp:939:15: warning: unused variable ‘old_k’ [-Wunused-variable] 2023-09-12T17:00:20,656 939 | int old_k = k_j[input_pointer]; 2023-09-12T17:00:20,657 | ^~~~~ 2023-09-12T17:00:20,676 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&)’: 2023-09-12T17:00:20,676 src/hapchat/hapchatcore.cpp:1114:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T17:00:20,677 1114 | (colJ[j].get_read_id() != -1) && 2023-09-12T17:00:20,678 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2023-09-12T17:00:20,678 src/hapchat/hapchatcore.cpp:1115:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T17:00:20,679 1115 | (colQ[i].get_read_id() != -1)) { 2023-09-12T17:00:20,680 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2023-09-12T17:00:20,681 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::represent_column(const Column&, BitColumn&, Counter&, BitColumn&, Counter&)’: 2023-09-12T17:00:20,681 src/hapchat/hapchatcore.cpp:1159:58: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T17:00:20,682 1159 | while(cov < column.size() && column[cov].get_read_id() != -1) { 2023-09-12T17:00:20,683 | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2023-09-12T17:00:20,686 src/hapchat/hapchatcore.cpp: In member function ‘int HapChatCore::compute_active_common(const Column&, const Column&, unsigned int&)’: 2023-09-12T17:00:20,687 src/hapchat/hapchatcore.cpp:1294:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T17:00:20,688 1294 | (colJ[j].get_read_id() != -1) && 2023-09-12T17:00:20,688 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2023-09-12T17:00:20,689 src/hapchat/hapchatcore.cpp:1295:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T17:00:20,690 1295 | (colQ[i].get_read_id() != -1)) { 2023-09-12T17:00:20,690 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2023-09-12T17:00:20,692 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&)’: 2023-09-12T17:00:20,692 src/hapchat/hapchatcore.cpp:1350:67: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T17:00:20,693 1350 | if(i < input[pointer].size() && input[pointer][i].get_read_id() != -1) 2023-09-12T17:00:20,694 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2023-09-12T17:00:21,789 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -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 2023-09-12T17:00:23,574 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -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 2023-09-12T17:00:25,144 In file included from /usr/include/c++/12/cassert:44, 2023-09-12T17:00:25,144 from src/pedigree.cpp:4: 2023-09-12T17:00:25,145 src/pedigree.cpp: In member function ‘void Pedigree::addIndividual(unsigned int, std::vector, std::vector)’: 2023-09-12T17:00:25,145 src/pedigree.cpp:32:33: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2023-09-12T17:00:25,146 32 | assert(genotypes.size() == variant_count); 2023-09-12T17:00:25,147 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2023-09-12T17:00:25,147 src/pedigree.cpp:33:44: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2023-09-12T17:00:25,148 33 | assert(genotype_likelihoods.size() == variant_count); 2023-09-12T17:00:25,148 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2023-09-12T17:00:25,166 src/pedigree.cpp: In member function ‘const Genotype* Pedigree::get_genotype_by_id(unsigned int, unsigned int) const’: 2023-09-12T17:00:25,167 src/pedigree.cpp:70:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] 2023-09-12T17:00:25,167 70 | assert(variant_index < variant_count); 2023-09-12T17:00:25,168 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2023-09-12T17:00:25,169 src/pedigree.cpp: In member function ‘const PhredGenotypeLikelihoods* Pedigree::get_genotype_likelihoods_by_id(unsigned int, unsigned int) const’: 2023-09-12T17:00:25,170 src/pedigree.cpp:81:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] 2023-09-12T17:00:25,171 81 | assert(variant_index < variant_count); 2023-09-12T17:00:25,171 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2023-09-12T17:00:25,180 src/pedigree.cpp: In member function ‘std::string Pedigree::toString() const’: 2023-09-12T17:00:25,181 src/pedigree.cpp:112:35: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘const int’ [-Wsign-compare] 2023-09-12T17:00:25,181 112 | for (size_t j=0; j&, size_t, const std::vector&, const Pedigree*, const PedigreePartitions&, bool)’: 2023-09-12T17:00:29,656 src/pedigreecolumncostcomputer.cpp:25:36: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-12T17:00:29,657 25 | for (unsigned int i = 0; i < (1< PedigreeColumnCostComputer::get_alleles()’: 2023-09-12T17:00:29,697 src/pedigreecolumncostcomputer.cpp:119:22: warning: unused variable ‘second_best_cost’ [-Wunused-variable] 2023-09-12T17:00:29,697 119 | unsigned int second_best_cost = numeric_limits < unsigned int >::max(); 2023-09-12T17:00:29,698 | ^~~~~~~~~~~~~~~~ 2023-09-12T17:00:30,943 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -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 2023-09-12T17:00:37,920 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -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 2023-09-12T17:00:40,069 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -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 2023-09-12T17:00:41,882 In file included from /usr/include/c++/12/vector:70, 2023-09-12T17:00:41,883 from src/genotype.h:4, 2023-09-12T17:00:41,884 from src/phredgenotypelikelihoods.h:5, 2023-09-12T17:00:41,884 from src/phredgenotypelikelihoods.cpp:4: 2023-09-12T17:00:41,885 /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]’: 2023-09-12T17:00:41,886 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-12T17:00:41,886 439 | vector<_Tp, _Alloc>:: 2023-09-12T17:00:41,887 | ^~~~~~~~~~~~~~~~~~~ 2023-09-12T17:00:41,918 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Genotype}; _Tp = Genotype; _Alloc = std::allocator]’, 2023-09-12T17:00:41,919 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, 2023-09-12T17:00:41,920 inlined from ‘void PhredGenotypeLikelihoods::get_genotypes(std::vector&) const’ at src/phredgenotypelikelihoods.cpp:53:22: 2023-09-12T17:00:41,920 /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 2023-09-12T17:00:41,921 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-12T17:00:41,922 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T17:00:42,042 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.11 -c src/polyphase/clustereditingsolution.cpp -o build/temp.linux-armv7l-cpython-311/src/polyphase/clustereditingsolution.o -std=c++11 -Werror=return-type -Werror=narrowing 2023-09-12T17:00:43,723 In file included from src/polyphase/clustereditingsolution.h:4, 2023-09-12T17:00:43,724 from src/polyphase/clustereditingsolution.cpp:1: 2023-09-12T17:00:43,725 src/polyphase/staticsparsegraph.h: In member function ‘std::string StaticSparseGraph::int2bin(uint64_t)’: 2023-09-12T17:00:43,725 src/polyphase/staticsparsegraph.h:225:30: warning: left shift count >= width of type [-Wshift-count-overflow] 2023-09-12T17:00:43,726 225 | uint64_t mask = (1UL << 63); // fill in values right-to-left 2023-09-12T17:00:43,726 | ~~~~^~~~~ 2023-09-12T17:00:44,212 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.11 -c src/polyphase/clustereditingsolver.cpp -o build/temp.linux-armv7l-cpython-311/src/polyphase/clustereditingsolver.o -std=c++11 -Werror=return-type -Werror=narrowing 2023-09-12T17:00:45,925 In file included from src/polyphase/clustereditingsolution.h:4, 2023-09-12T17:00:45,926 from src/polyphase/clustereditingsolver.h:10, 2023-09-12T17:00:45,926 from src/polyphase/clustereditingsolver.cpp:1: 2023-09-12T17:00:45,927 src/polyphase/staticsparsegraph.h: In member function ‘std::string StaticSparseGraph::int2bin(uint64_t)’: 2023-09-12T17:00:45,927 src/polyphase/staticsparsegraph.h:225:30: warning: left shift count >= width of type [-Wshift-count-overflow] 2023-09-12T17:00:45,928 225 | uint64_t mask = (1UL << 63); // fill in values right-to-left 2023-09-12T17:00:45,928 | ~~~~^~~~~ 2023-09-12T17:00:46,689 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.11 -c src/polyphase/edgeheap.cpp -o build/temp.linux-armv7l-cpython-311/src/polyphase/edgeheap.o -std=c++11 -Werror=return-type -Werror=narrowing 2023-09-12T17:00:48,377 In file included from src/polyphase/edgeheap.h:6, 2023-09-12T17:00:48,377 from src/polyphase/edgeheap.cpp:1: 2023-09-12T17:00:48,378 src/polyphase/staticsparsegraph.h: In member function ‘std::string StaticSparseGraph::int2bin(uint64_t)’: 2023-09-12T17:00:48,379 src/polyphase/staticsparsegraph.h:225:30: warning: left shift count >= width of type [-Wshift-count-overflow] 2023-09-12T17:00:48,379 225 | uint64_t mask = (1UL << 63); // fill in values right-to-left 2023-09-12T17:00:48,380 | ~~~~^~~~~ 2023-09-12T17:00:51,023 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -I/usr/include/python3.11 -c src/polyphase/haplothreader.cpp -o build/temp.linux-armv7l-cpython-311/src/polyphase/haplothreader.o -std=c++11 -Werror=return-type -Werror=narrowing 2023-09-12T17:00:52,564 In file included from src/polyphase/haplothreader.cpp:1: 2023-09-12T17:00:52,565 src/polyphase/haplothreader.h:30:50: warning: left shift count >= width of type [-Wshift-count-overflow] 2023-09-12T17:00:52,565 30 | 31UL << 20, 31UL << 25, 31UL << 30, 31UL << 35, 2023-09-12T17:00:52,566 | ~~~~~^~~~~ 2023-09-12T17:00:52,567 src/polyphase/haplothreader.h:31:14: warning: left shift count >= width of type [-Wshift-count-overflow] 2023-09-12T17:00:52,567 31 | 31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55}; 2023-09-12T17:00:52,568 | ~~~~~^~~~~ 2023-09-12T17:00:52,569 src/polyphase/haplothreader.h:31:26: warning: left shift count >= width of type [-Wshift-count-overflow] 2023-09-12T17:00:52,569 31 | 31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55}; 2023-09-12T17:00:52,570 | ~~~~~^~~~~ 2023-09-12T17:00:52,571 src/polyphase/haplothreader.h:31:38: warning: left shift count >= width of type [-Wshift-count-overflow] 2023-09-12T17:00:52,572 31 | 31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55}; 2023-09-12T17:00:52,572 | ~~~~~^~~~~ 2023-09-12T17:00:52,573 src/polyphase/haplothreader.h:31:50: warning: left shift count >= width of type [-Wshift-count-overflow] 2023-09-12T17:00:52,573 31 | 31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55}; 2023-09-12T17:00:52,574 | ~~~~~^~~~~ 2023-09-12T17:00:52,574 src/polyphase/haplothreader.h:30:50: error: right operand of shift expression ‘(31 << 35)’ is greater than or equal to the precision 32 of the left operand [-fpermissive] 2023-09-12T17:00:52,575 30 | 31UL << 20, 31UL << 25, 31UL << 30, 31UL << 35, 2023-09-12T17:00:52,575 | ~~~~~^~~~~ 2023-09-12T17:00:52,599 src/polyphase/haplothreader.h: In constructor ‘ClusterEntry::ClusterEntry()’: 2023-09-12T17:00:52,601 src/polyphase/haplothreader.h:194:16: error: ‘numeric_limits’ is not a member of ‘std’ 2023-09-12T17:00:52,603 194 | score(std::numeric_limits::infinity()), 2023-09-12T17:00:52,605 | ^~~~~~~~~~~~~~ 2023-09-12T17:00:52,607 src/polyphase/haplothreader.h:194:36: error: expected primary-expression before ‘>’ token 2023-09-12T17:00:52,609 194 | score(std::numeric_limits::infinity()), 2023-09-12T17:00:52,611 | ^ 2023-09-12T17:00:52,614 src/polyphase/haplothreader.h:194:39: error: ‘::infinity’ has not been declared; did you mean ‘finite’? 2023-09-12T17:00:52,616 194 | score(std::numeric_limits::infinity()), 2023-09-12T17:00:52,616 | ^~~~~~~~ 2023-09-12T17:00:52,617 | finite 2023-09-12T17:00:53,109 src/polyphase/haplothreader.cpp: In member function ‘std::vector > HaploThreader::computePaths(Position, Position, const std::vector >&, const std::vector >&, const std::vector >&, const std::vector >&, Position) const’: 2023-09-12T17:00:53,110 src/polyphase/haplothreader.cpp:253:18: warning: unused variable ‘allRows’ [-Wunused-variable] 2023-09-12T17:00:53,111 253 | uint32_t allRows = column.size(); 2023-09-12T17:00:53,112 | ^~~~~~~ 2023-09-12T17:00:54,037 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2023-09-12T17:00:54,152 ERROR: [present-rich] python setup.py bdist_wheel exited with 1 2023-09-12T17:00:54,168 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2023-09-12T17:00:54,168 exec(compile('"'"''"'"''"'"' 2023-09-12T17:00:54,168 # This is -- a caller that pip uses to run setup.py 2023-09-12T17:00:54,168 # 2023-09-12T17:00:54,168 # - It imports setuptools before invoking setup.py, to enable projects that directly 2023-09-12T17:00:54,168 # import from `distutils.core` to work with newer packaging standards. 2023-09-12T17:00:54,168 # - It provides a clear error message when setuptools is not installed. 2023-09-12T17:00:54,168 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2023-09-12T17:00:54,168 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2023-09-12T17:00:54,168 # manifest_maker: standard file '"'"'-c'"'"' not found". 2023-09-12T17:00:54,168 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2023-09-12T17:00:54,168 import os, sys, tokenize 2023-09-12T17:00:54,168 2023-09-12T17:00:54,168 try: 2023-09-12T17:00:54,168 import setuptools 2023-09-12T17:00:54,168 except ImportError as error: 2023-09-12T17:00:54,168 print( 2023-09-12T17:00:54,168 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2023-09-12T17:00:54,168 "the build environment.", 2023-09-12T17:00:54,168 file=sys.stderr, 2023-09-12T17:00:54,168 ) 2023-09-12T17:00:54,168 sys.exit(1) 2023-09-12T17:00:54,168 2023-09-12T17:00:54,168 __file__ = %r 2023-09-12T17:00:54,168 sys.argv[0] = __file__ 2023-09-12T17:00:54,168 2023-09-12T17:00:54,168 if os.path.exists(__file__): 2023-09-12T17:00:54,168 filename = __file__ 2023-09-12T17:00:54,168 with tokenize.open(__file__) as f: 2023-09-12T17:00:54,168 setup_py_code = f.read() 2023-09-12T17:00:54,168 else: 2023-09-12T17:00:54,168 filename = "" 2023-09-12T17:00:54,168 setup_py_code = "from setuptools import setup; setup()" 2023-09-12T17:00:54,168 2023-09-12T17:00:54,168 exec(compile(setup_py_code, filename, "exec")) 2023-09-12T17:00:54,168 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-5xn3kqpp/whatshap_c3a872ebe6cc43faa57522cdc0478878/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-m3fbg6he[/] 2023-09-12T17:00:54,168 [bold magenta]cwd[/]: /tmp/pip-wheel-5xn3kqpp/whatshap_c3a872ebe6cc43faa57522cdc0478878/ 2023-09-12T17:00:54,169 Building wheel for whatshap (setup.py): finished with status 'error' 2023-09-12T17:00:54,170 ERROR: Failed building wheel for whatshap 2023-09-12T17:00:54,171 Running setup.py clean for whatshap 2023-09-12T17:00:54,173 Running command python setup.py clean 2023-09-12T17:00:54,916 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2023-09-12T17:00:54,916 !! 2023-09-12T17:00:54,917 ******************************************************************************** 2023-09-12T17:00:54,918 Requirements should be satisfied by a PEP 517 installer. 2023-09-12T17:00:54,918 If you are using pip, you can try `pip install --use-pep517`. 2023-09-12T17:00:54,919 ******************************************************************************** 2023-09-12T17:00:54,920 !! 2023-09-12T17:00:54,921 dist.fetch_build_eggs(dist.setup_requires) 2023-09-12T17:00:55,541 running clean 2023-09-12T17:00:55,595 removing 'build/temp.linux-armv7l-cpython-311' (and everything under it) 2023-09-12T17:00:55,608 removing 'build/lib.linux-armv7l-cpython-311' (and everything under it) 2023-09-12T17:00:55,616 'build/bdist.linux-armv7l' does not exist -- can't clean it 2023-09-12T17:00:55,617 'build/scripts-3.11' does not exist -- can't clean it 2023-09-12T17:00:55,618 removing 'build' 2023-09-12T17:00:55,731 Failed to build whatshap 2023-09-12T17:00:55,732 ERROR: Failed to build one or more wheels 2023-09-12T17:00:55,734 Exception information: 2023-09-12T17:00:55,734 Traceback (most recent call last): 2023-09-12T17:00:55,734 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2023-09-12T17:00:55,734 status = run_func(*args) 2023-09-12T17:00:55,734 ^^^^^^^^^^^^^^^ 2023-09-12T17:00:55,734 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper 2023-09-12T17:00:55,734 return func(self, options, args) 2023-09-12T17:00:55,734 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-12T17:00:55,734 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run 2023-09-12T17:00:55,734 raise CommandError("Failed to build one or more wheels") 2023-09-12T17:00:55,734 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2023-09-12T17:00:55,738 Removed build tracker: '/tmp/pip-build-tracker-70xvopas'