2023-09-25T02:25:56,465 Created temporary directory: /tmp/pip-build-tracker-j7e15u6q
2023-09-25T02:25:56,466 Initialized build tracking at /tmp/pip-build-tracker-j7e15u6q
2023-09-25T02:25:56,466 Created build tracker: /tmp/pip-build-tracker-j7e15u6q
2023-09-25T02:25:56,467 Entered build tracker: /tmp/pip-build-tracker-j7e15u6q
2023-09-25T02:25:56,467 Created temporary directory: /tmp/pip-wheel-qqx546gj
2023-09-25T02:25:56,470 Created temporary directory: /tmp/pip-ephem-wheel-cache-4nnfu5c2
2023-09-25T02:25:56,492 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-09-25T02:25:56,496 2 location(s) to search for versions of whatshap:
2023-09-25T02:25:56,496 * https://pypi.org/simple/whatshap/
2023-09-25T02:25:56,496 * https://www.piwheels.org/simple/whatshap/
2023-09-25T02:25:56,497 Fetching project page and analyzing links: https://pypi.org/simple/whatshap/
2023-09-25T02:25:56,497 Getting page https://pypi.org/simple/whatshap/
2023-09-25T02:25:56,499 Found index url https://pypi.org/simple/
2023-09-25T02:25:56,769 Fetched page https://pypi.org/simple/whatshap/ as application/vnd.pypi.simple.v1+json
2023-09-25T02:25:56,781   Found link https://files.pythonhosted.org/packages/35/95/43ff2304cd59ade39e64aadaeaec48e8c12bbe6262bcbbbd7b7d89487757/whatshap-0.9.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.9
2023-09-25T02:25:56,782   Found link https://files.pythonhosted.org/packages/f0/4b/f2b882803ac66b969414d8427ee8b4ca2c29b17cfead0fd85f349dc66983/whatshap-0.10.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.10
2023-09-25T02:25:56,783   Found link https://files.pythonhosted.org/packages/fc/dc/30559c28fb54985773fb242f5768fc206e054e44e45962a32cf4fd29a794/whatshap-0.11.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.11
2023-09-25T02:25:56,783   Found link https://files.pythonhosted.org/packages/01/84/31a5ea338647d0256a4a5c57e98d7a563f387e6a47f1e26299b89e3f2da1/whatshap-0.12.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.12
2023-09-25T02:25:56,784   Found link https://files.pythonhosted.org/packages/e2/f3/c71cb4bc3ba3b1234ee0c5fe729c60440164e07437695ca09c61750e0e11/whatshap-0.13.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.13
2023-09-25T02:25:56,785   Found link https://files.pythonhosted.org/packages/cd/d3/a63285d15b0da196a259197e46d9f61a852d1b3c94800f4a82ca4e31e307/whatshap-0.14.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.14
2023-09-25T02:25:56,786   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
2023-09-25T02:25:56,786   Found link https://files.pythonhosted.org/packages/ca/13/6454e5e8f6c858a203378b3e22f13518f092ba85aa6d7a9a9796d22c28e0/whatshap-0.15.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.15
2023-09-25T02:25:56,787   Found link https://files.pythonhosted.org/packages/3d/cb/55730a8713ecba10f6d987dbd935ba31ded92f9af1ddd250896f3c1cfc3b/whatshap-0.16.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.16
2023-09-25T02:25:56,788   Found link https://files.pythonhosted.org/packages/79/11/79da12b8c23f43b00fab8a6206f75cc1cc8c1902ff30eca53c17abe2f633/whatshap-0.17.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.17
2023-09-25T02:25:56,788   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)
2023-09-25T02:25:56,789   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)
2023-09-25T02:25:56,790   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)
2023-09-25T02:25:56,790   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)
2023-09-25T02:25:56,791   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
2023-09-25T02:25:56,792   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)
2023-09-25T02:25:56,792   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)
2023-09-25T02:25:56,793   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)
2023-09-25T02:25:56,794   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
2023-09-25T02:25:56,794   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)
2023-09-25T02:25:56,795   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)
2023-09-25T02:25:56,796   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)
2023-09-25T02:25:56,796   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)
2023-09-25T02:25:56,797   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
2023-09-25T02:25:56,798   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)
2023-09-25T02:25:56,798   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)
2023-09-25T02:25:56,799   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)
2023-09-25T02:25:56,800   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)
2023-09-25T02:25:56,801   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
2023-09-25T02:25:56,801   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)
2023-09-25T02:25:56,802   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)
2023-09-25T02:25:56,802   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)
2023-09-25T02:25:56,803   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)
2023-09-25T02:25:56,804   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
2023-09-25T02:25:56,804   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)
2023-09-25T02:25:56,805   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)
2023-09-25T02:25:56,806   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)
2023-09-25T02:25:56,806   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)
2023-09-25T02:25:56,807   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
2023-09-25T02:25:56,808   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)
2023-09-25T02:25:56,808   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)
2023-09-25T02:25:56,809   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)
2023-09-25T02:25:56,810   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)
2023-09-25T02:25:56,811   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
2023-09-25T02:25:56,811   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)
2023-09-25T02:25:56,812   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)
2023-09-25T02:25:56,812   Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/be/b4/0b3c2b6952cf006809cc1133e3c4c4b907458949bd5fa263114d26ea1670/whatshap-1.5-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7)
2023-09-25T02:25:56,812   Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/63/d3/37e4980f972894b48ee1ec36c98e6c3a530b37eed7721bb9010626e920b6/whatshap-1.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7)
2023-09-25T02:25:56,813   Found link https://files.pythonhosted.org/packages/2a/0a/71c5db75b44c886e492294328b41f970bfcfdef1c409e8ed3981a0ff519e/whatshap-1.5.tar.gz (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7), version: 1.5
2023-09-25T02:25:56,814   Skipping link: No binaries permitted for whatshap: 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)
2023-09-25T02:25:56,815   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)
2023-09-25T02:25:56,815   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)
2023-09-25T02:25:56,816   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)
2023-09-25T02:25:56,817   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
2023-09-25T02:25:56,817   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)
2023-09-25T02:25:56,818   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)
2023-09-25T02:25:56,819   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)
2023-09-25T02:25:56,819   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)
2023-09-25T02:25:56,820   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
2023-09-25T02:25:56,820   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)
2023-09-25T02:25:56,821   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)
2023-09-25T02:25:56,822   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)
2023-09-25T02:25:56,822   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)
2023-09-25T02:25:56,823   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)
2023-09-25T02:25:56,824   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
2023-09-25T02:25:56,825 Fetching project page and analyzing links: https://www.piwheels.org/simple/whatshap/
2023-09-25T02:25:56,825 Getting page https://www.piwheels.org/simple/whatshap/
2023-09-25T02:25:56,827 Found index url https://www.piwheels.org/simple/
2023-09-25T02:25:56,994 Fetched page https://www.piwheels.org/simple/whatshap/ as text/html
2023-09-25T02:25:57,007   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)
2023-09-25T02:25:57,007   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)
2023-09-25T02:25:57,008   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)
2023-09-25T02:25:57,009   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)
2023-09-25T02:25:57,012   Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.18-cp35-cp35m-linux_armv6l.whl#sha256=a01e2ba831e1062cac18678005ed864422821a147a90381d1d561db6daaa240b (from https://www.piwheels.org/simple/whatshap/) (requires-python:>=3.4)
2023-09-25T02:25:57,012   Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.18-cp35-cp35m-linux_armv7l.whl#sha256=a01e2ba831e1062cac18678005ed864422821a147a90381d1d561db6daaa240b (from https://www.piwheels.org/simple/whatshap/) (requires-python:>=3.4)
2023-09-25T02:25:57,013   Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.17-cp37-cp37m-linux_armv6l.whl#sha256=a52131a2cecf121ac6b1d8a2f3d6b6f81722f159121dddb88c43589f05db1c48 (from https://www.piwheels.org/simple/whatshap/)
2023-09-25T02:25:57,013   Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.17-cp37-cp37m-linux_armv7l.whl#sha256=a52131a2cecf121ac6b1d8a2f3d6b6f81722f159121dddb88c43589f05db1c48 (from https://www.piwheels.org/simple/whatshap/)
2023-09-25T02:25:57,014   Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.17-cp35-cp35m-linux_armv6l.whl#sha256=bcc411757fef61409f32f77b8b87266850cb245c80f7e55030a701e7e8f9aaf2 (from https://www.piwheels.org/simple/whatshap/)
2023-09-25T02:25:57,015   Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.17-cp35-cp35m-linux_armv7l.whl#sha256=bcc411757fef61409f32f77b8b87266850cb245c80f7e55030a701e7e8f9aaf2 (from https://www.piwheels.org/simple/whatshap/)
2023-09-25T02:25:57,015   Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.17-cp34-cp34m-linux_armv7l.whl#sha256=57ed4c07b260ca5103118fe34d7875af69bcda84b3267f3c8a96147f5475b355 (from https://www.piwheels.org/simple/whatshap/)
2023-09-25T02:25:57,016   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/)
2023-09-25T02:25:57,016   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/)
2023-09-25T02:25:57,017   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/)
2023-09-25T02:25:57,017   Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.16-cp35-cp35m-linux_armv6l.whl#sha256=e89c850742d969409e79942e188b0ccef03000e5991929a628b61e75ccf48baa (from https://www.piwheels.org/simple/whatshap/)
2023-09-25T02:25:57,018   Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.16-cp35-cp35m-linux_armv7l.whl#sha256=e89c850742d969409e79942e188b0ccef03000e5991929a628b61e75ccf48baa (from https://www.piwheels.org/simple/whatshap/)
2023-09-25T02:25:57,019   Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.15-cp37-cp37m-linux_armv7l.whl#sha256=fe3e47cf1e67574d1d04b795d1d03a06c7c8248004a6f79aed017577f212dfac (from https://www.piwheels.org/simple/whatshap/)
2023-09-25T02:25:57,020   Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.15-cp37-cp37m-linux_armv6l.whl#sha256=fe3e47cf1e67574d1d04b795d1d03a06c7c8248004a6f79aed017577f212dfac (from https://www.piwheels.org/simple/whatshap/)
2023-09-25T02:25:57,020   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/)
2023-09-25T02:25:57,020   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/)
2023-09-25T02:25:57,021   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/)
2023-09-25T02:25:57,021   Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.15-cp34-cp34m-linux_armv6l.whl#sha256=8a603d7a9a636e78f0f8297e9ad41b9b829dc8bb2bed01428406d595852b7bb8 (from https://www.piwheels.org/simple/whatshap/)
2023-09-25T02:25:57,022   Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.14.1-cp34-cp34m-linux_armv6l.whl#sha256=22ddc6e868a47bcdfd91808303be8ad0d952e65ae74767ea3d49bdd16cdfb4f2 (from https://www.piwheels.org/simple/whatshap/)
2023-09-25T02:25:57,022   Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.14.1-cp34-cp34m-linux_armv7l.whl#sha256=22ddc6e868a47bcdfd91808303be8ad0d952e65ae74767ea3d49bdd16cdfb4f2 (from https://www.piwheels.org/simple/whatshap/)
2023-09-25T02:25:57,023   Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.14.1-cp35-cp35m-linux_armv6l.whl#sha256=d814d13967bc9b15f994573546cdeed83bac50694e44fb4105c3ae83bbfd97b7 (from https://www.piwheels.org/simple/whatshap/)
2023-09-25T02:25:57,023   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/)
2023-09-25T02:25:57,024   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/)
2023-09-25T02:25:57,024   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/)
2023-09-25T02:25:57,025   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/)
2023-09-25T02:25:57,025   Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.14-cp34-cp34m-linux_armv7l.whl#sha256=3ddde88fb4fed1664ec3d46039aca72142fa5dcde177a40f49c2cec09b407f9f (from https://www.piwheels.org/simple/whatshap/)
2023-09-25T02:25:57,026   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/)
2023-09-25T02:25:57,027   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/)
2023-09-25T02:25:57,027   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/)
2023-09-25T02:25:57,028   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/)
2023-09-25T02:25:57,028   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/)
2023-09-25T02:25:57,029   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/)
2023-09-25T02:25:57,029   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/)
2023-09-25T02:25:57,029   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/)
2023-09-25T02:25:57,030   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/)
2023-09-25T02:25:57,031   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/)
2023-09-25T02:25:57,031   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/)
2023-09-25T02:25:57,032   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/)
2023-09-25T02:25:57,032   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/)
2023-09-25T02:25:57,033   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/)
2023-09-25T02:25:57,033   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/)
2023-09-25T02:25:57,034   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/)
2023-09-25T02:25:57,035   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/)
2023-09-25T02:25:57,035   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/)
2023-09-25T02:25:57,036 Skipping link: not a file: https://www.piwheels.org/simple/whatshap/
2023-09-25T02:25:57,036 Skipping link: not a file: https://pypi.org/simple/whatshap/
2023-09-25T02:25:57,057 Given no hashes to check 1 links for project 'whatshap': discarding no candidates
2023-09-25T02:25:57,075 Collecting whatshap==2.0
2023-09-25T02:25:57,077   Created temporary directory: /tmp/pip-unpack-nyom73kz
2023-09-25T02:25:57,837   Downloading whatshap-2.0.tar.gz (5.4 MB)
2023-09-25T02:26:00,128   Added whatshap==2.0 from https://files.pythonhosted.org/packages/c3/10/b53674fa02c1d5b23887f5a6b0fbf6936ce35dcd08f65e994c18601b20cb/whatshap-2.0.tar.gz to build tracker '/tmp/pip-build-tracker-j7e15u6q'
2023-09-25T02:26:00,135   Created temporary directory: /tmp/pip-build-env-3llpxnu5
2023-09-25T02:26:00,139   Installing build dependencies: started
2023-09-25T02:26:00,140   Running command pip subprocess to install build dependencies
2023-09-25T02:26:01,273   Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11)
2023-09-25T02:26:01,761   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-09-25T02:26:03,279   Collecting setuptools>=63
2023-09-25T02:26:03,280     Obtaining dependency information for setuptools>=63 from https://files.pythonhosted.org/packages/bb/26/7945080113158354380a12ce26873dd6c1ebd88d47f5bc24e2c5bb38c16a/setuptools-68.2.2-py3-none-any.whl.metadata
2023-09-25T02:26:03,286     Using cached setuptools-68.2.2-py3-none-any.whl.metadata (6.3 kB)
2023-09-25T02:26:03,580   Collecting setuptools_scm[toml]
2023-09-25T02:26:03,581     Obtaining dependency information for setuptools_scm[toml] from https://files.pythonhosted.org/packages/ca/04/4ea91c627355ae6d976bf7f1fc2815372a96b1b87bf290c8d726d10a08a1/setuptools_scm-8.0.3-py3-none-any.whl.metadata
2023-09-25T02:26:03,586     Using cached setuptools_scm-8.0.3-py3-none-any.whl.metadata (6.1 kB)
2023-09-25T02:26:04,960   Collecting cython~=0.29.20
2023-09-25T02:26:04,961     Obtaining dependency information for cython~=0.29.20 from https://files.pythonhosted.org/packages/3f/d6/9eed523aeaca42acbaa3e6d3850edae780dc7f8da9df1bf6a2ceb851839c/Cython-0.29.36-py2.py3-none-any.whl.metadata
2023-09-25T02:26:04,967     Using cached Cython-0.29.36-py2.py3-none-any.whl.metadata (3.1 kB)
2023-09-25T02:26:05,530   Collecting packaging>=20 (from setuptools_scm[toml])
2023-09-25T02:26:05,545     Using cached https://www.piwheels.org/simple/packaging/packaging-23.1-py3-none-any.whl (48 kB)
2023-09-25T02:26:05,680   Using cached setuptools-68.2.2-py3-none-any.whl (807 kB)
2023-09-25T02:26:05,728   Using cached Cython-0.29.36-py2.py3-none-any.whl (988 kB)
2023-09-25T02:26:05,751   Using cached setuptools_scm-8.0.3-py3-none-any.whl (41 kB)
2023-09-25T02:26:08,210   Installing collected packages: setuptools, packaging, cython, setuptools_scm
2023-09-25T02:26:15,861     Creating /tmp/pip-build-env-3llpxnu5/overlay/local/bin
2023-09-25T02:26:15,863     changing mode of /tmp/pip-build-env-3llpxnu5/overlay/local/bin/cygdb to 755
2023-09-25T02:26:15,866     changing mode of /tmp/pip-build-env-3llpxnu5/overlay/local/bin/cython to 755
2023-09-25T02:26:15,868     changing mode of /tmp/pip-build-env-3llpxnu5/overlay/local/bin/cythonize to 755
2023-09-25T02:26:16,079   Successfully installed cython-0.29.36 packaging-23.1 setuptools-68.2.2 setuptools_scm-8.0.3
2023-09-25T02:26:16,663   Installing build dependencies: finished with status 'done'
2023-09-25T02:26:16,666   Getting requirements to build wheel: started
2023-09-25T02:26:16,667   Running command Getting requirements to build wheel
2023-09-25T02:26:26,768   warning: whatshap/priorityqueue.pyx:201:7: Unreachable code
2023-09-25T02:26:28,491   Compiling whatshap/core.pyx because it depends on /tmp/pip-build-env-3llpxnu5/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd.
2023-09-25T02:26:28,491   Compiling whatshap/polyphase/solver.pyx because it depends on /tmp/pip-build-env-3llpxnu5/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd.
2023-09-25T02:26:28,492   Compiling whatshap/readselect.pyx because it depends on /tmp/pip-build-env-3llpxnu5/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd.
2023-09-25T02:26:28,492   Compiling whatshap/priorityqueue.pyx because it depends on /tmp/pip-build-env-3llpxnu5/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd.
2023-09-25T02:26:28,492   Compiling whatshap/align.pyx because it depends on /tmp/pip-build-env-3llpxnu5/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libc/__init__.pxd.
2023-09-25T02:26:28,493   [1/5] Cythonizing whatshap/align.pyx
2023-09-25T02:26:28,493   [2/5] Cythonizing whatshap/core.pyx
2023-09-25T02:26:28,494   [3/5] Cythonizing whatshap/polyphase/solver.pyx
2023-09-25T02:26:28,494   [4/5] Cythonizing whatshap/priorityqueue.pyx
2023-09-25T02:26:28,495   [5/5] Cythonizing whatshap/readselect.pyx
2023-09-25T02:26:28,854   running egg_info
2023-09-25T02:26:28,860   writing whatshap.egg-info/PKG-INFO
2023-09-25T02:26:28,867   writing dependency_links to whatshap.egg-info/dependency_links.txt
2023-09-25T02:26:28,869   writing entry points to whatshap.egg-info/entry_points.txt
2023-09-25T02:26:28,873   writing requirements to whatshap.egg-info/requires.txt
2023-09-25T02:26:28,874   writing top-level names to whatshap.egg-info/top_level.txt
2023-09-25T02:26:28,923   ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any
2023-09-25T02:26:28,927   reading manifest file 'whatshap.egg-info/SOURCES.txt'
2023-09-25T02:26:28,938   reading manifest template 'MANIFEST.in'
2023-09-25T02:26:28,946   adding license file 'LICENSE'
2023-09-25T02:26:28,963   writing manifest file 'whatshap.egg-info/SOURCES.txt'
2023-09-25T02:26:29,872   Getting requirements to build wheel: finished with status 'done'
2023-09-25T02:26:29,884   Installing backend dependencies: started
2023-09-25T02:26:29,885   Running command pip subprocess to install backend dependencies
2023-09-25T02:26:31,027   Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11)
2023-09-25T02:26:31,514   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-09-25T02:26:32,019   Collecting wheel
2023-09-25T02:26:32,041     Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.2-py3-none-any.whl (64 kB)
2023-09-25T02:26:34,261   Installing collected packages: wheel
2023-09-25T02:26:34,480     Creating /tmp/pip-build-env-3llpxnu5/normal/local/bin
2023-09-25T02:26:34,483     changing mode of /tmp/pip-build-env-3llpxnu5/normal/local/bin/wheel to 755
2023-09-25T02:26:34,494   Successfully installed wheel-0.41.2
2023-09-25T02:26:34,960   Installing backend dependencies: finished with status 'done'
2023-09-25T02:26:34,962   Created temporary directory: /tmp/pip-modern-metadata-ezym0fuy
2023-09-25T02:26:34,964   Preparing metadata (pyproject.toml): started
2023-09-25T02:26:34,965   Running command Preparing metadata (pyproject.toml)
2023-09-25T02:26:36,479   running dist_info
2023-09-25T02:26:36,485   creating /tmp/pip-modern-metadata-ezym0fuy/whatshap.egg-info
2023-09-25T02:26:36,490   writing /tmp/pip-modern-metadata-ezym0fuy/whatshap.egg-info/PKG-INFO
2023-09-25T02:26:36,496   writing dependency_links to /tmp/pip-modern-metadata-ezym0fuy/whatshap.egg-info/dependency_links.txt
2023-09-25T02:26:36,499   writing entry points to /tmp/pip-modern-metadata-ezym0fuy/whatshap.egg-info/entry_points.txt
2023-09-25T02:26:36,502   writing requirements to /tmp/pip-modern-metadata-ezym0fuy/whatshap.egg-info/requires.txt
2023-09-25T02:26:36,503   writing top-level names to /tmp/pip-modern-metadata-ezym0fuy/whatshap.egg-info/top_level.txt
2023-09-25T02:26:36,504   writing manifest file '/tmp/pip-modern-metadata-ezym0fuy/whatshap.egg-info/SOURCES.txt'
2023-09-25T02:26:36,564   ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any
2023-09-25T02:26:36,568   reading manifest file '/tmp/pip-modern-metadata-ezym0fuy/whatshap.egg-info/SOURCES.txt'
2023-09-25T02:26:36,570   reading manifest template 'MANIFEST.in'
2023-09-25T02:26:36,584   adding license file 'LICENSE'
2023-09-25T02:26:36,591   writing manifest file '/tmp/pip-modern-metadata-ezym0fuy/whatshap.egg-info/SOURCES.txt'
2023-09-25T02:26:36,593   creating '/tmp/pip-modern-metadata-ezym0fuy/whatshap-2.0.dist-info'
2023-09-25T02:26:36,796   Preparing metadata (pyproject.toml): finished with status 'done'
2023-09-25T02:26:36,801   Source in /tmp/pip-wheel-qqx546gj/whatshap_20dbad9bb2f24af1b652bd285f25b10e has version 2.0, which satisfies requirement whatshap==2.0 from https://files.pythonhosted.org/packages/c3/10/b53674fa02c1d5b23887f5a6b0fbf6936ce35dcd08f65e994c18601b20cb/whatshap-2.0.tar.gz
2023-09-25T02:26:36,802   Removed whatshap==2.0 from https://files.pythonhosted.org/packages/c3/10/b53674fa02c1d5b23887f5a6b0fbf6936ce35dcd08f65e994c18601b20cb/whatshap-2.0.tar.gz from build tracker '/tmp/pip-build-tracker-j7e15u6q'
2023-09-25T02:26:36,807 Created temporary directory: /tmp/pip-unpack-mevn9htb
2023-09-25T02:26:36,809 Created temporary directory: /tmp/pip-unpack-b7aq891s
2023-09-25T02:26:36,845 Building wheels for collected packages: whatshap
2023-09-25T02:26:36,850   Created temporary directory: /tmp/pip-wheel-4l16z8pv
2023-09-25T02:26:36,850   Destination directory: /tmp/pip-wheel-4l16z8pv
2023-09-25T02:26:36,853   Building wheel for whatshap (pyproject.toml): started
2023-09-25T02:26:36,854   Running command Building wheel for whatshap (pyproject.toml)
2023-09-25T02:26:38,278   running bdist_wheel
2023-09-25T02:26:38,297   running build
2023-09-25T02:26:38,298   running build_py
2023-09-25T02:26:38,304   creating build
2023-09-25T02:26:38,305   creating build/lib.linux-armv7l-cpython-311
2023-09-25T02:26:38,306   creating build/lib.linux-armv7l-cpython-311/misc
2023-09-25T02:26:38,307   copying misc/example.py -> build/lib.linux-armv7l-cpython-311/misc
2023-09-25T02:26:38,311   creating build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,312   copying tests/test_run_phase.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,315   copying tests/test_run_haplotag.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,317   copying tests/test_pedigree.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,319   copying tests/test_genotyping.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,321   copying tests/test_run_genotype.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,324   copying tests/test_reorder.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,326   copying tests/test_pedigreephasing.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,329   copying tests/test_readselect.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,331   copying tests/test_pedreader.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,332   copying tests/test_main.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,334   copying tests/test_run_split.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,335   copying tests/test_bam.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,337   copying tests/test_geneticmap.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,339   copying tests/test_readscoring.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,340   copying tests/test_phasing.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,342   copying tests/test_variantselection.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,344   copying tests/test_graph.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,346   copying tests/test_reads.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,347   copying tests/test_priorityqueue.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,349   copying tests/test_pedigreegenotyping.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,352   copying tests/test_align.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,354   copying tests/test_run_unphase.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,355   copying tests/test_readsetreader.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,357   copying tests/test_run_find_snv_candidates.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,359   copying tests/test_offspringscoring.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,360   copying tests/test_vcf.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,363   copying tests/test_run_stats.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,365   copying tests/test_run_compare.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,367   copying tests/test_merge_reads.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,369   copying tests/test_run_polyphase.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,371   copying tests/test_allelematrix.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,373   copying tests/test_polyphasegenetic.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,375   copying tests/test_verification.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,376   copying tests/test_utils.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,378   copying tests/test_threading.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,380   copying tests/test_clusterediting.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,382   copying tests/test_run_hapcut2vcf.py -> build/lib.linux-armv7l-cpython-311/tests
2023-09-25T02:26:38,385   creating build/lib.linux-armv7l-cpython-311/whatshap
2023-09-25T02:26:38,385   copying whatshap/pedigree.py -> build/lib.linux-armv7l-cpython-311/whatshap
2023-09-25T02:26:38,388   copying whatshap/_version.py -> build/lib.linux-armv7l-cpython-311/whatshap
2023-09-25T02:26:38,389   copying whatshap/__init__.py -> build/lib.linux-armv7l-cpython-311/whatshap
2023-09-25T02:26:38,391   copying whatshap/testhelpers.py -> build/lib.linux-armv7l-cpython-311/whatshap
2023-09-25T02:26:38,393   copying whatshap/vcf.py -> build/lib.linux-armv7l-cpython-311/whatshap
2023-09-25T02:26:38,395   copying whatshap/coverage.py -> build/lib.linux-armv7l-cpython-311/whatshap
2023-09-25T02:26:38,397   copying whatshap/__main__.py -> build/lib.linux-armv7l-cpython-311/whatshap
2023-09-25T02:26:38,399   copying whatshap/args.py -> build/lib.linux-armv7l-cpython-311/whatshap
2023-09-25T02:26:38,400   copying whatshap/variants.py -> build/lib.linux-armv7l-cpython-311/whatshap
2023-09-25T02:26:38,403   copying whatshap/bam.py -> build/lib.linux-armv7l-cpython-311/whatshap
2023-09-25T02:26:38,405   copying whatshap/verification.py -> build/lib.linux-armv7l-cpython-311/whatshap
2023-09-25T02:26:38,406   copying whatshap/timer.py -> build/lib.linux-armv7l-cpython-311/whatshap
2023-09-25T02:26:38,408   copying whatshap/graph.py -> build/lib.linux-armv7l-cpython-311/whatshap
2023-09-25T02:26:38,410   copying whatshap/utils.py -> build/lib.linux-armv7l-cpython-311/whatshap
2023-09-25T02:26:38,411   copying whatshap/merge.py -> build/lib.linux-armv7l-cpython-311/whatshap
2023-09-25T02:26:38,413   copying whatshap/variant.py -> build/lib.linux-armv7l-cpython-311/whatshap
2023-09-25T02:26:38,415   creating build/lib.linux-armv7l-cpython-311/doc
2023-09-25T02:26:38,416   copying doc/conf.py -> build/lib.linux-armv7l-cpython-311/doc
2023-09-25T02:26:38,421   creating build/lib.linux-armv7l-cpython-311/whatshap/cli
2023-09-25T02:26:38,422   copying whatshap/cli/polyphase.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli
2023-09-25T02:26:38,424   copying whatshap/cli/hapcut2vcf.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli
2023-09-25T02:26:38,426   copying whatshap/cli/__init__.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli
2023-09-25T02:26:38,428   copying whatshap/cli/split.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli
2023-09-25T02:26:38,430   copying whatshap/cli/unphase.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli
2023-09-25T02:26:38,432   copying whatshap/cli/polyphasegenetic.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli
2023-09-25T02:26:38,434   copying whatshap/cli/stats.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli
2023-09-25T02:26:38,436   copying whatshap/cli/compare.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli
2023-09-25T02:26:38,439   copying whatshap/cli/haplotag.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli
2023-09-25T02:26:38,441   copying whatshap/cli/find_snv_candidates.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli
2023-09-25T02:26:38,443   copying whatshap/cli/genotype.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli
2023-09-25T02:26:38,446   copying whatshap/cli/phase.py -> build/lib.linux-armv7l-cpython-311/whatshap/cli
2023-09-25T02:26:38,449   creating build/lib.linux-armv7l-cpython-311/whatshap/polyphase
2023-09-25T02:26:38,450   copying whatshap/polyphase/offspringscoring.py -> build/lib.linux-armv7l-cpython-311/whatshap/polyphase
2023-09-25T02:26:38,452   copying whatshap/polyphase/reorder.py -> build/lib.linux-armv7l-cpython-311/whatshap/polyphase
2023-09-25T02:26:38,455   copying whatshap/polyphase/plots.py -> build/lib.linux-armv7l-cpython-311/whatshap/polyphase
2023-09-25T02:26:38,457   copying whatshap/polyphase/threading.py -> build/lib.linux-armv7l-cpython-311/whatshap/polyphase
2023-09-25T02:26:38,460   copying whatshap/polyphase/__init__.py -> build/lib.linux-armv7l-cpython-311/whatshap/polyphase
2023-09-25T02:26:38,462   copying whatshap/polyphase/clusterarrangement.py -> build/lib.linux-armv7l-cpython-311/whatshap/polyphase
2023-09-25T02:26:38,464   copying whatshap/polyphase/variantselection.py -> build/lib.linux-armv7l-cpython-311/whatshap/polyphase
2023-09-25T02:26:38,466   copying whatshap/polyphase/algorithm.py -> build/lib.linux-armv7l-cpython-311/whatshap/polyphase
2023-09-25T02:26:38,468   running egg_info
2023-09-25T02:26:38,473   writing whatshap.egg-info/PKG-INFO
2023-09-25T02:26:38,479   writing dependency_links to whatshap.egg-info/dependency_links.txt
2023-09-25T02:26:38,481   writing entry points to whatshap.egg-info/entry_points.txt
2023-09-25T02:26:38,484   writing requirements to whatshap.egg-info/requires.txt
2023-09-25T02:26:38,485   writing top-level names to whatshap.egg-info/top_level.txt
2023-09-25T02:26:38,521   ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any
2023-09-25T02:26:38,524   reading manifest file 'whatshap.egg-info/SOURCES.txt'
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2023-09-25T02:26:38,587   writing manifest file 'whatshap.egg-info/SOURCES.txt'
2023-09-25T02:26:38,608   creating build/lib.linux-armv7l-cpython-311/logo
2023-09-25T02:26:38,609   copying logo/Makefile -> build/lib.linux-armv7l-cpython-311/logo
2023-09-25T02:26:38,611   copying logo/README.md -> build/lib.linux-armv7l-cpython-311/logo
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2023-09-25T02:26:38,633   creating build/lib.linux-armv7l-cpython-311/src
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2023-09-25T02:26:39,391   copying tests/data/haplotag.supplementary.bam -> build/lib.linux-armv7l-cpython-311/tests/data
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2023-09-25T02:26:39,478   copying tests/data/haplotag_with_csi_index.vcf.gz -> build/lib.linux-armv7l-cpython-311/tests/data
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2023-09-25T02:26:39,483   copying tests/data/hexadecaploid.chr22.vcf -> build/lib.linux-armv7l-cpython-311/tests/data
2023-09-25T02:26:39,484   copying tests/data/indels.sam -> build/lib.linux-armv7l-cpython-311/tests/data
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2023-09-25T02:26:39,568   copying tests/data/phased_single_sample2.vcf -> build/lib.linux-armv7l-cpython-311/tests/data
2023-09-25T02:26:39,570   copying tests/data/phasedinput.vcf -> build/lib.linux-armv7l-cpython-311/tests/data
2023-09-25T02:26:39,572   copying tests/data/polyphasegenetic.ped1.txt -> build/lib.linux-armv7l-cpython-311/tests/data
2023-09-25T02:26:39,574   copying tests/data/polyphasegenetic.ped2.txt -> build/lib.linux-armv7l-cpython-311/tests/data
2023-09-25T02:26:39,576   copying tests/data/polyphasegenetic.test.parents.vcf -> build/lib.linux-armv7l-cpython-311/tests/data
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2023-09-25T02:26:39,583   copying tests/data/polyploid.chr22.42M.12k.bam -> build/lib.linux-armv7l-cpython-311/tests/data
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2023-09-25T02:26:39,593   copying tests/data/polyploid.chr22.42M.12k.vcf -> build/lib.linux-armv7l-cpython-311/tests/data
2023-09-25T02:26:39,595   copying tests/data/polyploid.chr22.inconsistent.vcf -> build/lib.linux-armv7l-cpython-311/tests/data
2023-09-25T02:26:39,597   copying tests/data/polyploid.chr22.phased.vcf -> build/lib.linux-armv7l-cpython-311/tests/data
2023-09-25T02:26:39,599   copying tests/data/polyploid.chr22.unphased.vcf -> build/lib.linux-armv7l-cpython-311/tests/data
2023-09-25T02:26:39,602   copying tests/data/polyploid.cuts.bam -> build/lib.linux-armv7l-cpython-311/tests/data
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2023-09-25T02:26:39,607   copying tests/data/polyploid.human1.chr22.42M.5k.bam -> build/lib.linux-armv7l-cpython-311/tests/data
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2023-09-25T02:26:39,619   copying tests/data/polyploid.human2.chr22.42M.5k.bam -> build/lib.linux-armv7l-cpython-311/tests/data
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2023-09-25T02:26:39,631   copying tests/data/polyploid.indels.bam -> build/lib.linux-armv7l-cpython-311/tests/data
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2023-09-25T02:26:39,638   copying tests/data/polyploid.multisample.chr22.42M.5k.vcf -> build/lib.linux-armv7l-cpython-311/tests/data
2023-09-25T02:26:39,640   copying tests/data/quartet.vcf.gz -> build/lib.linux-armv7l-cpython-311/tests/data
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2023-09-25T02:26:39,650   copying tests/data/random0.fasta -> build/lib.linux-armv7l-cpython-311/tests/data
2023-09-25T02:26:39,652   copying tests/data/random0.fasta.fai -> build/lib.linux-armv7l-cpython-311/tests/data
2023-09-25T02:26:39,655   copying tests/data/reads-no-sequence.bam -> build/lib.linux-armv7l-cpython-311/tests/data
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2023-09-25T02:26:39,659   copying tests/data/reads-no-sequence.haplotags.tsv -> build/lib.linux-armv7l-cpython-311/tests/data
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2023-09-25T02:26:39,672   copying tests/data/string_typed_ps_tag.vcf -> build/lib.linux-armv7l-cpython-311/tests/data
2023-09-25T02:26:39,674   copying tests/data/test_dist_geno.sam -> build/lib.linux-armv7l-cpython-311/tests/data
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2023-09-25T02:26:39,679   copying tests/data/trio-mendelian-conflict.vcf -> build/lib.linux-armv7l-cpython-311/tests/data
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2023-09-25T02:26:39,697   copying tests/data/trio-missing-genotypes.vcf -> build/lib.linux-armv7l-cpython-311/tests/data
2023-09-25T02:26:39,699   copying tests/data/trio-symbolic-alt.vcf -> build/lib.linux-armv7l-cpython-311/tests/data
2023-09-25T02:26:39,702   copying tests/data/trio-two-chromosomes.vcf -> build/lib.linux-armv7l-cpython-311/tests/data
2023-09-25T02:26:39,704   copying tests/data/trio.map -> build/lib.linux-armv7l-cpython-311/tests/data
2023-09-25T02:26:39,706   copying tests/data/trio.pacbio.sam -> build/lib.linux-armv7l-cpython-311/tests/data
2023-09-25T02:26:39,711   copying tests/data/trio.ped -> build/lib.linux-armv7l-cpython-311/tests/data
2023-09-25T02:26:39,713   copying tests/data/trio.vcf -> build/lib.linux-armv7l-cpython-311/tests/data
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2023-09-25T02:26:39,720   copying tests/data/trio_paired_end.ped -> build/lib.linux-armv7l-cpython-311/tests/data
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2023-09-25T02:26:39,729   copying tests/data/unphased.vcf -> build/lib.linux-armv7l-cpython-311/tests/data
2023-09-25T02:26:39,731   copying tests/data/zero-genetic-distance.map -> build/lib.linux-armv7l-cpython-311/tests/data
2023-09-25T02:26:39,734   creating build/lib.linux-armv7l-cpython-311/tests/data/short-genome
2023-09-25T02:26:39,735   copying tests/data/short-genome/.gitignore -> build/lib.linux-armv7l-cpython-311/tests/data/short-genome
2023-09-25T02:26:39,737   copying tests/data/short-genome/short-hap1.fasta -> build/lib.linux-armv7l-cpython-311/tests/data/short-genome
2023-09-25T02:26:39,739   copying tests/data/short-genome/short-hap2.fasta -> build/lib.linux-armv7l-cpython-311/tests/data/short-genome
2023-09-25T02:26:39,741   copying tests/data/short-genome/short-one-read-duplicate.sam -> build/lib.linux-armv7l-cpython-311/tests/data/short-genome
2023-09-25T02:26:39,743   copying tests/data/short-genome/short-reads.fasta -> build/lib.linux-armv7l-cpython-311/tests/data/short-genome
2023-09-25T02:26:39,745   copying tests/data/short-genome/short-ref.fasta -> build/lib.linux-armv7l-cpython-311/tests/data/short-genome
2023-09-25T02:26:39,747   copying tests/data/short-genome/short.sam -> build/lib.linux-armv7l-cpython-311/tests/data/short-genome
2023-09-25T02:26:39,750   copying tests/data/short-genome/short.vcf -> build/lib.linux-armv7l-cpython-311/tests/data/short-genome
2023-09-25T02:26:39,752   copying tests/data/short-genome/wrongchromosome.vcf -> build/lib.linux-armv7l-cpython-311/tests/data/short-genome
2023-09-25T02:26:39,754   creating build/lib.linux-armv7l-cpython-311/tests/data/pacbio
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2023-09-25T02:26:39,758   copying tests/data/pacbio/Makefile -> build/lib.linux-armv7l-cpython-311/tests/data/pacbio
2023-09-25T02:26:39,760   copying tests/data/pacbio/hapcut.txt -> build/lib.linux-armv7l-cpython-311/tests/data/pacbio
2023-09-25T02:26:39,762   copying tests/data/pacbio/haplotags.txt -> build/lib.linux-armv7l-cpython-311/tests/data/pacbio
2023-09-25T02:26:39,764   copying tests/data/pacbio/pacbio.bam -> build/lib.linux-armv7l-cpython-311/tests/data/pacbio
2023-09-25T02:26:39,768   copying tests/data/pacbio/pacbio.bam.bai -> build/lib.linux-armv7l-cpython-311/tests/data/pacbio
2023-09-25T02:26:39,771   copying tests/data/pacbio/pacbio.crai -> build/lib.linux-armv7l-cpython-311/tests/data/pacbio
2023-09-25T02:26:39,773   copying tests/data/pacbio/pacbio.cram -> build/lib.linux-armv7l-cpython-311/tests/data/pacbio
2023-09-25T02:26:39,776   copying tests/data/pacbio/phased.vcf -> build/lib.linux-armv7l-cpython-311/tests/data/pacbio
2023-09-25T02:26:39,779   copying tests/data/pacbio/phased.vcf.gz -> build/lib.linux-armv7l-cpython-311/tests/data/pacbio
2023-09-25T02:26:39,781   copying tests/data/pacbio/phased.vcf.gz.tbi -> build/lib.linux-armv7l-cpython-311/tests/data/pacbio
2023-09-25T02:26:39,783   copying tests/data/pacbio/phased_hapchat.vcf -> build/lib.linux-armv7l-cpython-311/tests/data/pacbio
2023-09-25T02:26:39,786   copying tests/data/pacbio/reference.fasta -> build/lib.linux-armv7l-cpython-311/tests/data/pacbio
2023-09-25T02:26:39,789   copying tests/data/pacbio/reference.fasta.fai -> build/lib.linux-armv7l-cpython-311/tests/data/pacbio
2023-09-25T02:26:39,791   copying tests/data/pacbio/variants.vcf -> build/lib.linux-armv7l-cpython-311/tests/data/pacbio
2023-09-25T02:26:39,794   copying whatshap/polyphase/solver.cpp -> build/lib.linux-armv7l-cpython-311/whatshap/polyphase
2023-09-25T02:26:39,807   copying whatshap/polyphase/solver.pxd -> build/lib.linux-armv7l-cpython-311/whatshap/polyphase
2023-09-25T02:26:39,809   copying whatshap/polyphase/solver.pyi -> build/lib.linux-armv7l-cpython-311/whatshap/polyphase
2023-09-25T02:26:39,811   copying whatshap/polyphase/solver.pyx -> build/lib.linux-armv7l-cpython-311/whatshap/polyphase
2023-09-25T02:26:39,813   creating build/lib.linux-armv7l-cpython-311/doc/_static
2023-09-25T02:26:39,814   copying doc/_static/gtf.png -> build/lib.linux-armv7l-cpython-311/doc/_static
2023-09-25T02:26:39,817   copying doc/_static/haplotagged-HP.png -> build/lib.linux-armv7l-cpython-311/doc/_static
2023-09-25T02:26:39,819   copying doc/_static/haplotagged-PS.png -> build/lib.linux-armv7l-cpython-311/doc/_static
2023-09-25T02:26:39,831   running build_ext
2023-09-25T02:26:39,836   building 'whatshap.core' extension
2023-09-25T02:26:39,837   creating build/temp.linux-armv7l-cpython-311
2023-09-25T02:26:39,837   creating build/temp.linux-armv7l-cpython-311/src
2023-09-25T02:26:39,839   creating build/temp.linux-armv7l-cpython-311/src/hapchat
2023-09-25T02:26:39,840   creating build/temp.linux-armv7l-cpython-311/whatshap
2023-09-25T02:26:39,840   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
2023-09-25T02:26:41,718   In file included from /usr/include/c++/12/cassert:44,
2023-09-25T02:26:41,719                    from src/backwardcolumniterator.cpp:1:
2023-09-25T02:26:41,720   src/backwardcolumniterator.cpp: In member function ‘void BackwardColumnIterator::jump_to_column(int)’:
2023-09-25T02:26:41,720   src/backwardcolumniterator.cpp:121:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<unsigned int>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-25T02:26:41,721     121 |         assert(k < positions->size());
2023-09-25T02:26:41,722         |                ~~^~~~~~~~~~~~~~~~~~~
2023-09-25T02:26:41,723   src/backwardcolumniterator.cpp:140:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-25T02:26:41,723     140 |                                 assert(active_entry < read->getVariantCount());
2023-09-25T02:26:41,724         |                                        ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-25T02:26:43,507   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -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
2023-09-25T02:26:43,826   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
2023-09-25T02:26:45,086   src/columnindexingiterator.cpp: In member function ‘unsigned int ColumnIndexingIterator::index_forward_projection(unsigned int)’:
2023-09-25T02:26:45,087   src/columnindexingiterator.cpp:90:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<unsigned int>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-25T02:26:45,087      90 |         for(int j=0; j< parent->read_ids.size(); ++j) {
2023-09-25T02:26:45,088         |                      ~^~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-25T02:26:45,089   src/columnindexingiterator.cpp:92:22: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2023-09-25T02:26:45,090      92 |                 if(m != -1) {
2023-09-25T02:26:45,090         |                    ~~^~~~~
2023-09-25T02:26:45,091   src/columnindexingiterator.cpp:89:22: warning: unused variable ‘s’ [-Wunused-variable]
2023-09-25T02:26:45,092      89 |         unsigned int s = 1;
2023-09-25T02:26:45,093         |                      ^
2023-09-25T02:26:45,397   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
2023-09-25T02:26:46,651   src/columnindexingscheme.cpp: In constructor ‘ColumnIndexingScheme::ColumnIndexingScheme(const ColumnIndexingScheme*, const std::vector<unsigned int>&)’:
2023-09-25T02:26:46,651   src/columnindexingscheme.cpp:22:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<unsigned int>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-25T02:26:46,652      22 |                 while ((i<previous_column->read_ids.size()) && (j<read_ids.size())) {
2023-09-25T02:26:46,652         |                         ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-25T02:26:46,653   src/columnindexingscheme.cpp:22:66: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<unsigned int>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-25T02:26:46,653      22 |                 while ((i<previous_column->read_ids.size()) && (j<read_ids.size())) {
2023-09-25T02:26:46,654         |                                                                 ~^~~~~~~~~~~~~~~~
2023-09-25T02:26:46,658   src/columnindexingscheme.cpp: In member function ‘void ColumnIndexingScheme::set_next_column(const ColumnIndexingScheme*)’:
2023-09-25T02:26:46,659   src/columnindexingscheme.cpp:71:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<unsigned int>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-25T02:26:46,659      71 |         while ((i<next_column->read_ids.size()) && (j<read_ids.size())) {
2023-09-25T02:26:46,660         |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-25T02:26:46,661   src/columnindexingscheme.cpp:71:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<unsigned int>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-25T02:26:46,661      71 |         while ((i<next_column->read_ids.size()) && (j<read_ids.size())) {
2023-09-25T02:26:46,662         |                                                     ~^~~~~~~~~~~~~~~~
2023-09-25T02:26:47,210   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/columniterator.cpp -o build/temp.linux-armv7l-cpython-311/src/columniterator.o -std=c++11 -Werror=return-type -Werror=narrowing
2023-09-25T02:26:49,034   In file included from /usr/include/c++/12/cassert:44,
2023-09-25T02:26:49,035                    from src/columniterator.cpp:1:
2023-09-25T02:26:49,035   src/columniterator.cpp: In member function ‘std::unique_ptr<std::vector<const Entry*> > ColumnIterator::get_next()’:
2023-09-25T02:26:49,036   src/columniterator.cpp:105:54: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-25T02:26:49,037     105 |                         assert(list_it->active_entry < read->getVariantCount());
2023-09-25T02:26:49,037         |                                ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-25T02:26:49,053   src/columniterator.cpp: In member function ‘void ColumnIterator::jump_to_column(size_t)’:
2023-09-25T02:26:49,054   src/columniterator.cpp:161:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-25T02:26:49,054     161 |                                 assert(active_entry < read->getVariantCount());
2023-09-25T02:26:49,055         |                                        ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-25T02:26:50,886   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
2023-09-25T02:26:52,019   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
2023-09-25T02:26:54,615   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
2023-09-25T02:26:57,818   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
2023-09-25T02:26:59,203   src/genotypedistribution.cpp: In member function ‘double GenotypeDistribution::errorProbability() const’:
2023-09-25T02:26:59,203   src/genotypedistribution.cpp:55:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-25T02:26:59,205      55 |                 if (i == best_index) continue;
2023-09-25T02:26:59,207         |                     ~~^~~~~~~~~~~~~
2023-09-25T02:26:59,759   In file included from /usr/include/c++/12/vector:70,
2023-09-25T02:26:59,760                    from src/genotypedistribution.h:4,
2023-09-25T02:26:59,760                    from src/genotypedistribution.cpp:5:
2023-09-25T02:26:59,761   /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<double>]’:
2023-09-25T02:26:59,761   /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
2023-09-25T02:26:59,762     439 |       vector<_Tp, _Alloc>::
2023-09-25T02:26:59,763         |       ^~~~~~~~~~~~~~~~~~~
2023-09-25T02:26:59,800   In file included from /usr/include/c++/12/vector:64:
2023-09-25T02:26:59,801   In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
2023-09-25T02:26:59,802       inlined from ‘GenotypeDistribution::GenotypeDistribution(double, double, double)’ at src/genotypedistribution.cpp:10:24:
2023-09-25T02:26:59,802   /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
2023-09-25T02:26:59,803    1287 |           _M_realloc_insert(end(), __x);
2023-09-25T02:26:59,803         |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
2023-09-25T02:26:59,804   In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
2023-09-25T02:26:59,805       inlined from ‘GenotypeDistribution::GenotypeDistribution(double, double, double)’ at src/genotypedistribution.cpp:11:24:
2023-09-25T02:26:59,805   /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
2023-09-25T02:26:59,806    1287 |           _M_realloc_insert(end(), __x);
2023-09-25T02:26:59,807         |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
2023-09-25T02:26:59,808   In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
2023-09-25T02:26:59,808       inlined from ‘GenotypeDistribution::GenotypeDistribution(double, double, double)’ at src/genotypedistribution.cpp:12:24:
2023-09-25T02:26:59,809   /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
2023-09-25T02:26:59,809    1287 |           _M_realloc_insert(end(), __x);
2023-09-25T02:26:59,809         |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
2023-09-25T02:26:59,972   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
2023-09-25T02:27:02,447   In file included from src/genotypedptable.cpp:11:
2023-09-25T02:27:02,448   src/genotypedptable.h: In member function ‘void GenotypeDPTable::genotype_likelihood_t::divide_likelihoods_by(long double&)’:
2023-09-25T02:27:02,449   src/genotypedptable.h:38:95: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = divides<long double>; _Tp = long double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
2023-09-25T02:27:02,449      38 |       std::transform(likelihoods.begin(), likelihoods.end(), likelihoods.begin(), std::bind2nd(std::divides<long double>(), val));
2023-09-25T02:27:02,450         |                                                                                   ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-25T02:27:02,451   In file included from /usr/include/c++/12/bits/stl_function.h:1438,
2023-09-25T02:27:02,451                    from /usr/include/c++/12/string:48,
2023-09-25T02:27:02,452                    from /usr/include/c++/12/stdexcept:39,
2023-09-25T02:27:02,453                    from src/genotypedptable.cpp:1:
2023-09-25T02:27:02,454   /usr/include/c++/12/backward/binders.h:172:5: note: declared here
2023-09-25T02:27:02,454     172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
2023-09-25T02:27:02,455         |     ^~~~~~~
2023-09-25T02:27:02,476   src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::clear_forward_table()’:
2023-09-25T02:27:02,477   src/genotypedptable.cpp:61:12: warning: unused variable ‘column_count’ [-Wunused-variable]
2023-09-25T02:27:02,478      61 |     size_t column_count = input_column_iterator.get_column_count();
2023-09-25T02:27:02,478         |            ^~~~~~~~~~~~
2023-09-25T02:27:02,525   src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_index()’:
2023-09-25T02:27:02,526   src/genotypedptable.cpp:91:18: warning: unused variable ‘transmission_configurations’ [-Wunused-variable]
2023-09-25T02:27:02,527      91 |     unsigned int transmission_configurations = pow(4, pedigree->triple_count());
2023-09-25T02:27:02,527         |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-25T02:27:02,531   src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_backward_prob()’:
2023-09-25T02:27:02,532   src/genotypedptable.cpp:152:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2023-09-25T02:27:02,532     152 |         if ((k>1) && (column_index < column_count-1) && (((column_index+1)%k) != 0)) {
2023-09-25T02:27:02,533         |                       ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
2023-09-25T02:27:02,536   src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_forward_prob()’:
2023-09-25T02:27:02,537   src/genotypedptable.cpp:178:12: warning: unused variable ‘k’ [-Wunused-variable]
2023-09-25T02:27:02,537     178 |     size_t k = (size_t)sqrt(input_column_iterator.get_column_count());
2023-09-25T02:27:02,538         |            ^
2023-09-25T02:27:02,709   In file included from src/genotypedptable.h:15:
2023-09-25T02:27:02,709   src/vector2d.h: In instantiation of ‘void Vector2D<T>::divide_entries_by(T) [with T = long double]’:
2023-09-25T02:27:02,710   src/genotypedptable.cpp:290:53:   required from here
2023-09-25T02:27:02,710   src/vector2d.h:40:28: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = divides<long double>; _Tp = long double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
2023-09-25T02:27:02,711      40 |                std::bind2nd(std::divides<T>(),val));
2023-09-25T02:27:02,712         |                ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
2023-09-25T02:27:02,712   /usr/include/c++/12/backward/binders.h:172:5: note: declared here
2023-09-25T02:27:02,713     172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
2023-09-25T02:27:02,713         |     ^~~~~~~
2023-09-25T02:27:06,500   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
2023-09-25T02:27:09,057   In file included from /usr/include/c++/12/vector:70,
2023-09-25T02:27:09,058                    from src/columniterator.h:4,
2023-09-25T02:27:09,058                    from src/genotyper.cpp:6:
2023-09-25T02:27:09,059   /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<Genotype>]’:
2023-09-25T02:27:09,060   /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<Genotype>::iterator’ changed in GCC 7.1
2023-09-25T02:27:09,061     439 |       vector<_Tp, _Alloc>::
2023-09-25T02:27:09,061         |       ^~~~~~~~~~~~~~~~~~~
2023-09-25T02:27:09,287   In file included from /usr/include/c++/12/vector:64:
2023-09-25T02:27:09,287   In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Genotype; _Alloc = std::allocator<Genotype>]’,
2023-09-25T02:27:09,288       inlined from ‘void compute_genotypes(const ReadSet&, std::vector<Genotype>*, std::vector<GenotypeDistribution>*, std::vector<unsigned int>*)’ at src/genotyper.cpp:48:23:
2023-09-25T02:27:09,289   /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Genotype*, std::vector<Genotype> >’ changed in GCC 7.1
2023-09-25T02:27:09,290    1287 |           _M_realloc_insert(end(), __x);
2023-09-25T02:27:09,290         |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
2023-09-25T02:27:09,633   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
2023-09-25T02:27:10,814   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
2023-09-25T02:27:16,190   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
2023-09-25T02:27:18,109   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
2023-09-25T02:27:20,990   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
2023-09-25T02:27:23,643   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
2023-09-25T02:27:26,319   src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::run_core()’:
2023-09-25T02:27:26,319   src/hapchat/hapchatcore.cpp:145:11: warning: variable ‘counter_columns’ set but not used [-Wunused-but-set-variable]
2023-09-25T02:27:26,320     145 |   Counter counter_columns;
2023-09-25T02:27:26,320         |           ^~~~~~~~~~~~~~~
2023-09-25T02:27:26,336   src/hapchat/hapchatcore.cpp: In member function ‘bool HapChatCore::check_end(HapChatColumnIterator, const std::vector<std::vector<Entry> >&, const Pointer&, const bool&)’:
2023-09-25T02:27:26,336   src/hapchat/hapchatcore.cpp:208:74: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2023-09-25T02:27:26,337     208 |   return (!re_run && (hap.is_ended() && (input[pointer][0].get_read_id() == -1)));
2023-09-25T02:27:26,338         |                                          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
2023-09-25T02:27:26,489   src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::dp(const constants_t&, std::vector<bool>&, std::vector<bool>&, Counter&, Cost&, Counter&, Counter&, Counter&, Counter&, HapChatColumnIterator)’:
2023-09-25T02:27:26,490   src/hapchat/hapchatcore.cpp:939:15: warning: unused variable ‘old_k’ [-Wunused-variable]
2023-09-25T02:27:26,491     939 |           int old_k = k_j[input_pointer];
2023-09-25T02:27:26,491         |               ^~~~~
2023-09-25T02:27:26,510   src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::intersect(const Column&, const Column&, const Pointer&, std::vector<std::vector<int> >&, std::vector<std::vector<int> >&, std::vector<std::bitset<64> >&, std::vector<unsigned int>&, const bool&)’:
2023-09-25T02:27:26,511   src/hapchat/hapchatcore.cpp:1114:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2023-09-25T02:27:26,512    1114 |          (colJ[j].get_read_id() != -1) &&
2023-09-25T02:27:26,513         |           ~~~~~~~~~~~~~~~~~~~~~~^~~~~
2023-09-25T02:27:26,513   src/hapchat/hapchatcore.cpp:1115:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2023-09-25T02:27:26,514    1115 |          (colQ[i].get_read_id() != -1)) {
2023-09-25T02:27:26,514         |           ~~~~~~~~~~~~~~~~~~~~~~^~~~~
2023-09-25T02:27:26,515   src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::represent_column(const Column&, BitColumn&, Counter&, BitColumn&, Counter&)’:
2023-09-25T02:27:26,516   src/hapchat/hapchatcore.cpp:1159:58: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2023-09-25T02:27:26,517    1159 |   while(cov < column.size() && column[cov].get_read_id() != -1) {
2023-09-25T02:27:26,518         |                                ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
2023-09-25T02:27:26,521   src/hapchat/hapchatcore.cpp: In member function ‘int HapChatCore::compute_active_common(const Column&, const Column&, unsigned int&)’:
2023-09-25T02:27:26,522   src/hapchat/hapchatcore.cpp:1294:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2023-09-25T02:27:26,522    1294 |          (colJ[j].get_read_id() != -1) &&
2023-09-25T02:27:26,523         |           ~~~~~~~~~~~~~~~~~~~~~~^~~~~
2023-09-25T02:27:26,523   src/hapchat/hapchatcore.cpp:1295:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2023-09-25T02:27:26,524    1295 |          (colQ[i].get_read_id() != -1)) {
2023-09-25T02:27:26,525         |           ~~~~~~~~~~~~~~~~~~~~~~^~~~~
2023-09-25T02:27:26,526   src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::insert_col_and_update(std::vector<std::vector<Entry> >&, std::vector<unsigned int>&, std::vector<unsigned int>&, std::vector<Cost>&, const Pointer&, const Column&, std::vector<bool>&, const Counter&)’:
2023-09-25T02:27:26,527   src/hapchat/hapchatcore.cpp:1350:67: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2023-09-25T02:27:26,527    1350 |   if(i < input[pointer].size() && input[pointer][i].get_read_id() != -1)
2023-09-25T02:27:26,528         |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
2023-09-25T02:27:27,631   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
2023-09-25T02:27:29,419   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
2023-09-25T02:27:30,780   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
2023-09-25T02:27:32,357   In file included from /usr/include/c++/12/cassert:44,
2023-09-25T02:27:32,358                    from src/pedigree.cpp:4:
2023-09-25T02:27:32,359   src/pedigree.cpp: In member function ‘void Pedigree::addIndividual(unsigned int, std::vector<Genotype*>, std::vector<PhredGenotypeLikelihoods*>)’:
2023-09-25T02:27:32,359   src/pedigree.cpp:32:33: warning: comparison of integer expressions of different signedness: ‘std::vector<Genotype*>::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-25T02:27:32,360      32 |         assert(genotypes.size() == variant_count);
2023-09-25T02:27:32,361         |                ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
2023-09-25T02:27:32,361   src/pedigree.cpp:33:44: warning: comparison of integer expressions of different signedness: ‘std::vector<PhredGenotypeLikelihoods*>::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-25T02:27:32,362      33 |         assert(genotype_likelihoods.size() == variant_count);
2023-09-25T02:27:32,363         |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
2023-09-25T02:27:32,380   src/pedigree.cpp: In member function ‘const Genotype* Pedigree::get_genotype_by_id(unsigned int, unsigned int) const’:
2023-09-25T02:27:32,381   src/pedigree.cpp:70:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
2023-09-25T02:27:32,381      70 |         assert(variant_index < variant_count);
2023-09-25T02:27:32,382         |                ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
2023-09-25T02:27:32,383   src/pedigree.cpp: In member function ‘const PhredGenotypeLikelihoods* Pedigree::get_genotype_likelihoods_by_id(unsigned int, unsigned int) const’:
2023-09-25T02:27:32,384   src/pedigree.cpp:81:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
2023-09-25T02:27:32,384      81 |         assert(variant_index < variant_count);
2023-09-25T02:27:32,385         |                ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
2023-09-25T02:27:32,394   src/pedigree.cpp: In member function ‘std::string Pedigree::toString() const’:
2023-09-25T02:27:32,394   src/pedigree.cpp:112:35: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘const int’ [-Wsign-compare]
2023-09-25T02:27:32,395     112 |                 for (size_t j=0; j<variant_count; ++j) {
2023-09-25T02:27:32,395         |                                  ~^~~~~~~~~~~~~~
2023-09-25T02:27:34,897   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/pedigreecolumncostcomputer.cpp -o build/temp.linux-armv7l-cpython-311/src/pedigreecolumncostcomputer.o -std=c++11 -Werror=return-type -Werror=narrowing
2023-09-25T02:27:36,893   src/pedigreecolumncostcomputer.cpp: In constructor ‘PedigreeColumnCostComputer::PedigreeColumnCostComputer(const std::vector<const Entry*>&, size_t, const std::vector<unsigned int>&, const Pedigree*, const PedigreePartitions&, bool)’:
2023-09-25T02:27:36,894   src/pedigreecolumncostcomputer.cpp:25:36: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2023-09-25T02:27:36,895      25 |         for (unsigned int i = 0; i < (1<<pedigree_partitions.count()); ++i) {
2023-09-25T02:27:36,895         |                                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-25T02:27:36,935   src/pedigreecolumncostcomputer.cpp: In member function ‘std::vector<PedigreeColumnCostComputer::phased_variant_t> PedigreeColumnCostComputer::get_alleles()’:
2023-09-25T02:27:36,935   src/pedigreecolumncostcomputer.cpp:119:22: warning: unused variable ‘second_best_cost’ [-Wunused-variable]
2023-09-25T02:27:36,936     119 |         unsigned int second_best_cost = numeric_limits < unsigned int >::max();
2023-09-25T02:27:36,937         |                      ^~~~~~~~~~~~~~~~
2023-09-25T02:27:38,166   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
2023-09-25T02:27:45,142   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
2023-09-25T02:27:47,308   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
2023-09-25T02:27:49,117   In file included from /usr/include/c++/12/vector:70,
2023-09-25T02:27:49,117                    from src/genotype.h:4,
2023-09-25T02:27:49,118                    from src/phredgenotypelikelihoods.h:5,
2023-09-25T02:27:49,119                    from src/phredgenotypelikelihoods.cpp:4:
2023-09-25T02:27:49,120   /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<Genotype>]’:
2023-09-25T02:27:49,120   /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<Genotype>::iterator’ changed in GCC 7.1
2023-09-25T02:27:49,121     439 |       vector<_Tp, _Alloc>::
2023-09-25T02:27:49,122         |       ^~~~~~~~~~~~~~~~~~~
2023-09-25T02:27:49,150   In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Genotype}; _Tp = Genotype; _Alloc = std::allocator<Genotype>]’,
2023-09-25T02:27:49,151       inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = Genotype; _Alloc = std::allocator<Genotype>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
2023-09-25T02:27:49,151       inlined from ‘void PhredGenotypeLikelihoods::get_genotypes(std::vector<Genotype>&) const’ at src/phredgenotypelikelihoods.cpp:53:22:
2023-09-25T02:27:49,152   /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Genotype*, std::vector<Genotype> >’ changed in GCC 7.1
2023-09-25T02:27:49,153     123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
2023-09-25T02:27:49,153         |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-25T02:27:49,272   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
2023-09-25T02:27:52,665   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
2023-09-25T02:27:57,738   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
2023-09-25T02:28:00,678   In file included from /usr/include/c++/12/vector:70,
2023-09-25T02:28:00,679                    from src/vector2d.h:5,
2023-09-25T02:28:00,679                    from src/transitionprobabilitycomputer.h:5,
2023-09-25T02:28:00,680                    from src/transitionprobabilitycomputer.cpp:1:
2023-09-25T02:28:00,681   /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<long double>]’:
2023-09-25T02:28:00,681   /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<long double, std::allocator<long double> >::iterator’ changed in GCC 7.1
2023-09-25T02:28:00,682     439 |       vector<_Tp, _Alloc>::
2023-09-25T02:28:00,682         |       ^~~~~~~~~~~~~~~~~~~
2023-09-25T02:28:01,277   In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator<long double>]’,
2023-09-25T02:28:01,278       inlined from ‘TransitionProbabilityComputer::TransitionProbabilityComputer(size_t, unsigned int, const Pedigree*, const std::vector<PedigreePartitions*>&)’ at src/transitionprobabilitycomputer.cpp:25:29:
2023-09-25T02:28:01,279   /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double, std::allocator<long double> > >’ changed in GCC 7.1
2023-09-25T02:28:01,279     123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
2023-09-25T02:28:01,280         |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-25T02:28:02,011   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
2023-09-25T02:28:05,641   In file included from whatshap/core.cpp:845:
2023-09-25T02:28:05,642   src/genotypedptable.h: In member function ‘void GenotypeDPTable::genotype_likelihood_t::divide_likelihoods_by(long double&)’:
2023-09-25T02:28:05,642   src/genotypedptable.h:38:95: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = divides<long double>; _Tp = long double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
2023-09-25T02:28:05,643      38 |       std::transform(likelihoods.begin(), likelihoods.end(), likelihoods.begin(), std::bind2nd(std::divides<long double>(), val));
2023-09-25T02:28:05,643         |                                                                                   ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-25T02:28:05,644   In file included from /usr/include/c++/12/bits/stl_function.h:1438,
2023-09-25T02:28:05,645                    from /usr/include/c++/12/string:48,
2023-09-25T02:28:05,645                    from whatshap/core.cpp:818:
2023-09-25T02:28:05,646   /usr/include/c++/12/backward/binders.h:172:5: note: declared here
2023-09-25T02:28:05,647     172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
2023-09-25T02:28:05,648         |     ^~~~~~~
2023-09-25T02:28:06,011   In file included from whatshap/core.cpp:849:
2023-09-25T02:28:06,012   src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::run_core()’:
2023-09-25T02:28:06,012   src/hapchat/hapchatcore.cpp:145:11: warning: variable ‘counter_columns’ set but not used [-Wunused-but-set-variable]
2023-09-25T02:28:06,013     145 |   Counter counter_columns;
2023-09-25T02:28:06,014         |           ^~~~~~~~~~~~~~~
2023-09-25T02:28:06,023   src/hapchat/hapchatcore.cpp: In member function ‘bool HapChatCore::check_end(HapChatColumnIterator, const std::vector<std::vector<Entry> >&, const Pointer&, const bool&)’:
2023-09-25T02:28:06,024   src/hapchat/hapchatcore.cpp:208:74: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2023-09-25T02:28:06,024     208 |   return (!re_run && (hap.is_ended() && (input[pointer][0].get_read_id() == -1)));
2023-09-25T02:28:06,025         |                                          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
2023-09-25T02:28:06,182   src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::dp(const constants_t&, std::vector<bool>&, std::vector<bool>&, Counter&, Cost&, Counter&, Counter&, Counter&, Counter&, HapChatColumnIterator)’:
2023-09-25T02:28:06,182   src/hapchat/hapchatcore.cpp:939:15: warning: unused variable ‘old_k’ [-Wunused-variable]
2023-09-25T02:28:06,183     939 |           int old_k = k_j[input_pointer];
2023-09-25T02:28:06,184         |               ^~~~~
2023-09-25T02:28:06,203   src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::intersect(const Column&, const Column&, const Pointer&, std::vector<std::vector<int> >&, std::vector<std::vector<int> >&, std::vector<std::bitset<64> >&, std::vector<unsigned int>&, const bool&)’:
2023-09-25T02:28:06,203   src/hapchat/hapchatcore.cpp:1114:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2023-09-25T02:28:06,204    1114 |          (colJ[j].get_read_id() != -1) &&
2023-09-25T02:28:06,205         |           ~~~~~~~~~~~~~~~~~~~~~~^~~~~
2023-09-25T02:28:06,206   src/hapchat/hapchatcore.cpp:1115:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2023-09-25T02:28:06,207    1115 |          (colQ[i].get_read_id() != -1)) {
2023-09-25T02:28:06,207         |           ~~~~~~~~~~~~~~~~~~~~~~^~~~~
2023-09-25T02:28:06,208   src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::represent_column(const Column&, BitColumn&, Counter&, BitColumn&, Counter&)’:
2023-09-25T02:28:06,208   src/hapchat/hapchatcore.cpp:1159:58: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2023-09-25T02:28:06,209    1159 |   while(cov < column.size() && column[cov].get_read_id() != -1) {
2023-09-25T02:28:06,210         |                                ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
2023-09-25T02:28:06,214   src/hapchat/hapchatcore.cpp: In member function ‘int HapChatCore::compute_active_common(const Column&, const Column&, unsigned int&)’:
2023-09-25T02:28:06,215   src/hapchat/hapchatcore.cpp:1294:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2023-09-25T02:28:06,215    1294 |          (colJ[j].get_read_id() != -1) &&
2023-09-25T02:28:06,216         |           ~~~~~~~~~~~~~~~~~~~~~~^~~~~
2023-09-25T02:28:06,217   src/hapchat/hapchatcore.cpp:1295:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2023-09-25T02:28:06,217    1295 |          (colQ[i].get_read_id() != -1)) {
2023-09-25T02:28:06,218         |           ~~~~~~~~~~~~~~~~~~~~~~^~~~~
2023-09-25T02:28:06,220   src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::insert_col_and_update(std::vector<std::vector<Entry> >&, std::vector<unsigned int>&, std::vector<unsigned int>&, std::vector<Cost>&, const Pointer&, const Column&, std::vector<bool>&, const Counter&)’:
2023-09-25T02:28:06,221   src/hapchat/hapchatcore.cpp:1350:67: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2023-09-25T02:28:06,221    1350 |   if(i < input[pointer].size() && input[pointer][i].get_read_id() != -1)
2023-09-25T02:28:06,222         |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
2023-09-25T02:28:06,373   In file included from src/polyphase/haplothreader.h:4,
2023-09-25T02:28:06,374                    from whatshap/core.cpp:855:
2023-09-25T02:28:06,375   src/polyphase/tuple.h: At global scope:
2023-09-25T02:28:06,375   src/polyphase/tuple.h:26:50: warning: left shift count >= width of type [-Wshift-count-overflow]
2023-09-25T02:28:06,376      26 |         31UL << 20, 31UL << 25, 31UL << 30, 31UL << 35,
2023-09-25T02:28:06,377         |                                             ~~~~~^~~~~
2023-09-25T02:28:06,377   src/polyphase/tuple.h:27:14: warning: left shift count >= width of type [-Wshift-count-overflow]
2023-09-25T02:28:06,378      27 |         31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55};
2023-09-25T02:28:06,379         |         ~~~~~^~~~~
2023-09-25T02:28:06,379   src/polyphase/tuple.h:27:26: warning: left shift count >= width of type [-Wshift-count-overflow]
2023-09-25T02:28:06,380      27 |         31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55};
2023-09-25T02:28:06,380         |                     ~~~~~^~~~~
2023-09-25T02:28:06,381   src/polyphase/tuple.h:27:38: warning: left shift count >= width of type [-Wshift-count-overflow]
2023-09-25T02:28:06,382      27 |         31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55};
2023-09-25T02:28:06,382         |                                 ~~~~~^~~~~
2023-09-25T02:28:06,383   src/polyphase/tuple.h:27:50: warning: left shift count >= width of type [-Wshift-count-overflow]
2023-09-25T02:28:06,384      27 |         31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55};
2023-09-25T02:28:06,385         |                                             ~~~~~^~~~~
2023-09-25T02:28:06,385   src/polyphase/tuple.h:26:50: error: right operand of shift expression ‘(31 << 35)’ is greater than or equal to the precision 32 of the left operand [-fpermissive]
2023-09-25T02:28:06,386      26 |         31UL << 20, 31UL << 25, 31UL << 30, 31UL << 35,
2023-09-25T02:28:06,387         |                                             ~~~~~^~~~~
2023-09-25T02:28:06,418   In file included from whatshap/core.cpp:856:
2023-09-25T02:28:06,419   src/polyphase/switchflipcalculator.h:31:14: warning: left shift count >= width of type [-Wshift-count-overflow]
2023-09-25T02:28:06,419      31 |         15UL << 32, 15UL << 36, 15UL << 40, 15UL << 44,
2023-09-25T02:28:06,420         |         ~~~~~^~~~~
2023-09-25T02:28:06,421   src/polyphase/switchflipcalculator.h:31:26: warning: left shift count >= width of type [-Wshift-count-overflow]
2023-09-25T02:28:06,421      31 |         15UL << 32, 15UL << 36, 15UL << 40, 15UL << 44,
2023-09-25T02:28:06,422         |                     ~~~~~^~~~~
2023-09-25T02:28:06,423   src/polyphase/switchflipcalculator.h:31:38: warning: left shift count >= width of type [-Wshift-count-overflow]
2023-09-25T02:28:06,423      31 |         15UL << 32, 15UL << 36, 15UL << 40, 15UL << 44,
2023-09-25T02:28:06,424         |                                 ~~~~~^~~~~
2023-09-25T02:28:06,424   src/polyphase/switchflipcalculator.h:31:50: warning: left shift count >= width of type [-Wshift-count-overflow]
2023-09-25T02:28:06,425      31 |         15UL << 32, 15UL << 36, 15UL << 40, 15UL << 44,
2023-09-25T02:28:06,426         |                                             ~~~~~^~~~~
2023-09-25T02:28:06,426   src/polyphase/switchflipcalculator.h:32:14: warning: left shift count >= width of type [-Wshift-count-overflow]
2023-09-25T02:28:06,427      32 |         15UL << 48, 15UL << 52, 15UL << 56, 15UL << 60
2023-09-25T02:28:06,427         |         ~~~~~^~~~~
2023-09-25T02:28:06,428   src/polyphase/switchflipcalculator.h:32:26: warning: left shift count >= width of type [-Wshift-count-overflow]
2023-09-25T02:28:06,429      32 |         15UL << 48, 15UL << 52, 15UL << 56, 15UL << 60
2023-09-25T02:28:06,430         |                     ~~~~~^~~~~
2023-09-25T02:28:06,431   src/polyphase/switchflipcalculator.h:32:38: warning: left shift count >= width of type [-Wshift-count-overflow]
2023-09-25T02:28:06,431      32 |         15UL << 48, 15UL << 52, 15UL << 56, 15UL << 60
2023-09-25T02:28:06,432         |                                 ~~~~~^~~~~
2023-09-25T02:28:06,433   src/polyphase/switchflipcalculator.h:32:50: warning: left shift count >= width of type [-Wshift-count-overflow]
2023-09-25T02:28:06,434      32 |         15UL << 48, 15UL << 52, 15UL << 56, 15UL << 60
2023-09-25T02:28:06,434         |                                             ~~~~~^~~~~
2023-09-25T02:28:06,435   src/polyphase/switchflipcalculator.h:31:14: error: right operand of shift expression ‘(15 << 32)’ is greater than or equal to the precision 32 of the left operand [-fpermissive]
2023-09-25T02:28:06,436      31 |         15UL << 32, 15UL << 36, 15UL << 40, 15UL << 44,
2023-09-25T02:28:06,436         |         ~~~~~^~~~~
2023-09-25T02:28:06,773   whatshap/core.cpp: In function ‘PyObject* __pyx_pf_8whatshap_4core_15PedigreeDPTable_4get_super_reads(__pyx_obj_8whatshap_4core_PedigreeDPTable*)’:
2023-09-25T02:28:06,774   whatshap/core.cpp:8979:33: warning: comparison of integer expressions of different signedness: ‘std::vector<ReadSet*>::size_type’ {aka ‘unsigned int’} and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare]
2023-09-25T02:28:06,775    8979 |   for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
2023-09-25T02:28:06,776         |                       ~~~~~~~~~~^~~~~~~~~~~
2023-09-25T02:28:07,090   whatshap/core.cpp: In function ‘PyObject* __pyx_pf_8whatshap_4core_11HapChatCore_6get_super_reads(__pyx_obj_8whatshap_4core_HapChatCore*)’:
2023-09-25T02:28:07,091   whatshap/core.cpp:15212:33: warning: comparison of integer expressions of different signedness: ‘std::vector<ReadSet*>::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-25T02:28:07,091   15212 |   for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
2023-09-25T02:28:07,092         |                       ~~~~~~~~~~^~~~~~~~~~~
2023-09-25T02:28:09,348   error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1
2023-09-25T02:28:09,509   ERROR: [present-rich] Building wheel for whatshap (pyproject.toml) exited with 1
2023-09-25T02:28:09,522   [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/tmp_pj77a2z[/]
2023-09-25T02:28:09,522   [bold magenta]cwd[/]: /tmp/pip-wheel-qqx546gj/whatshap_20dbad9bb2f24af1b652bd285f25b10e
2023-09-25T02:28:09,523   Building wheel for whatshap (pyproject.toml): finished with status 'error'
2023-09-25T02:28:09,525   ERROR: Failed building wheel for whatshap
2023-09-25T02:28:09,527 Failed to build whatshap
2023-09-25T02:28:09,529 ERROR: Failed to build one or more wheels
2023-09-25T02:28:09,530 Exception information:
2023-09-25T02:28:09,530 Traceback (most recent call last):
2023-09-25T02:28:09,530   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper
2023-09-25T02:28:09,530     status = run_func(*args)
2023-09-25T02:28:09,530              ^^^^^^^^^^^^^^^
2023-09-25T02:28:09,530   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper
2023-09-25T02:28:09,530     return func(self, options, args)
2023-09-25T02:28:09,530            ^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-25T02:28:09,530   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run
2023-09-25T02:28:09,530     raise CommandError("Failed to build one or more wheels")
2023-09-25T02:28:09,530 pip._internal.exceptions.CommandError: Failed to build one or more wheels
2023-09-25T02:28:09,534 Removed build tracker: '/tmp/pip-build-tracker-j7e15u6q'