2023-09-17T22:52:38,235 Created temporary directory: /tmp/pip-build-tracker-wqg8rx_i
2023-09-17T22:52:38,236 Initialized build tracking at /tmp/pip-build-tracker-wqg8rx_i
2023-09-17T22:52:38,237 Created build tracker: /tmp/pip-build-tracker-wqg8rx_i
2023-09-17T22:52:38,237 Entered build tracker: /tmp/pip-build-tracker-wqg8rx_i
2023-09-17T22:52:38,238 Created temporary directory: /tmp/pip-wheel-gwd83226
2023-09-17T22:52:38,241 Created temporary directory: /tmp/pip-ephem-wheel-cache-li4kcpho
2023-09-17T22:52:38,263 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-09-17T22:52:38,267 2 location(s) to search for versions of pytrimal:
2023-09-17T22:52:38,267 * https://pypi.org/simple/pytrimal/
2023-09-17T22:52:38,267 * https://www.piwheels.org/simple/pytrimal/
2023-09-17T22:52:38,267 Fetching project page and analyzing links: https://pypi.org/simple/pytrimal/
2023-09-17T22:52:38,268 Getting page https://pypi.org/simple/pytrimal/
2023-09-17T22:52:38,270 Found index url https://pypi.org/simple/
2023-09-17T22:52:38,530 Fetched page https://pypi.org/simple/pytrimal/ as application/vnd.pypi.simple.v1+json
2023-09-17T22:52:38,596   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/e7/92/deb27aec34cc7863b866ea29900d2e47e17511e771fd93e4a9f73ad6b8ac/pytrimal-0.1.0-cp310-cp310-macosx_10_15_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,597   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/ec/60/4797839372e3883bb134efc65c098c3c6c4d96d8022e41400a1a8a90bb0b/pytrimal-0.1.0-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,597   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/4b/f5/1d7233b1405054090c3b53605b27bad7119dd1c6238bdc174bb4b10b5df2/pytrimal-0.1.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,598   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/48/2f/69945d01f3d8af3f9a8442c7d5a0fa19f7c81361d568bc856bf502c8ae9a/pytrimal-0.1.0-cp35-cp35m-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,599   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/a9/c2/ccddd18f9a1918b79b346e0d856a2f08971ce68e25d780a9446e3a53860b/pytrimal-0.1.0-cp35-cp35m-manylinux2010_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,600   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/05/6b/cd4cd3b14e9b5644113e3e51cc15a839b3068231cec06441de8f99632b3a/pytrimal-0.1.0-cp36-cp36m-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,600   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/56/0f/65a63a8cbd8e7ee8e80afec55bda84b4e236841224f9a7221595c00a1dba/pytrimal-0.1.0-cp36-cp36m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,601   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/0a/38/92fb02233538de1e77eb533350ed7d14068ef1a6f031462f11bce08e05df/pytrimal-0.1.0-cp36-cp36m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,602   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/2e/4d/af840c124e2b391640d8df3045b4cdb2bb0eb4d952fe95acd65a0f9043e7/pytrimal-0.1.0-cp37-cp37m-macosx_10_15_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,602   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/75/3d/52511029b5d404a58457debf7d60a8fca6b4fd4322db7d2073d8026119b2/pytrimal-0.1.0-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,603   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/d1/cd/2b631d34ee040ffa60a48b58b0c38e5dc41d5f5251fd27f47a4f16650392/pytrimal-0.1.0-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,604   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/8b/6c/b9e93831941b14de3a41445333d9e09e2389378754527ab0743ff97ab5c7/pytrimal-0.1.0-cp38-cp38-macosx_10_15_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,604   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/94/1c/dab45d42e6fb9f9f2e8a4e76da1722faadf7eba1254c912b07e443398499/pytrimal-0.1.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,605   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/d9/f8/113e5e8ffc20f0477eb2c20d59e0e64c6d5dda295af95eb6979bd2efee93/pytrimal-0.1.0-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,605   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/cd/ca/e3bc1316c04c94ba11885b933473ce229863522b438a112c27b2fbfe080e/pytrimal-0.1.0-cp39-cp39-macosx_10_15_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,606   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/7c/15/c057ace451e9ccc70f96639e56461ca403ba2c829af6c6bbf777d36494df/pytrimal-0.1.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,606   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/6c/78/0a693856b86c7e419cfebe567e5c8ceafe8339b5600762d8cd8566607de9/pytrimal-0.1.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,607   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/2c/e4/b946aca9e551aa0dd6cd90705547b979e4834cb5a63834121f4f911461e3/pytrimal-0.1.0-pp36-pypy36_pp73-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,608   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/19/48/1283651eccc18b73c1f0c4af418db4a831d1ef949d9edbdbf8a47f40d2a8/pytrimal-0.1.0-pp37-pypy37_pp73-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,608   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/84/24/1bc90c83278945f66b31974a2aba5bf3e9d4b272d78790120748bf9485f5/pytrimal-0.1.0-pp37-pypy37_pp73-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,609   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/b1/6d/7d46cda527909bd41ead416342e24999e8cc63c82560bfaf5918fd708af7/pytrimal-0.1.0-pp38-pypy38_pp73-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,610   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/6a/aa/bae9c9761abe07e00fa0dc292ef343354f2e508e9ce37f72f8754dfb7903/pytrimal-0.1.0-pp39-pypy39_pp73-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,611   Found link https://files.pythonhosted.org/packages/39/09/11aae9fa483929539f100beb384da40724188ff102ee94517b4a3ccba5c8/pytrimal-0.1.0.tar.gz (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5), version: 0.1.0
2023-09-17T22:52:38,611   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/cd/95/15ba2a87e8ef78e2362fb9fa9900f0cee75d4938f92d2d889b0e8cd09f71/pytrimal-0.1.1-cp310-cp310-macosx_10_15_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,612   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/16/99/4b6ddc7537fa853cadf9d9ef81af95019c58003d5119febce6af8bddedcb/pytrimal-0.1.1-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,613   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/b5/c3/e1edfbe9450b0c2d23d36fa8e624dc28220d7f23ddaf3e46829c18c1725b/pytrimal-0.1.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,613   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/9b/c9/655540ff5e71515c6a37a61e71b5dcc9b3c29515a7ed7601dd40f7e5e8ce/pytrimal-0.1.1-cp35-cp35m-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,614   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/1c/85/3880bc8ccfc099b68d8e18baf2aa194127082c0cdf274833c13e83cee1a9/pytrimal-0.1.1-cp35-cp35m-manylinux2010_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,614   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/61/43/dc432a69a7f2a59f4e5e509c206f1178d56b401206cc661957179c9ddeae/pytrimal-0.1.1-cp36-cp36m-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,615   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/12/7a/53b39f4d3b3ae1da433bae3111d667d3d5813bece2a4b19bcc4a21fd11fa/pytrimal-0.1.1-cp36-cp36m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,615   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/77/8b/87f775f8f50c6f3b32813d272f7534fa00372db8cdb41ceda4971662368f/pytrimal-0.1.1-cp36-cp36m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,616   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/e5/e5/9bd5e09db10f69b2d749e985a5da7b66e98688f285bddf7f5a666301aff3/pytrimal-0.1.1-cp37-cp37m-macosx_10_15_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,617   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/da/35/5ce9cbae068eb2d7fb9c03aa07281308751a38c3d6bdb521c69345fefbda/pytrimal-0.1.1-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,617   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/74/22/25d73231abb8d9553a4be31493a8034544d1c16ee60204ab408c7406973d/pytrimal-0.1.1-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,618   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/72/34/deec927936c24cad8d5dd6b1d8e503e9087a9e08312ebe4cae88beb217ce/pytrimal-0.1.1-cp38-cp38-macosx_10_15_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,619   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/27/f7/10554d83d0ec45d5500b9e98eaca33706103b94ee91c6f6bf9964b0a380c/pytrimal-0.1.1-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,619   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/41/c7/044460829089c368091d78f9a8b99327e789d33fb1e7bd1803ea66b3113b/pytrimal-0.1.1-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,620   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/6f/9e/05203b6f71b87fb6ecd15c3e9c574abe49252c23207bffd33946e11dff82/pytrimal-0.1.1-cp39-cp39-macosx_10_15_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,620   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/bb/db/7c0fa4d3e5d996d2c9714a53e4391aba90f5fc2d532e43dce4af051da656/pytrimal-0.1.1-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,621   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/71/c2/de54862ac53e4644da95cc5d45c9e5dac1d461692ee5db20d380429b29df/pytrimal-0.1.1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,621   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/f3/9f/268de33e758c07ddaca562b49fc69e05e2754bcfebd1ebd981e259eeff6f/pytrimal-0.1.1-pp36-pypy36_pp73-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,622   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/36/58/d74103e669267602491f2ed32f9d2579844fa18da914f0397bf096daa911/pytrimal-0.1.1-pp37-pypy37_pp73-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,623   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/9c/63/539c1d358fe0952f7df82e2bb7bec9810385121673cc93859955b2c5aed1/pytrimal-0.1.1-pp37-pypy37_pp73-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,623   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/ae/ca/58bd8a813592f678c7d550bf0ddcc625922a2f891b4c53b2062c71aaa1a1/pytrimal-0.1.1-pp38-pypy38_pp73-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,624   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/c4/8b/f4066f88bce2590fbad7a52d52588c23a7410a07e5b278925ecf5b0bf934/pytrimal-0.1.1-pp39-pypy39_pp73-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,625   Found link https://files.pythonhosted.org/packages/86/c4/83edee2cc512ab4e6f48160b4f7e737681a8b0cabf4df5798ed32656e062/pytrimal-0.1.1.tar.gz (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5), version: 0.1.1
2023-09-17T22:52:38,626   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/24/1b/3c52d892348ffe2df0778d09e3650dc5f6e524d01333a1842067f14af62d/pytrimal-0.1.2-cp310-cp310-macosx_10_15_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,626   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/6d/3e/26e2fc28d6f07c55b6279ec9785098ba866ea41a892e542160efdeb1b755/pytrimal-0.1.2-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,627   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/c9/f7/fd0b169d7447de46c232e11e04a5b880448effa3e94e15121b5df4369106/pytrimal-0.1.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,627   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/8a/ed/fc33fc64e959980eb54d0b506d8983b4a92999f5f8ecf21a504fd22b25b3/pytrimal-0.1.2-cp35-cp35m-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,628   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/d5/fd/b234fd262c716f2c9b201cabc7b26f2ccdb60e34c9695034ddfdda347d00/pytrimal-0.1.2-cp35-cp35m-manylinux2010_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,629   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/b5/e6/a8bc5bea8875b2bb52a443d2467a8048e1ee4f99c8f35f3bd215c26b51b6/pytrimal-0.1.2-cp36-cp36m-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,629   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/91/c9/ba2d80eea0746c3bccd4ab0e1ebcbf520ef759430502e44f7c81fa53c651/pytrimal-0.1.2-cp36-cp36m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
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2023-09-17T22:52:38,811   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/2b/a6/a9571b0dc9e95d8dcdce37530298c8a8e0a6a3e7deb27928577281048987/pytrimal-0.6.0-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,811   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/36/e8/c05c45431eadf6da882c516522f2a49ccca46e3cbf4fe2526c67b361fa57/pytrimal-0.6.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
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2023-09-17T22:52:38,818   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/31/4a/d1c528ab58a3cb56783a37f0346314a1e4b03d4b10240e810a42a13a47af/pytrimal-0.6.0-pp38-pypy38_pp73-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
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2023-09-17T22:52:38,834   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/a5/e0/e4b4301c7c06889aa5c733f6724937e32e4baa33992bb9ff52f89d81b96c/pytrimal-0.7.0-cp39-cp39-macosx_11_0_arm64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,835   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/9c/d2/a6b14fc2c629142d94aae7d78f4c939b8063919f366a83e5db77da6ff59e/pytrimal-0.7.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,836   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/bd/a8/abfc394d3687be26591b5554e452a79f934c05c45beebf266d0886084421/pytrimal-0.7.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,836   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/40/f3/1514c62835d1a10f497367c476c1c63d899f814ab375bcd8cecc60c6dbbc/pytrimal-0.7.0-pp37-pypy37_pp73-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,837   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/da/60/30a3232263be603211853c9688748a28b1437054313c6eafb9bb6a870c73/pytrimal-0.7.0-pp37-pypy37_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,838   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/14/4f/98acfe0974a2efbf32ce38e5f013b7dbb688856fb5b356701d4c8b4263c3/pytrimal-0.7.0-pp37-pypy37_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,839   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/56/c7/f58e2a538d08108542822c21ac0557e520fbdfccb2f6fc4757e322d9be8e/pytrimal-0.7.0-pp38-pypy38_pp73-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,839   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/d8/66/3528b865040009edc3f7fa01ca755b2e8d9cfdb635a1bca04e530f061d96/pytrimal-0.7.0-pp38-pypy38_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,840   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/57/82/141872469d907ca4a4d6a3ff944f8e9d199039c6c0da44493e50073df9ba/pytrimal-0.7.0-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,840   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/be/f5/3a64ac65df88119888e3de4fd3d6305ff4c5fa3bbcb9ad95b112bf6a9090/pytrimal-0.7.0-pp39-pypy39_pp73-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,841   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/e8/43/3335546663062cb948c036321f50b4a87e149c55de683e545aeebe330ad5/pytrimal-0.7.0-pp39-pypy39_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,841   Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/83/f1/ee101daf3a0cf0420cbc6b843d5e8b43c4c14a4761c1fcbb90cf86e7f22e/pytrimal-0.7.0-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:38,843   Found link https://files.pythonhosted.org/packages/27/d4/b5f132426e1f6a3269f76527be6d7fff58ffe57df014720de60503f0aa27/pytrimal-0.7.0.tar.gz (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5), version: 0.7.0
2023-09-17T22:52:38,844 Fetching project page and analyzing links: https://www.piwheels.org/simple/pytrimal/
2023-09-17T22:52:38,845 Getting page https://www.piwheels.org/simple/pytrimal/
2023-09-17T22:52:38,846 Found index url https://www.piwheels.org/simple/
2023-09-17T22:52:39,118 Fetched page https://www.piwheels.org/simple/pytrimal/ as text/html
2023-09-17T22:52:39,135   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.7.0-cp39-cp39-linux_armv7l.whl#sha256=bba996dd781f64cd83d7719e0eb602313897c8435064cc0d7b6ba6bf8a0bfc9b (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,136   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.7.0-cp39-cp39-linux_armv6l.whl#sha256=bba996dd781f64cd83d7719e0eb602313897c8435064cc0d7b6ba6bf8a0bfc9b (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,136   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.6.0-cp39-cp39-linux_armv7l.whl#sha256=29720c9ebdd1832dc4c61ae6792460b69cb48d155266c995f0e4e7d2ad329b2b (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,137   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.6.0-cp39-cp39-linux_armv6l.whl#sha256=29720c9ebdd1832dc4c61ae6792460b69cb48d155266c995f0e4e7d2ad329b2b (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,137   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.5.5-cp39-cp39-linux_armv7l.whl#sha256=7cb3eeb8a73e979a4a7ba8284c74e59ca8b037430df30a59f03973c5b6f79aae (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,138   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.5.5-cp39-cp39-linux_armv6l.whl#sha256=7cb3eeb8a73e979a4a7ba8284c74e59ca8b037430df30a59f03973c5b6f79aae (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,139   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.5.4-cp39-cp39-linux_armv7l.whl#sha256=f057508a510a8b81ecbba935a0c1b246fab18e3b22b3ca8355229751d1ae812b (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,139   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.5.4-cp39-cp39-linux_armv6l.whl#sha256=f057508a510a8b81ecbba935a0c1b246fab18e3b22b3ca8355229751d1ae812b (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,140   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.5.4-cp37-cp37m-linux_armv7l.whl#sha256=3c4a238e9091e4af0f018445e263e367fcd09b80c5f113975345cb8d54621fc0 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,140   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.5.4-cp37-cp37m-linux_armv6l.whl#sha256=3c4a238e9091e4af0f018445e263e367fcd09b80c5f113975345cb8d54621fc0 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,141   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.5.3-cp39-cp39-linux_armv7l.whl#sha256=96414c6ad503cbafadc0cd909c065d410ab2460dc7ee7c1c664f2aab64c19323 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,141   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.5.3-cp39-cp39-linux_armv6l.whl#sha256=96414c6ad503cbafadc0cd909c065d410ab2460dc7ee7c1c664f2aab64c19323 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,142   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.5.3-cp37-cp37m-linux_armv7l.whl#sha256=790e0a5ba04a025d1521570bb479bbe5dd3f543fc0279b06d34b8dd8d78a9078 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,143   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.5.3-cp37-cp37m-linux_armv6l.whl#sha256=790e0a5ba04a025d1521570bb479bbe5dd3f543fc0279b06d34b8dd8d78a9078 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,143   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.5.2-cp39-cp39-linux_armv7l.whl#sha256=d8c4cbf91f4f60cc31cf104c877312bb091c4cedb0b11340fb15ec9409092560 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,144   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.5.2-cp39-cp39-linux_armv6l.whl#sha256=d8c4cbf91f4f60cc31cf104c877312bb091c4cedb0b11340fb15ec9409092560 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,144   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.5.2-cp37-cp37m-linux_armv7l.whl#sha256=4fcc57ac1551e91658c051a7f6a26c64e84e5c799c65c2c660b060a73649bbde (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,145   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.5.2-cp37-cp37m-linux_armv6l.whl#sha256=4fcc57ac1551e91658c051a7f6a26c64e84e5c799c65c2c660b060a73649bbde (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,146   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.5.1-cp39-cp39-linux_armv7l.whl#sha256=33634cd2d6a05efa31c4f7a64d98b50745ed67dd434f6f1a26d59d8380c782ed (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,147   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.5.1-cp39-cp39-linux_armv6l.whl#sha256=33634cd2d6a05efa31c4f7a64d98b50745ed67dd434f6f1a26d59d8380c782ed (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,147   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.5.1-cp37-cp37m-linux_armv7l.whl#sha256=7dc30c4514d830c7d50f5da9578ac26dc4c99658610a7a140859c6e95ffe5210 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,148   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.5.1-cp37-cp37m-linux_armv6l.whl#sha256=7dc30c4514d830c7d50f5da9578ac26dc4c99658610a7a140859c6e95ffe5210 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,148   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.5.0-cp39-cp39-linux_armv7l.whl#sha256=72fc3420a99a380479e4ed1919c0fbee2bbd9e00fe33238946ee59869bd9a9ba (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,149   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.5.0-cp39-cp39-linux_armv6l.whl#sha256=72fc3420a99a380479e4ed1919c0fbee2bbd9e00fe33238946ee59869bd9a9ba (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,149   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.5.0-cp37-cp37m-linux_armv7l.whl#sha256=49ce53bfa624c31e9f670a3442d3d4023bcc17f0e86c09dee3e81a901d0ef6b3 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,150   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.5.0-cp37-cp37m-linux_armv6l.whl#sha256=49ce53bfa624c31e9f670a3442d3d4023bcc17f0e86c09dee3e81a901d0ef6b3 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,150   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.4.0-cp39-cp39-linux_armv7l.whl#sha256=3cff96406b8ddeea7cbb51046bd603ab3ed9c0bb004cb90d1a665436624b2b56 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,151   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.4.0-cp39-cp39-linux_armv6l.whl#sha256=3cff96406b8ddeea7cbb51046bd603ab3ed9c0bb004cb90d1a665436624b2b56 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,152   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.4.0-cp37-cp37m-linux_armv7l.whl#sha256=7f78e36e834cd71b9c6157802ae3bf5bec7dd411d544fe6b2c01c05143727d59 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,152   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.4.0-cp37-cp37m-linux_armv6l.whl#sha256=7f78e36e834cd71b9c6157802ae3bf5bec7dd411d544fe6b2c01c05143727d59 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,153   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.2-cp39-cp39-linux_armv7l.whl#sha256=61a18089e1538bafb91947f7c54942052cdebd640068daae8f6fd8559ee1821c (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,153   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.2-cp39-cp39-linux_armv6l.whl#sha256=61a18089e1538bafb91947f7c54942052cdebd640068daae8f6fd8559ee1821c (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,154   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.2-cp37-cp37m-linux_armv7l.whl#sha256=5f3c8d40349fe09f1f02e9392a1bc6dfe598428ccca63cc687102270f4b8bcc7 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,154   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.2-cp37-cp37m-linux_armv6l.whl#sha256=5f3c8d40349fe09f1f02e9392a1bc6dfe598428ccca63cc687102270f4b8bcc7 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,155   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.2-cp35-cp35m-linux_armv7l.whl#sha256=2c89565387151ab91f065fd81e6801a59cb0a692e1d518a4bdbe1b819d4e3bb9 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,155   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.2-cp35-cp35m-linux_armv6l.whl#sha256=2c89565387151ab91f065fd81e6801a59cb0a692e1d518a4bdbe1b819d4e3bb9 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,156   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.1-cp39-cp39-linux_armv7l.whl#sha256=06890ee257c9d009b402620382086847b440e92a339043e6b759dda8545f6ff6 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,156   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.1-cp39-cp39-linux_armv6l.whl#sha256=06890ee257c9d009b402620382086847b440e92a339043e6b759dda8545f6ff6 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,157   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.1-cp37-cp37m-linux_armv7l.whl#sha256=87c41102be591a5dcb6efdf6807ea38a522ec3cc653f29af275f01d2b4e8d4fc (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,157   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.1-cp37-cp37m-linux_armv6l.whl#sha256=87c41102be591a5dcb6efdf6807ea38a522ec3cc653f29af275f01d2b4e8d4fc (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,158   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.1-cp35-cp35m-linux_armv7l.whl#sha256=7719393288e4b7d58df66be1b835f01bc962a0a64b61adab766ce32ffa6a3f0e (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,159   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.1-cp35-cp35m-linux_armv6l.whl#sha256=7719393288e4b7d58df66be1b835f01bc962a0a64b61adab766ce32ffa6a3f0e (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,159   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.0-cp39-cp39-linux_armv7l.whl#sha256=f5b150f17ead1887b6682721c33fa5cd7a8ab0d03d55d68176e11f3d0e17db43 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,160   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.0-cp39-cp39-linux_armv6l.whl#sha256=f5b150f17ead1887b6682721c33fa5cd7a8ab0d03d55d68176e11f3d0e17db43 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,160   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.0-cp37-cp37m-linux_armv7l.whl#sha256=b22cc6f8f6e39214cc9d6ef2778b8811ddb859aeca9ad030b64d78cc83816438 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,161   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.0-cp37-cp37m-linux_armv6l.whl#sha256=b22cc6f8f6e39214cc9d6ef2778b8811ddb859aeca9ad030b64d78cc83816438 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,162   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.0-cp35-cp35m-linux_armv7l.whl#sha256=c2e192c5e15e398eb8fcf987e378ac23645cf88ae7b43798f959edf36711e847 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,162   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.0-cp35-cp35m-linux_armv6l.whl#sha256=c2e192c5e15e398eb8fcf987e378ac23645cf88ae7b43798f959edf36711e847 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,163   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.1.2-cp39-cp39-linux_armv7l.whl#sha256=8335602183caad582c8928ea691b7be0671b701f02fd9489681d90efd6708863 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,163   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.1.2-cp39-cp39-linux_armv6l.whl#sha256=8335602183caad582c8928ea691b7be0671b701f02fd9489681d90efd6708863 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,163   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.1.2-cp37-cp37m-linux_armv7l.whl#sha256=37809e659b1a6d0ae65708c8315d044d8b3ed5fa169c916d23a800715869074c (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,164   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.1.2-cp37-cp37m-linux_armv6l.whl#sha256=37809e659b1a6d0ae65708c8315d044d8b3ed5fa169c916d23a800715869074c (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,164   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.1.2-cp35-cp35m-linux_armv7l.whl#sha256=4a3dcfa05641310e339af037687c7171ffa116dab65617ebd2d9661d937375ee (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,165   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.1.2-cp35-cp35m-linux_armv6l.whl#sha256=4a3dcfa05641310e339af037687c7171ffa116dab65617ebd2d9661d937375ee (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,166   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.1.1-cp39-cp39-linux_armv7l.whl#sha256=c54c9649d97022e8ce47cce412b180621f9a77399bf9c58ef855e08f913a237f (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,166   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.1.1-cp39-cp39-linux_armv6l.whl#sha256=c54c9649d97022e8ce47cce412b180621f9a77399bf9c58ef855e08f913a237f (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,167   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.1.1-cp37-cp37m-linux_armv7l.whl#sha256=37299a0c9633838823df1040fad4ea675ea5d693df9331240e4dc04f1797003c (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,167   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.1.1-cp37-cp37m-linux_armv6l.whl#sha256=37299a0c9633838823df1040fad4ea675ea5d693df9331240e4dc04f1797003c (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,168   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.1.1-cp35-cp35m-linux_armv7l.whl#sha256=ed62deb3aed080a21ff74516c43aecc431d77412aff60dbbc4ba6282beee2b7d (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,169   Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.1.1-cp35-cp35m-linux_armv6l.whl#sha256=ed62deb3aed080a21ff74516c43aecc431d77412aff60dbbc4ba6282beee2b7d (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5)
2023-09-17T22:52:39,169 Skipping link: not a file: https://www.piwheels.org/simple/pytrimal/
2023-09-17T22:52:39,170 Skipping link: not a file: https://pypi.org/simple/pytrimal/
2023-09-17T22:52:39,190 Given no hashes to check 1 links for project 'pytrimal': discarding no candidates
2023-09-17T22:52:39,207 Collecting pytrimal==0.1.0
2023-09-17T22:52:39,209   Created temporary directory: /tmp/pip-unpack-9d6yck1n
2023-09-17T22:52:39,912   Downloading pytrimal-0.1.0.tar.gz (8.5 MB)
2023-09-17T22:52:46,378   Added pytrimal==0.1.0 from https://files.pythonhosted.org/packages/39/09/11aae9fa483929539f100beb384da40724188ff102ee94517b4a3ccba5c8/pytrimal-0.1.0.tar.gz to build tracker '/tmp/pip-build-tracker-wqg8rx_i'
2023-09-17T22:52:46,382   Created temporary directory: /tmp/pip-build-env-4j5t91yl
2023-09-17T22:52:46,386   Installing build dependencies: started
2023-09-17T22:52:46,387   Running command pip subprocess to install build dependencies
2023-09-17T22:52:47,543   Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11)
2023-09-17T22:52:48,022   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-09-17T22:52:49,685   Collecting setuptools>=46.4
2023-09-17T22:52:49,686     Obtaining dependency information for setuptools>=46.4 from https://files.pythonhosted.org/packages/bb/26/7945080113158354380a12ce26873dd6c1ebd88d47f5bc24e2c5bb38c16a/setuptools-68.2.2-py3-none-any.whl.metadata
2023-09-17T22:52:49,692     Using cached setuptools-68.2.2-py3-none-any.whl.metadata (6.3 kB)
2023-09-17T22:52:51,073   Collecting cython~=0.29.16
2023-09-17T22:52:51,074     Obtaining dependency information for cython~=0.29.16 from https://files.pythonhosted.org/packages/3f/d6/9eed523aeaca42acbaa3e6d3850edae780dc7f8da9df1bf6a2ceb851839c/Cython-0.29.36-py2.py3-none-any.whl.metadata
2023-09-17T22:52:51,081     Using cached Cython-0.29.36-py2.py3-none-any.whl.metadata (3.1 kB)
2023-09-17T22:52:51,255   Using cached setuptools-68.2.2-py3-none-any.whl (807 kB)
2023-09-17T22:52:51,304   Using cached Cython-0.29.36-py2.py3-none-any.whl (988 kB)
2023-09-17T22:52:53,762   Installing collected packages: setuptools, cython
2023-09-17T22:52:58,354     Creating /tmp/pip-build-env-4j5t91yl/overlay/local/bin
2023-09-17T22:52:58,357     changing mode of /tmp/pip-build-env-4j5t91yl/overlay/local/bin/cygdb to 755
2023-09-17T22:52:58,359     changing mode of /tmp/pip-build-env-4j5t91yl/overlay/local/bin/cython to 755
2023-09-17T22:52:58,361     changing mode of /tmp/pip-build-env-4j5t91yl/overlay/local/bin/cythonize to 755
2023-09-17T22:52:58,382   Successfully installed cython-0.29.36 setuptools-68.2.2
2023-09-17T22:52:59,003   Installing build dependencies: finished with status 'done'
2023-09-17T22:52:59,006   Getting requirements to build wheel: started
2023-09-17T22:52:59,008   Running command Getting requirements to build wheel
2023-09-17T22:52:59,835   Getting requirements to build wheel: finished with status 'done'
2023-09-17T22:52:59,858   Installing backend dependencies: started
2023-09-17T22:52:59,859   Running command pip subprocess to install backend dependencies
2023-09-17T22:53:00,990   Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11)
2023-09-17T22:53:01,464   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-09-17T22:53:02,063   Collecting wheel
2023-09-17T22:53:02,079     Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.2-py3-none-any.whl (64 kB)
2023-09-17T22:53:04,293   Installing collected packages: wheel
2023-09-17T22:53:04,514     Creating /tmp/pip-build-env-4j5t91yl/normal/local/bin
2023-09-17T22:53:04,516     changing mode of /tmp/pip-build-env-4j5t91yl/normal/local/bin/wheel to 755
2023-09-17T22:53:04,527   Successfully installed wheel-0.41.2
2023-09-17T22:53:05,049   Installing backend dependencies: finished with status 'done'
2023-09-17T22:53:05,050   Created temporary directory: /tmp/pip-modern-metadata-xhd51wvf
2023-09-17T22:53:05,052   Preparing metadata (pyproject.toml): started
2023-09-17T22:53:05,054   Running command Preparing metadata (pyproject.toml)
2023-09-17T22:53:05,842   running dist_info
2023-09-17T22:53:05,859   creating /tmp/pip-modern-metadata-xhd51wvf/pytrimal.egg-info
2023-09-17T22:53:05,863   writing /tmp/pip-modern-metadata-xhd51wvf/pytrimal.egg-info/PKG-INFO
2023-09-17T22:53:05,867   writing dependency_links to /tmp/pip-modern-metadata-xhd51wvf/pytrimal.egg-info/dependency_links.txt
2023-09-17T22:53:05,869   writing top-level names to /tmp/pip-modern-metadata-xhd51wvf/pytrimal.egg-info/top_level.txt
2023-09-17T22:53:05,870   writing manifest file '/tmp/pip-modern-metadata-xhd51wvf/pytrimal.egg-info/SOURCES.txt'
2023-09-17T22:53:05,897   reading manifest file '/tmp/pip-modern-metadata-xhd51wvf/pytrimal.egg-info/SOURCES.txt'
2023-09-17T22:53:05,899   reading manifest template 'MANIFEST.in'
2023-09-17T22:53:06,191   warning: no files found matching '*.pyi' under directory 'pytrimal'
2023-09-17T22:53:06,210   warning: no files found matching '*.pxd' under directory 'pytrimal'
2023-09-17T22:53:06,219   warning: no files found matching '*.h' under directory 'pytrimal'
2023-09-17T22:53:06,225   warning: no files found matching 'py.typed' under directory 'pytrimal'
2023-09-17T22:53:06,226   warning: no previously-included files matching '*.html' found under directory 'pytrimal'
2023-09-17T22:53:06,228   warning: no files found matching '*.h' under directory 'pytrimal/patch'
2023-09-17T22:53:06,229   warning: no files found matching '*.pxd' under directory 'pytrimal/patch'
2023-09-17T22:53:06,230   adding license file 'COPYING'
2023-09-17T22:53:06,238   writing manifest file '/tmp/pip-modern-metadata-xhd51wvf/pytrimal.egg-info/SOURCES.txt'
2023-09-17T22:53:06,239   creating '/tmp/pip-modern-metadata-xhd51wvf/pytrimal-0.1.0.dist-info'
2023-09-17T22:53:06,421   Preparing metadata (pyproject.toml): finished with status 'done'
2023-09-17T22:53:06,427   Source in /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e has version 0.1.0, which satisfies requirement pytrimal==0.1.0 from https://files.pythonhosted.org/packages/39/09/11aae9fa483929539f100beb384da40724188ff102ee94517b4a3ccba5c8/pytrimal-0.1.0.tar.gz
2023-09-17T22:53:06,428   Removed pytrimal==0.1.0 from https://files.pythonhosted.org/packages/39/09/11aae9fa483929539f100beb384da40724188ff102ee94517b4a3ccba5c8/pytrimal-0.1.0.tar.gz from build tracker '/tmp/pip-build-tracker-wqg8rx_i'
2023-09-17T22:53:06,434 Created temporary directory: /tmp/pip-unpack-_f0lha0q
2023-09-17T22:53:06,436 Created temporary directory: /tmp/pip-unpack-r_vr1rp_
2023-09-17T22:53:06,440 Building wheels for collected packages: pytrimal
2023-09-17T22:53:06,443   Created temporary directory: /tmp/pip-wheel-kj3h_v1l
2023-09-17T22:53:06,444   Destination directory: /tmp/pip-wheel-kj3h_v1l
2023-09-17T22:53:06,446   Building wheel for pytrimal (pyproject.toml): started
2023-09-17T22:53:06,448   Running command Building wheel for pytrimal (pyproject.toml)
2023-09-17T22:53:07,259   running bdist_wheel
2023-09-17T22:53:07,296   running build
2023-09-17T22:53:07,297   running build_py
2023-09-17T22:53:07,304   creating build
2023-09-17T22:53:07,304   creating build/lib.linux-armv7l-cpython-311
2023-09-17T22:53:07,305   creating build/lib.linux-armv7l-cpython-311/pytrimal
2023-09-17T22:53:07,306   copying pytrimal/_version.py -> build/lib.linux-armv7l-cpython-311/pytrimal
2023-09-17T22:53:07,308   copying pytrimal/__init__.py -> build/lib.linux-armv7l-cpython-311/pytrimal
2023-09-17T22:53:07,310   creating build/lib.linux-armv7l-cpython-311/pytrimal/tests
2023-09-17T22:53:07,311   copying pytrimal/tests/test_automatic_trimmer.py -> build/lib.linux-armv7l-cpython-311/pytrimal/tests
2023-09-17T22:53:07,313   copying pytrimal/tests/test_manual_trimmer.py -> build/lib.linux-armv7l-cpython-311/pytrimal/tests
2023-09-17T22:53:07,314   copying pytrimal/tests/test_doctest.py -> build/lib.linux-armv7l-cpython-311/pytrimal/tests
2023-09-17T22:53:07,316   copying pytrimal/tests/test_similarity_matrix.py -> build/lib.linux-armv7l-cpython-311/pytrimal/tests
2023-09-17T22:53:07,318   copying pytrimal/tests/__init__.py -> build/lib.linux-armv7l-cpython-311/pytrimal/tests
2023-09-17T22:53:07,319   copying pytrimal/tests/test_alignment.py -> build/lib.linux-armv7l-cpython-311/pytrimal/tests
2023-09-17T22:53:07,321   copying pytrimal/tests/__main__.py -> build/lib.linux-armv7l-cpython-311/pytrimal/tests
2023-09-17T22:53:07,322   running egg_info
2023-09-17T22:53:07,326   writing pytrimal.egg-info/PKG-INFO
2023-09-17T22:53:07,329   writing dependency_links to pytrimal.egg-info/dependency_links.txt
2023-09-17T22:53:07,331   writing top-level names to pytrimal.egg-info/top_level.txt
2023-09-17T22:53:07,341   reading manifest file 'pytrimal.egg-info/SOURCES.txt'
2023-09-17T22:53:07,347   reading manifest template 'MANIFEST.in'
2023-09-17T22:53:07,625   warning: no files found matching '*.pyi' under directory 'pytrimal'
2023-09-17T22:53:07,642   warning: no files found matching '*.pxd' under directory 'pytrimal'
2023-09-17T22:53:07,651   warning: no files found matching '*.h' under directory 'pytrimal'
2023-09-17T22:53:07,656   warning: no files found matching 'py.typed' under directory 'pytrimal'
2023-09-17T22:53:07,658   warning: no previously-included files matching '*.html' found under directory 'pytrimal'
2023-09-17T22:53:07,660   warning: no files found matching '*.h' under directory 'pytrimal/patch'
2023-09-17T22:53:07,661   warning: no files found matching '*.pxd' under directory 'pytrimal/patch'
2023-09-17T22:53:07,661   adding license file 'COPYING'
2023-09-17T22:53:07,673   writing manifest file 'pytrimal.egg-info/SOURCES.txt'
2023-09-17T22:53:07,675   /tmp/pip-build-env-4j5t91yl/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'pytrimal.patch' is absent from the `packages` configuration.
2023-09-17T22:53:07,676   !!

2023-09-17T22:53:07,677           ********************************************************************************
2023-09-17T22:53:07,678           ############################
2023-09-17T22:53:07,678           # Package would be ignored #
2023-09-17T22:53:07,679           ############################
2023-09-17T22:53:07,680           Python recognizes 'pytrimal.patch' as an importable package[^1],
2023-09-17T22:53:07,680           but it is absent from setuptools' `packages` configuration.

2023-09-17T22:53:07,681           This leads to an ambiguous overall configuration. If you want to distribute this
2023-09-17T22:53:07,681           package, please make sure that 'pytrimal.patch' is explicitly added
2023-09-17T22:53:07,682           to the `packages` configuration field.

2023-09-17T22:53:07,683           Alternatively, you can also rely on setuptools' discovery methods
2023-09-17T22:53:07,683           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-09-17T22:53:07,684           instead of `find_packages(...)`/`find:`).

2023-09-17T22:53:07,685           You can read more about "package discovery" on setuptools documentation page:

2023-09-17T22:53:07,686           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-09-17T22:53:07,688           If you don't want 'pytrimal.patch' to be distributed and are
2023-09-17T22:53:07,688           already explicitly excluding 'pytrimal.patch' via
2023-09-17T22:53:07,689           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-09-17T22:53:07,690           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-09-17T22:53:07,690           combination with a more fine grained `package-data` configuration.

2023-09-17T22:53:07,691           You can read more about "package data files" on setuptools documentation page:

2023-09-17T22:53:07,692           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-09-17T22:53:07,694           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-09-17T22:53:07,694                 even if it does not contain any `.py` files.
2023-09-17T22:53:07,694                 On the other hand, currently there is no concept of package data
2023-09-17T22:53:07,695                 directory, all directories are treated like packages.
2023-09-17T22:53:07,695           ********************************************************************************

2023-09-17T22:53:07,696   !!
2023-09-17T22:53:07,697     check.warn(importable)
2023-09-17T22:53:07,697   /tmp/pip-build-env-4j5t91yl/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'pytrimal.tests.data' is absent from the `packages` configuration.
2023-09-17T22:53:07,699   !!

2023-09-17T22:53:07,700           ********************************************************************************
2023-09-17T22:53:07,701           ############################
2023-09-17T22:53:07,702           # Package would be ignored #
2023-09-17T22:53:07,702           ############################
2023-09-17T22:53:07,702           Python recognizes 'pytrimal.tests.data' as an importable package[^1],
2023-09-17T22:53:07,703           but it is absent from setuptools' `packages` configuration.

2023-09-17T22:53:07,707           This leads to an ambiguous overall configuration. If you want to distribute this
2023-09-17T22:53:07,708           package, please make sure that 'pytrimal.tests.data' is explicitly added
2023-09-17T22:53:07,709           to the `packages` configuration field.

2023-09-17T22:53:07,712           Alternatively, you can also rely on setuptools' discovery methods
2023-09-17T22:53:07,712           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-09-17T22:53:07,713           instead of `find_packages(...)`/`find:`).

2023-09-17T22:53:07,717           You can read more about "package discovery" on setuptools documentation page:

2023-09-17T22:53:07,719           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-09-17T22:53:07,720           If you don't want 'pytrimal.tests.data' to be distributed and are
2023-09-17T22:53:07,720           already explicitly excluding 'pytrimal.tests.data' via
2023-09-17T22:53:07,721           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-09-17T22:53:07,721           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-09-17T22:53:07,722           combination with a more fine grained `package-data` configuration.

2023-09-17T22:53:07,725           You can read more about "package data files" on setuptools documentation page:

2023-09-17T22:53:07,727           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-09-17T22:53:07,729           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-09-17T22:53:07,729                 even if it does not contain any `.py` files.
2023-09-17T22:53:07,730                 On the other hand, currently there is no concept of package data
2023-09-17T22:53:07,731                 directory, all directories are treated like packages.
2023-09-17T22:53:07,731           ********************************************************************************

2023-09-17T22:53:07,733   !!
2023-09-17T22:53:07,734     check.warn(importable)
2023-09-17T22:53:07,735   copying pytrimal/_trimal.pyx -> build/lib.linux-armv7l-cpython-311/pytrimal
2023-09-17T22:53:07,736   creating build/lib.linux-armv7l-cpython-311/pytrimal/patch
2023-09-17T22:53:07,737   copying pytrimal/patch/reportsystem.cpp -> build/lib.linux-armv7l-cpython-311/pytrimal/patch
2023-09-17T22:53:07,737   copying pytrimal/tests/requirements.txt -> build/lib.linux-armv7l-cpython-311/pytrimal/tests
2023-09-17T22:53:07,738   creating build/lib.linux-armv7l-cpython-311/pytrimal/tests/data
2023-09-17T22:53:07,738   copying pytrimal/tests/data/ENOG411BWBU.automated1.fasta -> build/lib.linux-armv7l-cpython-311/pytrimal/tests/data
2023-09-17T22:53:07,739   copying pytrimal/tests/data/ENOG411BWBU.cons40.gt40.fasta -> build/lib.linux-armv7l-cpython-311/pytrimal/tests/data
2023-09-17T22:53:07,739   copying pytrimal/tests/data/ENOG411BWBU.cons60.gt90.fasta -> build/lib.linux-armv7l-cpython-311/pytrimal/tests/data
2023-09-17T22:53:07,740   copying pytrimal/tests/data/ENOG411BWBU.fasta -> build/lib.linux-armv7l-cpython-311/pytrimal/tests/data
2023-09-17T22:53:07,743   copying pytrimal/tests/data/ENOG411BWBU.gappyout.fasta -> build/lib.linux-armv7l-cpython-311/pytrimal/tests/data
2023-09-17T22:53:07,744   copying pytrimal/tests/data/ENOG411BWBU.id50.fasta -> build/lib.linux-armv7l-cpython-311/pytrimal/tests/data
2023-09-17T22:53:07,744   copying pytrimal/tests/data/ENOG411BWBU.id70.fasta -> build/lib.linux-armv7l-cpython-311/pytrimal/tests/data
2023-09-17T22:53:07,745   copying pytrimal/tests/data/ENOG411BWBU.noallgaps.fasta -> build/lib.linux-armv7l-cpython-311/pytrimal/tests/data
2023-09-17T22:53:07,745   copying pytrimal/tests/data/ENOG411BWBU.strict.fasta -> build/lib.linux-armv7l-cpython-311/pytrimal/tests/data
2023-09-17T22:53:07,750   copying pytrimal/tests/data/ENOG411BWBU.strictplus.fasta -> build/lib.linux-armv7l-cpython-311/pytrimal/tests/data
2023-09-17T22:53:07,754   copying pytrimal/tests/data/__init__.py -> build/lib.linux-armv7l-cpython-311/pytrimal/tests/data
2023-09-17T22:53:07,756   copying pytrimal/tests/data/example.001.AA.clw -> build/lib.linux-armv7l-cpython-311/pytrimal/tests/data
2023-09-17T22:53:07,758   copying pytrimal/tests/data/halorhodopsin.afa -> build/lib.linux-armv7l-cpython-311/pytrimal/tests/data
2023-09-17T22:53:07,763   running build_clib
2023-09-17T22:53:07,767   creating build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,768   generating build/temp.linux-armv7l-cpython-311/libtrimal.a from vendor/trimal/source/Cleaner.cpp, vendor/trimal/source/Alignment/Alignment.cpp, vendor/trimal/source/Alignment/sequencesMatrix.cpp, vendor/trimal/source/Statistics/similarityMatrix.cpp, vendor/trimal/source/Statistics/Mold.cpp, vendor/trimal/source/Statistics/Gaps.cpp, vendor/trimal/source/Statistics/Manager.cpp, vendor/trimal/source/Statistics/Similarity.cpp, vendor/trimal/source/Statistics/Consistency.cpp, vendor/trimal/source/reportMessages/errorMessages.cpp, vendor/trimal/source/reportMessages/infoMessages.cpp, vendor/trimal/source/reportMessages/warningMessages.cpp, vendor/trimal/source/FormatHandling/phylip_paml_state.cpp, vendor/trimal/source/FormatHandling/fasta_m10_state.cpp, vendor/trimal/source/FormatHandling/fasta_state.cpp, vendor/trimal/source/FormatHandling/htmlreport_state.cpp, vendor/trimal/source/FormatHandling/mega_sequential_state.cpp, vendor/trimal/source/FormatHandling/nexus_m10_state.cpp, vendor/trimal/source/FormatHandling/pir_state.cpp, vendor/trimal/source/FormatHandling/clustal_state.cpp, vendor/trimal/source/FormatHandling/phylip40_m10_state.cpp, vendor/trimal/source/FormatHandling/phylip32_m10_state.cpp, vendor/trimal/source/FormatHandling/phylip40_state.cpp, vendor/trimal/source/FormatHandling/phylip32_state.cpp, vendor/trimal/source/FormatHandling/nexus_state.cpp, vendor/trimal/source/FormatHandling/phylip_paml_m10_state.cpp, vendor/trimal/source/FormatHandling/mega_interleaved_state.cpp, vendor/trimal/source/FormatHandling/BaseFormatHandler.cpp, vendor/trimal/source/utils.cpp, vendor/trimal/source/InternalBenchmarker.cpp, vendor/trimal/source/trimalManager.cpp, vendor/trimal/source/VCFHandler.cpp
2023-09-17T22:53:07,769   building trimal with unix compiler
2023-09-17T22:53:07,770   generating build/temp.linux-armv7l-cpython-311/defines.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/defines.h
2023-09-17T22:53:07,771   generating build/temp.linux-armv7l-cpython-311/trimalManager.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/trimalManager.h
2023-09-17T22:53:07,774   generating build/temp.linux-armv7l-cpython-311/VCFHandler.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/VCFHandler.h
2023-09-17T22:53:07,776   generating build/temp.linux-armv7l-cpython-311/reportsystem.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/reportsystem.h
2023-09-17T22:53:07,779   generating build/temp.linux-armv7l-cpython-311/values.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/values.h
2023-09-17T22:53:07,781   generating build/temp.linux-armv7l-cpython-311/InternalBenchmarker.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/InternalBenchmarker.h
2023-09-17T22:53:07,783   generating build/temp.linux-armv7l-cpython-311/utils.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/utils.h
2023-09-17T22:53:07,786   generating build/temp.linux-armv7l-cpython-311/Cleaner.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/Cleaner.h
2023-09-17T22:53:07,789   creating build/temp.linux-armv7l-cpython-311/FormatHandling
2023-09-17T22:53:07,790   generating build/temp.linux-armv7l-cpython-311/FormatHandling/phylip_paml_m10_state.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/FormatHandling/phylip_paml_m10_state.h
2023-09-17T22:53:07,792   generating build/temp.linux-armv7l-cpython-311/FormatHandling/phylip32_m10_state.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/FormatHandling/phylip32_m10_state.h
2023-09-17T22:53:07,794   generating build/temp.linux-armv7l-cpython-311/FormatHandling/FormatManager.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/FormatHandling/FormatManager.h
2023-09-17T22:53:07,796   generating build/temp.linux-armv7l-cpython-311/FormatHandling/nexus_state.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/FormatHandling/nexus_state.h
2023-09-17T22:53:07,798   generating build/temp.linux-armv7l-cpython-311/FormatHandling/mega_sequential_state.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/FormatHandling/mega_sequential_state.h
2023-09-17T22:53:07,800   generating build/temp.linux-armv7l-cpython-311/FormatHandling/phylip40_state.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/FormatHandling/phylip40_state.h
2023-09-17T22:53:07,802   generating build/temp.linux-armv7l-cpython-311/FormatHandling/nexus_m10_state.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/FormatHandling/nexus_m10_state.h
2023-09-17T22:53:07,804   generating build/temp.linux-armv7l-cpython-311/FormatHandling/pir_state.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/FormatHandling/pir_state.h
2023-09-17T22:53:07,806   generating build/temp.linux-armv7l-cpython-311/FormatHandling/htmlreport_state.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/FormatHandling/htmlreport_state.h
2023-09-17T22:53:07,808   generating build/temp.linux-armv7l-cpython-311/FormatHandling/phylip32_state.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/FormatHandling/phylip32_state.h
2023-09-17T22:53:07,809   generating build/temp.linux-armv7l-cpython-311/FormatHandling/BaseFormatHandler.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/FormatHandling/BaseFormatHandler.h
2023-09-17T22:53:07,812   generating build/temp.linux-armv7l-cpython-311/FormatHandling/fasta_state.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/FormatHandling/fasta_state.h
2023-09-17T22:53:07,814   generating build/temp.linux-armv7l-cpython-311/FormatHandling/mega_interleaved_state.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/FormatHandling/mega_interleaved_state.h
2023-09-17T22:53:07,815   generating build/temp.linux-armv7l-cpython-311/FormatHandling/clustal_state.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/FormatHandling/clustal_state.h
2023-09-17T22:53:07,817   generating build/temp.linux-armv7l-cpython-311/FormatHandling/phylip_paml_state.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/FormatHandling/phylip_paml_state.h
2023-09-17T22:53:07,819   generating build/temp.linux-armv7l-cpython-311/FormatHandling/formats_header.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/FormatHandling/formats_header.h
2023-09-17T22:53:07,821   generating build/temp.linux-armv7l-cpython-311/FormatHandling/phylip40_m10_state.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/FormatHandling/phylip40_m10_state.h
2023-09-17T22:53:07,822   generating build/temp.linux-armv7l-cpython-311/FormatHandling/fasta_m10_state.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/FormatHandling/fasta_m10_state.h
2023-09-17T22:53:07,824   creating build/temp.linux-armv7l-cpython-311/Statistics
2023-09-17T22:53:07,825   generating build/temp.linux-armv7l-cpython-311/Statistics/Gaps.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/Statistics/Gaps.h
2023-09-17T22:53:07,827   generating build/temp.linux-armv7l-cpython-311/Statistics/similarityMatrix.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/Statistics/similarityMatrix.h
2023-09-17T22:53:07,830   generating build/temp.linux-armv7l-cpython-311/Statistics/Consistency.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/Statistics/Consistency.h
2023-09-17T22:53:07,832   generating build/temp.linux-armv7l-cpython-311/Statistics/Similarity.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/Statistics/Similarity.h
2023-09-17T22:53:07,834   generating build/temp.linux-armv7l-cpython-311/Statistics/Mold.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/Statistics/Mold.h
2023-09-17T22:53:07,836   generating build/temp.linux-armv7l-cpython-311/Statistics/Manager.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/Statistics/Manager.h
2023-09-17T22:53:07,839   creating build/temp.linux-armv7l-cpython-311/Alignment
2023-09-17T22:53:07,840   generating build/temp.linux-armv7l-cpython-311/Alignment/sequencesMatrix.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/Alignment/sequencesMatrix.h
2023-09-17T22:53:07,842   generating build/temp.linux-armv7l-cpython-311/Alignment/Alignment.h from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/Alignment/Alignment.h
2023-09-17T22:53:07,844   creating build/temp.linux-armv7l-cpython-311/RawText
2023-09-17T22:53:07,846   generating build/temp.linux-armv7l-cpython-311/RawText/examples.txt from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/RawText/examples.txt
2023-09-17T22:53:07,848   generating build/temp.linux-armv7l-cpython-311/RawText/legacyMenu.txt from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/RawText/legacyMenu.txt
2023-09-17T22:53:07,850   generating build/temp.linux-armv7l-cpython-311/RawText/menu.txt from /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e/vendor/trimal/include/RawText/menu.txt
2023-09-17T22:53:07,853   generating build/temp.linux-armv7l-cpython-311/Cleaner.cpp from vendor/trimal/source/Cleaner.cpp
2023-09-17T22:53:07,854   copying vendor/trimal/source/Cleaner.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,858   generating build/temp.linux-armv7l-cpython-311/Alignment.cpp from vendor/trimal/source/Alignment/Alignment.cpp
2023-09-17T22:53:07,858   copying vendor/trimal/source/Alignment/Alignment.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,861   generating build/temp.linux-armv7l-cpython-311/sequencesMatrix.cpp from vendor/trimal/source/Alignment/sequencesMatrix.cpp
2023-09-17T22:53:07,862   copying vendor/trimal/source/Alignment/sequencesMatrix.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,864   generating build/temp.linux-armv7l-cpython-311/similarityMatrix.cpp from vendor/trimal/source/Statistics/similarityMatrix.cpp
2023-09-17T22:53:07,864   copying vendor/trimal/source/Statistics/similarityMatrix.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,866   generating build/temp.linux-armv7l-cpython-311/Mold.cpp from vendor/trimal/source/Statistics/Mold.cpp
2023-09-17T22:53:07,867   copying vendor/trimal/source/Statistics/Mold.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,869   generating build/temp.linux-armv7l-cpython-311/Gaps.cpp from vendor/trimal/source/Statistics/Gaps.cpp
2023-09-17T22:53:07,869   copying vendor/trimal/source/Statistics/Gaps.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,871   generating build/temp.linux-armv7l-cpython-311/Manager.cpp from vendor/trimal/source/Statistics/Manager.cpp
2023-09-17T22:53:07,872   copying vendor/trimal/source/Statistics/Manager.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,874   generating build/temp.linux-armv7l-cpython-311/Similarity.cpp from vendor/trimal/source/Statistics/Similarity.cpp
2023-09-17T22:53:07,874   copying vendor/trimal/source/Statistics/Similarity.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,877   generating build/temp.linux-armv7l-cpython-311/Consistency.cpp from vendor/trimal/source/Statistics/Consistency.cpp
2023-09-17T22:53:07,877   copying vendor/trimal/source/Statistics/Consistency.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,879   generating build/temp.linux-armv7l-cpython-311/errorMessages.cpp from vendor/trimal/source/reportMessages/errorMessages.cpp
2023-09-17T22:53:07,880   copying vendor/trimal/source/reportMessages/errorMessages.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,882   generating build/temp.linux-armv7l-cpython-311/infoMessages.cpp from vendor/trimal/source/reportMessages/infoMessages.cpp
2023-09-17T22:53:07,883   copying vendor/trimal/source/reportMessages/infoMessages.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,884   generating build/temp.linux-armv7l-cpython-311/warningMessages.cpp from vendor/trimal/source/reportMessages/warningMessages.cpp
2023-09-17T22:53:07,885   copying vendor/trimal/source/reportMessages/warningMessages.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,886   generating build/temp.linux-armv7l-cpython-311/phylip_paml_state.cpp from vendor/trimal/source/FormatHandling/phylip_paml_state.cpp
2023-09-17T22:53:07,887   copying vendor/trimal/source/FormatHandling/phylip_paml_state.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,888   generating build/temp.linux-armv7l-cpython-311/fasta_m10_state.cpp from vendor/trimal/source/FormatHandling/fasta_m10_state.cpp
2023-09-17T22:53:07,889   copying vendor/trimal/source/FormatHandling/fasta_m10_state.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,891   generating build/temp.linux-armv7l-cpython-311/fasta_state.cpp from vendor/trimal/source/FormatHandling/fasta_state.cpp
2023-09-17T22:53:07,891   copying vendor/trimal/source/FormatHandling/fasta_state.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,893   generating build/temp.linux-armv7l-cpython-311/htmlreport_state.cpp from vendor/trimal/source/FormatHandling/htmlreport_state.cpp
2023-09-17T22:53:07,894   copying vendor/trimal/source/FormatHandling/htmlreport_state.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,896   generating build/temp.linux-armv7l-cpython-311/mega_sequential_state.cpp from vendor/trimal/source/FormatHandling/mega_sequential_state.cpp
2023-09-17T22:53:07,896   copying vendor/trimal/source/FormatHandling/mega_sequential_state.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,898   generating build/temp.linux-armv7l-cpython-311/nexus_m10_state.cpp from vendor/trimal/source/FormatHandling/nexus_m10_state.cpp
2023-09-17T22:53:07,898   copying vendor/trimal/source/FormatHandling/nexus_m10_state.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,900   generating build/temp.linux-armv7l-cpython-311/pir_state.cpp from vendor/trimal/source/FormatHandling/pir_state.cpp
2023-09-17T22:53:07,901   copying vendor/trimal/source/FormatHandling/pir_state.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,903   generating build/temp.linux-armv7l-cpython-311/clustal_state.cpp from vendor/trimal/source/FormatHandling/clustal_state.cpp
2023-09-17T22:53:07,903   copying vendor/trimal/source/FormatHandling/clustal_state.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,905   generating build/temp.linux-armv7l-cpython-311/phylip40_m10_state.cpp from vendor/trimal/source/FormatHandling/phylip40_m10_state.cpp
2023-09-17T22:53:07,905   copying vendor/trimal/source/FormatHandling/phylip40_m10_state.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,907   generating build/temp.linux-armv7l-cpython-311/phylip32_m10_state.cpp from vendor/trimal/source/FormatHandling/phylip32_m10_state.cpp
2023-09-17T22:53:07,908   copying vendor/trimal/source/FormatHandling/phylip32_m10_state.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,910   generating build/temp.linux-armv7l-cpython-311/phylip40_state.cpp from vendor/trimal/source/FormatHandling/phylip40_state.cpp
2023-09-17T22:53:07,911   copying vendor/trimal/source/FormatHandling/phylip40_state.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,912   generating build/temp.linux-armv7l-cpython-311/phylip32_state.cpp from vendor/trimal/source/FormatHandling/phylip32_state.cpp
2023-09-17T22:53:07,913   copying vendor/trimal/source/FormatHandling/phylip32_state.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,915   generating build/temp.linux-armv7l-cpython-311/nexus_state.cpp from vendor/trimal/source/FormatHandling/nexus_state.cpp
2023-09-17T22:53:07,916   copying vendor/trimal/source/FormatHandling/nexus_state.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,918   generating build/temp.linux-armv7l-cpython-311/phylip_paml_m10_state.cpp from vendor/trimal/source/FormatHandling/phylip_paml_m10_state.cpp
2023-09-17T22:53:07,918   copying vendor/trimal/source/FormatHandling/phylip_paml_m10_state.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,920   generating build/temp.linux-armv7l-cpython-311/mega_interleaved_state.cpp from vendor/trimal/source/FormatHandling/mega_interleaved_state.cpp
2023-09-17T22:53:07,920   copying vendor/trimal/source/FormatHandling/mega_interleaved_state.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,922   generating build/temp.linux-armv7l-cpython-311/BaseFormatHandler.cpp from vendor/trimal/source/FormatHandling/BaseFormatHandler.cpp
2023-09-17T22:53:07,923   copying vendor/trimal/source/FormatHandling/BaseFormatHandler.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,925   generating build/temp.linux-armv7l-cpython-311/utils.cpp from vendor/trimal/source/utils.cpp
2023-09-17T22:53:07,926   copying vendor/trimal/source/utils.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,928   generating build/temp.linux-armv7l-cpython-311/InternalBenchmarker.cpp from vendor/trimal/source/InternalBenchmarker.cpp
2023-09-17T22:53:07,928   copying vendor/trimal/source/InternalBenchmarker.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,930   generating build/temp.linux-armv7l-cpython-311/trimalManager.cpp from vendor/trimal/source/trimalManager.cpp
2023-09-17T22:53:07,931   copying vendor/trimal/source/trimalManager.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,934   generating build/temp.linux-armv7l-cpython-311/VCFHandler.cpp from vendor/trimal/source/VCFHandler.cpp
2023-09-17T22:53:07,935   copying vendor/trimal/source/VCFHandler.cpp -> build/temp.linux-armv7l-cpython-311
2023-09-17T22:53:07,938   generating build/temp.linux-armv7l-cpython-311/Cleaner.o from build/temp.linux-armv7l-cpython-311/Cleaner.cpp
2023-09-17T22:53:07,938   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/Cleaner.cpp -o build/temp.linux-armv7l-cpython-311/Cleaner.o
2023-09-17T22:53:08,363   build/temp.linux-armv7l-cpython-311/Cleaner.cpp:1449: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
2023-09-17T22:53:08,364    1449 |     #pragma omp parallel for num_threads(NUMTHREADS) if(alig->originalNumberOfSequences>MINPARALLELSIZE)
2023-09-17T22:53:08,364         |
2023-09-17T22:53:08,365   build/temp.linux-armv7l-cpython-311/Cleaner.cpp:1457: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
2023-09-17T22:53:08,366    1457 |     #pragma omp parallel for num_threads(NUMTHREADS) private(j, k, hit, dst) if(alig->originalNumberOfSequences>MINPARALLELSIZE)
2023-09-17T22:53:08,366         |
2023-09-17T22:53:10,087   build/temp.linux-armv7l-cpython-311/Cleaner.cpp: In member function ‘Alignment* Cleaner::cleanStrict(int, const int*, float, const float*, bool, bool)’:
2023-09-17T22:53:10,088   build/temp.linux-armv7l-cpython-311/Cleaner.cpp:519:12: warning: unused variable ‘x’ [-Wunused-variable]
2023-09-17T22:53:10,088     519 |     int i, x, pos, counter, lenBlock;
2023-09-17T22:53:10,089         |            ^
2023-09-17T22:53:10,108   build/temp.linux-armv7l-cpython-311/Cleaner.cpp: In member function ‘Alignment* Cleaner::getClustering(float)’:
2023-09-17T22:53:10,109   build/temp.linux-armv7l-cpython-311/Cleaner.cpp:1217:12: warning: unused variable ‘j’ [-Wunused-variable]
2023-09-17T22:53:10,109    1217 |     int i, j, *clustering;
2023-09-17T22:53:10,110         |            ^
2023-09-17T22:53:10,115   build/temp.linux-armv7l-cpython-311/Cleaner.cpp: In member function ‘void Cleaner::removeAllGapsSeqsAndCols(bool, bool)’:
2023-09-17T22:53:10,116   build/temp.linux-armv7l-cpython-311/Cleaner.cpp:1382:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:53:10,117    1382 |             for (j = 0; j < alig->sequences[i].length(); j++) {
2023-09-17T22:53:10,118         |                         ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-17T22:53:10,118   build/temp.linux-armv7l-cpython-311/Cleaner.cpp:1393:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:53:10,119    1393 |             if (j == alig->sequences[i].length()) {
2023-09-17T22:53:10,120         |                 ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-17T22:53:14,753   generating build/temp.linux-armv7l-cpython-311/Alignment.o from build/temp.linux-armv7l-cpython-311/Alignment.cpp
2023-09-17T22:53:14,754   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/Alignment.cpp -o build/temp.linux-armv7l-cpython-311/Alignment.o
2023-09-17T22:53:15,140   build/temp.linux-armv7l-cpython-311/Alignment.cpp:395: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
2023-09-17T22:53:15,141     395 |     #pragma omp parallel for num_threads(NUMTHREADS) if(numberOfSequences>MINPARALLELSIZE)
2023-09-17T22:53:15,141         |
2023-09-17T22:53:15,141   build/temp.linux-armv7l-cpython-311/Alignment.cpp:398: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
2023-09-17T22:53:15,142     398 |     #pragma omp parallel for num_threads(NUMTHREADS) collapse(2) private(k, shared, referenceLength) if(numberOfSequences>MINPARALLELSIZE)
2023-09-17T22:53:15,142         |
2023-09-17T22:53:15,143   build/temp.linux-armv7l-cpython-311/Alignment.cpp:930: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
2023-09-17T22:53:15,143     930 |     #pragma omp parallel for private(k, mx, avg, pos) reduction(+: avgSeq, maxAvgSeq) num_threads(NUMTHREADS) if(originalNumberOfSequences>MINPARALLELSIZE)
2023-09-17T22:53:15,144         |
2023-09-17T22:53:16,840   build/temp.linux-armv7l-cpython-311/Alignment.cpp: In member function ‘Alignment* Alignment::getTranslationCDS(Alignment*)’:
2023-09-17T22:53:16,841   build/temp.linux-armv7l-cpython-311/Alignment.cpp:204:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:53:16,841     204 |         for (y = 0, counter = 0; y < ProtAlig->sequences[x].size(); y++) {
2023-09-17T22:53:16,842         |                                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-17T22:53:16,858   build/temp.linux-armv7l-cpython-311/Alignment.cpp: In member function ‘bool Alignment::prepareCodingSequence(bool, bool, Alignment*)’:
2023-09-17T22:53:16,858   build/temp.linux-armv7l-cpython-311/Alignment.cpp:614:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const std::__cxx11::basic_string<char>::size_type’ {aka ‘const unsigned int’} [-Wsign-compare]
2023-09-17T22:53:16,859     614 |             if ((found != string::npos) && (((int) found % 3) == 0)) {
2023-09-17T22:53:16,860         |                  ~~~~~~^~~~~~~~~~~~~~~
2023-09-17T22:53:16,862   build/temp.linux-armv7l-cpython-311/Alignment.cpp:641:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const std::__cxx11::basic_string<char>::size_type’ {aka ‘const unsigned int’} [-Wsign-compare]
2023-09-17T22:53:16,863     641 |         } while (found != string::npos);
2023-09-17T22:53:16,864         |                  ~~~~~~^~~~~~~~~~~~~~~
2023-09-17T22:53:16,865   build/temp.linux-armv7l-cpython-311/Alignment.cpp:651:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const std::__cxx11::basic_string<char>::size_type’ {aka ‘const unsigned int’} [-Wsign-compare]
2023-09-17T22:53:16,865     651 |             if ((found != string::npos) && (((int) found % 3) == 0)) {
2023-09-17T22:53:16,866         |                  ~~~~~~^~~~~~~~~~~~~~~
2023-09-17T22:53:16,868   build/temp.linux-armv7l-cpython-311/Alignment.cpp:676:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const std::__cxx11::basic_string<char>::size_type’ {aka ‘const unsigned int’} [-Wsign-compare]
2023-09-17T22:53:16,869     676 |         } while (found != string::npos);
2023-09-17T22:53:16,869         |                  ~~~~~~^~~~~~~~~~~~~~~
2023-09-17T22:53:16,870   build/temp.linux-armv7l-cpython-311/Alignment.cpp:685:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const std::__cxx11::basic_string<char>::size_type’ {aka ‘const unsigned int’} [-Wsign-compare]
2023-09-17T22:53:16,871     685 |             if ((found != string::npos) && (((int) found % 3) == 0)) {
2023-09-17T22:53:16,872         |                  ~~~~~~^~~~~~~~~~~~~~~
2023-09-17T22:53:16,874   build/temp.linux-armv7l-cpython-311/Alignment.cpp:711:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const std::__cxx11::basic_string<char>::size_type’ {aka ‘const unsigned int’} [-Wsign-compare]
2023-09-17T22:53:16,874     711 |         } while (found != string::npos);
2023-09-17T22:53:16,875         |                  ~~~~~~^~~~~~~~~~~~~~~
2023-09-17T22:53:16,885   build/temp.linux-armv7l-cpython-311/Alignment.cpp: In member function ‘bool Alignment::fillMatrices(bool, bool)’:
2023-09-17T22:53:16,886   build/temp.linux-armv7l-cpython-311/Alignment.cpp:810:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:53:16,886     810 |             for (j = 0; j < sequences[i].length(); j++)
2023-09-17T22:53:16,887         |                         ~~^~~~~~~~~~~~~~~~~~~~~~~
2023-09-17T22:53:16,889   build/temp.linux-armv7l-cpython-311/Alignment.cpp:837:35: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-17T22:53:16,889     837 |         if (sequences[i].length() != numberOfResidues) {
2023-09-17T22:53:16,890         |             ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
2023-09-17T22:53:16,892   build/temp.linux-armv7l-cpython-311/Alignment.cpp: In member function ‘void Alignment::printAlignmentInfo(std::ostream&)’:
2023-09-17T22:53:16,893   build/temp.linux-armv7l-cpython-311/Alignment.cpp:889:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:53:16,893     889 |         for (j = 0, valid_res = 0; j < sequences[i].length(); j++)
2023-09-17T22:53:16,894         |                                    ~~^~~~~~~~~~~~~~~~~~~~~~~
2023-09-17T22:53:29,731   generating build/temp.linux-armv7l-cpython-311/sequencesMatrix.o from build/temp.linux-armv7l-cpython-311/sequencesMatrix.cpp
2023-09-17T22:53:29,731   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/sequencesMatrix.cpp -o build/temp.linux-armv7l-cpython-311/sequencesMatrix.o
2023-09-17T22:53:32,218   generating build/temp.linux-armv7l-cpython-311/similarityMatrix.o from build/temp.linux-armv7l-cpython-311/similarityMatrix.cpp
2023-09-17T22:53:32,219   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/similarityMatrix.cpp -o build/temp.linux-armv7l-cpython-311/similarityMatrix.o
2023-09-17T22:53:35,058   generating build/temp.linux-armv7l-cpython-311/Mold.o from build/temp.linux-armv7l-cpython-311/Mold.cpp
2023-09-17T22:53:35,059   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/Mold.cpp -o build/temp.linux-armv7l-cpython-311/Mold.o
2023-09-17T22:53:39,034   generating build/temp.linux-armv7l-cpython-311/Gaps.o from build/temp.linux-armv7l-cpython-311/Gaps.cpp
2023-09-17T22:53:39,035   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/Gaps.cpp -o build/temp.linux-armv7l-cpython-311/Gaps.o
2023-09-17T22:53:43,366   generating build/temp.linux-armv7l-cpython-311/Manager.o from build/temp.linux-armv7l-cpython-311/Manager.cpp
2023-09-17T22:53:43,367   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/Manager.cpp -o build/temp.linux-armv7l-cpython-311/Manager.o
2023-09-17T22:53:45,620   generating build/temp.linux-armv7l-cpython-311/Similarity.o from build/temp.linux-armv7l-cpython-311/Similarity.cpp
2023-09-17T22:53:45,620   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/Similarity.cpp -o build/temp.linux-armv7l-cpython-311/Similarity.o
2023-09-17T22:53:45,972   build/temp.linux-armv7l-cpython-311/Similarity.cpp:115: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
2023-09-17T22:53:45,972     115 |         #pragma omp parallel for num_threads(NUMTHREADS) if(alig->originalNumberOfSequences>MINPARALLELSIZE)
2023-09-17T22:53:45,973         |
2023-09-17T22:53:45,973   build/temp.linux-armv7l-cpython-311/Similarity.cpp:124: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
2023-09-17T22:53:45,974     124 |         #pragma omp parallel for num_threads(NUMTHREADS) private(j, k, sum, length) if(alig->originalNumberOfSequences>MINPARALLELSIZE)
2023-09-17T22:53:45,974         |
2023-09-17T22:53:50,162   generating build/temp.linux-armv7l-cpython-311/Consistency.o from build/temp.linux-armv7l-cpython-311/Consistency.cpp
2023-09-17T22:53:50,163   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/Consistency.cpp -o build/temp.linux-armv7l-cpython-311/Consistency.o
2023-09-17T22:53:56,224   generating build/temp.linux-armv7l-cpython-311/errorMessages.o from build/temp.linux-armv7l-cpython-311/errorMessages.cpp
2023-09-17T22:53:56,224   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/errorMessages.cpp -o build/temp.linux-armv7l-cpython-311/errorMessages.o
2023-09-17T22:53:58,512   generating build/temp.linux-armv7l-cpython-311/infoMessages.o from build/temp.linux-armv7l-cpython-311/infoMessages.cpp
2023-09-17T22:53:58,513   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/infoMessages.cpp -o build/temp.linux-armv7l-cpython-311/infoMessages.o
2023-09-17T22:54:00,419   generating build/temp.linux-armv7l-cpython-311/warningMessages.o from build/temp.linux-armv7l-cpython-311/warningMessages.cpp
2023-09-17T22:54:00,420   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/warningMessages.cpp -o build/temp.linux-armv7l-cpython-311/warningMessages.o
2023-09-17T22:54:02,351   generating build/temp.linux-armv7l-cpython-311/phylip_paml_state.o from build/temp.linux-armv7l-cpython-311/phylip_paml_state.cpp
2023-09-17T22:54:02,352   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/phylip_paml_state.cpp -o build/temp.linux-armv7l-cpython-311/phylip_paml_state.o
2023-09-17T22:54:05,107   generating build/temp.linux-armv7l-cpython-311/fasta_m10_state.o from build/temp.linux-armv7l-cpython-311/fasta_m10_state.cpp
2023-09-17T22:54:05,108   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/fasta_m10_state.cpp -o build/temp.linux-armv7l-cpython-311/fasta_m10_state.o
2023-09-17T22:54:07,014   build/temp.linux-armv7l-cpython-311/fasta_m10_state.cpp: In member function ‘virtual bool FormatHandling::fasta_m10_state::SaveAlignment(const Alignment&, std::ostream*)’:
2023-09-17T22:54:07,015   build/temp.linux-armv7l-cpython-311/fasta_m10_state.cpp:95:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:54:07,016      95 |         for (j = 0, k = 0; j < alignment.sequences[i].length(); j++)
2023-09-17T22:54:07,016         |                            ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-17T22:54:07,017   build/temp.linux-armv7l-cpython-311/fasta_m10_state.cpp:99:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:54:07,018      99 |                 if (!lastcharIsnewline && j == alignment.sequences[i].length() -1 )
2023-09-17T22:54:07,018         |                                           ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-17T22:54:07,019   build/temp.linux-armv7l-cpython-311/fasta_m10_state.cpp:110:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:54:07,020     110 |                 if ((k % 60 == 0 || j == alignment.sequences[i].length() - 1))
2023-09-17T22:54:07,021         |                                     ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-17T22:54:07,779   generating build/temp.linux-armv7l-cpython-311/fasta_state.o from build/temp.linux-armv7l-cpython-311/fasta_state.cpp
2023-09-17T22:54:07,779   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/fasta_state.cpp -o build/temp.linux-armv7l-cpython-311/fasta_state.o
2023-09-17T22:54:09,674   build/temp.linux-armv7l-cpython-311/fasta_state.cpp: In member function ‘virtual bool FormatHandling::fasta_state::SaveAlignment(const Alignment&, std::ostream*)’:
2023-09-17T22:54:09,675   build/temp.linux-armv7l-cpython-311/fasta_state.cpp:197:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:54:09,675     197 |         for (j = 0, k = 0; j < alignment.sequences[i].length(); j++)
2023-09-17T22:54:09,676         |                            ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-17T22:54:09,677   build/temp.linux-armv7l-cpython-311/fasta_state.cpp:201:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:54:09,678     201 |                 if (!lastcharIsnewline && j == alignment.sequences[i].length() -1 )
2023-09-17T22:54:09,679         |                                           ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-17T22:54:09,679   build/temp.linux-armv7l-cpython-311/fasta_state.cpp:212:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:54:09,680     212 |                 if (k % 60 == 0 || j == alignment.sequences[i].length() -1 )
2023-09-17T22:54:09,680         |                                    ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-17T22:54:10,647   generating build/temp.linux-armv7l-cpython-311/htmlreport_state.o from build/temp.linux-armv7l-cpython-311/htmlreport_state.cpp
2023-09-17T22:54:10,647   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/htmlreport_state.cpp -o build/temp.linux-armv7l-cpython-311/htmlreport_state.o
2023-09-17T22:54:13,226   generating build/temp.linux-armv7l-cpython-311/mega_sequential_state.o from build/temp.linux-armv7l-cpython-311/mega_sequential_state.cpp
2023-09-17T22:54:13,227   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/mega_sequential_state.cpp -o build/temp.linux-armv7l-cpython-311/mega_sequential_state.o
2023-09-17T22:54:15,133   build/temp.linux-armv7l-cpython-311/mega_sequential_state.cpp: In member function ‘virtual bool FormatHandling::mega_sequential_state::SaveAlignment(const Alignment&, std::ostream*)’:
2023-09-17T22:54:15,133   build/temp.linux-armv7l-cpython-311/mega_sequential_state.cpp:335:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:54:15,134     335 |             for(j = 0, l = 0; j < alignment.sequences[i].length(); j ++)
2023-09-17T22:54:15,135         |                               ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-17T22:54:15,137   build/temp.linux-armv7l-cpython-311/mega_sequential_state.cpp:289:15: warning: unused variable ‘k’ [-Wunused-variable]
2023-09-17T22:54:15,137     289 |     int i, j, k, l, m;
2023-09-17T22:54:15,138         |               ^
2023-09-17T22:54:15,139   build/temp.linux-armv7l-cpython-311/mega_sequential_state.cpp:289:21: warning: unused variable ‘m’ [-Wunused-variable]
2023-09-17T22:54:15,140     289 |     int i, j, k, l, m;
2023-09-17T22:54:15,140         |                     ^
2023-09-17T22:54:16,306   generating build/temp.linux-armv7l-cpython-311/nexus_m10_state.o from build/temp.linux-armv7l-cpython-311/nexus_m10_state.cpp
2023-09-17T22:54:16,307   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/nexus_m10_state.cpp -o build/temp.linux-armv7l-cpython-311/nexus_m10_state.o
2023-09-17T22:54:19,603   generating build/temp.linux-armv7l-cpython-311/pir_state.o from build/temp.linux-armv7l-cpython-311/pir_state.cpp
2023-09-17T22:54:19,603   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/pir_state.cpp -o build/temp.linux-armv7l-cpython-311/pir_state.o
2023-09-17T22:54:21,500   build/temp.linux-armv7l-cpython-311/pir_state.cpp: In member function ‘virtual bool FormatHandling::pir_state::SaveAlignment(const Alignment&, std::ostream*)’:
2023-09-17T22:54:21,501   build/temp.linux-armv7l-cpython-311/pir_state.cpp:223:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:54:21,501     223 |         for (j = 0, k = 0, l = 0; j < alignment.sequences[i].length(); j++) {
2023-09-17T22:54:21,502         |                                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-17T22:54:21,504   build/temp.linux-armv7l-cpython-311/pir_state.cpp:231:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:54:21,504     231 |                 if (j == alignment.sequences[i].length() - 1);
2023-09-17T22:54:21,505         |                     ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-17T22:54:21,507   build/temp.linux-armv7l-cpython-311/pir_state.cpp:184:18: warning: variable ‘l’ set but not used [-Wunused-but-set-variable]
2023-09-17T22:54:21,508     184 |     int i, j, k, l;
2023-09-17T22:54:21,508         |                  ^
2023-09-17T22:54:22,491   generating build/temp.linux-armv7l-cpython-311/clustal_state.o from build/temp.linux-armv7l-cpython-311/clustal_state.cpp
2023-09-17T22:54:22,491   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/clustal_state.cpp -o build/temp.linux-armv7l-cpython-311/clustal_state.o
2023-09-17T22:54:25,466   generating build/temp.linux-armv7l-cpython-311/phylip40_m10_state.o from build/temp.linux-armv7l-cpython-311/phylip40_m10_state.cpp
2023-09-17T22:54:25,467   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/phylip40_m10_state.cpp -o build/temp.linux-armv7l-cpython-311/phylip40_m10_state.o
2023-09-17T22:54:27,842   build/temp.linux-armv7l-cpython-311/phylip40_m10_state.cpp: In member function ‘virtual bool FormatHandling::phylip40_m10_state::SaveAlignment(const Alignment&, std::ostream*)’:
2023-09-17T22:54:27,843   build/temp.linux-armv7l-cpython-311/phylip40_m10_state.cpp:104:19: warning: ‘k’ may be used uninitialized [-Wmaybe-uninitialized]
2023-09-17T22:54:27,844     104 |     for (i = k; i < alignment.originalNumberOfResidues; i=k)
2023-09-17T22:54:27,844         |                 ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-17T22:54:27,845   build/temp.linux-armv7l-cpython-311/phylip40_m10_state.cpp:52:15: note: ‘k’ was declared here
2023-09-17T22:54:27,845      52 |     int i, j, k, l, maxLongName;
2023-09-17T22:54:27,846         |               ^
2023-09-17T22:54:28,209   generating build/temp.linux-armv7l-cpython-311/phylip32_m10_state.o from build/temp.linux-armv7l-cpython-311/phylip32_m10_state.cpp
2023-09-17T22:54:28,210   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/phylip32_m10_state.cpp -o build/temp.linux-armv7l-cpython-311/phylip32_m10_state.o
2023-09-17T22:54:30,865   generating build/temp.linux-armv7l-cpython-311/phylip40_state.o from build/temp.linux-armv7l-cpython-311/phylip40_state.cpp
2023-09-17T22:54:30,866   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/phylip40_state.cpp -o build/temp.linux-armv7l-cpython-311/phylip40_state.o
2023-09-17T22:54:33,954   generating build/temp.linux-armv7l-cpython-311/phylip32_state.o from build/temp.linux-armv7l-cpython-311/phylip32_state.cpp
2023-09-17T22:54:33,955   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/phylip32_state.cpp -o build/temp.linux-armv7l-cpython-311/phylip32_state.o
2023-09-17T22:54:37,002   generating build/temp.linux-armv7l-cpython-311/nexus_state.o from build/temp.linux-armv7l-cpython-311/nexus_state.cpp
2023-09-17T22:54:37,002   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/nexus_state.cpp -o build/temp.linux-armv7l-cpython-311/nexus_state.o
2023-09-17T22:54:40,550   generating build/temp.linux-armv7l-cpython-311/phylip_paml_m10_state.o from build/temp.linux-armv7l-cpython-311/phylip_paml_m10_state.cpp
2023-09-17T22:54:40,550   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/phylip_paml_m10_state.cpp -o build/temp.linux-armv7l-cpython-311/phylip_paml_m10_state.o
2023-09-17T22:54:43,133   generating build/temp.linux-armv7l-cpython-311/mega_interleaved_state.o from build/temp.linux-armv7l-cpython-311/mega_interleaved_state.cpp
2023-09-17T22:54:43,134   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/mega_interleaved_state.cpp -o build/temp.linux-armv7l-cpython-311/mega_interleaved_state.o
2023-09-17T22:54:45,935   generating build/temp.linux-armv7l-cpython-311/BaseFormatHandler.o from build/temp.linux-armv7l-cpython-311/BaseFormatHandler.cpp
2023-09-17T22:54:45,936   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/BaseFormatHandler.cpp -o build/temp.linux-armv7l-cpython-311/BaseFormatHandler.o
2023-09-17T22:54:51,926   generating build/temp.linux-armv7l-cpython-311/utils.o from build/temp.linux-armv7l-cpython-311/utils.cpp
2023-09-17T22:54:51,927   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/utils.cpp -o build/temp.linux-armv7l-cpython-311/utils.o
2023-09-17T22:54:53,589   build/temp.linux-armv7l-cpython-311/utils.cpp: In function ‘std::string utils::removeCharacter(char, std::string)’:
2023-09-17T22:54:53,590   build/temp.linux-armv7l-cpython-311/utils.cpp:490:20: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-17T22:54:53,591     490 |         while (pos != (int) std::string::npos) {
2023-09-17T22:54:53,592         |                ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-17T22:54:53,601   build/temp.linux-armv7l-cpython-311/utils.cpp: In function ‘int* utils::readNumbers(const std::string&)’:
2023-09-17T22:54:53,602   build/temp.linux-armv7l-cpython-311/utils.cpp:632:52: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-17T22:54:53,602     632 |         while ((comma = line.find(',', comma + 1)) != (int) std::string::npos)
2023-09-17T22:54:53,603         |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-17T22:54:53,604   build/temp.linux-armv7l-cpython-311/utils.cpp:646:44: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-17T22:54:53,604     646 |             if (((separ < comma) || (comma == (int) std::string::npos)) && (separ != (int) std::string::npos)) {
2023-09-17T22:54:53,605         |                                      ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-17T22:54:53,605   build/temp.linux-armv7l-cpython-311/utils.cpp:646:83: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-17T22:54:53,606     646 |             if (((separ < comma) || (comma == (int) std::string::npos)) && (separ != (int) std::string::npos)) {
2023-09-17T22:54:53,607         |                                                                             ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-17T22:54:53,607   build/temp.linux-armv7l-cpython-311/utils.cpp:650:50: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-17T22:54:53,608     650 |             } else if ((separ > comma) || (separ == (int) std::string::npos)) {
2023-09-17T22:54:53,608         |                                            ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-17T22:54:53,609   build/temp.linux-armv7l-cpython-311/utils.cpp:666:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-17T22:54:53,610     666 |             if (comma == (int) std::string::npos)
2023-09-17T22:54:53,611         |                 ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-17T22:54:56,170   generating build/temp.linux-armv7l-cpython-311/InternalBenchmarker.o from build/temp.linux-armv7l-cpython-311/InternalBenchmarker.cpp
2023-09-17T22:54:56,172   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/InternalBenchmarker.cpp -o build/temp.linux-armv7l-cpython-311/InternalBenchmarker.o
2023-09-17T22:54:56,231   generating build/temp.linux-armv7l-cpython-311/trimalManager.o from build/temp.linux-armv7l-cpython-311/trimalManager.cpp
2023-09-17T22:54:56,233   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/trimalManager.cpp -o build/temp.linux-armv7l-cpython-311/trimalManager.o
2023-09-17T22:54:58,266   In file included from build/temp.linux-armv7l-cpython-311/trimalManager.cpp:42:
2023-09-17T22:54:58,266   build/temp.linux-armv7l-cpython-311/VCFHandler.h: In constructor ‘ngs::__internal::vcfFeature::vcfFeature()’:
2023-09-17T22:54:58,267   build/temp.linux-armv7l-cpython-311/VCFHandler.h:87:19: warning: ‘ngs::__internal::vcfFeature::quality’ will be initialized after [-Wreorder]
2023-09-17T22:54:58,268      87 |             float quality;
2023-09-17T22:54:58,269         |                   ^~~~~~~
2023-09-17T22:54:58,269   build/temp.linux-armv7l-cpython-311/VCFHandler.h:85:18: warning:   ‘bool ngs::__internal::vcfFeature::filter’ [-Wreorder]
2023-09-17T22:54:58,270      85 |             bool filter;
2023-09-17T22:54:58,271         |                  ^~~~~~
2023-09-17T22:54:58,271   build/temp.linux-armv7l-cpython-311/VCFHandler.h:96:13: warning:   when initialized here [-Wreorder]
2023-09-17T22:54:58,272      96 |             vcfFeature() : position(0), quality(0.0F), filter(false), readDepthIndex(0)
2023-09-17T22:54:58,273         |             ^~~~~~~~~~
2023-09-17T22:54:58,461   build/temp.linux-armv7l-cpython-311/trimalManager.cpp: In member function ‘bool trimAlManager::check_outputs_coincidence()’:
2023-09-17T22:54:58,462   build/temp.linux-armv7l-cpython-311/trimalManager.cpp:1419:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::array<char*, 4>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:54:58,462    1419 |     for (int i = 0, x = 0; i < outFiles.size(); i++) {
2023-09-17T22:54:58,463         |                            ~~^~~~~~~~~~~~~~~~~
2023-09-17T22:54:58,463   build/temp.linux-armv7l-cpython-311/trimalManager.cpp:1421:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::array<char*, 4>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:54:58,464    1421 |             for (x = i + 1; x < outFiles.size(); x++) {
2023-09-17T22:54:58,464         |                             ~~^~~~~~~~~~~~~~~~~
2023-09-17T22:55:07,839   generating build/temp.linux-armv7l-cpython-311/VCFHandler.o from build/temp.linux-armv7l-cpython-311/VCFHandler.cpp
2023-09-17T22:55:07,840   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c build/temp.linux-armv7l-cpython-311/VCFHandler.cpp -o build/temp.linux-armv7l-cpython-311/VCFHandler.o
2023-09-17T22:55:09,672   In file included from build/temp.linux-armv7l-cpython-311/VCFHandler.cpp:30:
2023-09-17T22:55:09,673   build/temp.linux-armv7l-cpython-311/VCFHandler.h: In constructor ‘ngs::__internal::vcfFeature::vcfFeature()’:
2023-09-17T22:55:09,674   build/temp.linux-armv7l-cpython-311/VCFHandler.h:87:19: warning: ‘ngs::__internal::vcfFeature::quality’ will be initialized after [-Wreorder]
2023-09-17T22:55:09,675      87 |             float quality;
2023-09-17T22:55:09,675         |                   ^~~~~~~
2023-09-17T22:55:09,679   build/temp.linux-armv7l-cpython-311/VCFHandler.h:85:18: warning:   ‘bool ngs::__internal::vcfFeature::filter’ [-Wreorder]
2023-09-17T22:55:09,679      85 |             bool filter;
2023-09-17T22:55:09,680         |                  ^~~~~~
2023-09-17T22:55:09,681   build/temp.linux-armv7l-cpython-311/VCFHandler.h:96:13: warning:   when initialized here [-Wreorder]
2023-09-17T22:55:09,681      96 |             vcfFeature() : position(0), quality(0.0F), filter(false), readDepthIndex(0)
2023-09-17T22:55:09,682         |             ^~~~~~~~~~
2023-09-17T22:55:09,700   build/temp.linux-armv7l-cpython-311/VCFHandler.cpp: In function ‘bool ngs::__internal::checkContigsWithReference(const ngs::AlignmentVector&, const ngs::StringVector&)’:
2023-09-17T22:55:09,701   build/temp.linux-armv7l-cpython-311/VCFHandler.cpp:153:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Alignment*>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:55:09,702     153 |                 for (i = 0; i < sources.size(); i++) {
2023-09-17T22:55:09,702         |                             ~~^~~~~~~~~~~~~~~~
2023-09-17T22:55:09,703   build/temp.linux-armv7l-cpython-311/VCFHandler.cpp:162:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Alignment*>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:55:09,704     162 |                 if (i == sources.size()) {
2023-09-17T22:55:09,705         |                     ~~^~~~~~~~~~~~~~~~~
2023-09-17T22:55:09,710   build/temp.linux-armv7l-cpython-311/VCFHandler.cpp: In function ‘void ngs::__internal::increaseSequencesInAlignment(const ngs::AlignmentVector&, const ngs::StringVector&)’:
2023-09-17T22:55:09,711   build/temp.linux-armv7l-cpython-311/VCFHandler.cpp:198:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:55:09,711     198 |                 for (int i = 1; i < donors.size() + 1; i++) {
2023-09-17T22:55:09,712         |                                 ~~^~~~~~~~~~~~~~~~~~~
2023-09-17T22:55:09,719   build/temp.linux-armv7l-cpython-311/VCFHandler.cpp: In function ‘void ngs::__internal::applyVariantCallingFiles(const ngs::AlignmentVector&, const ngs::StringVector&, const ngs::StringVector&, const std::vector<std::vector<int> >&, float, float, bool, const char*)’:
2023-09-17T22:55:09,720   build/temp.linux-armv7l-cpython-311/VCFHandler.cpp:337:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:55:09,720     337 |             for (int vcfIndex = 0; vcfIndex < filenames.size(); vcfIndex++) {
2023-09-17T22:55:09,721         |                                    ~~~~~~~~~^~~~~~~~~~~~~~~~~~
2023-09-17T22:55:09,721   build/temp.linux-armv7l-cpython-311/VCFHandler.cpp:360:59: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:55:09,722     360 |                         for (contigIndex = 0; contigIndex < contigs.size(); contigIndex++)
2023-09-17T22:55:09,723         |                                               ~~~~~~~~~~~~^~~~~~~~~~~~~~~~
2023-09-17T22:55:09,724   build/temp.linux-armv7l-cpython-311/VCFHandler.cpp:365:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:55:09,724     365 |                         if (contigIndex == contigs.size()) {
2023-09-17T22:55:09,725         |                             ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
2023-09-17T22:55:09,726   build/temp.linux-armv7l-cpython-311/VCFHandler.cpp:394:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:55:09,727     394 |                     for (int donorID = 0; donorID < feature.donorsInfo.size(); donorID++)
2023-09-17T22:55:09,728         |                                           ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-17T22:55:09,745   build/temp.linux-armv7l-cpython-311/VCFHandler.cpp:397:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:55:09,746     397 |                         if (donorID >= donorsPositions[vcfIndex].size())
2023-09-17T22:55:09,746         |                             ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-17T22:55:09,759   build/temp.linux-armv7l-cpython-311/VCFHandler.cpp: In function ‘void ngs::__internal::extractContigsFromLine(char*, ngs::StringVector&)’:
2023-09-17T22:55:09,760   build/temp.linux-armv7l-cpython-311/VCFHandler.cpp:528:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:55:09,760     528 |                 for (U = 0; U < contigs.size(); U++)
2023-09-17T22:55:09,761         |                             ~~^~~~~~~~~~~~~~~~
2023-09-17T22:55:09,762   build/temp.linux-armv7l-cpython-311/VCFHandler.cpp:533:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:55:09,763     533 |                 if (U == contigs.size())
2023-09-17T22:55:09,763         |                     ~~^~~~~~~~~~~~~~~~~
2023-09-17T22:55:09,764   build/temp.linux-armv7l-cpython-311/VCFHandler.cpp: In function ‘void ngs::__internal::extractDonorsFromLine(char*, std::vector<int>&, ngs::StringVector&)’:
2023-09-17T22:55:09,764   build/temp.linux-armv7l-cpython-311/VCFHandler.cpp:557:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:55:09,765     557 |                 for (U = 0; U < donors.size(); U++) {
2023-09-17T22:55:09,766         |                             ~~^~~~~~~~~~~~~~~
2023-09-17T22:55:09,766   build/temp.linux-armv7l-cpython-311/VCFHandler.cpp:564:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:55:09,767     564 |                 if (U == donors.size()) {
2023-09-17T22:55:09,767         |                     ~~^~~~~~~~~~~~~~~~
2023-09-17T22:55:09,768   build/temp.linux-armv7l-cpython-311/VCFHandler.cpp: In function ‘void ngs::__internal::obtainContigsAndDonors(const ngs::StringVector&, ngs::StringVector&, ngs::StringVector&, std::vector<std::vector<int> >&)’:
2023-09-17T22:55:09,768   build/temp.linux-armv7l-cpython-311/VCFHandler.cpp:591:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-17T22:55:09,769     591 |             for (int C = 0; C < filenames.size(); C++) {
2023-09-17T22:55:09,770         |                             ~~^~~~~~~~~~~~~~~~~~
2023-09-17T22:55:13,916   generating build/temp.linux-armv7l-cpython-311/libtrimal.a from build/temp.linux-armv7l-cpython-311/Cleaner.o, build/temp.linux-armv7l-cpython-311/Alignment.o, build/temp.linux-armv7l-cpython-311/sequencesMatrix.o, build/temp.linux-armv7l-cpython-311/similarityMatrix.o, build/temp.linux-armv7l-cpython-311/Mold.o, build/temp.linux-armv7l-cpython-311/Gaps.o, build/temp.linux-armv7l-cpython-311/Manager.o, build/temp.linux-armv7l-cpython-311/Similarity.o, build/temp.linux-armv7l-cpython-311/Consistency.o, build/temp.linux-armv7l-cpython-311/errorMessages.o, build/temp.linux-armv7l-cpython-311/infoMessages.o, build/temp.linux-armv7l-cpython-311/warningMessages.o, build/temp.linux-armv7l-cpython-311/phylip_paml_state.o, build/temp.linux-armv7l-cpython-311/fasta_m10_state.o, build/temp.linux-armv7l-cpython-311/fasta_state.o, build/temp.linux-armv7l-cpython-311/htmlreport_state.o, build/temp.linux-armv7l-cpython-311/mega_sequential_state.o, build/temp.linux-armv7l-cpython-311/nexus_m10_state.o, build/temp.linux-armv7l-cpython-311/pir_state.o, build/temp.linux-armv7l-cpython-311/clustal_state.o, build/temp.linux-armv7l-cpython-311/phylip40_m10_state.o, build/temp.linux-armv7l-cpython-311/phylip32_m10_state.o, build/temp.linux-armv7l-cpython-311/phylip40_state.o, build/temp.linux-armv7l-cpython-311/phylip32_state.o, build/temp.linux-armv7l-cpython-311/nexus_state.o, build/temp.linux-armv7l-cpython-311/phylip_paml_m10_state.o, build/temp.linux-armv7l-cpython-311/mega_interleaved_state.o, build/temp.linux-armv7l-cpython-311/BaseFormatHandler.o, build/temp.linux-armv7l-cpython-311/utils.o, build/temp.linux-armv7l-cpython-311/InternalBenchmarker.o, build/temp.linux-armv7l-cpython-311/trimalManager.o, build/temp.linux-armv7l-cpython-311/VCFHandler.o
2023-09-17T22:55:13,917   arm-linux-gnueabihf-gcc-ar rcs build/temp.linux-armv7l-cpython-311/libtrimal.a build/temp.linux-armv7l-cpython-311/Cleaner.o build/temp.linux-armv7l-cpython-311/Alignment.o build/temp.linux-armv7l-cpython-311/sequencesMatrix.o build/temp.linux-armv7l-cpython-311/similarityMatrix.o build/temp.linux-armv7l-cpython-311/Mold.o build/temp.linux-armv7l-cpython-311/Gaps.o build/temp.linux-armv7l-cpython-311/Manager.o build/temp.linux-armv7l-cpython-311/Similarity.o build/temp.linux-armv7l-cpython-311/Consistency.o build/temp.linux-armv7l-cpython-311/errorMessages.o build/temp.linux-armv7l-cpython-311/infoMessages.o build/temp.linux-armv7l-cpython-311/warningMessages.o build/temp.linux-armv7l-cpython-311/phylip_paml_state.o build/temp.linux-armv7l-cpython-311/fasta_m10_state.o build/temp.linux-armv7l-cpython-311/fasta_state.o build/temp.linux-armv7l-cpython-311/htmlreport_state.o build/temp.linux-armv7l-cpython-311/mega_sequential_state.o build/temp.linux-armv7l-cpython-311/nexus_m10_state.o build/temp.linux-armv7l-cpython-311/pir_state.o build/temp.linux-armv7l-cpython-311/clustal_state.o build/temp.linux-armv7l-cpython-311/phylip40_m10_state.o build/temp.linux-armv7l-cpython-311/phylip32_m10_state.o build/temp.linux-armv7l-cpython-311/phylip40_state.o build/temp.linux-armv7l-cpython-311/phylip32_state.o build/temp.linux-armv7l-cpython-311/nexus_state.o build/temp.linux-armv7l-cpython-311/phylip_paml_m10_state.o build/temp.linux-armv7l-cpython-311/mega_interleaved_state.o build/temp.linux-armv7l-cpython-311/BaseFormatHandler.o build/temp.linux-armv7l-cpython-311/utils.o build/temp.linux-armv7l-cpython-311/InternalBenchmarker.o build/temp.linux-armv7l-cpython-311/trimalManager.o build/temp.linux-armv7l-cpython-311/VCFHandler.o
2023-09-17T22:55:14,295   running build_ext

2023-09-17T22:55:15,246   Error compiling Cython file:
2023-09-17T22:55:15,247   ------------------------------------------------------------
2023-09-17T22:55:15,247   ...
2023-09-17T22:55:15,248   """

2023-09-17T22:55:15,249   # --- C imports --------------------------------------------------------------

2023-09-17T22:55:15,250   cimport cython
2023-09-17T22:55:15,250   from _unicode cimport (
2023-09-17T22:55:15,251   ^
2023-09-17T22:55:15,251   ------------------------------------------------------------

2023-09-17T22:55:15,252   pytrimal/_trimal.pyx:16:0: '_unicode.pxd' not found

2023-09-17T22:55:15,253   Error compiling Cython file:
2023-09-17T22:55:15,254   ------------------------------------------------------------
2023-09-17T22:55:15,254   ...
2023-09-17T22:55:15,255   """

2023-09-17T22:55:15,256   # --- C imports --------------------------------------------------------------

2023-09-17T22:55:15,257   cimport cython
2023-09-17T22:55:15,257   from _unicode cimport (
2023-09-17T22:55:15,258   ^
2023-09-17T22:55:15,258   ------------------------------------------------------------

2023-09-17T22:55:15,259   pytrimal/_trimal.pyx:16:0: '_unicode/PyUnicode_New.pxd' not found

2023-09-17T22:55:15,260   Error compiling Cython file:
2023-09-17T22:55:15,260   ------------------------------------------------------------
2023-09-17T22:55:15,261   ...
2023-09-17T22:55:15,262   """

2023-09-17T22:55:15,263   # --- C imports --------------------------------------------------------------

2023-09-17T22:55:15,264   cimport cython
2023-09-17T22:55:15,265   from _unicode cimport (
2023-09-17T22:55:15,266   ^
2023-09-17T22:55:15,266   ------------------------------------------------------------

2023-09-17T22:55:15,267   pytrimal/_trimal.pyx:16:0: '_unicode/PyUnicode_READY.pxd' not found

2023-09-17T22:55:15,268   Error compiling Cython file:
2023-09-17T22:55:15,269   ------------------------------------------------------------
2023-09-17T22:55:15,269   ...
2023-09-17T22:55:15,270   """

2023-09-17T22:55:15,271   # --- C imports --------------------------------------------------------------

2023-09-17T22:55:15,272   cimport cython
2023-09-17T22:55:15,273   from _unicode cimport (
2023-09-17T22:55:15,274   ^
2023-09-17T22:55:15,274   ------------------------------------------------------------

2023-09-17T22:55:15,275   pytrimal/_trimal.pyx:16:0: '_unicode/PyUnicode_KIND.pxd' not found

2023-09-17T22:55:15,276   Error compiling Cython file:
2023-09-17T22:55:15,276   ------------------------------------------------------------
2023-09-17T22:55:15,277   ...
2023-09-17T22:55:15,277   """

2023-09-17T22:55:15,278   # --- C imports --------------------------------------------------------------

2023-09-17T22:55:15,279   cimport cython
2023-09-17T22:55:15,279   from _unicode cimport (
2023-09-17T22:55:15,279   ^
2023-09-17T22:55:15,280   ------------------------------------------------------------

2023-09-17T22:55:15,281   pytrimal/_trimal.pyx:16:0: '_unicode/PyUnicode_DATA.pxd' not found

2023-09-17T22:55:15,282   Error compiling Cython file:
2023-09-17T22:55:15,283   ------------------------------------------------------------
2023-09-17T22:55:15,283   ...
2023-09-17T22:55:15,284   """

2023-09-17T22:55:15,286   # --- C imports --------------------------------------------------------------

2023-09-17T22:55:15,287   cimport cython
2023-09-17T22:55:15,288   from _unicode cimport (
2023-09-17T22:55:15,288   ^
2023-09-17T22:55:15,289   ------------------------------------------------------------

2023-09-17T22:55:15,290   pytrimal/_trimal.pyx:16:0: '_unicode/PyUnicode_WRITE.pxd' not found

2023-09-17T22:55:15,859   Error compiling Cython file:
2023-09-17T22:55:15,859   ------------------------------------------------------------
2023-09-17T22:55:15,860   ...

2023-09-17T22:55:15,861   from libc.math cimport NAN, isnan
2023-09-17T22:55:15,861   from libcpp cimport bool
2023-09-17T22:55:15,861   from libcpp.string cimport string

2023-09-17T22:55:15,862   cimport trimal
2023-09-17T22:55:15,863          ^
2023-09-17T22:55:15,863   ------------------------------------------------------------

2023-09-17T22:55:15,865   pytrimal/_trimal.pyx:32:8: 'trimal.pxd' not found

2023-09-17T22:55:15,866   Error compiling Cython file:
2023-09-17T22:55:15,866   ------------------------------------------------------------
2023-09-17T22:55:15,867   ...
2023-09-17T22:55:15,867   from libc.math cimport NAN, isnan
2023-09-17T22:55:15,868   from libcpp cimport bool
2023-09-17T22:55:15,868   from libcpp.string cimport string

2023-09-17T22:55:15,870   cimport trimal
2023-09-17T22:55:15,870   cimport trimal.alignment
2023-09-17T22:55:15,871          ^
2023-09-17T22:55:15,872   ------------------------------------------------------------

2023-09-17T22:55:15,873   pytrimal/_trimal.pyx:33:8: 'trimal/alignment.pxd' not found

2023-09-17T22:55:15,874   Error compiling Cython file:
2023-09-17T22:55:15,875   ------------------------------------------------------------
2023-09-17T22:55:15,876   ...
2023-09-17T22:55:15,876   from libcpp cimport bool
2023-09-17T22:55:15,877   from libcpp.string cimport string

2023-09-17T22:55:15,878   cimport trimal
2023-09-17T22:55:15,879   cimport trimal.alignment
2023-09-17T22:55:15,880   cimport trimal.format_manager
2023-09-17T22:55:15,880          ^
2023-09-17T22:55:15,881   ------------------------------------------------------------

2023-09-17T22:55:15,882   pytrimal/_trimal.pyx:34:8: 'trimal/format_manager.pxd' not found

2023-09-17T22:55:15,883   Error compiling Cython file:
2023-09-17T22:55:15,884   ------------------------------------------------------------
2023-09-17T22:55:15,884   ...
2023-09-17T22:55:15,885   from libcpp.string cimport string

2023-09-17T22:55:15,886   cimport trimal
2023-09-17T22:55:15,886   cimport trimal.alignment
2023-09-17T22:55:15,887   cimport trimal.format_manager
2023-09-17T22:55:15,888   cimport trimal.manager
2023-09-17T22:55:15,888          ^
2023-09-17T22:55:15,889   ------------------------------------------------------------

2023-09-17T22:55:15,890   pytrimal/_trimal.pyx:35:8: 'trimal/manager.pxd' not found

2023-09-17T22:55:15,892   Error compiling Cython file:
2023-09-17T22:55:15,892   ------------------------------------------------------------
2023-09-17T22:55:15,893   ...

2023-09-17T22:55:15,894   cimport trimal
2023-09-17T22:55:15,895   cimport trimal.alignment
2023-09-17T22:55:15,895   cimport trimal.format_manager
2023-09-17T22:55:15,896   cimport trimal.manager
2023-09-17T22:55:15,896   cimport trimal.report_system
2023-09-17T22:55:15,993          ^
2023-09-17T22:55:15,994   ------------------------------------------------------------

2023-09-17T22:55:15,995   pytrimal/_trimal.pyx:36:8: 'trimal/report_system.pxd' not found

2023-09-17T22:55:15,996   Error compiling Cython file:
2023-09-17T22:55:15,996   ------------------------------------------------------------
2023-09-17T22:55:15,996   ...
2023-09-17T22:55:15,997   cimport trimal
2023-09-17T22:55:15,997   cimport trimal.alignment
2023-09-17T22:55:15,997   cimport trimal.format_manager
2023-09-17T22:55:15,998   cimport trimal.manager
2023-09-17T22:55:15,998   cimport trimal.report_system
2023-09-17T22:55:15,999   cimport trimal.similarity_matrix
2023-09-17T22:55:15,999          ^
2023-09-17T22:55:15,999   ------------------------------------------------------------

2023-09-17T22:55:16,000   pytrimal/_trimal.pyx:37:8: 'trimal/similarity_matrix.pxd' not found

2023-09-17T22:55:16,001   Error compiling Cython file:
2023-09-17T22:55:16,001   ------------------------------------------------------------
2023-09-17T22:55:16,002   ...
2023-09-17T22:55:16,002             >>> sum(letter == '-' for seq in msa.sequences for letter in seq)
2023-09-17T22:55:16,002             43

2023-09-17T22:55:16,003         """

2023-09-17T22:55:16,004         cdef trimal.alignment.Alignment* _ali
2023-09-17T22:55:16,004             ^
2023-09-17T22:55:16,005   ------------------------------------------------------------

2023-09-17T22:55:16,006   pytrimal/_trimal.pyx:98:11: 'Alignment' is not a type identifier

2023-09-17T22:55:16,007   Error compiling Cython file:
2023-09-17T22:55:16,008   ------------------------------------------------------------
2023-09-17T22:55:16,008   ...
2023-09-17T22:55:16,009           >>> msa.residues[-1]
2023-09-17T22:55:16,009           'IIIIFL'

2023-09-17T22:55:16,010       """

2023-09-17T22:55:16,012       cdef trimal.alignment.Alignment* _ali
2023-09-17T22:55:16,012           ^
2023-09-17T22:55:16,013   ------------------------------------------------------------

2023-09-17T22:55:16,014   pytrimal/_trimal.pyx:165:9: 'Alignment' is not a type identifier

2023-09-17T22:55:16,015   Error compiling Cython file:
2023-09-17T22:55:16,015   ------------------------------------------------------------
2023-09-17T22:55:16,016   ...

2023-09-17T22:55:16,017   cdef class Alignment:
2023-09-17T22:55:16,018       """A multiple sequence alignment.
2023-09-17T22:55:16,018       """

2023-09-17T22:55:16,020       cdef trimal.alignment.Alignment* _ali
2023-09-17T22:55:16,020           ^
2023-09-17T22:55:16,021   ------------------------------------------------------------

2023-09-17T22:55:16,022   pytrimal/_trimal.pyx:218:9: 'Alignment' is not a type identifier

2023-09-17T22:55:16,023   Error compiling Cython file:
2023-09-17T22:55:16,023   ------------------------------------------------------------
2023-09-17T22:55:16,023   ...

2023-09-17T22:55:16,024           Create a new base trimmer.

2023-09-17T22:55:16,025           """

2023-09-17T22:55:16,026       cdef void _configure_manager(self, trimal.manager.trimAlManager* manager):
2023-09-17T22:55:16,027                                         ^
2023-09-17T22:55:16,027   ------------------------------------------------------------

2023-09-17T22:55:16,028   pytrimal/_trimal.pyx:573:39: 'trimAlManager' is not a type identifier

2023-09-17T22:55:16,029   Error compiling Cython file:
2023-09-17T22:55:16,030   ------------------------------------------------------------
2023-09-17T22:55:16,030   ...

2023-09-17T22:55:16,031           if method not in AUTOMATED_TRIMMER_METHODS:
2023-09-17T22:55:16,032               raise ValueError(f"Invalid value for `method`: {method!r}")
2023-09-17T22:55:16,033           self.method = method

2023-09-17T22:55:16,034       cdef void _configure_manager(self, trimal.manager.trimAlManager* manager):
2023-09-17T22:55:16,034                                         ^
2023-09-17T22:55:16,035   ------------------------------------------------------------

2023-09-17T22:55:16,036   pytrimal/_trimal.pyx:684:39: 'trimAlManager' is not a type identifier

2023-09-17T22:55:16,037   Error compiling Cython file:
2023-09-17T22:55:16,037   ------------------------------------------------------------
2023-09-17T22:55:16,038   ...
2023-09-17T22:55:16,038           if consistency_threshold is not None:
2023-09-17T22:55:16,038               self._consistency_threshold = _check_range(consistency_threshold, "consistency_threshold", 0, 1)
2023-09-17T22:55:16,039           if conservation_percentage is not None:
2023-09-17T22:55:16,039               self._conservation_percentage = _check_range(conservation_percentage, "conservation_percentage", 0, 100)

2023-09-17T22:55:16,040       cdef void _configure_manager(self, trimal.manager.trimAlManager* manager):
2023-09-17T22:55:16,040                                         ^
2023-09-17T22:55:16,041   ------------------------------------------------------------

2023-09-17T22:55:16,042   pytrimal/_trimal.pyx:781:39: 'trimAlManager' is not a type identifier

2023-09-17T22:55:16,042   Error compiling Cython file:
2023-09-17T22:55:16,043   ------------------------------------------------------------
2023-09-17T22:55:16,043   ...

2023-09-17T22:55:16,044   cdef class SimilarityMatrix:
2023-09-17T22:55:16,045       """A similarity matrix for biological sequence characters.
2023-09-17T22:55:16,045       """

2023-09-17T22:55:16,046       cdef trimal.similarity_matrix.similarityMatrix _smx
2023-09-17T22:55:16,047           ^
2023-09-17T22:55:16,047   ------------------------------------------------------------

2023-09-17T22:55:16,049   pytrimal/_trimal.pyx:797:9: 'similarityMatrix' is not a type identifier

2023-09-17T22:55:16,050   Error compiling Cython file:
2023-09-17T22:55:16,050   ------------------------------------------------------------
2023-09-17T22:55:16,051   ...
2023-09-17T22:55:16,052               >>> msa = Alignment.load("example.001.AA.clw")
2023-09-17T22:55:16,052               >>> msa.names
2023-09-17T22:55:16,053               [b'Sp8', b'Sp10', b'Sp26', b'Sp6', b'Sp17', b'Sp33']

2023-09-17T22:55:16,054           """
2023-09-17T22:55:16,055           cdef trimal.format_manager.FormatManager manager
2023-09-17T22:55:16,055               ^
2023-09-17T22:55:16,056   ------------------------------------------------------------

2023-09-17T22:55:16,057   pytrimal/_trimal.pyx:241:13: 'FormatManager' is not a type identifier

2023-09-17T22:55:16,058   Error compiling Cython file:
2023-09-17T22:55:16,059   ------------------------------------------------------------
2023-09-17T22:55:16,059   ...
2023-09-17T22:55:16,060               releasing the GIL.

2023-09-17T22:55:16,061           """
2023-09-17T22:55:16,061           # use a local manager object so that this method is re-entrant
2023-09-17T22:55:16,062           cdef Alignment                    copy
2023-09-17T22:55:16,062           cdef trimal.manager.trimAlManager manager
2023-09-17T22:55:16,063               ^
2023-09-17T22:55:16,063   ------------------------------------------------------------

2023-09-17T22:55:16,064   pytrimal/_trimal.pyx:596:13: 'trimAlManager' is not a type identifier

2023-09-17T22:55:16,213   Error compiling Cython file:
2023-09-17T22:55:16,213   ------------------------------------------------------------
2023-09-17T22:55:16,214   ...
2023-09-17T22:55:16,214                     if self._ali.saveResidues is NULL or self._ali.saveResidues[i] != -1:
2023-09-17T22:55:16,215                         data[x] = self._ali.sequences[index_][i]
2023-09-17T22:55:16,216                         x += 1
2023-09-17T22:55:16,216                 return seq.decode('ascii')
2023-09-17T22:55:16,217             ELSE:
2023-09-17T22:55:16,218                 cdef str      seq  = PyUnicode_New(self._ali.numberOfResidues, 0x7f)
2023-09-17T22:55:16,218                                     ^
2023-09-17T22:55:16,219   ------------------------------------------------------------

2023-09-17T22:55:16,220   pytrimal/_trimal.pyx:134:35: 'PyUnicode_New' is not a constant, variable or function identifier

2023-09-17T22:55:16,221   Error compiling Cython file:
2023-09-17T22:55:16,222   ------------------------------------------------------------
2023-09-17T22:55:16,222   ...
2023-09-17T22:55:16,222                         x += 1
2023-09-17T22:55:16,223                 return seq.decode('ascii')
2023-09-17T22:55:16,224             ELSE:
2023-09-17T22:55:16,224                 cdef str      seq  = PyUnicode_New(self._ali.numberOfResidues, 0x7f)
2023-09-17T22:55:16,224                 IF SYS_VERSION_INFO_MAJOR <= 3 and SYS_VERSION_INFO_MINOR < 12:
2023-09-17T22:55:16,225                     PyUnicode_READY(seq)
2023-09-17T22:55:16,225                    ^
2023-09-17T22:55:16,226   ------------------------------------------------------------

2023-09-17T22:55:16,227   pytrimal/_trimal.pyx:136:18: 'PyUnicode_READY' is not a constant, variable or function identifier

2023-09-17T22:55:16,228   Error compiling Cython file:
2023-09-17T22:55:16,228   ------------------------------------------------------------
2023-09-17T22:55:16,229   ...
2023-09-17T22:55:16,229                 return seq.decode('ascii')
2023-09-17T22:55:16,229             ELSE:
2023-09-17T22:55:16,230                 cdef str      seq  = PyUnicode_New(self._ali.numberOfResidues, 0x7f)
2023-09-17T22:55:16,230                 IF SYS_VERSION_INFO_MAJOR <= 3 and SYS_VERSION_INFO_MINOR < 12:
2023-09-17T22:55:16,231                     PyUnicode_READY(seq)
2023-09-17T22:55:16,231                 cdef void*    data = PyUnicode_DATA(seq)
2023-09-17T22:55:16,232                                     ^
2023-09-17T22:55:16,232   ------------------------------------------------------------

2023-09-17T22:55:16,233   pytrimal/_trimal.pyx:137:35: 'PyUnicode_DATA' is not a constant, variable or function identifier

2023-09-17T22:55:16,235   Error compiling Cython file:
2023-09-17T22:55:16,235   ------------------------------------------------------------
2023-09-17T22:55:16,236   ...
2023-09-17T22:55:16,237                 return seq.decode('ascii')
2023-09-17T22:55:16,237             ELSE:
2023-09-17T22:55:16,238                 cdef str      seq  = PyUnicode_New(self._ali.numberOfResidues, 0x7f)
2023-09-17T22:55:16,239                 IF SYS_VERSION_INFO_MAJOR <= 3 and SYS_VERSION_INFO_MINOR < 12:
2023-09-17T22:55:16,240                     PyUnicode_READY(seq)
2023-09-17T22:55:16,240                 cdef void*    data = PyUnicode_DATA(seq)
2023-09-17T22:55:16,241                                                   ^
2023-09-17T22:55:16,241   ------------------------------------------------------------

2023-09-17T22:55:16,243   pytrimal/_trimal.pyx:137:49: Cannot convert Python object to 'void *'

2023-09-17T22:55:16,244   Error compiling Cython file:
2023-09-17T22:55:16,244   ------------------------------------------------------------
2023-09-17T22:55:16,245   ...
2023-09-17T22:55:16,245                 return seq.decode('ascii')
2023-09-17T22:55:16,246             ELSE:
2023-09-17T22:55:16,246                 cdef str      seq  = PyUnicode_New(self._ali.numberOfResidues, 0x7f)
2023-09-17T22:55:16,247                 IF SYS_VERSION_INFO_MAJOR <= 3 and SYS_VERSION_INFO_MINOR < 12:
2023-09-17T22:55:16,248                     PyUnicode_READY(seq)
2023-09-17T22:55:16,248                 cdef void*    data = PyUnicode_DATA(seq)
2023-09-17T22:55:16,249                     ^
2023-09-17T22:55:16,249   ------------------------------------------------------------

2023-09-17T22:55:16,251   pytrimal/_trimal.pyx:137:19: Storing unsafe C derivative of temporary Python reference

2023-09-17T22:55:16,252   Error compiling Cython file:
2023-09-17T22:55:16,252   ------------------------------------------------------------
2023-09-17T22:55:16,253   ...
2023-09-17T22:55:16,254             ELSE:
2023-09-17T22:55:16,254                 cdef str      seq  = PyUnicode_New(self._ali.numberOfResidues, 0x7f)
2023-09-17T22:55:16,255                 IF SYS_VERSION_INFO_MAJOR <= 3 and SYS_VERSION_INFO_MINOR < 12:
2023-09-17T22:55:16,256                     PyUnicode_READY(seq)
2023-09-17T22:55:16,256                 cdef void*    data = PyUnicode_DATA(seq)
2023-09-17T22:55:16,257                 cdef int      kind = PyUnicode_KIND(seq)
2023-09-17T22:55:16,257                                     ^
2023-09-17T22:55:16,258   ------------------------------------------------------------

2023-09-17T22:55:16,258   pytrimal/_trimal.pyx:138:35: 'PyUnicode_KIND' is not a constant, variable or function identifier

2023-09-17T22:55:16,259   Error compiling Cython file:
2023-09-17T22:55:16,260   ------------------------------------------------------------
2023-09-17T22:55:16,260   ...
2023-09-17T22:55:16,261                     PyUnicode_READY(seq)
2023-09-17T22:55:16,261                 cdef void*    data = PyUnicode_DATA(seq)
2023-09-17T22:55:16,262                 cdef int      kind = PyUnicode_KIND(seq)
2023-09-17T22:55:16,262                 cdef size_t   x    = 0
2023-09-17T22:55:16,262                 for i in range(self._ali.originalNumberOfResidues):
2023-09-17T22:55:16,263                     if self._ali.saveResidues is NULL or self._ali.saveResidues[i] != -1:
2023-09-17T22:55:16,263                                              ^
2023-09-17T22:55:16,264   ------------------------------------------------------------

2023-09-17T22:55:16,265   pytrimal/_trimal.pyx:141:44: Invalid types for 'is' (Python object, void *)

2023-09-17T22:55:16,266   Error compiling Cython file:
2023-09-17T22:55:16,266   ------------------------------------------------------------
2023-09-17T22:55:16,267   ...
2023-09-17T22:55:16,267                 cdef void*    data = PyUnicode_DATA(seq)
2023-09-17T22:55:16,268                 cdef int      kind = PyUnicode_KIND(seq)
2023-09-17T22:55:16,268                 cdef size_t   x    = 0
2023-09-17T22:55:16,269                 for i in range(self._ali.originalNumberOfResidues):
2023-09-17T22:55:16,269                     if self._ali.saveResidues is NULL or self._ali.saveResidues[i] != -1:
2023-09-17T22:55:16,270                         PyUnicode_WRITE(kind, data, x, self._ali.sequences[index_][i])
2023-09-17T22:55:16,271                        ^
2023-09-17T22:55:16,271   ------------------------------------------------------------

2023-09-17T22:55:16,273   pytrimal/_trimal.pyx:142:22: 'PyUnicode_WRITE' is not a constant, variable or function identifier

2023-09-17T22:55:16,274   Error compiling Cython file:
2023-09-17T22:55:16,275   ------------------------------------------------------------
2023-09-17T22:55:16,276   ...
2023-09-17T22:55:16,276                 cdef void*    data = PyUnicode_DATA(seq)
2023-09-17T22:55:16,277                 cdef int      kind = PyUnicode_KIND(seq)
2023-09-17T22:55:16,278                 cdef size_t   x    = 0
2023-09-17T22:55:16,278                 for i in range(self._ali.originalNumberOfResidues):
2023-09-17T22:55:16,279                     if self._ali.saveResidues is NULL or self._ali.saveResidues[i] != -1:
2023-09-17T22:55:16,279                         PyUnicode_WRITE(kind, data, x, self._ali.sequences[index_][i])
2023-09-17T22:55:16,280                                              ^
2023-09-17T22:55:16,280   ------------------------------------------------------------

2023-09-17T22:55:16,281   pytrimal/_trimal.pyx:142:44: Cannot convert 'void *' to Python object

2023-09-17T22:55:16,283   Error compiling Cython file:
2023-09-17T22:55:16,283   ------------------------------------------------------------
2023-09-17T22:55:16,284   ...
2023-09-17T22:55:16,284                   if self._ali.saveSequences is NULL or self._ali.saveSequences[i] != -1:
2023-09-17T22:55:16,285                       data[x] = self._ali.sequences[i][index_]
2023-09-17T22:55:16,286                       x += 1
2023-09-17T22:55:16,286               return col.decode('ascii')
2023-09-17T22:55:16,287           ELSE:
2023-09-17T22:55:16,288               cdef str      col = PyUnicode_New(self._ali.numberOfSequences, 0x7f)
2023-09-17T22:55:16,288                                  ^
2023-09-17T22:55:16,289   ------------------------------------------------------------

2023-09-17T22:55:16,290   pytrimal/_trimal.pyx:201:32: 'PyUnicode_New' is not a constant, variable or function identifier

2023-09-17T22:55:16,291   Error compiling Cython file:
2023-09-17T22:55:16,292   ------------------------------------------------------------
2023-09-17T22:55:16,292   ...
2023-09-17T22:55:16,292                       x += 1
2023-09-17T22:55:16,293               return col.decode('ascii')
2023-09-17T22:55:16,293           ELSE:
2023-09-17T22:55:16,294               cdef str      col = PyUnicode_New(self._ali.numberOfSequences, 0x7f)
2023-09-17T22:55:16,294               IF SYS_VERSION_INFO_MAJOR <= 3 and SYS_VERSION_INFO_MINOR < 12:
2023-09-17T22:55:16,295                   PyUnicode_READY(col)
2023-09-17T22:55:16,295                  ^
2023-09-17T22:55:16,296   ------------------------------------------------------------

2023-09-17T22:55:16,297   pytrimal/_trimal.pyx:203:16: 'PyUnicode_READY' is not a constant, variable or function identifier

2023-09-17T22:55:16,297   Error compiling Cython file:
2023-09-17T22:55:16,298   ------------------------------------------------------------
2023-09-17T22:55:16,298   ...
2023-09-17T22:55:16,299               return col.decode('ascii')
2023-09-17T22:55:16,299           ELSE:
2023-09-17T22:55:16,300               cdef str      col = PyUnicode_New(self._ali.numberOfSequences, 0x7f)
2023-09-17T22:55:16,300               IF SYS_VERSION_INFO_MAJOR <= 3 and SYS_VERSION_INFO_MINOR < 12:
2023-09-17T22:55:16,301                   PyUnicode_READY(col)
2023-09-17T22:55:16,301               cdef void*    data = PyUnicode_DATA(col)
2023-09-17T22:55:16,302                                   ^
2023-09-17T22:55:16,302   ------------------------------------------------------------

2023-09-17T22:55:16,303   pytrimal/_trimal.pyx:204:33: 'PyUnicode_DATA' is not a constant, variable or function identifier

2023-09-17T22:55:16,305   Error compiling Cython file:
2023-09-17T22:55:16,306   ------------------------------------------------------------
2023-09-17T22:55:16,306   ...
2023-09-17T22:55:16,307               return col.decode('ascii')
2023-09-17T22:55:16,307           ELSE:
2023-09-17T22:55:16,308               cdef str      col = PyUnicode_New(self._ali.numberOfSequences, 0x7f)
2023-09-17T22:55:16,309               IF SYS_VERSION_INFO_MAJOR <= 3 and SYS_VERSION_INFO_MINOR < 12:
2023-09-17T22:55:16,309                   PyUnicode_READY(col)
2023-09-17T22:55:16,310               cdef void*    data = PyUnicode_DATA(col)
2023-09-17T22:55:16,311                                                 ^
2023-09-17T22:55:16,311   ------------------------------------------------------------

2023-09-17T22:55:16,313   pytrimal/_trimal.pyx:204:47: Cannot convert Python object to 'void *'

2023-09-17T22:55:16,314   Error compiling Cython file:
2023-09-17T22:55:16,314   ------------------------------------------------------------
2023-09-17T22:55:16,315   ...
2023-09-17T22:55:16,315               return col.decode('ascii')
2023-09-17T22:55:16,316           ELSE:
2023-09-17T22:55:16,316               cdef str      col = PyUnicode_New(self._ali.numberOfSequences, 0x7f)
2023-09-17T22:55:16,317               IF SYS_VERSION_INFO_MAJOR <= 3 and SYS_VERSION_INFO_MINOR < 12:
2023-09-17T22:55:16,318                   PyUnicode_READY(col)
2023-09-17T22:55:16,318               cdef void*    data = PyUnicode_DATA(col)
2023-09-17T22:55:16,319                   ^
2023-09-17T22:55:16,319   ------------------------------------------------------------

2023-09-17T22:55:16,321   pytrimal/_trimal.pyx:204:17: Storing unsafe C derivative of temporary Python reference

2023-09-17T22:55:16,322   Error compiling Cython file:
2023-09-17T22:55:16,323   ------------------------------------------------------------
2023-09-17T22:55:16,324   ...
2023-09-17T22:55:16,324           ELSE:
2023-09-17T22:55:16,325               cdef str      col = PyUnicode_New(self._ali.numberOfSequences, 0x7f)
2023-09-17T22:55:16,326               IF SYS_VERSION_INFO_MAJOR <= 3 and SYS_VERSION_INFO_MINOR < 12:
2023-09-17T22:55:16,326                   PyUnicode_READY(col)
2023-09-17T22:55:16,327               cdef void*    data = PyUnicode_DATA(col)
2023-09-17T22:55:16,327               cdef int      kind = PyUnicode_KIND(col)
2023-09-17T22:55:16,328                                   ^
2023-09-17T22:55:16,328   ------------------------------------------------------------

2023-09-17T22:55:16,329   pytrimal/_trimal.pyx:205:33: 'PyUnicode_KIND' is not a constant, variable or function identifier

2023-09-17T22:55:16,330   Error compiling Cython file:
2023-09-17T22:55:16,331   ------------------------------------------------------------
2023-09-17T22:55:16,331   ...
2023-09-17T22:55:16,331                   PyUnicode_READY(col)
2023-09-17T22:55:16,332               cdef void*    data = PyUnicode_DATA(col)
2023-09-17T22:55:16,332               cdef int      kind = PyUnicode_KIND(col)
2023-09-17T22:55:16,333               cdef size_t   x    = 0
2023-09-17T22:55:16,333               for i in range(self._ali.originalNumberOfSequences):
2023-09-17T22:55:16,334                   if self._ali.saveSequences is NULL or self._ali.saveSequences[i] != -1:
2023-09-17T22:55:16,334                                             ^
2023-09-17T22:55:16,335   ------------------------------------------------------------

2023-09-17T22:55:16,336   pytrimal/_trimal.pyx:208:43: Invalid types for 'is' (Python object, void *)

2023-09-17T22:55:16,337   Error compiling Cython file:
2023-09-17T22:55:16,337   ------------------------------------------------------------
2023-09-17T22:55:16,338   ...
2023-09-17T22:55:16,338               cdef void*    data = PyUnicode_DATA(col)
2023-09-17T22:55:16,339               cdef int      kind = PyUnicode_KIND(col)
2023-09-17T22:55:16,339               cdef size_t   x    = 0
2023-09-17T22:55:16,340               for i in range(self._ali.originalNumberOfSequences):
2023-09-17T22:55:16,341                   if self._ali.saveSequences is NULL or self._ali.saveSequences[i] != -1:
2023-09-17T22:55:16,341                       PyUnicode_WRITE(kind, data, x, self._ali.sequences[i][index_])
2023-09-17T22:55:16,342                      ^
2023-09-17T22:55:16,343   ------------------------------------------------------------

2023-09-17T22:55:16,344   pytrimal/_trimal.pyx:209:20: 'PyUnicode_WRITE' is not a constant, variable or function identifier

2023-09-17T22:55:16,345   Error compiling Cython file:
2023-09-17T22:55:16,346   ------------------------------------------------------------
2023-09-17T22:55:16,347   ...
2023-09-17T22:55:16,347               cdef void*    data = PyUnicode_DATA(col)
2023-09-17T22:55:16,348               cdef int      kind = PyUnicode_KIND(col)
2023-09-17T22:55:16,349               cdef size_t   x    = 0
2023-09-17T22:55:16,349               for i in range(self._ali.originalNumberOfSequences):
2023-09-17T22:55:16,350                   if self._ali.saveSequences is NULL or self._ali.saveSequences[i] != -1:
2023-09-17T22:55:16,350                       PyUnicode_WRITE(kind, data, x, self._ali.sequences[i][index_])
2023-09-17T22:55:16,351                                            ^
2023-09-17T22:55:16,351   ------------------------------------------------------------

2023-09-17T22:55:16,352   pytrimal/_trimal.pyx:209:42: Cannot convert 'void *' to Python object

2023-09-17T22:55:16,353   Error compiling Cython file:
2023-09-17T22:55:16,354   ------------------------------------------------------------
2023-09-17T22:55:16,355   ...
2023-09-17T22:55:16,355           self._sequences_mapping = NULL
2023-09-17T22:55:16,356           self._residues_mapping = NULL

2023-09-17T22:55:16,357       def __dealloc__(self):
2023-09-17T22:55:16,357           if self._ali is not NULL:
2023-09-17T22:55:16,358               del self._ali
2023-09-17T22:55:16,359                      ^
2023-09-17T22:55:16,359   ------------------------------------------------------------

2023-09-17T22:55:16,360   pytrimal/_trimal.pyx:260:20: Deletion of non-Python, non-C++ object

2023-09-17T22:55:16,361   Error compiling Cython file:
2023-09-17T22:55:16,362   ------------------------------------------------------------
2023-09-17T22:55:16,362   ...
2023-09-17T22:55:16,362           cdef int   nresidues = -1

2023-09-17T22:55:16,363           if len(names) != len(sequences):
2023-09-17T22:55:16,363               raise ValueError(f"`Alignment` given {len(names)!r} names but {len(sequences)!r} sequences")

2023-09-17T22:55:16,364           self._ali = new trimal.alignment.Alignment()
2023-09-17T22:55:16,365                          ^
2023-09-17T22:55:16,365   ------------------------------------------------------------

2023-09-17T22:55:16,366   pytrimal/_trimal.pyx:321:24: 'Alignment' is not a type identifier

2023-09-17T22:55:16,367   Error compiling Cython file:
2023-09-17T22:55:16,367   ------------------------------------------------------------
2023-09-17T22:55:16,368   ...
2023-09-17T22:55:16,368           cdef int   nresidues = -1

2023-09-17T22:55:16,369           if len(names) != len(sequences):
2023-09-17T22:55:16,369               raise ValueError(f"`Alignment` given {len(names)!r} names but {len(sequences)!r} sequences")

2023-09-17T22:55:16,370           self._ali = new trimal.alignment.Alignment()
2023-09-17T22:55:16,370                          ^
2023-09-17T22:55:16,371   ------------------------------------------------------------

2023-09-17T22:55:16,372   pytrimal/_trimal.pyx:321:24: new operator can only be applied to a C++ class

2023-09-17T22:55:16,373   Error compiling Cython file:
2023-09-17T22:55:16,373   ------------------------------------------------------------
2023-09-17T22:55:16,373   ...
2023-09-17T22:55:16,374           if len(names) != len(sequences):
2023-09-17T22:55:16,374               raise ValueError(f"`Alignment` given {len(names)!r} names but {len(sequences)!r} sequences")

2023-09-17T22:55:16,375           self._ali = new trimal.alignment.Alignment()
2023-09-17T22:55:16,376           self._ali.numberOfSequences = len(sequences)
2023-09-17T22:55:16,377           self._ali.seqsName  = new_array[string](self._ali.numberOfSequences)
2023-09-17T22:55:16,377                                                 ^
2023-09-17T22:55:16,378   ------------------------------------------------------------

2023-09-17T22:55:16,379   pytrimal/_trimal.pyx:323:47: Cannot convert 'string *' to Python object

2023-09-17T22:55:16,380   Error compiling Cython file:
2023-09-17T22:55:16,381   ------------------------------------------------------------
2023-09-17T22:55:16,381   ...
2023-09-17T22:55:16,382               raise ValueError(f"`Alignment` given {len(names)!r} names but {len(sequences)!r} sequences")

2023-09-17T22:55:16,383           self._ali = new trimal.alignment.Alignment()
2023-09-17T22:55:16,384           self._ali.numberOfSequences = len(sequences)
2023-09-17T22:55:16,384           self._ali.seqsName  = new_array[string](self._ali.numberOfSequences)
2023-09-17T22:55:16,385           self._ali.sequences = new_array[string](self._ali.numberOfSequences)
2023-09-17T22:55:16,385                                                 ^
2023-09-17T22:55:16,386   ------------------------------------------------------------

2023-09-17T22:55:16,387   pytrimal/_trimal.pyx:324:47: Cannot convert 'string *' to Python object

2023-09-17T22:55:16,388   Error compiling Cython file:
2023-09-17T22:55:16,389   ------------------------------------------------------------
2023-09-17T22:55:16,389   ...
2023-09-17T22:55:16,390           cdef int    x     = 0
2023-09-17T22:55:16,390           cdef bytes  name
2023-09-17T22:55:16,391           cdef object names = PyList_New(self._ali.numberOfSequences)

2023-09-17T22:55:16,392           for i in range(self._ali.originalNumberOfSequences):
2023-09-17T22:55:16,393               if self._ali.saveSequences is NULL or self._ali.saveSequences[i] != -1:
2023-09-17T22:55:16,393                                         ^
2023-09-17T22:55:16,394   ------------------------------------------------------------

2023-09-17T22:55:16,396   pytrimal/_trimal.pyx:359:39: Invalid types for 'is' (Python object, void *)

2023-09-17T22:55:16,396   Error compiling Cython file:
2023-09-17T22:55:16,397   ------------------------------------------------------------
2023-09-17T22:55:16,397   ...
2023-09-17T22:55:16,397           return AlignmentResidues(self)

2023-09-17T22:55:16,398       cpdef Alignment copy(self):
2023-09-17T22:55:16,399           assert self._ali is not NULL
2023-09-17T22:55:16,399           cdef Alignment copy = (type(self)).__new__(type(self))
2023-09-17T22:55:16,399           copy._ali = new trimal.alignment.Alignment(self._ali[0])
2023-09-17T22:55:16,400                          ^
2023-09-17T22:55:16,400   ------------------------------------------------------------

2023-09-17T22:55:16,401   pytrimal/_trimal.pyx:384:24: 'Alignment' is not a type identifier

2023-09-17T22:55:16,402   Error compiling Cython file:
2023-09-17T22:55:16,402   ------------------------------------------------------------
2023-09-17T22:55:16,402   ...
2023-09-17T22:55:16,403           return AlignmentResidues(self)

2023-09-17T22:55:16,404       cpdef Alignment copy(self):
2023-09-17T22:55:16,404           assert self._ali is not NULL
2023-09-17T22:55:16,404           cdef Alignment copy = (type(self)).__new__(type(self))
2023-09-17T22:55:16,405           copy._ali = new trimal.alignment.Alignment(self._ali[0])
2023-09-17T22:55:16,405                          ^
2023-09-17T22:55:16,406   ------------------------------------------------------------

2023-09-17T22:55:16,407   pytrimal/_trimal.pyx:384:24: new operator can only be applied to a C++ class

2023-09-17T22:55:16,408   Error compiling Cython file:
2023-09-17T22:55:16,408   ------------------------------------------------------------
2023-09-17T22:55:16,409   ...

2023-09-17T22:55:16,410           # mask sequences
2023-09-17T22:55:16,411           if sequences_mask is not None:
2023-09-17T22:55:16,411               if len(sequences_mask) != self._ali.originalNumberOfSequences:
2023-09-17T22:55:16,412                   raise ValueError("Sequences mask must have the same length as the sequences list")
2023-09-17T22:55:16,412               self._ali.saveSequences = new_array[int](self._ali.originalNumberOfSequences)
2023-09-17T22:55:16,413                                                      ^
2023-09-17T22:55:16,414   ------------------------------------------------------------

2023-09-17T22:55:16,415   pytrimal/_trimal.pyx:425:52: Cannot convert 'int *' to Python object

2023-09-17T22:55:16,416   Error compiling Cython file:
2023-09-17T22:55:16,417   ------------------------------------------------------------
2023-09-17T22:55:16,417   ...

2023-09-17T22:55:16,418           # mask residues
2023-09-17T22:55:16,419           if residues_mask is not None:
2023-09-17T22:55:16,420               if len(residues_mask) != self._ali.originalNumberOfResidues:
2023-09-17T22:55:16,420                   raise ValueError("Sequences mask must have the same length as the sequences list")
2023-09-17T22:55:16,421               self._ali.saveResidues = new_array[int](self._ali.originalNumberOfResidues)
2023-09-17T22:55:16,421                                                     ^
2023-09-17T22:55:16,422   ------------------------------------------------------------

2023-09-17T22:55:16,423   pytrimal/_trimal.pyx:437:51: Cannot convert 'int *' to Python object

2023-09-17T22:55:16,424   Error compiling Cython file:
2023-09-17T22:55:16,425   ------------------------------------------------------------
2023-09-17T22:55:16,425   ...
2023-09-17T22:55:16,426           self._sequences_mapping = <int*> PyMem_Malloc(self._ali.numberOfSequences * sizeof(int))
2023-09-17T22:55:16,426           if self._sequences_mapping is NULL:
2023-09-17T22:55:16,427               raise MemoryError()
2023-09-17T22:55:16,428           x = 0
2023-09-17T22:55:16,428           for i in range(self._ali.originalNumberOfSequences):
2023-09-17T22:55:16,429               if self._ali.saveSequences is NULL or self._ali.saveSequences[i] != -1:
2023-09-17T22:55:16,430                                         ^
2023-09-17T22:55:16,430   ------------------------------------------------------------

2023-09-17T22:55:16,431   pytrimal/_trimal.pyx:460:39: Invalid types for 'is' (Python object, void *)

2023-09-17T22:55:16,432   Error compiling Cython file:
2023-09-17T22:55:16,432   ------------------------------------------------------------
2023-09-17T22:55:16,433   ...
2023-09-17T22:55:16,433           self._residues_mapping = <int*> PyMem_Malloc(self._ali.numberOfResidues * sizeof(int))
2023-09-17T22:55:16,434           if self._residues_mapping is NULL:
2023-09-17T22:55:16,434               raise MemoryError()
2023-09-17T22:55:16,434           x = 0
2023-09-17T22:55:16,435           for i in range(self._ali.originalNumberOfResidues):
2023-09-17T22:55:16,435               if self._ali.saveResidues is NULL or self._ali.saveResidues[i] != -1:
2023-09-17T22:55:16,436                                        ^
2023-09-17T22:55:16,436   ------------------------------------------------------------

2023-09-17T22:55:16,437   pytrimal/_trimal.pyx:470:38: Invalid types for 'is' (Python object, void *)

2023-09-17T22:55:16,438   Error compiling Cython file:
2023-09-17T22:55:16,438   ------------------------------------------------------------
2023-09-17T22:55:16,439   ...
2023-09-17T22:55:16,439                   this trimmed alignment.

2023-09-17T22:55:16,440           """
2023-09-17T22:55:16,441           assert self._ali is not NULL
2023-09-17T22:55:16,441           cdef Alignment orig = Alignment.__new__(Alignment)
2023-09-17T22:55:16,441           orig._ali = new trimal.alignment.Alignment(self._ali[0])
2023-09-17T22:55:16,442                          ^
2023-09-17T22:55:16,442   ------------------------------------------------------------

2023-09-17T22:55:16,444   pytrimal/_trimal.pyx:486:24: 'Alignment' is not a type identifier

2023-09-17T22:55:16,445   Error compiling Cython file:
2023-09-17T22:55:16,446   ------------------------------------------------------------
2023-09-17T22:55:16,446   ...
2023-09-17T22:55:16,447                   this trimmed alignment.

2023-09-17T22:55:16,448           """
2023-09-17T22:55:16,449           assert self._ali is not NULL
2023-09-17T22:55:16,449           cdef Alignment orig = Alignment.__new__(Alignment)
2023-09-17T22:55:16,450           orig._ali = new trimal.alignment.Alignment(self._ali[0])
2023-09-17T22:55:16,450                          ^
2023-09-17T22:55:16,451   ------------------------------------------------------------

2023-09-17T22:55:16,452   pytrimal/_trimal.pyx:486:24: new operator can only be applied to a C++ class

2023-09-17T22:55:16,454   Error compiling Cython file:
2023-09-17T22:55:16,454   ------------------------------------------------------------
2023-09-17T22:55:16,455   ...

2023-09-17T22:55:16,456           """
2023-09-17T22:55:16,456           assert self._ali is not NULL
2023-09-17T22:55:16,457           cdef Alignment orig = Alignment.__new__(Alignment)
2023-09-17T22:55:16,457           orig._ali = new trimal.alignment.Alignment(self._ali[0])
2023-09-17T22:55:16,458           del_array[int](orig._ali.saveSequences)
2023-09-17T22:55:16,458                                  ^
2023-09-17T22:55:16,459   ------------------------------------------------------------

2023-09-17T22:55:16,460   pytrimal/_trimal.pyx:487:32: Cannot convert Python object to 'int *'

2023-09-17T22:55:16,461   Error compiling Cython file:
2023-09-17T22:55:16,461   ------------------------------------------------------------
2023-09-17T22:55:16,462   ...
2023-09-17T22:55:16,463           """
2023-09-17T22:55:16,463           assert self._ali is not NULL
2023-09-17T22:55:16,464           cdef Alignment orig = Alignment.__new__(Alignment)
2023-09-17T22:55:16,464           orig._ali = new trimal.alignment.Alignment(self._ali[0])
2023-09-17T22:55:16,465           del_array[int](orig._ali.saveSequences)
2023-09-17T22:55:16,466           del_array[int](orig._ali.saveResidues)
2023-09-17T22:55:16,466                                  ^
2023-09-17T22:55:16,467   ------------------------------------------------------------

2023-09-17T22:55:16,468   pytrimal/_trimal.pyx:488:32: Cannot convert Python object to 'int *'

2023-09-17T22:55:16,469   Error compiling Cython file:
2023-09-17T22:55:16,470   ------------------------------------------------------------
2023-09-17T22:55:16,470   ...
2023-09-17T22:55:16,470           assert self._ali is not NULL
2023-09-17T22:55:16,471           cdef Alignment orig = Alignment.__new__(Alignment)
2023-09-17T22:55:16,471           orig._ali = new trimal.alignment.Alignment(self._ali[0])
2023-09-17T22:55:16,472           del_array[int](orig._ali.saveSequences)
2023-09-17T22:55:16,472           del_array[int](orig._ali.saveResidues)
2023-09-17T22:55:16,472           orig._ali.saveSequences = NULL
2023-09-17T22:55:16,473                                    ^
2023-09-17T22:55:16,473   ------------------------------------------------------------

2023-09-17T22:55:16,474   pytrimal/_trimal.pyx:489:34: Cannot convert 'void *' to Python object

2023-09-17T22:55:16,475   Error compiling Cython file:
2023-09-17T22:55:16,475   ------------------------------------------------------------
2023-09-17T22:55:16,476   ...
2023-09-17T22:55:16,476           cdef Alignment orig = Alignment.__new__(Alignment)
2023-09-17T22:55:16,477           orig._ali = new trimal.alignment.Alignment(self._ali[0])
2023-09-17T22:55:16,477           del_array[int](orig._ali.saveSequences)
2023-09-17T22:55:16,478           del_array[int](orig._ali.saveResidues)
2023-09-17T22:55:16,478           orig._ali.saveSequences = NULL
2023-09-17T22:55:16,479           orig._ali.saveResidues = NULL
2023-09-17T22:55:16,479                                   ^
2023-09-17T22:55:16,479   ------------------------------------------------------------

2023-09-17T22:55:16,480   pytrimal/_trimal.pyx:490:33: Cannot convert 'void *' to Python object

2023-09-17T22:55:16,481   Error compiling Cython file:
2023-09-17T22:55:16,482   ------------------------------------------------------------
2023-09-17T22:55:16,483   ...
2023-09-17T22:55:16,483                   residues have been trimmed.

2023-09-17T22:55:16,484           """
2023-09-17T22:55:16,485           assert self._ali is not NULL
2023-09-17T22:55:16,486           cdef TrimmedAlignment term_only = TrimmedAlignment.__new__(TrimmedAlignment)
2023-09-17T22:55:16,486           term_only._ali = new trimal.alignment.Alignment(self._ali[0])
2023-09-17T22:55:16,487                               ^
2023-09-17T22:55:16,487   ------------------------------------------------------------

2023-09-17T22:55:16,489   pytrimal/_trimal.pyx:507:29: 'Alignment' is not a type identifier

2023-09-17T22:55:16,490   Error compiling Cython file:
2023-09-17T22:55:16,491   ------------------------------------------------------------
2023-09-17T22:55:16,491   ...
2023-09-17T22:55:16,492                   residues have been trimmed.

2023-09-17T22:55:16,493           """
2023-09-17T22:55:16,493           assert self._ali is not NULL
2023-09-17T22:55:16,494           cdef TrimmedAlignment term_only = TrimmedAlignment.__new__(TrimmedAlignment)
2023-09-17T22:55:16,494           term_only._ali = new trimal.alignment.Alignment(self._ali[0])
2023-09-17T22:55:16,495                               ^
2023-09-17T22:55:16,495   ------------------------------------------------------------

2023-09-17T22:55:16,497   pytrimal/_trimal.pyx:507:29: new operator can only be applied to a C++ class

2023-09-17T22:55:16,498   Error compiling Cython file:
2023-09-17T22:55:16,498   ------------------------------------------------------------
2023-09-17T22:55:16,499   ...
2023-09-17T22:55:16,499           term_only._build_index_mapping()
2023-09-17T22:55:16,500           return term_only

2023-09-17T22:55:16,501       cpdef TrimmedAlignment copy(self):
2023-09-17T22:55:16,502           cdef TrimmedAlignment copy = TrimmedAlignment.__new__(TrimmedAlignment)
2023-09-17T22:55:16,502           copy._ali = new trimal.alignment.Alignment(self._ali[0])
2023-09-17T22:55:16,503                          ^
2023-09-17T22:55:16,504   ------------------------------------------------------------

2023-09-17T22:55:16,505   pytrimal/_trimal.pyx:514:24: 'Alignment' is not a type identifier

2023-09-17T22:55:16,505   Error compiling Cython file:
2023-09-17T22:55:16,506   ------------------------------------------------------------
2023-09-17T22:55:16,506   ...
2023-09-17T22:55:16,506           term_only._build_index_mapping()
2023-09-17T22:55:16,507           return term_only

2023-09-17T22:55:16,508       cpdef TrimmedAlignment copy(self):
2023-09-17T22:55:16,508           cdef TrimmedAlignment copy = TrimmedAlignment.__new__(TrimmedAlignment)
2023-09-17T22:55:16,508           copy._ali = new trimal.alignment.Alignment(self._ali[0])
2023-09-17T22:55:16,509                          ^
2023-09-17T22:55:16,509   ------------------------------------------------------------

2023-09-17T22:55:16,510   pytrimal/_trimal.pyx:514:24: new operator can only be applied to a C++ class

2023-09-17T22:55:16,511   Error compiling Cython file:
2023-09-17T22:55:16,511   ------------------------------------------------------------
2023-09-17T22:55:16,512   ...

2023-09-17T22:55:16,512           cdef int    i
2023-09-17T22:55:16,513           cdef object mask = PyList_New(self._ali.originalNumberOfResidues)

2023-09-17T22:55:16,514           for i in range(self._ali.originalNumberOfResidues):
2023-09-17T22:55:16,514               if self._ali.saveResidues is NULL or self._ali.saveResidues[i] != -1:
2023-09-17T22:55:16,515                                        ^
2023-09-17T22:55:16,515   ------------------------------------------------------------

2023-09-17T22:55:16,516   pytrimal/_trimal.pyx:528:38: Invalid types for 'is' (Python object, void *)

2023-09-17T22:55:16,517   Error compiling Cython file:
2023-09-17T22:55:16,517   ------------------------------------------------------------
2023-09-17T22:55:16,518   ...

2023-09-17T22:55:16,519           cdef int    i
2023-09-17T22:55:16,520           cdef object mask = PyList_New(self._ali.originalNumberOfSequences)

2023-09-17T22:55:16,521           for i in range(self._ali.originalNumberOfSequences):
2023-09-17T22:55:16,521               if self._ali.saveSequences is NULL or self._ali.saveSequences[i] != -1:
2023-09-17T22:55:16,522                                         ^
2023-09-17T22:55:16,523   ------------------------------------------------------------

2023-09-17T22:55:16,524   pytrimal/_trimal.pyx:547:39: Invalid types for 'is' (Python object, void *)

2023-09-17T22:55:16,525   Error compiling Cython file:
2023-09-17T22:55:16,525   ------------------------------------------------------------
2023-09-17T22:55:16,526   ...
2023-09-17T22:55:16,527           if isinstance(alignment, TrimmedAlignment):
2023-09-17T22:55:16,527               copy = Alignment(alignment.names, alignment.sequences)
2023-09-17T22:55:16,528               manager.origAlig = copy._ali
2023-09-17T22:55:16,528               copy._ali = NULL
2023-09-17T22:55:16,529           else:
2023-09-17T22:55:16,529               manager.origAlig = new trimal.alignment.Alignment(alignment._ali[0])
2023-09-17T22:55:16,530                                     ^
2023-09-17T22:55:16,530   ------------------------------------------------------------

2023-09-17T22:55:16,531   pytrimal/_trimal.pyx:608:35: 'Alignment' is not a type identifier

2023-09-17T22:55:16,532   Error compiling Cython file:
2023-09-17T22:55:16,533   ------------------------------------------------------------
2023-09-17T22:55:16,533   ...
2023-09-17T22:55:16,534           if isinstance(alignment, TrimmedAlignment):
2023-09-17T22:55:16,534               copy = Alignment(alignment.names, alignment.sequences)
2023-09-17T22:55:16,535               manager.origAlig = copy._ali
2023-09-17T22:55:16,536               copy._ali = NULL
2023-09-17T22:55:16,536           else:
2023-09-17T22:55:16,537               manager.origAlig = new trimal.alignment.Alignment(alignment._ali[0])
2023-09-17T22:55:16,537                                     ^
2023-09-17T22:55:16,538   ------------------------------------------------------------

2023-09-17T22:55:16,540   pytrimal/_trimal.pyx:608:35: new operator can only be applied to a C++ class

2023-09-17T22:55:16,540   Error compiling Cython file:
2023-09-17T22:55:16,541   ------------------------------------------------------------
2023-09-17T22:55:16,541   ...

2023-09-17T22:55:16,542               manager.create_or_use_similarity_matrix()
2023-09-17T22:55:16,542               # self.manager.print_statistics()
2023-09-17T22:55:16,542               manager.clean_alignment()

2023-09-17T22:55:16,543               if manager.singleAlig == NULL:
2023-09-17T22:55:16,544                                    ^
2023-09-17T22:55:16,544   ------------------------------------------------------------

2023-09-17T22:55:16,545   pytrimal/_trimal.pyx:624:34: Invalid types for '==' (Python object, void *)

2023-09-17T22:55:16,546   Error compiling Cython file:
2023-09-17T22:55:16,546   ------------------------------------------------------------
2023-09-17T22:55:16,546   ...
2023-09-17T22:55:16,547               manager.create_or_use_similarity_matrix()
2023-09-17T22:55:16,547               # self.manager.print_statistics()
2023-09-17T22:55:16,548               manager.clean_alignment()

2023-09-17T22:55:16,548               if manager.singleAlig == NULL:
2023-09-17T22:55:16,549                   manager.singleAlig = manager.origAlig
2023-09-17T22:55:16,549                         ^
2023-09-17T22:55:16,550   ------------------------------------------------------------

2023-09-17T22:55:16,550   pytrimal/_trimal.pyx:625:23: Assignment of Python object not allowed without gil

2023-09-17T22:55:16,551   Error compiling Cython file:
2023-09-17T22:55:16,552   ------------------------------------------------------------
2023-09-17T22:55:16,552   ...
2023-09-17T22:55:16,553               # self.manager.print_statistics()
2023-09-17T22:55:16,553               manager.clean_alignment()

2023-09-17T22:55:16,554               if manager.singleAlig == NULL:
2023-09-17T22:55:16,555                   manager.singleAlig = manager.origAlig
2023-09-17T22:55:16,556                   manager.origAlig = NULL
2023-09-17T22:55:16,556                         ^
2023-09-17T22:55:16,557   ------------------------------------------------------------

2023-09-17T22:55:16,558   pytrimal/_trimal.pyx:626:23: Assignment of Python object not allowed without gil

2023-09-17T22:55:16,559   Error compiling Cython file:
2023-09-17T22:55:16,560   ------------------------------------------------------------
2023-09-17T22:55:16,560   ...
2023-09-17T22:55:16,561               # self.manager.print_statistics()
2023-09-17T22:55:16,562               manager.clean_alignment()

2023-09-17T22:55:16,563               if manager.singleAlig == NULL:
2023-09-17T22:55:16,564                   manager.singleAlig = manager.origAlig
2023-09-17T22:55:16,564                   manager.origAlig = NULL
2023-09-17T22:55:16,565                                     ^
2023-09-17T22:55:16,565   ------------------------------------------------------------

2023-09-17T22:55:16,566   pytrimal/_trimal.pyx:626:35: Cannot convert 'void *' to Python object

2023-09-17T22:55:16,568   Error compiling Cython file:
2023-09-17T22:55:16,568   ------------------------------------------------------------
2023-09-17T22:55:16,569   ...
2023-09-17T22:55:16,569               manager.postprocess_alignment()
2023-09-17T22:55:16,570               # manager.output_reports()
2023-09-17T22:55:16,570               # manager.save_alignment()

2023-09-17T22:55:16,571           cdef TrimmedAlignment trimmed = TrimmedAlignment.__new__(TrimmedAlignment)
2023-09-17T22:55:16,572           trimmed._ali = new trimal.alignment.Alignment(manager.singleAlig[0])
2023-09-17T22:55:16,572                             ^
2023-09-17T22:55:16,573   ------------------------------------------------------------

2023-09-17T22:55:16,574   pytrimal/_trimal.pyx:633:27: 'Alignment' is not a type identifier

2023-09-17T22:55:16,576   Error compiling Cython file:
2023-09-17T22:55:16,576   ------------------------------------------------------------
2023-09-17T22:55:16,577   ...
2023-09-17T22:55:16,578               manager.postprocess_alignment()
2023-09-17T22:55:16,578               # manager.output_reports()
2023-09-17T22:55:16,578               # manager.save_alignment()

2023-09-17T22:55:16,579           cdef TrimmedAlignment trimmed = TrimmedAlignment.__new__(TrimmedAlignment)
2023-09-17T22:55:16,580           trimmed._ali = new trimal.alignment.Alignment(manager.singleAlig[0])
2023-09-17T22:55:16,580                             ^
2023-09-17T22:55:16,580   ------------------------------------------------------------

2023-09-17T22:55:16,581   pytrimal/_trimal.pyx:633:27: new operator can only be applied to a C++ class

2023-09-17T22:55:16,597   Error compiling Cython file:
2023-09-17T22:55:16,597   ------------------------------------------------------------
2023-09-17T22:55:16,598   ...
2023-09-17T22:55:16,598           self._configure_manager(&manager)

2023-09-17T22:55:16,599           with nogil:
2023-09-17T22:55:16,599               # set flags
2023-09-17T22:55:16,600               # self.manager.origAlig.setKeepSequencesFlag(self.keep_sequences)
2023-09-17T22:55:16,600               manager.set_window_size()
2023-09-17T22:55:16,600                                     ^
2023-09-17T22:55:16,601   ------------------------------------------------------------

2023-09-17T22:55:16,602   pytrimal/_trimal.pyx:616:35: Discarding owned Python object not allowed without gil

2023-09-17T22:55:16,603   Error compiling Cython file:
2023-09-17T22:55:16,603   ------------------------------------------------------------
2023-09-17T22:55:16,604   ...
2023-09-17T22:55:16,604           self._configure_manager(&manager)

2023-09-17T22:55:16,605           with nogil:
2023-09-17T22:55:16,606               # set flags
2023-09-17T22:55:16,607               # self.manager.origAlig.setKeepSequencesFlag(self.keep_sequences)
2023-09-17T22:55:16,607               manager.set_window_size()
2023-09-17T22:55:16,608                                     ^
2023-09-17T22:55:16,609   ------------------------------------------------------------

2023-09-17T22:55:16,610   pytrimal/_trimal.pyx:616:35: Calling gil-requiring function not allowed without gil

2023-09-17T22:55:16,611   Error compiling Cython file:
2023-09-17T22:55:16,612   ------------------------------------------------------------
2023-09-17T22:55:16,613   ...
2023-09-17T22:55:16,613           self._configure_manager(&manager)

2023-09-17T22:55:16,614           with nogil:
2023-09-17T22:55:16,615               # set flags
2023-09-17T22:55:16,616               # self.manager.origAlig.setKeepSequencesFlag(self.keep_sequences)
2023-09-17T22:55:16,616               manager.set_window_size()
2023-09-17T22:55:16,617                     ^
2023-09-17T22:55:16,618   ------------------------------------------------------------

2023-09-17T22:55:16,619   pytrimal/_trimal.pyx:616:19: Accessing Python attribute not allowed without gil

2023-09-17T22:55:16,620   Error compiling Cython file:
2023-09-17T22:55:16,620   ------------------------------------------------------------
2023-09-17T22:55:16,621   ...
2023-09-17T22:55:16,621           self._configure_manager(&manager)

2023-09-17T22:55:16,623           with nogil:
2023-09-17T22:55:16,623               # set flags
2023-09-17T22:55:16,624               # self.manager.origAlig.setKeepSequencesFlag(self.keep_sequences)
2023-09-17T22:55:16,624               manager.set_window_size()
2023-09-17T22:55:16,625                                     ^
2023-09-17T22:55:16,625   ------------------------------------------------------------

2023-09-17T22:55:16,627   pytrimal/_trimal.pyx:616:35: Constructing Python tuple not allowed without gil

2023-09-17T22:55:16,628   Error compiling Cython file:
2023-09-17T22:55:16,629   ------------------------------------------------------------
2023-09-17T22:55:16,630   ...

2023-09-17T22:55:16,631           with nogil:
2023-09-17T22:55:16,632               # set flags
2023-09-17T22:55:16,632               # self.manager.origAlig.setKeepSequencesFlag(self.keep_sequences)
2023-09-17T22:55:16,633               manager.set_window_size()
2023-09-17T22:55:16,634               if manager.blockSize != -1:
2023-09-17T22:55:16,634                                   ^
2023-09-17T22:55:16,635   ------------------------------------------------------------

2023-09-17T22:55:16,636   pytrimal/_trimal.pyx:617:33: Truth-testing Python object not allowed without gil

2023-09-17T22:55:16,636   Error compiling Cython file:
2023-09-17T22:55:16,637   ------------------------------------------------------------
2023-09-17T22:55:16,637   ...

2023-09-17T22:55:16,638           with nogil:
2023-09-17T22:55:16,639               # set flags
2023-09-17T22:55:16,639               # self.manager.origAlig.setKeepSequencesFlag(self.keep_sequences)
2023-09-17T22:55:16,639               manager.set_window_size()
2023-09-17T22:55:16,640               if manager.blockSize != -1:
2023-09-17T22:55:16,640                                   ^
2023-09-17T22:55:16,641   ------------------------------------------------------------

2023-09-17T22:55:16,642   pytrimal/_trimal.pyx:617:33: Calling gil-requiring function not allowed without gil

2023-09-17T22:55:16,643   Error compiling Cython file:
2023-09-17T22:55:16,643   ------------------------------------------------------------
2023-09-17T22:55:16,643   ...

2023-09-17T22:55:16,644           with nogil:
2023-09-17T22:55:16,645               # set flags
2023-09-17T22:55:16,645               # self.manager.origAlig.setKeepSequencesFlag(self.keep_sequences)
2023-09-17T22:55:16,646               manager.set_window_size()
2023-09-17T22:55:16,646               if manager.blockSize != -1:
2023-09-17T22:55:16,647                        ^
2023-09-17T22:55:16,647   ------------------------------------------------------------

2023-09-17T22:55:16,648   pytrimal/_trimal.pyx:617:22: Accessing Python attribute not allowed without gil

2023-09-17T22:55:16,650   Error compiling Cython file:
2023-09-17T22:55:16,650   ------------------------------------------------------------
2023-09-17T22:55:16,651   ...
2023-09-17T22:55:16,652           with nogil:
2023-09-17T22:55:16,652               # set flags
2023-09-17T22:55:16,653               # self.manager.origAlig.setKeepSequencesFlag(self.keep_sequences)
2023-09-17T22:55:16,653               manager.set_window_size()
2023-09-17T22:55:16,654               if manager.blockSize != -1:
2023-09-17T22:55:16,655                   manager.origAlig.setBlockSize(manager.blockSize)
2023-09-17T22:55:16,655                                               ^
2023-09-17T22:55:16,656   ------------------------------------------------------------

2023-09-17T22:55:16,657   pytrimal/_trimal.pyx:618:45: Discarding owned Python object not allowed without gil

2023-09-17T22:55:16,658   Error compiling Cython file:
2023-09-17T22:55:16,659   ------------------------------------------------------------
2023-09-17T22:55:16,659   ...
2023-09-17T22:55:16,660           with nogil:
2023-09-17T22:55:16,660               # set flags
2023-09-17T22:55:16,661               # self.manager.origAlig.setKeepSequencesFlag(self.keep_sequences)
2023-09-17T22:55:16,661               manager.set_window_size()
2023-09-17T22:55:16,662               if manager.blockSize != -1:
2023-09-17T22:55:16,662                   manager.origAlig.setBlockSize(manager.blockSize)
2023-09-17T22:55:16,663                                               ^
2023-09-17T22:55:16,663   ------------------------------------------------------------

2023-09-17T22:55:16,664   pytrimal/_trimal.pyx:618:45: Calling gil-requiring function not allowed without gil

2023-09-17T22:55:16,666   Error compiling Cython file:
2023-09-17T22:55:16,666   ------------------------------------------------------------
2023-09-17T22:55:16,667   ...
2023-09-17T22:55:16,668           with nogil:
2023-09-17T22:55:16,668               # set flags
2023-09-17T22:55:16,669               # self.manager.origAlig.setKeepSequencesFlag(self.keep_sequences)
2023-09-17T22:55:16,670               manager.set_window_size()
2023-09-17T22:55:16,670               if manager.blockSize != -1:
2023-09-17T22:55:16,671                   manager.origAlig.setBlockSize(manager.blockSize)
2023-09-17T22:55:16,671                                  ^
2023-09-17T22:55:16,672   ------------------------------------------------------------

2023-09-17T22:55:16,673   pytrimal/_trimal.pyx:618:32: Accessing Python attribute not allowed without gil

2023-09-17T22:55:16,673   Error compiling Cython file:
2023-09-17T22:55:16,674   ------------------------------------------------------------
2023-09-17T22:55:16,674   ...
2023-09-17T22:55:16,675           with nogil:
2023-09-17T22:55:16,675               # set flags
2023-09-17T22:55:16,676               # self.manager.origAlig.setKeepSequencesFlag(self.keep_sequences)
2023-09-17T22:55:16,676               manager.set_window_size()
2023-09-17T22:55:16,677               if manager.blockSize != -1:
2023-09-17T22:55:16,677                   manager.origAlig.setBlockSize(manager.blockSize)
2023-09-17T22:55:16,678                         ^
2023-09-17T22:55:16,678   ------------------------------------------------------------

2023-09-17T22:55:16,679   pytrimal/_trimal.pyx:618:23: Accessing Python attribute not allowed without gil

2023-09-17T22:55:16,680   Error compiling Cython file:
2023-09-17T22:55:16,680   ------------------------------------------------------------
2023-09-17T22:55:16,681   ...
2023-09-17T22:55:16,681           with nogil:
2023-09-17T22:55:16,681               # set flags
2023-09-17T22:55:16,682               # self.manager.origAlig.setKeepSequencesFlag(self.keep_sequences)
2023-09-17T22:55:16,682               manager.set_window_size()
2023-09-17T22:55:16,683               if manager.blockSize != -1:
2023-09-17T22:55:16,684                   manager.origAlig.setBlockSize(manager.blockSize)
2023-09-17T22:55:16,684                                               ^
2023-09-17T22:55:16,685   ------------------------------------------------------------

2023-09-17T22:55:16,686   pytrimal/_trimal.pyx:618:45: Constructing Python tuple not allowed without gil

2023-09-17T22:55:16,687   Error compiling Cython file:
2023-09-17T22:55:16,688   ------------------------------------------------------------
2023-09-17T22:55:16,689   ...
2023-09-17T22:55:16,689           with nogil:
2023-09-17T22:55:16,690               # set flags
2023-09-17T22:55:16,690               # self.manager.origAlig.setKeepSequencesFlag(self.keep_sequences)
2023-09-17T22:55:16,691               manager.set_window_size()
2023-09-17T22:55:16,692               if manager.blockSize != -1:
2023-09-17T22:55:16,692                   manager.origAlig.setBlockSize(manager.blockSize)
2023-09-17T22:55:16,693                                                       ^
2023-09-17T22:55:16,694   ------------------------------------------------------------

2023-09-17T22:55:16,695   pytrimal/_trimal.pyx:618:53: Accessing Python attribute not allowed without gil

2023-09-17T22:55:16,696   Error compiling Cython file:
2023-09-17T22:55:16,696   ------------------------------------------------------------
2023-09-17T22:55:16,697   ...
2023-09-17T22:55:16,697               # self.manager.origAlig.setKeepSequencesFlag(self.keep_sequences)
2023-09-17T22:55:16,698               manager.set_window_size()
2023-09-17T22:55:16,698               if manager.blockSize != -1:
2023-09-17T22:55:16,699                   manager.origAlig.setBlockSize(manager.blockSize)

2023-09-17T22:55:16,700               manager.create_or_use_similarity_matrix()
2023-09-17T22:55:16,700                                                     ^
2023-09-17T22:55:16,701   ------------------------------------------------------------

2023-09-17T22:55:16,702   pytrimal/_trimal.pyx:620:51: Discarding owned Python object not allowed without gil

2023-09-17T22:55:16,703   Error compiling Cython file:
2023-09-17T22:55:16,704   ------------------------------------------------------------
2023-09-17T22:55:16,704   ...
2023-09-17T22:55:16,705               # self.manager.origAlig.setKeepSequencesFlag(self.keep_sequences)
2023-09-17T22:55:16,706               manager.set_window_size()
2023-09-17T22:55:16,707               if manager.blockSize != -1:
2023-09-17T22:55:16,707                   manager.origAlig.setBlockSize(manager.blockSize)

2023-09-17T22:55:16,708               manager.create_or_use_similarity_matrix()
2023-09-17T22:55:16,708                                                     ^
2023-09-17T22:55:16,709   ------------------------------------------------------------

2023-09-17T22:55:16,710   pytrimal/_trimal.pyx:620:51: Calling gil-requiring function not allowed without gil

2023-09-17T22:55:16,710   Error compiling Cython file:
2023-09-17T22:55:16,711   ------------------------------------------------------------
2023-09-17T22:55:16,711   ...
2023-09-17T22:55:16,712               # self.manager.origAlig.setKeepSequencesFlag(self.keep_sequences)
2023-09-17T22:55:16,712               manager.set_window_size()
2023-09-17T22:55:16,712               if manager.blockSize != -1:
2023-09-17T22:55:16,713                   manager.origAlig.setBlockSize(manager.blockSize)

2023-09-17T22:55:16,714               manager.create_or_use_similarity_matrix()
2023-09-17T22:55:16,714                     ^
2023-09-17T22:55:16,715   ------------------------------------------------------------

2023-09-17T22:55:16,716   pytrimal/_trimal.pyx:620:19: Accessing Python attribute not allowed without gil

2023-09-17T22:55:16,717   Error compiling Cython file:
2023-09-17T22:55:16,717   ------------------------------------------------------------
2023-09-17T22:55:16,717   ...
2023-09-17T22:55:16,718               # self.manager.origAlig.setKeepSequencesFlag(self.keep_sequences)
2023-09-17T22:55:16,719               manager.set_window_size()
2023-09-17T22:55:16,719               if manager.blockSize != -1:
2023-09-17T22:55:16,720                   manager.origAlig.setBlockSize(manager.blockSize)

2023-09-17T22:55:16,721               manager.create_or_use_similarity_matrix()
2023-09-17T22:55:16,721                                                     ^
2023-09-17T22:55:16,722   ------------------------------------------------------------

2023-09-17T22:55:16,723   pytrimal/_trimal.pyx:620:51: Constructing Python tuple not allowed without gil

2023-09-17T22:55:16,724   Error compiling Cython file:
2023-09-17T22:55:16,725   ------------------------------------------------------------
2023-09-17T22:55:16,726   ...
2023-09-17T22:55:16,727               if manager.blockSize != -1:
2023-09-17T22:55:16,728                   manager.origAlig.setBlockSize(manager.blockSize)

2023-09-17T22:55:16,730               manager.create_or_use_similarity_matrix()
2023-09-17T22:55:16,731               # self.manager.print_statistics()
2023-09-17T22:55:16,732               manager.clean_alignment()
2023-09-17T22:55:16,732                                     ^
2023-09-17T22:55:16,733   ------------------------------------------------------------

2023-09-17T22:55:16,735   pytrimal/_trimal.pyx:622:35: Discarding owned Python object not allowed without gil

2023-09-17T22:55:16,737   Error compiling Cython file:
2023-09-17T22:55:16,737   ------------------------------------------------------------
2023-09-17T22:55:16,738   ...
2023-09-17T22:55:16,739               if manager.blockSize != -1:
2023-09-17T22:55:16,740                   manager.origAlig.setBlockSize(manager.blockSize)

2023-09-17T22:55:16,741               manager.create_or_use_similarity_matrix()
2023-09-17T22:55:16,742               # self.manager.print_statistics()
2023-09-17T22:55:16,743               manager.clean_alignment()
2023-09-17T22:55:16,744                                     ^
2023-09-17T22:55:16,745   ------------------------------------------------------------

2023-09-17T22:55:16,747   pytrimal/_trimal.pyx:622:35: Calling gil-requiring function not allowed without gil

2023-09-17T22:55:16,748   Error compiling Cython file:
2023-09-17T22:55:16,749   ------------------------------------------------------------
2023-09-17T22:55:16,750   ...
2023-09-17T22:55:16,751               if manager.blockSize != -1:
2023-09-17T22:55:16,752                   manager.origAlig.setBlockSize(manager.blockSize)

2023-09-17T22:55:16,753               manager.create_or_use_similarity_matrix()
2023-09-17T22:55:16,753               # self.manager.print_statistics()
2023-09-17T22:55:16,754               manager.clean_alignment()
2023-09-17T22:55:16,755                     ^
2023-09-17T22:55:16,755   ------------------------------------------------------------

2023-09-17T22:55:16,756   pytrimal/_trimal.pyx:622:19: Accessing Python attribute not allowed without gil

2023-09-17T22:55:16,758   Error compiling Cython file:
2023-09-17T22:55:16,758   ------------------------------------------------------------
2023-09-17T22:55:16,759   ...
2023-09-17T22:55:16,760               if manager.blockSize != -1:
2023-09-17T22:55:16,760                   manager.origAlig.setBlockSize(manager.blockSize)

2023-09-17T22:55:16,762               manager.create_or_use_similarity_matrix()
2023-09-17T22:55:16,762               # self.manager.print_statistics()
2023-09-17T22:55:16,763               manager.clean_alignment()
2023-09-17T22:55:16,764                                     ^
2023-09-17T22:55:16,764   ------------------------------------------------------------

2023-09-17T22:55:16,766   pytrimal/_trimal.pyx:622:35: Constructing Python tuple not allowed without gil

2023-09-17T22:55:16,767   Error compiling Cython file:
2023-09-17T22:55:16,768   ------------------------------------------------------------
2023-09-17T22:55:16,768   ...

2023-09-17T22:55:16,770               manager.create_or_use_similarity_matrix()
2023-09-17T22:55:16,770               # self.manager.print_statistics()
2023-09-17T22:55:16,771               manager.clean_alignment()

2023-09-17T22:55:16,772               if manager.singleAlig == NULL:
2023-09-17T22:55:16,773                                    ^
2023-09-17T22:55:16,774   ------------------------------------------------------------

2023-09-17T22:55:16,776   pytrimal/_trimal.pyx:624:34: Truth-testing Python object not allowed without gil

2023-09-17T22:55:16,777   Error compiling Cython file:
2023-09-17T22:55:16,778   ------------------------------------------------------------
2023-09-17T22:55:16,779   ...

2023-09-17T22:55:16,781               manager.create_or_use_similarity_matrix()
2023-09-17T22:55:16,781               # self.manager.print_statistics()
2023-09-17T22:55:16,782               manager.clean_alignment()

2023-09-17T22:55:16,784               if manager.singleAlig == NULL:
2023-09-17T22:55:16,785                                    ^
2023-09-17T22:55:16,786   ------------------------------------------------------------

2023-09-17T22:55:16,788   pytrimal/_trimal.pyx:624:34: Operation not allowed without gil

2023-09-17T22:55:16,790   Error compiling Cython file:
2023-09-17T22:55:16,791   ------------------------------------------------------------
2023-09-17T22:55:16,791   ...

2023-09-17T22:55:16,793               manager.create_or_use_similarity_matrix()
2023-09-17T22:55:16,793               # self.manager.print_statistics()
2023-09-17T22:55:16,794               manager.clean_alignment()

2023-09-17T22:55:16,796               if manager.singleAlig == NULL:
2023-09-17T22:55:16,797                        ^
2023-09-17T22:55:16,798   ------------------------------------------------------------

2023-09-17T22:55:16,799   pytrimal/_trimal.pyx:624:22: Accessing Python attribute not allowed without gil

2023-09-17T22:55:16,800   Error compiling Cython file:
2023-09-17T22:55:16,801   ------------------------------------------------------------
2023-09-17T22:55:16,802   ...
2023-09-17T22:55:16,803               manager.create_or_use_similarity_matrix()
2023-09-17T22:55:16,804               # self.manager.print_statistics()
2023-09-17T22:55:16,804               manager.clean_alignment()

2023-09-17T22:55:16,806               if manager.singleAlig == NULL:
2023-09-17T22:55:16,807                   manager.singleAlig = manager.origAlig
2023-09-17T22:55:16,808                         ^
2023-09-17T22:55:16,809   ------------------------------------------------------------

2023-09-17T22:55:16,811   pytrimal/_trimal.pyx:625:23: Accessing Python attribute not allowed without gil

2023-09-17T22:55:16,812   Error compiling Cython file:
2023-09-17T22:55:16,813   ------------------------------------------------------------
2023-09-17T22:55:16,813   ...
2023-09-17T22:55:16,814               manager.create_or_use_similarity_matrix()
2023-09-17T22:55:16,815               # self.manager.print_statistics()
2023-09-17T22:55:16,815               manager.clean_alignment()

2023-09-17T22:55:16,817               if manager.singleAlig == NULL:
2023-09-17T22:55:16,817                   manager.singleAlig = manager.origAlig
2023-09-17T22:55:16,818                                              ^
2023-09-17T22:55:16,819   ------------------------------------------------------------

2023-09-17T22:55:16,820   pytrimal/_trimal.pyx:625:44: Accessing Python attribute not allowed without gil

2023-09-17T22:55:16,822   Error compiling Cython file:
2023-09-17T22:55:16,822   ------------------------------------------------------------
2023-09-17T22:55:16,823   ...
2023-09-17T22:55:16,824               # self.manager.print_statistics()
2023-09-17T22:55:16,824               manager.clean_alignment()

2023-09-17T22:55:16,826               if manager.singleAlig == NULL:
2023-09-17T22:55:16,827                   manager.singleAlig = manager.origAlig
2023-09-17T22:55:16,827                   manager.origAlig = NULL
2023-09-17T22:55:16,828                         ^
2023-09-17T22:55:16,829   ------------------------------------------------------------

2023-09-17T22:55:16,830   pytrimal/_trimal.pyx:626:23: Accessing Python attribute not allowed without gil

2023-09-17T22:55:16,832   Error compiling Cython file:
2023-09-17T22:55:16,832   ------------------------------------------------------------
2023-09-17T22:55:16,833   ...
2023-09-17T22:55:16,834               # self.manager.print_statistics()
2023-09-17T22:55:16,835               manager.clean_alignment()

2023-09-17T22:55:16,837               if manager.singleAlig == NULL:
2023-09-17T22:55:16,838                   manager.singleAlig = manager.origAlig
2023-09-17T22:55:16,839                   manager.origAlig = NULL
2023-09-17T22:55:16,840                                     ^
2023-09-17T22:55:16,841   ------------------------------------------------------------

2023-09-17T22:55:16,842   pytrimal/_trimal.pyx:626:35: Converting to Python object not allowed without gil

2023-09-17T22:55:16,844   Error compiling Cython file:
2023-09-17T22:55:16,845   ------------------------------------------------------------
2023-09-17T22:55:16,846   ...

2023-09-17T22:55:16,848               if manager.singleAlig == NULL:
2023-09-17T22:55:16,848                   manager.singleAlig = manager.origAlig
2023-09-17T22:55:16,849                   manager.origAlig = NULL

2023-09-17T22:55:16,851               manager.postprocess_alignment()
2023-09-17T22:55:16,851                                           ^
2023-09-17T22:55:16,852   ------------------------------------------------------------

2023-09-17T22:55:16,854   pytrimal/_trimal.pyx:628:41: Discarding owned Python object not allowed without gil

2023-09-17T22:55:16,855   Error compiling Cython file:
2023-09-17T22:55:16,856   ------------------------------------------------------------
2023-09-17T22:55:16,857   ...

2023-09-17T22:55:16,858               if manager.singleAlig == NULL:
2023-09-17T22:55:16,859                   manager.singleAlig = manager.origAlig
2023-09-17T22:55:16,860                   manager.origAlig = NULL

2023-09-17T22:55:16,861               manager.postprocess_alignment()
2023-09-17T22:55:16,862                                           ^
2023-09-17T22:55:16,863   ------------------------------------------------------------

2023-09-17T22:55:16,864   pytrimal/_trimal.pyx:628:41: Calling gil-requiring function not allowed without gil

2023-09-17T22:55:16,866   Error compiling Cython file:
2023-09-17T22:55:16,867   ------------------------------------------------------------
2023-09-17T22:55:16,868   ...

2023-09-17T22:55:16,869               if manager.singleAlig == NULL:
2023-09-17T22:55:16,870                   manager.singleAlig = manager.origAlig
2023-09-17T22:55:16,870                   manager.origAlig = NULL

2023-09-17T22:55:16,871               manager.postprocess_alignment()
2023-09-17T22:55:16,872                     ^
2023-09-17T22:55:16,872   ------------------------------------------------------------

2023-09-17T22:55:16,873   pytrimal/_trimal.pyx:628:19: Accessing Python attribute not allowed without gil

2023-09-17T22:55:16,874   Error compiling Cython file:
2023-09-17T22:55:16,875   ------------------------------------------------------------
2023-09-17T22:55:16,876   ...

2023-09-17T22:55:16,877               if manager.singleAlig == NULL:
2023-09-17T22:55:16,878                   manager.singleAlig = manager.origAlig
2023-09-17T22:55:16,879                   manager.origAlig = NULL

2023-09-17T22:55:16,880               manager.postprocess_alignment()
2023-09-17T22:55:16,881                                           ^
2023-09-17T22:55:16,882   ------------------------------------------------------------

2023-09-17T22:55:16,883   pytrimal/_trimal.pyx:628:41: Constructing Python tuple not allowed without gil

2023-09-17T22:55:16,885   Error compiling Cython file:
2023-09-17T22:55:16,885   ------------------------------------------------------------
2023-09-17T22:55:16,886   ...
2023-09-17T22:55:16,887           Create a default amino-acid similarity matrix (BLOSUM62).

2023-09-17T22:55:16,888           """
2023-09-17T22:55:16,889           cdef SimilarityMatrix matrix = cls.__new__(cls)
2023-09-17T22:55:16,890           with nogil:
2023-09-17T22:55:16,891               matrix._smx.defaultAASimMatrix()
2023-09-17T22:55:16,892                                            ^
2023-09-17T22:55:16,893   ------------------------------------------------------------

2023-09-17T22:55:16,894   pytrimal/_trimal.pyx:808:42: Discarding owned Python object not allowed without gil

2023-09-17T22:55:16,896   Error compiling Cython file:
2023-09-17T22:55:16,897   ------------------------------------------------------------
2023-09-17T22:55:16,898   ...
2023-09-17T22:55:16,899           Create a default amino-acid similarity matrix (BLOSUM62).

2023-09-17T22:55:16,901           """
2023-09-17T22:55:16,902           cdef SimilarityMatrix matrix = cls.__new__(cls)
2023-09-17T22:55:16,903           with nogil:
2023-09-17T22:55:16,904               matrix._smx.defaultAASimMatrix()
2023-09-17T22:55:16,905                                            ^
2023-09-17T22:55:16,906   ------------------------------------------------------------

2023-09-17T22:55:16,907   pytrimal/_trimal.pyx:808:42: Calling gil-requiring function not allowed without gil

2023-09-17T22:55:16,909   Error compiling Cython file:
2023-09-17T22:55:16,910   ------------------------------------------------------------
2023-09-17T22:55:16,911   ...
2023-09-17T22:55:16,911           Create a default amino-acid similarity matrix (BLOSUM62).

2023-09-17T22:55:16,913           """
2023-09-17T22:55:16,914           cdef SimilarityMatrix matrix = cls.__new__(cls)
2023-09-17T22:55:16,915           with nogil:
2023-09-17T22:55:16,916               matrix._smx.defaultAASimMatrix()
2023-09-17T22:55:16,916                         ^
2023-09-17T22:55:16,917   ------------------------------------------------------------

2023-09-17T22:55:16,919   pytrimal/_trimal.pyx:808:23: Accessing Python attribute not allowed without gil

2023-09-17T22:55:16,921   Error compiling Cython file:
2023-09-17T22:55:16,922   ------------------------------------------------------------
2023-09-17T22:55:16,923   ...
2023-09-17T22:55:16,923           Create a default amino-acid similarity matrix (BLOSUM62).

2023-09-17T22:55:16,925           """
2023-09-17T22:55:16,926           cdef SimilarityMatrix matrix = cls.__new__(cls)
2023-09-17T22:55:16,927           with nogil:
2023-09-17T22:55:16,928               matrix._smx.defaultAASimMatrix()
2023-09-17T22:55:16,929                                            ^
2023-09-17T22:55:16,930   ------------------------------------------------------------

2023-09-17T22:55:16,931   pytrimal/_trimal.pyx:808:42: Constructing Python tuple not allowed without gil

2023-09-17T22:55:16,932   Error compiling Cython file:
2023-09-17T22:55:16,933   ------------------------------------------------------------
2023-09-17T22:55:16,934   ...

2023-09-17T22:55:16,935           """
2023-09-17T22:55:16,936           cdef SimilarityMatrix matrix = cls.__new__(cls)
2023-09-17T22:55:16,936           with nogil:
2023-09-17T22:55:16,937               if degenerated:
2023-09-17T22:55:16,938                   matrix._smx.defaultNTSimMatrix()
2023-09-17T22:55:16,939                                                ^
2023-09-17T22:55:16,939   ------------------------------------------------------------

2023-09-17T22:55:16,941   pytrimal/_trimal.pyx:825:46: Discarding owned Python object not allowed without gil

2023-09-17T22:55:16,942   Error compiling Cython file:
2023-09-17T22:55:16,942   ------------------------------------------------------------
2023-09-17T22:55:16,943   ...

2023-09-17T22:55:16,944           """
2023-09-17T22:55:16,945           cdef SimilarityMatrix matrix = cls.__new__(cls)
2023-09-17T22:55:16,945           with nogil:
2023-09-17T22:55:16,946               if degenerated:
2023-09-17T22:55:16,946                   matrix._smx.defaultNTSimMatrix()
2023-09-17T22:55:16,947                                                ^
2023-09-17T22:55:16,947   ------------------------------------------------------------

2023-09-17T22:55:16,948   pytrimal/_trimal.pyx:825:46: Calling gil-requiring function not allowed without gil

2023-09-17T22:55:16,950   Error compiling Cython file:
2023-09-17T22:55:16,951   ------------------------------------------------------------
2023-09-17T22:55:16,952   ...

2023-09-17T22:55:16,953           """
2023-09-17T22:55:16,954           cdef SimilarityMatrix matrix = cls.__new__(cls)
2023-09-17T22:55:16,955           with nogil:
2023-09-17T22:55:16,955               if degenerated:
2023-09-17T22:55:16,956                   matrix._smx.defaultNTSimMatrix()
2023-09-17T22:55:16,957                             ^
2023-09-17T22:55:16,958   ------------------------------------------------------------

2023-09-17T22:55:16,959   pytrimal/_trimal.pyx:825:27: Accessing Python attribute not allowed without gil

2023-09-17T22:55:16,960   Error compiling Cython file:
2023-09-17T22:55:16,961   ------------------------------------------------------------
2023-09-17T22:55:16,962   ...

2023-09-17T22:55:16,963           """
2023-09-17T22:55:16,964           cdef SimilarityMatrix matrix = cls.__new__(cls)
2023-09-17T22:55:16,965           with nogil:
2023-09-17T22:55:16,966               if degenerated:
2023-09-17T22:55:16,966                   matrix._smx.defaultNTSimMatrix()
2023-09-17T22:55:16,967                                                ^
2023-09-17T22:55:16,968   ------------------------------------------------------------

2023-09-17T22:55:16,969   pytrimal/_trimal.pyx:825:46: Constructing Python tuple not allowed without gil

2023-09-17T22:55:16,970   Error compiling Cython file:
2023-09-17T22:55:16,971   ------------------------------------------------------------
2023-09-17T22:55:16,972   ...
2023-09-17T22:55:16,972           cdef SimilarityMatrix matrix = cls.__new__(cls)
2023-09-17T22:55:16,973           with nogil:
2023-09-17T22:55:16,974               if degenerated:
2023-09-17T22:55:16,974                   matrix._smx.defaultNTSimMatrix()
2023-09-17T22:55:16,975               else:
2023-09-17T22:55:16,976                   matrix._smx.defaultNTDegeneratedSimMatrix()
2023-09-17T22:55:16,976                                                           ^
2023-09-17T22:55:16,977   ------------------------------------------------------------

2023-09-17T22:55:16,979   pytrimal/_trimal.pyx:827:57: Discarding owned Python object not allowed without gil

2023-09-17T22:55:16,980   Error compiling Cython file:
2023-09-17T22:55:16,981   ------------------------------------------------------------
2023-09-17T22:55:16,982   ...
2023-09-17T22:55:16,982           cdef SimilarityMatrix matrix = cls.__new__(cls)
2023-09-17T22:55:16,983           with nogil:
2023-09-17T22:55:16,983               if degenerated:
2023-09-17T22:55:16,984                   matrix._smx.defaultNTSimMatrix()
2023-09-17T22:55:16,984               else:
2023-09-17T22:55:16,985                   matrix._smx.defaultNTDegeneratedSimMatrix()
2023-09-17T22:55:16,986                                                           ^
2023-09-17T22:55:16,986   ------------------------------------------------------------

2023-09-17T22:55:16,988   pytrimal/_trimal.pyx:827:57: Calling gil-requiring function not allowed without gil

2023-09-17T22:55:16,989   Error compiling Cython file:
2023-09-17T22:55:16,989   ------------------------------------------------------------
2023-09-17T22:55:16,990   ...
2023-09-17T22:55:16,991           cdef SimilarityMatrix matrix = cls.__new__(cls)
2023-09-17T22:55:16,991           with nogil:
2023-09-17T22:55:16,992               if degenerated:
2023-09-17T22:55:16,992                   matrix._smx.defaultNTSimMatrix()
2023-09-17T22:55:16,993               else:
2023-09-17T22:55:16,993                   matrix._smx.defaultNTDegeneratedSimMatrix()
2023-09-17T22:55:16,994                             ^
2023-09-17T22:55:16,994   ------------------------------------------------------------

2023-09-17T22:55:16,995   pytrimal/_trimal.pyx:827:27: Accessing Python attribute not allowed without gil

2023-09-17T22:55:16,996   Error compiling Cython file:
2023-09-17T22:55:16,997   ------------------------------------------------------------
2023-09-17T22:55:16,998   ...
2023-09-17T22:55:16,998           cdef SimilarityMatrix matrix = cls.__new__(cls)
2023-09-17T22:55:16,999           with nogil:
2023-09-17T22:55:16,999               if degenerated:
2023-09-17T22:55:17,000                   matrix._smx.defaultNTSimMatrix()
2023-09-17T22:55:17,001               else:
2023-09-17T22:55:17,001                   matrix._smx.defaultNTDegeneratedSimMatrix()
2023-09-17T22:55:17,002                                                           ^
2023-09-17T22:55:17,002   ------------------------------------------------------------

2023-09-17T22:55:17,004   pytrimal/_trimal.pyx:827:57: Constructing Python tuple not allowed without gil

2023-09-17T22:55:17,005   Error compiling Cython file:
2023-09-17T22:55:17,005   ------------------------------------------------------------
2023-09-17T22:55:17,006   ...
2023-09-17T22:55:17,006           """
2023-09-17T22:55:17,007           cdef float distance = 0.0
2023-09-17T22:55:17,008           cdef char  a_code   = ord(a)
2023-09-17T22:55:17,008           cdef char  b_code   = ord(b)
2023-09-17T22:55:17,009           with nogil:
2023-09-17T22:55:17,009               distance  = self._smx.getDistance(a_code, b_code)
2023-09-17T22:55:17,009                                               ^
2023-09-17T22:55:17,010   ------------------------------------------------------------

2023-09-17T22:55:17,011   pytrimal/_trimal.pyx:853:45: Coercion from Python not allowed without the GIL

2023-09-17T22:55:17,012   Error compiling Cython file:
2023-09-17T22:55:17,012   ------------------------------------------------------------
2023-09-17T22:55:17,013   ...
2023-09-17T22:55:17,013           """
2023-09-17T22:55:17,014           cdef float distance = 0.0
2023-09-17T22:55:17,014           cdef char  a_code   = ord(a)
2023-09-17T22:55:17,015           cdef char  b_code   = ord(b)
2023-09-17T22:55:17,015           with nogil:
2023-09-17T22:55:17,016               distance  = self._smx.getDistance(a_code, b_code)
2023-09-17T22:55:17,017                                               ^
2023-09-17T22:55:17,017   ------------------------------------------------------------

2023-09-17T22:55:17,019   pytrimal/_trimal.pyx:853:45: Calling gil-requiring function not allowed without gil

2023-09-17T22:55:17,022   Error compiling Cython file:
2023-09-17T22:55:17,022   ------------------------------------------------------------
2023-09-17T22:55:17,023   ...
2023-09-17T22:55:17,023           """
2023-09-17T22:55:17,023           cdef float distance = 0.0
2023-09-17T22:55:17,024           cdef char  a_code   = ord(a)
2023-09-17T22:55:17,024           cdef char  b_code   = ord(b)
2023-09-17T22:55:17,024           with nogil:
2023-09-17T22:55:17,025               distance  = self._smx.getDistance(a_code, b_code)
2023-09-17T22:55:17,025                                   ^
2023-09-17T22:55:17,025   ------------------------------------------------------------

2023-09-17T22:55:17,026   pytrimal/_trimal.pyx:853:33: Accessing Python attribute not allowed without gil

2023-09-17T22:55:17,027   Error compiling Cython file:
2023-09-17T22:55:17,027   ------------------------------------------------------------
2023-09-17T22:55:17,027   ...
2023-09-17T22:55:17,028           """
2023-09-17T22:55:17,028           cdef float distance = 0.0
2023-09-17T22:55:17,028           cdef char  a_code   = ord(a)
2023-09-17T22:55:17,029           cdef char  b_code   = ord(b)
2023-09-17T22:55:17,029           with nogil:
2023-09-17T22:55:17,029               distance  = self._smx.getDistance(a_code, b_code)
2023-09-17T22:55:17,030                                               ^
2023-09-17T22:55:17,030   ------------------------------------------------------------

2023-09-17T22:55:17,031   pytrimal/_trimal.pyx:853:45: Constructing Python tuple not allowed without gil

2023-09-17T22:55:17,031   Error compiling Cython file:
2023-09-17T22:55:17,032   ------------------------------------------------------------
2023-09-17T22:55:17,032   ...
2023-09-17T22:55:17,033           """
2023-09-17T22:55:17,033           cdef float distance = 0.0
2023-09-17T22:55:17,033           cdef char  a_code   = ord(a)
2023-09-17T22:55:17,034           cdef char  b_code   = ord(b)
2023-09-17T22:55:17,034           with nogil:
2023-09-17T22:55:17,035               distance  = self._smx.getDistance(a_code, b_code)
2023-09-17T22:55:17,035                                                ^
2023-09-17T22:55:17,036   ------------------------------------------------------------

2023-09-17T22:55:17,037   pytrimal/_trimal.pyx:853:46: Converting to Python object not allowed without gil

2023-09-17T22:55:17,038   Error compiling Cython file:
2023-09-17T22:55:17,038   ------------------------------------------------------------
2023-09-17T22:55:17,039   ...
2023-09-17T22:55:17,039           """
2023-09-17T22:55:17,040           cdef float distance = 0.0
2023-09-17T22:55:17,040           cdef char  a_code   = ord(a)
2023-09-17T22:55:17,041           cdef char  b_code   = ord(b)
2023-09-17T22:55:17,041           with nogil:
2023-09-17T22:55:17,042               distance  = self._smx.getDistance(a_code, b_code)
2023-09-17T22:55:17,042                                                        ^
2023-09-17T22:55:17,043   ------------------------------------------------------------

2023-09-17T22:55:17,044   pytrimal/_trimal.pyx:853:54: Converting to Python object not allowed without gil
2023-09-17T22:55:17,044   Compiling pytrimal/_trimal.pyx because it changed.
2023-09-17T22:55:17,045   [1/1] Cythonizing pytrimal/_trimal.pyx
2023-09-17T22:55:17,045   Traceback (most recent call last):
2023-09-17T22:55:17,045     File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
2023-09-17T22:55:17,046       main()
2023-09-17T22:55:17,046     File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
2023-09-17T22:55:17,047       json_out['return_val'] = hook(**hook_input['kwargs'])
2023-09-17T22:55:17,048                                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-17T22:55:17,048     File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel
2023-09-17T22:55:17,049       return _build_backend().build_wheel(wheel_directory, config_settings,
2023-09-17T22:55:17,049              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-17T22:55:17,050     File "/tmp/pip-build-env-4j5t91yl/overlay/local/lib/python3.11/dist-packages/setuptools/build_meta.py", line 434, in build_wheel
2023-09-17T22:55:17,050       return self._build_with_temp_dir(
2023-09-17T22:55:17,051              ^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-17T22:55:17,051     File "/tmp/pip-build-env-4j5t91yl/overlay/local/lib/python3.11/dist-packages/setuptools/build_meta.py", line 419, in _build_with_temp_dir
2023-09-17T22:55:17,051       self.run_setup()
2023-09-17T22:55:17,052     File "/tmp/pip-build-env-4j5t91yl/overlay/local/lib/python3.11/dist-packages/setuptools/build_meta.py", line 341, in run_setup
2023-09-17T22:55:17,052       exec(code, locals())
2023-09-17T22:55:17,052     File "<string>", line 294, in <module>
2023-09-17T22:55:17,053     File "/tmp/pip-build-env-4j5t91yl/overlay/local/lib/python3.11/dist-packages/setuptools/__init__.py", line 103, in setup
2023-09-17T22:55:17,053       return distutils.core.setup(**attrs)
2023-09-17T22:55:17,053              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-17T22:55:17,054     File "/tmp/pip-build-env-4j5t91yl/overlay/local/lib/python3.11/dist-packages/setuptools/_distutils/core.py", line 185, in setup
2023-09-17T22:55:17,054       return run_commands(dist)
2023-09-17T22:55:17,055              ^^^^^^^^^^^^^^^^^^
2023-09-17T22:55:17,055     File "/tmp/pip-build-env-4j5t91yl/overlay/local/lib/python3.11/dist-packages/setuptools/_distutils/core.py", line 201, in run_commands
2023-09-17T22:55:17,055       dist.run_commands()
2023-09-17T22:55:17,056     File "/tmp/pip-build-env-4j5t91yl/overlay/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py", line 969, in run_commands
2023-09-17T22:55:17,056       self.run_command(cmd)
2023-09-17T22:55:17,057     File "/tmp/pip-build-env-4j5t91yl/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py", line 989, in run_command
2023-09-17T22:55:17,057       super().run_command(command)
2023-09-17T22:55:17,058     File "/tmp/pip-build-env-4j5t91yl/overlay/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py", line 988, in run_command
2023-09-17T22:55:17,058       cmd_obj.run()
2023-09-17T22:55:17,059     File "/tmp/pip-build-env-4j5t91yl/normal/local/lib/python3.11/dist-packages/wheel/bdist_wheel.py", line 364, in run
2023-09-17T22:55:17,059       self.run_command("build")
2023-09-17T22:55:17,060     File "/tmp/pip-build-env-4j5t91yl/overlay/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py", line 318, in run_command
2023-09-17T22:55:17,060       self.distribution.run_command(command)
2023-09-17T22:55:17,061     File "/tmp/pip-build-env-4j5t91yl/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py", line 989, in run_command
2023-09-17T22:55:17,061       super().run_command(command)
2023-09-17T22:55:17,062     File "/tmp/pip-build-env-4j5t91yl/overlay/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py", line 988, in run_command
2023-09-17T22:55:17,062       cmd_obj.run()
2023-09-17T22:55:17,063     File "/tmp/pip-build-env-4j5t91yl/overlay/local/lib/python3.11/dist-packages/setuptools/_distutils/command/build.py", line 131, in run
2023-09-17T22:55:17,064       self.run_command(cmd_name)
2023-09-17T22:55:17,064     File "/tmp/pip-build-env-4j5t91yl/overlay/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py", line 318, in run_command
2023-09-17T22:55:17,064       self.distribution.run_command(command)
2023-09-17T22:55:17,065     File "/tmp/pip-build-env-4j5t91yl/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py", line 989, in run_command
2023-09-17T22:55:17,065       super().run_command(command)
2023-09-17T22:55:17,066     File "/tmp/pip-build-env-4j5t91yl/overlay/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py", line 988, in run_command
2023-09-17T22:55:17,067       cmd_obj.run()
2023-09-17T22:55:17,067     File "/tmp/pip-build-env-4j5t91yl/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_ext.py", line 88, in run
2023-09-17T22:55:17,068       _build_ext.run(self)
2023-09-17T22:55:17,068     File "/tmp/pip-build-env-4j5t91yl/overlay/local/lib/python3.11/dist-packages/Cython/Distutils/old_build_ext.py", line 186, in run
2023-09-17T22:55:17,069       _build_ext.build_ext.run(self)
2023-09-17T22:55:17,069     File "/tmp/pip-build-env-4j5t91yl/overlay/local/lib/python3.11/dist-packages/setuptools/_distutils/command/build_ext.py", line 345, in run
2023-09-17T22:55:17,069       self.build_extensions()
2023-09-17T22:55:17,070     File "<string>", line 151, in build_extensions
2023-09-17T22:55:17,070     File "/tmp/pip-build-env-4j5t91yl/overlay/local/lib/python3.11/dist-packages/Cython/Build/Dependencies.py", line 1115, in cythonize
2023-09-17T22:55:17,070       cythonize_one(*args)
2023-09-17T22:55:17,071     File "/tmp/pip-build-env-4j5t91yl/overlay/local/lib/python3.11/dist-packages/Cython/Build/Dependencies.py", line 1238, in cythonize_one
2023-09-17T22:55:17,071       raise CompileError(None, pyx_file)
2023-09-17T22:55:17,071   Cython.Compiler.Errors.CompileError: pytrimal/_trimal.pyx
2023-09-17T22:55:17,073   ERROR: [present-rich] Building wheel for pytrimal (pyproject.toml) exited with 1
2023-09-17T22:55:17,087   [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/tmpz7ou11p0[/]
2023-09-17T22:55:17,087   [bold magenta]cwd[/]: /tmp/pip-wheel-gwd83226/pytrimal_44ba82cfd0f046af8424f77a85f8784e
2023-09-17T22:55:17,088   Building wheel for pytrimal (pyproject.toml): finished with status 'error'
2023-09-17T22:55:17,090   ERROR: Failed building wheel for pytrimal
2023-09-17T22:55:17,092 Failed to build pytrimal
2023-09-17T22:55:17,093 ERROR: Failed to build one or more wheels
2023-09-17T22:55:17,095 Exception information:
2023-09-17T22:55:17,095 Traceback (most recent call last):
2023-09-17T22:55:17,095   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper
2023-09-17T22:55:17,095     status = run_func(*args)
2023-09-17T22:55:17,095              ^^^^^^^^^^^^^^^
2023-09-17T22:55:17,095   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper
2023-09-17T22:55:17,095     return func(self, options, args)
2023-09-17T22:55:17,095            ^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-17T22:55:17,095   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run
2023-09-17T22:55:17,095     raise CommandError("Failed to build one or more wheels")
2023-09-17T22:55:17,095 pip._internal.exceptions.CommandError: Failed to build one or more wheels
2023-09-17T22:55:17,099 Removed build tracker: '/tmp/pip-build-tracker-wqg8rx_i'