2022-06-03T13:32:02,865 Created temporary directory: /tmp/pip-ephem-wheel-cache-ox7z8mp_ 2022-06-03T13:32:02,871 Created temporary directory: /tmp/pip-build-tracker-tdsuykx6 2022-06-03T13:32:02,872 Initialized build tracking at /tmp/pip-build-tracker-tdsuykx6 2022-06-03T13:32:02,872 Created build tracker: /tmp/pip-build-tracker-tdsuykx6 2022-06-03T13:32:02,872 Entered build tracker: /tmp/pip-build-tracker-tdsuykx6 2022-06-03T13:32:02,873 Created temporary directory: /tmp/pip-wheel-uwsb9hxg 2022-06-03T13:32:02,942 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-06-03T13:32:02,951 2 location(s) to search for versions of pytrimal: 2022-06-03T13:32:02,951 * https://pypi.org/simple/pytrimal/ 2022-06-03T13:32:02,951 * https://www.piwheels.org/simple/pytrimal/ 2022-06-03T13:32:02,952 Fetching project page and analyzing links: https://pypi.org/simple/pytrimal/ 2022-06-03T13:32:02,953 Getting page https://pypi.org/simple/pytrimal/ 2022-06-03T13:32:02,956 Found index url https://pypi.org/simple 2022-06-03T13:32:03,103 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#sha256=7ac40ae8834c6246941caba5c28ceba9631310e96b740ace4bb344852f36a06b (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,104 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#sha256=77d22b9309c6394e026ef8fc6b1ece370675afe246210531846e7c22a27e16cd (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,105 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#sha256=14f1df21be7edec3b02a6f08b0a0ebf323d2fb24590dca90462ef7e11f367895 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,105 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#sha256=0a2042a306ffc01083b26cd2945b6d5ba89d9082db20ec93186717c054b4e1b1 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,106 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#sha256=2cabfe69e6cb6aaf76b37a39598b253c05412cd39f7c89deac90d56d42126692 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,106 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#sha256=ed3a1e341ba3c9678be46a8c3ae58fcbf2769e1a37baf901b4dca546382f1f83 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,107 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#sha256=cdaa9038a4aeb8eb2ba412951bb5621d328d83caa17181490764983269a13e3b (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,108 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#sha256=d8a629fcad2206efc074ab17e47b2a03d5a2df2d374be11ba53afda0c10c269f (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,108 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#sha256=444ef85979b7456875ece6c283930a2955244d7b3de09b894d1f893a19a5095e (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,109 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#sha256=8395af2505b928c812356425cc11eb1762542e53fdbc9a92c18477900f5939af (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,109 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#sha256=86445e44e5917738fffb693e162f5e6f7912b86a100e86b54d46c9f27f47d670 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,110 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#sha256=527a3b22729af435d86134d20cef0fbc54bc9bd7cc61531f4565f6b3787d88f9 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,110 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#sha256=8f0e6c857362571b1e859540dfaf3f2ad95b162ef06e16a90a5ee32a6c617237 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,111 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#sha256=3e4c96d07fab29f287e898b702ff1504ce4e5cac9378d79d51967a021e46e050 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,111 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#sha256=38d34b9f2e2afeccb4da9c7850260217e31062f0038f36978978bc90d9ffb3e1 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,112 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#sha256=e9bc72bde38b3e4fd075f1f8f8f7d9d5a8d7c0f7bbd42f72688c74e527327a32 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,112 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#sha256=0e62099e372edbc13fd5b4175a65254bab26850dbec6807cba86135a67add2b5 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,113 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#sha256=c8db855bc7409c535403bd81120fa8d623e52aeddb96d055e5fd826c8ee16dce (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,113 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#sha256=1fa01edbdce1d5bddbf98be5df21cd9dd59a703cf8365448ba5a634e7946bf1a (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,114 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#sha256=cb0ecf1eea08b25da60a2cbadc2015bd9393148d1c60918dd4e68f0ec84bfa39 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,114 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#sha256=f460c96c2a032554984102bb7e57c7d4cc61d1abf1069e1362747f65a49fdf96 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,115 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#sha256=30d6cf22157d9b29d5c3afb945f93f180c3c385e2b21ca688183d737ec7a48ff (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,117 Found link https://files.pythonhosted.org/packages/39/09/11aae9fa483929539f100beb384da40724188ff102ee94517b4a3ccba5c8/pytrimal-0.1.0.tar.gz#sha256=1af23728d26de53950644e1bdd1803a7fb8d9d6c6cb0c4aa38953c4fd0afe994 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5), version: 0.1.0 2022-06-03T13:32:03,117 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#sha256=cde8e4142c6ea1e5ebd35d81a4e93be816efb23a12c928d2522349577724a425 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,118 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#sha256=d037f9d14b4dec97c2fce851bad205c8c9ea46a3dde4a8fb7f0f39ed4a2d9e70 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,118 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#sha256=93b5ad25babcd407da31ff1dcea921de0dc18eafadbd17a9ab25e964a08d45df (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,119 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#sha256=5c7a6f54f525b5d8902660ad56ef89b460332c586a75fd1fd20efdc95cf22e97 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,120 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#sha256=9686c407bf596ef2a2d123d3b133cf1977562273c64a3b140a649403994ecb8d (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,120 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#sha256=2cbfd6359e677fad3885d99af6be30da10fe0d1e95cdbc65484b22ff3416fbc4 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,121 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#sha256=19ad1b204530940193eca5cb407cbc5a9caf9217ef09d66380e0a61adc15e7dd (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,121 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#sha256=25fe1d0d110d26bcbf2e1486c5df482e57eb04fb5afb2d846d87b3beed446822 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,122 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#sha256=29a4451db228da9f40e3d63bfd5fe957884d728ba4ca8f4b7ca84844dd9e0f90 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,122 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#sha256=425f1f9bf612e91c1f74b42578ac6d570737c099c220aa9cbea6448ee6b5bf31 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,123 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#sha256=3750218a87c26619134a2e3b683dbb0e3ac4931e2a36fde4924483e052372ea4 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,123 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#sha256=61f35b5ff95e57ae34eefff455903d142ce6483ea53dc119a46c183d97314899 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,124 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#sha256=65a2b64a8c0f97d3f612b68f0961b7d3f5433e383959b256543e0c0f73b20165 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,124 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#sha256=b37161d15b051c54970f4ec201de7b5eac97be854f94a8f6ead1959b8abb380b (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,125 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#sha256=79225c6ea3a4d5dbab116b470481b26e4704a33472f8ae4567ed4ce58605de74 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,125 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#sha256=20a99b74a063130d2f999cbf3723549715c502baab1dbe28339bcfe0dd2ade1a (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,126 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#sha256=2cc304e66208eeea4732f0fb751fa4212aa5a9606e62f289ecde42e8e95f5f7c (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,126 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#sha256=256a8ef5404d334442c82dabac708f970ec96bdc023087697220151238ecc4a2 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,127 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#sha256=6a44c2e9cab526603dbe45d2abacd973dab841c01b0deacfe2b618fa2abfa435 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,127 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#sha256=072dd3c338713e79d6cd327bbb6c83df30b05ea56884614cd16e637dfa3792ca (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,128 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#sha256=9a441f0a8810c42469e30086dace493dbf7c360a8c328ddb6719b3084b07101d (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,128 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#sha256=3c4d25b7ec0467576eeac127f2ec05912fca109c16e26e72726e8410a638496b (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-03T13:32:03,130 Found link https://files.pythonhosted.org/packages/86/c4/83edee2cc512ab4e6f48160b4f7e737681a8b0cabf4df5798ed32656e062/pytrimal-0.1.1.tar.gz#sha256=afaf88c657e631d573f3b951c845ac2d69d260b2a9c7a84b483f8fff2e9cce70 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5), version: 0.1.1 2022-06-03T13:32:03,131 Fetching project page and analyzing links: https://www.piwheels.org/simple/pytrimal/ 2022-06-03T13:32:03,131 Getting page https://www.piwheels.org/simple/pytrimal/ 2022-06-03T13:32:03,133 Found index url https://www.piwheels.org/simple 2022-06-03T13:32:03,342 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) 2022-06-03T13:32:03,343 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) 2022-06-03T13:32:03,343 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) 2022-06-03T13:32:03,344 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) 2022-06-03T13:32:03,344 Skipping link: not a file: https://www.piwheels.org/simple/pytrimal/ 2022-06-03T13:32:03,345 Skipping link: not a file: https://pypi.org/simple/pytrimal/ 2022-06-03T13:32:03,390 Given no hashes to check 1 links for project 'pytrimal': discarding no candidates 2022-06-03T13:32:03,433 Collecting pytrimal==0.1.1 2022-06-03T13:32:03,437 Created temporary directory: /tmp/pip-unpack-xvkw89sz 2022-06-03T13:32:03,529 Downloading pytrimal-0.1.1.tar.gz (8.5 MB) 2022-06-03T13:32:12,120 Added pytrimal==0.1.1 from https://files.pythonhosted.org/packages/86/c4/83edee2cc512ab4e6f48160b4f7e737681a8b0cabf4df5798ed32656e062/pytrimal-0.1.1.tar.gz#sha256=afaf88c657e631d573f3b951c845ac2d69d260b2a9c7a84b483f8fff2e9cce70 to build tracker '/tmp/pip-build-tracker-tdsuykx6' 2022-06-03T13:32:12,130 Created temporary directory: /tmp/pip-build-env-bde9bxs6 2022-06-03T13:32:12,150 Created temporary directory: /tmp/pip-standalone-pip-o3a39tyx 2022-06-03T13:32:14,548 Installing build dependencies: started 2022-06-03T13:32:14,551 Running command pip subprocess to install build dependencies 2022-06-03T13:32:25,799 Using pip 22.1 from /tmp/pip-standalone-pip-o3a39tyx/__env_pip__.zip/pip (python 3.9) 2022-06-03T13:32:27,376 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-06-03T13:32:31,297 Collecting setuptools>=46.4 2022-06-03T13:32:31,576 Using cached https://www.piwheels.org/simple/setuptools/setuptools-62.3.2-py3-none-any.whl (1.2 MB) 2022-06-03T13:32:35,217 Collecting cython~=0.29.16 2022-06-03T13:32:36,274 Using cached https://www.piwheels.org/simple/cython/Cython-0.29.30-cp39-cp39-linux_armv7l.whl (5.0 MB) 2022-06-03T13:32:41,681 Installing collected packages: setuptools, cython 2022-06-03T13:32:53,215 Creating /tmp/pip-build-env-bde9bxs6/overlay/bin 2022-06-03T13:32:53,220 changing mode of /tmp/pip-build-env-bde9bxs6/overlay/bin/cygdb to 755 2022-06-03T13:32:53,224 changing mode of /tmp/pip-build-env-bde9bxs6/overlay/bin/cython to 755 2022-06-03T13:32:53,229 changing mode of /tmp/pip-build-env-bde9bxs6/overlay/bin/cythonize to 755 2022-06-03T13:32:53,276 Successfully installed cython-0.29.30 setuptools-62.3.2 2022-06-03T13:32:53,470 WARNING: There was an error checking the latest version of pip. 2022-06-03T13:32:54,031 Installing build dependencies: finished with status 'done' 2022-06-03T13:32:54,059 Getting requirements to build wheel: started 2022-06-03T13:32:54,061 Running command Getting requirements to build wheel 2022-06-03T13:32:56,938 Getting requirements to build wheel: finished with status 'done' 2022-06-03T13:32:56,977 Created temporary directory: /tmp/pip-standalone-pip-u5hnx_02 2022-06-03T13:32:59,177 Installing backend dependencies: started 2022-06-03T13:32:59,179 Running command pip subprocess to install backend dependencies 2022-06-03T13:33:10,440 Using pip 22.1 from /tmp/pip-standalone-pip-u5hnx_02/__env_pip__.zip/pip (python 3.9) 2022-06-03T13:33:12,010 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-06-03T13:33:12,892 Collecting wheel 2022-06-03T13:33:12,927 Using cached https://www.piwheels.org/simple/wheel/wheel-0.37.1-py2.py3-none-any.whl (35 kB) 2022-06-03T13:33:17,201 Installing collected packages: wheel 2022-06-03T13:33:17,493 Creating /tmp/pip-build-env-bde9bxs6/normal/bin 2022-06-03T13:33:17,498 changing mode of /tmp/pip-build-env-bde9bxs6/normal/bin/wheel to 755 2022-06-03T13:33:17,526 Successfully installed wheel-0.37.1 2022-06-03T13:33:17,716 WARNING: There was an error checking the latest version of pip. 2022-06-03T13:33:18,152 Installing backend dependencies: finished with status 'done' 2022-06-03T13:33:18,173 Created temporary directory: /tmp/pip-modern-metadata-2rh3fsan 2022-06-03T13:33:18,180 Preparing metadata (pyproject.toml): started 2022-06-03T13:33:18,182 Running command Preparing metadata (pyproject.toml) 2022-06-03T13:33:23,043 running dist_info 2022-06-03T13:33:23,650 creating /tmp/pip-modern-metadata-2rh3fsan/pytrimal.egg-info 2022-06-03T13:33:24,238 writing /tmp/pip-modern-metadata-2rh3fsan/pytrimal.egg-info/PKG-INFO 2022-06-03T13:33:24,796 writing dependency_links to /tmp/pip-modern-metadata-2rh3fsan/pytrimal.egg-info/dependency_links.txt 2022-06-03T13:33:28,115 writing top-level names to /tmp/pip-modern-metadata-2rh3fsan/pytrimal.egg-info/top_level.txt 2022-06-03T13:33:28,118 writing manifest file '/tmp/pip-modern-metadata-2rh3fsan/pytrimal.egg-info/SOURCES.txt' 2022-06-03T13:33:28,799 reading manifest file '/tmp/pip-modern-metadata-2rh3fsan/pytrimal.egg-info/SOURCES.txt' 2022-06-03T13:33:28,802 reading manifest template 'MANIFEST.in' 2022-06-03T13:33:29,621 warning: no files found matching '*.h' under directory 'pytrimal' 2022-06-03T13:33:29,641 warning: no previously-included files matching '*.html' found under directory 'pytrimal' 2022-06-03T13:33:29,645 warning: no files found matching '*.h' under directory 'pytrimal/patch' 2022-06-03T13:33:29,647 warning: no files found matching '*.pxd' under directory 'pytrimal/patch' 2022-06-03T13:33:29,647 adding license file 'COPYING' 2022-06-03T13:33:29,672 writing manifest file '/tmp/pip-modern-metadata-2rh3fsan/pytrimal.egg-info/SOURCES.txt' 2022-06-03T13:33:29,675 creating '/tmp/pip-modern-metadata-2rh3fsan/pytrimal-0.1.1.dist-info' 2022-06-03T13:33:29,869 adding license file "COPYING" (matched pattern "COPYING*") 2022-06-03T13:33:30,119 Preparing metadata (pyproject.toml): finished with status 'done' 2022-06-03T13:33:30,135 Source in /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959 has version 0.1.1, which satisfies requirement pytrimal==0.1.1 from https://files.pythonhosted.org/packages/86/c4/83edee2cc512ab4e6f48160b4f7e737681a8b0cabf4df5798ed32656e062/pytrimal-0.1.1.tar.gz#sha256=afaf88c657e631d573f3b951c845ac2d69d260b2a9c7a84b483f8fff2e9cce70 2022-06-03T13:33:30,137 Removed pytrimal==0.1.1 from https://files.pythonhosted.org/packages/86/c4/83edee2cc512ab4e6f48160b4f7e737681a8b0cabf4df5798ed32656e062/pytrimal-0.1.1.tar.gz#sha256=afaf88c657e631d573f3b951c845ac2d69d260b2a9c7a84b483f8fff2e9cce70 from build tracker '/tmp/pip-build-tracker-tdsuykx6' 2022-06-03T13:33:30,152 Created temporary directory: /tmp/pip-unpack-m78j1xx9 2022-06-03T13:33:30,153 Building wheels for collected packages: pytrimal 2022-06-03T13:33:30,162 Created temporary directory: /tmp/pip-wheel-kskaf1sv 2022-06-03T13:33:30,163 Destination directory: /tmp/pip-wheel-kskaf1sv 2022-06-03T13:33:30,168 Building wheel for pytrimal (pyproject.toml): started 2022-06-03T13:33:30,170 Running command Building wheel for pytrimal (pyproject.toml) 2022-06-03T13:33:34,643 running bdist_wheel 2022-06-03T13:33:34,740 running build 2022-06-03T13:33:34,740 running build_py 2022-06-03T13:33:35,334 creating build 2022-06-03T13:33:35,335 creating build/lib.linux-armv7l-cpython-39 2022-06-03T13:33:35,336 creating build/lib.linux-armv7l-cpython-39/pytrimal 2022-06-03T13:33:35,338 copying pytrimal/_version.py -> build/lib.linux-armv7l-cpython-39/pytrimal 2022-06-03T13:33:35,342 copying pytrimal/__init__.py -> build/lib.linux-armv7l-cpython-39/pytrimal 2022-06-03T13:33:35,347 creating build/lib.linux-armv7l-cpython-39/pytrimal/tests 2022-06-03T13:33:35,349 copying pytrimal/tests/test_alignment.py -> build/lib.linux-armv7l-cpython-39/pytrimal/tests 2022-06-03T13:33:35,353 copying pytrimal/tests/test_doctest.py -> build/lib.linux-armv7l-cpython-39/pytrimal/tests 2022-06-03T13:33:35,356 copying pytrimal/tests/__main__.py -> build/lib.linux-armv7l-cpython-39/pytrimal/tests 2022-06-03T13:33:35,360 copying pytrimal/tests/test_similarity_matrix.py -> build/lib.linux-armv7l-cpython-39/pytrimal/tests 2022-06-03T13:33:35,363 copying pytrimal/tests/test_automatic_trimmer.py -> build/lib.linux-armv7l-cpython-39/pytrimal/tests 2022-06-03T13:33:35,366 copying pytrimal/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/pytrimal/tests 2022-06-03T13:33:35,370 copying pytrimal/tests/test_manual_trimmer.py -> build/lib.linux-armv7l-cpython-39/pytrimal/tests 2022-06-03T13:33:35,372 running egg_info 2022-06-03T13:33:36,557 writing pytrimal.egg-info/PKG-INFO 2022-06-03T13:33:37,109 writing dependency_links to pytrimal.egg-info/dependency_links.txt 2022-06-03T13:33:40,429 writing top-level names to pytrimal.egg-info/top_level.txt 2022-06-03T13:33:40,481 reading manifest file 'pytrimal.egg-info/SOURCES.txt' 2022-06-03T13:33:40,537 reading manifest template 'MANIFEST.in' 2022-06-03T13:33:41,319 warning: no files found matching '*.h' under directory 'pytrimal' 2022-06-03T13:33:41,339 warning: no previously-included files matching '*.html' found under directory 'pytrimal' 2022-06-03T13:33:41,343 warning: no files found matching '*.h' under directory 'pytrimal/patch' 2022-06-03T13:33:41,345 warning: no files found matching '*.pxd' under directory 'pytrimal/patch' 2022-06-03T13:33:41,345 adding license file 'COPYING' 2022-06-03T13:33:41,380 writing manifest file 'pytrimal.egg-info/SOURCES.txt' 2022-06-03T13:33:41,386 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-06-03T13:33:41,387 ############################ 2022-06-03T13:33:41,387 # Package would be ignored # 2022-06-03T13:33:41,388 ############################ 2022-06-03T13:33:41,388 Python recognizes 'pytrimal.patch' as an importable package, however it is 2022-06-03T13:33:41,388 included in the distribution as "data". 2022-06-03T13:33:41,388 This behavior is likely to change in future versions of setuptools (and 2022-06-03T13:33:41,389 therefore is considered deprecated). 2022-06-03T13:33:41,389 Please make sure that 'pytrimal.patch' is included as a package by using 2022-06-03T13:33:41,390 setuptools' `packages` configuration field or the proper discovery methods. 2022-06-03T13:33:41,390 You can read more about "package discovery" and "data files" on setuptools 2022-06-03T13:33:41,390 documentation page. 2022-06-03T13:33:41,391 !! 2022-06-03T13:33:41,392 check.warn(importable) 2022-06-03T13:33:41,392 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-06-03T13:33:41,393 ############################ 2022-06-03T13:33:41,393 # Package would be ignored # 2022-06-03T13:33:41,394 ############################ 2022-06-03T13:33:41,394 Python recognizes 'pytrimal.tests.data' as an importable package, however it is 2022-06-03T13:33:41,394 included in the distribution as "data". 2022-06-03T13:33:41,394 This behavior is likely to change in future versions of setuptools (and 2022-06-03T13:33:41,395 therefore is considered deprecated). 2022-06-03T13:33:41,395 Please make sure that 'pytrimal.tests.data' is included as a package by using 2022-06-03T13:33:41,395 setuptools' `packages` configuration field or the proper discovery methods. 2022-06-03T13:33:41,396 You can read more about "package discovery" and "data files" on setuptools 2022-06-03T13:33:41,396 documentation page. 2022-06-03T13:33:41,397 !! 2022-06-03T13:33:41,398 check.warn(importable) 2022-06-03T13:33:41,411 copying pytrimal/_trimal.pxd -> build/lib.linux-armv7l-cpython-39/pytrimal 2022-06-03T13:33:41,415 copying pytrimal/_trimal.pyi -> build/lib.linux-armv7l-cpython-39/pytrimal 2022-06-03T13:33:41,419 copying pytrimal/_trimal.pyx -> build/lib.linux-armv7l-cpython-39/pytrimal 2022-06-03T13:33:41,424 copying pytrimal/py.typed -> build/lib.linux-armv7l-cpython-39/pytrimal 2022-06-03T13:33:41,427 creating build/lib.linux-armv7l-cpython-39/pytrimal/patch 2022-06-03T13:33:41,429 copying pytrimal/patch/reportsystem.cpp -> build/lib.linux-armv7l-cpython-39/pytrimal/patch 2022-06-03T13:33:41,434 copying pytrimal/tests/requirements.txt -> build/lib.linux-armv7l-cpython-39/pytrimal/tests 2022-06-03T13:33:41,438 creating build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-03T13:33:41,439 copying pytrimal/tests/data/ENOG411BWBU.automated1.fasta -> build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-03T13:33:41,452 copying pytrimal/tests/data/ENOG411BWBU.cons40.gt40.fasta -> build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-03T13:33:41,466 copying pytrimal/tests/data/ENOG411BWBU.cons60.gt90.fasta -> build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-03T13:33:41,479 copying pytrimal/tests/data/ENOG411BWBU.fasta -> build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-03T13:33:41,502 copying pytrimal/tests/data/ENOG411BWBU.gappyout.fasta -> build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-03T13:33:41,516 copying pytrimal/tests/data/ENOG411BWBU.id50.fasta -> build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-03T13:33:41,522 copying pytrimal/tests/data/ENOG411BWBU.id70.fasta -> build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-03T13:33:41,531 copying pytrimal/tests/data/ENOG411BWBU.noallgaps.fasta -> build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-03T13:33:41,549 copying pytrimal/tests/data/ENOG411BWBU.strict.fasta -> build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-03T13:33:41,561 copying pytrimal/tests/data/ENOG411BWBU.strictplus.fasta -> build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-03T13:33:41,575 copying pytrimal/tests/data/__init__.py -> build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-03T13:33:41,579 copying pytrimal/tests/data/example.001.AA.clw -> build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-03T13:33:41,583 copying pytrimal/tests/data/halorhodopsin.afa -> build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-03T13:33:41,598 running build_clib 2022-06-03T13:33:41,610 creating build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,612 generating build/temp.linux-armv7l-cpython-39/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/fasta_m10_state.cpp, vendor/trimal/source/FormatHandling/phylip32_state.cpp, vendor/trimal/source/FormatHandling/mega_interleaved_state.cpp, vendor/trimal/source/FormatHandling/mega_sequential_state.cpp, vendor/trimal/source/FormatHandling/fasta_state.cpp, vendor/trimal/source/FormatHandling/phylip_paml_state.cpp, vendor/trimal/source/FormatHandling/pir_state.cpp, vendor/trimal/source/FormatHandling/phylip_paml_m10_state.cpp, vendor/trimal/source/FormatHandling/clustal_state.cpp, vendor/trimal/source/FormatHandling/htmlreport_state.cpp, vendor/trimal/source/FormatHandling/nexus_state.cpp, vendor/trimal/source/FormatHandling/phylip40_m10_state.cpp, vendor/trimal/source/FormatHandling/nexus_m10_state.cpp, vendor/trimal/source/FormatHandling/phylip40_state.cpp, vendor/trimal/source/FormatHandling/phylip32_m10_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 2022-06-03T13:33:41,612 building trimal with unix compiler 2022-06-03T13:33:41,613 generating build/temp.linux-armv7l-cpython-39/utils.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/utils.h 2022-06-03T13:33:41,618 generating build/temp.linux-armv7l-cpython-39/Cleaner.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/Cleaner.h 2022-06-03T13:33:41,623 generating build/temp.linux-armv7l-cpython-39/trimalManager.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/trimalManager.h 2022-06-03T13:33:41,628 generating build/temp.linux-armv7l-cpython-39/reportsystem.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/reportsystem.h 2022-06-03T13:33:41,634 generating build/temp.linux-armv7l-cpython-39/defines.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/defines.h 2022-06-03T13:33:41,637 generating build/temp.linux-armv7l-cpython-39/values.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/values.h 2022-06-03T13:33:41,641 generating build/temp.linux-armv7l-cpython-39/VCFHandler.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/VCFHandler.h 2022-06-03T13:33:41,645 generating build/temp.linux-armv7l-cpython-39/InternalBenchmarker.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/InternalBenchmarker.h 2022-06-03T13:33:41,649 creating build/temp.linux-armv7l-cpython-39/Statistics 2022-06-03T13:33:41,650 generating build/temp.linux-armv7l-cpython-39/Statistics/similarityMatrix.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/Statistics/similarityMatrix.h 2022-06-03T13:33:41,654 generating build/temp.linux-armv7l-cpython-39/Statistics/Gaps.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/Statistics/Gaps.h 2022-06-03T13:33:41,657 generating build/temp.linux-armv7l-cpython-39/Statistics/Manager.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/Statistics/Manager.h 2022-06-03T13:33:41,661 generating build/temp.linux-armv7l-cpython-39/Statistics/Consistency.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/Statistics/Consistency.h 2022-06-03T13:33:41,666 generating build/temp.linux-armv7l-cpython-39/Statistics/Mold.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/Statistics/Mold.h 2022-06-03T13:33:41,669 generating build/temp.linux-armv7l-cpython-39/Statistics/Similarity.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/Statistics/Similarity.h 2022-06-03T13:33:41,673 creating build/temp.linux-armv7l-cpython-39/FormatHandling 2022-06-03T13:33:41,674 generating build/temp.linux-armv7l-cpython-39/FormatHandling/nexus_state.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/FormatHandling/nexus_state.h 2022-06-03T13:33:41,677 generating build/temp.linux-armv7l-cpython-39/FormatHandling/fasta_m10_state.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/FormatHandling/fasta_m10_state.h 2022-06-03T13:33:41,680 generating build/temp.linux-armv7l-cpython-39/FormatHandling/formats_header.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/FormatHandling/formats_header.h 2022-06-03T13:33:41,682 generating build/temp.linux-armv7l-cpython-39/FormatHandling/BaseFormatHandler.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/FormatHandling/BaseFormatHandler.h 2022-06-03T13:33:41,686 generating build/temp.linux-armv7l-cpython-39/FormatHandling/phylip32_m10_state.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/FormatHandling/phylip32_m10_state.h 2022-06-03T13:33:41,689 generating build/temp.linux-armv7l-cpython-39/FormatHandling/phylip_paml_state.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/FormatHandling/phylip_paml_state.h 2022-06-03T13:33:41,691 generating build/temp.linux-armv7l-cpython-39/FormatHandling/phylip40_m10_state.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/FormatHandling/phylip40_m10_state.h 2022-06-03T13:33:41,694 generating build/temp.linux-armv7l-cpython-39/FormatHandling/mega_sequential_state.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/FormatHandling/mega_sequential_state.h 2022-06-03T13:33:41,697 generating build/temp.linux-armv7l-cpython-39/FormatHandling/htmlreport_state.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/FormatHandling/htmlreport_state.h 2022-06-03T13:33:41,700 generating build/temp.linux-armv7l-cpython-39/FormatHandling/mega_interleaved_state.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/FormatHandling/mega_interleaved_state.h 2022-06-03T13:33:41,703 generating build/temp.linux-armv7l-cpython-39/FormatHandling/phylip32_state.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/FormatHandling/phylip32_state.h 2022-06-03T13:33:41,705 generating build/temp.linux-armv7l-cpython-39/FormatHandling/clustal_state.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/FormatHandling/clustal_state.h 2022-06-03T13:33:41,708 generating build/temp.linux-armv7l-cpython-39/FormatHandling/FormatManager.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/FormatHandling/FormatManager.h 2022-06-03T13:33:41,712 generating build/temp.linux-armv7l-cpython-39/FormatHandling/phylip_paml_m10_state.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/FormatHandling/phylip_paml_m10_state.h 2022-06-03T13:33:41,715 generating build/temp.linux-armv7l-cpython-39/FormatHandling/pir_state.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/FormatHandling/pir_state.h 2022-06-03T13:33:41,718 generating build/temp.linux-armv7l-cpython-39/FormatHandling/fasta_state.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/FormatHandling/fasta_state.h 2022-06-03T13:33:41,720 generating build/temp.linux-armv7l-cpython-39/FormatHandling/nexus_m10_state.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/FormatHandling/nexus_m10_state.h 2022-06-03T13:33:41,723 generating build/temp.linux-armv7l-cpython-39/FormatHandling/phylip40_state.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/FormatHandling/phylip40_state.h 2022-06-03T13:33:41,726 creating build/temp.linux-armv7l-cpython-39/Alignment 2022-06-03T13:33:41,727 generating build/temp.linux-armv7l-cpython-39/Alignment/sequencesMatrix.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/Alignment/sequencesMatrix.h 2022-06-03T13:33:41,731 generating build/temp.linux-armv7l-cpython-39/Alignment/Alignment.h from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/Alignment/Alignment.h 2022-06-03T13:33:41,734 creating build/temp.linux-armv7l-cpython-39/RawText 2022-06-03T13:33:41,735 generating build/temp.linux-armv7l-cpython-39/RawText/menu.txt from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/RawText/menu.txt 2022-06-03T13:33:41,740 generating build/temp.linux-armv7l-cpython-39/RawText/legacyMenu.txt from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/RawText/legacyMenu.txt 2022-06-03T13:33:41,744 generating build/temp.linux-armv7l-cpython-39/RawText/examples.txt from /tmp/pip-wheel-uwsb9hxg/pytrimal_f89ce11b61214c018ee80e7dc316e959/vendor/trimal/include/RawText/examples.txt 2022-06-03T13:33:41,747 generating build/temp.linux-armv7l-cpython-39/Cleaner.cpp from vendor/trimal/source/Cleaner.cpp 2022-06-03T13:33:41,747 copying vendor/trimal/source/Cleaner.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,754 generating build/temp.linux-armv7l-cpython-39/Alignment.cpp from vendor/trimal/source/Alignment/Alignment.cpp 2022-06-03T13:33:41,754 copying vendor/trimal/source/Alignment/Alignment.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,763 generating build/temp.linux-armv7l-cpython-39/sequencesMatrix.cpp from vendor/trimal/source/Alignment/sequencesMatrix.cpp 2022-06-03T13:33:41,763 copying vendor/trimal/source/Alignment/sequencesMatrix.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,768 generating build/temp.linux-armv7l-cpython-39/similarityMatrix.cpp from vendor/trimal/source/Statistics/similarityMatrix.cpp 2022-06-03T13:33:41,768 copying vendor/trimal/source/Statistics/similarityMatrix.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,772 generating build/temp.linux-armv7l-cpython-39/Mold.cpp from vendor/trimal/source/Statistics/Mold.cpp 2022-06-03T13:33:41,773 copying vendor/trimal/source/Statistics/Mold.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,777 generating build/temp.linux-armv7l-cpython-39/Gaps.cpp from vendor/trimal/source/Statistics/Gaps.cpp 2022-06-03T13:33:41,777 copying vendor/trimal/source/Statistics/Gaps.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,782 generating build/temp.linux-armv7l-cpython-39/Manager.cpp from vendor/trimal/source/Statistics/Manager.cpp 2022-06-03T13:33:41,782 copying vendor/trimal/source/Statistics/Manager.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,786 generating build/temp.linux-armv7l-cpython-39/Similarity.cpp from vendor/trimal/source/Statistics/Similarity.cpp 2022-06-03T13:33:41,787 copying vendor/trimal/source/Statistics/Similarity.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,791 generating build/temp.linux-armv7l-cpython-39/Consistency.cpp from vendor/trimal/source/Statistics/Consistency.cpp 2022-06-03T13:33:41,792 copying vendor/trimal/source/Statistics/Consistency.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,796 generating build/temp.linux-armv7l-cpython-39/errorMessages.cpp from vendor/trimal/source/reportMessages/errorMessages.cpp 2022-06-03T13:33:41,797 copying vendor/trimal/source/reportMessages/errorMessages.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,801 generating build/temp.linux-armv7l-cpython-39/infoMessages.cpp from vendor/trimal/source/reportMessages/infoMessages.cpp 2022-06-03T13:33:41,802 copying vendor/trimal/source/reportMessages/infoMessages.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,805 generating build/temp.linux-armv7l-cpython-39/warningMessages.cpp from vendor/trimal/source/reportMessages/warningMessages.cpp 2022-06-03T13:33:41,805 copying vendor/trimal/source/reportMessages/warningMessages.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,808 generating build/temp.linux-armv7l-cpython-39/fasta_m10_state.cpp from vendor/trimal/source/FormatHandling/fasta_m10_state.cpp 2022-06-03T13:33:41,808 copying vendor/trimal/source/FormatHandling/fasta_m10_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,812 generating build/temp.linux-armv7l-cpython-39/phylip32_state.cpp from vendor/trimal/source/FormatHandling/phylip32_state.cpp 2022-06-03T13:33:41,812 copying vendor/trimal/source/FormatHandling/phylip32_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,817 generating build/temp.linux-armv7l-cpython-39/mega_interleaved_state.cpp from vendor/trimal/source/FormatHandling/mega_interleaved_state.cpp 2022-06-03T13:33:41,817 copying vendor/trimal/source/FormatHandling/mega_interleaved_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,821 generating build/temp.linux-armv7l-cpython-39/mega_sequential_state.cpp from vendor/trimal/source/FormatHandling/mega_sequential_state.cpp 2022-06-03T13:33:41,821 copying vendor/trimal/source/FormatHandling/mega_sequential_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,825 generating build/temp.linux-armv7l-cpython-39/fasta_state.cpp from vendor/trimal/source/FormatHandling/fasta_state.cpp 2022-06-03T13:33:41,826 copying vendor/trimal/source/FormatHandling/fasta_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,829 generating build/temp.linux-armv7l-cpython-39/phylip_paml_state.cpp from vendor/trimal/source/FormatHandling/phylip_paml_state.cpp 2022-06-03T13:33:41,830 copying vendor/trimal/source/FormatHandling/phylip_paml_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,832 generating build/temp.linux-armv7l-cpython-39/pir_state.cpp from vendor/trimal/source/FormatHandling/pir_state.cpp 2022-06-03T13:33:41,833 copying vendor/trimal/source/FormatHandling/pir_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,837 generating build/temp.linux-armv7l-cpython-39/phylip_paml_m10_state.cpp from vendor/trimal/source/FormatHandling/phylip_paml_m10_state.cpp 2022-06-03T13:33:41,837 copying vendor/trimal/source/FormatHandling/phylip_paml_m10_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,840 generating build/temp.linux-armv7l-cpython-39/clustal_state.cpp from vendor/trimal/source/FormatHandling/clustal_state.cpp 2022-06-03T13:33:41,840 copying vendor/trimal/source/FormatHandling/clustal_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,844 generating build/temp.linux-armv7l-cpython-39/htmlreport_state.cpp from vendor/trimal/source/FormatHandling/htmlreport_state.cpp 2022-06-03T13:33:41,845 copying vendor/trimal/source/FormatHandling/htmlreport_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,848 generating build/temp.linux-armv7l-cpython-39/nexus_state.cpp from vendor/trimal/source/FormatHandling/nexus_state.cpp 2022-06-03T13:33:41,849 copying vendor/trimal/source/FormatHandling/nexus_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,853 generating build/temp.linux-armv7l-cpython-39/phylip40_m10_state.cpp from vendor/trimal/source/FormatHandling/phylip40_m10_state.cpp 2022-06-03T13:33:41,853 copying vendor/trimal/source/FormatHandling/phylip40_m10_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,857 generating build/temp.linux-armv7l-cpython-39/nexus_m10_state.cpp from vendor/trimal/source/FormatHandling/nexus_m10_state.cpp 2022-06-03T13:33:41,857 copying vendor/trimal/source/FormatHandling/nexus_m10_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,861 generating build/temp.linux-armv7l-cpython-39/phylip40_state.cpp from vendor/trimal/source/FormatHandling/phylip40_state.cpp 2022-06-03T13:33:41,861 copying vendor/trimal/source/FormatHandling/phylip40_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,865 generating build/temp.linux-armv7l-cpython-39/phylip32_m10_state.cpp from vendor/trimal/source/FormatHandling/phylip32_m10_state.cpp 2022-06-03T13:33:41,866 copying vendor/trimal/source/FormatHandling/phylip32_m10_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,870 generating build/temp.linux-armv7l-cpython-39/BaseFormatHandler.cpp from vendor/trimal/source/FormatHandling/BaseFormatHandler.cpp 2022-06-03T13:33:41,870 copying vendor/trimal/source/FormatHandling/BaseFormatHandler.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,874 generating build/temp.linux-armv7l-cpython-39/utils.cpp from vendor/trimal/source/utils.cpp 2022-06-03T13:33:41,874 copying vendor/trimal/source/utils.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,879 generating build/temp.linux-armv7l-cpython-39/InternalBenchmarker.cpp from vendor/trimal/source/InternalBenchmarker.cpp 2022-06-03T13:33:41,880 copying vendor/trimal/source/InternalBenchmarker.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,883 generating build/temp.linux-armv7l-cpython-39/trimalManager.cpp from vendor/trimal/source/trimalManager.cpp 2022-06-03T13:33:41,884 copying vendor/trimal/source/trimalManager.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,891 generating build/temp.linux-armv7l-cpython-39/VCFHandler.cpp from vendor/trimal/source/VCFHandler.cpp 2022-06-03T13:33:41,892 copying vendor/trimal/source/VCFHandler.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-03T13:33:41,897 generating build/temp.linux-armv7l-cpython-39/Cleaner.o from build/temp.linux-armv7l-cpython-39/Cleaner.cpp 2022-06-03T13:33:41,898 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/Cleaner.cpp -o build/temp.linux-armv7l-cpython-39/Cleaner.o 2022-06-03T13:33:43,009 build/temp.linux-armv7l-cpython-39/Cleaner.cpp:1449: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2022-06-03T13:33:43,009 1449 | #pragma omp parallel for num_threads(NUMTHREADS) if(alig->originalNumberOfSequences>MINPARALLELSIZE) 2022-06-03T13:33:43,010 | 2022-06-03T13:33:43,010 build/temp.linux-armv7l-cpython-39/Cleaner.cpp:1457: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2022-06-03T13:33:43,010 1457 | #pragma omp parallel for num_threads(NUMTHREADS) private(j, k, hit, dst) if(alig->originalNumberOfSequences>MINPARALLELSIZE) 2022-06-03T13:33:43,011 | 2022-06-03T13:33:46,235 build/temp.linux-armv7l-cpython-39/Cleaner.cpp: In member function ‘Alignment* Cleaner::cleanStrict(int, const int*, float, const float*, bool, bool)’: 2022-06-03T13:33:46,236 build/temp.linux-armv7l-cpython-39/Cleaner.cpp:519:12: warning: unused variable ‘x’ [-Wunused-variable] 2022-06-03T13:33:46,236 519 | int i, x, pos, counter, lenBlock; 2022-06-03T13:33:46,237 | ^ 2022-06-03T13:33:46,274 build/temp.linux-armv7l-cpython-39/Cleaner.cpp: In member function ‘Alignment* Cleaner::getClustering(float)’: 2022-06-03T13:33:46,275 build/temp.linux-armv7l-cpython-39/Cleaner.cpp:1217:12: warning: unused variable ‘j’ [-Wunused-variable] 2022-06-03T13:33:46,275 1217 | int i, j, *clustering; 2022-06-03T13:33:46,275 | ^ 2022-06-03T13:33:46,287 build/temp.linux-armv7l-cpython-39/Cleaner.cpp: In member function ‘void Cleaner::removeAllGapsSeqsAndCols(bool, bool)’: 2022-06-03T13:33:46,288 build/temp.linux-armv7l-cpython-39/Cleaner.cpp:1382:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:33:46,288 1382 | for (j = 0; j < alig->sequences[i].length(); j++) { 2022-06-03T13:33:46,289 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-03T13:33:46,289 build/temp.linux-armv7l-cpython-39/Cleaner.cpp:1393:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:33:46,290 1393 | if (j == alig->sequences[i].length()) { 2022-06-03T13:33:46,290 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-03T13:33:55,386 generating build/temp.linux-armv7l-cpython-39/Alignment.o from build/temp.linux-armv7l-cpython-39/Alignment.cpp 2022-06-03T13:33:55,388 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/Alignment.cpp -o build/temp.linux-armv7l-cpython-39/Alignment.o 2022-06-03T13:33:56,297 build/temp.linux-armv7l-cpython-39/Alignment.cpp:395: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2022-06-03T13:33:56,298 395 | #pragma omp parallel for num_threads(NUMTHREADS) if(numberOfSequences>MINPARALLELSIZE) 2022-06-03T13:33:56,298 | 2022-06-03T13:33:56,299 build/temp.linux-armv7l-cpython-39/Alignment.cpp:398: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2022-06-03T13:33:56,299 398 | #pragma omp parallel for num_threads(NUMTHREADS) collapse(2) private(k, shared, referenceLength) if(numberOfSequences>MINPARALLELSIZE) 2022-06-03T13:33:56,299 | 2022-06-03T13:33:56,300 build/temp.linux-armv7l-cpython-39/Alignment.cpp:930: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2022-06-03T13:33:56,300 930 | #pragma omp parallel for private(k, mx, avg, pos) reduction(+: avgSeq, maxAvgSeq) num_threads(NUMTHREADS) if(originalNumberOfSequences>MINPARALLELSIZE) 2022-06-03T13:33:56,301 | 2022-06-03T13:33:59,429 build/temp.linux-armv7l-cpython-39/Alignment.cpp: In member function ‘Alignment* Alignment::getTranslationCDS(Alignment*)’: 2022-06-03T13:33:59,430 build/temp.linux-armv7l-cpython-39/Alignment.cpp:204:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:33:59,430 204 | for (y = 0, counter = 0; y < ProtAlig->sequences[x].size(); y++) { 2022-06-03T13:33:59,431 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-03T13:33:59,457 build/temp.linux-armv7l-cpython-39/Alignment.cpp: In member function ‘bool Alignment::prepareCodingSequence(bool, bool, Alignment*)’: 2022-06-03T13:33:59,458 build/temp.linux-armv7l-cpython-39/Alignment.cpp:614:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const size_type’ {aka ‘const unsigned int’} [-Wsign-compare] 2022-06-03T13:33:59,458 614 | if ((found != string::npos) && (((int) found % 3) == 0)) { 2022-06-03T13:33:59,459 | ~~~~~~^~~~~~~~~~~~~~~ 2022-06-03T13:33:59,464 build/temp.linux-armv7l-cpython-39/Alignment.cpp:641:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const size_type’ {aka ‘const unsigned int’} [-Wsign-compare] 2022-06-03T13:33:59,465 641 | } while (found != string::npos); 2022-06-03T13:33:59,465 | ~~~~~~^~~~~~~~~~~~~~~ 2022-06-03T13:33:59,466 build/temp.linux-armv7l-cpython-39/Alignment.cpp:651:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const size_type’ {aka ‘const unsigned int’} [-Wsign-compare] 2022-06-03T13:33:59,466 651 | if ((found != string::npos) && (((int) found % 3) == 0)) { 2022-06-03T13:33:59,467 | ~~~~~~^~~~~~~~~~~~~~~ 2022-06-03T13:33:59,472 build/temp.linux-armv7l-cpython-39/Alignment.cpp:676:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const size_type’ {aka ‘const unsigned int’} [-Wsign-compare] 2022-06-03T13:33:59,473 676 | } while (found != string::npos); 2022-06-03T13:33:59,473 | ~~~~~~^~~~~~~~~~~~~~~ 2022-06-03T13:33:59,474 build/temp.linux-armv7l-cpython-39/Alignment.cpp:685:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const size_type’ {aka ‘const unsigned int’} [-Wsign-compare] 2022-06-03T13:33:59,474 685 | if ((found != string::npos) && (((int) found % 3) == 0)) { 2022-06-03T13:33:59,474 | ~~~~~~^~~~~~~~~~~~~~~ 2022-06-03T13:33:59,480 build/temp.linux-armv7l-cpython-39/Alignment.cpp:711:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const size_type’ {aka ‘const unsigned int’} [-Wsign-compare] 2022-06-03T13:33:59,481 711 | } while (found != string::npos); 2022-06-03T13:33:59,481 | ~~~~~~^~~~~~~~~~~~~~~ 2022-06-03T13:33:59,501 build/temp.linux-armv7l-cpython-39/Alignment.cpp: In member function ‘bool Alignment::fillMatrices(bool, bool)’: 2022-06-03T13:33:59,502 build/temp.linux-armv7l-cpython-39/Alignment.cpp:810:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:33:59,502 810 | for (j = 0; j < sequences[i].length(); j++) 2022-06-03T13:33:59,502 | ~~^~~~~~~~~~~~~~~~~~~~~~~ 2022-06-03T13:33:59,506 build/temp.linux-armv7l-cpython-39/Alignment.cpp:837:35: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2022-06-03T13:33:59,506 837 | if (sequences[i].length() != numberOfResidues) { 2022-06-03T13:33:59,507 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2022-06-03T13:33:59,511 build/temp.linux-armv7l-cpython-39/Alignment.cpp: In member function ‘void Alignment::printAlignmentInfo(std::ostream&)’: 2022-06-03T13:33:59,512 build/temp.linux-armv7l-cpython-39/Alignment.cpp:889:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:33:59,512 889 | for (j = 0, valid_res = 0; j < sequences[i].length(); j++) 2022-06-03T13:33:59,513 | ~~^~~~~~~~~~~~~~~~~~~~~~~ 2022-06-03T13:34:26,232 generating build/temp.linux-armv7l-cpython-39/sequencesMatrix.o from build/temp.linux-armv7l-cpython-39/sequencesMatrix.cpp 2022-06-03T13:34:26,234 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/sequencesMatrix.cpp -o build/temp.linux-armv7l-cpython-39/sequencesMatrix.o 2022-06-03T13:34:31,112 generating build/temp.linux-armv7l-cpython-39/similarityMatrix.o from build/temp.linux-armv7l-cpython-39/similarityMatrix.cpp 2022-06-03T13:34:31,114 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/similarityMatrix.cpp -o build/temp.linux-armv7l-cpython-39/similarityMatrix.o 2022-06-03T13:34:36,461 generating build/temp.linux-armv7l-cpython-39/Mold.o from build/temp.linux-armv7l-cpython-39/Mold.cpp 2022-06-03T13:34:36,462 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/Mold.cpp -o build/temp.linux-armv7l-cpython-39/Mold.o 2022-06-03T13:34:44,490 generating build/temp.linux-armv7l-cpython-39/Gaps.o from build/temp.linux-armv7l-cpython-39/Gaps.cpp 2022-06-03T13:34:44,491 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/Gaps.cpp -o build/temp.linux-armv7l-cpython-39/Gaps.o 2022-06-03T13:34:53,140 generating build/temp.linux-armv7l-cpython-39/Manager.o from build/temp.linux-armv7l-cpython-39/Manager.cpp 2022-06-03T13:34:53,141 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/Manager.cpp -o build/temp.linux-armv7l-cpython-39/Manager.o 2022-06-03T13:34:57,655 generating build/temp.linux-armv7l-cpython-39/Similarity.o from build/temp.linux-armv7l-cpython-39/Similarity.cpp 2022-06-03T13:34:57,657 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/Similarity.cpp -o build/temp.linux-armv7l-cpython-39/Similarity.o 2022-06-03T13:34:58,472 build/temp.linux-armv7l-cpython-39/Similarity.cpp:115: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2022-06-03T13:34:58,473 115 | #pragma omp parallel for num_threads(NUMTHREADS) if(alig->originalNumberOfSequences>MINPARALLELSIZE) 2022-06-03T13:34:58,473 | 2022-06-03T13:34:58,473 build/temp.linux-armv7l-cpython-39/Similarity.cpp:124: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2022-06-03T13:34:58,474 124 | #pragma omp parallel for num_threads(NUMTHREADS) private(j, k, sum, length) if(alig->originalNumberOfSequences>MINPARALLELSIZE) 2022-06-03T13:34:58,474 | 2022-06-03T13:35:06,712 generating build/temp.linux-armv7l-cpython-39/Consistency.o from build/temp.linux-armv7l-cpython-39/Consistency.cpp 2022-06-03T13:35:06,714 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/Consistency.cpp -o build/temp.linux-armv7l-cpython-39/Consistency.o 2022-06-03T13:35:19,152 generating build/temp.linux-armv7l-cpython-39/errorMessages.o from build/temp.linux-armv7l-cpython-39/errorMessages.cpp 2022-06-03T13:35:19,153 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/errorMessages.cpp -o build/temp.linux-armv7l-cpython-39/errorMessages.o 2022-06-03T13:35:23,876 generating build/temp.linux-armv7l-cpython-39/infoMessages.o from build/temp.linux-armv7l-cpython-39/infoMessages.cpp 2022-06-03T13:35:23,877 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/infoMessages.cpp -o build/temp.linux-armv7l-cpython-39/infoMessages.o 2022-06-03T13:35:27,786 generating build/temp.linux-armv7l-cpython-39/warningMessages.o from build/temp.linux-armv7l-cpython-39/warningMessages.cpp 2022-06-03T13:35:27,787 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/warningMessages.cpp -o build/temp.linux-armv7l-cpython-39/warningMessages.o 2022-06-03T13:35:31,767 generating build/temp.linux-armv7l-cpython-39/fasta_m10_state.o from build/temp.linux-armv7l-cpython-39/fasta_m10_state.cpp 2022-06-03T13:35:31,769 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/fasta_m10_state.cpp -o build/temp.linux-armv7l-cpython-39/fasta_m10_state.o 2022-06-03T13:35:35,496 build/temp.linux-armv7l-cpython-39/fasta_m10_state.cpp: In member function ‘virtual bool FormatHandling::fasta_m10_state::SaveAlignment(const Alignment&, std::ostream*)’: 2022-06-03T13:35:35,497 build/temp.linux-armv7l-cpython-39/fasta_m10_state.cpp:95:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:35:35,497 95 | for (j = 0, k = 0; j < alignment.sequences[i].length(); j++) 2022-06-03T13:35:35,498 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-03T13:35:35,498 build/temp.linux-armv7l-cpython-39/fasta_m10_state.cpp:99:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:35:35,499 99 | if (!lastcharIsnewline && j == alignment.sequences[i].length() -1 ) 2022-06-03T13:35:35,499 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-03T13:35:35,501 build/temp.linux-armv7l-cpython-39/fasta_m10_state.cpp:110:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:35:35,501 110 | if ((k % 60 == 0 || j == alignment.sequences[i].length() - 1)) 2022-06-03T13:35:35,501 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-03T13:35:37,086 generating build/temp.linux-armv7l-cpython-39/phylip32_state.o from build/temp.linux-armv7l-cpython-39/phylip32_state.cpp 2022-06-03T13:35:37,087 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/phylip32_state.cpp -o build/temp.linux-armv7l-cpython-39/phylip32_state.o 2022-06-03T13:35:43,176 generating build/temp.linux-armv7l-cpython-39/mega_interleaved_state.o from build/temp.linux-armv7l-cpython-39/mega_interleaved_state.cpp 2022-06-03T13:35:43,178 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/mega_interleaved_state.cpp -o build/temp.linux-armv7l-cpython-39/mega_interleaved_state.o 2022-06-03T13:35:48,834 generating build/temp.linux-armv7l-cpython-39/mega_sequential_state.o from build/temp.linux-armv7l-cpython-39/mega_sequential_state.cpp 2022-06-03T13:35:48,835 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/mega_sequential_state.cpp -o build/temp.linux-armv7l-cpython-39/mega_sequential_state.o 2022-06-03T13:35:52,589 build/temp.linux-armv7l-cpython-39/mega_sequential_state.cpp: In member function ‘virtual bool FormatHandling::mega_sequential_state::SaveAlignment(const Alignment&, std::ostream*)’: 2022-06-03T13:35:52,590 build/temp.linux-armv7l-cpython-39/mega_sequential_state.cpp:335:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:35:52,590 335 | for(j = 0, l = 0; j < alignment.sequences[i].length(); j ++) 2022-06-03T13:35:52,591 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-03T13:35:52,596 build/temp.linux-armv7l-cpython-39/mega_sequential_state.cpp:289:15: warning: unused variable ‘k’ [-Wunused-variable] 2022-06-03T13:35:52,597 289 | int i, j, k, l, m; 2022-06-03T13:35:52,597 | ^ 2022-06-03T13:35:52,597 build/temp.linux-armv7l-cpython-39/mega_sequential_state.cpp:289:21: warning: unused variable ‘m’ [-Wunused-variable] 2022-06-03T13:35:52,598 289 | int i, j, k, l, m; 2022-06-03T13:35:52,598 | ^ 2022-06-03T13:35:54,982 generating build/temp.linux-armv7l-cpython-39/fasta_state.o from build/temp.linux-armv7l-cpython-39/fasta_state.cpp 2022-06-03T13:35:54,984 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/fasta_state.cpp -o build/temp.linux-armv7l-cpython-39/fasta_state.o 2022-06-03T13:35:58,696 build/temp.linux-armv7l-cpython-39/fasta_state.cpp: In member function ‘virtual bool FormatHandling::fasta_state::SaveAlignment(const Alignment&, std::ostream*)’: 2022-06-03T13:35:58,696 build/temp.linux-armv7l-cpython-39/fasta_state.cpp:197:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:35:58,697 197 | for (j = 0, k = 0; j < alignment.sequences[i].length(); j++) 2022-06-03T13:35:58,697 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-03T13:35:58,698 build/temp.linux-armv7l-cpython-39/fasta_state.cpp:201:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:35:58,698 201 | if (!lastcharIsnewline && j == alignment.sequences[i].length() -1 ) 2022-06-03T13:35:58,698 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-03T13:35:58,700 build/temp.linux-armv7l-cpython-39/fasta_state.cpp:212:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:35:58,701 212 | if (k % 60 == 0 || j == alignment.sequences[i].length() -1 ) 2022-06-03T13:35:58,701 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-03T13:36:00,719 generating build/temp.linux-armv7l-cpython-39/phylip_paml_state.o from build/temp.linux-armv7l-cpython-39/phylip_paml_state.cpp 2022-06-03T13:36:00,721 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/phylip_paml_state.cpp -o build/temp.linux-armv7l-cpython-39/phylip_paml_state.o 2022-06-03T13:36:05,856 generating build/temp.linux-armv7l-cpython-39/pir_state.o from build/temp.linux-armv7l-cpython-39/pir_state.cpp 2022-06-03T13:36:05,857 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/pir_state.cpp -o build/temp.linux-armv7l-cpython-39/pir_state.o 2022-06-03T13:36:09,598 build/temp.linux-armv7l-cpython-39/pir_state.cpp: In member function ‘virtual bool FormatHandling::pir_state::SaveAlignment(const Alignment&, std::ostream*)’: 2022-06-03T13:36:09,599 build/temp.linux-armv7l-cpython-39/pir_state.cpp:223:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:36:09,599 223 | for (j = 0, k = 0, l = 0; j < alignment.sequences[i].length(); j++) { 2022-06-03T13:36:09,600 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-03T13:36:09,602 build/temp.linux-armv7l-cpython-39/pir_state.cpp:231:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:36:09,602 231 | if (j == alignment.sequences[i].length() - 1); 2022-06-03T13:36:09,603 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-03T13:36:09,606 build/temp.linux-armv7l-cpython-39/pir_state.cpp:184:18: warning: variable ‘l’ set but not used [-Wunused-but-set-variable] 2022-06-03T13:36:09,607 184 | int i, j, k, l; 2022-06-03T13:36:09,607 | ^ 2022-06-03T13:36:11,646 generating build/temp.linux-armv7l-cpython-39/phylip_paml_m10_state.o from build/temp.linux-armv7l-cpython-39/phylip_paml_m10_state.cpp 2022-06-03T13:36:11,647 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/phylip_paml_m10_state.cpp -o build/temp.linux-armv7l-cpython-39/phylip_paml_m10_state.o 2022-06-03T13:36:16,763 generating build/temp.linux-armv7l-cpython-39/clustal_state.o from build/temp.linux-armv7l-cpython-39/clustal_state.cpp 2022-06-03T13:36:16,766 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/clustal_state.cpp -o build/temp.linux-armv7l-cpython-39/clustal_state.o 2022-06-03T13:36:22,663 generating build/temp.linux-armv7l-cpython-39/htmlreport_state.o from build/temp.linux-armv7l-cpython-39/htmlreport_state.cpp 2022-06-03T13:36:22,665 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/htmlreport_state.cpp -o build/temp.linux-armv7l-cpython-39/htmlreport_state.o 2022-06-03T13:36:27,837 generating build/temp.linux-armv7l-cpython-39/nexus_state.o from build/temp.linux-armv7l-cpython-39/nexus_state.cpp 2022-06-03T13:36:27,838 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/nexus_state.cpp -o build/temp.linux-armv7l-cpython-39/nexus_state.o 2022-06-03T13:36:35,016 generating build/temp.linux-armv7l-cpython-39/phylip40_m10_state.o from build/temp.linux-armv7l-cpython-39/phylip40_m10_state.cpp 2022-06-03T13:36:35,017 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/phylip40_m10_state.cpp -o build/temp.linux-armv7l-cpython-39/phylip40_m10_state.o 2022-06-03T13:36:39,568 build/temp.linux-armv7l-cpython-39/phylip40_m10_state.cpp: In member function ‘virtual bool FormatHandling::phylip40_m10_state::SaveAlignment(const Alignment&, std::ostream*)’: 2022-06-03T13:36:39,569 build/temp.linux-armv7l-cpython-39/phylip40_m10_state.cpp:104:19: warning: ‘k’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-06-03T13:36:39,569 104 | for (i = k; i < alignment.originalNumberOfResidues; i=k) 2022-06-03T13:36:39,569 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-03T13:36:40,296 generating build/temp.linux-armv7l-cpython-39/nexus_m10_state.o from build/temp.linux-armv7l-cpython-39/nexus_m10_state.cpp 2022-06-03T13:36:40,298 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/nexus_m10_state.cpp -o build/temp.linux-armv7l-cpython-39/nexus_m10_state.o 2022-06-03T13:36:46,980 generating build/temp.linux-armv7l-cpython-39/phylip40_state.o from build/temp.linux-armv7l-cpython-39/phylip40_state.cpp 2022-06-03T13:36:46,983 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/phylip40_state.cpp -o build/temp.linux-armv7l-cpython-39/phylip40_state.o 2022-06-03T13:36:53,046 generating build/temp.linux-armv7l-cpython-39/phylip32_m10_state.o from build/temp.linux-armv7l-cpython-39/phylip32_m10_state.cpp 2022-06-03T13:36:53,048 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/phylip32_m10_state.cpp -o build/temp.linux-armv7l-cpython-39/phylip32_m10_state.o 2022-06-03T13:36:58,289 generating build/temp.linux-armv7l-cpython-39/BaseFormatHandler.o from build/temp.linux-armv7l-cpython-39/BaseFormatHandler.cpp 2022-06-03T13:36:58,292 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/BaseFormatHandler.cpp -o build/temp.linux-armv7l-cpython-39/BaseFormatHandler.o 2022-06-03T13:37:10,394 generating build/temp.linux-armv7l-cpython-39/utils.o from build/temp.linux-armv7l-cpython-39/utils.cpp 2022-06-03T13:37:10,397 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/utils.cpp -o build/temp.linux-armv7l-cpython-39/utils.o 2022-06-03T13:37:13,597 build/temp.linux-armv7l-cpython-39/utils.cpp: In function ‘std::string utils::removeCharacter(char, std::string)’: 2022-06-03T13:37:13,598 build/temp.linux-armv7l-cpython-39/utils.cpp:490:20: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2022-06-03T13:37:13,599 490 | while (pos != (int) std::string::npos) { 2022-06-03T13:37:13,599 | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-03T13:37:13,619 build/temp.linux-armv7l-cpython-39/utils.cpp: In function ‘int* utils::readNumbers(const string&)’: 2022-06-03T13:37:13,620 build/temp.linux-armv7l-cpython-39/utils.cpp:632:52: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2022-06-03T13:37:13,620 632 | while ((comma = line.find(',', comma + 1)) != (int) std::string::npos) 2022-06-03T13:37:13,621 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-03T13:37:13,621 build/temp.linux-armv7l-cpython-39/utils.cpp:646:44: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2022-06-03T13:37:13,621 646 | if (((separ < comma) || (comma == (int) std::string::npos)) && (separ != (int) std::string::npos)) { 2022-06-03T13:37:13,622 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-03T13:37:13,622 build/temp.linux-armv7l-cpython-39/utils.cpp:646:83: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2022-06-03T13:37:13,623 646 | if (((separ < comma) || (comma == (int) std::string::npos)) && (separ != (int) std::string::npos)) { 2022-06-03T13:37:13,623 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-03T13:37:13,623 build/temp.linux-armv7l-cpython-39/utils.cpp:650:50: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2022-06-03T13:37:13,624 650 | } else if ((separ > comma) || (separ == (int) std::string::npos)) { 2022-06-03T13:37:13,624 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-03T13:37:13,624 build/temp.linux-armv7l-cpython-39/utils.cpp:666:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2022-06-03T13:37:13,625 666 | if (comma == (int) std::string::npos) 2022-06-03T13:37:13,625 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-03T13:37:19,536 generating build/temp.linux-armv7l-cpython-39/InternalBenchmarker.o from build/temp.linux-armv7l-cpython-39/InternalBenchmarker.cpp 2022-06-03T13:37:19,538 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/InternalBenchmarker.cpp -o build/temp.linux-armv7l-cpython-39/InternalBenchmarker.o 2022-06-03T13:37:19,713 generating build/temp.linux-armv7l-cpython-39/trimalManager.o from build/temp.linux-armv7l-cpython-39/trimalManager.cpp 2022-06-03T13:37:19,715 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/trimalManager.cpp -o build/temp.linux-armv7l-cpython-39/trimalManager.o 2022-06-03T13:37:23,695 In file included from build/temp.linux-armv7l-cpython-39/trimalManager.cpp:42: 2022-06-03T13:37:23,695 build/temp.linux-armv7l-cpython-39/VCFHandler.h: In constructor ‘ngs::__internal::vcfFeature::vcfFeature()’: 2022-06-03T13:37:23,696 build/temp.linux-armv7l-cpython-39/VCFHandler.h:87:19: warning: ‘ngs::__internal::vcfFeature::quality’ will be initialized after [-Wreorder] 2022-06-03T13:37:23,696 87 | float quality; 2022-06-03T13:37:23,696 | ^~~~~~~ 2022-06-03T13:37:23,697 build/temp.linux-armv7l-cpython-39/VCFHandler.h:85:18: warning: ‘bool ngs::__internal::vcfFeature::filter’ [-Wreorder] 2022-06-03T13:37:23,697 85 | bool filter; 2022-06-03T13:37:23,698 | ^~~~~~ 2022-06-03T13:37:23,698 build/temp.linux-armv7l-cpython-39/VCFHandler.h:96:13: warning: when initialized here [-Wreorder] 2022-06-03T13:37:23,698 96 | vcfFeature() : position(0), quality(0.0F), filter(false), readDepthIndex(0) 2022-06-03T13:37:23,699 | ^~~~~~~~~~ 2022-06-03T13:37:24,057 build/temp.linux-armv7l-cpython-39/trimalManager.cpp: In member function ‘bool trimAlManager::check_outputs_coincidence()’: 2022-06-03T13:37:24,058 build/temp.linux-armv7l-cpython-39/trimalManager.cpp:1419:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::array::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:37:24,058 1419 | for (int i = 0, x = 0; i < outFiles.size(); i++) { 2022-06-03T13:37:24,058 | ~~^~~~~~~~~~~~~~~~~ 2022-06-03T13:37:24,059 build/temp.linux-armv7l-cpython-39/trimalManager.cpp:1421:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::array::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:37:24,059 1421 | for (x = i + 1; x < outFiles.size(); x++) { 2022-06-03T13:37:24,059 | ~~^~~~~~~~~~~~~~~~~ 2022-06-03T13:37:45,770 generating build/temp.linux-armv7l-cpython-39/VCFHandler.o from build/temp.linux-armv7l-cpython-39/VCFHandler.cpp 2022-06-03T13:37:45,772 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -std=c++11 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/VCFHandler.cpp -o build/temp.linux-armv7l-cpython-39/VCFHandler.o 2022-06-03T13:37:49,347 In file included from build/temp.linux-armv7l-cpython-39/VCFHandler.cpp:30: 2022-06-03T13:37:49,347 build/temp.linux-armv7l-cpython-39/VCFHandler.h: In constructor ‘ngs::__internal::vcfFeature::vcfFeature()’: 2022-06-03T13:37:49,347 build/temp.linux-armv7l-cpython-39/VCFHandler.h:87:19: warning: ‘ngs::__internal::vcfFeature::quality’ will be initialized after [-Wreorder] 2022-06-03T13:37:49,348 87 | float quality; 2022-06-03T13:37:49,348 | ^~~~~~~ 2022-06-03T13:37:49,349 build/temp.linux-armv7l-cpython-39/VCFHandler.h:85:18: warning: ‘bool ngs::__internal::vcfFeature::filter’ [-Wreorder] 2022-06-03T13:37:49,349 85 | bool filter; 2022-06-03T13:37:49,349 | ^~~~~~ 2022-06-03T13:37:49,350 build/temp.linux-armv7l-cpython-39/VCFHandler.h:96:13: warning: when initialized here [-Wreorder] 2022-06-03T13:37:49,350 96 | vcfFeature() : position(0), quality(0.0F), filter(false), readDepthIndex(0) 2022-06-03T13:37:49,350 | ^~~~~~~~~~ 2022-06-03T13:37:49,395 build/temp.linux-armv7l-cpython-39/VCFHandler.cpp: In function ‘bool ngs::__internal::checkContigsWithReference(const AlignmentVector&, const StringVector&)’: 2022-06-03T13:37:49,395 build/temp.linux-armv7l-cpython-39/VCFHandler.cpp:153:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:37:49,396 153 | for (i = 0; i < sources.size(); i++) { 2022-06-03T13:37:49,396 | ~~^~~~~~~~~~~~~~~~ 2022-06-03T13:37:49,396 build/temp.linux-armv7l-cpython-39/VCFHandler.cpp:162:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:37:49,397 162 | if (i == sources.size()) { 2022-06-03T13:37:49,397 | ~~^~~~~~~~~~~~~~~~~ 2022-06-03T13:37:49,410 build/temp.linux-armv7l-cpython-39/VCFHandler.cpp: In function ‘void ngs::__internal::increaseSequencesInAlignment(const AlignmentVector&, const StringVector&)’: 2022-06-03T13:37:49,411 build/temp.linux-armv7l-cpython-39/VCFHandler.cpp:198:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:37:49,411 198 | for (int i = 1; i < donors.size() + 1; i++) { 2022-06-03T13:37:49,411 | ~~^~~~~~~~~~~~~~~~~~~ 2022-06-03T13:37:49,425 build/temp.linux-armv7l-cpython-39/VCFHandler.cpp: In function ‘void ngs::__internal::applyVariantCallingFiles(const AlignmentVector&, const StringVector&, const StringVector&, const std::vector >&, float, float, bool, const char*)’: 2022-06-03T13:37:49,426 build/temp.linux-armv7l-cpython-39/VCFHandler.cpp:337:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:37:49,426 337 | for (int vcfIndex = 0; vcfIndex < filenames.size(); vcfIndex++) { 2022-06-03T13:37:49,427 | ~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2022-06-03T13:37:49,427 build/temp.linux-armv7l-cpython-39/VCFHandler.cpp:360:59: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:37:49,428 360 | for (contigIndex = 0; contigIndex < contigs.size(); contigIndex++) 2022-06-03T13:37:49,428 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2022-06-03T13:37:49,429 build/temp.linux-armv7l-cpython-39/VCFHandler.cpp:365:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:37:49,429 365 | if (contigIndex == contigs.size()) { 2022-06-03T13:37:49,430 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2022-06-03T13:37:49,434 build/temp.linux-armv7l-cpython-39/VCFHandler.cpp:394:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:37:49,434 394 | for (int donorID = 0; donorID < feature.donorsInfo.size(); donorID++) 2022-06-03T13:37:49,435 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-03T13:37:49,482 build/temp.linux-armv7l-cpython-39/VCFHandler.cpp:397:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:37:49,482 397 | if (donorID >= donorsPositions[vcfIndex].size()) 2022-06-03T13:37:49,483 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-03T13:37:49,507 build/temp.linux-armv7l-cpython-39/VCFHandler.cpp: In function ‘void ngs::__internal::extractContigsFromLine(char*, ngs::StringVector&)’: 2022-06-03T13:37:49,507 build/temp.linux-armv7l-cpython-39/VCFHandler.cpp:528:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:37:49,508 528 | for (U = 0; U < contigs.size(); U++) 2022-06-03T13:37:49,508 | ~~^~~~~~~~~~~~~~~~ 2022-06-03T13:37:49,508 build/temp.linux-armv7l-cpython-39/VCFHandler.cpp:533:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:37:49,509 533 | if (U == contigs.size()) 2022-06-03T13:37:49,509 | ~~^~~~~~~~~~~~~~~~~ 2022-06-03T13:37:49,511 build/temp.linux-armv7l-cpython-39/VCFHandler.cpp: In function ‘void ngs::__internal::extractDonorsFromLine(char*, std::vector&, ngs::StringVector&)’: 2022-06-03T13:37:49,511 build/temp.linux-armv7l-cpython-39/VCFHandler.cpp:557:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:37:49,512 557 | for (U = 0; U < donors.size(); U++) { 2022-06-03T13:37:49,512 | ~~^~~~~~~~~~~~~~~ 2022-06-03T13:37:49,512 build/temp.linux-armv7l-cpython-39/VCFHandler.cpp:564:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:37:49,513 564 | if (U == donors.size()) { 2022-06-03T13:37:49,513 | ~~^~~~~~~~~~~~~~~~ 2022-06-03T13:37:49,515 build/temp.linux-armv7l-cpython-39/VCFHandler.cpp: In function ‘void ngs::__internal::obtainContigsAndDonors(const StringVector&, ngs::StringVector&, ngs::StringVector&, std::vector >&)’: 2022-06-03T13:37:49,515 build/temp.linux-armv7l-cpython-39/VCFHandler.cpp:591:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-03T13:37:49,515 591 | for (int C = 0; C < filenames.size(); C++) { 2022-06-03T13:37:49,516 | ~~^~~~~~~~~~~~~~~~~~ 2022-06-03T13:37:57,842 generating build/temp.linux-armv7l-cpython-39/libtrimal.a from build/temp.linux-armv7l-cpython-39/Cleaner.o, build/temp.linux-armv7l-cpython-39/Alignment.o, build/temp.linux-armv7l-cpython-39/sequencesMatrix.o, build/temp.linux-armv7l-cpython-39/similarityMatrix.o, build/temp.linux-armv7l-cpython-39/Mold.o, build/temp.linux-armv7l-cpython-39/Gaps.o, build/temp.linux-armv7l-cpython-39/Manager.o, build/temp.linux-armv7l-cpython-39/Similarity.o, build/temp.linux-armv7l-cpython-39/Consistency.o, build/temp.linux-armv7l-cpython-39/errorMessages.o, build/temp.linux-armv7l-cpython-39/infoMessages.o, build/temp.linux-armv7l-cpython-39/warningMessages.o, build/temp.linux-armv7l-cpython-39/fasta_m10_state.o, build/temp.linux-armv7l-cpython-39/phylip32_state.o, build/temp.linux-armv7l-cpython-39/mega_interleaved_state.o, build/temp.linux-armv7l-cpython-39/mega_sequential_state.o, build/temp.linux-armv7l-cpython-39/fasta_state.o, build/temp.linux-armv7l-cpython-39/phylip_paml_state.o, build/temp.linux-armv7l-cpython-39/pir_state.o, build/temp.linux-armv7l-cpython-39/phylip_paml_m10_state.o, build/temp.linux-armv7l-cpython-39/clustal_state.o, build/temp.linux-armv7l-cpython-39/htmlreport_state.o, build/temp.linux-armv7l-cpython-39/nexus_state.o, build/temp.linux-armv7l-cpython-39/phylip40_m10_state.o, build/temp.linux-armv7l-cpython-39/nexus_m10_state.o, build/temp.linux-armv7l-cpython-39/phylip40_state.o, build/temp.linux-armv7l-cpython-39/phylip32_m10_state.o, build/temp.linux-armv7l-cpython-39/BaseFormatHandler.o, build/temp.linux-armv7l-cpython-39/utils.o, build/temp.linux-armv7l-cpython-39/InternalBenchmarker.o, build/temp.linux-armv7l-cpython-39/trimalManager.o, build/temp.linux-armv7l-cpython-39/VCFHandler.o 2022-06-03T13:37:57,843 arm-linux-gnueabihf-gcc-ar rcs build/temp.linux-armv7l-cpython-39/libtrimal.a build/temp.linux-armv7l-cpython-39/Cleaner.o build/temp.linux-armv7l-cpython-39/Alignment.o build/temp.linux-armv7l-cpython-39/sequencesMatrix.o build/temp.linux-armv7l-cpython-39/similarityMatrix.o build/temp.linux-armv7l-cpython-39/Mold.o build/temp.linux-armv7l-cpython-39/Gaps.o build/temp.linux-armv7l-cpython-39/Manager.o build/temp.linux-armv7l-cpython-39/Similarity.o build/temp.linux-armv7l-cpython-39/Consistency.o build/temp.linux-armv7l-cpython-39/errorMessages.o build/temp.linux-armv7l-cpython-39/infoMessages.o build/temp.linux-armv7l-cpython-39/warningMessages.o build/temp.linux-armv7l-cpython-39/fasta_m10_state.o build/temp.linux-armv7l-cpython-39/phylip32_state.o build/temp.linux-armv7l-cpython-39/mega_interleaved_state.o build/temp.linux-armv7l-cpython-39/mega_sequential_state.o build/temp.linux-armv7l-cpython-39/fasta_state.o build/temp.linux-armv7l-cpython-39/phylip_paml_state.o build/temp.linux-armv7l-cpython-39/pir_state.o build/temp.linux-armv7l-cpython-39/phylip_paml_m10_state.o build/temp.linux-armv7l-cpython-39/clustal_state.o build/temp.linux-armv7l-cpython-39/htmlreport_state.o build/temp.linux-armv7l-cpython-39/nexus_state.o build/temp.linux-armv7l-cpython-39/phylip40_m10_state.o build/temp.linux-armv7l-cpython-39/nexus_m10_state.o build/temp.linux-armv7l-cpython-39/phylip40_state.o build/temp.linux-armv7l-cpython-39/phylip32_m10_state.o build/temp.linux-armv7l-cpython-39/BaseFormatHandler.o build/temp.linux-armv7l-cpython-39/utils.o build/temp.linux-armv7l-cpython-39/InternalBenchmarker.o build/temp.linux-armv7l-cpython-39/trimalManager.o build/temp.linux-armv7l-cpython-39/VCFHandler.o 2022-06-03T13:37:58,502 running build_ext 2022-06-03T13:38:04,713 Compiling pytrimal/_trimal.pyx because it changed. 2022-06-03T13:38:04,713 [1/1] Cythonizing pytrimal/_trimal.pyx 2022-06-03T13:38:04,714 building pytrimal._trimal with unix compiler 2022-06-03T13:38:04,727 building 'pytrimal._trimal' extension 2022-06-03T13:38:04,728 creating build/temp.linux-armv7l-cpython-39/pytrimal 2022-06-03T13:38:04,731 creating build/temp.linux-armv7l-cpython-39/pytrimal/patch 2022-06-03T13:38:04,733 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DCYTHON_WITHOUT_ASSERTIONS=1 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c pytrimal/_trimal.cpp -o build/temp.linux-armv7l-cpython-39/pytrimal/_trimal.o -std=c++11 2022-06-03T13:38:39,916 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DCYTHON_WITHOUT_ASSERTIONS=1 -Ipytrimal/patch -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c pytrimal/patch/reportsystem.cpp -o build/temp.linux-armv7l-cpython-39/pytrimal/patch/reportsystem.o -std=c++11 2022-06-03T13:38:43,266 pytrimal/patch/reportsystem.cpp: In member function ‘void reporting::reportManager::report(ErrorCode, const char*)’: 2022-06-03T13:38:43,267 pytrimal/patch/reportsystem.cpp:120:11: warning: unused variable ‘counter’ [-Wunused-variable] 2022-06-03T13:38:43,267 120 | int counter = 0; 2022-06-03T13:38:43,268 | ^~~~~~~ 2022-06-03T13:38:43,309 pytrimal/patch/reportsystem.cpp: In member function ‘void reporting::reportManager::report(WarningCode, const char*)’: 2022-06-03T13:38:43,310 pytrimal/patch/reportsystem.cpp:162:11: warning: unused variable ‘counter’ [-Wunused-variable] 2022-06-03T13:38:43,310 162 | int counter = 0; 2022-06-03T13:38:43,311 | ^~~~~~~ 2022-06-03T13:38:47,137 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/pytrimal/_trimal.o build/temp.linux-armv7l-cpython-39/pytrimal/patch/reportsystem.o build/temp.linux-armv7l-cpython-39/libtrimal.a -L/usr/lib -Lbuild/temp.linux-armv7l-cpython-39 -ltrimal -ltrimal -o build/lib.linux-armv7l-cpython-39/pytrimal/_trimal.cpython-39-arm-linux-gnueabihf.so 2022-06-03T13:38:50,678 installing to build/bdist.linux-armv7l/wheel 2022-06-03T13:38:50,679 running install 2022-06-03T13:38:50,741 running install_lib 2022-06-03T13:38:51,332 creating build/bdist.linux-armv7l 2022-06-03T13:38:51,333 creating build/bdist.linux-armv7l/wheel 2022-06-03T13:38:51,336 creating build/bdist.linux-armv7l/wheel/pytrimal 2022-06-03T13:38:51,338 copying build/lib.linux-armv7l-cpython-39/pytrimal/_version.py -> build/bdist.linux-armv7l/wheel/pytrimal 2022-06-03T13:38:51,343 creating build/bdist.linux-armv7l/wheel/pytrimal/tests 2022-06-03T13:38:51,345 creating build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-03T13:38:51,347 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/data/ENOG411BWBU.cons60.gt90.fasta -> build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-03T13:38:51,360 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/data/ENOG411BWBU.id70.fasta -> build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-03T13:38:51,370 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/data/ENOG411BWBU.cons40.gt40.fasta -> build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-03T13:38:51,385 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/data/ENOG411BWBU.strictplus.fasta -> build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-03T13:38:51,396 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/data/halorhodopsin.afa -> build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-03T13:38:51,407 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/data/ENOG411BWBU.gappyout.fasta -> build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-03T13:38:51,422 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/data/ENOG411BWBU.strict.fasta -> build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-03T13:38:51,434 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/data/example.001.AA.clw -> build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-03T13:38:51,439 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/data/ENOG411BWBU.id50.fasta -> build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-03T13:38:51,444 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/data/ENOG411BWBU.fasta -> build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-03T13:38:51,462 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/data/ENOG411BWBU.automated1.fasta -> build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-03T13:38:51,476 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/data/ENOG411BWBU.noallgaps.fasta -> build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-03T13:38:51,494 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/data/__init__.py -> build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-03T13:38:51,497 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/test_alignment.py -> build/bdist.linux-armv7l/wheel/pytrimal/tests 2022-06-03T13:38:51,501 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/test_doctest.py -> build/bdist.linux-armv7l/wheel/pytrimal/tests 2022-06-03T13:38:51,504 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/requirements.txt -> build/bdist.linux-armv7l/wheel/pytrimal/tests 2022-06-03T13:38:51,508 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/__main__.py -> build/bdist.linux-armv7l/wheel/pytrimal/tests 2022-06-03T13:38:51,511 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/test_similarity_matrix.py -> build/bdist.linux-armv7l/wheel/pytrimal/tests 2022-06-03T13:38:51,514 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/test_automatic_trimmer.py -> build/bdist.linux-armv7l/wheel/pytrimal/tests 2022-06-03T13:38:51,517 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/__init__.py -> build/bdist.linux-armv7l/wheel/pytrimal/tests 2022-06-03T13:38:51,521 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/test_manual_trimmer.py -> build/bdist.linux-armv7l/wheel/pytrimal/tests 2022-06-03T13:38:51,524 copying build/lib.linux-armv7l-cpython-39/pytrimal/_trimal.pyx -> build/bdist.linux-armv7l/wheel/pytrimal 2022-06-03T13:38:51,530 copying build/lib.linux-armv7l-cpython-39/pytrimal/_trimal.pyi -> build/bdist.linux-armv7l/wheel/pytrimal 2022-06-03T13:38:51,534 creating build/bdist.linux-armv7l/wheel/pytrimal/patch 2022-06-03T13:38:51,537 copying build/lib.linux-armv7l-cpython-39/pytrimal/patch/reportsystem.cpp -> build/bdist.linux-armv7l/wheel/pytrimal/patch 2022-06-03T13:38:51,542 copying build/lib.linux-armv7l-cpython-39/pytrimal/py.typed -> build/bdist.linux-armv7l/wheel/pytrimal 2022-06-03T13:38:51,545 copying build/lib.linux-armv7l-cpython-39/pytrimal/__init__.py -> build/bdist.linux-armv7l/wheel/pytrimal 2022-06-03T13:38:51,549 copying build/lib.linux-armv7l-cpython-39/pytrimal/_trimal.pxd -> build/bdist.linux-armv7l/wheel/pytrimal 2022-06-03T13:38:51,553 copying build/lib.linux-armv7l-cpython-39/pytrimal/_trimal.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pytrimal 2022-06-03T13:38:51,916 running install_egg_info 2022-06-03T13:38:52,516 Copying pytrimal.egg-info to build/bdist.linux-armv7l/wheel/pytrimal-0.1.1-py3.9.egg-info 2022-06-03T13:38:52,541 running install_scripts 2022-06-03T13:38:52,677 adding license file "COPYING" (matched pattern "COPYING*") 2022-06-03T13:38:52,732 creating build/bdist.linux-armv7l/wheel/pytrimal-0.1.1.dist-info/WHEEL 2022-06-03T13:38:52,738 creating '/tmp/pip-wheel-kskaf1sv/tmpmlkhnnyf/pytrimal-0.1.1-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2022-06-03T13:38:52,742 adding 'pytrimal/__init__.py' 2022-06-03T13:38:56,069 adding 'pytrimal/_trimal.cpython-39-arm-linux-gnueabihf.so' 2022-06-03T13:38:56,217 adding 'pytrimal/_trimal.pxd' 2022-06-03T13:38:56,220 adding 'pytrimal/_trimal.pyi' 2022-06-03T13:38:56,228 adding 'pytrimal/_trimal.pyx' 2022-06-03T13:38:56,231 adding 'pytrimal/_version.py' 2022-06-03T13:38:56,233 adding 'pytrimal/py.typed' 2022-06-03T13:38:56,238 adding 'pytrimal/patch/reportsystem.cpp' 2022-06-03T13:38:56,241 adding 'pytrimal/tests/__init__.py' 2022-06-03T13:38:56,243 adding 'pytrimal/tests/__main__.py' 2022-06-03T13:38:56,246 adding 'pytrimal/tests/requirements.txt' 2022-06-03T13:38:56,248 adding 'pytrimal/tests/test_alignment.py' 2022-06-03T13:38:56,251 adding 'pytrimal/tests/test_automatic_trimmer.py' 2022-06-03T13:38:56,253 adding 'pytrimal/tests/test_doctest.py' 2022-06-03T13:38:56,256 adding 'pytrimal/tests/test_manual_trimmer.py' 2022-06-03T13:38:56,258 adding 'pytrimal/tests/test_similarity_matrix.py' 2022-06-03T13:38:56,288 adding 'pytrimal/tests/data/ENOG411BWBU.automated1.fasta' 2022-06-03T13:38:56,320 adding 'pytrimal/tests/data/ENOG411BWBU.cons40.gt40.fasta' 2022-06-03T13:38:56,349 adding 'pytrimal/tests/data/ENOG411BWBU.cons60.gt90.fasta' 2022-06-03T13:38:56,393 adding 'pytrimal/tests/data/ENOG411BWBU.fasta' 2022-06-03T13:38:56,427 adding 'pytrimal/tests/data/ENOG411BWBU.gappyout.fasta' 2022-06-03T13:38:56,434 adding 'pytrimal/tests/data/ENOG411BWBU.id50.fasta' 2022-06-03T13:38:56,448 adding 'pytrimal/tests/data/ENOG411BWBU.id70.fasta' 2022-06-03T13:38:56,484 adding 'pytrimal/tests/data/ENOG411BWBU.noallgaps.fasta' 2022-06-03T13:38:56,511 adding 'pytrimal/tests/data/ENOG411BWBU.strict.fasta' 2022-06-03T13:38:56,533 adding 'pytrimal/tests/data/ENOG411BWBU.strictplus.fasta' 2022-06-03T13:38:56,537 adding 'pytrimal/tests/data/__init__.py' 2022-06-03T13:38:56,540 adding 'pytrimal/tests/data/example.001.AA.clw' 2022-06-03T13:38:56,556 adding 'pytrimal/tests/data/halorhodopsin.afa' 2022-06-03T13:38:56,575 adding 'pytrimal-0.1.1.dist-info/COPYING' 2022-06-03T13:38:56,579 adding 'pytrimal-0.1.1.dist-info/METADATA' 2022-06-03T13:38:56,581 adding 'pytrimal-0.1.1.dist-info/WHEEL' 2022-06-03T13:38:56,583 adding 'pytrimal-0.1.1.dist-info/top_level.txt' 2022-06-03T13:38:56,585 adding 'pytrimal-0.1.1.dist-info/RECORD' 2022-06-03T13:38:56,693 removing build/bdist.linux-armv7l/wheel 2022-06-03T13:38:57,274 Building wheel for pytrimal (pyproject.toml): finished with status 'done' 2022-06-03T13:38:57,422 Created wheel for pytrimal: filename=pytrimal-0.1.1-cp39-cp39-linux_armv7l.whl size=2776511 sha256=c54c9649d97022e8ce47cce412b180621f9a77399bf9c58ef855e08f913a237f 2022-06-03T13:38:57,424 Stored in directory: /tmp/pip-ephem-wheel-cache-ox7z8mp_/wheels/2e/4b/9e/c3019c88609bd77286a6eafbfd219060afd775ab9d24eb3d20 2022-06-03T13:38:57,455 Successfully built pytrimal 2022-06-03T13:38:57,641 Removed build tracker: '/tmp/pip-build-tracker-tdsuykx6'