2022-06-09T06:47:14,900 Created temporary directory: /tmp/pip-ephem-wheel-cache-f7fhxn0e 2022-06-09T06:47:14,905 Created temporary directory: /tmp/pip-build-tracker-t7xntenv 2022-06-09T06:47:14,906 Initialized build tracking at /tmp/pip-build-tracker-t7xntenv 2022-06-09T06:47:14,906 Created build tracker: /tmp/pip-build-tracker-t7xntenv 2022-06-09T06:47:14,907 Entered build tracker: /tmp/pip-build-tracker-t7xntenv 2022-06-09T06:47:14,908 Created temporary directory: /tmp/pip-wheel-kox7n9ta 2022-06-09T06:47:14,977 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-06-09T06:47:14,985 2 location(s) to search for versions of pytrimal: 2022-06-09T06:47:14,985 * https://pypi.org/simple/pytrimal/ 2022-06-09T06:47:14,985 * https://www.piwheels.org/simple/pytrimal/ 2022-06-09T06:47:14,986 Fetching project page and analyzing links: https://pypi.org/simple/pytrimal/ 2022-06-09T06:47:14,987 Getting page https://pypi.org/simple/pytrimal/ 2022-06-09T06:47:14,991 Found 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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) 2022-06-09T06:47:15,205 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) 2022-06-09T06:47:15,206 Skipping link: No binaries permitted for pytrimal: 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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) 2022-06-09T06:47:15,208 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) 2022-06-09T06:47:15,209 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) 2022-06-09T06:47:15,210 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 2022-06-09T06:47:15,211 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) 2022-06-09T06:47:15,212 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) 2022-06-09T06:47:15,213 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) 2022-06-09T06:47:15,213 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) 2022-06-09T06:47:15,214 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) 2022-06-09T06:47:15,214 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) 2022-06-09T06:47:15,215 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) 2022-06-09T06:47:15,215 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) 2022-06-09T06:47:15,216 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) 2022-06-09T06:47:15,216 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) 2022-06-09T06:47:15,217 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) 2022-06-09T06:47:15,217 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) 2022-06-09T06:47:15,218 Skipping link: No binaries permitted for pytrimal: 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2022-06-09T06:47:15,267 Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/a1/1d/ad4e31bd0fb9b2ab5a0d60cb8b7fef043b92ad520a983ed489bcf7889a49/pytrimal-0.2.2-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl#sha256=b410f74c694de690b5b64bbb13062b4fcbbe1716de40320d5f4fe86d494136b8 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,268 Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/d4/cf/90a3e7b18eb3f95d3eed938e61b541fe069ceb1ca74a705b46163a4d283e/pytrimal-0.2.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl#sha256=5f926a5c7624f5d16f451276db5d81ab1c1cda5c3f396629c551271b7b819796 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,268 Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/a9/d5/30847595f3f27dd3dac9351cecdd32ebdeb3f9b007da13841f3b60ddf40d/pytrimal-0.2.2-cp35-cp35m-macosx_10_14_x86_64.whl#sha256=600ce96c1bb9d43ba3290ede8230393041d196681457c9cb58c44902b141b8e1 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,269 Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/72/d4/27360c3b8847b77d84e6da35e0d2609fa6e80501611da718488212448351/pytrimal-0.2.2-cp35-cp35m-manylinux2010_x86_64.whl#sha256=e27ece3efc94be63e74a34c29eab395025b924483e6b210e1f75372347fc429e (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,270 Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/47/ee/2fe3fca8f8b03c996a5fda1c5d98dc00340d7797020ccb564cdcbc20ae64/pytrimal-0.2.2-cp36-cp36m-macosx_10_14_x86_64.whl#sha256=d7acddaf5782ee20c8444cf240dc46dbc158d536928d203986a977af28777e00 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,270 Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/c6/53/4ad50d221e3bc82e14539a5f41bc08d26218ad175b8e1d1ff7fd5bfad470/pytrimal-0.2.2-cp36-cp36m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl#sha256=99dea606c3868aceab7b51495c31d4f4d56859388edced678422241c3af5c688 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,271 Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/d1/27/18e0e9ed84b9927be1d6bfd5686632d08339a2d2d3b21b761d23a0d0d3b1/pytrimal-0.2.2-cp36-cp36m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl#sha256=0d484e4765b3c2e9d261c50663de9df1762c6d79d8595f977a8e77320c14e085 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,271 Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/b8/97/072913e40df143dfdd8928464e081ffa2dea8751e4581f3ecc60dea88fbc/pytrimal-0.2.2-cp37-cp37m-macosx_10_15_x86_64.whl#sha256=8da97b0b40be9281aa22091f1790dd490603b2b02bb48174af3c3e13c8a9252e (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,272 Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/86/88/c4eddb78eba46accb803dfcd28d5088e3656196c87f3ad4c484e4a9bea2a/pytrimal-0.2.2-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl#sha256=74444df150401492f309b882355633aee6f83a57e130b2920522ed25ca247e3f (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,272 Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/be/ad/c3309a44f3a6a73cbffdc5705b309d384588f226eb31d2aa97c6cf9b45e2/pytrimal-0.2.2-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl#sha256=3df1903e7dabbc8c21c8512e0f9eae8f742988d822d75e4c61f8243ae81ebd9f (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,273 Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/d3/5c/aebb342d4ca926b1933e097cf3349db72252835a592b35026c551fa8acb2/pytrimal-0.2.2-cp38-cp38-macosx_10_15_x86_64.whl#sha256=bf1b43df63af100e4d5dbdc3340a95c2d9080d7d031c2adeee69ae91bec16861 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,273 Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/09/66/e9e6990ae0d87a9821d2662507b11432977b79b4fed5f08ebf37c1567741/pytrimal-0.2.2-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl#sha256=16a713d82f69525dcdc8d9f7c51d019b53d4a02ec24f14a94fd15defc210fb10 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,274 Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/34/19/7d2f7891b4bdaed950115fd4bf102542478fb71382913341af769a8618ea/pytrimal-0.2.2-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl#sha256=646af6f86854852eee84aa60d94d3d7e487e26be51639165077bee81aa418c45 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,274 Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/fc/ba/bee3467f3bbbe045bdf91e444d446865a1a040f23b57d69a90cf74d33746/pytrimal-0.2.2-cp39-cp39-macosx_10_15_x86_64.whl#sha256=ccadc5146426b78e5553fac58e1c86720af7bdada141f756e3dee5da45df6646 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,275 Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/27/84/47b834914b887200fae78c873cf5cecabd16f5ab29d3ec7c6e6b6bd269c5/pytrimal-0.2.2-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl#sha256=9d4b6b38f14fe128a67ab873d128b109b53854ba4e3388a254c37f4654b2f14d (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,275 Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/79/9e/a30f9e5ed67d6340e7e6b14adbb9785c07e6be638e7e174fa90e21346b9e/pytrimal-0.2.2-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl#sha256=795c839f1367758c7bca92cb970170aca9033884afc1cd9096cb95a81b3ee699 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,276 Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/c1/fc/99342fcc0f8aeff6de1ae17d246b23f7b859ff0c2a18c73bb2fac83951d4/pytrimal-0.2.2-pp36-pypy36_pp73-manylinux_2_12_x86_64.manylinux2010_x86_64.whl#sha256=5af3f51efd57435143cfa749ab5438e83ba1e3dd92aa58cf2fafab04f1230359 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,276 Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/f1/f6/e16ecf929a4d93adb49a4b1371d4899e220eec8a7eacb449daca0ede6a45/pytrimal-0.2.2-pp37-pypy37_pp73-macosx_10_9_x86_64.whl#sha256=4c1597aee1c1ff7f5584d86e3dc3e6bd9720df3dde3393a56561e5ab74b9e3a1 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,277 Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/78/1d/63137814c76bdbc122fe35494e64d8c0f5b1f05e5adb2a988c15a20be541/pytrimal-0.2.2-pp37-pypy37_pp73-manylinux_2_12_x86_64.manylinux2010_x86_64.whl#sha256=e815abbf943283d2cd9c68de56f38a84b84b8f4f5f4dac9671b67f5a19941412 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,277 Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/ff/ed/af317c698e535d923630672e06a7795612554b587d9532962425ef41c94a/pytrimal-0.2.2-pp38-pypy38_pp73-macosx_10_9_x86_64.whl#sha256=e72c9aa401d23ecb610059b868c5216851e33aa0039c2b53d1cdcd214c1aed66 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,278 Skipping link: No binaries permitted for pytrimal: https://files.pythonhosted.org/packages/0c/16/6cacd068c92dddfdadbecb04b33222546c3168552a6013c167cdba086414/pytrimal-0.2.2-pp39-pypy39_pp73-macosx_10_9_x86_64.whl#sha256=17fe07a744d3b0777f423031a17d28318c43f08b7091e07fbe415719776859a1 (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,279 Found link https://files.pythonhosted.org/packages/52/96/0cc493d018f9d4f17bd5445727c45f5860a9460c5a766ab4f64514405514/pytrimal-0.2.2.tar.gz#sha256=36a69a4faab2813ff7d3b3f4eed3c6556a17c37ad339509e28ba9f65b5cb7ccf (from https://pypi.org/simple/pytrimal/) (requires-python:>=3.5), version: 0.2.2 2022-06-09T06:47:15,280 Fetching project page and analyzing links: https://www.piwheels.org/simple/pytrimal/ 2022-06-09T06:47:15,281 Getting page https://www.piwheels.org/simple/pytrimal/ 2022-06-09T06:47:15,283 Found index url https://www.piwheels.org/simple 2022-06-09T06:47:15,592 Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.2-cp37-cp37m-linux_armv7l.whl#sha256=5f3c8d40349fe09f1f02e9392a1bc6dfe598428ccca63cc687102270f4b8bcc7 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,593 Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.2-cp37-cp37m-linux_armv6l.whl#sha256=5f3c8d40349fe09f1f02e9392a1bc6dfe598428ccca63cc687102270f4b8bcc7 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,593 Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.2-cp35-cp35m-linux_armv7l.whl#sha256=2c89565387151ab91f065fd81e6801a59cb0a692e1d518a4bdbe1b819d4e3bb9 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,594 Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.2-cp35-cp35m-linux_armv6l.whl#sha256=2c89565387151ab91f065fd81e6801a59cb0a692e1d518a4bdbe1b819d4e3bb9 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,594 Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.1-cp39-cp39-linux_armv7l.whl#sha256=06890ee257c9d009b402620382086847b440e92a339043e6b759dda8545f6ff6 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,595 Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.1-cp39-cp39-linux_armv6l.whl#sha256=06890ee257c9d009b402620382086847b440e92a339043e6b759dda8545f6ff6 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,595 Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.1-cp37-cp37m-linux_armv7l.whl#sha256=87c41102be591a5dcb6efdf6807ea38a522ec3cc653f29af275f01d2b4e8d4fc (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,596 Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.1-cp37-cp37m-linux_armv6l.whl#sha256=87c41102be591a5dcb6efdf6807ea38a522ec3cc653f29af275f01d2b4e8d4fc (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,596 Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.1-cp35-cp35m-linux_armv7l.whl#sha256=7719393288e4b7d58df66be1b835f01bc962a0a64b61adab766ce32ffa6a3f0e (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,597 Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.1-cp35-cp35m-linux_armv6l.whl#sha256=7719393288e4b7d58df66be1b835f01bc962a0a64b61adab766ce32ffa6a3f0e (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,597 Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.0-cp39-cp39-linux_armv7l.whl#sha256=f5b150f17ead1887b6682721c33fa5cd7a8ab0d03d55d68176e11f3d0e17db43 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,598 Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.0-cp39-cp39-linux_armv6l.whl#sha256=f5b150f17ead1887b6682721c33fa5cd7a8ab0d03d55d68176e11f3d0e17db43 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,598 Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.0-cp37-cp37m-linux_armv7l.whl#sha256=b22cc6f8f6e39214cc9d6ef2778b8811ddb859aeca9ad030b64d78cc83816438 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,599 Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.0-cp37-cp37m-linux_armv6l.whl#sha256=b22cc6f8f6e39214cc9d6ef2778b8811ddb859aeca9ad030b64d78cc83816438 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,599 Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.0-cp35-cp35m-linux_armv7l.whl#sha256=c2e192c5e15e398eb8fcf987e378ac23645cf88ae7b43798f959edf36711e847 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,600 Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.2.0-cp35-cp35m-linux_armv6l.whl#sha256=c2e192c5e15e398eb8fcf987e378ac23645cf88ae7b43798f959edf36711e847 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,600 Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.1.2-cp39-cp39-linux_armv7l.whl#sha256=8335602183caad582c8928ea691b7be0671b701f02fd9489681d90efd6708863 (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,601 Skipping link: No binaries permitted for pytrimal: 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https://www.piwheels.org/simple/pytrimal/pytrimal-0.1.2-cp35-cp35m-linux_armv7l.whl#sha256=4a3dcfa05641310e339af037687c7171ffa116dab65617ebd2d9661d937375ee (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,603 Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.1.2-cp35-cp35m-linux_armv6l.whl#sha256=4a3dcfa05641310e339af037687c7171ffa116dab65617ebd2d9661d937375ee (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,603 Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.1.1-cp39-cp39-linux_armv7l.whl#sha256=c54c9649d97022e8ce47cce412b180621f9a77399bf9c58ef855e08f913a237f (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,604 Skipping link: No binaries permitted for pytrimal: https://www.piwheels.org/simple/pytrimal/pytrimal-0.1.1-cp39-cp39-linux_armv6l.whl#sha256=c54c9649d97022e8ce47cce412b180621f9a77399bf9c58ef855e08f913a237f (from https://www.piwheels.org/simple/pytrimal/) (requires-python:>=3.5) 2022-06-09T06:47:15,604 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) 2022-06-09T06:47:15,605 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) 2022-06-09T06:47:15,605 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) 2022-06-09T06:47:15,606 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) 2022-06-09T06:47:15,607 Skipping link: not a file: https://www.piwheels.org/simple/pytrimal/ 2022-06-09T06:47:15,607 Skipping link: not a file: https://pypi.org/simple/pytrimal/ 2022-06-09T06:47:15,653 Given no hashes to check 1 links for project 'pytrimal': discarding no candidates 2022-06-09T06:47:15,696 Collecting pytrimal==0.2.2 2022-06-09T06:47:15,700 Created temporary directory: /tmp/pip-unpack-1z6ohg5h 2022-06-09T06:47:15,791 Downloading pytrimal-0.2.2.tar.gz (8.6 MB) 2022-06-09T06:47:24,956 Added pytrimal==0.2.2 from https://files.pythonhosted.org/packages/52/96/0cc493d018f9d4f17bd5445727c45f5860a9460c5a766ab4f64514405514/pytrimal-0.2.2.tar.gz#sha256=36a69a4faab2813ff7d3b3f4eed3c6556a17c37ad339509e28ba9f65b5cb7ccf to build tracker '/tmp/pip-build-tracker-t7xntenv' 2022-06-09T06:47:24,966 Created temporary directory: /tmp/pip-build-env-9l9z77vd 2022-06-09T06:47:24,986 Created temporary directory: /tmp/pip-standalone-pip-o1nu3a4s 2022-06-09T06:47:27,281 Installing build dependencies: started 2022-06-09T06:47:27,283 Running command pip subprocess to install build dependencies 2022-06-09T06:47:38,860 Using pip 22.1 from /tmp/pip-standalone-pip-o1nu3a4s/__env_pip__.zip/pip (python 3.9) 2022-06-09T06:47:40,441 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-06-09T06:47:44,376 Collecting setuptools>=46.4 2022-06-09T06:47:44,654 Using cached https://www.piwheels.org/simple/setuptools/setuptools-62.3.3-py3-none-any.whl (1.2 MB) 2022-06-09T06:47:48,324 Collecting cython~=0.29.16 2022-06-09T06:47:49,351 Using cached https://www.piwheels.org/simple/cython/Cython-0.29.30-cp39-cp39-linux_armv7l.whl (5.0 MB) 2022-06-09T06:47:54,782 Installing collected packages: setuptools, cython 2022-06-09T06:48:06,254 Creating /tmp/pip-build-env-9l9z77vd/overlay/bin 2022-06-09T06:48:06,258 changing mode of /tmp/pip-build-env-9l9z77vd/overlay/bin/cygdb to 755 2022-06-09T06:48:06,262 changing mode of /tmp/pip-build-env-9l9z77vd/overlay/bin/cython to 755 2022-06-09T06:48:06,267 changing mode of /tmp/pip-build-env-9l9z77vd/overlay/bin/cythonize to 755 2022-06-09T06:48:06,312 Successfully installed cython-0.29.30 setuptools-62.3.3 2022-06-09T06:48:06,508 WARNING: There was an error checking the latest version of pip. 2022-06-09T06:48:07,068 Installing build dependencies: finished with status 'done' 2022-06-09T06:48:07,095 Getting requirements to build wheel: started 2022-06-09T06:48:07,097 Running command Getting requirements to build wheel 2022-06-09T06:48:09,871 Getting requirements to build wheel: finished with status 'done' 2022-06-09T06:48:09,910 Created temporary directory: /tmp/pip-standalone-pip-u8rcqdn3 2022-06-09T06:48:12,101 Installing backend dependencies: started 2022-06-09T06:48:12,104 Running command pip subprocess to install backend dependencies 2022-06-09T06:48:23,328 Using pip 22.1 from /tmp/pip-standalone-pip-u8rcqdn3/__env_pip__.zip/pip (python 3.9) 2022-06-09T06:48:24,903 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-06-09T06:48:25,779 Collecting wheel 2022-06-09T06:48:25,812 Using cached https://www.piwheels.org/simple/wheel/wheel-0.37.1-py2.py3-none-any.whl (35 kB) 2022-06-09T06:48:30,195 Installing collected packages: wheel 2022-06-09T06:48:30,487 Creating /tmp/pip-build-env-9l9z77vd/normal/bin 2022-06-09T06:48:30,492 changing mode of /tmp/pip-build-env-9l9z77vd/normal/bin/wheel to 755 2022-06-09T06:48:30,519 Successfully installed wheel-0.37.1 2022-06-09T06:48:30,710 WARNING: There was an error checking the latest version of pip. 2022-06-09T06:48:31,133 Installing backend dependencies: finished with status 'done' 2022-06-09T06:48:31,155 Created temporary directory: /tmp/pip-modern-metadata-87w33arq 2022-06-09T06:48:31,161 Preparing metadata (pyproject.toml): started 2022-06-09T06:48:31,163 Running command Preparing metadata (pyproject.toml) 2022-06-09T06:48:36,087 running dist_info 2022-06-09T06:48:36,697 creating /tmp/pip-modern-metadata-87w33arq/pytrimal.egg-info 2022-06-09T06:48:37,293 writing /tmp/pip-modern-metadata-87w33arq/pytrimal.egg-info/PKG-INFO 2022-06-09T06:48:37,854 writing dependency_links to /tmp/pip-modern-metadata-87w33arq/pytrimal.egg-info/dependency_links.txt 2022-06-09T06:48:41,210 writing top-level names to /tmp/pip-modern-metadata-87w33arq/pytrimal.egg-info/top_level.txt 2022-06-09T06:48:41,214 writing manifest file '/tmp/pip-modern-metadata-87w33arq/pytrimal.egg-info/SOURCES.txt' 2022-06-09T06:48:41,920 reading manifest file '/tmp/pip-modern-metadata-87w33arq/pytrimal.egg-info/SOURCES.txt' 2022-06-09T06:48:41,924 reading manifest template 'MANIFEST.in' 2022-06-09T06:48:42,928 warning: no previously-included files matching '*.html' found under directory 'pytrimal' 2022-06-09T06:48:42,936 warning: no files found matching '*.pxd' under directory 'pytrimal/patch' 2022-06-09T06:48:42,958 adding license file 'COPYING' 2022-06-09T06:48:42,989 writing manifest file '/tmp/pip-modern-metadata-87w33arq/pytrimal.egg-info/SOURCES.txt' 2022-06-09T06:48:42,993 creating '/tmp/pip-modern-metadata-87w33arq/pytrimal-0.2.2.dist-info' 2022-06-09T06:48:43,185 adding license file "COPYING" (matched pattern "COPYING*") 2022-06-09T06:48:43,432 Preparing metadata (pyproject.toml): finished with status 'done' 2022-06-09T06:48:43,489 Source in /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d has version 0.2.2, which satisfies requirement pytrimal==0.2.2 from https://files.pythonhosted.org/packages/52/96/0cc493d018f9d4f17bd5445727c45f5860a9460c5a766ab4f64514405514/pytrimal-0.2.2.tar.gz#sha256=36a69a4faab2813ff7d3b3f4eed3c6556a17c37ad339509e28ba9f65b5cb7ccf 2022-06-09T06:48:43,491 Removed pytrimal==0.2.2 from https://files.pythonhosted.org/packages/52/96/0cc493d018f9d4f17bd5445727c45f5860a9460c5a766ab4f64514405514/pytrimal-0.2.2.tar.gz#sha256=36a69a4faab2813ff7d3b3f4eed3c6556a17c37ad339509e28ba9f65b5cb7ccf from build tracker '/tmp/pip-build-tracker-t7xntenv' 2022-06-09T06:48:43,507 Created temporary directory: /tmp/pip-unpack-2x0fyc48 2022-06-09T06:48:43,508 Building wheels for collected packages: pytrimal 2022-06-09T06:48:43,517 Created temporary directory: /tmp/pip-wheel-ii2n35sg 2022-06-09T06:48:43,518 Destination directory: /tmp/pip-wheel-ii2n35sg 2022-06-09T06:48:43,523 Building wheel for pytrimal (pyproject.toml): started 2022-06-09T06:48:43,525 Running command Building wheel for pytrimal (pyproject.toml) 2022-06-09T06:48:48,384 running bdist_wheel 2022-06-09T06:48:48,479 running build 2022-06-09T06:48:48,480 running build_py 2022-06-09T06:48:49,078 creating build 2022-06-09T06:48:49,079 creating build/lib.linux-armv7l-cpython-39 2022-06-09T06:48:49,080 creating build/lib.linux-armv7l-cpython-39/pytrimal 2022-06-09T06:48:49,082 copying pytrimal/__init__.py -> build/lib.linux-armv7l-cpython-39/pytrimal 2022-06-09T06:48:49,086 copying pytrimal/_version.py -> build/lib.linux-armv7l-cpython-39/pytrimal 2022-06-09T06:48:49,091 creating build/lib.linux-armv7l-cpython-39/pytrimal/tests 2022-06-09T06:48:49,093 copying pytrimal/tests/test_doctest.py -> build/lib.linux-armv7l-cpython-39/pytrimal/tests 2022-06-09T06:48:49,096 copying pytrimal/tests/test_manual_trimmer.py -> build/lib.linux-armv7l-cpython-39/pytrimal/tests 2022-06-09T06:48:49,100 copying pytrimal/tests/__main__.py -> build/lib.linux-armv7l-cpython-39/pytrimal/tests 2022-06-09T06:48:49,104 copying pytrimal/tests/test_similarity_matrix.py -> build/lib.linux-armv7l-cpython-39/pytrimal/tests 2022-06-09T06:48:49,107 copying pytrimal/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/pytrimal/tests 2022-06-09T06:48:49,110 copying pytrimal/tests/test_automatic_trimmer.py -> build/lib.linux-armv7l-cpython-39/pytrimal/tests 2022-06-09T06:48:49,114 copying pytrimal/tests/test_alignment.py -> build/lib.linux-armv7l-cpython-39/pytrimal/tests 2022-06-09T06:48:49,119 creating build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-09T06:48:49,121 copying pytrimal/tests/data/__init__.py -> build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-09T06:48:49,137 copying pytrimal/py.typed -> build/lib.linux-armv7l-cpython-39/pytrimal 2022-06-09T06:48:49,140 copying pytrimal/_trimal.pyi -> build/lib.linux-armv7l-cpython-39/pytrimal 2022-06-09T06:48:49,144 copying pytrimal/tests/requirements.txt -> build/lib.linux-armv7l-cpython-39/pytrimal/tests 2022-06-09T06:48:49,148 copying pytrimal/tests/data/ENOG411BWBU.id50.fasta -> build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-09T06:48:49,154 copying pytrimal/tests/data/ENOG411BWBU.fasta -> build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-09T06:48:49,172 copying pytrimal/tests/data/halorhodopsin.afa -> build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-09T06:48:49,188 copying pytrimal/tests/data/ENOG411BWBU.strict.fasta -> build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-09T06:48:49,207 copying pytrimal/tests/data/example.001.gt90.w3.fasta -> build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-09T06:48:49,210 copying pytrimal/tests/data/pam70.json -> build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-09T06:48:49,214 copying pytrimal/tests/data/ENOG411BWBU.noallgaps.fasta -> build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-09T06:48:49,233 copying pytrimal/tests/data/ENOG411BWBU.strictplus.fasta -> build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-09T06:48:49,244 copying pytrimal/tests/data/ENOG411BWBU.id70.fasta -> build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-09T06:48:49,252 copying pytrimal/tests/data/ENOG411BWBU.cons40.gt40.fasta -> build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-09T06:48:49,265 copying pytrimal/tests/data/example.001.AA.clw -> build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-09T06:48:49,269 copying pytrimal/tests/data/ENOG411BWBU.cons60.gt90.fasta -> build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-09T06:48:49,282 copying pytrimal/tests/data/ENOG411BWBU.gappyout.fasta -> build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-09T06:48:49,295 copying pytrimal/tests/data/ENOG411BWBU.automated1.fasta -> build/lib.linux-armv7l-cpython-39/pytrimal/tests/data 2022-06-09T06:48:49,313 running build_clib 2022-06-09T06:48:49,326 creating build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:49,328 generating build/temp.linux-armv7l-cpython-39/libcpu_features.a from vendor/cpu_features/src/impl_arm_linux_or_android.c, vendor/cpu_features/src/filesystem.c, vendor/cpu_features/src/stack_line_reader.c, vendor/cpu_features/src/string_view.c, vendor/cpu_features/src/copy.inl, vendor/cpu_features/src/define_introspection.inl, vendor/cpu_features/src/define_introspection_and_hwcaps.inl, vendor/cpu_features/src/equals.inl, vendor/cpu_features/src/impl_x86__base_implementation.inl 2022-06-09T06:48:49,328 building cpu_features with unix compiler 2022-06-09T06:48:49,329 generating build/temp.linux-armv7l-cpython-39/impl_arm_linux_or_android.c from vendor/cpu_features/src/impl_arm_linux_or_android.c 2022-06-09T06:48:49,330 copying vendor/cpu_features/src/impl_arm_linux_or_android.c -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:49,333 generating build/temp.linux-armv7l-cpython-39/filesystem.c from vendor/cpu_features/src/filesystem.c 2022-06-09T06:48:49,334 copying vendor/cpu_features/src/filesystem.c -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:49,337 generating build/temp.linux-armv7l-cpython-39/stack_line_reader.c from vendor/cpu_features/src/stack_line_reader.c 2022-06-09T06:48:49,338 copying vendor/cpu_features/src/stack_line_reader.c -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:49,342 generating build/temp.linux-armv7l-cpython-39/string_view.c from vendor/cpu_features/src/string_view.c 2022-06-09T06:48:49,342 copying vendor/cpu_features/src/string_view.c -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:49,346 generating build/temp.linux-armv7l-cpython-39/copy.inl from vendor/cpu_features/src/copy.inl 2022-06-09T06:48:49,347 copying vendor/cpu_features/src/copy.inl -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:49,350 generating build/temp.linux-armv7l-cpython-39/define_introspection.inl from vendor/cpu_features/src/define_introspection.inl 2022-06-09T06:48:49,351 copying vendor/cpu_features/src/define_introspection.inl -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:49,353 generating build/temp.linux-armv7l-cpython-39/define_introspection_and_hwcaps.inl from vendor/cpu_features/src/define_introspection_and_hwcaps.inl 2022-06-09T06:48:49,354 copying vendor/cpu_features/src/define_introspection_and_hwcaps.inl -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:49,357 generating build/temp.linux-armv7l-cpython-39/equals.inl from vendor/cpu_features/src/equals.inl 2022-06-09T06:48:49,358 copying vendor/cpu_features/src/equals.inl -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:49,361 generating build/temp.linux-armv7l-cpython-39/impl_x86__base_implementation.inl from vendor/cpu_features/src/impl_x86__base_implementation.inl 2022-06-09T06:48:49,362 copying vendor/cpu_features/src/impl_x86__base_implementation.inl -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:49,370 generating build/temp.linux-armv7l-cpython-39/impl_arm_linux_or_android.o from build/temp.linux-armv7l-cpython-39/impl_arm_linux_or_android.c 2022-06-09T06:48:49,371 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 -DSTACK_LINE_READER_BUFFER_SIZE=1024 -Ivendor/cpu_features/include -Ibuild/temp.linux-armv7l-cpython-39 -c build/temp.linux-armv7l-cpython-39/impl_arm_linux_or_android.c -o build/temp.linux-armv7l-cpython-39/impl_arm_linux_or_android.o 2022-06-09T06:48:50,631 generating build/temp.linux-armv7l-cpython-39/filesystem.o from build/temp.linux-armv7l-cpython-39/filesystem.c 2022-06-09T06:48:50,633 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 -DSTACK_LINE_READER_BUFFER_SIZE=1024 -Ivendor/cpu_features/include -Ibuild/temp.linux-armv7l-cpython-39 -c build/temp.linux-armv7l-cpython-39/filesystem.c -o build/temp.linux-armv7l-cpython-39/filesystem.o 2022-06-09T06:48:51,004 generating build/temp.linux-armv7l-cpython-39/stack_line_reader.o from build/temp.linux-armv7l-cpython-39/stack_line_reader.c 2022-06-09T06:48:51,006 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 -DSTACK_LINE_READER_BUFFER_SIZE=1024 -Ivendor/cpu_features/include -Ibuild/temp.linux-armv7l-cpython-39 -c build/temp.linux-armv7l-cpython-39/stack_line_reader.c -o build/temp.linux-armv7l-cpython-39/stack_line_reader.o 2022-06-09T06:48:51,440 generating build/temp.linux-armv7l-cpython-39/string_view.o from build/temp.linux-armv7l-cpython-39/string_view.c 2022-06-09T06:48:51,441 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 -DSTACK_LINE_READER_BUFFER_SIZE=1024 -Ivendor/cpu_features/include -Ibuild/temp.linux-armv7l-cpython-39 -c build/temp.linux-armv7l-cpython-39/string_view.c -o build/temp.linux-armv7l-cpython-39/string_view.o 2022-06-09T06:48:52,319 generating build/temp.linux-armv7l-cpython-39/libcpu_features.a from build/temp.linux-armv7l-cpython-39/impl_arm_linux_or_android.o, build/temp.linux-armv7l-cpython-39/filesystem.o, build/temp.linux-armv7l-cpython-39/stack_line_reader.o, build/temp.linux-armv7l-cpython-39/string_view.o, build/temp.linux-armv7l-cpython-39/copy.inl, build/temp.linux-armv7l-cpython-39/define_introspection.inl, build/temp.linux-armv7l-cpython-39/define_introspection_and_hwcaps.inl, build/temp.linux-armv7l-cpython-39/equals.inl, build/temp.linux-armv7l-cpython-39/impl_x86__base_implementation.inl 2022-06-09T06:48:52,320 arm-linux-gnueabihf-gcc-ar rcs build/temp.linux-armv7l-cpython-39/libcpu_features.a build/temp.linux-armv7l-cpython-39/impl_arm_linux_or_android.o build/temp.linux-armv7l-cpython-39/filesystem.o build/temp.linux-armv7l-cpython-39/stack_line_reader.o build/temp.linux-armv7l-cpython-39/string_view.o build/temp.linux-armv7l-cpython-39/copy.inl build/temp.linux-armv7l-cpython-39/define_introspection.inl build/temp.linux-armv7l-cpython-39/define_introspection_and_hwcaps.inl build/temp.linux-armv7l-cpython-39/equals.inl build/temp.linux-armv7l-cpython-39/impl_x86__base_implementation.inl 2022-06-09T06:48:52,397 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/phylip_paml_m10_state.cpp, vendor/trimal/source/FormatHandling/nexus_state.cpp, vendor/trimal/source/FormatHandling/mega_sequential_state.cpp, vendor/trimal/source/FormatHandling/mega_interleaved_state.cpp, vendor/trimal/source/FormatHandling/nexus_m10_state.cpp, vendor/trimal/source/FormatHandling/fasta_state.cpp, vendor/trimal/source/FormatHandling/clustal_state.cpp, vendor/trimal/source/FormatHandling/htmlreport_state.cpp, vendor/trimal/source/FormatHandling/fasta_m10_state.cpp, vendor/trimal/source/FormatHandling/phylip32_state.cpp, vendor/trimal/source/FormatHandling/pir_state.cpp, vendor/trimal/source/FormatHandling/phylip40_state.cpp, vendor/trimal/source/FormatHandling/phylip_paml_state.cpp, vendor/trimal/source/FormatHandling/phylip32_m10_state.cpp, vendor/trimal/source/FormatHandling/phylip40_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 2022-06-09T06:48:52,398 building trimal with unix compiler 2022-06-09T06:48:52,399 generating build/temp.linux-armv7l-cpython-39/InternalBenchmarker.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/InternalBenchmarker.h 2022-06-09T06:48:52,407 generating build/temp.linux-armv7l-cpython-39/Cleaner.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/Cleaner.h 2022-06-09T06:48:52,421 generating build/temp.linux-armv7l-cpython-39/defines.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/defines.h 2022-06-09T06:48:52,426 generating build/temp.linux-armv7l-cpython-39/trimalManager.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/trimalManager.h 2022-06-09T06:48:52,436 generating build/temp.linux-armv7l-cpython-39/utils.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/utils.h 2022-06-09T06:48:52,447 generating build/temp.linux-armv7l-cpython-39/reportsystem.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/reportsystem.h 2022-06-09T06:48:52,460 generating build/temp.linux-armv7l-cpython-39/values.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/values.h 2022-06-09T06:48:52,466 generating build/temp.linux-armv7l-cpython-39/VCFHandler.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/VCFHandler.h 2022-06-09T06:48:52,476 creating build/temp.linux-armv7l-cpython-39/Statistics 2022-06-09T06:48:52,478 generating build/temp.linux-armv7l-cpython-39/Statistics/Similarity.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/Statistics/Similarity.h 2022-06-09T06:48:52,484 generating build/temp.linux-armv7l-cpython-39/Statistics/Mold.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/Statistics/Mold.h 2022-06-09T06:48:52,489 generating build/temp.linux-armv7l-cpython-39/Statistics/Consistency.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/Statistics/Consistency.h 2022-06-09T06:48:52,496 generating build/temp.linux-armv7l-cpython-39/Statistics/Manager.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/Statistics/Manager.h 2022-06-09T06:48:52,503 generating build/temp.linux-armv7l-cpython-39/Statistics/Gaps.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/Statistics/Gaps.h 2022-06-09T06:48:52,508 generating build/temp.linux-armv7l-cpython-39/Statistics/similarityMatrix.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/Statistics/similarityMatrix.h 2022-06-09T06:48:52,514 creating build/temp.linux-armv7l-cpython-39/FormatHandling 2022-06-09T06:48:52,516 generating build/temp.linux-armv7l-cpython-39/FormatHandling/FormatManager.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/FormatHandling/FormatManager.h 2022-06-09T06:48:52,524 generating build/temp.linux-armv7l-cpython-39/FormatHandling/mega_interleaved_state.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/FormatHandling/mega_interleaved_state.h 2022-06-09T06:48:52,528 generating build/temp.linux-armv7l-cpython-39/FormatHandling/formats_header.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/FormatHandling/formats_header.h 2022-06-09T06:48:52,532 generating build/temp.linux-armv7l-cpython-39/FormatHandling/fasta_state.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/FormatHandling/fasta_state.h 2022-06-09T06:48:52,535 generating build/temp.linux-armv7l-cpython-39/FormatHandling/nexus_state.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/FormatHandling/nexus_state.h 2022-06-09T06:48:52,539 generating build/temp.linux-armv7l-cpython-39/FormatHandling/nexus_m10_state.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/FormatHandling/nexus_m10_state.h 2022-06-09T06:48:52,543 generating build/temp.linux-armv7l-cpython-39/FormatHandling/phylip_paml_m10_state.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/FormatHandling/phylip_paml_m10_state.h 2022-06-09T06:48:52,546 generating build/temp.linux-armv7l-cpython-39/FormatHandling/phylip_paml_state.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/FormatHandling/phylip_paml_state.h 2022-06-09T06:48:52,550 generating build/temp.linux-armv7l-cpython-39/FormatHandling/mega_sequential_state.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/FormatHandling/mega_sequential_state.h 2022-06-09T06:48:52,553 generating build/temp.linux-armv7l-cpython-39/FormatHandling/BaseFormatHandler.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/FormatHandling/BaseFormatHandler.h 2022-06-09T06:48:52,559 generating build/temp.linux-armv7l-cpython-39/FormatHandling/fasta_m10_state.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/FormatHandling/fasta_m10_state.h 2022-06-09T06:48:52,562 generating build/temp.linux-armv7l-cpython-39/FormatHandling/phylip40_state.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/FormatHandling/phylip40_state.h 2022-06-09T06:48:52,566 generating build/temp.linux-armv7l-cpython-39/FormatHandling/phylip32_m10_state.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/FormatHandling/phylip32_m10_state.h 2022-06-09T06:48:52,569 generating build/temp.linux-armv7l-cpython-39/FormatHandling/phylip32_state.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/FormatHandling/phylip32_state.h 2022-06-09T06:48:52,573 generating build/temp.linux-armv7l-cpython-39/FormatHandling/phylip40_m10_state.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/FormatHandling/phylip40_m10_state.h 2022-06-09T06:48:52,576 generating build/temp.linux-armv7l-cpython-39/FormatHandling/pir_state.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/FormatHandling/pir_state.h 2022-06-09T06:48:52,580 generating build/temp.linux-armv7l-cpython-39/FormatHandling/htmlreport_state.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/FormatHandling/htmlreport_state.h 2022-06-09T06:48:52,583 generating build/temp.linux-armv7l-cpython-39/FormatHandling/clustal_state.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/FormatHandling/clustal_state.h 2022-06-09T06:48:52,587 creating build/temp.linux-armv7l-cpython-39/Alignment 2022-06-09T06:48:52,588 generating build/temp.linux-armv7l-cpython-39/Alignment/Alignment.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/Alignment/Alignment.h 2022-06-09T06:48:52,594 generating build/temp.linux-armv7l-cpython-39/Alignment/sequencesMatrix.h from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/Alignment/sequencesMatrix.h 2022-06-09T06:48:52,600 creating build/temp.linux-armv7l-cpython-39/RawText 2022-06-09T06:48:52,601 generating build/temp.linux-armv7l-cpython-39/RawText/examples.txt from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/RawText/examples.txt 2022-06-09T06:48:52,605 generating build/temp.linux-armv7l-cpython-39/RawText/legacyMenu.txt from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/RawText/legacyMenu.txt 2022-06-09T06:48:52,611 generating build/temp.linux-armv7l-cpython-39/RawText/menu.txt from /tmp/pip-wheel-kox7n9ta/pytrimal_0d2e68dbe9fe49069837addedaa7c18d/vendor/trimal/include/RawText/menu.txt 2022-06-09T06:48:52,621 generating build/temp.linux-armv7l-cpython-39/Cleaner.cpp from vendor/trimal/source/Cleaner.cpp 2022-06-09T06:48:52,622 copying vendor/trimal/source/Cleaner.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,629 generating build/temp.linux-armv7l-cpython-39/Alignment.cpp from vendor/trimal/source/Alignment/Alignment.cpp 2022-06-09T06:48:52,630 copying vendor/trimal/source/Alignment/Alignment.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,640 generating build/temp.linux-armv7l-cpython-39/sequencesMatrix.cpp from vendor/trimal/source/Alignment/sequencesMatrix.cpp 2022-06-09T06:48:52,641 copying vendor/trimal/source/Alignment/sequencesMatrix.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,645 generating build/temp.linux-armv7l-cpython-39/similarityMatrix.cpp from vendor/trimal/source/Statistics/similarityMatrix.cpp 2022-06-09T06:48:52,645 copying vendor/trimal/source/Statistics/similarityMatrix.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,650 generating build/temp.linux-armv7l-cpython-39/Mold.cpp from vendor/trimal/source/Statistics/Mold.cpp 2022-06-09T06:48:52,650 copying vendor/trimal/source/Statistics/Mold.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,655 generating build/temp.linux-armv7l-cpython-39/Gaps.cpp from vendor/trimal/source/Statistics/Gaps.cpp 2022-06-09T06:48:52,655 copying vendor/trimal/source/Statistics/Gaps.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,660 generating build/temp.linux-armv7l-cpython-39/Manager.cpp from vendor/trimal/source/Statistics/Manager.cpp 2022-06-09T06:48:52,662 copying vendor/trimal/source/Statistics/Manager.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,666 generating build/temp.linux-armv7l-cpython-39/Similarity.cpp from vendor/trimal/source/Statistics/Similarity.cpp 2022-06-09T06:48:52,667 copying vendor/trimal/source/Statistics/Similarity.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,672 generating build/temp.linux-armv7l-cpython-39/Consistency.cpp from vendor/trimal/source/Statistics/Consistency.cpp 2022-06-09T06:48:52,674 copying vendor/trimal/source/Statistics/Consistency.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,680 generating build/temp.linux-armv7l-cpython-39/errorMessages.cpp from vendor/trimal/source/reportMessages/errorMessages.cpp 2022-06-09T06:48:52,681 copying vendor/trimal/source/reportMessages/errorMessages.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,686 generating build/temp.linux-armv7l-cpython-39/infoMessages.cpp from vendor/trimal/source/reportMessages/infoMessages.cpp 2022-06-09T06:48:52,688 copying vendor/trimal/source/reportMessages/infoMessages.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,691 generating build/temp.linux-armv7l-cpython-39/warningMessages.cpp from vendor/trimal/source/reportMessages/warningMessages.cpp 2022-06-09T06:48:52,692 copying vendor/trimal/source/reportMessages/warningMessages.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,696 generating build/temp.linux-armv7l-cpython-39/phylip_paml_m10_state.cpp from vendor/trimal/source/FormatHandling/phylip_paml_m10_state.cpp 2022-06-09T06:48:52,697 copying vendor/trimal/source/FormatHandling/phylip_paml_m10_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,701 generating build/temp.linux-armv7l-cpython-39/nexus_state.cpp from vendor/trimal/source/FormatHandling/nexus_state.cpp 2022-06-09T06:48:52,701 copying vendor/trimal/source/FormatHandling/nexus_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,706 generating build/temp.linux-armv7l-cpython-39/mega_sequential_state.cpp from vendor/trimal/source/FormatHandling/mega_sequential_state.cpp 2022-06-09T06:48:52,706 copying vendor/trimal/source/FormatHandling/mega_sequential_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,710 generating build/temp.linux-armv7l-cpython-39/mega_interleaved_state.cpp from vendor/trimal/source/FormatHandling/mega_interleaved_state.cpp 2022-06-09T06:48:52,711 copying vendor/trimal/source/FormatHandling/mega_interleaved_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,715 generating build/temp.linux-armv7l-cpython-39/nexus_m10_state.cpp from vendor/trimal/source/FormatHandling/nexus_m10_state.cpp 2022-06-09T06:48:52,715 copying vendor/trimal/source/FormatHandling/nexus_m10_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,719 generating build/temp.linux-armv7l-cpython-39/fasta_state.cpp from vendor/trimal/source/FormatHandling/fasta_state.cpp 2022-06-09T06:48:52,720 copying vendor/trimal/source/FormatHandling/fasta_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,723 generating build/temp.linux-armv7l-cpython-39/clustal_state.cpp from vendor/trimal/source/FormatHandling/clustal_state.cpp 2022-06-09T06:48:52,724 copying vendor/trimal/source/FormatHandling/clustal_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,727 generating build/temp.linux-armv7l-cpython-39/htmlreport_state.cpp from vendor/trimal/source/FormatHandling/htmlreport_state.cpp 2022-06-09T06:48:52,728 copying vendor/trimal/source/FormatHandling/htmlreport_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,732 generating build/temp.linux-armv7l-cpython-39/fasta_m10_state.cpp from vendor/trimal/source/FormatHandling/fasta_m10_state.cpp 2022-06-09T06:48:52,732 copying vendor/trimal/source/FormatHandling/fasta_m10_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,736 generating build/temp.linux-armv7l-cpython-39/phylip32_state.cpp from vendor/trimal/source/FormatHandling/phylip32_state.cpp 2022-06-09T06:48:52,736 copying vendor/trimal/source/FormatHandling/phylip32_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,740 generating build/temp.linux-armv7l-cpython-39/pir_state.cpp from vendor/trimal/source/FormatHandling/pir_state.cpp 2022-06-09T06:48:52,741 copying vendor/trimal/source/FormatHandling/pir_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,744 generating build/temp.linux-armv7l-cpython-39/phylip40_state.cpp from vendor/trimal/source/FormatHandling/phylip40_state.cpp 2022-06-09T06:48:52,745 copying vendor/trimal/source/FormatHandling/phylip40_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,749 generating build/temp.linux-armv7l-cpython-39/phylip_paml_state.cpp from vendor/trimal/source/FormatHandling/phylip_paml_state.cpp 2022-06-09T06:48:52,749 copying vendor/trimal/source/FormatHandling/phylip_paml_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,752 generating build/temp.linux-armv7l-cpython-39/phylip32_m10_state.cpp from vendor/trimal/source/FormatHandling/phylip32_m10_state.cpp 2022-06-09T06:48:52,753 copying vendor/trimal/source/FormatHandling/phylip32_m10_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,756 generating build/temp.linux-armv7l-cpython-39/phylip40_m10_state.cpp from vendor/trimal/source/FormatHandling/phylip40_m10_state.cpp 2022-06-09T06:48:52,757 copying vendor/trimal/source/FormatHandling/phylip40_m10_state.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,760 generating build/temp.linux-armv7l-cpython-39/BaseFormatHandler.cpp from vendor/trimal/source/FormatHandling/BaseFormatHandler.cpp 2022-06-09T06:48:52,761 copying vendor/trimal/source/FormatHandling/BaseFormatHandler.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,764 generating build/temp.linux-armv7l-cpython-39/utils.cpp from vendor/trimal/source/utils.cpp 2022-06-09T06:48:52,765 copying vendor/trimal/source/utils.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,770 generating build/temp.linux-armv7l-cpython-39/InternalBenchmarker.cpp from vendor/trimal/source/InternalBenchmarker.cpp 2022-06-09T06:48:52,771 copying vendor/trimal/source/InternalBenchmarker.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,776 generating build/temp.linux-armv7l-cpython-39/trimalManager.cpp from vendor/trimal/source/trimalManager.cpp 2022-06-09T06:48:52,777 copying vendor/trimal/source/trimalManager.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,787 generating build/temp.linux-armv7l-cpython-39/VCFHandler.cpp from vendor/trimal/source/VCFHandler.cpp 2022-06-09T06:48:52,788 copying vendor/trimal/source/VCFHandler.cpp -> build/temp.linux-armv7l-cpython-39 2022-06-09T06:48:52,794 generating build/temp.linux-armv7l-cpython-39/Cleaner.o from build/temp.linux-armv7l-cpython-39/Cleaner.cpp 2022-06-09T06:48:52,796 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 -c build/temp.linux-armv7l-cpython-39/Cleaner.cpp -o build/temp.linux-armv7l-cpython-39/Cleaner.o 2022-06-09T06:48:53,960 build/temp.linux-armv7l-cpython-39/Cleaner.cpp:1449: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2022-06-09T06:48:53,960 1449 | #pragma omp parallel for num_threads(NUMTHREADS) if(alig->originalNumberOfSequences>MINPARALLELSIZE) 2022-06-09T06:48:53,961 | 2022-06-09T06:48:53,961 build/temp.linux-armv7l-cpython-39/Cleaner.cpp:1457: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2022-06-09T06:48:53,962 1457 | #pragma omp parallel for num_threads(NUMTHREADS) private(j, k, hit, dst) if(alig->originalNumberOfSequences>MINPARALLELSIZE) 2022-06-09T06:48:53,962 | 2022-06-09T06:48:57,160 build/temp.linux-armv7l-cpython-39/Cleaner.cpp: In member function ‘Alignment* Cleaner::cleanStrict(int, const int*, float, const float*, bool, bool)’: 2022-06-09T06:48:57,161 build/temp.linux-armv7l-cpython-39/Cleaner.cpp:519:12: warning: unused variable ‘x’ [-Wunused-variable] 2022-06-09T06:48:57,161 519 | int i, x, pos, counter, lenBlock; 2022-06-09T06:48:57,162 | ^ 2022-06-09T06:48:57,201 build/temp.linux-armv7l-cpython-39/Cleaner.cpp: In member function ‘Alignment* Cleaner::getClustering(float)’: 2022-06-09T06:48:57,201 build/temp.linux-armv7l-cpython-39/Cleaner.cpp:1217:12: warning: unused variable ‘j’ [-Wunused-variable] 2022-06-09T06:48:57,202 1217 | int i, j, *clustering; 2022-06-09T06:48:57,202 | ^ 2022-06-09T06:48:57,215 build/temp.linux-armv7l-cpython-39/Cleaner.cpp: In member function ‘void Cleaner::removeAllGapsSeqsAndCols(bool, bool)’: 2022-06-09T06:48:57,215 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] 2022-06-09T06:48:57,216 1382 | for (j = 0; j < alig->sequences[i].length(); j++) { 2022-06-09T06:48:57,216 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T06:48:57,217 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] 2022-06-09T06:48:57,217 1393 | if (j == alig->sequences[i].length()) { 2022-06-09T06:48:57,218 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T06:49:05,945 generating build/temp.linux-armv7l-cpython-39/Alignment.o from build/temp.linux-armv7l-cpython-39/Alignment.cpp 2022-06-09T06:49:05,946 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 -c build/temp.linux-armv7l-cpython-39/Alignment.cpp -o build/temp.linux-armv7l-cpython-39/Alignment.o 2022-06-09T06:49:06,899 build/temp.linux-armv7l-cpython-39/Alignment.cpp:395: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2022-06-09T06:49:06,900 395 | #pragma omp parallel for num_threads(NUMTHREADS) if(numberOfSequences>MINPARALLELSIZE) 2022-06-09T06:49:06,900 | 2022-06-09T06:49:06,900 build/temp.linux-armv7l-cpython-39/Alignment.cpp:398: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2022-06-09T06:49:06,901 398 | #pragma omp parallel for num_threads(NUMTHREADS) collapse(2) private(k, shared, referenceLength) if(numberOfSequences>MINPARALLELSIZE) 2022-06-09T06:49:06,901 | 2022-06-09T06:49:06,902 build/temp.linux-armv7l-cpython-39/Alignment.cpp:930: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2022-06-09T06:49:06,902 930 | #pragma omp parallel for private(k, mx, avg, pos) reduction(+: avgSeq, maxAvgSeq) num_threads(NUMTHREADS) if(originalNumberOfSequences>MINPARALLELSIZE) 2022-06-09T06:49:06,903 | 2022-06-09T06:49:10,023 build/temp.linux-armv7l-cpython-39/Alignment.cpp: In member function ‘Alignment* Alignment::getTranslationCDS(Alignment*)’: 2022-06-09T06:49:10,023 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] 2022-06-09T06:49:10,024 204 | for (y = 0, counter = 0; y < ProtAlig->sequences[x].size(); y++) { 2022-06-09T06:49:10,024 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T06:49:10,051 build/temp.linux-armv7l-cpython-39/Alignment.cpp: In member function ‘bool Alignment::prepareCodingSequence(bool, bool, Alignment*)’: 2022-06-09T06:49:10,051 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] 2022-06-09T06:49:10,052 614 | if ((found != string::npos) && (((int) found % 3) == 0)) { 2022-06-09T06:49:10,052 | ~~~~~~^~~~~~~~~~~~~~~ 2022-06-09T06:49:10,058 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] 2022-06-09T06:49:10,058 641 | } while (found != string::npos); 2022-06-09T06:49:10,059 | ~~~~~~^~~~~~~~~~~~~~~ 2022-06-09T06:49:10,059 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] 2022-06-09T06:49:10,059 651 | if ((found != string::npos) && (((int) found % 3) == 0)) { 2022-06-09T06:49:10,060 | ~~~~~~^~~~~~~~~~~~~~~ 2022-06-09T06:49:10,066 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] 2022-06-09T06:49:10,066 676 | } while (found != string::npos); 2022-06-09T06:49:10,066 | ~~~~~~^~~~~~~~~~~~~~~ 2022-06-09T06:49:10,067 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] 2022-06-09T06:49:10,067 685 | if ((found != string::npos) && (((int) found % 3) == 0)) { 2022-06-09T06:49:10,068 | ~~~~~~^~~~~~~~~~~~~~~ 2022-06-09T06:49:10,073 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] 2022-06-09T06:49:10,074 711 | } while (found != string::npos); 2022-06-09T06:49:10,074 | ~~~~~~^~~~~~~~~~~~~~~ 2022-06-09T06:49:10,094 build/temp.linux-armv7l-cpython-39/Alignment.cpp: In member function ‘bool Alignment::fillMatrices(bool, bool)’: 2022-06-09T06:49:10,095 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] 2022-06-09T06:49:10,095 810 | for (j = 0; j < sequences[i].length(); j++) 2022-06-09T06:49:10,096 | ~~^~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T06:49:10,099 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] 2022-06-09T06:49:10,100 837 | if (sequences[i].length() != numberOfResidues) { 2022-06-09T06:49:10,100 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2022-06-09T06:49:10,105 build/temp.linux-armv7l-cpython-39/Alignment.cpp: In member function ‘void Alignment::printAlignmentInfo(std::ostream&)’: 2022-06-09T06:49:10,105 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] 2022-06-09T06:49:10,105 889 | for (j = 0, valid_res = 0; j < sequences[i].length(); j++) 2022-06-09T06:49:10,106 | ~~^~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T06:49:36,648 generating build/temp.linux-armv7l-cpython-39/sequencesMatrix.o from build/temp.linux-armv7l-cpython-39/sequencesMatrix.cpp 2022-06-09T06:49:36,650 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 -c build/temp.linux-armv7l-cpython-39/sequencesMatrix.cpp -o build/temp.linux-armv7l-cpython-39/sequencesMatrix.o 2022-06-09T06:49:41,481 generating build/temp.linux-armv7l-cpython-39/similarityMatrix.o from build/temp.linux-armv7l-cpython-39/similarityMatrix.cpp 2022-06-09T06:49:41,483 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 -c build/temp.linux-armv7l-cpython-39/similarityMatrix.cpp -o build/temp.linux-armv7l-cpython-39/similarityMatrix.o 2022-06-09T06:49:46,859 generating build/temp.linux-armv7l-cpython-39/Mold.o from build/temp.linux-armv7l-cpython-39/Mold.cpp 2022-06-09T06:49:46,860 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 -c build/temp.linux-armv7l-cpython-39/Mold.cpp -o build/temp.linux-armv7l-cpython-39/Mold.o 2022-06-09T06:49:55,080 generating build/temp.linux-armv7l-cpython-39/Gaps.o from build/temp.linux-armv7l-cpython-39/Gaps.cpp 2022-06-09T06:49:55,081 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 -c build/temp.linux-armv7l-cpython-39/Gaps.cpp -o build/temp.linux-armv7l-cpython-39/Gaps.o 2022-06-09T06:50:03,842 generating build/temp.linux-armv7l-cpython-39/Manager.o from build/temp.linux-armv7l-cpython-39/Manager.cpp 2022-06-09T06:50:03,843 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 -c build/temp.linux-armv7l-cpython-39/Manager.cpp -o build/temp.linux-armv7l-cpython-39/Manager.o 2022-06-09T06:50:07,469 build/temp.linux-armv7l-cpython-39/Manager.cpp: In destructor ‘statistics::Manager::~Manager()’: 2022-06-09T06:50:07,470 build/temp.linux-armv7l-cpython-39/Manager.cpp:219:9: warning: deleting object of polymorphic class type ‘statistics::Similarity’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 2022-06-09T06:50:07,470 219 | delete similarity; 2022-06-09T06:50:07,471 | ^~~~~~~~~~~~~~~~~ 2022-06-09T06:50:08,326 generating build/temp.linux-armv7l-cpython-39/Similarity.o from build/temp.linux-armv7l-cpython-39/Similarity.cpp 2022-06-09T06:50:08,327 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 -c build/temp.linux-armv7l-cpython-39/Similarity.cpp -o build/temp.linux-armv7l-cpython-39/Similarity.o 2022-06-09T06:50:09,137 build/temp.linux-armv7l-cpython-39/Similarity.cpp:115: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2022-06-09T06:50:09,138 115 | #pragma omp parallel for num_threads(NUMTHREADS) if(alig->originalNumberOfSequences>MINPARALLELSIZE) 2022-06-09T06:50:09,138 | 2022-06-09T06:50:09,139 build/temp.linux-armv7l-cpython-39/Similarity.cpp:124: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2022-06-09T06:50:09,139 124 | #pragma omp parallel for num_threads(NUMTHREADS) private(j, k, sum, length) if(alig->originalNumberOfSequences>MINPARALLELSIZE) 2022-06-09T06:50:09,140 | 2022-06-09T06:50:17,509 generating build/temp.linux-armv7l-cpython-39/Consistency.o from build/temp.linux-armv7l-cpython-39/Consistency.cpp 2022-06-09T06:50:17,510 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 -c build/temp.linux-armv7l-cpython-39/Consistency.cpp -o build/temp.linux-armv7l-cpython-39/Consistency.o 2022-06-09T06:50:30,164 generating build/temp.linux-armv7l-cpython-39/errorMessages.o from build/temp.linux-armv7l-cpython-39/errorMessages.cpp 2022-06-09T06:50:30,166 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 -c build/temp.linux-armv7l-cpython-39/errorMessages.cpp -o build/temp.linux-armv7l-cpython-39/errorMessages.o 2022-06-09T06:50:34,902 generating build/temp.linux-armv7l-cpython-39/infoMessages.o from build/temp.linux-armv7l-cpython-39/infoMessages.cpp 2022-06-09T06:50:34,903 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 -c build/temp.linux-armv7l-cpython-39/infoMessages.cpp -o build/temp.linux-armv7l-cpython-39/infoMessages.o 2022-06-09T06:50:38,784 generating build/temp.linux-armv7l-cpython-39/warningMessages.o from build/temp.linux-armv7l-cpython-39/warningMessages.cpp 2022-06-09T06:50:38,785 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 -c build/temp.linux-armv7l-cpython-39/warningMessages.cpp -o build/temp.linux-armv7l-cpython-39/warningMessages.o 2022-06-09T06:50:42,741 generating build/temp.linux-armv7l-cpython-39/phylip_paml_m10_state.o from build/temp.linux-armv7l-cpython-39/phylip_paml_m10_state.cpp 2022-06-09T06:50:42,743 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 -c build/temp.linux-armv7l-cpython-39/phylip_paml_m10_state.cpp -o build/temp.linux-armv7l-cpython-39/phylip_paml_m10_state.o 2022-06-09T06:50:47,898 generating build/temp.linux-armv7l-cpython-39/nexus_state.o from build/temp.linux-armv7l-cpython-39/nexus_state.cpp 2022-06-09T06:50:47,900 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 -c build/temp.linux-armv7l-cpython-39/nexus_state.cpp -o build/temp.linux-armv7l-cpython-39/nexus_state.o 2022-06-09T06:50:55,048 generating build/temp.linux-armv7l-cpython-39/mega_sequential_state.o from build/temp.linux-armv7l-cpython-39/mega_sequential_state.cpp 2022-06-09T06:50:55,050 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 -c build/temp.linux-armv7l-cpython-39/mega_sequential_state.cpp -o build/temp.linux-armv7l-cpython-39/mega_sequential_state.o 2022-06-09T06:50:58,810 build/temp.linux-armv7l-cpython-39/mega_sequential_state.cpp: In member function ‘virtual bool FormatHandling::mega_sequential_state::SaveAlignment(const Alignment&, std::ostream*)’: 2022-06-09T06:50:58,810 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] 2022-06-09T06:50:58,811 335 | for(j = 0, l = 0; j < alignment.sequences[i].length(); j ++) 2022-06-09T06:50:58,811 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T06:50:58,817 build/temp.linux-armv7l-cpython-39/mega_sequential_state.cpp:289:15: warning: unused variable ‘k’ [-Wunused-variable] 2022-06-09T06:50:58,817 289 | int i, j, k, l, m; 2022-06-09T06:50:58,817 | ^ 2022-06-09T06:50:58,818 build/temp.linux-armv7l-cpython-39/mega_sequential_state.cpp:289:21: warning: unused variable ‘m’ [-Wunused-variable] 2022-06-09T06:50:58,818 289 | int i, j, k, l, m; 2022-06-09T06:50:58,819 | ^ 2022-06-09T06:51:01,206 generating build/temp.linux-armv7l-cpython-39/mega_interleaved_state.o from build/temp.linux-armv7l-cpython-39/mega_interleaved_state.cpp 2022-06-09T06:51:01,208 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 -c build/temp.linux-armv7l-cpython-39/mega_interleaved_state.cpp -o build/temp.linux-armv7l-cpython-39/mega_interleaved_state.o 2022-06-09T06:51:06,828 generating build/temp.linux-armv7l-cpython-39/nexus_m10_state.o from build/temp.linux-armv7l-cpython-39/nexus_m10_state.cpp 2022-06-09T06:51:06,830 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 -c build/temp.linux-armv7l-cpython-39/nexus_m10_state.cpp -o build/temp.linux-armv7l-cpython-39/nexus_m10_state.o 2022-06-09T06:51:13,438 generating build/temp.linux-armv7l-cpython-39/fasta_state.o from build/temp.linux-armv7l-cpython-39/fasta_state.cpp 2022-06-09T06:51:13,440 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 -c build/temp.linux-armv7l-cpython-39/fasta_state.cpp -o build/temp.linux-armv7l-cpython-39/fasta_state.o 2022-06-09T06:51:17,164 build/temp.linux-armv7l-cpython-39/fasta_state.cpp: In member function ‘virtual bool FormatHandling::fasta_state::SaveAlignment(const Alignment&, std::ostream*)’: 2022-06-09T06:51:17,165 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] 2022-06-09T06:51:17,165 197 | for (j = 0, k = 0; j < alignment.sequences[i].length(); j++) 2022-06-09T06:51:17,166 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T06:51:17,166 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] 2022-06-09T06:51:17,167 201 | if (!lastcharIsnewline && j == alignment.sequences[i].length() -1 ) 2022-06-09T06:51:17,167 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T06:51:17,169 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] 2022-06-09T06:51:17,169 212 | if (k % 60 == 0 || j == alignment.sequences[i].length() -1 ) 2022-06-09T06:51:17,170 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T06:51:19,182 generating build/temp.linux-armv7l-cpython-39/clustal_state.o from build/temp.linux-armv7l-cpython-39/clustal_state.cpp 2022-06-09T06:51:19,183 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 -c build/temp.linux-armv7l-cpython-39/clustal_state.cpp -o build/temp.linux-armv7l-cpython-39/clustal_state.o 2022-06-09T06:51:25,085 generating build/temp.linux-armv7l-cpython-39/htmlreport_state.o from build/temp.linux-armv7l-cpython-39/htmlreport_state.cpp 2022-06-09T06:51:25,087 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 -c build/temp.linux-armv7l-cpython-39/htmlreport_state.cpp -o build/temp.linux-armv7l-cpython-39/htmlreport_state.o 2022-06-09T06:51:30,366 generating build/temp.linux-armv7l-cpython-39/fasta_m10_state.o from build/temp.linux-armv7l-cpython-39/fasta_m10_state.cpp 2022-06-09T06:51:30,368 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 -c build/temp.linux-armv7l-cpython-39/fasta_m10_state.cpp -o build/temp.linux-armv7l-cpython-39/fasta_m10_state.o 2022-06-09T06:51:34,077 build/temp.linux-armv7l-cpython-39/fasta_m10_state.cpp: In member function ‘virtual bool FormatHandling::fasta_m10_state::SaveAlignment(const Alignment&, std::ostream*)’: 2022-06-09T06:51:34,078 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] 2022-06-09T06:51:34,079 95 | for (j = 0, k = 0; j < alignment.sequences[i].length(); j++) 2022-06-09T06:51:34,079 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T06:51:34,079 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] 2022-06-09T06:51:34,080 99 | if (!lastcharIsnewline && j == alignment.sequences[i].length() -1 ) 2022-06-09T06:51:34,080 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T06:51:34,082 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] 2022-06-09T06:51:34,082 110 | if ((k % 60 == 0 || j == alignment.sequences[i].length() - 1)) 2022-06-09T06:51:34,083 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T06:51:35,680 generating build/temp.linux-armv7l-cpython-39/phylip32_state.o from build/temp.linux-armv7l-cpython-39/phylip32_state.cpp 2022-06-09T06:51:35,682 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 -c build/temp.linux-armv7l-cpython-39/phylip32_state.cpp -o build/temp.linux-armv7l-cpython-39/phylip32_state.o 2022-06-09T06:51:41,717 generating build/temp.linux-armv7l-cpython-39/pir_state.o from build/temp.linux-armv7l-cpython-39/pir_state.cpp 2022-06-09T06:51:41,719 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 -c build/temp.linux-armv7l-cpython-39/pir_state.cpp -o build/temp.linux-armv7l-cpython-39/pir_state.o 2022-06-09T06:51:45,436 build/temp.linux-armv7l-cpython-39/pir_state.cpp: In member function ‘virtual bool FormatHandling::pir_state::SaveAlignment(const Alignment&, std::ostream*)’: 2022-06-09T06:51:45,437 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] 2022-06-09T06:51:45,437 223 | for (j = 0, k = 0, l = 0; j < alignment.sequences[i].length(); j++) { 2022-06-09T06:51:45,437 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T06:51:45,440 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] 2022-06-09T06:51:45,440 231 | if (j == alignment.sequences[i].length() - 1); 2022-06-09T06:51:45,441 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T06:51:45,444 build/temp.linux-armv7l-cpython-39/pir_state.cpp:184:18: warning: variable ‘l’ set but not used [-Wunused-but-set-variable] 2022-06-09T06:51:45,445 184 | int i, j, k, l; 2022-06-09T06:51:45,445 | ^ 2022-06-09T06:51:47,470 generating build/temp.linux-armv7l-cpython-39/phylip40_state.o from build/temp.linux-armv7l-cpython-39/phylip40_state.cpp 2022-06-09T06:51:47,471 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 -c build/temp.linux-armv7l-cpython-39/phylip40_state.cpp -o build/temp.linux-armv7l-cpython-39/phylip40_state.o 2022-06-09T06:51:53,595 generating build/temp.linux-armv7l-cpython-39/phylip_paml_state.o from build/temp.linux-armv7l-cpython-39/phylip_paml_state.cpp 2022-06-09T06:51:53,597 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 -c build/temp.linux-armv7l-cpython-39/phylip_paml_state.cpp -o build/temp.linux-armv7l-cpython-39/phylip_paml_state.o 2022-06-09T06:51:58,697 generating build/temp.linux-armv7l-cpython-39/phylip32_m10_state.o from build/temp.linux-armv7l-cpython-39/phylip32_m10_state.cpp 2022-06-09T06:51:58,699 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 -c build/temp.linux-armv7l-cpython-39/phylip32_m10_state.cpp -o build/temp.linux-armv7l-cpython-39/phylip32_m10_state.o 2022-06-09T06:52:03,969 generating build/temp.linux-armv7l-cpython-39/phylip40_m10_state.o from build/temp.linux-armv7l-cpython-39/phylip40_m10_state.cpp 2022-06-09T06:52:03,970 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 -c build/temp.linux-armv7l-cpython-39/phylip40_m10_state.cpp -o build/temp.linux-armv7l-cpython-39/phylip40_m10_state.o 2022-06-09T06:52:08,588 build/temp.linux-armv7l-cpython-39/phylip40_m10_state.cpp: In member function ‘virtual bool FormatHandling::phylip40_m10_state::SaveAlignment(const Alignment&, std::ostream*)’: 2022-06-09T06:52:08,589 build/temp.linux-armv7l-cpython-39/phylip40_m10_state.cpp:104:19: warning: ‘k’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-06-09T06:52:08,589 104 | for (i = k; i < alignment.originalNumberOfResidues; i=k) 2022-06-09T06:52:08,589 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T06:52:09,329 generating build/temp.linux-armv7l-cpython-39/BaseFormatHandler.o from build/temp.linux-armv7l-cpython-39/BaseFormatHandler.cpp 2022-06-09T06:52:09,331 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 -c build/temp.linux-armv7l-cpython-39/BaseFormatHandler.cpp -o build/temp.linux-armv7l-cpython-39/BaseFormatHandler.o 2022-06-09T06:52:21,411 generating build/temp.linux-armv7l-cpython-39/utils.o from build/temp.linux-armv7l-cpython-39/utils.cpp 2022-06-09T06:52:21,412 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 -c build/temp.linux-armv7l-cpython-39/utils.cpp -o build/temp.linux-armv7l-cpython-39/utils.o 2022-06-09T06:52:24,590 build/temp.linux-armv7l-cpython-39/utils.cpp: In function ‘std::string utils::removeCharacter(char, std::string)’: 2022-06-09T06:52:24,591 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] 2022-06-09T06:52:24,591 490 | while (pos != (int) std::string::npos) { 2022-06-09T06:52:24,591 | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T06:52:24,612 build/temp.linux-armv7l-cpython-39/utils.cpp: In function ‘int* utils::readNumbers(const string&)’: 2022-06-09T06:52:24,612 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] 2022-06-09T06:52:24,613 632 | while ((comma = line.find(',', comma + 1)) != (int) std::string::npos) 2022-06-09T06:52:24,613 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T06:52:24,614 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] 2022-06-09T06:52:24,614 646 | if (((separ < comma) || (comma == (int) std::string::npos)) && (separ != (int) std::string::npos)) { 2022-06-09T06:52:24,614 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T06:52:24,615 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] 2022-06-09T06:52:24,615 646 | if (((separ < comma) || (comma == (int) std::string::npos)) && (separ != (int) std::string::npos)) { 2022-06-09T06:52:24,615 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T06:52:24,616 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] 2022-06-09T06:52:24,616 650 | } else if ((separ > comma) || (separ == (int) std::string::npos)) { 2022-06-09T06:52:24,616 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T06:52:24,617 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] 2022-06-09T06:52:24,617 666 | if (comma == (int) std::string::npos) 2022-06-09T06:52:24,618 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T06:52:30,497 generating build/temp.linux-armv7l-cpython-39/InternalBenchmarker.o from build/temp.linux-armv7l-cpython-39/InternalBenchmarker.cpp 2022-06-09T06:52:30,499 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 -c build/temp.linux-armv7l-cpython-39/InternalBenchmarker.cpp -o build/temp.linux-armv7l-cpython-39/InternalBenchmarker.o 2022-06-09T06:52:30,676 generating build/temp.linux-armv7l-cpython-39/trimalManager.o from build/temp.linux-armv7l-cpython-39/trimalManager.cpp 2022-06-09T06:52:30,678 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 -c build/temp.linux-armv7l-cpython-39/trimalManager.cpp -o build/temp.linux-armv7l-cpython-39/trimalManager.o 2022-06-09T06:52:34,653 In file included from build/temp.linux-armv7l-cpython-39/trimalManager.cpp:42: 2022-06-09T06:52:34,653 build/temp.linux-armv7l-cpython-39/VCFHandler.h: In constructor ‘ngs::__internal::vcfFeature::vcfFeature()’: 2022-06-09T06:52:34,654 build/temp.linux-armv7l-cpython-39/VCFHandler.h:87:19: warning: ‘ngs::__internal::vcfFeature::quality’ will be initialized after [-Wreorder] 2022-06-09T06:52:34,654 87 | float quality; 2022-06-09T06:52:34,654 | ^~~~~~~ 2022-06-09T06:52:34,655 build/temp.linux-armv7l-cpython-39/VCFHandler.h:85:18: warning: ‘bool ngs::__internal::vcfFeature::filter’ [-Wreorder] 2022-06-09T06:52:34,655 85 | bool filter; 2022-06-09T06:52:34,655 | ^~~~~~ 2022-06-09T06:52:34,656 build/temp.linux-armv7l-cpython-39/VCFHandler.h:96:13: warning: when initialized here [-Wreorder] 2022-06-09T06:52:34,656 96 | vcfFeature() : position(0), quality(0.0F), filter(false), readDepthIndex(0) 2022-06-09T06:52:34,656 | ^~~~~~~~~~ 2022-06-09T06:52:35,008 build/temp.linux-armv7l-cpython-39/trimalManager.cpp: In member function ‘bool trimAlManager::check_outputs_coincidence()’: 2022-06-09T06:52:35,008 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] 2022-06-09T06:52:35,009 1419 | for (int i = 0, x = 0; i < outFiles.size(); i++) { 2022-06-09T06:52:35,009 | ~~^~~~~~~~~~~~~~~~~ 2022-06-09T06:52:35,009 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] 2022-06-09T06:52:35,010 1421 | for (x = i + 1; x < outFiles.size(); x++) { 2022-06-09T06:52:35,010 | ~~^~~~~~~~~~~~~~~~~ 2022-06-09T06:52:35,250 build/temp.linux-armv7l-cpython-39/trimalManager.cpp: In member function ‘void trimAlManager::CleanSequences()’: 2022-06-09T06:52:35,251 build/temp.linux-armv7l-cpython-39/trimalManager.cpp:2100:9: warning: deleting object of polymorphic class type ‘statistics::Similarity’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 2022-06-09T06:52:35,251 2100 | delete singleAlig->Statistics->similarity; 2022-06-09T06:52:35,252 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T06:52:56,894 generating build/temp.linux-armv7l-cpython-39/VCFHandler.o from build/temp.linux-armv7l-cpython-39/VCFHandler.cpp 2022-06-09T06:52:56,895 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 -c build/temp.linux-armv7l-cpython-39/VCFHandler.cpp -o build/temp.linux-armv7l-cpython-39/VCFHandler.o 2022-06-09T06:53:00,449 In file included from build/temp.linux-armv7l-cpython-39/VCFHandler.cpp:30: 2022-06-09T06:53:00,449 build/temp.linux-armv7l-cpython-39/VCFHandler.h: In constructor ‘ngs::__internal::vcfFeature::vcfFeature()’: 2022-06-09T06:53:00,450 build/temp.linux-armv7l-cpython-39/VCFHandler.h:87:19: warning: ‘ngs::__internal::vcfFeature::quality’ will be initialized after [-Wreorder] 2022-06-09T06:53:00,450 87 | float quality; 2022-06-09T06:53:00,450 | ^~~~~~~ 2022-06-09T06:53:00,451 build/temp.linux-armv7l-cpython-39/VCFHandler.h:85:18: warning: ‘bool ngs::__internal::vcfFeature::filter’ [-Wreorder] 2022-06-09T06:53:00,451 85 | bool filter; 2022-06-09T06:53:00,452 | ^~~~~~ 2022-06-09T06:53:00,452 build/temp.linux-armv7l-cpython-39/VCFHandler.h:96:13: warning: when initialized here [-Wreorder] 2022-06-09T06:53:00,453 96 | vcfFeature() : position(0), quality(0.0F), filter(false), readDepthIndex(0) 2022-06-09T06:53:00,453 | ^~~~~~~~~~ 2022-06-09T06:53:00,501 build/temp.linux-armv7l-cpython-39/VCFHandler.cpp: In function ‘bool ngs::__internal::checkContigsWithReference(const AlignmentVector&, const StringVector&)’: 2022-06-09T06:53:00,501 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] 2022-06-09T06:53:00,502 153 | for (i = 0; i < sources.size(); i++) { 2022-06-09T06:53:00,502 | ~~^~~~~~~~~~~~~~~~ 2022-06-09T06:53:00,504 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] 2022-06-09T06:53:00,504 162 | if (i == sources.size()) { 2022-06-09T06:53:00,505 | ~~^~~~~~~~~~~~~~~~~ 2022-06-09T06:53:00,519 build/temp.linux-armv7l-cpython-39/VCFHandler.cpp: In function ‘void ngs::__internal::increaseSequencesInAlignment(const AlignmentVector&, const StringVector&)’: 2022-06-09T06:53:00,520 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] 2022-06-09T06:53:00,520 198 | for (int i = 1; i < donors.size() + 1; i++) { 2022-06-09T06:53:00,521 | ~~^~~~~~~~~~~~~~~~~~~ 2022-06-09T06:53:00,536 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*)’: 2022-06-09T06:53:00,537 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] 2022-06-09T06:53:00,537 337 | for (int vcfIndex = 0; vcfIndex < filenames.size(); vcfIndex++) { 2022-06-09T06:53:00,537 | ~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2022-06-09T06:53:00,540 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] 2022-06-09T06:53:00,540 360 | for (contigIndex = 0; contigIndex < contigs.size(); contigIndex++) 2022-06-09T06:53:00,540 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2022-06-09T06:53:00,543 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] 2022-06-09T06:53:00,543 365 | if (contigIndex == contigs.size()) { 2022-06-09T06:53:00,543 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2022-06-09T06:53:00,549 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] 2022-06-09T06:53:00,549 394 | for (int donorID = 0; donorID < feature.donorsInfo.size(); donorID++) 2022-06-09T06:53:00,550 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T06:53:00,598 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] 2022-06-09T06:53:00,599 397 | if (donorID >= donorsPositions[vcfIndex].size()) 2022-06-09T06:53:00,599 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-09T06:53:00,624 build/temp.linux-armv7l-cpython-39/VCFHandler.cpp: In function ‘void ngs::__internal::extractContigsFromLine(char*, ngs::StringVector&)’: 2022-06-09T06:53:00,625 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] 2022-06-09T06:53:00,625 528 | for (U = 0; U < contigs.size(); U++) 2022-06-09T06:53:00,625 | ~~^~~~~~~~~~~~~~~~ 2022-06-09T06:53:00,627 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] 2022-06-09T06:53:00,628 533 | if (U == contigs.size()) 2022-06-09T06:53:00,628 | ~~^~~~~~~~~~~~~~~~~ 2022-06-09T06:53:00,631 build/temp.linux-armv7l-cpython-39/VCFHandler.cpp: In function ‘void ngs::__internal::extractDonorsFromLine(char*, std::vector&, ngs::StringVector&)’: 2022-06-09T06:53:00,632 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] 2022-06-09T06:53:00,632 557 | for (U = 0; U < donors.size(); U++) { 2022-06-09T06:53:00,632 | ~~^~~~~~~~~~~~~~~ 2022-06-09T06:53:00,633 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] 2022-06-09T06:53:00,633 564 | if (U == donors.size()) { 2022-06-09T06:53:00,634 | ~~^~~~~~~~~~~~~~~~ 2022-06-09T06:53:00,635 build/temp.linux-armv7l-cpython-39/VCFHandler.cpp: In function ‘void ngs::__internal::obtainContigsAndDonors(const StringVector&, ngs::StringVector&, ngs::StringVector&, std::vector >&)’: 2022-06-09T06:53:00,635 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] 2022-06-09T06:53:00,636 591 | for (int C = 0; C < filenames.size(); C++) { 2022-06-09T06:53:00,636 | ~~^~~~~~~~~~~~~~~~~~ 2022-06-09T06:53:08,945 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/phylip_paml_m10_state.o, build/temp.linux-armv7l-cpython-39/nexus_state.o, build/temp.linux-armv7l-cpython-39/mega_sequential_state.o, build/temp.linux-armv7l-cpython-39/mega_interleaved_state.o, build/temp.linux-armv7l-cpython-39/nexus_m10_state.o, build/temp.linux-armv7l-cpython-39/fasta_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/fasta_m10_state.o, build/temp.linux-armv7l-cpython-39/phylip32_state.o, build/temp.linux-armv7l-cpython-39/pir_state.o, build/temp.linux-armv7l-cpython-39/phylip40_state.o, build/temp.linux-armv7l-cpython-39/phylip_paml_state.o, build/temp.linux-armv7l-cpython-39/phylip32_m10_state.o, build/temp.linux-armv7l-cpython-39/phylip40_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 2022-06-09T06:53:08,948 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/phylip_paml_m10_state.o build/temp.linux-armv7l-cpython-39/nexus_state.o build/temp.linux-armv7l-cpython-39/mega_sequential_state.o build/temp.linux-armv7l-cpython-39/mega_interleaved_state.o build/temp.linux-armv7l-cpython-39/nexus_m10_state.o build/temp.linux-armv7l-cpython-39/fasta_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/fasta_m10_state.o build/temp.linux-armv7l-cpython-39/phylip32_state.o build/temp.linux-armv7l-cpython-39/pir_state.o build/temp.linux-armv7l-cpython-39/phylip40_state.o build/temp.linux-armv7l-cpython-39/phylip_paml_state.o build/temp.linux-armv7l-cpython-39/phylip32_m10_state.o build/temp.linux-armv7l-cpython-39/phylip40_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 2022-06-09T06:53:09,614 running build_ext 2022-06-09T06:53:18,370 Compiling pytrimal/_trimal.pyx because it changed. 2022-06-09T06:53:18,370 [1/1] Cythonizing pytrimal/_trimal.pyx 2022-06-09T06:53:18,371 building pytrimal._trimal with unix compiler 2022-06-09T06:53:18,372 building 'pytrimal._trimal' extension 2022-06-09T06:53:18,373 creating build/temp.linux-armv7l-cpython-39/pytrimal 2022-06-09T06:53:18,375 creating build/temp.linux-armv7l-cpython-39/pytrimal/fileobj 2022-06-09T06:53:18,376 creating build/temp.linux-armv7l-cpython-39/pytrimal/patch 2022-06-09T06:53:18,377 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/fileobj -Ipytrimal/impl -Ivendor/cpu_features/include -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 2022-06-09T06:54:10,577 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/fileobj -Ipytrimal/impl -Ivendor/cpu_features/include -Ipytrimal -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c pytrimal/fileobj/pyfilebuf.cpp -o build/temp.linux-armv7l-cpython-39/pytrimal/fileobj/pyfilebuf.o -std=c++11 2022-06-09T06:54:13,199 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/fileobj -Ipytrimal/impl -Ivendor/cpu_features/include -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 2022-06-09T06:54:20,493 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/fileobj/pyfilebuf.o build/temp.linux-armv7l-cpython-39/pytrimal/patch/reportsystem.o build/temp.linux-armv7l-cpython-39/libcpu_features.a build/temp.linux-armv7l-cpython-39/libtrimal.a -L/usr/lib -Lbuild/temp.linux-armv7l-cpython-39 -lcpu_features -ltrimal -lcpu_features -ltrimal -o build/lib.linux-armv7l-cpython-39/pytrimal/_trimal.cpython-39-arm-linux-gnueabihf.so -Wno-alloc-size-larger-than 2022-06-09T06:54:24,407 installing to build/bdist.linux-armv7l/wheel 2022-06-09T06:54:24,407 running install 2022-06-09T06:54:24,470 running install_lib 2022-06-09T06:54:25,108 creating build/bdist.linux-armv7l 2022-06-09T06:54:25,109 creating build/bdist.linux-armv7l/wheel 2022-06-09T06:54:25,112 creating build/bdist.linux-armv7l/wheel/pytrimal 2022-06-09T06:54:25,113 copying build/lib.linux-armv7l-cpython-39/pytrimal/_trimal.pyi -> build/bdist.linux-armv7l/wheel/pytrimal 2022-06-09T06:54:25,117 copying build/lib.linux-armv7l-cpython-39/pytrimal/__init__.py -> build/bdist.linux-armv7l/wheel/pytrimal 2022-06-09T06:54:25,121 copying build/lib.linux-armv7l-cpython-39/pytrimal/_trimal.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pytrimal 2022-06-09T06:54:25,502 creating build/bdist.linux-armv7l/wheel/pytrimal/tests 2022-06-09T06:54:25,504 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/test_doctest.py -> build/bdist.linux-armv7l/wheel/pytrimal/tests 2022-06-09T06:54:25,509 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/test_manual_trimmer.py -> build/bdist.linux-armv7l/wheel/pytrimal/tests 2022-06-09T06:54:25,513 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/__main__.py -> build/bdist.linux-armv7l/wheel/pytrimal/tests 2022-06-09T06:54:25,516 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/test_similarity_matrix.py -> build/bdist.linux-armv7l/wheel/pytrimal/tests 2022-06-09T06:54:25,521 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/__init__.py -> build/bdist.linux-armv7l/wheel/pytrimal/tests 2022-06-09T06:54:25,524 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/test_automatic_trimmer.py -> build/bdist.linux-armv7l/wheel/pytrimal/tests 2022-06-09T06:54:25,530 creating build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-09T06:54:25,532 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/data/ENOG411BWBU.id50.fasta -> build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-09T06:54:25,537 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/data/ENOG411BWBU.fasta -> build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-09T06:54:25,557 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/data/halorhodopsin.afa -> build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-09T06:54:25,570 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/data/ENOG411BWBU.strict.fasta -> build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-09T06:54:25,583 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/data/example.001.gt90.w3.fasta -> build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-09T06:54:25,586 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/data/pam70.json -> build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-09T06:54:25,589 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/data/ENOG411BWBU.noallgaps.fasta -> build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-09T06:54:25,606 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/data/ENOG411BWBU.strictplus.fasta -> build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-09T06:54:25,616 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/data/ENOG411BWBU.id70.fasta -> build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-09T06:54:25,625 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/data/ENOG411BWBU.cons40.gt40.fasta -> build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-09T06:54:25,637 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/data/example.001.AA.clw -> build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-09T06:54:25,641 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/data/ENOG411BWBU.cons60.gt90.fasta -> build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-09T06:54:25,662 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/data/ENOG411BWBU.gappyout.fasta -> build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-09T06:54:25,678 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/data/__init__.py -> build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-09T06:54:25,680 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/data/ENOG411BWBU.automated1.fasta -> build/bdist.linux-armv7l/wheel/pytrimal/tests/data 2022-06-09T06:54:25,694 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/requirements.txt -> build/bdist.linux-armv7l/wheel/pytrimal/tests 2022-06-09T06:54:25,697 copying build/lib.linux-armv7l-cpython-39/pytrimal/tests/test_alignment.py -> build/bdist.linux-armv7l/wheel/pytrimal/tests 2022-06-09T06:54:25,701 copying build/lib.linux-armv7l-cpython-39/pytrimal/_version.py -> build/bdist.linux-armv7l/wheel/pytrimal 2022-06-09T06:54:25,704 copying build/lib.linux-armv7l-cpython-39/pytrimal/py.typed -> build/bdist.linux-armv7l/wheel/pytrimal 2022-06-09T06:54:25,706 running install_egg_info 2022-06-09T06:54:26,924 running egg_info 2022-06-09T06:54:27,518 writing pytrimal.egg-info/PKG-INFO 2022-06-09T06:54:28,087 writing dependency_links to pytrimal.egg-info/dependency_links.txt 2022-06-09T06:54:31,473 writing top-level names to pytrimal.egg-info/top_level.txt 2022-06-09T06:54:31,544 reading manifest file 'pytrimal.egg-info/SOURCES.txt' 2022-06-09T06:54:31,625 reading manifest template 'MANIFEST.in' 2022-06-09T06:54:32,570 warning: no previously-included files matching '*.html' found under directory 'pytrimal' 2022-06-09T06:54:32,578 warning: no files found matching '*.pxd' under directory 'pytrimal/patch' 2022-06-09T06:54:32,605 adding license file 'COPYING' 2022-06-09T06:54:32,649 writing manifest file 'pytrimal.egg-info/SOURCES.txt' 2022-06-09T06:54:32,654 Copying pytrimal.egg-info to build/bdist.linux-armv7l/wheel/pytrimal-0.2.2-py3.9.egg-info 2022-06-09T06:54:32,675 running install_scripts 2022-06-09T06:54:32,805 adding license file "COPYING" (matched pattern "COPYING*") 2022-06-09T06:54:32,860 creating build/bdist.linux-armv7l/wheel/pytrimal-0.2.2.dist-info/WHEEL 2022-06-09T06:54:32,866 creating '/tmp/pip-wheel-ii2n35sg/tmpbkjy5qij/pytrimal-0.2.2-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2022-06-09T06:54:32,871 adding 'pytrimal/__init__.py' 2022-06-09T06:54:36,357 adding 'pytrimal/_trimal.cpython-39-arm-linux-gnueabihf.so' 2022-06-09T06:54:36,514 adding 'pytrimal/_trimal.pyi' 2022-06-09T06:54:36,517 adding 'pytrimal/_version.py' 2022-06-09T06:54:36,519 adding 'pytrimal/py.typed' 2022-06-09T06:54:36,523 adding 'pytrimal/tests/__init__.py' 2022-06-09T06:54:36,526 adding 'pytrimal/tests/__main__.py' 2022-06-09T06:54:36,529 adding 'pytrimal/tests/requirements.txt' 2022-06-09T06:54:36,532 adding 'pytrimal/tests/test_alignment.py' 2022-06-09T06:54:36,535 adding 'pytrimal/tests/test_automatic_trimmer.py' 2022-06-09T06:54:36,539 adding 'pytrimal/tests/test_doctest.py' 2022-06-09T06:54:36,542 adding 'pytrimal/tests/test_manual_trimmer.py' 2022-06-09T06:54:36,545 adding 'pytrimal/tests/test_similarity_matrix.py' 2022-06-09T06:54:36,575 adding 'pytrimal/tests/data/ENOG411BWBU.automated1.fasta' 2022-06-09T06:54:36,608 adding 'pytrimal/tests/data/ENOG411BWBU.cons40.gt40.fasta' 2022-06-09T06:54:36,638 adding 'pytrimal/tests/data/ENOG411BWBU.cons60.gt90.fasta' 2022-06-09T06:54:36,675 adding 'pytrimal/tests/data/ENOG411BWBU.fasta' 2022-06-09T06:54:36,709 adding 'pytrimal/tests/data/ENOG411BWBU.gappyout.fasta' 2022-06-09T06:54:36,716 adding 'pytrimal/tests/data/ENOG411BWBU.id50.fasta' 2022-06-09T06:54:36,730 adding 'pytrimal/tests/data/ENOG411BWBU.id70.fasta' 2022-06-09T06:54:36,766 adding 'pytrimal/tests/data/ENOG411BWBU.noallgaps.fasta' 2022-06-09T06:54:36,793 adding 'pytrimal/tests/data/ENOG411BWBU.strict.fasta' 2022-06-09T06:54:36,815 adding 'pytrimal/tests/data/ENOG411BWBU.strictplus.fasta' 2022-06-09T06:54:36,819 adding 'pytrimal/tests/data/__init__.py' 2022-06-09T06:54:36,822 adding 'pytrimal/tests/data/example.001.AA.clw' 2022-06-09T06:54:36,824 adding 'pytrimal/tests/data/example.001.gt90.w3.fasta' 2022-06-09T06:54:36,840 adding 'pytrimal/tests/data/halorhodopsin.afa' 2022-06-09T06:54:36,846 adding 'pytrimal/tests/data/pam70.json' 2022-06-09T06:54:36,862 adding 'pytrimal-0.2.2.dist-info/COPYING' 2022-06-09T06:54:36,866 adding 'pytrimal-0.2.2.dist-info/METADATA' 2022-06-09T06:54:36,869 adding 'pytrimal-0.2.2.dist-info/WHEEL' 2022-06-09T06:54:36,870 adding 'pytrimal-0.2.2.dist-info/top_level.txt' 2022-06-09T06:54:36,872 adding 'pytrimal-0.2.2.dist-info/RECORD' 2022-06-09T06:54:36,988 removing build/bdist.linux-armv7l/wheel 2022-06-09T06:54:37,600 Building wheel for pytrimal (pyproject.toml): finished with status 'done' 2022-06-09T06:54:37,785 Created wheel for pytrimal: filename=pytrimal-0.2.2-cp39-cp39-linux_armv7l.whl size=2938431 sha256=61a18089e1538bafb91947f7c54942052cdebd640068daae8f6fd8559ee1821c 2022-06-09T06:54:37,787 Stored in directory: /tmp/pip-ephem-wheel-cache-f7fhxn0e/wheels/a5/a5/45/d5fcbe62f7252c7435a0523fd14777141c1fe30d8b01639414 2022-06-09T06:54:37,819 Successfully built pytrimal 2022-06-09T06:54:38,041 Removed build tracker: '/tmp/pip-build-tracker-t7xntenv'