2024-01-07T19:28:02,480 Created temporary directory: /tmp/pip-build-tracker-mzn0kkrb 2024-01-07T19:28:02,481 Initialized build tracking at /tmp/pip-build-tracker-mzn0kkrb 2024-01-07T19:28:02,482 Created build tracker: /tmp/pip-build-tracker-mzn0kkrb 2024-01-07T19:28:02,482 Entered build tracker: /tmp/pip-build-tracker-mzn0kkrb 2024-01-07T19:28:02,483 Created temporary directory: /tmp/pip-wheel-tfg4rksr 2024-01-07T19:28:02,486 Created temporary directory: /tmp/pip-ephem-wheel-cache-4prrtrp1 2024-01-07T19:28:02,508 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-01-07T19:28:02,512 2 location(s) to search for versions of mitos: 2024-01-07T19:28:02,512 * https://pypi.org/simple/mitos/ 2024-01-07T19:28:02,512 * https://www.piwheels.org/simple/mitos/ 2024-01-07T19:28:02,513 Fetching project page and analyzing links: https://pypi.org/simple/mitos/ 2024-01-07T19:28:02,513 Getting page https://pypi.org/simple/mitos/ 2024-01-07T19:28:02,515 Found index url https://pypi.org/simple/ 2024-01-07T19:28:02,748 Fetched page https://pypi.org/simple/mitos/ as application/vnd.pypi.simple.v1+json 2024-01-07T19:28:02,754 Skipping link: No binaries permitted for mitos: https://files.pythonhosted.org/packages/ae/2d/5f1e66a046e59cf6088f44d4a02cae66d498e226365af5fd42e2d660a814/mitos-1.0-py2-none-any.whl (from https://pypi.org/simple/mitos/) 2024-01-07T19:28:02,755 Found link https://files.pythonhosted.org/packages/c5/6e/e1aae4079b0ebbce64897f54f5cd4a3953a0cb741026d16e14e7ae272a48/mitos-1.0.tar.gz (from https://pypi.org/simple/mitos/), version: 1.0 2024-01-07T19:28:02,756 Found link https://files.pythonhosted.org/packages/d7/19/816780e09ecc6a783f146d80bcde73eb7940d074f4feea137ec954bfd437/mitos-1.0.1.tar.gz (from https://pypi.org/simple/mitos/), version: 1.0.1 2024-01-07T19:28:02,756 Found link https://files.pythonhosted.org/packages/38/c7/3dd90bcf0d61c69226ef1632baa3ad0e96d798de36053b4b56ed7660dfdb/mitos-1.0.2.tar.gz (from https://pypi.org/simple/mitos/), version: 1.0.2 2024-01-07T19:28:02,757 Found link https://files.pythonhosted.org/packages/e2/d4/864af2605cc1f45cc78cfed740bbdfba1da59ea9a42c24ef5077c9218501/mitos-1.0.3.tar.gz (from https://pypi.org/simple/mitos/), version: 1.0.3 2024-01-07T19:28:02,758 Found link https://files.pythonhosted.org/packages/8d/32/1aa5eb88f964c3cf5441622648cc4ae30f115db32bdd5dc5bf194a3c112c/mitos-1.0.4.tar.gz (from https://pypi.org/simple/mitos/), version: 1.0.4 2024-01-07T19:28:02,758 Found link https://files.pythonhosted.org/packages/ff/49/f4c711126604aa86abeeda44378786a0903bc53970acf4afa5feb68f72b8/mitos-1.0.5.tar.gz (from https://pypi.org/simple/mitos/), version: 1.0.5 2024-01-07T19:28:02,759 Skipping link: No binaries permitted for mitos: https://files.pythonhosted.org/packages/c3/cd/96e0e1ad1551b8fff56ab89e61231809494dec3ee80f51117b4f5d432452/mitos-1.1.0-py3-none-any.whl (from https://pypi.org/simple/mitos/) 2024-01-07T19:28:02,759 Found link https://files.pythonhosted.org/packages/ce/33/46fd40fd9f4c11f5bf296c2c092f59e36dee233d71a0f032b34c2a64c7ba/mitos-1.1.0.tar.gz (from https://pypi.org/simple/mitos/), version: 1.1.0 2024-01-07T19:28:02,760 Found link https://files.pythonhosted.org/packages/b3/a0/5268d8fec841240195c19e704b552a8b3060768c6710c67c67350ea60f13/mitos-1.1.1.tar.gz (from https://pypi.org/simple/mitos/), version: 1.1.1 2024-01-07T19:28:02,761 Found link https://files.pythonhosted.org/packages/7c/38/4431d42c178a65b3710531867f10ae50c5a49408ccab6c058af277e83e5d/mitos-1.1.2.tar.gz (from https://pypi.org/simple/mitos/), version: 1.1.2 2024-01-07T19:28:02,762 Found link https://files.pythonhosted.org/packages/76/40/e0db56e8dfc65a2a13c8f613c4b5839247b918a1cd5d83b384a6c957928e/mitos-1.1.3.tar.gz (from https://pypi.org/simple/mitos/), version: 1.1.3 2024-01-07T19:28:02,762 Found link https://files.pythonhosted.org/packages/fc/39/368668a4250e85f2a596f996a4067528a2e13ad69d18404d4dac5ca4118f/mitos-1.1.4.tar.gz (from https://pypi.org/simple/mitos/), version: 1.1.4 2024-01-07T19:28:02,763 Found link https://files.pythonhosted.org/packages/f3/fa/7e2b9cef0d99e7792077a4c1116dc9bbe4c085e7b89ea79b74474c00b2b1/mitos-2.0.1.tar.gz (from https://pypi.org/simple/mitos/), version: 2.0.1 2024-01-07T19:28:02,764 Found link https://files.pythonhosted.org/packages/d7/53/5d215fe8689055dd329a27202f9dc7f66e23548f3d2ad3fa55d98dc56988/mitos-2.0.2.tar.gz (from https://pypi.org/simple/mitos/), version: 2.0.2 2024-01-07T19:28:02,765 Found link https://files.pythonhosted.org/packages/cd/97/a8bf95d5e26b51071d9f342dc475891425b223b6add347a6dbf9412937f1/mitos-2.0.3.tar.gz (from https://pypi.org/simple/mitos/), version: 2.0.3 2024-01-07T19:28:02,765 Found link https://files.pythonhosted.org/packages/39/9f/6cdac19a8d50915e2e5285b447077459af9c6524f980ded6657dc205593d/mitos-2.0.4.tar.gz (from https://pypi.org/simple/mitos/), version: 2.0.4 2024-01-07T19:28:02,766 Found link https://files.pythonhosted.org/packages/d0/16/8040a37887377e3992b0874ab441af54e16030fd23eb844bbf5293597c99/mitos-2.0.5.tar.gz (from https://pypi.org/simple/mitos/), version: 2.0.5 2024-01-07T19:28:02,766 Found link https://files.pythonhosted.org/packages/40/ef/5a93579c1ebc63ca8fe71cfe541bca389a0f9410b9a2c1ceff148f83af79/mitos-2.0.6.tar.gz (from https://pypi.org/simple/mitos/), version: 2.0.6 2024-01-07T19:28:02,767 Found link https://files.pythonhosted.org/packages/1f/a2/32eb96227aae3a719794cc922d839b8c38ee5c315087bf095792c48f996d/mitos-2.0.7.tar.gz (from https://pypi.org/simple/mitos/), version: 2.0.7 2024-01-07T19:28:02,767 Found link https://files.pythonhosted.org/packages/d5/7f/b3e5c5c83352beb13677186899379de3c50a2222dc8faac16632f600d4b6/mitos-2.0.8.tar.gz (from https://pypi.org/simple/mitos/), version: 2.0.8 2024-01-07T19:28:02,768 Skipping link: No binaries permitted for mitos: https://files.pythonhosted.org/packages/9d/93/5f2a1097bfa507acbf7dd6ac677f6df14df61692cccb42d28c34edb7ca5b/mitos-2.1.0-py3-none-any.whl (from https://pypi.org/simple/mitos/) 2024-01-07T19:28:02,768 Found link https://files.pythonhosted.org/packages/f8/f4/2950dea175f0bda896b88ac2ac13007a1d007252a583ddd328b176fb54a5/mitos-2.1.0.tar.gz (from https://pypi.org/simple/mitos/), version: 2.1.0 2024-01-07T19:28:02,769 Found link https://files.pythonhosted.org/packages/57/78/2fde036a6c767aa5fb8c1102526af749ee13ad426b295289265c548384f9/mitos-2.1.1.tar.gz (from https://pypi.org/simple/mitos/), version: 2.1.1 2024-01-07T19:28:02,769 Found link https://files.pythonhosted.org/packages/74/63/f90f359df86c01e68f5c678eef30d929b9311e7bb80f16071a1532515a0a/mitos-2.1.2.tar.gz (from https://pypi.org/simple/mitos/), version: 2.1.2 2024-01-07T19:28:02,770 Found link https://files.pythonhosted.org/packages/d6/1f/b6dbc4704555e91e3efa3184fc90b04e901dc6e787c37091d445dd50bd4b/mitos-2.1.3.tar.gz (from https://pypi.org/simple/mitos/), version: 2.1.3 2024-01-07T19:28:02,771 Found link https://files.pythonhosted.org/packages/ff/1f/af7beaaaa133f2f55cdbfbf5430c0e9a3102b101dd0a8d2c6f22376af56b/mitos-2.1.4.tar.gz (from https://pypi.org/simple/mitos/), version: 2.1.4 2024-01-07T19:28:02,772 Found link https://files.pythonhosted.org/packages/c9/6d/853d05a3ec8c81c73bb23ba0862ded05aa4c2fdc74cdc796c982c6896476/mitos-2.1.5.tar.gz (from https://pypi.org/simple/mitos/), version: 2.1.5 2024-01-07T19:28:02,772 Found link https://files.pythonhosted.org/packages/96/9a/97d5e59e6680b450e24d0c3313f112b8818f7d2f6c6fbc90d685cf7fe47c/mitos-2.1.6.tar.gz (from https://pypi.org/simple/mitos/), version: 2.1.6 2024-01-07T19:28:02,773 Fetching project page and analyzing links: https://www.piwheels.org/simple/mitos/ 2024-01-07T19:28:02,774 Getting page https://www.piwheels.org/simple/mitos/ 2024-01-07T19:28:02,775 Found index url https://www.piwheels.org/simple/ 2024-01-07T19:28:02,933 Fetched page https://www.piwheels.org/simple/mitos/ as text/html 2024-01-07T19:28:02,940 Skipping link: No binaries permitted for mitos: https://www.piwheels.org/simple/mitos/mitos-2.1.5-py3-none-any.whl#sha256=c404e62da7a2d919a7cf0999ba3ce479541d935e38999ed75c09dc9a38f6b6bd (from https://www.piwheels.org/simple/mitos/) 2024-01-07T19:28:02,941 Skipping link: No binaries permitted for mitos: https://www.piwheels.org/simple/mitos/mitos-2.1.4-py3-none-any.whl#sha256=249c87e42350fbefa1e3281d0e81f795c7710a95303b226bdc818b51615162e0 (from https://www.piwheels.org/simple/mitos/) 2024-01-07T19:28:02,942 Skipping link: No binaries permitted for mitos: https://www.piwheels.org/simple/mitos/mitos-2.1.3-py3-none-any.whl#sha256=dd19f4a9b02b695465d7d7861d7f611d1c73f231e6205b881d1617cd733bdd87 (from https://www.piwheels.org/simple/mitos/) 2024-01-07T19:28:02,942 Skipping link: No binaries permitted for mitos: https://www.piwheels.org/simple/mitos/mitos-2.1.2-py3-none-any.whl#sha256=c98234624cb7939861858030fbac10b88073159ea24b334b42e1cfd70254088d (from https://www.piwheels.org/simple/mitos/) 2024-01-07T19:28:02,943 Skipping link: No binaries permitted for mitos: https://www.piwheels.org/simple/mitos/mitos-2.1.1-py3-none-any.whl#sha256=698670abccda0918af0b490888cb195f86172e217766c9672bfedae33666ac82 (from https://www.piwheels.org/simple/mitos/) 2024-01-07T19:28:02,943 Skipping link: No binaries permitted for mitos: https://www.piwheels.org/simple/mitos/mitos-2.1.0-py3-none-any.whl#sha256=d4b006045b98620155cbed38de6ecf0d0ffb030cebc4d6e6e947cb015b8ce746 (from https://www.piwheels.org/simple/mitos/) 2024-01-07T19:28:02,943 Skipping link: No binaries permitted for mitos: https://www.piwheels.org/simple/mitos/mitos-2.0.8-py3-none-any.whl#sha256=5e88aa49c5bba746d511e0e619295e3c59916c71ba94246f984e44dcfef6a06c (from https://www.piwheels.org/simple/mitos/) 2024-01-07T19:28:02,944 Skipping link: No binaries permitted for mitos: https://www.piwheels.org/simple/mitos/mitos-2.0.7-py3-none-any.whl#sha256=97e98856e946735f44b3df83d67645e0dac8b411edb7774df74c00a44832e1d6 (from https://www.piwheels.org/simple/mitos/) 2024-01-07T19:28:02,944 Skipping link: No binaries permitted for mitos: https://www.piwheels.org/simple/mitos/mitos-2.0.6-py3-none-any.whl#sha256=8fba2e7cf9c22c6a728a1f8141764a77a6a4a27d7f7e50106b6e43832857b149 (from https://www.piwheels.org/simple/mitos/) 2024-01-07T19:28:02,945 Skipping link: No binaries permitted for mitos: https://www.piwheels.org/simple/mitos/mitos-2.0.5-py3-none-any.whl#sha256=ed4998969ebae7bf1688b78cdac8f19ca359f123ea79c2acd2654dd454a53f22 (from https://www.piwheels.org/simple/mitos/) 2024-01-07T19:28:02,945 Skipping link: No binaries permitted for mitos: https://www.piwheels.org/simple/mitos/mitos-2.0.4-py3-none-any.whl#sha256=71ac10ffdc0a236d68e4fd82a700ae35a92f0b23a09242c8b99485ccbadb10cc (from https://www.piwheels.org/simple/mitos/) 2024-01-07T19:28:02,946 Skipping link: No binaries permitted for mitos: https://www.piwheels.org/simple/mitos/mitos-2.0.3-py3-none-any.whl#sha256=4da7d3530901e0732adc63ab4afa0c5d9a40558469b2ccee71ea4fbad466603b (from https://www.piwheels.org/simple/mitos/) 2024-01-07T19:28:02,946 Skipping link: No binaries permitted for mitos: https://www.piwheels.org/simple/mitos/mitos-2.0.2-py3-none-any.whl#sha256=0cd775b72e2dca4acf2f9c6f4d591abaeb00b983e4882fcf536d934a8263d342 (from https://www.piwheels.org/simple/mitos/) 2024-01-07T19:28:02,947 Skipping link: No binaries permitted for mitos: https://www.piwheels.org/simple/mitos/mitos-2.0.1-py3-none-any.whl#sha256=307713427f698c0f3449d782d86287f1494fd2ff773a9fc407fbd29a0de53aed (from https://www.piwheels.org/simple/mitos/) 2024-01-07T19:28:02,948 Skipping link: No binaries permitted for mitos: https://www.piwheels.org/simple/mitos/mitos-1.1.3-py3-none-any.whl#sha256=92bec0ea93c83f4d494767e69401c1dcc1dd8f562917c3d110ec0a525d142a6a (from https://www.piwheels.org/simple/mitos/) 2024-01-07T19:28:02,948 Skipping link: No binaries permitted for mitos: https://www.piwheels.org/simple/mitos/mitos-1.1.2-py3-none-any.whl#sha256=b237b128b553848c12c5d387b10a20bbcb734b8672b3bf56fb2f3995e169c03d (from https://www.piwheels.org/simple/mitos/) 2024-01-07T19:28:02,949 Skipping link: No binaries permitted for mitos: https://www.piwheels.org/simple/mitos/mitos-1.1.1-py3-none-any.whl#sha256=f0970e0e530a2a7759daafc81f1c79460dc85d15c1f34551d8394dce187dfe1c (from https://www.piwheels.org/simple/mitos/) 2024-01-07T19:28:02,949 Skipping link: No binaries permitted for mitos: https://www.piwheels.org/simple/mitos/mitos-1.1.0-py3-none-any.whl#sha256=424b5172258baf2837d8a45e89224c12fdc3cc2a8f4ba0894e5c74111e754e5d (from https://www.piwheels.org/simple/mitos/) 2024-01-07T19:28:02,950 Skipping link: No binaries permitted for mitos: https://www.piwheels.org/simple/mitos/mitos-1.0.5-py3-none-any.whl#sha256=f27a041efc520420cbffbb63a6c428a2ace092d6ffdc47942d6b9c434a281629 (from https://www.piwheels.org/simple/mitos/) 2024-01-07T19:28:02,951 Skipping link: No binaries permitted for mitos: https://www.piwheels.org/simple/mitos/mitos-1.0.4-py3-none-any.whl#sha256=4c35b6595c7a62189502f6becaed4b2fe147f7ed6c6ee8d6b69fb4fda5e2139a (from https://www.piwheels.org/simple/mitos/) 2024-01-07T19:28:02,952 Skipping link: No binaries permitted for mitos: https://www.piwheels.org/simple/mitos/mitos-1.0.3-py3-none-any.whl#sha256=7b62f2fcef8414d2a429f2f3c033e85c9377805612113e7103fa6793aa083cbc (from https://www.piwheels.org/simple/mitos/) 2024-01-07T19:28:02,952 Skipping link: No binaries permitted for mitos: https://www.piwheels.org/simple/mitos/mitos-1.0.2-py3-none-any.whl#sha256=ba6a5f7a1d3a0a95106d401e13f7639c5ed2ecb367ab7899e2204b14aa9930a1 (from https://www.piwheels.org/simple/mitos/) 2024-01-07T19:28:02,952 Skipping link: No binaries permitted for mitos: https://www.piwheels.org/simple/mitos/mitos-1.0.1-py3-none-any.whl#sha256=d216729f10eb3463d947658451c8f70fd97a9b2ca94cea55221f7a50f85749e2 (from https://www.piwheels.org/simple/mitos/) 2024-01-07T19:28:02,953 Skipping link: No binaries permitted for mitos: https://www.piwheels.org/simple/mitos/mitos-1.0-py3-none-any.whl#sha256=4f914c63f700f85163b395353782bcb87e49392f63c151f387dd4514694d0ac1 (from https://www.piwheels.org/simple/mitos/) 2024-01-07T19:28:02,953 Skipping link: not a file: https://www.piwheels.org/simple/mitos/ 2024-01-07T19:28:02,954 Skipping link: not a file: https://pypi.org/simple/mitos/ 2024-01-07T19:28:02,975 Given no hashes to check 1 links for project 'mitos': discarding no candidates 2024-01-07T19:28:02,993 Collecting mitos==2.1.6 2024-01-07T19:28:02,996 Created temporary directory: /tmp/pip-unpack-ciu5jizv 2024-01-07T19:28:03,214 Downloading mitos-2.1.6.tar.gz (273 kB) 2024-01-07T19:28:03,483 Added mitos==2.1.6 from https://files.pythonhosted.org/packages/96/9a/97d5e59e6680b450e24d0c3313f112b8818f7d2f6c6fbc90d685cf7fe47c/mitos-2.1.6.tar.gz to build tracker '/tmp/pip-build-tracker-mzn0kkrb' 2024-01-07T19:28:03,485 Running setup.py (path:/tmp/pip-wheel-tfg4rksr/mitos_57934bd777864142a9e1e2630dc1391a/setup.py) egg_info for package mitos 2024-01-07T19:28:03,486 Created temporary directory: /tmp/pip-pip-egg-info-xiqnu667 2024-01-07T19:28:03,486 Preparing metadata (setup.py): started 2024-01-07T19:28:03,488 Running command python setup.py egg_info 2024-01-07T19:28:04,503 running egg_info 2024-01-07T19:28:04,504 creating /tmp/pip-pip-egg-info-xiqnu667/mitos.egg-info 2024-01-07T19:28:04,529 writing /tmp/pip-pip-egg-info-xiqnu667/mitos.egg-info/PKG-INFO 2024-01-07T19:28:04,532 writing dependency_links to /tmp/pip-pip-egg-info-xiqnu667/mitos.egg-info/dependency_links.txt 2024-01-07T19:28:04,534 writing requirements to /tmp/pip-pip-egg-info-xiqnu667/mitos.egg-info/requires.txt 2024-01-07T19:28:04,536 writing top-level names to /tmp/pip-pip-egg-info-xiqnu667/mitos.egg-info/top_level.txt 2024-01-07T19:28:04,537 writing manifest file '/tmp/pip-pip-egg-info-xiqnu667/mitos.egg-info/SOURCES.txt' 2024-01-07T19:28:04,660 reading manifest file '/tmp/pip-pip-egg-info-xiqnu667/mitos.egg-info/SOURCES.txt' 2024-01-07T19:28:04,661 reading manifest template 'MANIFEST.in' 2024-01-07T19:28:04,662 warning: no files found matching 'mitos/codons/gc.prt' 2024-01-07T19:28:04,665 adding license file 'LICENSE' 2024-01-07T19:28:04,668 writing manifest file '/tmp/pip-pip-egg-info-xiqnu667/mitos.egg-info/SOURCES.txt' 2024-01-07T19:28:04,774 Preparing metadata (setup.py): finished with status 'done' 2024-01-07T19:28:04,778 Source in /tmp/pip-wheel-tfg4rksr/mitos_57934bd777864142a9e1e2630dc1391a has version 2.1.6, which satisfies requirement mitos==2.1.6 from https://files.pythonhosted.org/packages/96/9a/97d5e59e6680b450e24d0c3313f112b8818f7d2f6c6fbc90d685cf7fe47c/mitos-2.1.6.tar.gz 2024-01-07T19:28:04,779 Removed mitos==2.1.6 from https://files.pythonhosted.org/packages/96/9a/97d5e59e6680b450e24d0c3313f112b8818f7d2f6c6fbc90d685cf7fe47c/mitos-2.1.6.tar.gz from build tracker '/tmp/pip-build-tracker-mzn0kkrb' 2024-01-07T19:28:04,783 Created temporary directory: /tmp/pip-unpack-u8ih25yp 2024-01-07T19:28:04,784 Created temporary directory: /tmp/pip-unpack-r2hsc46s 2024-01-07T19:28:04,788 Building wheels for collected packages: mitos 2024-01-07T19:28:04,792 Created temporary directory: /tmp/pip-wheel-a7jfihc1 2024-01-07T19:28:04,793 Building wheel for mitos (setup.py): started 2024-01-07T19:28:04,794 Destination directory: /tmp/pip-wheel-a7jfihc1 2024-01-07T19:28:04,795 Running command python setup.py bdist_wheel 2024-01-07T19:28:05,796 running bdist_wheel 2024-01-07T19:28:05,891 running build 2024-01-07T19:28:05,892 running build_py 2024-01-07T19:28:05,919 creating build 2024-01-07T19:28:05,919 creating build/lib 2024-01-07T19:28:05,920 creating build/lib/mitos 2024-01-07T19:28:05,922 copying mitos/mitos-extension.py -> build/lib/mitos 2024-01-07T19:28:05,924 copying mitos/update-mitolog.py -> build/lib/mitos 2024-01-07T19:28:05,926 copying mitos/codoncount.py -> build/lib/mitos 2024-01-07T19:28:05,928 copying mitos/cmsearch_parse_separate.py -> build/lib/mitos 2024-01-07T19:28:05,930 copying mitos/trnascan_parse_separate.py -> build/lib/mitos 2024-01-07T19:28:05,932 copying mitos/inihit.py -> build/lib/mitos 2024-01-07T19:28:05,934 copying mitos/convert_tree.py -> build/lib/mitos 2024-01-07T19:28:05,937 copying mitos/names.py -> build/lib/mitos 2024-01-07T19:28:05,939 copying mitos/prepareFiles.py -> build/lib/mitos 2024-01-07T19:28:05,941 copying mitos/trna-cm.py -> build/lib/mitos 2024-01-07T19:28:05,948 copying mitos/booreparser.py -> build/lib/mitos 2024-01-07T19:28:05,950 copying mitos/skew.py -> build/lib/mitos 2024-01-07T19:28:05,953 copying mitos/mitoch_revisions.py -> build/lib/mitos 2024-01-07T19:28:05,956 copying mitos/__init__.py -> build/lib/mitos 2024-01-07T19:28:05,958 copying mitos/create_prot_fasta.py -> build/lib/mitos 2024-01-07T19:28:05,960 copying mitos/mitos-extension2.py -> build/lib/mitos 2024-01-07T19:28:05,963 copying mitos/mumcmp.py -> build/lib/mitos 2024-01-07T19:28:05,965 copying mitos/merge_results.py -> build/lib/mitos 2024-01-07T19:28:05,968 copying mitos/ogre-geneorder.py -> build/lib/mitos 2024-01-07T19:28:05,970 copying mitos/CONFIG.py -> build/lib/mitos 2024-01-07T19:28:05,972 copying mitos/trnadist.py -> build/lib/mitos 2024-01-07T19:28:05,975 copying mitos/mitoloc.py -> build/lib/mitos 2024-01-07T19:28:05,977 copying mitos/get-wancy.py -> build/lib/mitos 2024-01-07T19:28:05,979 copying mitos/removegene.py -> build/lib/mitos 2024-01-07T19:28:05,982 creating build/lib/mitos/tbl 2024-01-07T19:28:05,983 copying mitos/tbl/__init__.py -> build/lib/mitos/tbl 2024-01-07T19:28:05,986 creating build/lib/mitos/blast 2024-01-07T19:28:05,988 copying mitos/blast/__init__.py -> build/lib/mitos/blast 2024-01-07T19:28:05,992 creating build/lib/mitos/rna 2024-01-07T19:28:05,993 copying mitos/rna/vienna.py -> build/lib/mitos/rna 2024-01-07T19:28:05,995 copying mitos/rna/forester.py -> build/lib/mitos/rna 2024-01-07T19:28:05,997 copying mitos/rna/__init__.py -> build/lib/mitos/rna 2024-01-07T19:28:05,999 creating build/lib/mitos/webserver 2024-01-07T19:28:06,000 copying mitos/webserver/__init__.py -> build/lib/mitos/webserver 2024-01-07T19:28:06,002 creating build/lib/mitos/mergefeature 2024-01-07T19:28:06,003 copying mitos/mergefeature/__init__.py -> build/lib/mitos/mergefeature 2024-01-07T19:28:06,006 creating build/lib/mitos/protfeat 2024-01-07T19:28:06,007 copying mitos/protfeat/__init__.py -> build/lib/mitos/protfeat 2024-01-07T19:28:06,011 creating build/lib/mitos/update 2024-01-07T19:28:06,012 copying mitos/update/__init__.py -> build/lib/mitos/update 2024-01-07T19:28:06,015 creating build/lib/mitos/mito 2024-01-07T19:28:06,016 copying mitos/mito/__init__.py -> build/lib/mitos/mito 2024-01-07T19:28:06,018 creating build/lib/mitos/draw 2024-01-07T19:28:06,019 copying mitos/draw/__init__.py -> build/lib/mitos/draw 2024-01-07T19:28:06,021 creating build/lib/mitos/sequin 2024-01-07T19:28:06,022 copying mitos/sequin/__init__.py -> build/lib/mitos/sequin 2024-01-07T19:28:06,025 creating build/lib/mitos/bedfile 2024-01-07T19:28:06,026 copying mitos/bedfile/__init__.py -> build/lib/mitos/bedfile 2024-01-07T19:28:06,028 creating build/lib/mitos/mitofile 2024-01-07T19:28:06,029 copying mitos/mitofile/__init__.py -> build/lib/mitos/mitofile 2024-01-07T19:28:06,031 creating build/lib/mitos/trna 2024-01-07T19:28:06,032 copying mitos/trna/trnascan.py -> build/lib/mitos/trna 2024-01-07T19:28:06,035 copying mitos/trna/__init__.py -> build/lib/mitos/trna 2024-01-07T19:28:06,037 copying mitos/trna/arwenscan.py -> build/lib/mitos/trna 2024-01-07T19:28:06,039 creating build/lib/mitos/gfffile 2024-01-07T19:28:06,040 copying mitos/gfffile/__init__.py -> build/lib/mitos/gfffile 2024-01-07T19:28:06,042 creating build/lib/mitos/gb 2024-01-07T19:28:06,043 copying mitos/gb/__init__.py -> build/lib/mitos/gb 2024-01-07T19:28:06,046 copying mitos/gb/unify.py -> build/lib/mitos/gb 2024-01-07T19:28:06,048 creating build/lib/mitos/extprog 2024-01-07T19:28:06,049 copying mitos/extprog/__init__.py -> build/lib/mitos/extprog 2024-01-07T19:28:06,052 creating build/lib/mitos/feature 2024-01-07T19:28:06,053 copying mitos/feature/__init__.py -> build/lib/mitos/feature 2024-01-07T19:28:06,056 creating build/lib/mitos/mitfi 2024-01-07T19:28:06,057 copying mitos/mitfi/__init__.py -> build/lib/mitos/mitfi 2024-01-07T19:28:06,060 creating build/lib/mitos/sequence 2024-01-07T19:28:06,061 copying mitos/sequence/__init__.py -> build/lib/mitos/sequence 2024-01-07T19:28:06,064 copying mitos/sequence/degenerate.py -> build/lib/mitos/sequence 2024-01-07T19:28:06,066 creating build/lib/mitos/util 2024-01-07T19:28:06,067 copying mitos/util/__init__.py -> build/lib/mitos/util 2024-01-07T19:28:06,069 creating build/lib/mitos/tax 2024-01-07T19:28:06,070 copying mitos/tax/__init__.py -> build/lib/mitos/tax 2024-01-07T19:28:06,072 running egg_info 2024-01-07T19:28:06,127 writing mitos.egg-info/PKG-INFO 2024-01-07T19:28:06,130 writing dependency_links to mitos.egg-info/dependency_links.txt 2024-01-07T19:28:06,132 writing requirements to mitos.egg-info/requires.txt 2024-01-07T19:28:06,133 writing top-level names to mitos.egg-info/top_level.txt 2024-01-07T19:28:06,176 reading manifest file 'mitos.egg-info/SOURCES.txt' 2024-01-07T19:28:06,180 reading manifest template 'MANIFEST.in' 2024-01-07T19:28:06,181 warning: no files found matching 'mitos/codons/gc.prt' 2024-01-07T19:28:06,182 adding license file 'LICENSE' 2024-01-07T19:28:06,187 writing manifest file 'mitos.egg-info/SOURCES.txt' 2024-01-07T19:28:06,189 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'mitos.mitfi.parser' is absent from the `packages` configuration. 2024-01-07T19:28:06,190 !! 2024-01-07T19:28:06,191 ******************************************************************************** 2024-01-07T19:28:06,192 ############################ 2024-01-07T19:28:06,192 # Package would be ignored # 2024-01-07T19:28:06,193 ############################ 2024-01-07T19:28:06,193 Python recognizes 'mitos.mitfi.parser' as an importable package[^1], 2024-01-07T19:28:06,194 but it is absent from setuptools' `packages` configuration. 2024-01-07T19:28:06,195 This leads to an ambiguous overall configuration. If you want to distribute this 2024-01-07T19:28:06,196 package, please make sure that 'mitos.mitfi.parser' is explicitly added 2024-01-07T19:28:06,196 to the `packages` configuration field. 2024-01-07T19:28:06,197 Alternatively, you can also rely on setuptools' discovery methods 2024-01-07T19:28:06,198 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-01-07T19:28:06,198 instead of `find_packages(...)`/`find:`). 2024-01-07T19:28:06,199 You can read more about "package discovery" on setuptools documentation page: 2024-01-07T19:28:06,200 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-01-07T19:28:06,201 If you don't want 'mitos.mitfi.parser' to be distributed and are 2024-01-07T19:28:06,202 already explicitly excluding 'mitos.mitfi.parser' via 2024-01-07T19:28:06,202 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-01-07T19:28:06,202 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-01-07T19:28:06,203 combination with a more fine grained `package-data` configuration. 2024-01-07T19:28:06,204 You can read more about "package data files" on setuptools documentation page: 2024-01-07T19:28:06,204 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-01-07T19:28:06,206 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-01-07T19:28:06,206 even if it does not contain any `.py` files. 2024-01-07T19:28:06,207 On the other hand, currently there is no concept of package data 2024-01-07T19:28:06,207 directory, all directories are treated like packages. 2024-01-07T19:28:06,207 ******************************************************************************** 2024-01-07T19:28:06,208 !! 2024-01-07T19:28:06,209 check.warn(importable) 2024-01-07T19:28:06,209 copying mitos/plotprot.R -> build/lib/mitos 2024-01-07T19:28:06,210 copying mitos/plotrna.R -> build/lib/mitos 2024-01-07T19:28:06,211 copying mitos/plotstst.R -> build/lib/mitos 2024-01-07T19:28:06,212 copying mitos/webserver/help.txt -> build/lib/mitos/webserver 2024-01-07T19:28:06,215 copying mitos/webserver/history.txt -> build/lib/mitos/webserver 2024-01-07T19:28:06,217 copying mitos/webserver/index.txt -> build/lib/mitos/webserver 2024-01-07T19:28:06,220 copying mitos/webserver/news.txt -> build/lib/mitos/webserver 2024-01-07T19:28:06,222 copying mitos/webserver/upload.txt -> build/lib/mitos/webserver 2024-01-07T19:28:06,224 copying mitos/webserver/wait.txt -> build/lib/mitos/webserver 2024-01-07T19:28:06,226 creating build/lib/mitos/mitfi/parser 2024-01-07T19:28:06,227 copying mitos/mitfi/parser/improve_infernal_structure.jar -> build/lib/mitos/mitfi/parser 2024-01-07T19:28:06,230 copying mitos/mitfi/parser/mitfiGeneticCodes -> build/lib/mitos/mitfi/parser 2024-01-07T19:28:06,232 copying mitos/mitfi/parser/mitfi_import-1.1.jar -> build/lib/mitos/mitfi/parser 2024-01-07T19:28:06,235 copying mitos/mitfi/parser/mitfi_import-1.1.jar.old -> build/lib/mitos/mitfi/parser 2024-01-07T19:28:06,238 copying mitos/mitfi/parser/mitfi_import-1.1.jar.org -> build/lib/mitos/mitfi/parser 2024-01-07T19:28:06,241 copying mitos/mitfi/parser/mitfi_import-1.1.jar.org.pre-circ -> build/lib/mitos/mitfi/parser 2024-01-07T19:28:06,244 copying mitos/mitfi/parser/mitfi_import.jar -> build/lib/mitos/mitfi/parser 2024-01-07T19:28:06,254 running build_scripts 2024-01-07T19:28:06,255 creating build/scripts-3.11 2024-01-07T19:28:06,256 copying and adjusting runmitos.py -> build/scripts-3.11 2024-01-07T19:28:06,260 copying and adjusting drawmitos.py -> build/scripts-3.11 2024-01-07T19:28:06,261 copying and adjusting analyse.py -> build/scripts-3.11 2024-01-07T19:28:06,264 copying and adjusting gcpp.py -> build/scripts-3.11 2024-01-07T19:28:06,266 copying and adjusting geneorder.py -> build/scripts-3.11 2024-01-07T19:28:06,268 copying and adjusting getfeatures.py -> build/scripts-3.11 2024-01-07T19:28:06,271 copying and adjusting getinfo.py -> build/scripts-3.11 2024-01-07T19:28:06,272 copying and adjusting refseqsplit.py -> build/scripts-3.11 2024-01-07T19:28:06,274 copying and adjusting subseq.py -> build/scripts-3.11 2024-01-07T19:28:06,276 copying and adjusting taxtree.py -> build/scripts-3.11 2024-01-07T19:28:06,278 copying update-blastdb.py -> build/scripts-3.11 2024-01-07T19:28:06,280 copying mitos/plotprot.R -> build/scripts-3.11 2024-01-07T19:28:06,282 copying mitos/plotstst.R -> build/scripts-3.11 2024-01-07T19:28:06,285 copying mitos/plotrna.R -> build/scripts-3.11 2024-01-07T19:28:06,286 changing mode of build/scripts-3.11/runmitos.py from 644 to 755 2024-01-07T19:28:06,287 changing mode of build/scripts-3.11/drawmitos.py from 644 to 755 2024-01-07T19:28:06,287 changing mode of build/scripts-3.11/analyse.py from 644 to 755 2024-01-07T19:28:06,288 changing mode of build/scripts-3.11/gcpp.py from 644 to 755 2024-01-07T19:28:06,288 changing mode of build/scripts-3.11/geneorder.py from 644 to 755 2024-01-07T19:28:06,288 changing mode of build/scripts-3.11/getfeatures.py from 644 to 755 2024-01-07T19:28:06,289 changing mode of build/scripts-3.11/getinfo.py from 644 to 755 2024-01-07T19:28:06,289 changing mode of build/scripts-3.11/refseqsplit.py from 644 to 755 2024-01-07T19:28:06,290 changing mode of build/scripts-3.11/subseq.py from 644 to 755 2024-01-07T19:28:06,290 changing mode of build/scripts-3.11/taxtree.py from 644 to 755 2024-01-07T19:28:06,291 changing mode of build/scripts-3.11/update-blastdb.py from 644 to 755 2024-01-07T19:28:06,314 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-01-07T19:28:06,314 !! 2024-01-07T19:28:06,316 ******************************************************************************** 2024-01-07T19:28:06,316 Please avoid running ``setup.py`` directly. 2024-01-07T19:28:06,317 Instead, use pypa/build, pypa/installer or other 2024-01-07T19:28:06,317 standards-based tools. 2024-01-07T19:28:06,318 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-01-07T19:28:06,319 ******************************************************************************** 2024-01-07T19:28:06,320 !! 2024-01-07T19:28:06,320 self.initialize_options() 2024-01-07T19:28:06,338 installing to build/bdist.linux-armv7l/wheel 2024-01-07T19:28:06,339 running install 2024-01-07T19:28:06,363 running install_lib 2024-01-07T19:28:06,387 creating build/bdist.linux-armv7l 2024-01-07T19:28:06,388 creating build/bdist.linux-armv7l/wheel 2024-01-07T19:28:06,390 creating build/bdist.linux-armv7l/wheel/mitos 2024-01-07T19:28:06,391 creating build/bdist.linux-armv7l/wheel/mitos/tbl 2024-01-07T19:28:06,392 copying build/lib/mitos/tbl/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/tbl 2024-01-07T19:28:06,395 creating build/bdist.linux-armv7l/wheel/mitos/blast 2024-01-07T19:28:06,396 copying build/lib/mitos/blast/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/blast 2024-01-07T19:28:06,400 copying build/lib/mitos/mitos-extension.py -> build/bdist.linux-armv7l/wheel/mitos 2024-01-07T19:28:06,402 copying build/lib/mitos/update-mitolog.py -> build/bdist.linux-armv7l/wheel/mitos 2024-01-07T19:28:06,404 copying build/lib/mitos/codoncount.py -> build/bdist.linux-armv7l/wheel/mitos 2024-01-07T19:28:06,407 copying build/lib/mitos/cmsearch_parse_separate.py -> build/bdist.linux-armv7l/wheel/mitos 2024-01-07T19:28:06,409 copying build/lib/mitos/trnascan_parse_separate.py -> build/bdist.linux-armv7l/wheel/mitos 2024-01-07T19:28:06,411 copying build/lib/mitos/inihit.py -> build/bdist.linux-armv7l/wheel/mitos 2024-01-07T19:28:06,413 copying build/lib/mitos/plotstst.R -> build/bdist.linux-armv7l/wheel/mitos 2024-01-07T19:28:06,415 copying build/lib/mitos/convert_tree.py -> build/bdist.linux-armv7l/wheel/mitos 2024-01-07T19:28:06,418 copying build/lib/mitos/names.py -> build/bdist.linux-armv7l/wheel/mitos 2024-01-07T19:28:06,421 creating build/bdist.linux-armv7l/wheel/mitos/rna 2024-01-07T19:28:06,422 copying build/lib/mitos/rna/vienna.py -> build/bdist.linux-armv7l/wheel/mitos/rna 2024-01-07T19:28:06,424 copying build/lib/mitos/rna/forester.py -> build/bdist.linux-armv7l/wheel/mitos/rna 2024-01-07T19:28:06,426 copying build/lib/mitos/rna/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/rna 2024-01-07T19:28:06,427 copying build/lib/mitos/prepareFiles.py -> build/bdist.linux-armv7l/wheel/mitos 2024-01-07T19:28:06,429 creating build/bdist.linux-armv7l/wheel/mitos/webserver 2024-01-07T19:28:06,430 copying build/lib/mitos/webserver/upload.txt -> build/bdist.linux-armv7l/wheel/mitos/webserver 2024-01-07T19:28:06,432 copying build/lib/mitos/webserver/help.txt -> build/bdist.linux-armv7l/wheel/mitos/webserver 2024-01-07T19:28:06,435 copying build/lib/mitos/webserver/news.txt -> build/bdist.linux-armv7l/wheel/mitos/webserver 2024-01-07T19:28:06,436 copying build/lib/mitos/webserver/index.txt -> build/bdist.linux-armv7l/wheel/mitos/webserver 2024-01-07T19:28:06,439 copying build/lib/mitos/webserver/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/webserver 2024-01-07T19:28:06,441 copying build/lib/mitos/webserver/history.txt -> build/bdist.linux-armv7l/wheel/mitos/webserver 2024-01-07T19:28:06,442 copying build/lib/mitos/webserver/wait.txt -> build/bdist.linux-armv7l/wheel/mitos/webserver 2024-01-07T19:28:06,444 creating build/bdist.linux-armv7l/wheel/mitos/mergefeature 2024-01-07T19:28:06,445 copying build/lib/mitos/mergefeature/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/mergefeature 2024-01-07T19:28:06,449 creating build/bdist.linux-armv7l/wheel/mitos/protfeat 2024-01-07T19:28:06,449 copying build/lib/mitos/protfeat/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/protfeat 2024-01-07T19:28:06,452 copying build/lib/mitos/trna-cm.py -> build/bdist.linux-armv7l/wheel/mitos 2024-01-07T19:28:06,458 copying build/lib/mitos/booreparser.py -> build/bdist.linux-armv7l/wheel/mitos 2024-01-07T19:28:06,461 creating build/bdist.linux-armv7l/wheel/mitos/update 2024-01-07T19:28:06,462 copying build/lib/mitos/update/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/update 2024-01-07T19:28:06,465 copying build/lib/mitos/skew.py -> build/bdist.linux-armv7l/wheel/mitos 2024-01-07T19:28:06,468 creating build/bdist.linux-armv7l/wheel/mitos/mito 2024-01-07T19:28:06,469 copying build/lib/mitos/mito/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/mito 2024-01-07T19:28:06,471 copying build/lib/mitos/mitoch_revisions.py -> build/bdist.linux-armv7l/wheel/mitos 2024-01-07T19:28:06,474 copying build/lib/mitos/__init__.py -> build/bdist.linux-armv7l/wheel/mitos 2024-01-07T19:28:06,476 copying build/lib/mitos/create_prot_fasta.py -> build/bdist.linux-armv7l/wheel/mitos 2024-01-07T19:28:06,479 creating build/bdist.linux-armv7l/wheel/mitos/draw 2024-01-07T19:28:06,480 copying build/lib/mitos/draw/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/draw 2024-01-07T19:28:06,482 creating build/bdist.linux-armv7l/wheel/mitos/sequin 2024-01-07T19:28:06,483 copying build/lib/mitos/sequin/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/sequin 2024-01-07T19:28:06,485 copying build/lib/mitos/mitos-extension2.py -> build/bdist.linux-armv7l/wheel/mitos 2024-01-07T19:28:06,488 creating build/bdist.linux-armv7l/wheel/mitos/bedfile 2024-01-07T19:28:06,489 copying build/lib/mitos/bedfile/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/bedfile 2024-01-07T19:28:06,491 copying build/lib/mitos/mumcmp.py -> build/bdist.linux-armv7l/wheel/mitos 2024-01-07T19:28:06,493 creating build/bdist.linux-armv7l/wheel/mitos/mitofile 2024-01-07T19:28:06,494 copying build/lib/mitos/mitofile/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/mitofile 2024-01-07T19:28:06,497 creating build/bdist.linux-armv7l/wheel/mitos/trna 2024-01-07T19:28:06,498 copying build/lib/mitos/trna/trnascan.py -> build/bdist.linux-armv7l/wheel/mitos/trna 2024-01-07T19:28:06,500 copying build/lib/mitos/trna/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/trna 2024-01-07T19:28:06,503 copying build/lib/mitos/trna/arwenscan.py -> build/bdist.linux-armv7l/wheel/mitos/trna 2024-01-07T19:28:06,506 creating build/bdist.linux-armv7l/wheel/mitos/gfffile 2024-01-07T19:28:06,507 copying build/lib/mitos/gfffile/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/gfffile 2024-01-07T19:28:06,509 creating build/bdist.linux-armv7l/wheel/mitos/gb 2024-01-07T19:28:06,510 copying build/lib/mitos/gb/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/gb 2024-01-07T19:28:06,513 copying build/lib/mitos/gb/unify.py -> build/bdist.linux-armv7l/wheel/mitos/gb 2024-01-07T19:28:06,515 copying build/lib/mitos/merge_results.py -> build/bdist.linux-armv7l/wheel/mitos 2024-01-07T19:28:06,518 creating build/bdist.linux-armv7l/wheel/mitos/extprog 2024-01-07T19:28:06,518 copying build/lib/mitos/extprog/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/extprog 2024-01-07T19:28:06,521 copying build/lib/mitos/plotprot.R -> build/bdist.linux-armv7l/wheel/mitos 2024-01-07T19:28:06,523 creating build/bdist.linux-armv7l/wheel/mitos/feature 2024-01-07T19:28:06,524 copying build/lib/mitos/feature/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/feature 2024-01-07T19:28:06,527 copying build/lib/mitos/ogre-geneorder.py -> build/bdist.linux-armv7l/wheel/mitos 2024-01-07T19:28:06,529 copying build/lib/mitos/CONFIG.py -> build/bdist.linux-armv7l/wheel/mitos 2024-01-07T19:28:06,531 copying build/lib/mitos/trnadist.py -> build/bdist.linux-armv7l/wheel/mitos 2024-01-07T19:28:06,534 creating build/bdist.linux-armv7l/wheel/mitos/mitfi 2024-01-07T19:28:06,535 copying build/lib/mitos/mitfi/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/mitfi 2024-01-07T19:28:06,538 creating build/bdist.linux-armv7l/wheel/mitos/mitfi/parser 2024-01-07T19:28:06,539 copying build/lib/mitos/mitfi/parser/mitfi_import-1.1.jar.org.pre-circ -> build/bdist.linux-armv7l/wheel/mitos/mitfi/parser 2024-01-07T19:28:06,542 copying build/lib/mitos/mitfi/parser/mitfi_import-1.1.jar.old -> build/bdist.linux-armv7l/wheel/mitos/mitfi/parser 2024-01-07T19:28:06,544 copying build/lib/mitos/mitfi/parser/mitfi_import-1.1.jar -> build/bdist.linux-armv7l/wheel/mitos/mitfi/parser 2024-01-07T19:28:06,547 copying build/lib/mitos/mitfi/parser/mitfiGeneticCodes -> build/bdist.linux-armv7l/wheel/mitos/mitfi/parser 2024-01-07T19:28:06,549 copying build/lib/mitos/mitfi/parser/improve_infernal_structure.jar -> build/bdist.linux-armv7l/wheel/mitos/mitfi/parser 2024-01-07T19:28:06,551 copying build/lib/mitos/mitfi/parser/mitfi_import.jar -> build/bdist.linux-armv7l/wheel/mitos/mitfi/parser 2024-01-07T19:28:06,554 copying build/lib/mitos/mitfi/parser/mitfi_import-1.1.jar.org -> build/bdist.linux-armv7l/wheel/mitos/mitfi/parser 2024-01-07T19:28:06,557 creating build/bdist.linux-armv7l/wheel/mitos/sequence 2024-01-07T19:28:06,558 copying build/lib/mitos/sequence/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/sequence 2024-01-07T19:28:06,561 copying build/lib/mitos/sequence/degenerate.py -> build/bdist.linux-armv7l/wheel/mitos/sequence 2024-01-07T19:28:06,563 creating build/bdist.linux-armv7l/wheel/mitos/util 2024-01-07T19:28:06,564 copying build/lib/mitos/util/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/util 2024-01-07T19:28:06,566 copying build/lib/mitos/mitoloc.py -> build/bdist.linux-armv7l/wheel/mitos 2024-01-07T19:28:06,568 copying build/lib/mitos/get-wancy.py -> build/bdist.linux-armv7l/wheel/mitos 2024-01-07T19:28:06,571 copying build/lib/mitos/plotrna.R -> build/bdist.linux-armv7l/wheel/mitos 2024-01-07T19:28:06,572 copying build/lib/mitos/removegene.py -> build/bdist.linux-armv7l/wheel/mitos 2024-01-07T19:28:06,574 creating build/bdist.linux-armv7l/wheel/mitos/tax 2024-01-07T19:28:06,575 copying build/lib/mitos/tax/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/tax 2024-01-07T19:28:06,577 running install_egg_info 2024-01-07T19:28:06,607 Copying mitos.egg-info to build/bdist.linux-armv7l/wheel/mitos-2.1.6-py3.11.egg-info 2024-01-07T19:28:06,618 running install_scripts 2024-01-07T19:28:06,619 creating build/bdist.linux-armv7l/wheel/mitos-2.1.6.data 2024-01-07T19:28:06,620 creating build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts 2024-01-07T19:28:06,622 copying build/scripts-3.11/refseqsplit.py -> build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts 2024-01-07T19:28:06,623 copying build/scripts-3.11/analyse.py -> build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts 2024-01-07T19:28:06,626 copying build/scripts-3.11/plotstst.R -> build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts 2024-01-07T19:28:06,628 copying build/scripts-3.11/runmitos.py -> build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts 2024-01-07T19:28:06,631 copying build/scripts-3.11/taxtree.py -> build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts 2024-01-07T19:28:06,633 copying build/scripts-3.11/gcpp.py -> build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts 2024-01-07T19:28:06,635 copying build/scripts-3.11/getfeatures.py -> build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts 2024-01-07T19:28:06,638 copying build/scripts-3.11/getinfo.py -> build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts 2024-01-07T19:28:06,640 copying build/scripts-3.11/plotprot.R -> build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts 2024-01-07T19:28:06,642 copying build/scripts-3.11/drawmitos.py -> build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts 2024-01-07T19:28:06,643 copying build/scripts-3.11/subseq.py -> build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts 2024-01-07T19:28:06,646 copying build/scripts-3.11/update-blastdb.py -> build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts 2024-01-07T19:28:06,647 copying build/scripts-3.11/plotrna.R -> build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts 2024-01-07T19:28:06,649 copying build/scripts-3.11/geneorder.py -> build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts 2024-01-07T19:28:06,652 changing mode of build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts/refseqsplit.py to 755 2024-01-07T19:28:06,652 changing mode of build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts/analyse.py to 755 2024-01-07T19:28:06,653 changing mode of build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts/plotstst.R to 755 2024-01-07T19:28:06,653 changing mode of build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts/runmitos.py to 755 2024-01-07T19:28:06,654 changing mode of build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts/taxtree.py to 755 2024-01-07T19:28:06,654 changing mode of build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts/gcpp.py to 755 2024-01-07T19:28:06,655 changing mode of build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts/getfeatures.py to 755 2024-01-07T19:28:06,655 changing mode of build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts/getinfo.py to 755 2024-01-07T19:28:06,656 changing mode of build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts/plotprot.R to 755 2024-01-07T19:28:06,656 changing mode of build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts/drawmitos.py to 755 2024-01-07T19:28:06,657 changing mode of build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts/subseq.py to 755 2024-01-07T19:28:06,657 changing mode of build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts/update-blastdb.py to 755 2024-01-07T19:28:06,658 changing mode of build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts/plotrna.R to 755 2024-01-07T19:28:06,658 changing mode of build/bdist.linux-armv7l/wheel/mitos-2.1.6.data/scripts/geneorder.py to 755 2024-01-07T19:28:06,670 creating build/bdist.linux-armv7l/wheel/mitos-2.1.6.dist-info/WHEEL 2024-01-07T19:28:06,673 creating '/tmp/pip-wheel-a7jfihc1/mitos-2.1.6-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-01-07T19:28:06,676 adding 'mitos/CONFIG.py' 2024-01-07T19:28:06,677 adding 'mitos/__init__.py' 2024-01-07T19:28:06,679 adding 'mitos/booreparser.py' 2024-01-07T19:28:06,681 adding 'mitos/cmsearch_parse_separate.py' 2024-01-07T19:28:06,682 adding 'mitos/codoncount.py' 2024-01-07T19:28:06,686 adding 'mitos/convert_tree.py' 2024-01-07T19:28:06,688 adding 'mitos/create_prot_fasta.py' 2024-01-07T19:28:06,690 adding 'mitos/get-wancy.py' 2024-01-07T19:28:06,691 adding 'mitos/inihit.py' 2024-01-07T19:28:06,693 adding 'mitos/merge_results.py' 2024-01-07T19:28:06,698 adding 'mitos/mitoch_revisions.py' 2024-01-07T19:28:06,700 adding 'mitos/mitoloc.py' 2024-01-07T19:28:06,702 adding 'mitos/mitos-extension.py' 2024-01-07T19:28:06,705 adding 'mitos/mitos-extension2.py' 2024-01-07T19:28:06,706 adding 'mitos/mumcmp.py' 2024-01-07T19:28:06,707 adding 'mitos/names.py' 2024-01-07T19:28:06,709 adding 'mitos/ogre-geneorder.py' 2024-01-07T19:28:06,710 adding 'mitos/plotprot.R' 2024-01-07T19:28:06,712 adding 'mitos/plotrna.R' 2024-01-07T19:28:06,713 adding 'mitos/plotstst.R' 2024-01-07T19:28:06,714 adding 'mitos/prepareFiles.py' 2024-01-07T19:28:06,716 adding 'mitos/removegene.py' 2024-01-07T19:28:06,718 adding 'mitos/skew.py' 2024-01-07T19:28:06,733 adding 'mitos/trna-cm.py' 2024-01-07T19:28:06,737 adding 'mitos/trnadist.py' 2024-01-07T19:28:06,739 adding 'mitos/trnascan_parse_separate.py' 2024-01-07T19:28:06,740 adding 'mitos/update-mitolog.py' 2024-01-07T19:28:06,742 adding 'mitos/bedfile/__init__.py' 2024-01-07T19:28:06,753 adding 'mitos/blast/__init__.py' 2024-01-07T19:28:06,756 adding 'mitos/draw/__init__.py' 2024-01-07T19:28:06,757 adding 'mitos/extprog/__init__.py' 2024-01-07T19:28:06,763 adding 'mitos/feature/__init__.py' 2024-01-07T19:28:06,769 adding 'mitos/gb/__init__.py' 2024-01-07T19:28:06,771 adding 'mitos/gb/unify.py' 2024-01-07T19:28:06,773 adding 'mitos/gfffile/__init__.py' 2024-01-07T19:28:06,777 adding 'mitos/mergefeature/__init__.py' 2024-01-07T19:28:06,780 adding 'mitos/mitfi/__init__.py' 2024-01-07T19:28:06,783 adding 'mitos/mitfi/parser/improve_infernal_structure.jar' 2024-01-07T19:28:06,784 adding 'mitos/mitfi/parser/mitfiGeneticCodes' 2024-01-07T19:28:06,788 adding 'mitos/mitfi/parser/mitfi_import-1.1.jar' 2024-01-07T19:28:06,793 adding 'mitos/mitfi/parser/mitfi_import-1.1.jar.old' 2024-01-07T19:28:06,796 adding 'mitos/mitfi/parser/mitfi_import-1.1.jar.org' 2024-01-07T19:28:06,801 adding 'mitos/mitfi/parser/mitfi_import-1.1.jar.org.pre-circ' 2024-01-07T19:28:06,805 adding 'mitos/mitfi/parser/mitfi_import.jar' 2024-01-07T19:28:06,807 adding 'mitos/mito/__init__.py' 2024-01-07T19:28:06,809 adding 'mitos/mitofile/__init__.py' 2024-01-07T19:28:06,813 adding 'mitos/protfeat/__init__.py' 2024-01-07T19:28:06,815 adding 'mitos/rna/__init__.py' 2024-01-07T19:28:06,816 adding 'mitos/rna/forester.py' 2024-01-07T19:28:06,817 adding 'mitos/rna/vienna.py' 2024-01-07T19:28:06,820 adding 'mitos/sequence/__init__.py' 2024-01-07T19:28:06,822 adding 'mitos/sequence/degenerate.py' 2024-01-07T19:28:06,823 adding 'mitos/sequin/__init__.py' 2024-01-07T19:28:06,825 adding 'mitos/tax/__init__.py' 2024-01-07T19:28:06,827 adding 'mitos/tbl/__init__.py' 2024-01-07T19:28:06,829 adding 'mitos/trna/__init__.py' 2024-01-07T19:28:06,831 adding 'mitos/trna/arwenscan.py' 2024-01-07T19:28:06,833 adding 'mitos/trna/trnascan.py' 2024-01-07T19:28:06,837 adding 'mitos/update/__init__.py' 2024-01-07T19:28:06,839 adding 'mitos/util/__init__.py' 2024-01-07T19:28:06,841 adding 'mitos/webserver/__init__.py' 2024-01-07T19:28:06,845 adding 'mitos/webserver/help.txt' 2024-01-07T19:28:06,847 adding 'mitos/webserver/history.txt' 2024-01-07T19:28:06,848 adding 'mitos/webserver/index.txt' 2024-01-07T19:28:06,849 adding 'mitos/webserver/news.txt' 2024-01-07T19:28:06,851 adding 'mitos/webserver/upload.txt' 2024-01-07T19:28:06,852 adding 'mitos/webserver/wait.txt' 2024-01-07T19:28:06,855 adding 'mitos-2.1.6.data/scripts/analyse.py' 2024-01-07T19:28:06,856 adding 'mitos-2.1.6.data/scripts/drawmitos.py' 2024-01-07T19:28:06,858 adding 'mitos-2.1.6.data/scripts/gcpp.py' 2024-01-07T19:28:06,860 adding 'mitos-2.1.6.data/scripts/geneorder.py' 2024-01-07T19:28:06,862 adding 'mitos-2.1.6.data/scripts/getfeatures.py' 2024-01-07T19:28:06,864 adding 'mitos-2.1.6.data/scripts/getinfo.py' 2024-01-07T19:28:06,865 adding 'mitos-2.1.6.data/scripts/plotprot.R' 2024-01-07T19:28:06,866 adding 'mitos-2.1.6.data/scripts/plotrna.R' 2024-01-07T19:28:06,868 adding 'mitos-2.1.6.data/scripts/plotstst.R' 2024-01-07T19:28:06,869 adding 'mitos-2.1.6.data/scripts/refseqsplit.py' 2024-01-07T19:28:06,874 adding 'mitos-2.1.6.data/scripts/runmitos.py' 2024-01-07T19:28:06,876 adding 'mitos-2.1.6.data/scripts/subseq.py' 2024-01-07T19:28:06,877 adding 'mitos-2.1.6.data/scripts/taxtree.py' 2024-01-07T19:28:06,879 adding 'mitos-2.1.6.data/scripts/update-blastdb.py' 2024-01-07T19:28:06,881 adding 'mitos-2.1.6.dist-info/LICENSE' 2024-01-07T19:28:06,882 adding 'mitos-2.1.6.dist-info/METADATA' 2024-01-07T19:28:06,883 adding 'mitos-2.1.6.dist-info/WHEEL' 2024-01-07T19:28:06,883 adding 'mitos-2.1.6.dist-info/top_level.txt' 2024-01-07T19:28:06,885 adding 'mitos-2.1.6.dist-info/RECORD' 2024-01-07T19:28:06,891 removing build/bdist.linux-armv7l/wheel 2024-01-07T19:28:07,031 Building wheel for mitos (setup.py): finished with status 'done' 2024-01-07T19:28:07,039 Created wheel for mitos: filename=mitos-2.1.6-py3-none-any.whl size=332534 sha256=bed8aeda4eebf1ce891081ec67cf34897f2e5da8800cfb51c78593616a3304ea 2024-01-07T19:28:07,040 Stored in directory: /tmp/pip-ephem-wheel-cache-4prrtrp1/wheels/55/30/29/079ba63ff92bccedd61f9f69637852978523470b94e7428c89 2024-01-07T19:28:07,056 Successfully built mitos 2024-01-07T19:28:07,077 Removed build tracker: '/tmp/pip-build-tracker-mzn0kkrb'