2023-12-27T16:39:49,931 Created temporary directory: /tmp/pip-build-tracker-j6o7r1zb 2023-12-27T16:39:49,933 Initialized build tracking at /tmp/pip-build-tracker-j6o7r1zb 2023-12-27T16:39:49,933 Created build tracker: /tmp/pip-build-tracker-j6o7r1zb 2023-12-27T16:39:49,934 Entered build tracker: /tmp/pip-build-tracker-j6o7r1zb 2023-12-27T16:39:49,934 Created temporary directory: /tmp/pip-wheel-aeo_f2us 2023-12-27T16:39:49,937 Created temporary directory: /tmp/pip-ephem-wheel-cache-du7y2_1k 2023-12-27T16:39:49,960 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-12-27T16:39:49,963 2 location(s) to search for versions of mitos: 2023-12-27T16:39:49,963 * https://pypi.org/simple/mitos/ 2023-12-27T16:39:49,963 * https://www.piwheels.org/simple/mitos/ 2023-12-27T16:39:49,964 Fetching project page and analyzing links: https://pypi.org/simple/mitos/ 2023-12-27T16:39:49,965 Getting page https://pypi.org/simple/mitos/ 2023-12-27T16:39:49,966 Found index url https://pypi.org/simple/ 2023-12-27T16:39:50,217 Fetched page https://pypi.org/simple/mitos/ as application/vnd.pypi.simple.v1+json 2023-12-27T16:39:50,222 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/) 2023-12-27T16:39:50,223 Found link https://files.pythonhosted.org/packages/c5/6e/e1aae4079b0ebbce64897f54f5cd4a3953a0cb741026d16e14e7ae272a48/mitos-1.0.tar.gz (from https://pypi.org/simple/mitos/), version: 1.0 2023-12-27T16:39:50,224 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 2023-12-27T16:39:50,224 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 2023-12-27T16:39:50,225 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 2023-12-27T16:39:50,226 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 2023-12-27T16:39:50,227 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 2023-12-27T16:39:50,227 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/) 2023-12-27T16:39:50,228 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 2023-12-27T16:39:50,229 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 2023-12-27T16:39:50,230 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 2023-12-27T16:39:50,230 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 2023-12-27T16:39:50,231 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 2023-12-27T16:39:50,232 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 2023-12-27T16:39:50,232 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 2023-12-27T16:39:50,233 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 2023-12-27T16:39:50,234 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 2023-12-27T16:39:50,234 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 2023-12-27T16:39:50,235 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 2023-12-27T16:39:50,235 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 2023-12-27T16:39:50,236 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/) 2023-12-27T16:39:50,236 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 2023-12-27T16:39:50,237 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 2023-12-27T16:39:50,237 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 2023-12-27T16:39:50,238 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 2023-12-27T16:39:50,239 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 2023-12-27T16:39:50,240 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 2023-12-27T16:39:50,241 Fetching project page and analyzing links: https://www.piwheels.org/simple/mitos/ 2023-12-27T16:39:50,241 Getting page https://www.piwheels.org/simple/mitos/ 2023-12-27T16:39:50,243 Found index url https://www.piwheels.org/simple/ 2023-12-27T16:39:50,395 Fetched page https://www.piwheels.org/simple/mitos/ as text/html 2023-12-27T16:39:50,401 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/) 2023-12-27T16:39:50,402 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/) 2023-12-27T16:39:50,402 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/) 2023-12-27T16:39:50,403 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/) 2023-12-27T16:39:50,404 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/) 2023-12-27T16:39:50,404 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/) 2023-12-27T16:39:50,405 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/) 2023-12-27T16:39:50,405 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/) 2023-12-27T16:39:50,406 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/) 2023-12-27T16:39:50,406 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/) 2023-12-27T16:39:50,407 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/) 2023-12-27T16:39:50,407 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/) 2023-12-27T16:39:50,408 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/) 2023-12-27T16:39:50,408 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/) 2023-12-27T16:39:50,409 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/) 2023-12-27T16:39:50,409 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/) 2023-12-27T16:39:50,410 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/) 2023-12-27T16:39:50,410 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/) 2023-12-27T16:39:50,411 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/) 2023-12-27T16:39:50,412 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/) 2023-12-27T16:39:50,412 Skipping link: not a file: https://www.piwheels.org/simple/mitos/ 2023-12-27T16:39:50,413 Skipping link: not a file: https://pypi.org/simple/mitos/ 2023-12-27T16:39:50,436 Given no hashes to check 1 links for project 'mitos': discarding no candidates 2023-12-27T16:39:50,455 Collecting mitos==2.1.4 2023-12-27T16:39:50,458 Created temporary directory: /tmp/pip-unpack-6e7d38rl 2023-12-27T16:39:50,833 Downloading mitos-2.1.4.tar.gz (278 kB) 2023-12-27T16:39:51,108 Added mitos==2.1.4 from https://files.pythonhosted.org/packages/ff/1f/af7beaaaa133f2f55cdbfbf5430c0e9a3102b101dd0a8d2c6f22376af56b/mitos-2.1.4.tar.gz to build tracker '/tmp/pip-build-tracker-j6o7r1zb' 2023-12-27T16:39:51,110 Running setup.py (path:/tmp/pip-wheel-aeo_f2us/mitos_fe47385c8f7a43faa7c720ba8ebed566/setup.py) egg_info for package mitos 2023-12-27T16:39:51,111 Created temporary directory: /tmp/pip-pip-egg-info-q12nu4rw 2023-12-27T16:39:51,111 Preparing metadata (setup.py): started 2023-12-27T16:39:51,113 Running command python setup.py egg_info 2023-12-27T16:39:51,983 running egg_info 2023-12-27T16:39:51,984 creating /tmp/pip-pip-egg-info-q12nu4rw/mitos.egg-info 2023-12-27T16:39:52,009 writing /tmp/pip-pip-egg-info-q12nu4rw/mitos.egg-info/PKG-INFO 2023-12-27T16:39:52,012 writing dependency_links to /tmp/pip-pip-egg-info-q12nu4rw/mitos.egg-info/dependency_links.txt 2023-12-27T16:39:52,013 writing requirements to /tmp/pip-pip-egg-info-q12nu4rw/mitos.egg-info/requires.txt 2023-12-27T16:39:52,014 writing top-level names to /tmp/pip-pip-egg-info-q12nu4rw/mitos.egg-info/top_level.txt 2023-12-27T16:39:52,016 writing manifest file '/tmp/pip-pip-egg-info-q12nu4rw/mitos.egg-info/SOURCES.txt' 2023-12-27T16:39:52,136 reading manifest file '/tmp/pip-pip-egg-info-q12nu4rw/mitos.egg-info/SOURCES.txt' 2023-12-27T16:39:52,138 reading manifest template 'MANIFEST.in' 2023-12-27T16:39:52,139 warning: no files found matching 'mitos/codons/gc.prt' 2023-12-27T16:39:52,141 adding license file 'LICENSE' 2023-12-27T16:39:52,144 writing manifest file '/tmp/pip-pip-egg-info-q12nu4rw/mitos.egg-info/SOURCES.txt' 2023-12-27T16:39:52,243 Preparing metadata (setup.py): finished with status 'done' 2023-12-27T16:39:52,247 Source in /tmp/pip-wheel-aeo_f2us/mitos_fe47385c8f7a43faa7c720ba8ebed566 has version 2.1.4, which satisfies requirement mitos==2.1.4 from https://files.pythonhosted.org/packages/ff/1f/af7beaaaa133f2f55cdbfbf5430c0e9a3102b101dd0a8d2c6f22376af56b/mitos-2.1.4.tar.gz 2023-12-27T16:39:52,248 Removed mitos==2.1.4 from https://files.pythonhosted.org/packages/ff/1f/af7beaaaa133f2f55cdbfbf5430c0e9a3102b101dd0a8d2c6f22376af56b/mitos-2.1.4.tar.gz from build tracker '/tmp/pip-build-tracker-j6o7r1zb' 2023-12-27T16:39:52,252 Created temporary directory: /tmp/pip-unpack-nqgmgpui 2023-12-27T16:39:52,253 Created temporary directory: /tmp/pip-unpack-ddbu449h 2023-12-27T16:39:52,257 Building wheels for collected packages: mitos 2023-12-27T16:39:52,261 Created temporary directory: /tmp/pip-wheel-2dwjhmdi 2023-12-27T16:39:52,262 Building wheel for mitos (setup.py): started 2023-12-27T16:39:52,263 Destination directory: /tmp/pip-wheel-2dwjhmdi 2023-12-27T16:39:52,264 Running command python setup.py bdist_wheel 2023-12-27T16:39:53,075 running bdist_wheel 2023-12-27T16:39:53,207 running build 2023-12-27T16:39:53,207 running build_py 2023-12-27T16:39:53,236 creating build 2023-12-27T16:39:53,236 creating build/lib 2023-12-27T16:39:53,237 creating build/lib/mitos 2023-12-27T16:39:53,239 copying mitos/cmsearch_parse_separate.py -> build/lib/mitos 2023-12-27T16:39:53,241 copying mitos/merge_results.py -> build/lib/mitos 2023-12-27T16:39:53,243 copying mitos/mitoch_revisions.py -> build/lib/mitos 2023-12-27T16:39:53,246 copying mitos/trna-cm.py -> build/lib/mitos 2023-12-27T16:39:53,250 copying mitos/__init__.py -> build/lib/mitos 2023-12-27T16:39:53,252 copying mitos/mitoloc.py -> build/lib/mitos 2023-12-27T16:39:53,254 copying mitos/removegene.py -> build/lib/mitos 2023-12-27T16:39:53,256 copying mitos/convert_tree.py -> build/lib/mitos 2023-12-27T16:39:53,258 copying mitos/prepareFiles.py -> build/lib/mitos 2023-12-27T16:39:53,260 copying mitos/names.py -> build/lib/mitos 2023-12-27T16:39:53,262 copying mitos/CONFIG.py -> build/lib/mitos 2023-12-27T16:39:53,264 copying mitos/trnascan_parse_separate.py -> build/lib/mitos 2023-12-27T16:39:53,266 copying mitos/mitos-extension.py -> build/lib/mitos 2023-12-27T16:39:53,268 copying mitos/trnadist.py -> build/lib/mitos 2023-12-27T16:39:53,271 copying mitos/get-wancy.py -> build/lib/mitos 2023-12-27T16:39:53,273 copying mitos/create_prot_fasta.py -> build/lib/mitos 2023-12-27T16:39:53,275 copying mitos/codoncount.py -> build/lib/mitos 2023-12-27T16:39:53,276 copying mitos/skew.py -> build/lib/mitos 2023-12-27T16:39:53,279 copying mitos/mitos-extension2.py -> build/lib/mitos 2023-12-27T16:39:53,281 copying mitos/ogre-geneorder.py -> build/lib/mitos 2023-12-27T16:39:53,283 copying mitos/inihit.py -> build/lib/mitos 2023-12-27T16:39:53,285 copying mitos/booreparser.py -> build/lib/mitos 2023-12-27T16:39:53,287 copying mitos/mumcmp.py -> build/lib/mitos 2023-12-27T16:39:53,289 copying mitos/update-mitolog.py -> build/lib/mitos 2023-12-27T16:39:53,291 creating build/lib/mitos/mitofile 2023-12-27T16:39:53,292 copying mitos/mitofile/__init__.py -> build/lib/mitos/mitofile 2023-12-27T16:39:53,295 creating build/lib/mitos/gfffile 2023-12-27T16:39:53,295 copying mitos/gfffile/__init__.py -> build/lib/mitos/gfffile 2023-12-27T16:39:53,298 creating build/lib/mitos/sequin 2023-12-27T16:39:53,298 copying mitos/sequin/__init__.py -> build/lib/mitos/sequin 2023-12-27T16:39:53,301 creating build/lib/mitos/bedfile 2023-12-27T16:39:53,301 copying mitos/bedfile/__init__.py -> build/lib/mitos/bedfile 2023-12-27T16:39:53,304 creating build/lib/mitos/tax 2023-12-27T16:39:53,305 copying mitos/tax/__init__.py -> build/lib/mitos/tax 2023-12-27T16:39:53,307 creating build/lib/mitos/mito 2023-12-27T16:39:53,308 copying mitos/mito/__init__.py -> build/lib/mitos/mito 2023-12-27T16:39:53,311 creating build/lib/mitos/blast 2023-12-27T16:39:53,312 copying mitos/blast/__init__.py -> build/lib/mitos/blast 2023-12-27T16:39:53,316 creating build/lib/mitos/draw 2023-12-27T16:39:53,316 copying mitos/draw/__init__.py -> build/lib/mitos/draw 2023-12-27T16:39:53,319 creating build/lib/mitos/protfeat 2023-12-27T16:39:53,320 copying mitos/protfeat/__init__.py -> build/lib/mitos/protfeat 2023-12-27T16:39:53,323 creating build/lib/mitos/gb 2023-12-27T16:39:53,324 copying mitos/gb/__init__.py -> build/lib/mitos/gb 2023-12-27T16:39:53,327 copying mitos/gb/unify.py -> build/lib/mitos/gb 2023-12-27T16:39:53,329 creating build/lib/mitos/tbl 2023-12-27T16:39:53,331 copying mitos/tbl/__init__.py -> build/lib/mitos/tbl 2023-12-27T16:39:53,333 creating build/lib/mitos/rna 2023-12-27T16:39:53,334 copying mitos/rna/__init__.py -> build/lib/mitos/rna 2023-12-27T16:39:53,336 copying mitos/rna/vienna.py -> build/lib/mitos/rna 2023-12-27T16:39:53,338 copying mitos/rna/forester.py -> build/lib/mitos/rna 2023-12-27T16:39:53,341 creating build/lib/mitos/extprog 2023-12-27T16:39:53,342 copying mitos/extprog/__init__.py -> build/lib/mitos/extprog 2023-12-27T16:39:53,344 creating build/lib/mitos/update 2023-12-27T16:39:53,345 copying mitos/update/__init__.py -> build/lib/mitos/update 2023-12-27T16:39:53,348 creating build/lib/mitos/webserver 2023-12-27T16:39:53,349 copying mitos/webserver/__init__.py -> build/lib/mitos/webserver 2023-12-27T16:39:53,352 creating build/lib/mitos/feature 2023-12-27T16:39:53,353 copying mitos/feature/__init__.py -> build/lib/mitos/feature 2023-12-27T16:39:53,356 creating build/lib/mitos/trna 2023-12-27T16:39:53,357 copying mitos/trna/arwenscan.py -> build/lib/mitos/trna 2023-12-27T16:39:53,360 copying mitos/trna/trnascan.py -> build/lib/mitos/trna 2023-12-27T16:39:53,362 copying mitos/trna/__init__.py -> build/lib/mitos/trna 2023-12-27T16:39:53,364 creating build/lib/mitos/mitfi 2023-12-27T16:39:53,365 copying mitos/mitfi/__init__.py -> build/lib/mitos/mitfi 2023-12-27T16:39:53,368 creating build/lib/mitos/util 2023-12-27T16:39:53,369 copying mitos/util/__init__.py -> build/lib/mitos/util 2023-12-27T16:39:53,371 creating build/lib/mitos/mergefeature 2023-12-27T16:39:53,372 copying mitos/mergefeature/__init__.py -> build/lib/mitos/mergefeature 2023-12-27T16:39:53,375 creating build/lib/mitos/sequence 2023-12-27T16:39:53,375 copying mitos/sequence/__init__.py -> build/lib/mitos/sequence 2023-12-27T16:39:53,378 copying mitos/sequence/degenerate.py -> build/lib/mitos/sequence 2023-12-27T16:39:53,379 running egg_info 2023-12-27T16:39:53,404 writing mitos.egg-info/PKG-INFO 2023-12-27T16:39:53,407 writing dependency_links to mitos.egg-info/dependency_links.txt 2023-12-27T16:39:53,408 writing requirements to mitos.egg-info/requires.txt 2023-12-27T16:39:53,410 writing top-level names to mitos.egg-info/top_level.txt 2023-12-27T16:39:53,451 reading manifest file 'mitos.egg-info/SOURCES.txt' 2023-12-27T16:39:53,455 reading manifest template 'MANIFEST.in' 2023-12-27T16:39:53,455 warning: no files found matching 'mitos/codons/gc.prt' 2023-12-27T16:39:53,457 adding license file 'LICENSE' 2023-12-27T16:39:53,462 writing manifest file 'mitos.egg-info/SOURCES.txt' 2023-12-27T16:39:53,464 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'mitos.mitfi.parser' is absent from the `packages` configuration. 2023-12-27T16:39:53,465 !! 2023-12-27T16:39:53,466 ******************************************************************************** 2023-12-27T16:39:53,466 ############################ 2023-12-27T16:39:53,467 # Package would be ignored # 2023-12-27T16:39:53,467 ############################ 2023-12-27T16:39:53,468 Python recognizes 'mitos.mitfi.parser' as an importable package[^1], 2023-12-27T16:39:53,468 but it is absent from setuptools' `packages` configuration. 2023-12-27T16:39:53,470 This leads to an ambiguous overall configuration. If you want to distribute this 2023-12-27T16:39:53,470 package, please make sure that 'mitos.mitfi.parser' is explicitly added 2023-12-27T16:39:53,471 to the `packages` configuration field. 2023-12-27T16:39:53,472 Alternatively, you can also rely on setuptools' discovery methods 2023-12-27T16:39:53,472 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-12-27T16:39:53,473 instead of `find_packages(...)`/`find:`). 2023-12-27T16:39:53,474 You can read more about "package discovery" on setuptools documentation page: 2023-12-27T16:39:53,475 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-12-27T16:39:53,476 If you don't want 'mitos.mitfi.parser' to be distributed and are 2023-12-27T16:39:53,476 already explicitly excluding 'mitos.mitfi.parser' via 2023-12-27T16:39:53,477 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-12-27T16:39:53,477 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-12-27T16:39:53,478 combination with a more fine grained `package-data` configuration. 2023-12-27T16:39:53,479 You can read more about "package data files" on setuptools documentation page: 2023-12-27T16:39:53,480 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-12-27T16:39:53,481 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-12-27T16:39:53,482 even if it does not contain any `.py` files. 2023-12-27T16:39:53,482 On the other hand, currently there is no concept of package data 2023-12-27T16:39:53,483 directory, all directories are treated like packages. 2023-12-27T16:39:53,484 ******************************************************************************** 2023-12-27T16:39:53,484 !! 2023-12-27T16:39:53,485 check.warn(importable) 2023-12-27T16:39:53,485 copying mitos/plotprot.R -> build/lib/mitos 2023-12-27T16:39:53,486 copying mitos/plotrna.R -> build/lib/mitos 2023-12-27T16:39:53,486 copying mitos/plotstst.R -> build/lib/mitos 2023-12-27T16:39:53,487 copying mitos/webserver/help.txt -> build/lib/mitos/webserver 2023-12-27T16:39:53,490 copying mitos/webserver/history.txt -> build/lib/mitos/webserver 2023-12-27T16:39:53,491 copying mitos/webserver/index.txt -> build/lib/mitos/webserver 2023-12-27T16:39:53,494 copying mitos/webserver/news.txt -> build/lib/mitos/webserver 2023-12-27T16:39:53,495 copying mitos/webserver/upload.txt -> build/lib/mitos/webserver 2023-12-27T16:39:53,497 copying mitos/webserver/wait.txt -> build/lib/mitos/webserver 2023-12-27T16:39:53,499 creating build/lib/mitos/mitfi/parser 2023-12-27T16:39:53,500 copying mitos/mitfi/parser/improve_infernal_structure.jar -> build/lib/mitos/mitfi/parser 2023-12-27T16:39:53,502 copying mitos/mitfi/parser/mitfiGeneticCodes -> build/lib/mitos/mitfi/parser 2023-12-27T16:39:53,505 copying mitos/mitfi/parser/mitfi_import-1.1.jar -> build/lib/mitos/mitfi/parser 2023-12-27T16:39:53,507 copying mitos/mitfi/parser/mitfi_import-1.1.jar.old -> build/lib/mitos/mitfi/parser 2023-12-27T16:39:53,510 copying mitos/mitfi/parser/mitfi_import-1.1.jar.org -> build/lib/mitos/mitfi/parser 2023-12-27T16:39:53,513 copying mitos/mitfi/parser/mitfi_import-1.1.jar.org.pre-circ -> build/lib/mitos/mitfi/parser 2023-12-27T16:39:53,516 copying mitos/mitfi/parser/mitfi_import.jar -> build/lib/mitos/mitfi/parser 2023-12-27T16:39:53,525 running build_scripts 2023-12-27T16:39:53,526 creating build/scripts-3.11 2023-12-27T16:39:53,527 copying and adjusting runmitos.py -> build/scripts-3.11 2023-12-27T16:39:53,531 copying and adjusting drawmitos.py -> build/scripts-3.11 2023-12-27T16:39:53,532 copying and adjusting analyse.py -> build/scripts-3.11 2023-12-27T16:39:53,534 copying and adjusting gcpp.py -> build/scripts-3.11 2023-12-27T16:39:53,536 copying and adjusting geneorder.py -> build/scripts-3.11 2023-12-27T16:39:53,539 copying and adjusting getfeatures.py -> build/scripts-3.11 2023-12-27T16:39:53,540 copying and adjusting getinfo.py -> build/scripts-3.11 2023-12-27T16:39:53,542 copying and adjusting refseqsplit.py -> build/scripts-3.11 2023-12-27T16:39:53,543 copying and adjusting subseq.py -> build/scripts-3.11 2023-12-27T16:39:53,545 copying and adjusting taxtree.py -> build/scripts-3.11 2023-12-27T16:39:53,547 copying update-blastdb.py -> build/scripts-3.11 2023-12-27T16:39:53,549 copying mitos/plotprot.R -> build/scripts-3.11 2023-12-27T16:39:53,551 copying mitos/plotstst.R -> build/scripts-3.11 2023-12-27T16:39:53,554 copying mitos/plotrna.R -> build/scripts-3.11 2023-12-27T16:39:53,555 changing mode of build/scripts-3.11/runmitos.py from 644 to 755 2023-12-27T16:39:53,556 changing mode of build/scripts-3.11/drawmitos.py from 644 to 755 2023-12-27T16:39:53,556 changing mode of build/scripts-3.11/analyse.py from 644 to 755 2023-12-27T16:39:53,557 changing mode of build/scripts-3.11/gcpp.py from 644 to 755 2023-12-27T16:39:53,557 changing mode of build/scripts-3.11/geneorder.py from 644 to 755 2023-12-27T16:39:53,558 changing mode of build/scripts-3.11/getfeatures.py from 644 to 755 2023-12-27T16:39:53,558 changing mode of build/scripts-3.11/getinfo.py from 644 to 755 2023-12-27T16:39:53,559 changing mode of build/scripts-3.11/refseqsplit.py from 644 to 755 2023-12-27T16:39:53,559 changing mode of build/scripts-3.11/subseq.py from 644 to 755 2023-12-27T16:39:53,560 changing mode of build/scripts-3.11/taxtree.py from 644 to 755 2023-12-27T16:39:53,561 changing mode of build/scripts-3.11/update-blastdb.py from 644 to 755 2023-12-27T16:39:53,585 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-12-27T16:39:53,586 !! 2023-12-27T16:39:53,586 ******************************************************************************** 2023-12-27T16:39:53,587 Please avoid running ``setup.py`` directly. 2023-12-27T16:39:53,587 Instead, use pypa/build, pypa/installer or other 2023-12-27T16:39:53,588 standards-based tools. 2023-12-27T16:39:53,589 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-12-27T16:39:53,589 ******************************************************************************** 2023-12-27T16:39:53,590 !! 2023-12-27T16:39:53,590 self.initialize_options() 2023-12-27T16:39:53,611 installing to build/bdist.linux-armv7l/wheel 2023-12-27T16:39:53,612 running install 2023-12-27T16:39:53,636 running install_lib 2023-12-27T16:39:53,661 creating build/bdist.linux-armv7l 2023-12-27T16:39:53,662 creating build/bdist.linux-armv7l/wheel 2023-12-27T16:39:53,664 creating build/bdist.linux-armv7l/wheel/mitos 2023-12-27T16:39:53,664 copying build/lib/mitos/cmsearch_parse_separate.py -> build/bdist.linux-armv7l/wheel/mitos 2023-12-27T16:39:53,666 copying build/lib/mitos/merge_results.py -> build/bdist.linux-armv7l/wheel/mitos 2023-12-27T16:39:53,669 creating build/bdist.linux-armv7l/wheel/mitos/mitofile 2023-12-27T16:39:53,670 copying build/lib/mitos/mitofile/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/mitofile 2023-12-27T16:39:53,672 creating build/bdist.linux-armv7l/wheel/mitos/gfffile 2023-12-27T16:39:53,673 copying build/lib/mitos/gfffile/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/gfffile 2023-12-27T16:39:53,675 creating build/bdist.linux-armv7l/wheel/mitos/sequin 2023-12-27T16:39:53,676 copying build/lib/mitos/sequin/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/sequin 2023-12-27T16:39:53,678 creating build/bdist.linux-armv7l/wheel/mitos/bedfile 2023-12-27T16:39:53,679 copying build/lib/mitos/bedfile/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/bedfile 2023-12-27T16:39:53,682 creating build/bdist.linux-armv7l/wheel/mitos/tax 2023-12-27T16:39:53,682 copying build/lib/mitos/tax/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/tax 2023-12-27T16:39:53,684 copying build/lib/mitos/mitoch_revisions.py -> build/bdist.linux-armv7l/wheel/mitos 2023-12-27T16:39:53,687 copying build/lib/mitos/trna-cm.py -> build/bdist.linux-armv7l/wheel/mitos 2023-12-27T16:39:53,692 copying build/lib/mitos/__init__.py -> build/bdist.linux-armv7l/wheel/mitos 2023-12-27T16:39:53,693 copying build/lib/mitos/mitoloc.py -> build/bdist.linux-armv7l/wheel/mitos 2023-12-27T16:39:53,695 copying build/lib/mitos/removegene.py -> build/bdist.linux-armv7l/wheel/mitos 2023-12-27T16:39:53,697 creating build/bdist.linux-armv7l/wheel/mitos/mito 2023-12-27T16:39:53,698 copying build/lib/mitos/mito/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/mito 2023-12-27T16:39:53,701 creating build/bdist.linux-armv7l/wheel/mitos/blast 2023-12-27T16:39:53,702 copying build/lib/mitos/blast/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/blast 2023-12-27T16:39:53,706 creating build/bdist.linux-armv7l/wheel/mitos/draw 2023-12-27T16:39:53,707 copying build/lib/mitos/draw/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/draw 2023-12-27T16:39:53,710 copying build/lib/mitos/convert_tree.py -> build/bdist.linux-armv7l/wheel/mitos 2023-12-27T16:39:53,712 copying build/lib/mitos/prepareFiles.py -> build/bdist.linux-armv7l/wheel/mitos 2023-12-27T16:39:53,714 copying build/lib/mitos/names.py -> build/bdist.linux-armv7l/wheel/mitos 2023-12-27T16:39:53,716 creating build/bdist.linux-armv7l/wheel/mitos/protfeat 2023-12-27T16:39:53,717 copying build/lib/mitos/protfeat/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/protfeat 2023-12-27T16:39:53,720 copying build/lib/mitos/CONFIG.py -> build/bdist.linux-armv7l/wheel/mitos 2023-12-27T16:39:53,722 copying build/lib/mitos/trnascan_parse_separate.py -> build/bdist.linux-armv7l/wheel/mitos 2023-12-27T16:39:53,724 copying build/lib/mitos/mitos-extension.py -> build/bdist.linux-armv7l/wheel/mitos 2023-12-27T16:39:53,726 copying build/lib/mitos/trnadist.py -> build/bdist.linux-armv7l/wheel/mitos 2023-12-27T16:39:53,729 copying build/lib/mitos/get-wancy.py -> build/bdist.linux-armv7l/wheel/mitos 2023-12-27T16:39:53,731 creating build/bdist.linux-armv7l/wheel/mitos/gb 2023-12-27T16:39:53,732 copying build/lib/mitos/gb/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/gb 2023-12-27T16:39:53,735 copying build/lib/mitos/gb/unify.py -> build/bdist.linux-armv7l/wheel/mitos/gb 2023-12-27T16:39:53,737 creating build/bdist.linux-armv7l/wheel/mitos/tbl 2023-12-27T16:39:53,738 copying build/lib/mitos/tbl/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/tbl 2023-12-27T16:39:53,741 creating build/bdist.linux-armv7l/wheel/mitos/rna 2023-12-27T16:39:53,741 copying build/lib/mitos/rna/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/rna 2023-12-27T16:39:53,743 copying build/lib/mitos/rna/vienna.py -> build/bdist.linux-armv7l/wheel/mitos/rna 2023-12-27T16:39:53,745 copying build/lib/mitos/rna/forester.py -> build/bdist.linux-armv7l/wheel/mitos/rna 2023-12-27T16:39:53,747 copying build/lib/mitos/plotstst.R -> build/bdist.linux-armv7l/wheel/mitos 2023-12-27T16:39:53,749 copying build/lib/mitos/create_prot_fasta.py -> build/bdist.linux-armv7l/wheel/mitos 2023-12-27T16:39:53,752 creating build/bdist.linux-armv7l/wheel/mitos/extprog 2023-12-27T16:39:53,753 copying build/lib/mitos/extprog/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/extprog 2023-12-27T16:39:53,755 creating build/bdist.linux-armv7l/wheel/mitos/update 2023-12-27T16:39:53,756 copying build/lib/mitos/update/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/update 2023-12-27T16:39:53,760 creating build/bdist.linux-armv7l/wheel/mitos/webserver 2023-12-27T16:39:53,760 copying build/lib/mitos/webserver/news.txt -> build/bdist.linux-armv7l/wheel/mitos/webserver 2023-12-27T16:39:53,762 copying build/lib/mitos/webserver/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/webserver 2023-12-27T16:39:53,764 copying build/lib/mitos/webserver/index.txt -> build/bdist.linux-armv7l/wheel/mitos/webserver 2023-12-27T16:39:53,767 copying build/lib/mitos/webserver/upload.txt -> build/bdist.linux-armv7l/wheel/mitos/webserver 2023-12-27T16:39:53,768 copying build/lib/mitos/webserver/history.txt -> build/bdist.linux-armv7l/wheel/mitos/webserver 2023-12-27T16:39:53,770 copying build/lib/mitos/webserver/wait.txt -> build/bdist.linux-armv7l/wheel/mitos/webserver 2023-12-27T16:39:53,772 copying build/lib/mitos/webserver/help.txt -> build/bdist.linux-armv7l/wheel/mitos/webserver 2023-12-27T16:39:53,775 creating build/bdist.linux-armv7l/wheel/mitos/feature 2023-12-27T16:39:53,776 copying build/lib/mitos/feature/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/feature 2023-12-27T16:39:53,779 copying build/lib/mitos/codoncount.py -> build/bdist.linux-armv7l/wheel/mitos 2023-12-27T16:39:53,781 copying build/lib/mitos/skew.py -> build/bdist.linux-armv7l/wheel/mitos 2023-12-27T16:39:53,783 copying build/lib/mitos/plotprot.R -> build/bdist.linux-armv7l/wheel/mitos 2023-12-27T16:39:53,785 copying build/lib/mitos/mitos-extension2.py -> build/bdist.linux-armv7l/wheel/mitos 2023-12-27T16:39:53,788 creating build/bdist.linux-armv7l/wheel/mitos/trna 2023-12-27T16:39:53,789 copying build/lib/mitos/trna/arwenscan.py -> build/bdist.linux-armv7l/wheel/mitos/trna 2023-12-27T16:39:53,791 copying build/lib/mitos/trna/trnascan.py -> build/bdist.linux-armv7l/wheel/mitos/trna 2023-12-27T16:39:53,794 copying build/lib/mitos/trna/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/trna 2023-12-27T16:39:53,796 copying build/lib/mitos/ogre-geneorder.py -> build/bdist.linux-armv7l/wheel/mitos 2023-12-27T16:39:53,798 creating build/bdist.linux-armv7l/wheel/mitos/mitfi 2023-12-27T16:39:53,799 copying build/lib/mitos/mitfi/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/mitfi 2023-12-27T16:39:53,802 creating build/bdist.linux-armv7l/wheel/mitos/mitfi/parser 2023-12-27T16:39:53,803 copying build/lib/mitos/mitfi/parser/improve_infernal_structure.jar -> build/bdist.linux-armv7l/wheel/mitos/mitfi/parser 2023-12-27T16:39:53,805 copying build/lib/mitos/mitfi/parser/mitfi_import-1.1.jar.old -> build/bdist.linux-armv7l/wheel/mitos/mitfi/parser 2023-12-27T16:39:53,808 copying build/lib/mitos/mitfi/parser/mitfiGeneticCodes -> build/bdist.linux-armv7l/wheel/mitos/mitfi/parser 2023-12-27T16:39:53,811 copying build/lib/mitos/mitfi/parser/mitfi_import-1.1.jar.org.pre-circ -> build/bdist.linux-armv7l/wheel/mitos/mitfi/parser 2023-12-27T16:39:53,813 copying build/lib/mitos/mitfi/parser/mitfi_import-1.1.jar -> build/bdist.linux-armv7l/wheel/mitos/mitfi/parser 2023-12-27T16:39:53,816 copying build/lib/mitos/mitfi/parser/mitfi_import.jar -> build/bdist.linux-armv7l/wheel/mitos/mitfi/parser 2023-12-27T16:39:53,819 copying build/lib/mitos/mitfi/parser/mitfi_import-1.1.jar.org -> build/bdist.linux-armv7l/wheel/mitos/mitfi/parser 2023-12-27T16:39:53,821 copying build/lib/mitos/inihit.py -> build/bdist.linux-armv7l/wheel/mitos 2023-12-27T16:39:53,823 copying build/lib/mitos/plotrna.R -> build/bdist.linux-armv7l/wheel/mitos 2023-12-27T16:39:53,825 copying build/lib/mitos/booreparser.py -> build/bdist.linux-armv7l/wheel/mitos 2023-12-27T16:39:53,827 copying build/lib/mitos/mumcmp.py -> build/bdist.linux-armv7l/wheel/mitos 2023-12-27T16:39:53,829 creating build/bdist.linux-armv7l/wheel/mitos/util 2023-12-27T16:39:53,830 copying build/lib/mitos/util/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/util 2023-12-27T16:39:53,832 creating build/bdist.linux-armv7l/wheel/mitos/mergefeature 2023-12-27T16:39:53,833 copying build/lib/mitos/mergefeature/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/mergefeature 2023-12-27T16:39:53,836 copying build/lib/mitos/update-mitolog.py -> build/bdist.linux-armv7l/wheel/mitos 2023-12-27T16:39:53,839 creating build/bdist.linux-armv7l/wheel/mitos/sequence 2023-12-27T16:39:53,840 copying build/lib/mitos/sequence/__init__.py -> build/bdist.linux-armv7l/wheel/mitos/sequence 2023-12-27T16:39:53,842 copying build/lib/mitos/sequence/degenerate.py -> build/bdist.linux-armv7l/wheel/mitos/sequence 2023-12-27T16:39:53,844 running install_egg_info 2023-12-27T16:39:53,875 Copying mitos.egg-info to build/bdist.linux-armv7l/wheel/mitos-2.1.4-py3.11.egg-info 2023-12-27T16:39:53,884 running install_scripts 2023-12-27T16:39:53,886 creating build/bdist.linux-armv7l/wheel/mitos-2.1.4.data 2023-12-27T16:39:53,886 creating build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts 2023-12-27T16:39:53,887 copying build/scripts-3.11/subseq.py -> build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts 2023-12-27T16:39:53,890 copying build/scripts-3.11/runmitos.py -> build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts 2023-12-27T16:39:53,894 copying build/scripts-3.11/drawmitos.py -> build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts 2023-12-27T16:39:53,896 copying build/scripts-3.11/getfeatures.py -> build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts 2023-12-27T16:39:53,898 copying build/scripts-3.11/getinfo.py -> build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts 2023-12-27T16:39:53,900 copying build/scripts-3.11/update-blastdb.py -> build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts 2023-12-27T16:39:53,902 copying build/scripts-3.11/plotstst.R -> build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts 2023-12-27T16:39:53,905 copying build/scripts-3.11/taxtree.py -> build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts 2023-12-27T16:39:53,907 copying build/scripts-3.11/analyse.py -> build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts 2023-12-27T16:39:53,909 copying build/scripts-3.11/refseqsplit.py -> build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts 2023-12-27T16:39:53,911 copying build/scripts-3.11/plotprot.R -> build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts 2023-12-27T16:39:53,913 copying build/scripts-3.11/gcpp.py -> build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts 2023-12-27T16:39:53,915 copying build/scripts-3.11/plotrna.R -> build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts 2023-12-27T16:39:53,917 copying build/scripts-3.11/geneorder.py -> build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts 2023-12-27T16:39:53,919 changing mode of build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts/subseq.py to 755 2023-12-27T16:39:53,919 changing mode of build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts/runmitos.py to 755 2023-12-27T16:39:53,920 changing mode of build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts/drawmitos.py to 755 2023-12-27T16:39:53,920 changing mode of build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts/getfeatures.py to 755 2023-12-27T16:39:53,921 changing mode of build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts/getinfo.py to 755 2023-12-27T16:39:53,921 changing mode of build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts/update-blastdb.py to 755 2023-12-27T16:39:53,922 changing mode of build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts/plotstst.R to 755 2023-12-27T16:39:53,922 changing mode of build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts/taxtree.py to 755 2023-12-27T16:39:53,922 changing mode of build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts/analyse.py to 755 2023-12-27T16:39:53,923 changing mode of build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts/refseqsplit.py to 755 2023-12-27T16:39:53,923 changing mode of build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts/plotprot.R to 755 2023-12-27T16:39:53,924 changing mode of build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts/gcpp.py to 755 2023-12-27T16:39:53,924 changing mode of build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts/plotrna.R to 755 2023-12-27T16:39:53,925 changing mode of build/bdist.linux-armv7l/wheel/mitos-2.1.4.data/scripts/geneorder.py to 755 2023-12-27T16:39:53,936 creating build/bdist.linux-armv7l/wheel/mitos-2.1.4.dist-info/WHEEL 2023-12-27T16:39:53,938 creating '/tmp/pip-wheel-2dwjhmdi/mitos-2.1.4-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-12-27T16:39:53,941 adding 'mitos/CONFIG.py' 2023-12-27T16:39:53,943 adding 'mitos/__init__.py' 2023-12-27T16:39:53,944 adding 'mitos/booreparser.py' 2023-12-27T16:39:53,946 adding 'mitos/cmsearch_parse_separate.py' 2023-12-27T16:39:53,947 adding 'mitos/codoncount.py' 2023-12-27T16:39:53,951 adding 'mitos/convert_tree.py' 2023-12-27T16:39:53,953 adding 'mitos/create_prot_fasta.py' 2023-12-27T16:39:53,954 adding 'mitos/get-wancy.py' 2023-12-27T16:39:53,956 adding 'mitos/inihit.py' 2023-12-27T16:39:53,958 adding 'mitos/merge_results.py' 2023-12-27T16:39:53,963 adding 'mitos/mitoch_revisions.py' 2023-12-27T16:39:53,965 adding 'mitos/mitoloc.py' 2023-12-27T16:39:53,967 adding 'mitos/mitos-extension.py' 2023-12-27T16:39:53,969 adding 'mitos/mitos-extension2.py' 2023-12-27T16:39:53,970 adding 'mitos/mumcmp.py' 2023-12-27T16:39:53,972 adding 'mitos/names.py' 2023-12-27T16:39:53,973 adding 'mitos/ogre-geneorder.py' 2023-12-27T16:39:53,974 adding 'mitos/plotprot.R' 2023-12-27T16:39:53,976 adding 'mitos/plotrna.R' 2023-12-27T16:39:53,977 adding 'mitos/plotstst.R' 2023-12-27T16:39:53,979 adding 'mitos/prepareFiles.py' 2023-12-27T16:39:53,980 adding 'mitos/removegene.py' 2023-12-27T16:39:53,982 adding 'mitos/skew.py' 2023-12-27T16:39:53,998 adding 'mitos/trna-cm.py' 2023-12-27T16:39:54,002 adding 'mitos/trnadist.py' 2023-12-27T16:39:54,003 adding 'mitos/trnascan_parse_separate.py' 2023-12-27T16:39:54,005 adding 'mitos/update-mitolog.py' 2023-12-27T16:39:54,007 adding 'mitos/bedfile/__init__.py' 2023-12-27T16:39:54,018 adding 'mitos/blast/__init__.py' 2023-12-27T16:39:54,020 adding 'mitos/draw/__init__.py' 2023-12-27T16:39:54,022 adding 'mitos/extprog/__init__.py' 2023-12-27T16:39:54,028 adding 'mitos/feature/__init__.py' 2023-12-27T16:39:54,034 adding 'mitos/gb/__init__.py' 2023-12-27T16:39:54,036 adding 'mitos/gb/unify.py' 2023-12-27T16:39:54,038 adding 'mitos/gfffile/__init__.py' 2023-12-27T16:39:54,042 adding 'mitos/mergefeature/__init__.py' 2023-12-27T16:39:54,045 adding 'mitos/mitfi/__init__.py' 2023-12-27T16:39:54,047 adding 'mitos/mitfi/parser/improve_infernal_structure.jar' 2023-12-27T16:39:54,049 adding 'mitos/mitfi/parser/mitfiGeneticCodes' 2023-12-27T16:39:54,053 adding 'mitos/mitfi/parser/mitfi_import-1.1.jar' 2023-12-27T16:39:54,057 adding 'mitos/mitfi/parser/mitfi_import-1.1.jar.old' 2023-12-27T16:39:54,060 adding 'mitos/mitfi/parser/mitfi_import-1.1.jar.org' 2023-12-27T16:39:54,064 adding 'mitos/mitfi/parser/mitfi_import-1.1.jar.org.pre-circ' 2023-12-27T16:39:54,068 adding 'mitos/mitfi/parser/mitfi_import.jar' 2023-12-27T16:39:54,070 adding 'mitos/mito/__init__.py' 2023-12-27T16:39:54,072 adding 'mitos/mitofile/__init__.py' 2023-12-27T16:39:54,076 adding 'mitos/protfeat/__init__.py' 2023-12-27T16:39:54,077 adding 'mitos/rna/__init__.py' 2023-12-27T16:39:54,079 adding 'mitos/rna/forester.py' 2023-12-27T16:39:54,081 adding 'mitos/rna/vienna.py' 2023-12-27T16:39:54,085 adding 'mitos/sequence/__init__.py' 2023-12-27T16:39:54,086 adding 'mitos/sequence/degenerate.py' 2023-12-27T16:39:54,087 adding 'mitos/sequin/__init__.py' 2023-12-27T16:39:54,089 adding 'mitos/tax/__init__.py' 2023-12-27T16:39:54,091 adding 'mitos/tbl/__init__.py' 2023-12-27T16:39:54,093 adding 'mitos/trna/__init__.py' 2023-12-27T16:39:54,095 adding 'mitos/trna/arwenscan.py' 2023-12-27T16:39:54,097 adding 'mitos/trna/trnascan.py' 2023-12-27T16:39:54,100 adding 'mitos/update/__init__.py' 2023-12-27T16:39:54,102 adding 'mitos/util/__init__.py' 2023-12-27T16:39:54,105 adding 'mitos/webserver/__init__.py' 2023-12-27T16:39:54,109 adding 'mitos/webserver/help.txt' 2023-12-27T16:39:54,110 adding 'mitos/webserver/history.txt' 2023-12-27T16:39:54,111 adding 'mitos/webserver/index.txt' 2023-12-27T16:39:54,113 adding 'mitos/webserver/news.txt' 2023-12-27T16:39:54,114 adding 'mitos/webserver/upload.txt' 2023-12-27T16:39:54,115 adding 'mitos/webserver/wait.txt' 2023-12-27T16:39:54,118 adding 'mitos-2.1.4.data/scripts/analyse.py' 2023-12-27T16:39:54,119 adding 'mitos-2.1.4.data/scripts/drawmitos.py' 2023-12-27T16:39:54,121 adding 'mitos-2.1.4.data/scripts/gcpp.py' 2023-12-27T16:39:54,123 adding 'mitos-2.1.4.data/scripts/geneorder.py' 2023-12-27T16:39:54,125 adding 'mitos-2.1.4.data/scripts/getfeatures.py' 2023-12-27T16:39:54,126 adding 'mitos-2.1.4.data/scripts/getinfo.py' 2023-12-27T16:39:54,128 adding 'mitos-2.1.4.data/scripts/plotprot.R' 2023-12-27T16:39:54,129 adding 'mitos-2.1.4.data/scripts/plotrna.R' 2023-12-27T16:39:54,130 adding 'mitos-2.1.4.data/scripts/plotstst.R' 2023-12-27T16:39:54,132 adding 'mitos-2.1.4.data/scripts/refseqsplit.py' 2023-12-27T16:39:54,137 adding 'mitos-2.1.4.data/scripts/runmitos.py' 2023-12-27T16:39:54,139 adding 'mitos-2.1.4.data/scripts/subseq.py' 2023-12-27T16:39:54,140 adding 'mitos-2.1.4.data/scripts/taxtree.py' 2023-12-27T16:39:54,142 adding 'mitos-2.1.4.data/scripts/update-blastdb.py' 2023-12-27T16:39:54,144 adding 'mitos-2.1.4.dist-info/LICENSE' 2023-12-27T16:39:54,145 adding 'mitos-2.1.4.dist-info/METADATA' 2023-12-27T16:39:54,145 adding 'mitos-2.1.4.dist-info/WHEEL' 2023-12-27T16:39:54,146 adding 'mitos-2.1.4.dist-info/top_level.txt' 2023-12-27T16:39:54,148 adding 'mitos-2.1.4.dist-info/RECORD' 2023-12-27T16:39:54,153 removing build/bdist.linux-armv7l/wheel 2023-12-27T16:39:54,280 Building wheel for mitos (setup.py): finished with status 'done' 2023-12-27T16:39:54,286 Created wheel for mitos: filename=mitos-2.1.4-py3-none-any.whl size=338606 sha256=249c87e42350fbefa1e3281d0e81f795c7710a95303b226bdc818b51615162e0 2023-12-27T16:39:54,287 Stored in directory: /tmp/pip-ephem-wheel-cache-du7y2_1k/wheels/df/b9/66/71d404889f14c8a75214f2d3e0f318914a4ca3ba6bebba00d3 2023-12-27T16:39:54,300 Successfully built mitos 2023-12-27T16:39:54,315 Removed build tracker: '/tmp/pip-build-tracker-j6o7r1zb'