2020-07-10T20:31:11,849 Created temporary directory: /tmp/pip-ephem-wheel-cache-l2k5kpld
2020-07-10T20:31:11,853 Created temporary directory: /tmp/pip-req-tracker-3riayoip
2020-07-10T20:31:11,854 Initialized build tracking at /tmp/pip-req-tracker-3riayoip
2020-07-10T20:31:11,856 Created build tracker: /tmp/pip-req-tracker-3riayoip
2020-07-10T20:31:11,856 Entered build tracker: /tmp/pip-req-tracker-3riayoip
2020-07-10T20:31:11,858 Created temporary directory: /tmp/pip-wheel-z0gk5hkm
2020-07-10T20:31:11,873 1 location(s) to search for versions of pubrunner:
2020-07-10T20:31:11,873 * https://pypi.org/simple/pubrunner/
2020-07-10T20:31:11,874 Fetching project page and analyzing links: https://pypi.org/simple/pubrunner/
2020-07-10T20:31:11,876 Getting page https://pypi.org/simple/pubrunner/
2020-07-10T20:31:11,880 Found index url https://pypi.org/simple
2020-07-10T20:31:12,243   Found link https://files.pythonhosted.org/packages/6c/6a/f4513b14bf4b854168da41463202748b7b83e30620bcbf9b7383b296ab6f/pubrunner-0.1.0.tar.gz#sha256=be2491692e40e08ce626952036cdb86ae8203feb731dd5edc7bc8bca8bd0f40e (from https://pypi.org/simple/pubrunner/), version: 0.1.0
2020-07-10T20:31:12,244   Found link https://files.pythonhosted.org/packages/2e/2e/c0afbe541e12079600714dda307e94e588aec4922b090dfc6291165279e7/pubrunner-0.1.1.tar.gz#sha256=376b64a184629c36913e327df57c907643edd74d8674b2a93a704afb818012d8 (from https://pypi.org/simple/pubrunner/), version: 0.1.1
2020-07-10T20:31:12,245   Found link https://files.pythonhosted.org/packages/cf/f4/9f91597f3cb2696b925a00deccccf12264581673d0bb3e5227a4e71df0a6/pubrunner-0.1.2.tar.gz#sha256=62f31647a9f2ab1159873ed3d8599ef18155f56cd3528af77f6ced4f98071860 (from https://pypi.org/simple/pubrunner/), version: 0.1.2
2020-07-10T20:31:12,246   Found link https://files.pythonhosted.org/packages/5a/fd/22d3d1c74696d65a22840664bf801293c88d4c90a333e644924166808fe3/pubrunner-0.1.3.tar.gz#sha256=14571a822b12f518da29fe5ebb3cd5944be1725011bbb8f8ca34cacb28ca2a64 (from https://pypi.org/simple/pubrunner/), version: 0.1.3
2020-07-10T20:31:12,247   Found link https://files.pythonhosted.org/packages/91/35/a1241e6b019f5e0f2f6d45ca07b625abe6eb5b30d6e896360fae9f2d7a2e/pubrunner-0.1.4.tar.gz#sha256=7e395d8c49c5045bc4d117ad022e38c97861d3de796e0d0318d90c753895ac13 (from https://pypi.org/simple/pubrunner/), version: 0.1.4
2020-07-10T20:31:12,248   Found link https://files.pythonhosted.org/packages/d1/b1/46b464a545a276af16dc8a47a166fbe735206d7f462886355a81c18ef514/pubrunner-0.2.0.tar.gz#sha256=f7f81b4ad16d9a552c22c1d31e55c02c60392f535b3e16450ea8c2aa8e258f77 (from https://pypi.org/simple/pubrunner/), version: 0.2.0
2020-07-10T20:31:12,249   Found link https://files.pythonhosted.org/packages/29/47/732d656446cd15808d0da8449d38c2934567c1042a269c90ca4e8b104a57/pubrunner-0.2.1.tar.gz#sha256=b5cb2f084133ca05786c5af71ac535dc4a6ce7b0b1119fb5fe2ee402c9372aef (from https://pypi.org/simple/pubrunner/), version: 0.2.1
2020-07-10T20:31:12,250   Found link https://files.pythonhosted.org/packages/cb/76/0c5a020ce4a75d492169b84f556b9fa8fe2bbcca2cef06e30bb0e0e4c77b/pubrunner-0.2.2.tar.gz#sha256=0dfa2d818cc18c8a7462806314aef7f827e1e69be7e7c20bbdb843da2b52d79d (from https://pypi.org/simple/pubrunner/), version: 0.2.2
2020-07-10T20:31:12,250   Found link https://files.pythonhosted.org/packages/e1/cc/d0724faf35d387b9d0dfc5abe82364b41a427e39a277c87e0fc35d24b559/pubrunner-0.2.3.tar.gz#sha256=62d04ab630e7176f009c97361b8961d19268d6c2828657b449481b2e917abe44 (from https://pypi.org/simple/pubrunner/), version: 0.2.3
2020-07-10T20:31:12,251   Found link https://files.pythonhosted.org/packages/95/ce/0bf8f0c2567dbbe983d3d391e329b83dd01ff9c457840716ded424cdbf2c/pubrunner-0.2.4.tar.gz#sha256=26c58d1445e4f17694e94c360b0a28856a32731bb7657e4e14ef61c51b677783 (from https://pypi.org/simple/pubrunner/), version: 0.2.4
2020-07-10T20:31:12,252   Found link https://files.pythonhosted.org/packages/96/43/545b6671f97ab059a24619f7702efdab0eb886ca7e4601ca0aeffedc1584/pubrunner-0.3.0.tar.gz#sha256=1b4d015dfd47ae4e1c0cfe630fafbfcfd698d5eaaa01c7ad3dbea975a316df79 (from https://pypi.org/simple/pubrunner/), version: 0.3.0
2020-07-10T20:31:12,253   Found link https://files.pythonhosted.org/packages/3c/8f/dc2020fa728d151dc1e1e4bd792d6c3b76967a4ed6c72d177cb7594e0a90/pubrunner-0.3.1.tar.gz#sha256=5e043f51ede4f732a2a6b5516faefbf12631e5c6fdff5b776794c0581efc1055 (from https://pypi.org/simple/pubrunner/), version: 0.3.1
2020-07-10T20:31:12,254   Found link https://files.pythonhosted.org/packages/cd/c3/4d78d3bd5bfbed4b8fb655e21abf49f5f5abfe58f4bb5cebd2cef5852236/pubrunner-0.4.0.tar.gz#sha256=ca1753ac3431f5422b376d2440208e8152e01e9300b8ccd355c64d82754781f5 (from https://pypi.org/simple/pubrunner/), version: 0.4.0
2020-07-10T20:31:12,255   Found link https://files.pythonhosted.org/packages/c4/fc/92d4622d775dfc3403c8a0bbb71bc81dea207c1bf44584400190bf55fe27/pubrunner-0.4.1.tar.gz#sha256=c7cc560bfaf4c8688ef14692ff9cb53c65eb7e20c70cf5dd7213516a43c4b8e0 (from https://pypi.org/simple/pubrunner/), version: 0.4.1
2020-07-10T20:31:12,255   Found link https://files.pythonhosted.org/packages/18/5a/2673256b80c7090c86de8ce53f9a171223cf99c021bd424f09b8cf566393/pubrunner-0.5.0.tar.gz#sha256=3d3cfd5fbb4d5c48bb7770c10a0b19ec066d6cc888ade969e1b29872aea79bfc (from https://pypi.org/simple/pubrunner/), version: 0.5.0
2020-07-10T20:31:12,256   Found link https://files.pythonhosted.org/packages/cb/2e/f4c4efccacea847f0f61eb1adcf871983a61185daaa4cb5e86972698dedd/pubrunner-0.5.1.tar.gz#sha256=0f571317236ac929f77e4e34c8af0d3074010b3d30e665de6ba38f17f949cc52 (from https://pypi.org/simple/pubrunner/), version: 0.5.1
2020-07-10T20:31:12,257   Found link https://files.pythonhosted.org/packages/85/97/347fc7c8be6b94add82d4f6354f162b2650dfaa058e6461937757dd14389/pubrunner-0.5.2.tar.gz#sha256=1dd7f58069a086810abd074bedfc0dfc34b2ccdc941cc28cc2c22b80d3442f28 (from https://pypi.org/simple/pubrunner/), version: 0.5.2
2020-07-10T20:31:12,258   Found link https://files.pythonhosted.org/packages/70/62/043242dcbcc9d3db22cd9ef151f62d9986745ab6d015688319e19c9bb5dd/pubrunner-0.5.3.tar.gz#sha256=19e4e0a6e6b23cebcc7357c9e13a3504c5f4567c57494fbf815aa6a25ff70972 (from https://pypi.org/simple/pubrunner/), version: 0.5.3
2020-07-10T20:31:12,259   Found link https://files.pythonhosted.org/packages/b6/66/e8e10bd44527d4ec29b182e641ccf59b9bf99a590cd06a0da798a471d456/pubrunner-0.5.4.tar.gz#sha256=d1eb2388b30ae431dd9f42f65f00ab96230b5c298f4a08d6676c38228733eed4 (from https://pypi.org/simple/pubrunner/), version: 0.5.4
2020-07-10T20:31:12,277 Given no hashes to check 1 links for project 'pubrunner': discarding no candidates
2020-07-10T20:31:12,279 Using version 0.5.4 (newest of versions: 0.5.4)
2020-07-10T20:31:12,285 Collecting pubrunner==0.5.4
2020-07-10T20:31:12,290   Created temporary directory: /tmp/pip-unpack-7je7zknu
2020-07-10T20:31:12,517   Downloading pubrunner-0.5.4.tar.gz (30 kB)
2020-07-10T20:31:12,725   Added pubrunner==0.5.4 from https://files.pythonhosted.org/packages/b6/66/e8e10bd44527d4ec29b182e641ccf59b9bf99a590cd06a0da798a471d456/pubrunner-0.5.4.tar.gz#sha256=d1eb2388b30ae431dd9f42f65f00ab96230b5c298f4a08d6676c38228733eed4 to build tracker '/tmp/pip-req-tracker-3riayoip'
2020-07-10T20:31:12,727     Running setup.py (path:/tmp/pip-wheel-z0gk5hkm/pubrunner/setup.py) egg_info for package pubrunner
2020-07-10T20:31:12,729     Created temporary directory: /tmp/pip-pip-egg-info-m0cji8pn
2020-07-10T20:31:12,729     Running command python setup.py egg_info
2020-07-10T20:31:14,967     running egg_info
2020-07-10T20:31:14,972     creating /tmp/pip-pip-egg-info-m0cji8pn/pubrunner.egg-info
2020-07-10T20:31:14,975     writing requirements to /tmp/pip-pip-egg-info-m0cji8pn/pubrunner.egg-info/requires.txt
2020-07-10T20:31:14,977     writing /tmp/pip-pip-egg-info-m0cji8pn/pubrunner.egg-info/PKG-INFO
2020-07-10T20:31:14,984     writing entry points to /tmp/pip-pip-egg-info-m0cji8pn/pubrunner.egg-info/entry_points.txt
2020-07-10T20:31:14,986     writing dependency_links to /tmp/pip-pip-egg-info-m0cji8pn/pubrunner.egg-info/dependency_links.txt
2020-07-10T20:31:14,989     writing top-level names to /tmp/pip-pip-egg-info-m0cji8pn/pubrunner.egg-info/top_level.txt
2020-07-10T20:31:14,994     writing manifest file '/tmp/pip-pip-egg-info-m0cji8pn/pubrunner.egg-info/SOURCES.txt'
2020-07-10T20:31:15,361     reading manifest file '/tmp/pip-pip-egg-info-m0cji8pn/pubrunner.egg-info/SOURCES.txt'
2020-07-10T20:31:15,365     reading manifest template 'MANIFEST.in'
2020-07-10T20:31:15,367     warning: no files found matching 'README.rst'
2020-07-10T20:31:15,379     writing manifest file '/tmp/pip-pip-egg-info-m0cji8pn/pubrunner.egg-info/SOURCES.txt'
2020-07-10T20:31:15,518   Source in /tmp/pip-wheel-z0gk5hkm/pubrunner has version 0.5.4, which satisfies requirement pubrunner==0.5.4 from https://files.pythonhosted.org/packages/b6/66/e8e10bd44527d4ec29b182e641ccf59b9bf99a590cd06a0da798a471d456/pubrunner-0.5.4.tar.gz#sha256=d1eb2388b30ae431dd9f42f65f00ab96230b5c298f4a08d6676c38228733eed4
2020-07-10T20:31:15,520   Removed pubrunner==0.5.4 from https://files.pythonhosted.org/packages/b6/66/e8e10bd44527d4ec29b182e641ccf59b9bf99a590cd06a0da798a471d456/pubrunner-0.5.4.tar.gz#sha256=d1eb2388b30ae431dd9f42f65f00ab96230b5c298f4a08d6676c38228733eed4 from build tracker '/tmp/pip-req-tracker-3riayoip'
2020-07-10T20:31:15,525 Building wheels for collected packages: pubrunner
2020-07-10T20:31:15,534   Created temporary directory: /tmp/pip-wheel-vf2xpxct
2020-07-10T20:31:15,535   Building wheel for pubrunner (setup.py): started
2020-07-10T20:31:15,536   Destination directory: /tmp/pip-wheel-vf2xpxct
2020-07-10T20:31:15,536   Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-z0gk5hkm/pubrunner/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-z0gk5hkm/pubrunner/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-vf2xpxct
2020-07-10T20:31:17,792   running bdist_wheel
2020-07-10T20:31:17,807   running build
2020-07-10T20:31:17,808   running build_py
2020-07-10T20:31:18,151   creating build
2020-07-10T20:31:18,152   creating build/lib
2020-07-10T20:31:18,154   creating build/lib/pubrunner
2020-07-10T20:31:18,156   copying pubrunner/convert.py -> build/lib/pubrunner
2020-07-10T20:31:18,163   copying pubrunner/command_line.py -> build/lib/pubrunner
2020-07-10T20:31:18,168   copying pubrunner/globalsettings.py -> build/lib/pubrunner
2020-07-10T20:31:18,173   copying pubrunner/getresource.py -> build/lib/pubrunner
2020-07-10T20:31:18,180   copying pubrunner/pubrun.py -> build/lib/pubrunner
2020-07-10T20:31:18,188   copying pubrunner/pubmed_hash.py -> build/lib/pubrunner
2020-07-10T20:31:18,193   copying pubrunner/__init__.py -> build/lib/pubrunner
2020-07-10T20:31:18,198   copying pubrunner/upload.py -> build/lib/pubrunner
2020-07-10T20:31:18,205   copying pubrunner/gather_pmids.py -> build/lib/pubrunner
2020-07-10T20:31:18,211   copying pubrunner/snakemake.py -> build/lib/pubrunner
2020-07-10T20:31:18,217   copying pubrunner/convertBioCToTSV.py -> build/lib/pubrunner
2020-07-10T20:31:18,220   running egg_info
2020-07-10T20:31:18,252   writing pubrunner.egg-info/PKG-INFO
2020-07-10T20:31:18,257   writing top-level names to pubrunner.egg-info/top_level.txt
2020-07-10T20:31:18,259   writing dependency_links to pubrunner.egg-info/dependency_links.txt
2020-07-10T20:31:18,262   writing entry points to pubrunner.egg-info/entry_points.txt
2020-07-10T20:31:18,265   writing requirements to pubrunner.egg-info/requires.txt
2020-07-10T20:31:18,279   reading manifest file 'pubrunner.egg-info/SOURCES.txt'
2020-07-10T20:31:18,287   reading manifest template 'MANIFEST.in'
2020-07-10T20:31:18,289   warning: no files found matching 'README.rst'
2020-07-10T20:31:18,304   writing manifest file 'pubrunner.egg-info/SOURCES.txt'
2020-07-10T20:31:18,311   copying pubrunner/pubrunner.settings.default.yml -> build/lib/pubrunner
2020-07-10T20:31:18,316   creating build/lib/pubrunner/Snakefiles
2020-07-10T20:31:18,318   copying pubrunner/Snakefiles/Convert.py -> build/lib/pubrunner/Snakefiles
2020-07-10T20:31:18,323   copying pubrunner/Snakefiles/PubmedHashes.py -> build/lib/pubrunner/Snakefiles
2020-07-10T20:31:18,328   copying pubrunner/Snakefiles/Run.py -> build/lib/pubrunner/Snakefiles
2020-07-10T20:31:18,334   creating build/lib/pubrunner/resources
2020-07-10T20:31:18,336   copying pubrunner/resources/DISEASE_ONTOLOGY.yml -> build/lib/pubrunner/resources
2020-07-10T20:31:18,343   copying pubrunner/resources/FOODON.yml -> build/lib/pubrunner/resources
2020-07-10T20:31:18,350   copying pubrunner/resources/METATHESAURUS_EMPTY.yml -> build/lib/pubrunner/resources
2020-07-10T20:31:18,356   copying pubrunner/resources/NCBI_GENE.yml -> build/lib/pubrunner/resources
2020-07-10T20:31:18,362   copying pubrunner/resources/NCBI_GENE_TEST.yml -> build/lib/pubrunner/resources
2020-07-10T20:31:18,369   copying pubrunner/resources/PMCAMC.yml -> build/lib/pubrunner/resources
2020-07-10T20:31:18,376   copying pubrunner/resources/PMCOA.yml -> build/lib/pubrunner/resources
2020-07-10T20:31:18,383   copying pubrunner/resources/PMCOA_TWOJOURNALS.yml -> build/lib/pubrunner/resources
2020-07-10T20:31:18,390   copying pubrunner/resources/PUBCHEM.yml -> build/lib/pubrunner/resources
2020-07-10T20:31:18,396   copying pubrunner/resources/PUBMED.yml -> build/lib/pubrunner/resources
2020-07-10T20:31:18,403   copying pubrunner/resources/PUBMED_TWOFILES.yml -> build/lib/pubrunner/resources
2020-07-10T20:31:18,423   installing to build/bdist.linux-armv7l/wheel
2020-07-10T20:31:18,424   running install
2020-07-10T20:31:18,425   running install_lib
2020-07-10T20:31:18,433   creating build/bdist.linux-armv7l
2020-07-10T20:31:18,434   creating build/bdist.linux-armv7l/wheel
2020-07-10T20:31:18,438   creating build/bdist.linux-armv7l/wheel/pubrunner
2020-07-10T20:31:18,441   copying build/lib/pubrunner/convert.py -> build/bdist.linux-armv7l/wheel/pubrunner
2020-07-10T20:31:18,448   copying build/lib/pubrunner/command_line.py -> build/bdist.linux-armv7l/wheel/pubrunner
2020-07-10T20:31:18,453   copying build/lib/pubrunner/globalsettings.py -> build/bdist.linux-armv7l/wheel/pubrunner
2020-07-10T20:31:18,457   copying build/lib/pubrunner/getresource.py -> build/bdist.linux-armv7l/wheel/pubrunner
2020-07-10T20:31:18,464   copying build/lib/pubrunner/pubrun.py -> build/bdist.linux-armv7l/wheel/pubrunner
2020-07-10T20:31:18,473   creating build/bdist.linux-armv7l/wheel/pubrunner/Snakefiles
2020-07-10T20:31:18,475   copying build/lib/pubrunner/Snakefiles/Convert.py -> build/bdist.linux-armv7l/wheel/pubrunner/Snakefiles
2020-07-10T20:31:18,481   copying build/lib/pubrunner/Snakefiles/PubmedHashes.py -> build/bdist.linux-armv7l/wheel/pubrunner/Snakefiles
2020-07-10T20:31:18,487   copying build/lib/pubrunner/Snakefiles/Run.py -> build/bdist.linux-armv7l/wheel/pubrunner/Snakefiles
2020-07-10T20:31:18,494   copying build/lib/pubrunner/pubmed_hash.py -> build/bdist.linux-armv7l/wheel/pubrunner
2020-07-10T20:31:18,500   copying build/lib/pubrunner/__init__.py -> build/bdist.linux-armv7l/wheel/pubrunner
2020-07-10T20:31:18,505   copying build/lib/pubrunner/upload.py -> build/bdist.linux-armv7l/wheel/pubrunner
2020-07-10T20:31:18,512   copying build/lib/pubrunner/gather_pmids.py -> build/bdist.linux-armv7l/wheel/pubrunner
2020-07-10T20:31:18,518   copying build/lib/pubrunner/snakemake.py -> build/bdist.linux-armv7l/wheel/pubrunner
2020-07-10T20:31:18,524   copying build/lib/pubrunner/convertBioCToTSV.py -> build/bdist.linux-armv7l/wheel/pubrunner
2020-07-10T20:31:18,531   creating build/bdist.linux-armv7l/wheel/pubrunner/resources
2020-07-10T20:31:18,533   copying build/lib/pubrunner/resources/PMCOA_TWOJOURNALS.yml -> build/bdist.linux-armv7l/wheel/pubrunner/resources
2020-07-10T20:31:18,539   copying build/lib/pubrunner/resources/NCBI_GENE.yml -> build/bdist.linux-armv7l/wheel/pubrunner/resources
2020-07-10T20:31:18,545   copying build/lib/pubrunner/resources/PUBMED.yml -> build/bdist.linux-armv7l/wheel/pubrunner/resources
2020-07-10T20:31:18,550   copying build/lib/pubrunner/resources/PUBMED_TWOFILES.yml -> build/bdist.linux-armv7l/wheel/pubrunner/resources
2020-07-10T20:31:18,555   copying build/lib/pubrunner/resources/DISEASE_ONTOLOGY.yml -> build/bdist.linux-armv7l/wheel/pubrunner/resources
2020-07-10T20:31:18,560   copying build/lib/pubrunner/resources/FOODON.yml -> build/bdist.linux-armv7l/wheel/pubrunner/resources
2020-07-10T20:31:18,566   copying build/lib/pubrunner/resources/PMCAMC.yml -> build/bdist.linux-armv7l/wheel/pubrunner/resources
2020-07-10T20:31:18,571   copying build/lib/pubrunner/resources/PUBCHEM.yml -> build/bdist.linux-armv7l/wheel/pubrunner/resources
2020-07-10T20:31:18,576   copying build/lib/pubrunner/resources/PMCOA.yml -> build/bdist.linux-armv7l/wheel/pubrunner/resources
2020-07-10T20:31:18,582   copying build/lib/pubrunner/resources/NCBI_GENE_TEST.yml -> build/bdist.linux-armv7l/wheel/pubrunner/resources
2020-07-10T20:31:18,587   copying build/lib/pubrunner/resources/METATHESAURUS_EMPTY.yml -> build/bdist.linux-armv7l/wheel/pubrunner/resources
2020-07-10T20:31:18,592   copying build/lib/pubrunner/pubrunner.settings.default.yml -> build/bdist.linux-armv7l/wheel/pubrunner
2020-07-10T20:31:18,597   running install_egg_info
2020-07-10T20:31:18,620   Copying pubrunner.egg-info to build/bdist.linux-armv7l/wheel/pubrunner-0.5.4-py3.5.egg-info
2020-07-10T20:31:18,654   running install_scripts
2020-07-10T20:31:18,869   creating build/bdist.linux-armv7l/wheel/pubrunner-0.5.4.dist-info/WHEEL
2020-07-10T20:31:19,183   Building wheel for pubrunner (setup.py): finished with status 'done'
2020-07-10T20:31:19,188   Created wheel for pubrunner: filename=pubrunner-0.5.4-py3-none-any.whl size=40548 sha256=3fbedc3767c1d42b9eee9f7872e4a4c1aeee0bad919cb2c659f87b049795cbee
2020-07-10T20:31:19,188   Stored in directory: /tmp/pip-ephem-wheel-cache-l2k5kpld/wheels/f2/09/40/9c2301f02f16eeb85b621ea17fbaca4fcdad5d2fad248c85c3
2020-07-10T20:31:19,192 Successfully built pubrunner
2020-07-10T20:31:19,205 Removed build tracker: '/tmp/pip-req-tracker-3riayoip'