2024-11-28T15:58:33,875 Created temporary directory: /tmp/pip-build-tracker-1hy8b93_
2024-11-28T15:58:33,877 Initialized build tracking at /tmp/pip-build-tracker-1hy8b93_
2024-11-28T15:58:33,877 Created build tracker: /tmp/pip-build-tracker-1hy8b93_
2024-11-28T15:58:33,878 Entered build tracker: /tmp/pip-build-tracker-1hy8b93_
2024-11-28T15:58:33,878 Created temporary directory: /tmp/pip-wheel-o5tlhh90
2024-11-28T15:58:33,882 Created temporary directory: /tmp/pip-ephem-wheel-cache-alrl053z
2024-11-28T15:58:33,929 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2024-11-28T15:58:33,931 2 location(s) to search for versions of coralme:
2024-11-28T15:58:33,931 * https://pypi.org/simple/coralme/
2024-11-28T15:58:33,931 * https://www.piwheels.org/simple/coralme/
2024-11-28T15:58:33,932 Fetching project page and analyzing links: https://pypi.org/simple/coralme/
2024-11-28T15:58:33,933 Getting page https://pypi.org/simple/coralme/
2024-11-28T15:58:33,934 Found index url https://pypi.org/simple/
2024-11-28T15:58:34,078 Fetched page https://pypi.org/simple/coralme/ as application/vnd.pypi.simple.v1+json
2024-11-28T15:58:34,084   Skipping link: No binaries permitted for coralme: https://files.pythonhosted.org/packages/b3/cd/5d6128384de97cd66728ffb9077a3a317b05284b8fc55ed2892abde04988/coralME-1.0.0-py3-none-any.whl (from https://pypi.org/simple/coralme/) (requires-python:~=3.0)
2024-11-28T15:58:34,086   Found link https://files.pythonhosted.org/packages/31/32/3bc2eec17165d6d1ccf75a42851f2c1e54c1656e16c05c2ff70d203d9a2d/coralME-1.0.tar.gz (from https://pypi.org/simple/coralme/) (requires-python:~=3.0), version: 1.0
2024-11-28T15:58:34,086   Skipping link: No binaries permitted for coralme: https://files.pythonhosted.org/packages/64/d9/437302ea3967819d104b01255c506132b78fe7d6c40e9f7b5fb1fda1471b/coralME-1.0.0.post1-py3-none-any.whl (from https://pypi.org/simple/coralme/) (requires-python:~=3.0)
2024-11-28T15:58:34,087   Found link https://files.pythonhosted.org/packages/0a/a6/69e5b9146c97f78f52ff4ae7cabce9cf6ba53af5a1437f16980d55175efb/coralme-1.0.0.post1.tar.gz (from https://pypi.org/simple/coralme/) (requires-python:~=3.0), version: 1.0.0.post1
2024-11-28T15:58:34,088   Skipping link: No binaries permitted for coralme: https://files.pythonhosted.org/packages/04/8b/c4dad0d0a44e9c73db1d04ad85c781aaa52b44036536b775a27af1cfd5d4/coralME-1.0.0.post2-py3-none-any.whl (from https://pypi.org/simple/coralme/) (requires-python:~=3.0)
2024-11-28T15:58:34,089   Found link https://files.pythonhosted.org/packages/b4/1d/9ce7e27ad95f141fabe37512ae3791a24d04932d6f538494f291a9212071/coralme-1.0.0.post2.tar.gz (from https://pypi.org/simple/coralme/) (requires-python:~=3.0), version: 1.0.0.post2
2024-11-28T15:58:34,090   Skipping link: No binaries permitted for coralme: https://files.pythonhosted.org/packages/b9/ad/b75b4ee52cccd105f07480a024983ef9e047ba3d62580ff54cf6b968fd11/coralME-1.0.0.post3-py3-none-any.whl (from https://pypi.org/simple/coralme/) (requires-python:~=3.0)
2024-11-28T15:58:34,091   Found link https://files.pythonhosted.org/packages/57/b5/2bf10653857fc4ac9c8ce4f4641f93e1ba667ccacdddc8c4698ef289c827/coralme-1.0.0.post3.tar.gz (from https://pypi.org/simple/coralme/) (requires-python:~=3.0), version: 1.0.0.post3
2024-11-28T15:58:34,091   Skipping link: No binaries permitted for coralme: https://files.pythonhosted.org/packages/4e/04/d529fcbb6f321c75110be5aee42bbf9ea2e8a48c1533991fc8520039e9cf/coralME-1.1.0-py3-none-any.whl (from https://pypi.org/simple/coralme/) (requires-python:~=3.0)
2024-11-28T15:58:34,093   Found link https://files.pythonhosted.org/packages/ae/02/61a2270de794f05a442da6780ef4829137667292927808e2169c577a8ee2/coralme-1.1.0.tar.gz (from https://pypi.org/simple/coralme/) (requires-python:~=3.0), version: 1.1.0
2024-11-28T15:58:34,093   Skipping link: No binaries permitted for coralme: https://files.pythonhosted.org/packages/b3/02/b26931a4161c042cf9c734be57c701e5d76981ead5832796531510a5baa0/coralME-1.1.1-py3-none-any.whl (from https://pypi.org/simple/coralme/) (requires-python:~=3.0)
2024-11-28T15:58:34,094   Found link https://files.pythonhosted.org/packages/e5/6b/9faa456a1bafe9b7e6a3f7ed85b0c863d5b2a3027b09f9e1e541d90e5d01/coralme-1.1.1.tar.gz (from https://pypi.org/simple/coralme/) (requires-python:~=3.0), version: 1.1.1
2024-11-28T15:58:34,095   Skipping link: No binaries permitted for coralme: https://files.pythonhosted.org/packages/2f/5b/580385e954d6fc42d8eac064daa33c0a694988dfc52da8fd5ca298e5d6b0/coralME-1.1.2-py3-none-any.whl (from https://pypi.org/simple/coralme/) (requires-python:~=3.0)
2024-11-28T15:58:34,096   Found link https://files.pythonhosted.org/packages/d9/d5/f085dc517f64026bdabe8410cfc95d8bc5898cac172b3b982cec59c1e188/coralme-1.1.2.tar.gz (from https://pypi.org/simple/coralme/) (requires-python:~=3.0), version: 1.1.2
2024-11-28T15:58:34,097   Skipping link: No binaries permitted for coralme: https://files.pythonhosted.org/packages/33/71/b4cf0bf6dd4b4645c38d7b726b17542a1384a2314abee9a36b6acc35c392/coralME-1.1.3-py3-none-any.whl (from https://pypi.org/simple/coralme/) (requires-python:~=3.0)
2024-11-28T15:58:34,098   Found link https://files.pythonhosted.org/packages/67/ac/47f0c031808a891828f3b12123ea21f050ba08bd1ec205584e640ff31fcc/coralme-1.1.3.tar.gz (from https://pypi.org/simple/coralme/) (requires-python:~=3.0), version: 1.1.3
2024-11-28T15:58:34,099   Skipping link: No binaries permitted for coralme: https://files.pythonhosted.org/packages/f6/18/b7e43d27132dceb7bf5e4d13d8957769d66b565b8e14687fed09fc4c1dd8/coralME-1.1.4-py3-none-any.whl (from https://pypi.org/simple/coralme/) (requires-python:~=3.0)
2024-11-28T15:58:34,099   Found link https://files.pythonhosted.org/packages/c2/76/ef2eb4ecec6b7d25043b8ef022422f87b4f1abc4277841e75a6305038255/coralme-1.1.4.tar.gz (from https://pypi.org/simple/coralme/) (requires-python:~=3.0), version: 1.1.4
2024-11-28T15:58:34,100   Skipping link: No binaries permitted for coralme: https://files.pythonhosted.org/packages/34/25/6f2e739d39d35df071d2df2fb6a63f17783f3ed665b72c9d10fb7905351e/coralME-1.1.5-py3-none-any.whl (from https://pypi.org/simple/coralme/) (requires-python:~=3.0)
2024-11-28T15:58:34,101   Found link https://files.pythonhosted.org/packages/c2/0d/52301c9c25ba738621b9cf7a8e086b59b06aaeaf79c840c8b166860639e4/coralme-1.1.5.tar.gz (from https://pypi.org/simple/coralme/) (requires-python:~=3.0), version: 1.1.5
2024-11-28T15:58:34,102   Skipping link: No binaries permitted for coralme: https://files.pythonhosted.org/packages/6b/6c/5a024da74985e9873476a19920176a01654af72b598b1d907c89f78d90c5/coralME-1.1.6-py3-none-any.whl (from https://pypi.org/simple/coralme/) (requires-python:~=3.0)
2024-11-28T15:58:34,103   Found link https://files.pythonhosted.org/packages/96/06/89189c3ed663403e91f8327f84e25955352b5245a96fa5161f7eedb8f4b3/coralme-1.1.6.tar.gz (from https://pypi.org/simple/coralme/) (requires-python:~=3.0), version: 1.1.6
2024-11-28T15:58:34,103   Skipping link: No binaries permitted for coralme: https://files.pythonhosted.org/packages/32/6a/dfae77f81cd50687546994bb33f27ce9fe38fda570f0238e6f2339a2f175/coralME-1.1.7-py3-none-any.whl (from https://pypi.org/simple/coralme/) (requires-python:~=3.0)
2024-11-28T15:58:34,104   Found link https://files.pythonhosted.org/packages/28/e4/b8069af59f572f85a8b33d89cd0c569844aeee8a280964edf25d032222ff/coralme-1.1.7.tar.gz (from https://pypi.org/simple/coralme/) (requires-python:~=3.0), version: 1.1.7
2024-11-28T15:58:34,105   Skipping link: No binaries permitted for coralme: https://files.pythonhosted.org/packages/de/5a/30d173d1c0e90dd186a08df34f8f4e7a8b7d3e8751b94e70a85171247d22/coralME-1.1.8-py3-none-any.whl (from https://pypi.org/simple/coralme/) (requires-python:~=3.0)
2024-11-28T15:58:34,106   Found link https://files.pythonhosted.org/packages/0c/5b/88567312519cba67e30c9e9f9022dbae29836c86768d8b756facca23e9a5/coralme-1.1.8.tar.gz (from https://pypi.org/simple/coralme/) (requires-python:~=3.0), version: 1.1.8
2024-11-28T15:58:34,106   Skipping link: No binaries permitted for coralme: https://files.pythonhosted.org/packages/d5/8d/9b3f98c74bf48666afe24cd99f89218c553fc7ce4e6d48621db8b1f690e3/coralME-1.1.9-py3-none-any.whl (from https://pypi.org/simple/coralme/) (requires-python:~=3.0)
2024-11-28T15:58:34,107   Found link https://files.pythonhosted.org/packages/f5/eb/8b47f9001cab3069c2bceeb9d52630790140f4aaed5c885422cbc14e7703/coralme-1.1.9.tar.gz (from https://pypi.org/simple/coralme/) (requires-python:~=3.0), version: 1.1.9
2024-11-28T15:58:34,109 Fetching project page and analyzing links: https://www.piwheels.org/simple/coralme/
2024-11-28T15:58:34,109 Getting page https://www.piwheels.org/simple/coralme/
2024-11-28T15:58:34,110 Found index url https://www.piwheels.org/simple/
2024-11-28T15:58:34,278 Fetched page https://www.piwheels.org/simple/coralme/ as text/html
2024-11-28T15:58:34,280   Skipping link: No binaries permitted for coralme: https://www.piwheels.org/simple/coralme/coralME-1.0.0.post1-py3-none-any.whl#sha256=c013e324d5a89b8680ae4f14dd2f583a419ca4093cab14d5f01c3f075eb12d95 (from https://www.piwheels.org/simple/coralme/) (requires-python:~=3.0)
2024-11-28T15:58:34,281   Skipping link: No binaries permitted for coralme: https://www.piwheels.org/simple/coralme/coralME-1.0-py3-none-any.whl#sha256=97369c482c958763a4b73fcacba5460503c28762eb9a63b98e4a176aee42e308 (from https://www.piwheels.org/simple/coralme/) (requires-python:~=3.0)
2024-11-28T15:58:34,281 Skipping link: not a file: https://www.piwheels.org/simple/coralme/
2024-11-28T15:58:34,282 Skipping link: not a file: https://pypi.org/simple/coralme/
2024-11-28T15:58:34,302 Given no hashes to check 1 links for project 'coralme': discarding no candidates
2024-11-28T15:58:34,305 Collecting coralme==1.0.0.post2
2024-11-28T15:58:34,307   Created temporary directory: /tmp/pip-unpack-kzhcgv_k
2024-11-28T15:58:34,447   Downloading coralme-1.0.0.post2.tar.gz (8.5 MB)
2024-11-28T15:58:36,407   Added coralme==1.0.0.post2 from https://files.pythonhosted.org/packages/b4/1d/9ce7e27ad95f141fabe37512ae3791a24d04932d6f538494f291a9212071/coralme-1.0.0.post2.tar.gz to build tracker '/tmp/pip-build-tracker-1hy8b93_'
2024-11-28T15:58:36,409   Running setup.py (path:/tmp/pip-wheel-o5tlhh90/coralme_029a59c5b46449ef838867945c368a9a/setup.py) egg_info for package coralme
2024-11-28T15:58:36,410   Created temporary directory: /tmp/pip-pip-egg-info-vtjga2ja
2024-11-28T15:58:36,411   Preparing metadata (setup.py): started
2024-11-28T15:58:36,412   Running command python setup.py egg_info
2024-11-28T15:58:37,526   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:337: InformationOnly: Normalizing '1.0.0-2' to '1.0.0.post2'
2024-11-28T15:58:37,526     self.metadata.version = self._normalize_version(self.metadata.version)
2024-11-28T15:58:37,580   running egg_info
2024-11-28T15:58:37,608   creating /tmp/pip-pip-egg-info-vtjga2ja/coralME.egg-info
2024-11-28T15:58:37,609   writing /tmp/pip-pip-egg-info-vtjga2ja/coralME.egg-info/PKG-INFO
2024-11-28T15:58:37,613   writing dependency_links to /tmp/pip-pip-egg-info-vtjga2ja/coralME.egg-info/dependency_links.txt
2024-11-28T15:58:37,615   writing requirements to /tmp/pip-pip-egg-info-vtjga2ja/coralME.egg-info/requires.txt
2024-11-28T15:58:37,616   writing top-level names to /tmp/pip-pip-egg-info-vtjga2ja/coralME.egg-info/top_level.txt
2024-11-28T15:58:37,618   writing manifest file '/tmp/pip-pip-egg-info-vtjga2ja/coralME.egg-info/SOURCES.txt'
2024-11-28T15:58:37,723   reading manifest file '/tmp/pip-pip-egg-info-vtjga2ja/coralME.egg-info/SOURCES.txt'
2024-11-28T15:58:37,725   adding license file 'LICENSE'
2024-11-28T15:58:37,731   writing manifest file '/tmp/pip-pip-egg-info-vtjga2ja/coralME.egg-info/SOURCES.txt'
2024-11-28T15:58:37,840   Preparing metadata (setup.py): finished with status 'done'
2024-11-28T15:58:37,845   Source in /tmp/pip-wheel-o5tlhh90/coralme_029a59c5b46449ef838867945c368a9a has version 1.0.0.post2, which satisfies requirement coralme==1.0.0.post2 from https://files.pythonhosted.org/packages/b4/1d/9ce7e27ad95f141fabe37512ae3791a24d04932d6f538494f291a9212071/coralme-1.0.0.post2.tar.gz
2024-11-28T15:58:37,846   Removed coralme==1.0.0.post2 from https://files.pythonhosted.org/packages/b4/1d/9ce7e27ad95f141fabe37512ae3791a24d04932d6f538494f291a9212071/coralme-1.0.0.post2.tar.gz from build tracker '/tmp/pip-build-tracker-1hy8b93_'
2024-11-28T15:58:37,855 Created temporary directory: /tmp/pip-unpack-8ef0jghe
2024-11-28T15:58:37,857 Created temporary directory: /tmp/pip-unpack-l2f2k47_
2024-11-28T15:58:37,857 Building wheels for collected packages: coralme
2024-11-28T15:58:37,861   Created temporary directory: /tmp/pip-wheel-b2suttkw
2024-11-28T15:58:37,862   Building wheel for coralme (setup.py): started
2024-11-28T15:58:37,863   Destination directory: /tmp/pip-wheel-b2suttkw
2024-11-28T15:58:37,864   Running command python setup.py bdist_wheel
2024-11-28T15:58:38,911   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:337: InformationOnly: Normalizing '1.0.0-2' to '1.0.0.post2'
2024-11-28T15:58:38,911     self.metadata.version = self._normalize_version(self.metadata.version)
2024-11-28T15:58:38,939   running bdist_wheel
2024-11-28T15:58:39,079   running build
2024-11-28T15:58:39,079   running build_py
2024-11-28T15:58:39,109   creating build/lib/coralme
2024-11-28T15:58:39,111   copying coralme/__init__.py -> build/lib/coralme
2024-11-28T15:58:39,114   copying coralme/_version.py -> build/lib/coralme
2024-11-28T15:58:39,117   creating build/lib/coralme/builder
2024-11-28T15:58:39,118   copying coralme/builder/translocation.py -> build/lib/coralme/builder
2024-11-28T15:58:39,120   copying coralme/builder/dictionaries.py -> build/lib/coralme/builder
2024-11-28T15:58:39,123   copying coralme/builder/trna_charging.py -> build/lib/coralme/builder
2024-11-28T15:58:39,125   copying coralme/builder/curation.py -> build/lib/coralme/builder
2024-11-28T15:58:39,129   copying coralme/builder/transcription.py -> build/lib/coralme/builder
2024-11-28T15:58:39,130   copying coralme/builder/__init__.py -> build/lib/coralme/builder
2024-11-28T15:58:39,132   copying coralme/builder/organism.py -> build/lib/coralme/builder
2024-11-28T15:58:39,136   copying coralme/builder/modifications.py -> build/lib/coralme/builder
2024-11-28T15:58:39,138   copying coralme/builder/flat_files.py -> build/lib/coralme/builder
2024-11-28T15:58:39,141   copying coralme/builder/main.py -> build/lib/coralme/builder
2024-11-28T15:58:39,145   copying coralme/builder/ribosome.py -> build/lib/coralme/builder
2024-11-28T15:58:39,147   copying coralme/builder/preprocess_inputs.py -> build/lib/coralme/builder
2024-11-28T15:58:39,150   copying coralme/builder/dna_replication.py -> build/lib/coralme/builder
2024-11-28T15:58:39,152   copying coralme/builder/formulas.py -> build/lib/coralme/builder
2024-11-28T15:58:39,154   copying coralme/builder/helper_functions.py -> build/lib/coralme/builder
2024-11-28T15:58:39,156   copying coralme/builder/compartments.py -> build/lib/coralme/builder
2024-11-28T15:58:39,158   copying coralme/builder/translation.py -> build/lib/coralme/builder
2024-11-28T15:58:39,160   copying coralme/builder/homology.py -> build/lib/coralme/builder
2024-11-28T15:58:39,163   creating build/lib/coralme/core
2024-11-28T15:58:39,164   copying coralme/core/__init__.py -> build/lib/coralme/core
2024-11-28T15:58:39,166   copying coralme/core/model.py -> build/lib/coralme/core
2024-11-28T15:58:39,169   copying coralme/core/reaction.py -> build/lib/coralme/core
2024-11-28T15:58:39,173   copying coralme/core/component.py -> build/lib/coralme/core
2024-11-28T15:58:39,176   copying coralme/core/processdata.py -> build/lib/coralme/core
2024-11-28T15:58:39,179   creating build/lib/coralme/io
2024-11-28T15:58:39,181   copying coralme/io/__init__.py -> build/lib/coralme/io
2024-11-28T15:58:39,183   copying coralme/io/dict.py -> build/lib/coralme/io
2024-11-28T15:58:39,186   copying coralme/io/json.py -> build/lib/coralme/io
2024-11-28T15:58:39,188   copying coralme/io/pickle.py -> build/lib/coralme/io
2024-11-28T15:58:39,191   creating build/lib/coralme/solver
2024-11-28T15:58:39,192   copying coralme/solver/__init__.py -> build/lib/coralme/solver
2024-11-28T15:58:39,194   copying coralme/solver/solver.py -> build/lib/coralme/solver
2024-11-28T15:58:39,197   creating build/lib/coralme/util
2024-11-28T15:58:39,198   copying coralme/util/building.py -> build/lib/coralme/util
2024-11-28T15:58:39,201   copying coralme/util/__init__.py -> build/lib/coralme/util
2024-11-28T15:58:39,203   copying coralme/util/dogma.py -> build/lib/coralme/util
2024-11-28T15:58:39,206   copying coralme/util/massbalance.py -> build/lib/coralme/util
2024-11-28T15:58:39,217   creating build/lib/coralme/iJL1678b-ME
2024-11-28T15:58:39,218   copying coralme/iJL1678b-ME/BarEven_subsystem_classification.csv -> build/lib/coralme/iJL1678b-ME
2024-11-28T15:58:39,221   creating build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,222   copying coralme/iJL1678b-ME/building_data/genes.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,229   copying coralme/iJL1678b-ME/building_data/protein_complexes.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,232   copying coralme/iJL1678b-ME/building_data/proteins.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,236   copying coralme/iJL1678b-ME/building_data/keffs.json -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,244   copying coralme/iJL1678b-ME/building_data/reaction_corrections.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,246   copying coralme/iJL1678b-ME/building_data/me_metabolites.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,249   copying coralme/iJL1678b-ME/building_data/rna_modification.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,251   copying coralme/iJL1678b-ME/building_data/codon_usage.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,253   copying coralme/iJL1678b-ME/building_data/rho_independent.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,255   copying coralme/iJL1678b-ME/building_data/termination_subreactions.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,258   copying coralme/iJL1678b-ME/building_data/modification.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,260   copying coralme/iJL1678b-ME/building_data/special_modifications.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,262   copying coralme/iJL1678b-ME/building_data/amino_acid_trna_synthetase.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,263   copying coralme/iJL1678b-ME/building_data/post_transcriptional_modification_of_RNA.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,266   copying coralme/iJL1678b-ME/building_data/folding_chaperones.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,268   copying coralme/iJL1678b-ME/building_data/ribosome_subreactions.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,271   copying coralme/iJL1678b-ME/building_data/enzyme_reaction_association.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,275   copying coralme/iJL1678b-ME/building_data/subsystem_classification.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,277   copying coralme/iJL1678b-ME/building_data/metabolites.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,281   copying coralme/iJL1678b-ME/building_data/excision_machinery.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,283   copying coralme/iJL1678b-ME/building_data/special_trna_subreactions.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,286   copying coralme/iJL1678b-ME/building_data/rrna_modifications.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,288   copying coralme/iJL1678b-ME/building_data/ribosomal_proteins.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,290   copying coralme/iJL1678b-ME/building_data/elongation_subreactions.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,292   copying coralme/iJL1678b-ME/building_data/trna_modification.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,295   copying coralme/iJL1678b-ME/building_data/sigma_factors.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,297   copying coralme/iJL1678b-ME/building_data/genome.gb -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,481   copying coralme/iJL1678b-ME/building_data/lipid_modifications.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,484   copying coralme/iJL1678b-ME/building_data/metabolite_corrections.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,486   copying coralme/iJL1678b-ME/building_data/initiation_subreactions.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,488   copying coralme/iJL1678b-ME/building_data/stable_RNAs.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,491   copying coralme/iJL1678b-ME/building_data/keffs.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,497   copying coralme/iJL1678b-ME/building_data/folding_dict.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,499   copying coralme/iJL1678b-ME/building_data/m_model.json -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,515   copying coralme/iJL1678b-ME/building_data/cleaved_methionine.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,517   copying coralme/iJL1678b-ME/building_data/iJO1366b.json -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,534   copying coralme/iJL1678b-ME/building_data/orphan_and_spont_reactions.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,536   copying coralme/iJL1678b-ME/building_data/translocation_multipliers.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,538   copying coralme/iJL1678b-ME/building_data/m_to_me_mets.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,541   copying coralme/iJL1678b-ME/building_data/reference_tRNAs.fna -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,618   copying coralme/iJL1678b-ME/building_data/lipoprotein_precursors.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,620   copying coralme/iJL1678b-ME/building_data/TUs.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,625   copying coralme/iJL1678b-ME/building_data/generic_dict.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,627   copying coralme/iJL1678b-ME/building_data/translocation_pathways.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,629   copying coralme/iJL1678b-ME/building_data/protein_modification.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,632   copying coralme/iJL1678b-ME/building_data/protein_corrections.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,635   copying coralme/iJL1678b-ME/building_data/RNAs.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,637   copying coralme/iJL1678b-ME/building_data/TUs_from_biocyc.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,642   copying coralme/iJL1678b-ME/building_data/rna_degradosome.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,644   copying coralme/iJL1678b-ME/building_data/reaction_matrix.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,647   copying coralme/iJL1678b-ME/building_data/subreaction_matrix.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,650   copying coralme/iJL1678b-ME/building_data/transcription_subreactions.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,652   copying coralme/iJL1678b-ME/building_data/peptide_release_factors.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,655   copying coralme/iJL1678b-ME/building_data/_TUs_from_biocyc.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,661   copying coralme/iJL1678b-ME/building_data/peptide_compartment_and_pathways.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:39,664   copying coralme/solver/warmLP.cpython-37m-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:58:39,674   copying coralme/solver/warmLP.cpython-39-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:58:39,686   copying coralme/solver/qvaryME.cpython-37m-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:58:39,698   copying coralme/solver/warmLP.cpython-310-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:58:39,709   copying coralme/solver/qwarmLP.cpython-37m-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:58:39,719   copying coralme/solver/qsolveME.cpython-310-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:58:39,723   copying coralme/solver/qmatrixA.cpython-37m-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:58:39,727   copying coralme/solver/qmatrixA.cpython-310-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:58:39,731   copying coralme/solver/qwarmLP.cpython-38-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:58:39,740   copying coralme/solver/qvaryME.cpython-310-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:58:39,750   copying coralme/solver/qmatrixA.cpython-38-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:58:39,754   copying coralme/solver/qsolveME.cpython-38-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:58:39,758   copying coralme/solver/qmatrixA.cpython-39-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:58:39,762   copying coralme/solver/warmLP.cpython-38-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:58:39,772   copying coralme/solver/qwarmLP.cpython-39-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:58:39,782   copying coralme/solver/qvaryME.cpython-38-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:58:39,796   copying coralme/solver/qwarmLP.cpython-310-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:58:39,806   copying coralme/solver/qvaryME.cpython-39-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:58:39,816   copying coralme/solver/qsolveME.cpython-37m-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:58:39,820   copying coralme/solver/qsolveME.cpython-39-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:58:39,824   copying coralme/io/JSONSCHEMA -> build/lib/coralme/io
2024-11-28T15:58:39,827   copying coralme/builder/column_format.json -> build/lib/coralme/builder
2024-11-28T15:58:39,830   creating build/lib/coralme/licenses
2024-11-28T15:58:39,831   copying coralme/licenses/LICENSE-solvemepy -> build/lib/coralme/licenses
2024-11-28T15:58:39,833   copying coralme/licenses/LICENSE-cobrame -> build/lib/coralme/licenses
2024-11-28T15:58:39,835   copying coralme/licenses/LICENSE-ecolime -> build/lib/coralme/licenses
2024-11-28T15:58:39,867   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2024-11-28T15:58:39,868   !!

2024-11-28T15:58:39,869           ********************************************************************************
2024-11-28T15:58:39,870           Please avoid running ``setup.py`` directly.
2024-11-28T15:58:39,870           Instead, use pypa/build, pypa/installer or other
2024-11-28T15:58:39,871           standards-based tools.

2024-11-28T15:58:39,872           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2024-11-28T15:58:39,872           ********************************************************************************

2024-11-28T15:58:39,874   !!
2024-11-28T15:58:39,874     self.initialize_options()
2024-11-28T15:58:39,896   installing to build/bdist.linux-armv7l/wheel
2024-11-28T15:58:39,896   running install
2024-11-28T15:58:39,920   running install_lib
2024-11-28T15:58:39,950   creating build/bdist.linux-armv7l/wheel
2024-11-28T15:58:39,953   creating build/bdist.linux-armv7l/wheel/coralme
2024-11-28T15:58:39,955   creating build/bdist.linux-armv7l/wheel/coralme/licenses
2024-11-28T15:58:39,956   copying build/lib/coralme/licenses/LICENSE-solvemepy -> build/bdist.linux-armv7l/wheel/./coralme/licenses
2024-11-28T15:58:39,958   copying build/lib/coralme/licenses/LICENSE-cobrame -> build/bdist.linux-armv7l/wheel/./coralme/licenses
2024-11-28T15:58:39,960   copying build/lib/coralme/licenses/LICENSE-ecolime -> build/bdist.linux-armv7l/wheel/./coralme/licenses
2024-11-28T15:58:39,962   creating build/bdist.linux-armv7l/wheel/coralme/builder
2024-11-28T15:58:39,963   copying build/lib/coralme/builder/translocation.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:58:39,966   copying build/lib/coralme/builder/dictionaries.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:58:39,969   copying build/lib/coralme/builder/trna_charging.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:58:39,970   copying build/lib/coralme/builder/curation.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:58:39,974   copying build/lib/coralme/builder/column_format.json -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:58:39,976   copying build/lib/coralme/builder/transcription.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:58:39,977   copying build/lib/coralme/builder/__init__.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:58:39,979   copying build/lib/coralme/builder/organism.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:58:39,983   copying build/lib/coralme/builder/modifications.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:58:39,985   copying build/lib/coralme/builder/flat_files.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:58:39,988   copying build/lib/coralme/builder/main.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:58:39,994   copying build/lib/coralme/builder/ribosome.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:58:39,996   copying build/lib/coralme/builder/preprocess_inputs.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:58:40,000   copying build/lib/coralme/builder/dna_replication.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:58:40,002   copying build/lib/coralme/builder/formulas.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:58:40,004   copying build/lib/coralme/builder/helper_functions.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:58:40,007   copying build/lib/coralme/builder/compartments.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:58:40,009   copying build/lib/coralme/builder/translation.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:58:40,011   copying build/lib/coralme/builder/homology.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:58:40,014   creating build/bdist.linux-armv7l/wheel/coralme/core
2024-11-28T15:58:40,015   copying build/lib/coralme/core/__init__.py -> build/bdist.linux-armv7l/wheel/./coralme/core
2024-11-28T15:58:40,017   copying build/lib/coralme/core/model.py -> build/bdist.linux-armv7l/wheel/./coralme/core
2024-11-28T15:58:40,021   copying build/lib/coralme/core/reaction.py -> build/bdist.linux-armv7l/wheel/./coralme/core
2024-11-28T15:58:40,025   copying build/lib/coralme/core/component.py -> build/bdist.linux-armv7l/wheel/./coralme/core
2024-11-28T15:58:40,027   copying build/lib/coralme/core/processdata.py -> build/bdist.linux-armv7l/wheel/./coralme/core
2024-11-28T15:58:40,031   copying build/lib/coralme/__init__.py -> build/bdist.linux-armv7l/wheel/./coralme
2024-11-28T15:58:40,033   creating build/bdist.linux-armv7l/wheel/coralme/iJL1678b-ME
2024-11-28T15:58:40,034   copying build/lib/coralme/iJL1678b-ME/BarEven_subsystem_classification.csv -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME
2024-11-28T15:58:40,039   creating build/bdist.linux-armv7l/wheel/coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,040   copying build/lib/coralme/iJL1678b-ME/building_data/genes.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,047   copying build/lib/coralme/iJL1678b-ME/building_data/protein_complexes.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,052   copying build/lib/coralme/iJL1678b-ME/building_data/proteins.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,057   copying build/lib/coralme/iJL1678b-ME/building_data/keffs.json -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,065   copying build/lib/coralme/iJL1678b-ME/building_data/reaction_corrections.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,067   copying build/lib/coralme/iJL1678b-ME/building_data/me_metabolites.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,069   copying build/lib/coralme/iJL1678b-ME/building_data/rna_modification.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,071   copying build/lib/coralme/iJL1678b-ME/building_data/codon_usage.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,072   copying build/lib/coralme/iJL1678b-ME/building_data/rho_independent.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,075   copying build/lib/coralme/iJL1678b-ME/building_data/termination_subreactions.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,076   copying build/lib/coralme/iJL1678b-ME/building_data/modification.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,078   copying build/lib/coralme/iJL1678b-ME/building_data/special_modifications.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,080   copying build/lib/coralme/iJL1678b-ME/building_data/amino_acid_trna_synthetase.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,082   copying build/lib/coralme/iJL1678b-ME/building_data/post_transcriptional_modification_of_RNA.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,084   copying build/lib/coralme/iJL1678b-ME/building_data/folding_chaperones.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,086   copying build/lib/coralme/iJL1678b-ME/building_data/ribosome_subreactions.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,088   copying build/lib/coralme/iJL1678b-ME/building_data/enzyme_reaction_association.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,091   copying build/lib/coralme/iJL1678b-ME/building_data/subsystem_classification.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,093   copying build/lib/coralme/iJL1678b-ME/building_data/metabolites.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,097   copying build/lib/coralme/iJL1678b-ME/building_data/excision_machinery.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,099   copying build/lib/coralme/iJL1678b-ME/building_data/special_trna_subreactions.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,100   copying build/lib/coralme/iJL1678b-ME/building_data/rrna_modifications.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,102   copying build/lib/coralme/iJL1678b-ME/building_data/ribosomal_proteins.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,104   copying build/lib/coralme/iJL1678b-ME/building_data/elongation_subreactions.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,106   copying build/lib/coralme/iJL1678b-ME/building_data/trna_modification.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,108   copying build/lib/coralme/iJL1678b-ME/building_data/sigma_factors.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,110   copying build/lib/coralme/iJL1678b-ME/building_data/genome.gb -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,307   copying build/lib/coralme/iJL1678b-ME/building_data/lipid_modifications.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,309   copying build/lib/coralme/iJL1678b-ME/building_data/metabolite_corrections.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,311   copying build/lib/coralme/iJL1678b-ME/building_data/initiation_subreactions.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,312   copying build/lib/coralme/iJL1678b-ME/building_data/stable_RNAs.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,314   copying build/lib/coralme/iJL1678b-ME/building_data/keffs.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,320   copying build/lib/coralme/iJL1678b-ME/building_data/folding_dict.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,322   copying build/lib/coralme/iJL1678b-ME/building_data/m_model.json -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,337   copying build/lib/coralme/iJL1678b-ME/building_data/cleaved_methionine.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,339   copying build/lib/coralme/iJL1678b-ME/building_data/iJO1366b.json -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,360   copying build/lib/coralme/iJL1678b-ME/building_data/orphan_and_spont_reactions.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,362   copying build/lib/coralme/iJL1678b-ME/building_data/translocation_multipliers.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,363   copying build/lib/coralme/iJL1678b-ME/building_data/m_to_me_mets.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,366   copying build/lib/coralme/iJL1678b-ME/building_data/reference_tRNAs.fna -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,436   copying build/lib/coralme/iJL1678b-ME/building_data/lipoprotein_precursors.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,438   copying build/lib/coralme/iJL1678b-ME/building_data/TUs.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,441   copying build/lib/coralme/iJL1678b-ME/building_data/generic_dict.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,443   copying build/lib/coralme/iJL1678b-ME/building_data/translocation_pathways.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,445   copying build/lib/coralme/iJL1678b-ME/building_data/protein_modification.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,448   copying build/lib/coralme/iJL1678b-ME/building_data/protein_corrections.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,450   copying build/lib/coralme/iJL1678b-ME/building_data/RNAs.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,452   copying build/lib/coralme/iJL1678b-ME/building_data/TUs_from_biocyc.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,457   copying build/lib/coralme/iJL1678b-ME/building_data/rna_degradosome.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,459   copying build/lib/coralme/iJL1678b-ME/building_data/reaction_matrix.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,462   copying build/lib/coralme/iJL1678b-ME/building_data/subreaction_matrix.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,464   copying build/lib/coralme/iJL1678b-ME/building_data/transcription_subreactions.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,466   copying build/lib/coralme/iJL1678b-ME/building_data/peptide_release_factors.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,467   copying build/lib/coralme/iJL1678b-ME/building_data/_TUs_from_biocyc.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,473   copying build/lib/coralme/iJL1678b-ME/building_data/peptide_compartment_and_pathways.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:58:40,477   creating build/bdist.linux-armv7l/wheel/coralme/io
2024-11-28T15:58:40,478   copying build/lib/coralme/io/__init__.py -> build/bdist.linux-armv7l/wheel/./coralme/io
2024-11-28T15:58:40,480   copying build/lib/coralme/io/dict.py -> build/bdist.linux-armv7l/wheel/./coralme/io
2024-11-28T15:58:40,483   copying build/lib/coralme/io/json.py -> build/bdist.linux-armv7l/wheel/./coralme/io
2024-11-28T15:58:40,485   copying build/lib/coralme/io/pickle.py -> build/bdist.linux-armv7l/wheel/./coralme/io
2024-11-28T15:58:40,487   copying build/lib/coralme/io/JSONSCHEMA -> build/bdist.linux-armv7l/wheel/./coralme/io
2024-11-28T15:58:40,490   copying build/lib/coralme/_version.py -> build/bdist.linux-armv7l/wheel/./coralme
2024-11-28T15:58:40,494   creating build/bdist.linux-armv7l/wheel/coralme/solver
2024-11-28T15:58:40,495   copying build/lib/coralme/solver/warmLP.cpython-37m-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:58:40,506   copying build/lib/coralme/solver/warmLP.cpython-39-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:58:40,515   copying build/lib/coralme/solver/qvaryME.cpython-37m-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:58:40,526   copying build/lib/coralme/solver/__init__.py -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:58:40,528   copying build/lib/coralme/solver/warmLP.cpython-310-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:58:40,538   copying build/lib/coralme/solver/qwarmLP.cpython-37m-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:58:40,548   copying build/lib/coralme/solver/qsolveME.cpython-310-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:58:40,552   copying build/lib/coralme/solver/qmatrixA.cpython-37m-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:58:40,555   copying build/lib/coralme/solver/qmatrixA.cpython-310-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:58:40,559   copying build/lib/coralme/solver/qwarmLP.cpython-38-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:58:40,569   copying build/lib/coralme/solver/qvaryME.cpython-310-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:58:40,578   copying build/lib/coralme/solver/qmatrixA.cpython-38-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:58:40,582   copying build/lib/coralme/solver/qsolveME.cpython-38-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:58:40,586   copying build/lib/coralme/solver/qmatrixA.cpython-39-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:58:40,590   copying build/lib/coralme/solver/warmLP.cpython-38-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:58:40,638   copying build/lib/coralme/solver/qwarmLP.cpython-39-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:58:40,647   copying build/lib/coralme/solver/qvaryME.cpython-38-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:58:40,657   copying build/lib/coralme/solver/qwarmLP.cpython-310-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:58:40,667   copying build/lib/coralme/solver/qvaryME.cpython-39-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:58:40,677   copying build/lib/coralme/solver/qsolveME.cpython-37m-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:58:40,681   copying build/lib/coralme/solver/qsolveME.cpython-39-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:58:40,685   copying build/lib/coralme/solver/solver.py -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:58:40,688   creating build/bdist.linux-armv7l/wheel/coralme/util
2024-11-28T15:58:40,689   copying build/lib/coralme/util/building.py -> build/bdist.linux-armv7l/wheel/./coralme/util
2024-11-28T15:58:40,692   copying build/lib/coralme/util/__init__.py -> build/bdist.linux-armv7l/wheel/./coralme/util
2024-11-28T15:58:40,694   copying build/lib/coralme/util/dogma.py -> build/bdist.linux-armv7l/wheel/./coralme/util
2024-11-28T15:58:40,696   copying build/lib/coralme/util/massbalance.py -> build/bdist.linux-armv7l/wheel/./coralme/util
2024-11-28T15:58:40,698   running install_egg_info
2024-11-28T15:58:40,730   running egg_info
2024-11-28T15:58:40,757   writing coralME.egg-info/PKG-INFO
2024-11-28T15:58:40,761   writing dependency_links to coralME.egg-info/dependency_links.txt
2024-11-28T15:58:40,762   writing requirements to coralME.egg-info/requires.txt
2024-11-28T15:58:40,764   writing top-level names to coralME.egg-info/top_level.txt
2024-11-28T15:58:40,807   reading manifest file 'coralME.egg-info/SOURCES.txt'
2024-11-28T15:58:40,815   adding license file 'LICENSE'
2024-11-28T15:58:40,823   writing manifest file 'coralME.egg-info/SOURCES.txt'
2024-11-28T15:58:40,824   Copying coralME.egg-info to build/bdist.linux-armv7l/wheel/./coralME-1.0.0.post2-py3.11.egg-info
2024-11-28T15:58:40,834   running install_scripts
2024-11-28T15:58:40,850   creating build/bdist.linux-armv7l/wheel/coralME-1.0.0.post2.dist-info/WHEEL
2024-11-28T15:58:40,853   creating '/tmp/pip-wheel-b2suttkw/coralME-1.0.0.post2-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2024-11-28T15:58:40,856   adding 'coralme/__init__.py'
2024-11-28T15:58:40,859   adding 'coralme/_version.py'
2024-11-28T15:58:40,861   adding 'coralme/builder/__init__.py'
2024-11-28T15:58:40,862   adding 'coralme/builder/column_format.json'
2024-11-28T15:58:40,864   adding 'coralme/builder/compartments.py'
2024-11-28T15:58:40,868   adding 'coralme/builder/curation.py'
2024-11-28T15:58:40,871   adding 'coralme/builder/dictionaries.py'
2024-11-28T15:58:40,873   adding 'coralme/builder/dna_replication.py'
2024-11-28T15:58:40,876   adding 'coralme/builder/flat_files.py'
2024-11-28T15:58:40,877   adding 'coralme/builder/formulas.py'
2024-11-28T15:58:40,881   adding 'coralme/builder/helper_functions.py'
2024-11-28T15:58:40,883   adding 'coralme/builder/homology.py'
2024-11-28T15:58:40,901   adding 'coralme/builder/main.py'
2024-11-28T15:58:40,904   adding 'coralme/builder/modifications.py'
2024-11-28T15:58:40,914   adding 'coralme/builder/organism.py'
2024-11-28T15:58:40,919   adding 'coralme/builder/preprocess_inputs.py'
2024-11-28T15:58:40,921   adding 'coralme/builder/ribosome.py'
2024-11-28T15:58:40,922   adding 'coralme/builder/transcription.py'
2024-11-28T15:58:40,924   adding 'coralme/builder/translation.py'
2024-11-28T15:58:40,925   adding 'coralme/builder/translocation.py'
2024-11-28T15:58:40,927   adding 'coralme/builder/trna_charging.py'
2024-11-28T15:58:40,929   adding 'coralme/core/__init__.py'
2024-11-28T15:58:40,930   adding 'coralme/core/component.py'
2024-11-28T15:58:40,937   adding 'coralme/core/model.py'
2024-11-28T15:58:40,942   adding 'coralme/core/processdata.py'
2024-11-28T15:58:40,951   adding 'coralme/core/reaction.py'
2024-11-28T15:58:40,955   adding 'coralme/iJL1678b-ME/BarEven_subsystem_classification.csv'
2024-11-28T15:58:40,959   adding 'coralme/iJL1678b-ME/building_data/RNAs.txt'
2024-11-28T15:58:40,977   adding 'coralme/iJL1678b-ME/building_data/TUs.txt'
2024-11-28T15:58:40,997   adding 'coralme/iJL1678b-ME/building_data/TUs_from_biocyc.txt'
2024-11-28T15:58:41,021   adding 'coralme/iJL1678b-ME/building_data/_TUs_from_biocyc.txt'
2024-11-28T15:58:41,024   adding 'coralme/iJL1678b-ME/building_data/amino_acid_trna_synthetase.txt'
2024-11-28T15:58:41,025   adding 'coralme/iJL1678b-ME/building_data/cleaved_methionine.txt'
2024-11-28T15:58:41,027   adding 'coralme/iJL1678b-ME/building_data/codon_usage.txt'
2024-11-28T15:58:41,028   adding 'coralme/iJL1678b-ME/building_data/elongation_subreactions.txt'
2024-11-28T15:58:41,036   adding 'coralme/iJL1678b-ME/building_data/enzyme_reaction_association.txt'
2024-11-28T15:58:41,038   adding 'coralme/iJL1678b-ME/building_data/excision_machinery.txt'
2024-11-28T15:58:41,039   adding 'coralme/iJL1678b-ME/building_data/folding_chaperones.txt'
2024-11-28T15:58:41,040   adding 'coralme/iJL1678b-ME/building_data/folding_dict.txt'
2024-11-28T15:58:41,041   adding 'coralme/iJL1678b-ME/building_data/generic_dict.txt'
2024-11-28T15:58:41,097   adding 'coralme/iJL1678b-ME/building_data/genes.txt'
2024-11-28T15:58:45,208   adding 'coralme/iJL1678b-ME/building_data/genome.gb'
2024-11-28T15:58:45,339   adding 'coralme/iJL1678b-ME/building_data/iJO1366b.json'
2024-11-28T15:58:45,345   adding 'coralme/iJL1678b-ME/building_data/initiation_subreactions.txt'
2024-11-28T15:58:45,370   adding 'coralme/iJL1678b-ME/building_data/keffs.json'
2024-11-28T15:58:45,395   adding 'coralme/iJL1678b-ME/building_data/keffs.txt'
2024-11-28T15:58:45,398   adding 'coralme/iJL1678b-ME/building_data/lipid_modifications.txt'
2024-11-28T15:58:45,399   adding 'coralme/iJL1678b-ME/building_data/lipoprotein_precursors.txt'
2024-11-28T15:58:45,450   adding 'coralme/iJL1678b-ME/building_data/m_model.json'
2024-11-28T15:58:45,456   adding 'coralme/iJL1678b-ME/building_data/m_to_me_mets.txt'
2024-11-28T15:58:45,458   adding 'coralme/iJL1678b-ME/building_data/me_metabolites.txt'
2024-11-28T15:58:45,459   adding 'coralme/iJL1678b-ME/building_data/metabolite_corrections.txt'
2024-11-28T15:58:45,467   adding 'coralme/iJL1678b-ME/building_data/metabolites.txt'
2024-11-28T15:58:45,468   adding 'coralme/iJL1678b-ME/building_data/modification.txt'
2024-11-28T15:58:45,470   adding 'coralme/iJL1678b-ME/building_data/orphan_and_spont_reactions.txt'
2024-11-28T15:58:45,472   adding 'coralme/iJL1678b-ME/building_data/peptide_compartment_and_pathways.txt'
2024-11-28T15:58:45,474   adding 'coralme/iJL1678b-ME/building_data/peptide_release_factors.txt'
2024-11-28T15:58:45,476   adding 'coralme/iJL1678b-ME/building_data/post_transcriptional_modification_of_RNA.txt'
2024-11-28T15:58:45,483   adding 'coralme/iJL1678b-ME/building_data/protein_complexes.txt'
2024-11-28T15:58:45,485   adding 'coralme/iJL1678b-ME/building_data/protein_corrections.txt'
2024-11-28T15:58:45,489   adding 'coralme/iJL1678b-ME/building_data/protein_modification.txt'
2024-11-28T15:58:45,497   adding 'coralme/iJL1678b-ME/building_data/proteins.txt'
2024-11-28T15:58:45,499   adding 'coralme/iJL1678b-ME/building_data/reaction_corrections.txt'
2024-11-28T15:58:45,502   adding 'coralme/iJL1678b-ME/building_data/reaction_matrix.txt'
2024-11-28T15:58:48,016   adding 'coralme/iJL1678b-ME/building_data/reference_tRNAs.fna'
2024-11-28T15:58:48,046   adding 'coralme/iJL1678b-ME/building_data/rho_independent.txt'
2024-11-28T15:58:48,048   adding 'coralme/iJL1678b-ME/building_data/ribosomal_proteins.txt'
2024-11-28T15:58:48,049   adding 'coralme/iJL1678b-ME/building_data/ribosome_subreactions.txt'
2024-11-28T15:58:48,050   adding 'coralme/iJL1678b-ME/building_data/rna_degradosome.txt'
2024-11-28T15:58:48,052   adding 'coralme/iJL1678b-ME/building_data/rna_modification.txt'
2024-11-28T15:58:48,053   adding 'coralme/iJL1678b-ME/building_data/rrna_modifications.txt'
2024-11-28T15:58:48,055   adding 'coralme/iJL1678b-ME/building_data/sigma_factors.txt'
2024-11-28T15:58:48,056   adding 'coralme/iJL1678b-ME/building_data/special_modifications.txt'
2024-11-28T15:58:48,057   adding 'coralme/iJL1678b-ME/building_data/special_trna_subreactions.txt'
2024-11-28T15:58:48,058   adding 'coralme/iJL1678b-ME/building_data/stable_RNAs.txt'
2024-11-28T15:58:48,060   adding 'coralme/iJL1678b-ME/building_data/subreaction_matrix.txt'
2024-11-28T15:58:48,061   adding 'coralme/iJL1678b-ME/building_data/subsystem_classification.txt'
2024-11-28T15:58:48,062   adding 'coralme/iJL1678b-ME/building_data/termination_subreactions.txt'
2024-11-28T15:58:48,064   adding 'coralme/iJL1678b-ME/building_data/transcription_subreactions.txt'
2024-11-28T15:58:48,065   adding 'coralme/iJL1678b-ME/building_data/translocation_multipliers.txt'
2024-11-28T15:58:48,066   adding 'coralme/iJL1678b-ME/building_data/translocation_pathways.txt'
2024-11-28T15:58:48,068   adding 'coralme/iJL1678b-ME/building_data/trna_modification.txt'
2024-11-28T15:58:48,070   adding 'coralme/io/JSONSCHEMA'
2024-11-28T15:58:48,071   adding 'coralme/io/__init__.py'
2024-11-28T15:58:48,073   adding 'coralme/io/dict.py'
2024-11-28T15:58:48,075   adding 'coralme/io/json.py'
2024-11-28T15:58:48,076   adding 'coralme/io/pickle.py'
2024-11-28T15:58:48,078   adding 'coralme/licenses/LICENSE-cobrame'
2024-11-28T15:58:48,079   adding 'coralme/licenses/LICENSE-ecolime'
2024-11-28T15:58:48,080   adding 'coralme/licenses/LICENSE-solvemepy'
2024-11-28T15:58:48,082   adding 'coralme/solver/__init__.py'
2024-11-28T15:58:48,098   adding 'coralme/solver/qmatrixA.cpython-310-x86_64-linux-gnu.so'
2024-11-28T15:58:48,114   adding 'coralme/solver/qmatrixA.cpython-37m-x86_64-linux-gnu.so'
2024-11-28T15:58:48,131   adding 'coralme/solver/qmatrixA.cpython-38-x86_64-linux-gnu.so'
2024-11-28T15:58:48,148   adding 'coralme/solver/qmatrixA.cpython-39-x86_64-linux-gnu.so'
2024-11-28T15:58:48,165   adding 'coralme/solver/qsolveME.cpython-310-x86_64-linux-gnu.so'
2024-11-28T15:58:48,181   adding 'coralme/solver/qsolveME.cpython-37m-x86_64-linux-gnu.so'
2024-11-28T15:58:48,198   adding 'coralme/solver/qsolveME.cpython-38-x86_64-linux-gnu.so'
2024-11-28T15:58:48,214   adding 'coralme/solver/qsolveME.cpython-39-x86_64-linux-gnu.so'
2024-11-28T15:58:48,314   adding 'coralme/solver/qvaryME.cpython-310-x86_64-linux-gnu.so'
2024-11-28T15:58:48,414   adding 'coralme/solver/qvaryME.cpython-37m-x86_64-linux-gnu.so'
2024-11-28T15:58:48,524   adding 'coralme/solver/qvaryME.cpython-38-x86_64-linux-gnu.so'
2024-11-28T15:58:48,627   adding 'coralme/solver/qvaryME.cpython-39-x86_64-linux-gnu.so'
2024-11-28T15:58:48,729   adding 'coralme/solver/qwarmLP.cpython-310-x86_64-linux-gnu.so'
2024-11-28T15:58:48,829   adding 'coralme/solver/qwarmLP.cpython-37m-x86_64-linux-gnu.so'
2024-11-28T15:58:48,931   adding 'coralme/solver/qwarmLP.cpython-38-x86_64-linux-gnu.so'
2024-11-28T15:58:49,032   adding 'coralme/solver/qwarmLP.cpython-39-x86_64-linux-gnu.so'
2024-11-28T15:58:49,037   adding 'coralme/solver/solver.py'
2024-11-28T15:58:49,142   adding 'coralme/solver/warmLP.cpython-310-x86_64-linux-gnu.so'
2024-11-28T15:58:49,250   adding 'coralme/solver/warmLP.cpython-37m-x86_64-linux-gnu.so'
2024-11-28T15:58:49,358   adding 'coralme/solver/warmLP.cpython-38-x86_64-linux-gnu.so'
2024-11-28T15:58:49,467   adding 'coralme/solver/warmLP.cpython-39-x86_64-linux-gnu.so'
2024-11-28T15:58:49,472   adding 'coralme/util/__init__.py'
2024-11-28T15:58:49,478   adding 'coralme/util/building.py'
2024-11-28T15:58:49,480   adding 'coralme/util/dogma.py'
2024-11-28T15:58:49,482   adding 'coralme/util/massbalance.py'
2024-11-28T15:58:49,483   adding 'coralME-1.0.0.post2.dist-info/LICENSE'
2024-11-28T15:58:49,484   adding 'coralME-1.0.0.post2.dist-info/METADATA'
2024-11-28T15:58:49,485   adding 'coralME-1.0.0.post2.dist-info/WHEEL'
2024-11-28T15:58:49,486   adding 'coralME-1.0.0.post2.dist-info/top_level.txt'
2024-11-28T15:58:49,488   adding 'coralME-1.0.0.post2.dist-info/RECORD'
2024-11-28T15:58:49,640   removing build/bdist.linux-armv7l/wheel
2024-11-28T15:58:49,811   Building wheel for coralme (setup.py): finished with status 'done'
2024-11-28T15:58:49,900   Created wheel for coralme: filename=coralME-1.0.0.post2-py3-none-any.whl size=8697073 sha256=3aa90c51300fda98a82676c82c521489145f64178c9efc2d3fb67daba9e06033
2024-11-28T15:58:49,901   Stored in directory: /tmp/pip-ephem-wheel-cache-alrl053z/wheels/d2/b1/86/328b7547ad9ab013b5684ccb4acc2a6b0e9e2a18e8f2caa648
2024-11-28T15:58:49,918 Successfully built coralme
2024-11-28T15:58:50,122 Removed build tracker: '/tmp/pip-build-tracker-1hy8b93_'