2024-11-28T15:49:14,493 Created temporary directory: /tmp/pip-build-tracker-po2dlbwu
2024-11-28T15:49:14,845 Initialized build tracking at /tmp/pip-build-tracker-po2dlbwu
2024-11-28T15:49:14,846 Created build tracker: /tmp/pip-build-tracker-po2dlbwu
2024-11-28T15:49:14,848 Entered build tracker: /tmp/pip-build-tracker-po2dlbwu
2024-11-28T15:49:14,851 Created temporary directory: /tmp/pip-wheel-f5gfgv25
2024-11-28T15:49:14,862 Created temporary directory: /tmp/pip-ephem-wheel-cache-mvcty4gc
2024-11-28T15:49:14,942 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2024-11-28T15:49:14,946 2 location(s) to search for versions of coralme:
2024-11-28T15:49:14,946 * https://pypi.org/simple/coralme/
2024-11-28T15:49:14,946 * https://www.piwheels.org/simple/coralme/
2024-11-28T15:49:14,947 Fetching project page and analyzing links: https://pypi.org/simple/coralme/
2024-11-28T15:49:14,948 Getting page https://pypi.org/simple/coralme/
2024-11-28T15:49:14,950 Found index url https://pypi.org/simple/
2024-11-28T15:49:15,185 Fetched page https://pypi.org/simple/coralme/ as application/vnd.pypi.simple.v1+json
2024-11-28T15:49:15,192   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)
2024-11-28T15:49:15,193   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
2024-11-28T15:49:15,194   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)
2024-11-28T15:49:15,195   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
2024-11-28T15:49:15,196   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)
2024-11-28T15:49:15,197   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
2024-11-28T15:49:15,198   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)
2024-11-28T15:49:15,200   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
2024-11-28T15:49:15,201   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)
2024-11-28T15:49:15,202   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
2024-11-28T15:49:15,202   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)
2024-11-28T15:49:15,204   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
2024-11-28T15:49:15,205   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)
2024-11-28T15:49:15,206   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
2024-11-28T15:49:15,207   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)
2024-11-28T15:49:15,208   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
2024-11-28T15:49:15,209   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)
2024-11-28T15:49:15,210   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
2024-11-28T15:49:15,211   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)
2024-11-28T15:49:15,212   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
2024-11-28T15:49:15,212   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)
2024-11-28T15:49:15,214   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
2024-11-28T15:49:15,214   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)
2024-11-28T15:49:15,216   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
2024-11-28T15:49:15,216   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)
2024-11-28T15:49:15,218   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
2024-11-28T15:49:15,218   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)
2024-11-28T15:49:15,220   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
2024-11-28T15:49:15,221 Fetching project page and analyzing links: https://www.piwheels.org/simple/coralme/
2024-11-28T15:49:15,222 Getting page https://www.piwheels.org/simple/coralme/
2024-11-28T15:49:15,223 Found index url https://www.piwheels.org/simple/
2024-11-28T15:49:15,384 Fetched page https://www.piwheels.org/simple/coralme/ as text/html
2024-11-28T15:49:15,386   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)
2024-11-28T15:49:15,387 Skipping link: not a file: https://www.piwheels.org/simple/coralme/
2024-11-28T15:49:15,387 Skipping link: not a file: https://pypi.org/simple/coralme/
2024-11-28T15:49:15,408 Given no hashes to check 1 links for project 'coralme': discarding no candidates
2024-11-28T15:49:15,410 Collecting coralme==1.0.0.post1
2024-11-28T15:49:15,412   Created temporary directory: /tmp/pip-unpack-lmmcz1l4
2024-11-28T15:49:15,639   Downloading coralme-1.0.0.post1.tar.gz (8.5 MB)
2024-11-28T15:49:18,836   Added coralme==1.0.0.post1 from https://files.pythonhosted.org/packages/0a/a6/69e5b9146c97f78f52ff4ae7cabce9cf6ba53af5a1437f16980d55175efb/coralme-1.0.0.post1.tar.gz to build tracker '/tmp/pip-build-tracker-po2dlbwu'
2024-11-28T15:49:18,838   Running setup.py (path:/tmp/pip-wheel-f5gfgv25/coralme_5be67c24ec534022b5ce8ecd29af7ab7/setup.py) egg_info for package coralme
2024-11-28T15:49:18,839   Created temporary directory: /tmp/pip-pip-egg-info-w_5atkcd
2024-11-28T15:49:18,839   Preparing metadata (setup.py): started
2024-11-28T15:49:18,841   Running command python setup.py egg_info
2024-11-28T15:49:19,903   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:337: InformationOnly: Normalizing '1.0.0-1' to '1.0.0.post1'
2024-11-28T15:49:19,903     self.metadata.version = self._normalize_version(self.metadata.version)
2024-11-28T15:49:19,957   running egg_info
2024-11-28T15:49:19,985   creating /tmp/pip-pip-egg-info-w_5atkcd/coralME.egg-info
2024-11-28T15:49:19,986   writing /tmp/pip-pip-egg-info-w_5atkcd/coralME.egg-info/PKG-INFO
2024-11-28T15:49:19,989   writing dependency_links to /tmp/pip-pip-egg-info-w_5atkcd/coralME.egg-info/dependency_links.txt
2024-11-28T15:49:19,991   writing requirements to /tmp/pip-pip-egg-info-w_5atkcd/coralME.egg-info/requires.txt
2024-11-28T15:49:19,992   writing top-level names to /tmp/pip-pip-egg-info-w_5atkcd/coralME.egg-info/top_level.txt
2024-11-28T15:49:19,994   writing manifest file '/tmp/pip-pip-egg-info-w_5atkcd/coralME.egg-info/SOURCES.txt'
2024-11-28T15:49:20,099   reading manifest file '/tmp/pip-pip-egg-info-w_5atkcd/coralME.egg-info/SOURCES.txt'
2024-11-28T15:49:20,100   adding license file 'LICENSE'
2024-11-28T15:49:20,106   writing manifest file '/tmp/pip-pip-egg-info-w_5atkcd/coralME.egg-info/SOURCES.txt'
2024-11-28T15:49:20,215   Preparing metadata (setup.py): finished with status 'done'
2024-11-28T15:49:20,220   Source in /tmp/pip-wheel-f5gfgv25/coralme_5be67c24ec534022b5ce8ecd29af7ab7 has version 1.0.0.post1, which satisfies requirement coralme==1.0.0.post1 from https://files.pythonhosted.org/packages/0a/a6/69e5b9146c97f78f52ff4ae7cabce9cf6ba53af5a1437f16980d55175efb/coralme-1.0.0.post1.tar.gz
2024-11-28T15:49:20,221   Removed coralme==1.0.0.post1 from https://files.pythonhosted.org/packages/0a/a6/69e5b9146c97f78f52ff4ae7cabce9cf6ba53af5a1437f16980d55175efb/coralme-1.0.0.post1.tar.gz from build tracker '/tmp/pip-build-tracker-po2dlbwu'
2024-11-28T15:49:20,229 Created temporary directory: /tmp/pip-unpack-qi55113b
2024-11-28T15:49:20,230 Created temporary directory: /tmp/pip-unpack-bhivb0lk
2024-11-28T15:49:20,231 Building wheels for collected packages: coralme
2024-11-28T15:49:20,235   Created temporary directory: /tmp/pip-wheel-3qa2xji7
2024-11-28T15:49:20,236   Building wheel for coralme (setup.py): started
2024-11-28T15:49:20,237   Destination directory: /tmp/pip-wheel-3qa2xji7
2024-11-28T15:49:20,237   Running command python setup.py bdist_wheel
2024-11-28T15:49:21,281   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:337: InformationOnly: Normalizing '1.0.0-1' to '1.0.0.post1'
2024-11-28T15:49:21,281     self.metadata.version = self._normalize_version(self.metadata.version)
2024-11-28T15:49:21,309   running bdist_wheel
2024-11-28T15:49:21,444   running build
2024-11-28T15:49:21,445   running build_py
2024-11-28T15:49:21,476   creating build/lib/coralme
2024-11-28T15:49:21,478   copying coralme/_version.py -> build/lib/coralme
2024-11-28T15:49:21,480   copying coralme/__init__.py -> build/lib/coralme
2024-11-28T15:49:21,483   creating build/lib/coralme/io
2024-11-28T15:49:21,484   copying coralme/io/dict.py -> build/lib/coralme/io
2024-11-28T15:49:21,487   copying coralme/io/pickle.py -> build/lib/coralme/io
2024-11-28T15:49:21,489   copying coralme/io/json.py -> build/lib/coralme/io
2024-11-28T15:49:21,491   copying coralme/io/__init__.py -> build/lib/coralme/io
2024-11-28T15:49:21,494   creating build/lib/coralme/builder
2024-11-28T15:49:21,495   copying coralme/builder/curation.py -> build/lib/coralme/builder
2024-11-28T15:49:21,499   copying coralme/builder/organism.py -> build/lib/coralme/builder
2024-11-28T15:49:21,503   copying coralme/builder/translocation.py -> build/lib/coralme/builder
2024-11-28T15:49:21,506   copying coralme/builder/flat_files.py -> build/lib/coralme/builder
2024-11-28T15:49:21,508   copying coralme/builder/homology.py -> build/lib/coralme/builder
2024-11-28T15:49:21,510   copying coralme/builder/transcription.py -> build/lib/coralme/builder
2024-11-28T15:49:21,512   copying coralme/builder/dictionaries.py -> build/lib/coralme/builder
2024-11-28T15:49:21,515   copying coralme/builder/helper_functions.py -> build/lib/coralme/builder
2024-11-28T15:49:21,518   copying coralme/builder/ribosome.py -> build/lib/coralme/builder
2024-11-28T15:49:21,520   copying coralme/builder/modifications.py -> build/lib/coralme/builder
2024-11-28T15:49:21,522   copying coralme/builder/main.py -> build/lib/coralme/builder
2024-11-28T15:49:21,528   copying coralme/builder/translation.py -> build/lib/coralme/builder
2024-11-28T15:49:21,530   copying coralme/builder/dna_replication.py -> build/lib/coralme/builder
2024-11-28T15:49:21,532   copying coralme/builder/__init__.py -> build/lib/coralme/builder
2024-11-28T15:49:21,534   copying coralme/builder/compartments.py -> build/lib/coralme/builder
2024-11-28T15:49:21,537   copying coralme/builder/trna_charging.py -> build/lib/coralme/builder
2024-11-28T15:49:21,538   copying coralme/builder/preprocess_inputs.py -> build/lib/coralme/builder
2024-11-28T15:49:21,542   copying coralme/builder/formulas.py -> build/lib/coralme/builder
2024-11-28T15:49:21,544   creating build/lib/coralme/util
2024-11-28T15:49:21,545   copying coralme/util/building.py -> build/lib/coralme/util
2024-11-28T15:49:21,548   copying coralme/util/massbalance.py -> build/lib/coralme/util
2024-11-28T15:49:21,551   copying coralme/util/dogma.py -> build/lib/coralme/util
2024-11-28T15:49:21,553   copying coralme/util/__init__.py -> build/lib/coralme/util
2024-11-28T15:49:21,555   creating build/lib/coralme/core
2024-11-28T15:49:21,556   copying coralme/core/component.py -> build/lib/coralme/core
2024-11-28T15:49:21,559   copying coralme/core/processdata.py -> build/lib/coralme/core
2024-11-28T15:49:21,562   copying coralme/core/reaction.py -> build/lib/coralme/core
2024-11-28T15:49:21,566   copying coralme/core/__init__.py -> build/lib/coralme/core
2024-11-28T15:49:21,567   copying coralme/core/model.py -> build/lib/coralme/core
2024-11-28T15:49:21,572   creating build/lib/coralme/solver
2024-11-28T15:49:21,573   copying coralme/solver/solver.py -> build/lib/coralme/solver
2024-11-28T15:49:21,576   copying coralme/solver/__init__.py -> build/lib/coralme/solver
2024-11-28T15:49:21,587   creating build/lib/coralme/iJL1678b-ME
2024-11-28T15:49:21,589   copying coralme/iJL1678b-ME/BarEven_subsystem_classification.csv -> build/lib/coralme/iJL1678b-ME
2024-11-28T15:49:21,592   creating build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,593   copying coralme/iJL1678b-ME/building_data/TUs_from_biocyc.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,599   copying coralme/iJL1678b-ME/building_data/ribosomal_proteins.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,601   copying coralme/iJL1678b-ME/building_data/lipid_modifications.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,603   copying coralme/iJL1678b-ME/building_data/reference_tRNAs.fna -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,672   copying coralme/iJL1678b-ME/building_data/metabolite_corrections.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,674   copying coralme/iJL1678b-ME/building_data/protein_complexes.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,678   copying coralme/iJL1678b-ME/building_data/stable_RNAs.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,680   copying coralme/iJL1678b-ME/building_data/codon_usage.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,682   copying coralme/iJL1678b-ME/building_data/amino_acid_trna_synthetase.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,685   copying coralme/iJL1678b-ME/building_data/post_transcriptional_modification_of_RNA.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,687   copying coralme/iJL1678b-ME/building_data/elongation_subreactions.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,689   copying coralme/iJL1678b-ME/building_data/metabolites.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,693   copying coralme/iJL1678b-ME/building_data/iJO1366b.json -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,710   copying coralme/iJL1678b-ME/building_data/enzyme_reaction_association.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,714   copying coralme/iJL1678b-ME/building_data/proteins.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,718   copying coralme/iJL1678b-ME/building_data/sigma_factors.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,721   copying coralme/iJL1678b-ME/building_data/me_metabolites.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,725   copying coralme/iJL1678b-ME/building_data/transcription_subreactions.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,727   copying coralme/iJL1678b-ME/building_data/subreaction_matrix.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,730   copying coralme/iJL1678b-ME/building_data/genome.gb -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,915   copying coralme/iJL1678b-ME/building_data/translocation_multipliers.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,918   copying coralme/iJL1678b-ME/building_data/trna_modification.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,920   copying coralme/iJL1678b-ME/building_data/m_model.json -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,935   copying coralme/iJL1678b-ME/building_data/protein_corrections.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,937   copying coralme/iJL1678b-ME/building_data/cleaved_methionine.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,940   copying coralme/iJL1678b-ME/building_data/genes.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,947   copying coralme/iJL1678b-ME/building_data/orphan_and_spont_reactions.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,949   copying coralme/iJL1678b-ME/building_data/translocation_pathways.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,951   copying coralme/iJL1678b-ME/building_data/rna_modification.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,953   copying coralme/iJL1678b-ME/building_data/TUs.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,958   copying coralme/iJL1678b-ME/building_data/generic_dict.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,960   copying coralme/iJL1678b-ME/building_data/RNAs.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,962   copying coralme/iJL1678b-ME/building_data/_TUs_from_biocyc.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,969   copying coralme/iJL1678b-ME/building_data/reaction_matrix.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,972   copying coralme/iJL1678b-ME/building_data/rna_degradosome.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,974   copying coralme/iJL1678b-ME/building_data/lipoprotein_precursors.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,976   copying coralme/iJL1678b-ME/building_data/folding_dict.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,978   copying coralme/iJL1678b-ME/building_data/excision_machinery.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,980   copying coralme/iJL1678b-ME/building_data/special_modifications.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,982   copying coralme/iJL1678b-ME/building_data/peptide_compartment_and_pathways.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,985   copying coralme/iJL1678b-ME/building_data/rho_independent.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,987   copying coralme/iJL1678b-ME/building_data/special_trna_subreactions.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,989   copying coralme/iJL1678b-ME/building_data/termination_subreactions.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,991   copying coralme/iJL1678b-ME/building_data/peptide_release_factors.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,993   copying coralme/iJL1678b-ME/building_data/reaction_corrections.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,995   copying coralme/iJL1678b-ME/building_data/m_to_me_mets.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:21,998   copying coralme/iJL1678b-ME/building_data/folding_chaperones.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,000   copying coralme/iJL1678b-ME/building_data/rrna_modifications.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,002   copying coralme/iJL1678b-ME/building_data/modification.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,004   copying coralme/iJL1678b-ME/building_data/protein_modification.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,007   copying coralme/iJL1678b-ME/building_data/keffs.json -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,018   copying coralme/iJL1678b-ME/building_data/keffs.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,025   copying coralme/iJL1678b-ME/building_data/ribosome_subreactions.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,026   copying coralme/iJL1678b-ME/building_data/initiation_subreactions.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,029   copying coralme/iJL1678b-ME/building_data/subsystem_classification.txt -> build/lib/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,031   copying coralme/solver/qvaryME.cpython-39-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:49:22,041   copying coralme/solver/qsolveME.cpython-310-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:49:22,045   copying coralme/solver/qwarmLP.cpython-38-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:49:22,056   copying coralme/solver/warmLP.cpython-37m-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:49:22,067   copying coralme/solver/qwarmLP.cpython-39-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:49:22,078   copying coralme/solver/qsolveME.cpython-39-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:49:22,082   copying coralme/solver/warmLP.cpython-310-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:49:22,093   copying coralme/solver/qsolveME.cpython-37m-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:49:22,097   copying coralme/solver/qvaryME.cpython-37m-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:49:22,107   copying coralme/solver/qmatrixA.cpython-310-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:49:22,112   copying coralme/solver/warmLP.cpython-39-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:49:22,125   copying coralme/solver/qwarmLP.cpython-310-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:49:22,135   copying coralme/solver/qmatrixA.cpython-38-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:49:22,140   copying coralme/solver/qvaryME.cpython-38-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:49:22,150   copying coralme/solver/warmLP.cpython-38-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:49:22,161   copying coralme/solver/qmatrixA.cpython-39-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:49:22,166   copying coralme/solver/qsolveME.cpython-38-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:49:22,170   copying coralme/solver/qwarmLP.cpython-37m-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:49:22,180   copying coralme/solver/qvaryME.cpython-310-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:49:22,190   copying coralme/solver/qmatrixA.cpython-37m-x86_64-linux-gnu.so -> build/lib/coralme/solver
2024-11-28T15:49:22,194   copying coralme/io/JSONSCHEMA -> build/lib/coralme/io
2024-11-28T15:49:22,198   copying coralme/builder/column_format.json -> build/lib/coralme/builder
2024-11-28T15:49:22,201   creating build/lib/coralme/licenses
2024-11-28T15:49:22,202   copying coralme/licenses/LICENSE-cobrame -> build/lib/coralme/licenses
2024-11-28T15:49:22,205   copying coralme/licenses/LICENSE-ecolime -> build/lib/coralme/licenses
2024-11-28T15:49:22,207   copying coralme/licenses/LICENSE-solvemepy -> build/lib/coralme/licenses
2024-11-28T15:49:22,240   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2024-11-28T15:49:22,241   !!

2024-11-28T15:49:22,242           ********************************************************************************
2024-11-28T15:49:22,243           Please avoid running ``setup.py`` directly.
2024-11-28T15:49:22,243           Instead, use pypa/build, pypa/installer or other
2024-11-28T15:49:22,244           standards-based tools.

2024-11-28T15:49:22,245           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2024-11-28T15:49:22,246           ********************************************************************************

2024-11-28T15:49:22,247   !!
2024-11-28T15:49:22,247     self.initialize_options()
2024-11-28T15:49:22,273   installing to build/bdist.linux-armv7l/wheel
2024-11-28T15:49:22,273   running install
2024-11-28T15:49:22,298   running install_lib
2024-11-28T15:49:22,327   creating build/bdist.linux-armv7l/wheel
2024-11-28T15:49:22,330   creating build/bdist.linux-armv7l/wheel/coralme
2024-11-28T15:49:22,332   creating build/bdist.linux-armv7l/wheel/coralme/iJL1678b-ME
2024-11-28T15:49:22,334   copying build/lib/coralme/iJL1678b-ME/BarEven_subsystem_classification.csv -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME
2024-11-28T15:49:22,338   creating build/bdist.linux-armv7l/wheel/coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,339   copying build/lib/coralme/iJL1678b-ME/building_data/TUs_from_biocyc.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,346   copying build/lib/coralme/iJL1678b-ME/building_data/ribosomal_proteins.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,348   copying build/lib/coralme/iJL1678b-ME/building_data/lipid_modifications.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,349   copying build/lib/coralme/iJL1678b-ME/building_data/reference_tRNAs.fna -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,422   copying build/lib/coralme/iJL1678b-ME/building_data/metabolite_corrections.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,424   copying build/lib/coralme/iJL1678b-ME/building_data/protein_complexes.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,428   copying build/lib/coralme/iJL1678b-ME/building_data/stable_RNAs.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,430   copying build/lib/coralme/iJL1678b-ME/building_data/codon_usage.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,431   copying build/lib/coralme/iJL1678b-ME/building_data/amino_acid_trna_synthetase.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,433   copying build/lib/coralme/iJL1678b-ME/building_data/post_transcriptional_modification_of_RNA.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,435   copying build/lib/coralme/iJL1678b-ME/building_data/elongation_subreactions.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,437   copying build/lib/coralme/iJL1678b-ME/building_data/metabolites.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,441   copying build/lib/coralme/iJL1678b-ME/building_data/iJO1366b.json -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,456   copying build/lib/coralme/iJL1678b-ME/building_data/enzyme_reaction_association.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,460   copying build/lib/coralme/iJL1678b-ME/building_data/proteins.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,463   copying build/lib/coralme/iJL1678b-ME/building_data/sigma_factors.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,465   copying build/lib/coralme/iJL1678b-ME/building_data/me_metabolites.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,468   copying build/lib/coralme/iJL1678b-ME/building_data/transcription_subreactions.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,469   copying build/lib/coralme/iJL1678b-ME/building_data/subreaction_matrix.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,472   copying build/lib/coralme/iJL1678b-ME/building_data/genome.gb -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,671   copying build/lib/coralme/iJL1678b-ME/building_data/translocation_multipliers.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,673   copying build/lib/coralme/iJL1678b-ME/building_data/trna_modification.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,675   copying build/lib/coralme/iJL1678b-ME/building_data/m_model.json -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,690   copying build/lib/coralme/iJL1678b-ME/building_data/protein_corrections.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,692   copying build/lib/coralme/iJL1678b-ME/building_data/cleaved_methionine.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,694   copying build/lib/coralme/iJL1678b-ME/building_data/genes.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,700   copying build/lib/coralme/iJL1678b-ME/building_data/orphan_and_spont_reactions.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,702   copying build/lib/coralme/iJL1678b-ME/building_data/translocation_pathways.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,704   copying build/lib/coralme/iJL1678b-ME/building_data/rna_modification.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,706   copying build/lib/coralme/iJL1678b-ME/building_data/TUs.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,709   copying build/lib/coralme/iJL1678b-ME/building_data/generic_dict.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,711   copying build/lib/coralme/iJL1678b-ME/building_data/RNAs.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,714   copying build/lib/coralme/iJL1678b-ME/building_data/_TUs_from_biocyc.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,721   copying build/lib/coralme/iJL1678b-ME/building_data/reaction_matrix.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,724   copying build/lib/coralme/iJL1678b-ME/building_data/rna_degradosome.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,726   copying build/lib/coralme/iJL1678b-ME/building_data/lipoprotein_precursors.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,727   copying build/lib/coralme/iJL1678b-ME/building_data/folding_dict.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,729   copying build/lib/coralme/iJL1678b-ME/building_data/excision_machinery.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,731   copying build/lib/coralme/iJL1678b-ME/building_data/special_modifications.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,733   copying build/lib/coralme/iJL1678b-ME/building_data/peptide_compartment_and_pathways.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,735   copying build/lib/coralme/iJL1678b-ME/building_data/rho_independent.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,737   copying build/lib/coralme/iJL1678b-ME/building_data/special_trna_subreactions.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,739   copying build/lib/coralme/iJL1678b-ME/building_data/termination_subreactions.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,741   copying build/lib/coralme/iJL1678b-ME/building_data/peptide_release_factors.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,743   copying build/lib/coralme/iJL1678b-ME/building_data/reaction_corrections.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,744   copying build/lib/coralme/iJL1678b-ME/building_data/m_to_me_mets.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,747   copying build/lib/coralme/iJL1678b-ME/building_data/folding_chaperones.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,749   copying build/lib/coralme/iJL1678b-ME/building_data/rrna_modifications.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,750   copying build/lib/coralme/iJL1678b-ME/building_data/modification.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,752   copying build/lib/coralme/iJL1678b-ME/building_data/protein_modification.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,755   copying build/lib/coralme/iJL1678b-ME/building_data/keffs.json -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,763   copying build/lib/coralme/iJL1678b-ME/building_data/keffs.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,769   copying build/lib/coralme/iJL1678b-ME/building_data/ribosome_subreactions.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,771   copying build/lib/coralme/iJL1678b-ME/building_data/initiation_subreactions.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,773   copying build/lib/coralme/iJL1678b-ME/building_data/subsystem_classification.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data
2024-11-28T15:49:22,775   creating build/bdist.linux-armv7l/wheel/coralme/io
2024-11-28T15:49:22,776   copying build/lib/coralme/io/JSONSCHEMA -> build/bdist.linux-armv7l/wheel/./coralme/io
2024-11-28T15:49:22,779   copying build/lib/coralme/io/dict.py -> build/bdist.linux-armv7l/wheel/./coralme/io
2024-11-28T15:49:22,781   copying build/lib/coralme/io/pickle.py -> build/bdist.linux-armv7l/wheel/./coralme/io
2024-11-28T15:49:22,783   copying build/lib/coralme/io/json.py -> build/bdist.linux-armv7l/wheel/./coralme/io
2024-11-28T15:49:22,786   copying build/lib/coralme/io/__init__.py -> build/bdist.linux-armv7l/wheel/./coralme/io
2024-11-28T15:49:22,789   creating build/bdist.linux-armv7l/wheel/coralme/builder
2024-11-28T15:49:22,790   copying build/lib/coralme/builder/curation.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:49:22,794   copying build/lib/coralme/builder/organism.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:49:22,798   copying build/lib/coralme/builder/translocation.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:49:22,800   copying build/lib/coralme/builder/flat_files.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:49:22,803   copying build/lib/coralme/builder/homology.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:49:22,805   copying build/lib/coralme/builder/transcription.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:49:22,807   copying build/lib/coralme/builder/dictionaries.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:49:22,810   copying build/lib/coralme/builder/helper_functions.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:49:22,813   copying build/lib/coralme/builder/ribosome.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:49:22,815   copying build/lib/coralme/builder/modifications.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:49:22,818   copying build/lib/coralme/builder/main.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:49:22,822   copying build/lib/coralme/builder/translation.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:49:22,824   copying build/lib/coralme/builder/dna_replication.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:49:22,826   copying build/lib/coralme/builder/__init__.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:49:22,828   copying build/lib/coralme/builder/compartments.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:49:22,830   copying build/lib/coralme/builder/trna_charging.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:49:22,832   copying build/lib/coralme/builder/preprocess_inputs.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:49:22,835   copying build/lib/coralme/builder/formulas.py -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:49:22,837   copying build/lib/coralme/builder/column_format.json -> build/bdist.linux-armv7l/wheel/./coralme/builder
2024-11-28T15:49:22,839   creating build/bdist.linux-armv7l/wheel/coralme/util
2024-11-28T15:49:22,840   copying build/lib/coralme/util/building.py -> build/bdist.linux-armv7l/wheel/./coralme/util
2024-11-28T15:49:22,843   copying build/lib/coralme/util/massbalance.py -> build/bdist.linux-armv7l/wheel/./coralme/util
2024-11-28T15:49:22,846   copying build/lib/coralme/util/dogma.py -> build/bdist.linux-armv7l/wheel/./coralme/util
2024-11-28T15:49:22,848   copying build/lib/coralme/util/__init__.py -> build/bdist.linux-armv7l/wheel/./coralme/util
2024-11-28T15:49:22,850   copying build/lib/coralme/_version.py -> build/bdist.linux-armv7l/wheel/./coralme
2024-11-28T15:49:22,854   creating build/bdist.linux-armv7l/wheel/coralme/licenses
2024-11-28T15:49:22,855   copying build/lib/coralme/licenses/LICENSE-cobrame -> build/bdist.linux-armv7l/wheel/./coralme/licenses
2024-11-28T15:49:22,857   copying build/lib/coralme/licenses/LICENSE-ecolime -> build/bdist.linux-armv7l/wheel/./coralme/licenses
2024-11-28T15:49:22,859   copying build/lib/coralme/licenses/LICENSE-solvemepy -> build/bdist.linux-armv7l/wheel/./coralme/licenses
2024-11-28T15:49:22,861   copying build/lib/coralme/__init__.py -> build/bdist.linux-armv7l/wheel/./coralme
2024-11-28T15:49:22,863   creating build/bdist.linux-armv7l/wheel/coralme/core
2024-11-28T15:49:22,865   copying build/lib/coralme/core/component.py -> build/bdist.linux-armv7l/wheel/./coralme/core
2024-11-28T15:49:22,867   copying build/lib/coralme/core/processdata.py -> build/bdist.linux-armv7l/wheel/./coralme/core
2024-11-28T15:49:22,871   copying build/lib/coralme/core/reaction.py -> build/bdist.linux-armv7l/wheel/./coralme/core
2024-11-28T15:49:22,876   copying build/lib/coralme/core/__init__.py -> build/bdist.linux-armv7l/wheel/./coralme/core
2024-11-28T15:49:22,880   copying build/lib/coralme/core/model.py -> build/bdist.linux-armv7l/wheel/./coralme/core
2024-11-28T15:49:22,885   creating build/bdist.linux-armv7l/wheel/coralme/solver
2024-11-28T15:49:22,887   copying build/lib/coralme/solver/qvaryME.cpython-39-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:49:22,897   copying build/lib/coralme/solver/qsolveME.cpython-310-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:49:22,902   copying build/lib/coralme/solver/qwarmLP.cpython-38-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:49:22,915   copying build/lib/coralme/solver/warmLP.cpython-37m-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:49:22,928   copying build/lib/coralme/solver/qwarmLP.cpython-39-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:49:22,937   copying build/lib/coralme/solver/qsolveME.cpython-39-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:49:22,941   copying build/lib/coralme/solver/warmLP.cpython-310-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:49:22,950   copying build/lib/coralme/solver/qsolveME.cpython-37m-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:49:22,954   copying build/lib/coralme/solver/qvaryME.cpython-37m-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:49:22,963   copying build/lib/coralme/solver/qmatrixA.cpython-310-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:49:22,968   copying build/lib/coralme/solver/warmLP.cpython-39-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:49:22,979   copying build/lib/coralme/solver/qwarmLP.cpython-310-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:49:22,989   copying build/lib/coralme/solver/qmatrixA.cpython-38-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:49:22,993   copying build/lib/coralme/solver/qvaryME.cpython-38-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:49:23,005   copying build/lib/coralme/solver/solver.py -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:49:23,008   copying build/lib/coralme/solver/__init__.py -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:49:23,011   copying build/lib/coralme/solver/warmLP.cpython-38-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:49:23,032   copying build/lib/coralme/solver/qmatrixA.cpython-39-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:49:23,039   copying build/lib/coralme/solver/qsolveME.cpython-38-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:49:23,045   copying build/lib/coralme/solver/qwarmLP.cpython-37m-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:49:23,065   copying build/lib/coralme/solver/qvaryME.cpython-310-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:49:23,084   copying build/lib/coralme/solver/qmatrixA.cpython-37m-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver
2024-11-28T15:49:23,090   running install_egg_info
2024-11-28T15:49:23,127   running egg_info
2024-11-28T15:49:23,155   writing coralME.egg-info/PKG-INFO
2024-11-28T15:49:23,159   writing dependency_links to coralME.egg-info/dependency_links.txt
2024-11-28T15:49:23,161   writing requirements to coralME.egg-info/requires.txt
2024-11-28T15:49:23,162   writing top-level names to coralME.egg-info/top_level.txt
2024-11-28T15:49:23,206   reading manifest file 'coralME.egg-info/SOURCES.txt'
2024-11-28T15:49:23,214   adding license file 'LICENSE'
2024-11-28T15:49:23,222   writing manifest file 'coralME.egg-info/SOURCES.txt'
2024-11-28T15:49:23,225   Copying coralME.egg-info to build/bdist.linux-armv7l/wheel/./coralME-1.0.0.post1-py3.11.egg-info
2024-11-28T15:49:23,235   running install_scripts
2024-11-28T15:49:23,251   creating build/bdist.linux-armv7l/wheel/coralME-1.0.0.post1.dist-info/WHEEL
2024-11-28T15:49:23,254   creating '/tmp/pip-wheel-3qa2xji7/coralME-1.0.0.post1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2024-11-28T15:49:23,257   adding 'coralme/__init__.py'
2024-11-28T15:49:23,261   adding 'coralme/_version.py'
2024-11-28T15:49:23,263   adding 'coralme/builder/__init__.py'
2024-11-28T15:49:23,265   adding 'coralme/builder/column_format.json'
2024-11-28T15:49:23,267   adding 'coralme/builder/compartments.py'
2024-11-28T15:49:23,272   adding 'coralme/builder/curation.py'
2024-11-28T15:49:23,275   adding 'coralme/builder/dictionaries.py'
2024-11-28T15:49:23,278   adding 'coralme/builder/dna_replication.py'
2024-11-28T15:49:23,280   adding 'coralme/builder/flat_files.py'
2024-11-28T15:49:23,282   adding 'coralme/builder/formulas.py'
2024-11-28T15:49:23,287   adding 'coralme/builder/helper_functions.py'
2024-11-28T15:49:23,289   adding 'coralme/builder/homology.py'
2024-11-28T15:49:23,308   adding 'coralme/builder/main.py'
2024-11-28T15:49:23,311   adding 'coralme/builder/modifications.py'
2024-11-28T15:49:23,323   adding 'coralme/builder/organism.py'
2024-11-28T15:49:23,328   adding 'coralme/builder/preprocess_inputs.py'
2024-11-28T15:49:23,330   adding 'coralme/builder/ribosome.py'
2024-11-28T15:49:23,332   adding 'coralme/builder/transcription.py'
2024-11-28T15:49:23,334   adding 'coralme/builder/translation.py'
2024-11-28T15:49:23,336   adding 'coralme/builder/translocation.py'
2024-11-28T15:49:23,338   adding 'coralme/builder/trna_charging.py'
2024-11-28T15:49:23,340   adding 'coralme/core/__init__.py'
2024-11-28T15:49:23,342   adding 'coralme/core/component.py'
2024-11-28T15:49:23,350   adding 'coralme/core/model.py'
2024-11-28T15:49:23,356   adding 'coralme/core/processdata.py'
2024-11-28T15:49:23,365   adding 'coralme/core/reaction.py'
2024-11-28T15:49:23,369   adding 'coralme/iJL1678b-ME/BarEven_subsystem_classification.csv'
2024-11-28T15:49:23,373   adding 'coralme/iJL1678b-ME/building_data/RNAs.txt'
2024-11-28T15:49:23,392   adding 'coralme/iJL1678b-ME/building_data/TUs.txt'
2024-11-28T15:49:23,412   adding 'coralme/iJL1678b-ME/building_data/TUs_from_biocyc.txt'
2024-11-28T15:49:23,439   adding 'coralme/iJL1678b-ME/building_data/_TUs_from_biocyc.txt'
2024-11-28T15:49:23,442   adding 'coralme/iJL1678b-ME/building_data/amino_acid_trna_synthetase.txt'
2024-11-28T15:49:23,443   adding 'coralme/iJL1678b-ME/building_data/cleaved_methionine.txt'
2024-11-28T15:49:23,444   adding 'coralme/iJL1678b-ME/building_data/codon_usage.txt'
2024-11-28T15:49:23,445   adding 'coralme/iJL1678b-ME/building_data/elongation_subreactions.txt'
2024-11-28T15:49:23,454   adding 'coralme/iJL1678b-ME/building_data/enzyme_reaction_association.txt'
2024-11-28T15:49:23,456   adding 'coralme/iJL1678b-ME/building_data/excision_machinery.txt'
2024-11-28T15:49:23,457   adding 'coralme/iJL1678b-ME/building_data/folding_chaperones.txt'
2024-11-28T15:49:23,458   adding 'coralme/iJL1678b-ME/building_data/folding_dict.txt'
2024-11-28T15:49:23,459   adding 'coralme/iJL1678b-ME/building_data/generic_dict.txt'
2024-11-28T15:49:23,514   adding 'coralme/iJL1678b-ME/building_data/genes.txt'
2024-11-28T15:49:27,629   adding 'coralme/iJL1678b-ME/building_data/genome.gb'
2024-11-28T15:49:27,760   adding 'coralme/iJL1678b-ME/building_data/iJO1366b.json'
2024-11-28T15:49:27,766   adding 'coralme/iJL1678b-ME/building_data/initiation_subreactions.txt'
2024-11-28T15:49:27,791   adding 'coralme/iJL1678b-ME/building_data/keffs.json'
2024-11-28T15:49:27,816   adding 'coralme/iJL1678b-ME/building_data/keffs.txt'
2024-11-28T15:49:27,819   adding 'coralme/iJL1678b-ME/building_data/lipid_modifications.txt'
2024-11-28T15:49:27,820   adding 'coralme/iJL1678b-ME/building_data/lipoprotein_precursors.txt'
2024-11-28T15:49:27,871   adding 'coralme/iJL1678b-ME/building_data/m_model.json'
2024-11-28T15:49:27,878   adding 'coralme/iJL1678b-ME/building_data/m_to_me_mets.txt'
2024-11-28T15:49:27,879   adding 'coralme/iJL1678b-ME/building_data/me_metabolites.txt'
2024-11-28T15:49:27,881   adding 'coralme/iJL1678b-ME/building_data/metabolite_corrections.txt'
2024-11-28T15:49:27,890   adding 'coralme/iJL1678b-ME/building_data/metabolites.txt'
2024-11-28T15:49:27,891   adding 'coralme/iJL1678b-ME/building_data/modification.txt'
2024-11-28T15:49:27,893   adding 'coralme/iJL1678b-ME/building_data/orphan_and_spont_reactions.txt'
2024-11-28T15:49:27,895   adding 'coralme/iJL1678b-ME/building_data/peptide_compartment_and_pathways.txt'
2024-11-28T15:49:27,897   adding 'coralme/iJL1678b-ME/building_data/peptide_release_factors.txt'
2024-11-28T15:49:27,899   adding 'coralme/iJL1678b-ME/building_data/post_transcriptional_modification_of_RNA.txt'
2024-11-28T15:49:27,906   adding 'coralme/iJL1678b-ME/building_data/protein_complexes.txt'
2024-11-28T15:49:27,908   adding 'coralme/iJL1678b-ME/building_data/protein_corrections.txt'
2024-11-28T15:49:27,912   adding 'coralme/iJL1678b-ME/building_data/protein_modification.txt'
2024-11-28T15:49:27,920   adding 'coralme/iJL1678b-ME/building_data/proteins.txt'
2024-11-28T15:49:27,922   adding 'coralme/iJL1678b-ME/building_data/reaction_corrections.txt'
2024-11-28T15:49:27,926   adding 'coralme/iJL1678b-ME/building_data/reaction_matrix.txt'
2024-11-28T15:49:30,466   adding 'coralme/iJL1678b-ME/building_data/reference_tRNAs.fna'
2024-11-28T15:49:30,496   adding 'coralme/iJL1678b-ME/building_data/rho_independent.txt'
2024-11-28T15:49:30,497   adding 'coralme/iJL1678b-ME/building_data/ribosomal_proteins.txt'
2024-11-28T15:49:30,499   adding 'coralme/iJL1678b-ME/building_data/ribosome_subreactions.txt'
2024-11-28T15:49:30,500   adding 'coralme/iJL1678b-ME/building_data/rna_degradosome.txt'
2024-11-28T15:49:30,502   adding 'coralme/iJL1678b-ME/building_data/rna_modification.txt'
2024-11-28T15:49:30,503   adding 'coralme/iJL1678b-ME/building_data/rrna_modifications.txt'
2024-11-28T15:49:30,504   adding 'coralme/iJL1678b-ME/building_data/sigma_factors.txt'
2024-11-28T15:49:30,506   adding 'coralme/iJL1678b-ME/building_data/special_modifications.txt'
2024-11-28T15:49:30,507   adding 'coralme/iJL1678b-ME/building_data/special_trna_subreactions.txt'
2024-11-28T15:49:30,509   adding 'coralme/iJL1678b-ME/building_data/stable_RNAs.txt'
2024-11-28T15:49:30,510   adding 'coralme/iJL1678b-ME/building_data/subreaction_matrix.txt'
2024-11-28T15:49:30,511   adding 'coralme/iJL1678b-ME/building_data/subsystem_classification.txt'
2024-11-28T15:49:30,513   adding 'coralme/iJL1678b-ME/building_data/termination_subreactions.txt'
2024-11-28T15:49:30,514   adding 'coralme/iJL1678b-ME/building_data/transcription_subreactions.txt'
2024-11-28T15:49:30,515   adding 'coralme/iJL1678b-ME/building_data/translocation_multipliers.txt'
2024-11-28T15:49:30,517   adding 'coralme/iJL1678b-ME/building_data/translocation_pathways.txt'
2024-11-28T15:49:30,518   adding 'coralme/iJL1678b-ME/building_data/trna_modification.txt'
2024-11-28T15:49:30,520   adding 'coralme/io/JSONSCHEMA'
2024-11-28T15:49:30,522   adding 'coralme/io/__init__.py'
2024-11-28T15:49:30,524   adding 'coralme/io/dict.py'
2024-11-28T15:49:30,525   adding 'coralme/io/json.py'
2024-11-28T15:49:30,527   adding 'coralme/io/pickle.py'
2024-11-28T15:49:30,528   adding 'coralme/licenses/LICENSE-cobrame'
2024-11-28T15:49:30,530   adding 'coralme/licenses/LICENSE-ecolime'
2024-11-28T15:49:30,531   adding 'coralme/licenses/LICENSE-solvemepy'
2024-11-28T15:49:30,533   adding 'coralme/solver/__init__.py'
2024-11-28T15:49:30,549   adding 'coralme/solver/qmatrixA.cpython-310-x86_64-linux-gnu.so'
2024-11-28T15:49:30,565   adding 'coralme/solver/qmatrixA.cpython-37m-x86_64-linux-gnu.so'
2024-11-28T15:49:30,582   adding 'coralme/solver/qmatrixA.cpython-38-x86_64-linux-gnu.so'
2024-11-28T15:49:30,599   adding 'coralme/solver/qmatrixA.cpython-39-x86_64-linux-gnu.so'
2024-11-28T15:49:30,616   adding 'coralme/solver/qsolveME.cpython-310-x86_64-linux-gnu.so'
2024-11-28T15:49:30,632   adding 'coralme/solver/qsolveME.cpython-37m-x86_64-linux-gnu.so'
2024-11-28T15:49:30,649   adding 'coralme/solver/qsolveME.cpython-38-x86_64-linux-gnu.so'
2024-11-28T15:49:30,666   adding 'coralme/solver/qsolveME.cpython-39-x86_64-linux-gnu.so'
2024-11-28T15:49:30,766   adding 'coralme/solver/qvaryME.cpython-310-x86_64-linux-gnu.so'
2024-11-28T15:49:30,867   adding 'coralme/solver/qvaryME.cpython-37m-x86_64-linux-gnu.so'
2024-11-28T15:49:30,970   adding 'coralme/solver/qvaryME.cpython-38-x86_64-linux-gnu.so'
2024-11-28T15:49:31,072   adding 'coralme/solver/qvaryME.cpython-39-x86_64-linux-gnu.so'
2024-11-28T15:49:31,174   adding 'coralme/solver/qwarmLP.cpython-310-x86_64-linux-gnu.so'
2024-11-28T15:49:31,276   adding 'coralme/solver/qwarmLP.cpython-37m-x86_64-linux-gnu.so'
2024-11-28T15:49:31,385   adding 'coralme/solver/qwarmLP.cpython-38-x86_64-linux-gnu.so'
2024-11-28T15:49:31,488   adding 'coralme/solver/qwarmLP.cpython-39-x86_64-linux-gnu.so'
2024-11-28T15:49:31,493   adding 'coralme/solver/solver.py'
2024-11-28T15:49:31,599   adding 'coralme/solver/warmLP.cpython-310-x86_64-linux-gnu.so'
2024-11-28T15:49:31,707   adding 'coralme/solver/warmLP.cpython-37m-x86_64-linux-gnu.so'
2024-11-28T15:49:31,816   adding 'coralme/solver/warmLP.cpython-38-x86_64-linux-gnu.so'
2024-11-28T15:49:31,924   adding 'coralme/solver/warmLP.cpython-39-x86_64-linux-gnu.so'
2024-11-28T15:49:31,929   adding 'coralme/util/__init__.py'
2024-11-28T15:49:31,936   adding 'coralme/util/building.py'
2024-11-28T15:49:31,938   adding 'coralme/util/dogma.py'
2024-11-28T15:49:31,939   adding 'coralme/util/massbalance.py'
2024-11-28T15:49:31,941   adding 'coralME-1.0.0.post1.dist-info/LICENSE'
2024-11-28T15:49:31,942   adding 'coralME-1.0.0.post1.dist-info/METADATA'
2024-11-28T15:49:31,943   adding 'coralME-1.0.0.post1.dist-info/WHEEL'
2024-11-28T15:49:31,944   adding 'coralME-1.0.0.post1.dist-info/top_level.txt'
2024-11-28T15:49:31,946   adding 'coralME-1.0.0.post1.dist-info/RECORD'
2024-11-28T15:49:32,034   removing build/bdist.linux-armv7l/wheel
2024-11-28T15:49:32,184   Building wheel for coralme (setup.py): finished with status 'done'
2024-11-28T15:49:32,272   Created wheel for coralme: filename=coralME-1.0.0.post1-py3-none-any.whl size=8697071 sha256=c013e324d5a89b8680ae4f14dd2f583a419ca4093cab14d5f01c3f075eb12d95
2024-11-28T15:49:32,274   Stored in directory: /tmp/pip-ephem-wheel-cache-mvcty4gc/wheels/9b/60/71/e9172df221c7457ad4daf64b04055dc7c566add821118cf7d7
2024-11-28T15:49:32,291 Successfully built coralme
2024-11-28T15:49:32,516 Removed build tracker: '/tmp/pip-build-tracker-po2dlbwu'