2024-11-28T15:58:43,869 Created temporary directory: /tmp/pip-build-tracker-khe0obb4 2024-11-28T15:58:43,871 Initialized build tracking at /tmp/pip-build-tracker-khe0obb4 2024-11-28T15:58:43,871 Created build tracker: /tmp/pip-build-tracker-khe0obb4 2024-11-28T15:58:43,872 Entered build tracker: /tmp/pip-build-tracker-khe0obb4 2024-11-28T15:58:43,872 Created temporary directory: /tmp/pip-wheel-10pfgneb 2024-11-28T15:58:43,876 Created temporary directory: /tmp/pip-ephem-wheel-cache-xjr9xc8t 2024-11-28T15:58:43,921 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-11-28T15:58:43,923 2 location(s) to search for versions of coralme: 2024-11-28T15:58:43,923 * https://pypi.org/simple/coralme/ 2024-11-28T15:58:43,923 * https://www.piwheels.org/simple/coralme/ 2024-11-28T15:58:43,924 Fetching project page and analyzing links: https://pypi.org/simple/coralme/ 2024-11-28T15:58:43,925 Getting page https://pypi.org/simple/coralme/ 2024-11-28T15:58:43,926 Found index url https://pypi.org/simple/ 2024-11-28T15:58:44,145 Fetched page https://pypi.org/simple/coralme/ as application/vnd.pypi.simple.v1+json 2024-11-28T15:58:44,151 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) 2024-11-28T15:58:44,152 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 2024-11-28T15:58:44,153 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) 2024-11-28T15:58:44,154 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 2024-11-28T15:58:44,155 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) 2024-11-28T15:58:44,156 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 2024-11-28T15:58:44,157 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) 2024-11-28T15:58:44,158 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 2024-11-28T15:58:44,158 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) 2024-11-28T15:58:44,159 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 2024-11-28T15:58:44,160 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) 2024-11-28T15:58:44,161 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 2024-11-28T15:58:44,162 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) 2024-11-28T15:58:44,163 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 2024-11-28T15:58:44,164 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) 2024-11-28T15:58:44,165 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 2024-11-28T15:58:44,166 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) 2024-11-28T15:58:44,166 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 2024-11-28T15:58:44,167 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) 2024-11-28T15:58:44,168 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 2024-11-28T15:58:44,169 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) 2024-11-28T15:58:44,170 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 2024-11-28T15:58:44,170 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) 2024-11-28T15:58:44,171 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 2024-11-28T15:58:44,172 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) 2024-11-28T15:58:44,173 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 2024-11-28T15:58:44,174 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) 2024-11-28T15:58:44,175 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 2024-11-28T15:58:44,176 Fetching project page and analyzing links: https://www.piwheels.org/simple/coralme/ 2024-11-28T15:58:44,177 Getting page https://www.piwheels.org/simple/coralme/ 2024-11-28T15:58:44,178 Found index url https://www.piwheels.org/simple/ 2024-11-28T15:58:44,344 Fetched page https://www.piwheels.org/simple/coralme/ as text/html 2024-11-28T15:58:44,346 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) 2024-11-28T15:58:44,346 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) 2024-11-28T15:58:44,347 Skipping link: not a file: https://www.piwheels.org/simple/coralme/ 2024-11-28T15:58:44,347 Skipping link: not a file: https://pypi.org/simple/coralme/ 2024-11-28T15:58:44,368 Given no hashes to check 1 links for project 'coralme': discarding no candidates 2024-11-28T15:58:44,370 Collecting coralme==1.0.0.post3 2024-11-28T15:58:44,372 Created temporary directory: /tmp/pip-unpack-_d0ps6hk 2024-11-28T15:58:44,513 Downloading coralme-1.0.0.post3.tar.gz (8.5 MB) 2024-11-28T15:58:46,580 Added coralme==1.0.0.post3 from https://files.pythonhosted.org/packages/57/b5/2bf10653857fc4ac9c8ce4f4641f93e1ba667ccacdddc8c4698ef289c827/coralme-1.0.0.post3.tar.gz to build tracker '/tmp/pip-build-tracker-khe0obb4' 2024-11-28T15:58:46,582 Running setup.py (path:/tmp/pip-wheel-10pfgneb/coralme_898fc7e021d74a34adc5580f087f8094/setup.py) egg_info for package coralme 2024-11-28T15:58:46,583 Created temporary directory: /tmp/pip-pip-egg-info-m7igdk_v 2024-11-28T15:58:46,584 Preparing metadata (setup.py): started 2024-11-28T15:58:46,585 Running command python setup.py egg_info 2024-11-28T15:58:47,638 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:337: InformationOnly: Normalizing '1.0.0-3' to '1.0.0.post3' 2024-11-28T15:58:47,638 self.metadata.version = self._normalize_version(self.metadata.version) 2024-11-28T15:58:47,691 running egg_info 2024-11-28T15:58:47,717 creating /tmp/pip-pip-egg-info-m7igdk_v/coralME.egg-info 2024-11-28T15:58:47,718 writing /tmp/pip-pip-egg-info-m7igdk_v/coralME.egg-info/PKG-INFO 2024-11-28T15:58:47,722 writing dependency_links to /tmp/pip-pip-egg-info-m7igdk_v/coralME.egg-info/dependency_links.txt 2024-11-28T15:58:47,724 writing requirements to /tmp/pip-pip-egg-info-m7igdk_v/coralME.egg-info/requires.txt 2024-11-28T15:58:47,725 writing top-level names to /tmp/pip-pip-egg-info-m7igdk_v/coralME.egg-info/top_level.txt 2024-11-28T15:58:47,726 writing manifest file '/tmp/pip-pip-egg-info-m7igdk_v/coralME.egg-info/SOURCES.txt' 2024-11-28T15:58:47,827 reading manifest file '/tmp/pip-pip-egg-info-m7igdk_v/coralME.egg-info/SOURCES.txt' 2024-11-28T15:58:47,829 adding license file 'LICENSE' 2024-11-28T15:58:47,835 writing manifest file '/tmp/pip-pip-egg-info-m7igdk_v/coralME.egg-info/SOURCES.txt' 2024-11-28T15:58:47,945 Preparing metadata (setup.py): finished with status 'done' 2024-11-28T15:58:47,949 Source in /tmp/pip-wheel-10pfgneb/coralme_898fc7e021d74a34adc5580f087f8094 has version 1.0.0.post3, which satisfies requirement coralme==1.0.0.post3 from https://files.pythonhosted.org/packages/57/b5/2bf10653857fc4ac9c8ce4f4641f93e1ba667ccacdddc8c4698ef289c827/coralme-1.0.0.post3.tar.gz 2024-11-28T15:58:47,950 Removed coralme==1.0.0.post3 from https://files.pythonhosted.org/packages/57/b5/2bf10653857fc4ac9c8ce4f4641f93e1ba667ccacdddc8c4698ef289c827/coralme-1.0.0.post3.tar.gz from build tracker '/tmp/pip-build-tracker-khe0obb4' 2024-11-28T15:58:47,959 Created temporary directory: /tmp/pip-unpack-cqci86_3 2024-11-28T15:58:47,960 Created temporary directory: /tmp/pip-unpack-lnzl4tfw 2024-11-28T15:58:47,960 Building wheels for collected packages: coralme 2024-11-28T15:58:47,964 Created temporary directory: /tmp/pip-wheel-mtdgfdf3 2024-11-28T15:58:47,965 Building wheel for coralme (setup.py): started 2024-11-28T15:58:47,966 Destination directory: /tmp/pip-wheel-mtdgfdf3 2024-11-28T15:58:47,966 Running command python setup.py bdist_wheel 2024-11-28T15:58:48,995 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:337: InformationOnly: Normalizing '1.0.0-3' to '1.0.0.post3' 2024-11-28T15:58:48,995 self.metadata.version = self._normalize_version(self.metadata.version) 2024-11-28T15:58:49,022 running bdist_wheel 2024-11-28T15:58:49,152 running build 2024-11-28T15:58:49,153 running build_py 2024-11-28T15:58:49,182 creating build/lib/coralme 2024-11-28T15:58:49,185 copying coralme/__init__.py -> build/lib/coralme 2024-11-28T15:58:49,187 copying coralme/_version.py -> build/lib/coralme 2024-11-28T15:58:49,190 creating build/lib/coralme/io 2024-11-28T15:58:49,191 copying coralme/io/json.py -> build/lib/coralme/io 2024-11-28T15:58:49,193 copying coralme/io/__init__.py -> build/lib/coralme/io 2024-11-28T15:58:49,195 copying coralme/io/pickle.py -> build/lib/coralme/io 2024-11-28T15:58:49,197 copying coralme/io/dict.py -> build/lib/coralme/io 2024-11-28T15:58:49,200 creating build/lib/coralme/util 2024-11-28T15:58:49,201 copying coralme/util/__init__.py -> build/lib/coralme/util 2024-11-28T15:58:49,203 copying coralme/util/dogma.py -> build/lib/coralme/util 2024-11-28T15:58:49,205 copying coralme/util/building.py -> build/lib/coralme/util 2024-11-28T15:58:49,208 copying coralme/util/massbalance.py -> build/lib/coralme/util 2024-11-28T15:58:49,211 creating build/lib/coralme/builder 2024-11-28T15:58:49,212 copying coralme/builder/preprocess_inputs.py -> build/lib/coralme/builder 2024-11-28T15:58:49,215 copying coralme/builder/flat_files.py -> build/lib/coralme/builder 2024-11-28T15:58:49,217 copying coralme/builder/dna_replication.py -> build/lib/coralme/builder 2024-11-28T15:58:49,219 copying coralme/builder/__init__.py -> build/lib/coralme/builder 2024-11-28T15:58:49,221 copying coralme/builder/compartments.py -> build/lib/coralme/builder 2024-11-28T15:58:49,223 copying coralme/builder/formulas.py -> build/lib/coralme/builder 2024-11-28T15:58:49,225 copying coralme/builder/dictionaries.py -> build/lib/coralme/builder 2024-11-28T15:58:49,228 copying coralme/builder/helper_functions.py -> build/lib/coralme/builder 2024-11-28T15:58:49,230 copying coralme/builder/translation.py -> build/lib/coralme/builder 2024-11-28T15:58:49,233 copying coralme/builder/trna_charging.py -> build/lib/coralme/builder 2024-11-28T15:58:49,234 copying coralme/builder/modifications.py -> build/lib/coralme/builder 2024-11-28T15:58:49,237 copying coralme/builder/transcription.py -> build/lib/coralme/builder 2024-11-28T15:58:49,239 copying coralme/builder/main.py -> build/lib/coralme/builder 2024-11-28T15:58:49,243 copying coralme/builder/homology.py -> build/lib/coralme/builder 2024-11-28T15:58:49,245 copying coralme/builder/ribosome.py -> build/lib/coralme/builder 2024-11-28T15:58:49,247 copying coralme/builder/curation.py -> build/lib/coralme/builder 2024-11-28T15:58:49,250 copying coralme/builder/translocation.py -> build/lib/coralme/builder 2024-11-28T15:58:49,253 copying coralme/builder/organism.py -> build/lib/coralme/builder 2024-11-28T15:58:49,257 creating build/lib/coralme/core 2024-11-28T15:58:49,258 copying coralme/core/model.py -> build/lib/coralme/core 2024-11-28T15:58:49,262 copying coralme/core/__init__.py -> build/lib/coralme/core 2024-11-28T15:58:49,263 copying coralme/core/reaction.py -> build/lib/coralme/core 2024-11-28T15:58:49,267 copying coralme/core/processdata.py -> build/lib/coralme/core 2024-11-28T15:58:49,270 copying coralme/core/component.py -> build/lib/coralme/core 2024-11-28T15:58:49,272 creating build/lib/coralme/solver 2024-11-28T15:58:49,273 copying coralme/solver/solver.py -> build/lib/coralme/solver 2024-11-28T15:58:49,276 copying coralme/solver/__init__.py -> build/lib/coralme/solver 2024-11-28T15:58:49,287 creating build/lib/coralme/iJL1678b-ME 2024-11-28T15:58:49,289 copying coralme/iJL1678b-ME/BarEven_subsystem_classification.csv -> build/lib/coralme/iJL1678b-ME 2024-11-28T15:58:49,291 creating build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,293 copying coralme/iJL1678b-ME/building_data/generic_dict.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,295 copying coralme/iJL1678b-ME/building_data/orphan_and_spont_reactions.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,297 copying coralme/iJL1678b-ME/building_data/metabolites.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,301 copying coralme/iJL1678b-ME/building_data/proteins.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,305 copying coralme/iJL1678b-ME/building_data/transcription_subreactions.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,307 copying coralme/iJL1678b-ME/building_data/genes.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,313 copying coralme/iJL1678b-ME/building_data/folding_dict.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,315 copying coralme/iJL1678b-ME/building_data/protein_complexes.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,319 copying coralme/iJL1678b-ME/building_data/rna_degradosome.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,321 copying coralme/iJL1678b-ME/building_data/stable_RNAs.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,323 copying coralme/iJL1678b-ME/building_data/post_transcriptional_modification_of_RNA.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,326 copying coralme/iJL1678b-ME/building_data/excision_machinery.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,328 copying coralme/iJL1678b-ME/building_data/initiation_subreactions.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,330 copying coralme/iJL1678b-ME/building_data/termination_subreactions.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,332 copying coralme/iJL1678b-ME/building_data/trna_modification.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,334 copying coralme/iJL1678b-ME/building_data/subreaction_matrix.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,337 copying coralme/iJL1678b-ME/building_data/me_metabolites.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,340 copying coralme/iJL1678b-ME/building_data/reaction_corrections.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,342 copying coralme/iJL1678b-ME/building_data/peptide_compartment_and_pathways.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,345 copying coralme/iJL1678b-ME/building_data/keffs.json -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,354 copying coralme/iJL1678b-ME/building_data/special_modifications.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,356 copying coralme/iJL1678b-ME/building_data/ribosomal_proteins.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,358 copying coralme/iJL1678b-ME/building_data/reference_tRNAs.fna -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,431 copying coralme/iJL1678b-ME/building_data/genome.gb -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,690 copying coralme/iJL1678b-ME/building_data/rna_modification.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,692 copying coralme/iJL1678b-ME/building_data/ribosome_subreactions.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,694 copying coralme/iJL1678b-ME/building_data/codon_usage.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,697 copying coralme/iJL1678b-ME/building_data/elongation_subreactions.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,699 copying coralme/iJL1678b-ME/building_data/protein_corrections.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,702 copying coralme/iJL1678b-ME/building_data/TUs.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,706 copying coralme/iJL1678b-ME/building_data/protein_modification.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,709 copying coralme/iJL1678b-ME/building_data/folding_chaperones.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,712 copying coralme/iJL1678b-ME/building_data/amino_acid_trna_synthetase.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,714 copying coralme/iJL1678b-ME/building_data/modification.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,717 copying coralme/iJL1678b-ME/building_data/m_to_me_mets.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,719 copying coralme/iJL1678b-ME/building_data/translocation_multipliers.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,722 copying coralme/iJL1678b-ME/building_data/RNAs.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,725 copying coralme/iJL1678b-ME/building_data/iJO1366b.json -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,741 copying coralme/iJL1678b-ME/building_data/_TUs_from_biocyc.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,748 copying coralme/iJL1678b-ME/building_data/rrna_modifications.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,750 copying coralme/iJL1678b-ME/building_data/keffs.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,755 copying coralme/iJL1678b-ME/building_data/lipid_modifications.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,758 copying coralme/iJL1678b-ME/building_data/subsystem_classification.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,760 copying coralme/iJL1678b-ME/building_data/TUs_from_biocyc.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,765 copying coralme/iJL1678b-ME/building_data/enzyme_reaction_association.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,768 copying coralme/iJL1678b-ME/building_data/cleaved_methionine.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,771 copying coralme/iJL1678b-ME/building_data/m_model.json -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,787 copying coralme/iJL1678b-ME/building_data/translocation_pathways.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,789 copying coralme/iJL1678b-ME/building_data/special_trna_subreactions.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,791 copying coralme/iJL1678b-ME/building_data/metabolite_corrections.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,794 copying coralme/iJL1678b-ME/building_data/peptide_release_factors.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,796 copying coralme/iJL1678b-ME/building_data/rho_independent.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,798 copying coralme/iJL1678b-ME/building_data/lipoprotein_precursors.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,800 copying coralme/iJL1678b-ME/building_data/sigma_factors.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,803 copying coralme/iJL1678b-ME/building_data/reaction_matrix.txt -> build/lib/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:49,806 copying coralme/solver/qwarmLP.cpython-38-x86_64-linux-gnu.so -> build/lib/coralme/solver 2024-11-28T15:58:49,817 copying coralme/solver/qsolveME.cpython-38-x86_64-linux-gnu.so -> build/lib/coralme/solver 2024-11-28T15:58:49,822 copying coralme/solver/qvaryME.cpython-37m-x86_64-linux-gnu.so -> build/lib/coralme/solver 2024-11-28T15:58:49,836 copying coralme/solver/warmLP.cpython-37m-x86_64-linux-gnu.so -> build/lib/coralme/solver 2024-11-28T15:58:49,850 copying coralme/solver/warmLP.cpython-310-x86_64-linux-gnu.so -> build/lib/coralme/solver 2024-11-28T15:58:49,863 copying coralme/solver/qmatrixA.cpython-310-x86_64-linux-gnu.so -> build/lib/coralme/solver 2024-11-28T15:58:49,869 copying coralme/solver/warmLP.cpython-39-x86_64-linux-gnu.so -> build/lib/coralme/solver 2024-11-28T15:58:50,103 copying coralme/solver/qmatrixA.cpython-38-x86_64-linux-gnu.so -> build/lib/coralme/solver 2024-11-28T15:58:50,119 copying coralme/solver/warmLP.cpython-38-x86_64-linux-gnu.so -> build/lib/coralme/solver 2024-11-28T15:58:50,141 copying coralme/solver/qsolveME.cpython-37m-x86_64-linux-gnu.so -> build/lib/coralme/solver 2024-11-28T15:58:50,149 copying coralme/solver/qsolveME.cpython-310-x86_64-linux-gnu.so -> build/lib/coralme/solver 2024-11-28T15:58:50,157 copying coralme/solver/qmatrixA.cpython-37m-x86_64-linux-gnu.so -> build/lib/coralme/solver 2024-11-28T15:58:50,166 copying coralme/solver/qsolveME.cpython-39-x86_64-linux-gnu.so -> build/lib/coralme/solver 2024-11-28T15:58:50,174 copying coralme/solver/qwarmLP.cpython-39-x86_64-linux-gnu.so -> build/lib/coralme/solver 2024-11-28T15:58:50,199 copying coralme/solver/qvaryME.cpython-39-x86_64-linux-gnu.so -> build/lib/coralme/solver 2024-11-28T15:58:50,222 copying coralme/solver/qvaryME.cpython-310-x86_64-linux-gnu.so -> build/lib/coralme/solver 2024-11-28T15:58:50,232 copying coralme/solver/qwarmLP.cpython-310-x86_64-linux-gnu.so -> build/lib/coralme/solver 2024-11-28T15:58:50,242 copying coralme/solver/qmatrixA.cpython-39-x86_64-linux-gnu.so -> build/lib/coralme/solver 2024-11-28T15:58:50,246 copying coralme/solver/qwarmLP.cpython-37m-x86_64-linux-gnu.so -> build/lib/coralme/solver 2024-11-28T15:58:50,256 copying coralme/solver/qvaryME.cpython-38-x86_64-linux-gnu.so -> build/lib/coralme/solver 2024-11-28T15:58:50,268 copying coralme/io/JSONSCHEMA -> build/lib/coralme/io 2024-11-28T15:58:50,271 copying coralme/builder/column_format.json -> build/lib/coralme/builder 2024-11-28T15:58:50,273 creating build/lib/coralme/licenses 2024-11-28T15:58:50,275 copying coralme/licenses/LICENSE-ecolime -> build/lib/coralme/licenses 2024-11-28T15:58:50,277 copying coralme/licenses/LICENSE-cobrame -> build/lib/coralme/licenses 2024-11-28T15:58:50,280 copying coralme/licenses/LICENSE-solvemepy -> build/lib/coralme/licenses 2024-11-28T15:58:50,312 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-11-28T15:58:50,312 !! 2024-11-28T15:58:50,314 ******************************************************************************** 2024-11-28T15:58:50,314 Please avoid running ``setup.py`` directly. 2024-11-28T15:58:50,315 Instead, use pypa/build, pypa/installer or other 2024-11-28T15:58:50,315 standards-based tools. 2024-11-28T15:58:50,317 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-11-28T15:58:50,317 ******************************************************************************** 2024-11-28T15:58:50,318 !! 2024-11-28T15:58:50,319 self.initialize_options() 2024-11-28T15:58:50,342 installing to build/bdist.linux-armv7l/wheel 2024-11-28T15:58:50,343 running install 2024-11-28T15:58:50,368 running install_lib 2024-11-28T15:58:50,396 creating build/bdist.linux-armv7l/wheel 2024-11-28T15:58:50,398 creating build/bdist.linux-armv7l/wheel/coralme 2024-11-28T15:58:50,400 copying build/lib/coralme/__init__.py -> build/bdist.linux-armv7l/wheel/./coralme 2024-11-28T15:58:50,403 creating build/bdist.linux-armv7l/wheel/coralme/io 2024-11-28T15:58:50,404 copying build/lib/coralme/io/JSONSCHEMA -> build/bdist.linux-armv7l/wheel/./coralme/io 2024-11-28T15:58:50,407 copying build/lib/coralme/io/json.py -> build/bdist.linux-armv7l/wheel/./coralme/io 2024-11-28T15:58:50,409 copying build/lib/coralme/io/__init__.py -> build/bdist.linux-armv7l/wheel/./coralme/io 2024-11-28T15:58:50,411 copying build/lib/coralme/io/pickle.py -> build/bdist.linux-armv7l/wheel/./coralme/io 2024-11-28T15:58:50,413 copying build/lib/coralme/io/dict.py -> build/bdist.linux-armv7l/wheel/./coralme/io 2024-11-28T15:58:50,416 creating build/bdist.linux-armv7l/wheel/coralme/licenses 2024-11-28T15:58:50,417 copying build/lib/coralme/licenses/LICENSE-ecolime -> build/bdist.linux-armv7l/wheel/./coralme/licenses 2024-11-28T15:58:50,419 copying build/lib/coralme/licenses/LICENSE-cobrame -> build/bdist.linux-armv7l/wheel/./coralme/licenses 2024-11-28T15:58:50,421 copying build/lib/coralme/licenses/LICENSE-solvemepy -> build/bdist.linux-armv7l/wheel/./coralme/licenses 2024-11-28T15:58:50,423 creating build/bdist.linux-armv7l/wheel/coralme/iJL1678b-ME 2024-11-28T15:58:50,424 copying build/lib/coralme/iJL1678b-ME/BarEven_subsystem_classification.csv -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME 2024-11-28T15:58:50,428 creating build/bdist.linux-armv7l/wheel/coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,429 copying build/lib/coralme/iJL1678b-ME/building_data/generic_dict.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,431 copying build/lib/coralme/iJL1678b-ME/building_data/orphan_and_spont_reactions.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,433 copying build/lib/coralme/iJL1678b-ME/building_data/metabolites.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,436 copying build/lib/coralme/iJL1678b-ME/building_data/proteins.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,440 copying build/lib/coralme/iJL1678b-ME/building_data/transcription_subreactions.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,441 copying build/lib/coralme/iJL1678b-ME/building_data/genes.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,449 copying build/lib/coralme/iJL1678b-ME/building_data/folding_dict.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,451 copying build/lib/coralme/iJL1678b-ME/building_data/protein_complexes.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,454 copying build/lib/coralme/iJL1678b-ME/building_data/rna_degradosome.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,456 copying build/lib/coralme/iJL1678b-ME/building_data/stable_RNAs.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,458 copying build/lib/coralme/iJL1678b-ME/building_data/post_transcriptional_modification_of_RNA.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,460 copying build/lib/coralme/iJL1678b-ME/building_data/excision_machinery.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,462 copying build/lib/coralme/iJL1678b-ME/building_data/initiation_subreactions.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,463 copying build/lib/coralme/iJL1678b-ME/building_data/termination_subreactions.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,465 copying build/lib/coralme/iJL1678b-ME/building_data/trna_modification.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,467 copying build/lib/coralme/iJL1678b-ME/building_data/subreaction_matrix.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,469 copying build/lib/coralme/iJL1678b-ME/building_data/me_metabolites.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,472 copying build/lib/coralme/iJL1678b-ME/building_data/reaction_corrections.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,474 copying build/lib/coralme/iJL1678b-ME/building_data/peptide_compartment_and_pathways.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,476 copying build/lib/coralme/iJL1678b-ME/building_data/keffs.json -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,485 copying build/lib/coralme/iJL1678b-ME/building_data/special_modifications.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,487 copying build/lib/coralme/iJL1678b-ME/building_data/ribosomal_proteins.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,489 copying build/lib/coralme/iJL1678b-ME/building_data/reference_tRNAs.fna -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,559 copying build/lib/coralme/iJL1678b-ME/building_data/genome.gb -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,751 copying build/lib/coralme/iJL1678b-ME/building_data/rna_modification.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,753 copying build/lib/coralme/iJL1678b-ME/building_data/ribosome_subreactions.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,755 copying build/lib/coralme/iJL1678b-ME/building_data/codon_usage.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,757 copying build/lib/coralme/iJL1678b-ME/building_data/elongation_subreactions.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,759 copying build/lib/coralme/iJL1678b-ME/building_data/protein_corrections.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,761 copying build/lib/coralme/iJL1678b-ME/building_data/TUs.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,765 copying build/lib/coralme/iJL1678b-ME/building_data/protein_modification.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,768 copying build/lib/coralme/iJL1678b-ME/building_data/folding_chaperones.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,770 copying build/lib/coralme/iJL1678b-ME/building_data/amino_acid_trna_synthetase.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,772 copying build/lib/coralme/iJL1678b-ME/building_data/modification.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,774 copying build/lib/coralme/iJL1678b-ME/building_data/m_to_me_mets.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,777 copying build/lib/coralme/iJL1678b-ME/building_data/translocation_multipliers.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,779 copying build/lib/coralme/iJL1678b-ME/building_data/RNAs.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,786 copying build/lib/coralme/iJL1678b-ME/building_data/iJO1366b.json -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,800 copying build/lib/coralme/iJL1678b-ME/building_data/_TUs_from_biocyc.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,806 copying build/lib/coralme/iJL1678b-ME/building_data/rrna_modifications.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,807 copying build/lib/coralme/iJL1678b-ME/building_data/keffs.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,814 copying build/lib/coralme/iJL1678b-ME/building_data/lipid_modifications.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,816 copying build/lib/coralme/iJL1678b-ME/building_data/subsystem_classification.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,818 copying build/lib/coralme/iJL1678b-ME/building_data/TUs_from_biocyc.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,822 copying build/lib/coralme/iJL1678b-ME/building_data/enzyme_reaction_association.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,826 copying build/lib/coralme/iJL1678b-ME/building_data/cleaved_methionine.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,828 copying build/lib/coralme/iJL1678b-ME/building_data/m_model.json -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,842 copying build/lib/coralme/iJL1678b-ME/building_data/translocation_pathways.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,844 copying build/lib/coralme/iJL1678b-ME/building_data/special_trna_subreactions.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,846 copying build/lib/coralme/iJL1678b-ME/building_data/metabolite_corrections.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,848 copying build/lib/coralme/iJL1678b-ME/building_data/peptide_release_factors.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,850 copying build/lib/coralme/iJL1678b-ME/building_data/rho_independent.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,852 copying build/lib/coralme/iJL1678b-ME/building_data/lipoprotein_precursors.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,853 copying build/lib/coralme/iJL1678b-ME/building_data/sigma_factors.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,855 copying build/lib/coralme/iJL1678b-ME/building_data/reaction_matrix.txt -> build/bdist.linux-armv7l/wheel/./coralme/iJL1678b-ME/building_data 2024-11-28T15:58:50,859 creating build/bdist.linux-armv7l/wheel/coralme/util 2024-11-28T15:58:50,860 copying build/lib/coralme/util/__init__.py -> build/bdist.linux-armv7l/wheel/./coralme/util 2024-11-28T15:58:50,862 copying build/lib/coralme/util/dogma.py -> build/bdist.linux-armv7l/wheel/./coralme/util 2024-11-28T15:58:50,865 copying build/lib/coralme/util/building.py -> build/bdist.linux-armv7l/wheel/./coralme/util 2024-11-28T15:58:50,868 copying build/lib/coralme/util/massbalance.py -> build/bdist.linux-armv7l/wheel/./coralme/util 2024-11-28T15:58:50,871 creating build/bdist.linux-armv7l/wheel/coralme/builder 2024-11-28T15:58:50,872 copying build/lib/coralme/builder/preprocess_inputs.py -> build/bdist.linux-armv7l/wheel/./coralme/builder 2024-11-28T15:58:50,875 copying build/lib/coralme/builder/flat_files.py -> build/bdist.linux-armv7l/wheel/./coralme/builder 2024-11-28T15:58:50,878 copying build/lib/coralme/builder/dna_replication.py -> build/bdist.linux-armv7l/wheel/./coralme/builder 2024-11-28T15:58:50,880 copying build/lib/coralme/builder/__init__.py -> build/bdist.linux-armv7l/wheel/./coralme/builder 2024-11-28T15:58:50,882 copying build/lib/coralme/builder/compartments.py -> build/bdist.linux-armv7l/wheel/./coralme/builder 2024-11-28T15:58:50,884 copying build/lib/coralme/builder/formulas.py -> build/bdist.linux-armv7l/wheel/./coralme/builder 2024-11-28T15:58:50,886 copying build/lib/coralme/builder/dictionaries.py -> build/bdist.linux-armv7l/wheel/./coralme/builder 2024-11-28T15:58:50,889 copying build/lib/coralme/builder/helper_functions.py -> build/bdist.linux-armv7l/wheel/./coralme/builder 2024-11-28T15:58:50,892 copying build/lib/coralme/builder/translation.py -> build/bdist.linux-armv7l/wheel/./coralme/builder 2024-11-28T15:58:50,894 copying build/lib/coralme/builder/trna_charging.py -> build/bdist.linux-armv7l/wheel/./coralme/builder 2024-11-28T15:58:50,896 copying build/lib/coralme/builder/modifications.py -> build/bdist.linux-armv7l/wheel/./coralme/builder 2024-11-28T15:58:50,898 copying build/lib/coralme/builder/transcription.py -> build/bdist.linux-armv7l/wheel/./coralme/builder 2024-11-28T15:58:50,900 copying build/lib/coralme/builder/main.py -> build/bdist.linux-armv7l/wheel/./coralme/builder 2024-11-28T15:58:50,905 copying build/lib/coralme/builder/homology.py -> build/bdist.linux-armv7l/wheel/./coralme/builder 2024-11-28T15:58:50,907 copying build/lib/coralme/builder/ribosome.py -> build/bdist.linux-armv7l/wheel/./coralme/builder 2024-11-28T15:58:50,909 copying build/lib/coralme/builder/curation.py -> build/bdist.linux-armv7l/wheel/./coralme/builder 2024-11-28T15:58:50,912 copying build/lib/coralme/builder/translocation.py -> build/bdist.linux-armv7l/wheel/./coralme/builder 2024-11-28T15:58:50,915 copying build/lib/coralme/builder/column_format.json -> build/bdist.linux-armv7l/wheel/./coralme/builder 2024-11-28T15:58:50,916 copying build/lib/coralme/builder/organism.py -> build/bdist.linux-armv7l/wheel/./coralme/builder 2024-11-28T15:58:50,921 creating build/bdist.linux-armv7l/wheel/coralme/core 2024-11-28T15:58:50,922 copying build/lib/coralme/core/model.py -> build/bdist.linux-armv7l/wheel/./coralme/core 2024-11-28T15:58:50,926 copying build/lib/coralme/core/__init__.py -> build/bdist.linux-armv7l/wheel/./coralme/core 2024-11-28T15:58:50,928 copying build/lib/coralme/core/reaction.py -> build/bdist.linux-armv7l/wheel/./coralme/core 2024-11-28T15:58:50,932 copying build/lib/coralme/core/processdata.py -> build/bdist.linux-armv7l/wheel/./coralme/core 2024-11-28T15:58:50,935 copying build/lib/coralme/core/component.py -> build/bdist.linux-armv7l/wheel/./coralme/core 2024-11-28T15:58:50,939 copying build/lib/coralme/_version.py -> build/bdist.linux-armv7l/wheel/./coralme 2024-11-28T15:58:50,943 creating build/bdist.linux-armv7l/wheel/coralme/solver 2024-11-28T15:58:50,945 copying build/lib/coralme/solver/qwarmLP.cpython-38-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver 2024-11-28T15:58:50,958 copying build/lib/coralme/solver/solver.py -> build/bdist.linux-armv7l/wheel/./coralme/solver 2024-11-28T15:58:50,961 copying build/lib/coralme/solver/qsolveME.cpython-38-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver 2024-11-28T15:58:50,966 copying build/lib/coralme/solver/qvaryME.cpython-37m-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver 2024-11-28T15:58:50,988 copying build/lib/coralme/solver/__init__.py -> build/bdist.linux-armv7l/wheel/./coralme/solver 2024-11-28T15:58:50,990 copying build/lib/coralme/solver/warmLP.cpython-37m-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver 2024-11-28T15:58:51,007 copying build/lib/coralme/solver/warmLP.cpython-310-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver 2024-11-28T15:58:51,022 copying build/lib/coralme/solver/qmatrixA.cpython-310-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver 2024-11-28T15:58:51,028 copying build/lib/coralme/solver/warmLP.cpython-39-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver 2024-11-28T15:58:51,039 copying build/lib/coralme/solver/qmatrixA.cpython-38-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver 2024-11-28T15:58:51,043 copying build/lib/coralme/solver/warmLP.cpython-38-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver 2024-11-28T15:58:51,053 copying build/lib/coralme/solver/qsolveME.cpython-37m-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver 2024-11-28T15:58:51,057 copying build/lib/coralme/solver/qsolveME.cpython-310-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver 2024-11-28T15:58:51,061 copying build/lib/coralme/solver/qmatrixA.cpython-37m-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver 2024-11-28T15:58:51,065 copying build/lib/coralme/solver/qsolveME.cpython-39-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver 2024-11-28T15:58:51,069 copying build/lib/coralme/solver/qwarmLP.cpython-39-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver 2024-11-28T15:58:51,079 copying build/lib/coralme/solver/qvaryME.cpython-39-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver 2024-11-28T15:58:51,089 copying build/lib/coralme/solver/qvaryME.cpython-310-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver 2024-11-28T15:58:51,098 copying build/lib/coralme/solver/qwarmLP.cpython-310-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver 2024-11-28T15:58:51,108 copying build/lib/coralme/solver/qmatrixA.cpython-39-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver 2024-11-28T15:58:51,111 copying build/lib/coralme/solver/qwarmLP.cpython-37m-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver 2024-11-28T15:58:51,121 copying build/lib/coralme/solver/qvaryME.cpython-38-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./coralme/solver 2024-11-28T15:58:51,130 running install_egg_info 2024-11-28T15:58:51,161 running egg_info 2024-11-28T15:58:51,189 writing coralME.egg-info/PKG-INFO 2024-11-28T15:58:51,192 writing dependency_links to coralME.egg-info/dependency_links.txt 2024-11-28T15:58:51,194 writing requirements to coralME.egg-info/requires.txt 2024-11-28T15:58:51,195 writing top-level names to coralME.egg-info/top_level.txt 2024-11-28T15:58:51,237 reading manifest file 'coralME.egg-info/SOURCES.txt' 2024-11-28T15:58:51,245 adding license file 'LICENSE' 2024-11-28T15:58:51,252 writing manifest file 'coralME.egg-info/SOURCES.txt' 2024-11-28T15:58:51,254 Copying coralME.egg-info to build/bdist.linux-armv7l/wheel/./coralME-1.0.0.post3-py3.11.egg-info 2024-11-28T15:58:51,264 running install_scripts 2024-11-28T15:58:51,280 creating build/bdist.linux-armv7l/wheel/coralME-1.0.0.post3.dist-info/WHEEL 2024-11-28T15:58:51,283 creating '/tmp/pip-wheel-mtdgfdf3/coralME-1.0.0.post3-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-11-28T15:58:51,286 adding 'coralme/__init__.py' 2024-11-28T15:58:51,289 adding 'coralme/_version.py' 2024-11-28T15:58:51,291 adding 'coralme/builder/__init__.py' 2024-11-28T15:58:51,292 adding 'coralme/builder/column_format.json' 2024-11-28T15:58:51,293 adding 'coralme/builder/compartments.py' 2024-11-28T15:58:51,298 adding 'coralme/builder/curation.py' 2024-11-28T15:58:51,301 adding 'coralme/builder/dictionaries.py' 2024-11-28T15:58:51,303 adding 'coralme/builder/dna_replication.py' 2024-11-28T15:58:51,305 adding 'coralme/builder/flat_files.py' 2024-11-28T15:58:51,307 adding 'coralme/builder/formulas.py' 2024-11-28T15:58:51,311 adding 'coralme/builder/helper_functions.py' 2024-11-28T15:58:51,313 adding 'coralme/builder/homology.py' 2024-11-28T15:58:51,331 adding 'coralme/builder/main.py' 2024-11-28T15:58:51,334 adding 'coralme/builder/modifications.py' 2024-11-28T15:58:51,345 adding 'coralme/builder/organism.py' 2024-11-28T15:58:51,350 adding 'coralme/builder/preprocess_inputs.py' 2024-11-28T15:58:51,352 adding 'coralme/builder/ribosome.py' 2024-11-28T15:58:51,353 adding 'coralme/builder/transcription.py' 2024-11-28T15:58:51,355 adding 'coralme/builder/translation.py' 2024-11-28T15:58:51,357 adding 'coralme/builder/translocation.py' 2024-11-28T15:58:51,358 adding 'coralme/builder/trna_charging.py' 2024-11-28T15:58:51,360 adding 'coralme/core/__init__.py' 2024-11-28T15:58:51,362 adding 'coralme/core/component.py' 2024-11-28T15:58:51,369 adding 'coralme/core/model.py' 2024-11-28T15:58:51,374 adding 'coralme/core/processdata.py' 2024-11-28T15:58:51,383 adding 'coralme/core/reaction.py' 2024-11-28T15:58:51,387 adding 'coralme/iJL1678b-ME/BarEven_subsystem_classification.csv' 2024-11-28T15:58:51,390 adding 'coralme/iJL1678b-ME/building_data/RNAs.txt' 2024-11-28T15:58:51,408 adding 'coralme/iJL1678b-ME/building_data/TUs.txt' 2024-11-28T15:58:51,428 adding 'coralme/iJL1678b-ME/building_data/TUs_from_biocyc.txt' 2024-11-28T15:58:51,452 adding 'coralme/iJL1678b-ME/building_data/_TUs_from_biocyc.txt' 2024-11-28T15:58:51,455 adding 'coralme/iJL1678b-ME/building_data/amino_acid_trna_synthetase.txt' 2024-11-28T15:58:51,456 adding 'coralme/iJL1678b-ME/building_data/cleaved_methionine.txt' 2024-11-28T15:58:51,457 adding 'coralme/iJL1678b-ME/building_data/codon_usage.txt' 2024-11-28T15:58:51,459 adding 'coralme/iJL1678b-ME/building_data/elongation_subreactions.txt' 2024-11-28T15:58:51,467 adding 'coralme/iJL1678b-ME/building_data/enzyme_reaction_association.txt' 2024-11-28T15:58:51,469 adding 'coralme/iJL1678b-ME/building_data/excision_machinery.txt' 2024-11-28T15:58:51,470 adding 'coralme/iJL1678b-ME/building_data/folding_chaperones.txt' 2024-11-28T15:58:51,472 adding 'coralme/iJL1678b-ME/building_data/folding_dict.txt' 2024-11-28T15:58:51,473 adding 'coralme/iJL1678b-ME/building_data/generic_dict.txt' 2024-11-28T15:58:51,527 adding 'coralme/iJL1678b-ME/building_data/genes.txt' 2024-11-28T15:58:55,665 adding 'coralme/iJL1678b-ME/building_data/genome.gb' 2024-11-28T15:58:55,797 adding 'coralme/iJL1678b-ME/building_data/iJO1366b.json' 2024-11-28T15:58:55,803 adding 'coralme/iJL1678b-ME/building_data/initiation_subreactions.txt' 2024-11-28T15:58:55,829 adding 'coralme/iJL1678b-ME/building_data/keffs.json' 2024-11-28T15:58:55,854 adding 'coralme/iJL1678b-ME/building_data/keffs.txt' 2024-11-28T15:58:55,857 adding 'coralme/iJL1678b-ME/building_data/lipid_modifications.txt' 2024-11-28T15:58:55,858 adding 'coralme/iJL1678b-ME/building_data/lipoprotein_precursors.txt' 2024-11-28T15:58:55,909 adding 'coralme/iJL1678b-ME/building_data/m_model.json' 2024-11-28T15:58:55,916 adding 'coralme/iJL1678b-ME/building_data/m_to_me_mets.txt' 2024-11-28T15:58:55,917 adding 'coralme/iJL1678b-ME/building_data/me_metabolites.txt' 2024-11-28T15:58:55,919 adding 'coralme/iJL1678b-ME/building_data/metabolite_corrections.txt' 2024-11-28T15:58:55,926 adding 'coralme/iJL1678b-ME/building_data/metabolites.txt' 2024-11-28T15:58:55,928 adding 'coralme/iJL1678b-ME/building_data/modification.txt' 2024-11-28T15:58:55,929 adding 'coralme/iJL1678b-ME/building_data/orphan_and_spont_reactions.txt' 2024-11-28T15:58:55,932 adding 'coralme/iJL1678b-ME/building_data/peptide_compartment_and_pathways.txt' 2024-11-28T15:58:55,934 adding 'coralme/iJL1678b-ME/building_data/peptide_release_factors.txt' 2024-11-28T15:58:55,936 adding 'coralme/iJL1678b-ME/building_data/post_transcriptional_modification_of_RNA.txt' 2024-11-28T15:58:55,943 adding 'coralme/iJL1678b-ME/building_data/protein_complexes.txt' 2024-11-28T15:58:55,945 adding 'coralme/iJL1678b-ME/building_data/protein_corrections.txt' 2024-11-28T15:58:55,949 adding 'coralme/iJL1678b-ME/building_data/protein_modification.txt' 2024-11-28T15:58:55,957 adding 'coralme/iJL1678b-ME/building_data/proteins.txt' 2024-11-28T15:58:55,959 adding 'coralme/iJL1678b-ME/building_data/reaction_corrections.txt' 2024-11-28T15:58:55,963 adding 'coralme/iJL1678b-ME/building_data/reaction_matrix.txt' 2024-11-28T15:58:58,512 adding 'coralme/iJL1678b-ME/building_data/reference_tRNAs.fna' 2024-11-28T15:58:58,542 adding 'coralme/iJL1678b-ME/building_data/rho_independent.txt' 2024-11-28T15:58:58,544 adding 'coralme/iJL1678b-ME/building_data/ribosomal_proteins.txt' 2024-11-28T15:58:58,545 adding 'coralme/iJL1678b-ME/building_data/ribosome_subreactions.txt' 2024-11-28T15:58:58,547 adding 'coralme/iJL1678b-ME/building_data/rna_degradosome.txt' 2024-11-28T15:58:58,548 adding 'coralme/iJL1678b-ME/building_data/rna_modification.txt' 2024-11-28T15:58:58,549 adding 'coralme/iJL1678b-ME/building_data/rrna_modifications.txt' 2024-11-28T15:58:58,551 adding 'coralme/iJL1678b-ME/building_data/sigma_factors.txt' 2024-11-28T15:58:58,552 adding 'coralme/iJL1678b-ME/building_data/special_modifications.txt' 2024-11-28T15:58:58,553 adding 'coralme/iJL1678b-ME/building_data/special_trna_subreactions.txt' 2024-11-28T15:58:58,555 adding 'coralme/iJL1678b-ME/building_data/stable_RNAs.txt' 2024-11-28T15:58:58,556 adding 'coralme/iJL1678b-ME/building_data/subreaction_matrix.txt' 2024-11-28T15:58:58,558 adding 'coralme/iJL1678b-ME/building_data/subsystem_classification.txt' 2024-11-28T15:58:58,559 adding 'coralme/iJL1678b-ME/building_data/termination_subreactions.txt' 2024-11-28T15:58:58,560 adding 'coralme/iJL1678b-ME/building_data/transcription_subreactions.txt' 2024-11-28T15:58:58,561 adding 'coralme/iJL1678b-ME/building_data/translocation_multipliers.txt' 2024-11-28T15:58:58,562 adding 'coralme/iJL1678b-ME/building_data/translocation_pathways.txt' 2024-11-28T15:58:58,564 adding 'coralme/iJL1678b-ME/building_data/trna_modification.txt' 2024-11-28T15:58:58,567 adding 'coralme/io/JSONSCHEMA' 2024-11-28T15:58:58,568 adding 'coralme/io/__init__.py' 2024-11-28T15:58:58,570 adding 'coralme/io/dict.py' 2024-11-28T15:58:58,572 adding 'coralme/io/json.py' 2024-11-28T15:58:58,573 adding 'coralme/io/pickle.py' 2024-11-28T15:58:58,574 adding 'coralme/licenses/LICENSE-cobrame' 2024-11-28T15:58:58,576 adding 'coralme/licenses/LICENSE-ecolime' 2024-11-28T15:58:58,577 adding 'coralme/licenses/LICENSE-solvemepy' 2024-11-28T15:58:58,579 adding 'coralme/solver/__init__.py' 2024-11-28T15:58:58,596 adding 'coralme/solver/qmatrixA.cpython-310-x86_64-linux-gnu.so' 2024-11-28T15:58:58,612 adding 'coralme/solver/qmatrixA.cpython-37m-x86_64-linux-gnu.so' 2024-11-28T15:58:58,629 adding 'coralme/solver/qmatrixA.cpython-38-x86_64-linux-gnu.so' 2024-11-28T15:58:58,647 adding 'coralme/solver/qmatrixA.cpython-39-x86_64-linux-gnu.so' 2024-11-28T15:58:58,664 adding 'coralme/solver/qsolveME.cpython-310-x86_64-linux-gnu.so' 2024-11-28T15:58:58,680 adding 'coralme/solver/qsolveME.cpython-37m-x86_64-linux-gnu.so' 2024-11-28T15:58:58,698 adding 'coralme/solver/qsolveME.cpython-38-x86_64-linux-gnu.so' 2024-11-28T15:58:58,715 adding 'coralme/solver/qsolveME.cpython-39-x86_64-linux-gnu.so' 2024-11-28T15:58:58,815 adding 'coralme/solver/qvaryME.cpython-310-x86_64-linux-gnu.so' 2024-11-28T15:58:58,915 adding 'coralme/solver/qvaryME.cpython-37m-x86_64-linux-gnu.so' 2024-11-28T15:58:59,017 adding 'coralme/solver/qvaryME.cpython-38-x86_64-linux-gnu.so' 2024-11-28T15:58:59,119 adding 'coralme/solver/qvaryME.cpython-39-x86_64-linux-gnu.so' 2024-11-28T15:58:59,221 adding 'coralme/solver/qwarmLP.cpython-310-x86_64-linux-gnu.so' 2024-11-28T15:58:59,321 adding 'coralme/solver/qwarmLP.cpython-37m-x86_64-linux-gnu.so' 2024-11-28T15:58:59,422 adding 'coralme/solver/qwarmLP.cpython-38-x86_64-linux-gnu.so' 2024-11-28T15:58:59,523 adding 'coralme/solver/qwarmLP.cpython-39-x86_64-linux-gnu.so' 2024-11-28T15:58:59,529 adding 'coralme/solver/solver.py' 2024-11-28T15:58:59,634 adding 'coralme/solver/warmLP.cpython-310-x86_64-linux-gnu.so' 2024-11-28T15:58:59,740 adding 'coralme/solver/warmLP.cpython-37m-x86_64-linux-gnu.so' 2024-11-28T15:58:59,849 adding 'coralme/solver/warmLP.cpython-38-x86_64-linux-gnu.so' 2024-11-28T15:58:59,956 adding 'coralme/solver/warmLP.cpython-39-x86_64-linux-gnu.so' 2024-11-28T15:58:59,962 adding 'coralme/util/__init__.py' 2024-11-28T15:58:59,968 adding 'coralme/util/building.py' 2024-11-28T15:58:59,970 adding 'coralme/util/dogma.py' 2024-11-28T15:58:59,971 adding 'coralme/util/massbalance.py' 2024-11-28T15:58:59,973 adding 'coralME-1.0.0.post3.dist-info/LICENSE' 2024-11-28T15:58:59,974 adding 'coralME-1.0.0.post3.dist-info/METADATA' 2024-11-28T15:58:59,975 adding 'coralME-1.0.0.post3.dist-info/WHEEL' 2024-11-28T15:58:59,976 adding 'coralME-1.0.0.post3.dist-info/top_level.txt' 2024-11-28T15:58:59,978 adding 'coralME-1.0.0.post3.dist-info/RECORD' 2024-11-28T15:59:00,079 removing build/bdist.linux-armv7l/wheel 2024-11-28T15:59:00,233 Building wheel for coralme (setup.py): finished with status 'done' 2024-11-28T15:59:00,321 Created wheel for coralme: filename=coralME-1.0.0.post3-py3-none-any.whl size=8697075 sha256=2a7524cb2590adcaf6cafe9d0ab5f117e23be674a620bb52aee42767ce2da140 2024-11-28T15:59:00,322 Stored in directory: /tmp/pip-ephem-wheel-cache-xjr9xc8t/wheels/5c/66/af/92a81edebc16b117459b2ca34266d5d06e3e04c3d4ef7b8bee 2024-11-28T15:59:00,341 Successfully built coralme 2024-11-28T15:59:00,541 Removed build tracker: '/tmp/pip-build-tracker-khe0obb4'