cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
Other
159 stars 53 forks source link

Having issues with cyanobacteria universe in latest version, and cplex installation for carveme version 1.4 #195

Open marlaux opened 10 months ago

marlaux commented 10 months ago

Hello The cyanobacteria universe is not working with the latest carve version, is that right? So I found out that I should user carve version 1.4. For the latest carve version I was using the scip solver. However, for carve 1.4 it has to be CPLEX, so I downloaded and installed the academic CPLEX. When trying to set up the python API, I noticed that I would need to create a python 3.10 environment, because I have the latest, so I did. Within the py310 environment, when I run: python /opt/ibm/ILOG/CPLEX_Studio2211/python/setup.py install I have the following error:

############################################################################### Invoking ['/home/marlaux/anaconda3/envs/py310/bin/python', '-m', 'pip', 'install', '.'] in /opt/ibm/ILOG/CPLEX_Studio2211/cplex/python/3.10/x86-64_linux Processing /opt/ibm/ILOG/CPLEX_Studio2211/cplex/python/3.10/x86-64_linux Preparing metadata (setup.py) ... done Building wheels for collected packages: cplex Building wheel for cplex (setup.py) ... error error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully. │ exit code: 1 ╰─> [1 lines of output] error: could not delete 'build/lib/cplex/constant_class.py': Permission denied [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for cplex Running setup.py clean for cplex Failed to build cplex ERROR: Could not build wheels for cplex, which is required to install pyproject.toml-based projects Could not install CPLEX, code = 1 ###############################################################################

I search all I could find about this issue trying to solve it, and after almost a entire day trying, I'm here asking for your help. Could anyone maybe try to help me? Thank you very much Below some details about my OS and py310 env: Ubuntu 22.04 (on WSL and VS code) cplex file downloaded: cplex_studio2211.linux_x86_64.bin Path to cplex (default): /opt/ibm/ILOG/CPLEX_Studio2211/cplex/bin/x86-64_linux

conda activate py310 python --version Python 3.10.13 pip list Package Version


asttokens 2.4.1 carveme 1.4.1 certifi 2023.11.17 chardet 5.2.0 charset-normalizer 3.3.2 comm 0.2.1 contourpy 1.2.0 cycler 0.12.1 debugpy 1.8.0 decorator 5.1.1 docplex 2.25.236 exceptiongroup 1.2.0 executing 2.0.1 fonttools 4.47.2 future 0.18.3 futures 3.0.5 idna 3.6 ipykernel 6.28.0 ipython 8.20.0 jedi 0.19.1 jupyter_client 8.6.0 jupyter_core 5.7.1 kiwisolver 1.4.5 matplotlib 3.8.2 matplotlib-inline 0.1.6 mpmath 1.3.0 nest-asyncio 1.5.8 numpy 1.26.3 packaging 23.2 pandas 2.1.4 parso 0.8.3 pexpect 4.9.0 pillow 10.2.0 pip 23.3.2 prompt-toolkit 3.0.43 psutil 5.9.7 ptyprocess 0.7.0 pure-eval 0.2.2 Pygments 2.17.2 PySCIPOpt 3.5.0 python-dateutil 2.8.2 python-libsbml 5.20.2 pytz 2023.3.post1 pyzmq 25.1.2 reframed 1.5.0 requests 2.31.0 scipy 1.11.4 seaborn 0.13.1 setuptools 69.0.3 six 1.16.0 stack-data 0.6.3 sympy 1.12 tornado 6.4 traitlets 5.14.1 tzdata 2023.4 urllib3 2.1.0 wcwidth 0.2.13 wheel 0.42.0