This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Failed building wheel for mminte

I want to create metabolic network from 16S data. So, I tried to install MMinte

~$ pip install mminte

but I got error alert.

 Failed building wheel for mminte
  Running setup.py clean for mminte
  Running setup.py bdist_wheel for future ... done
  Stored in directory: /home/usr/.cache/pip/wheels/0c/61/d2/d6b7317325828fbb39ee6ad559dbe4664d0896da4721bf379e
  Running setup.py bdist_wheel for mpmath ... done
  Stored in directory: /home/usr/.cache/pip/wheels/63/9d/8e/37c3f6506ed3f152733a699e92d8e0c9f5e5f01dea262f80ad
Successfully built future mpmath
Failed to build mminte

How can I solve this problem? or any tools to construct network? Thanks.

modeling rna-seq metabolomics software error
• 4,744 views • link
updated by htaherkhani • htaherkhani • written by mmaetha • mmaetha

Which python version are you using?

• 0 views • link
written by WouterDeCoster WouterDeCoster

python2.7.15 and python3.6.7

• 0 views • link
written by mmaetha • mmaetha

Is what you posted the full error message?

• 0 views • link
written by WouterDeCoster WouterDeCoster

These are all message

~$ pip install mminte


 ...
    Building wheels for collected packages: mminte, future, mpmath
      Running setup.py bdist_wheel for mminte ... error
      Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-V3RzfI/mminte/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /tmp/tmpIAHs0Mpip-wheel- --python-tag cp27:
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build/lib.linux-x86_64-2.7
      creating build/lib.linux-x86_64-2.7/mminte
      copying mminte/__init__.py -> build/lib.linux-x86_64-2.7/mminte
      copying mminte/community.py -> build/lib.linux-x86_64-2.7/mminte
      copying mminte/interaction_analysis.py -> build/lib.linux-x86_64-2.7/mminte
      ...
      copying build/lib.linux-x86_64-2.7/mminte/test/data/western.json -> build/bdist.linux-x86_64/wheel/mminte/test/data
      copying build/lib.linux-x86_64-2.7/mminte/test/test_interactions.py -> build/bdist.linux-x86_64/wheel/mminte/test
      copying build/lib.linux-x86_64-2.7/mminte/test/test_representative.py -> build/bdist.linux-x86_64/wheel/mminte/test
      copying build/lib.linux-x86_64-2.7/mminte/visualize.py -> build/bdist.linux-x86_64/wheel/mminte
      running install_egg_info
      running egg_info
      writing requirements to mminte.egg-info/requires.txt
      writing mminte.egg-info/PKG-INFO
      writing top-level names to mminte.egg-info/top_level.txt
      writing dependency_links to mminte.egg-info/dependency_links.txt
      reading manifest file 'mminte.egg-info/SOURCES.txt'
      writing manifest file 'mminte.egg-info/SOURCES.txt'
      Copying mminte.egg-info to build/bdist.linux-x86_64/wheel/mminte-1.0.3-py2.7.egg-info
      running install_scripts
      creating build/bdist.linux-x86_64/wheel/mminte-1.0.3.data
      creating build/bdist.linux-x86_64/wheel/mminte-1.0.3.data/scripts
      copying build/scripts-2.7/launchMMinte -> build/bdist.linux-x86_64/wheel/mminte-1.0.3.data/scripts
      changing mode of build/bdist.linux-x86_64/wheel/mminte-1.0.3.data/scripts/launchMMinte to 777
      adding link at /usr/bin/blastn to /home/maemae/.local/bin
      error: [Errno 13] Permission denied

      ----------------------------------------
      Failed building wheel for mminte
      Running setup.py clean for mminte
      Running setup.py bdist_wheel for future ... done
      Stored in directory: /home/maemae/.cache/pip/wheels/0c/61/d2/d6b7317325828fbb39ee6ad559dbe4664d0896da4721bf379e
      Running setup.py bdist_wheel for mpmath ... done
      Stored in directory: /home/maemae/.cache/pip/wheels/63/9d/8e/37c3f6506ed3f152733a699e92d8e0c9f5e5f01dea262f80ad
    Successfully built future mpmath
    Failed to build mminte
    Installing collected packages: numpy, biopython, six, pytz, python-dateutil, pandas, ruamel.ordereddict, ruamel.yaml, swiglpk, mpmath, sympy, optlang, future, pip, pipdeptree, depinfo, python-libsbml-experimental, tabulate, cobra, lxml, urllib3, certifi, chardet, idna, requests, configparser, mackinac, decorator, networkx, python-libsbml, scipy, mminte
      Running setup.py install for mminte ... done
    Successfully installed biopython-1.73 certifi-2019.3.9 chardet-3.0.4 cobra-0.15.3 configparser-3.7.4 decorator-4.4.0 depinfo-1.5.1 future-0.17.1 idna-2.8 lxml-4.3.3 mackinac-0.8.4 mminte-1.0.3 mpmath-1.1.0 networkx-2.2 numpy-1.16.3 optlang-1.4.4 pandas-0.24.2 pip-19.1.1 pipdeptree-0.13.2 python-dateutil-2.8.0 python-libsbml-5.18.0 python-libsbml-experimental-5.18.0 pytz-2019.1 requests-2.21.0 ruamel.ordereddict-0.4.13 ruamel.yaml-0.15.94 scipy-1.2.1 six-1.12.0 swiglpk-4.65.0 sympy-1.4 tabulate-0.8.3 urllib3-1.24.3
• 0 views • link
written by mmaetha • mmaetha

That was important. Don't just show half of the error message.

I believe things start going wrong here:

adding link at /usr/bin/blastn to /home/maemae/.local/bin
error: [Errno 13] Permission denied

Do /usr/bin/blastn and /home/maemae/.local/bin exist? Do you have write permission there?

• 0 views • link
written by WouterDeCoster WouterDeCoster

/usr/bin/blastn don't exist. Oh! how can I do? and if I want to change to other model construction program, can you give me an advice?

• 0 views • link
written by mmaetha • mmaetha

So what was wrong was in the error message, all along. You could try to make sure /usr/bin/blast does exist by installing it, if you have those permissions. But a tool which expects a hardcoded path to a dependency is a tool I wouldn't trust any further. This is a bug which you should/could raise on GitHub.

I know nothing about model construction.

• 0 views • link
written by WouterDeCoster WouterDeCoster

Thank you for your answer.

• 0 views • link
written by mmaetha • mmaetha

I want to create metabolic network from 16S data. So, I tried to install MMinte but I have a problem in widget3 When I run this widget I see this Error

Sorry, something went wrong creating metabolic model using ModelSEED. Exeption; Call get_token() to obtain an authentication token

• 0 views • link
written by htaherkhani • htaherkhani

0 answers

No answers yet.

Log in to answer this question.

More posts like this