unable to Create a miniconda2 environment #71

amitjc · 2020-04-02T19:27:23Z

amitjc
Apr 2, 2020

Dear Experts,

I tried installing connectomemapper 3 on a MacBook after failed attempt on linux. However, I'm unable to Create a miniconda2 environment, as suggested in the documentation.

Please find the log below and advice.

Thank you,

Best Regards,
Amit.

(base) Amitkumars-MacBook-Pro:Applications amitjc$ conda env create -f connectomemapper3/environment.yml
Collecting package metadata (repodata.json): done
Solving environment: failed

ResolvePackageNotFound:

git-annex=7.20190219

(base) Amitkumars-MacBook-Pro:Applications amitjc$

Answered by sebastientourbier

May 29, 2020

it seems there is no exisitng conda package for git-annex on Mac.
Git-annex could indeed be installed on MacOSX using brew (https://brew.sh/index_fr):
$brew install git-annex
However, git-annex should be installed only if you wish to use BIDS datasets managed by Datalad (https://www.datalad.org/), which is a very experimental feature which I would not recommend to use right now as it has been a long time I did not test it.

So, you can without any problem delete or comment the line git-annex=7.20190219 in the environment.yml and this should then work.

Info added to documentation (commit 4f418f2)

View full answer

sebastientourbier · 2020-04-03T16:13:08Z

sebastientourbier
Apr 3, 2020
Maintainer

Hi Amit,

I should document this error happening on Mac but it seems there is no exisitng conda package for git-annex on Mac.
Git-annex could indeed be installed on MacOSX using brew (https://brew.sh/index_fr):

$brew install git-annex

However, git-annex should be installed only if you wish to use BIDS datasets managed by Datalad (https://www.datalad.org/), which is a very experimental feature which I would not recommend to use right now as it has been a long time I did not test it.

So, you can without any problem delete or comment the line git-annex=7.20190219 in the environment.yml and this should then work.

Concerning your failed attempt of installation of CMP3 on Linux (#29), please check my last reply (#29 (comment)) which should make the installation on your machine successful.

0 replies

amitjc · 2020-04-04T06:09:52Z

amitjc
Apr 4, 2020
Author

Hello Sébastien,

Brew installed git-annex. However, received the same error as earlier.

Then deleted git-annex=7.20190219 from environment.yml and reran conda env create -f connectomemapper3/environment.yml; yet had CondaEnvException: Pip failed.

Pasting the entire process below.

Looking forward to your continued support.

Thank you,

Best Regards,
Amit.

(base) Amitkumars-MacBook-Pro:Applications amitjc$ conda env create -f connectomemapper3/environment.yml
Collecting package metadata (repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.2
  latest version: 4.8.3

Please update conda by running

    $ conda update -n base -c defaults conda



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Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Ran pip subprocess with arguments:
['/Users/amitjc/opt/miniconda3/envs/py27cmp-gui/bin/python', '-m', 'pip', 'install', '-U', '-r', '/Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt']
Pip subprocess output:
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Requirement already satisfied, skipping upgrade: six in /Users/amitjc/opt/miniconda3/envs/py27cmp-gui/lib/python2.7/site-packages (from duecredit==0.7.0->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 2)) (1.13.0)
Requirement already satisfied, skipping upgrade: nibabel>=2.3.0 in /Users/amitjc/opt/miniconda3/envs/py27cmp-gui/lib/python2.7/site-packages (from dipy==0.15.0->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 3)) (2.5.1)
Requirement already satisfied, skipping upgrade: scipy>=0.9 in /Users/amitjc/opt/miniconda3/envs/py27cmp-gui/lib/python2.7/site-packages (from dipy==0.15.0->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 3)) (1.2.1)
Requirement already satisfied, skipping upgrade: h5py>=2.4.0 in /Users/amitjc/opt/miniconda3/envs/py27cmp-gui/lib/python2.7/site-packages (from dipy==0.15.0->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 3)) (2.9.0)
Requirement already satisfied, skipping upgrade: future>=0.12.4 in /Users/amitjc/opt/miniconda3/envs/py27cmp-gui/lib/python2.7/site-packages (from obspy==1.1.1->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 5)) (0.18.2)
Requirement already satisfied, skipping upgrade: numpy>=1.6.1 in /Users/amitjc/opt/miniconda3/envs/py27cmp-gui/lib/python2.7/site-packages (from obspy==1.1.1->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 5)) (1.15.4)
Requirement already satisfied, skipping upgrade: matplotlib>=1.1.0 in /Users/amitjc/opt/miniconda3/envs/py27cmp-gui/lib/python2.7/site-packages (from obspy==1.1.1->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 5)) (2.2.3)
Requirement already satisfied, skipping upgrade: lxml in /Users/amitjc/opt/miniconda3/envs/py27cmp-gui/lib/python2.7/site-packages (from obspy==1.1.1->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 5)) (4.4.2)
Requirement already satisfied, skipping upgrade: setuptools in /Users/amitjc/opt/miniconda3/envs/py27cmp-gui/lib/python2.7/site-packages (from obspy==1.1.1->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 5)) (44.0.0.post20200106)
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  Installing build dependencies: started
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Requirement already satisfied, skipping upgrade: decorator in /Users/amitjc/opt/miniconda3/envs/py27cmp-gui/lib/python2.7/site-packages (from obspy==1.1.1->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 5)) (4.4.2)
Collecting appdirs (from datalad[full]==0.11.4->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 6))
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Collecting chardet>=3.0.4 (from datalad[full]==0.11.4->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 6))
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Collecting GitPython>=2.1.8 (from datalad[full]==0.11.4->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 6))
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Requirement already satisfied, skipping upgrade: python-dateutil in /Users/amitjc/opt/miniconda3/envs/py27cmp-gui/lib/python2.7/site-packages (from datalad[full]==0.11.4->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 6)) (2.8.1)
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Requirement already satisfied, skipping upgrade: pydicom in /Users/amitjc/opt/miniconda3/envs/py27cmp-gui/lib/python2.7/site-packages (from datalad_neuroimaging==0.2.0->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 9)) (1.4.2)
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Collecting num2words (from pybids==0.9.1->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 10))
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Collecting patsy (from pybids==0.9.1->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 10))
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Requirement already satisfied, skipping upgrade: traitsui in /Users/amitjc/opt/miniconda3/envs/py27cmp-gui/lib/python2.7/site-packages (from apptools==4.4.0->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 11)) (6.0.0)
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Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /Users/amitjc/opt/miniconda3/envs/py27cmp-gui/lib/python2.7/site-packages (from sphinx==1.8.5->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 14)) (2.5.2)
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Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /Users/amitjc/opt/miniconda3/envs/py27cmp-gui/lib/python2.7/site-packages (from matplotlib>=1.1.0->obspy==1.1.1->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 5)) (2.4.6)
Requirement already satisfied, skipping upgrade: pytz in /Users/amitjc/opt/miniconda3/envs/py27cmp-gui/lib/python2.7/site-packages (from matplotlib>=1.1.0->obspy==1.1.1->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 5)) (2019.3)
Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /Users/amitjc/opt/miniconda3/envs/py27cmp-gui/lib/python2.7/site-packages (from matplotlib>=1.1.0->obspy==1.1.1->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 5)) (1.1.0)
Requirement already satisfied, skipping upgrade: backports.functools_lru_cache in /Users/amitjc/opt/miniconda3/envs/py27cmp-gui/lib/python2.7/site-packages (from matplotlib>=1.1.0->obspy==1.1.1->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 5)) (1.6.1)
Requirement already satisfied, skipping upgrade: subprocess32 in /Users/amitjc/opt/miniconda3/envs/py27cmp-gui/lib/python2.7/site-packages (from matplotlib>=1.1.0->obspy==1.1.1->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 5)) (3.5.4)
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Requirement already satisfied, skipping upgrade: funcsigs>=1; python_version < "3.3" in /Users/amitjc/opt/miniconda3/envs/py27cmp-gui/lib/python2.7/site-packages (from mock>=1.0.1->datalad[full]==0.11.4->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 6)) (1.0.2)
Collecting entrypoints (from keyring>=8.0->datalad[full]==0.11.4->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 6))
  Downloading https://files.pythonhosted.org/packages/ac/c6/44694103f8c221443ee6b0041f69e2740d89a25641e62fb4f2ee568f2f9c/entrypoints-0.3-py2.py3-none-any.whl
Collecting deprecated (from PyGithub->datalad[full]==0.11.4->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 6))
  Downloading https://files.pythonhosted.org/packages/f6/89/62912e01f3cede11edcc0abf81298e3439d9c06c8dce644369380ed13f6d/Deprecated-1.2.7-py2.py3-none-any.whl
Collecting pyjwt (from PyGithub->datalad[full]==0.11.4->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 6))
  Downloading https://files.pythonhosted.org/packages/87/8b/6a9f14b5f781697e51259d81657e6048fd31a113229cf346880bb7545565/PyJWT-1.7.1-py2.py3-none-any.whl
Collecting soupsieve>=1.2 (from BeautifulSoup4->datalad[full]==0.11.4->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 6))
  Downloading https://files.pythonhosted.org/packages/81/94/03c0f04471fc245d08d0a99f7946ac228ca98da4fa75796c507f61e688c2/soupsieve-1.9.5-py2.py3-none-any.whl
Collecting contextlib2; python_version == "2.7" (from vcrpy->datalad[full]==0.11.4->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 6))
  Downloading https://files.pythonhosted.org/packages/85/60/370352f7ef6aa96c52fb001831622f50f923c1d575427d021b8ab3311236/contextlib2-0.6.0.post1-py2.py3-none-any.whl
Collecting scandir; python_version < "3.5" (from pathlib2; python_version < "3.0"->datalad-revolution==0.6.0->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 7))
  Downloading https://files.pythonhosted.org/packages/df/f5/9c052db7bd54d0cbf1bc0bb6554362bba1012d03e5888950a4f5c5dadc4e/scandir-1.10.0.tar.gz
Collecting docopt>=0.6.2 (from num2words->pybids==0.9.1->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 10))
  Downloading https://files.pythonhosted.org/packages/a2/55/8f8cab2afd404cf578136ef2cc5dfb50baa1761b68c9da1fb1e4eed343c9/docopt-0.6.2.tar.gz
Requirement already satisfied, skipping upgrade: traits in /Users/amitjc/opt/miniconda3/envs/py27cmp-gui/lib/python2.7/site-packages (from traitsui->apptools==4.4.0->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 11)) (5.1.2)
Requirement already satisfied, skipping upgrade: pyface>=6.0.0 in /Users/amitjc/opt/miniconda3/envs/py27cmp-gui/lib/python2.7/site-packages (from traitsui->apptools==4.4.0->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 11)) (6.1.2)
Collecting MarkupSafe>=0.23 (from Jinja2>=2.3->sphinx==1.8.5->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 14))
  Downloading https://files.pythonhosted.org/packages/6d/d2/0ccd2c0e2cd93b35e765d9b3205cd6602e6b202b522fc7997531353715b3/MarkupSafe-1.1.1-cp27-cp27m-macosx_10_6_intel.whl
Collecting smmap2>=2.0.0 (from gitdb2<3,>=2->GitPython>=2.1.8->datalad[full]==0.11.4->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 6))
  Downloading https://files.pythonhosted.org/packages/88/77/b1542b654fa594580fa82a1e0af4bf81074323d272a50a838c943e3de7b4/smmap2-3.0.1.tar.gz
Requirement already satisfied, skipping upgrade: configparser>=3.5; python_version == "2.7" in /Users/amitjc/opt/miniconda3/envs/py27cmp-gui/lib/python2.7/site-packages (from entrypoints->keyring>=8.0->datalad[full]==0.11.4->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 6)) (4.0.2)
Collecting smmap>=3.0.1 (from smmap2>=2.0.0->gitdb2<3,>=2->GitPython>=2.1.8->datalad[full]==0.11.4->-r /Volumes/Macintosh HD 1/Applications/connectomemapper3/condaenv.t_z9e54b.requirements.txt (line 6))
  Downloading https://files.pythonhosted.org/packages/35/d2/27777ab463cd44842c78305fa8097dfba0d94768abbb7e1c4d88f1fa1a0b/smmap-3.0.1-py2.py3-none-any.whl
Building wheels for collected packages: sqlalchemy
Failed to build sqlalchemy

Pip subprocess error:
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
The directory '/Users/amitjc/Library/Caches/pip/http' or its parent directory is not owned by the current user and the cache has been disabled. Please check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
The directory '/Users/amitjc/Library/Caches/pip' or its parent directory is not owned by the current user and caching wheels has been disabled. check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
  Building wheel for sqlalchemy failed: [Errno 13] Permission denied: '/Users/amitjc/Library/Caches/pip/wheels/24'
Could not build wheels for sqlalchemy which use PEP 517 and cannot be installed directly


CondaEnvException: Pip failed

(base) Amitkumars-MacBook-Pro:Applications amitjc$ sudo conda env create -f connectomemapper3/environment.yml
Password:

CondaValueError: prefix already exists: /Users/amitjc/opt/miniconda3/envs/py27cmp-gui

(base) Amitkumars-MacBook-Pro:Applications amitjc$ sudo -H conda env create -f connectomemapper3/environment.yml

CondaValueError: prefix already exists: /Users/amitjc/opt/miniconda3/envs/py27cmp-gui

(base) Amitkumars-MacBook-Pro:Applications amitjc$

0 replies

amitjc · 2020-04-04T06:33:23Z

amitjc
Apr 4, 2020
Author

The directory '/Users/amitjc/Library/Caches/pip/http' or its parent directory is not owned by the current user and the cache has been disabled. Please check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
The directory '/Users/amitjc/Library/Caches/pip' or its parent directory is not owned by the current user and caching wheels has been disabled. check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.

No such directory exists.

Also tried the sudo -H, but in vain.

0 replies

sebastientourbier · 2020-04-06T21:14:05Z

sebastientourbier
Apr 6, 2020
Maintainer

Hi Amit,

To fix the error:

CondaValueError: prefix already exists: /Users/amitjc/opt/miniconda3/envs/py27cmp-gui

You would have to remove by hand the folder contained the environment py27cmp-gui, i.e:

$ (sudo) rm -R  /Users/amitjc/opt/miniconda3/envs/py27cmp-gui

Not sure if you would need to be root (sudo).

It seems the error related to sqlalchemy, i.e.

Building wheel for sqlalchemy failed: [Errno 13] Permission denied: '/Users/amitjc/Library/Caches/pip/wheels/24'
Could not build wheels for sqlalchemy which use PEP 517 and cannot be installed directly

is a dependency of Datalad. So maybe comment/remove all the lines in the environment.yml related to Datalad.

Also, I would advise you to never run commands such as conda env create ... as root. This might just create at some other levels new permission denied errors.

Hope this would work eventually.

0 replies

sebastientourbier · 2020-05-26T12:43:01Z

sebastientourbier
May 26, 2020
Maintainer

Any update on this @amitjc ?
If not I will considered this issue as solved and will close it

0 replies

sebastientourbier · 2020-05-29T14:26:55Z

sebastientourbier
May 29, 2020
Maintainer

it seems there is no exisitng conda package for git-annex on Mac.
Git-annex could indeed be installed on MacOSX using brew (https://brew.sh/index_fr):
$brew install git-annex
However, git-annex should be installed only if you wish to use BIDS datasets managed by Datalad (https://www.datalad.org/), which is a very experimental feature which I would not recommend to use right now as it has been a long time I did not test it.

So, you can without any problem delete or comment the line git-annex=7.20190219 in the environment.yml and this should then work.

Info added to documentation (commit 4f418f2)

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unable to Create a miniconda2 environment #71

amitjc Apr 2, 2020

Replies: 6 comments

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