CODEWITHSUNDEEP
pythonanacondaconda
Charlie Parker
Charlie Parker

Reputation: 5111

How does one fix the issue of not writable paths with conda?

Why do I see the following error when using conda (usually when installing packages or making new envs) and how do I fix it:

Verifying transaction: | WARNING conda.core.path_actions:verify(963): Unable to create environments file. Path not writable.
  environment location: /Users/brandomiranda/.conda/environments.txt

or

Preparing transaction: done
Verifying transaction: - WARNING conda.core.path_actions:verify(963): Unable to create environments file. Path not writable.
  environment location: /Users/brandomiranda/.conda/environments.txt

done
Executing transaction: - WARNING conda.core.envs_manager:register_env(52): Unable to register environment. Path not writable or missing.
  environment location: /Users/brandomiranda/miniconda3/envs/myenv
  registry file: /Users/brandomiranda/.conda/environments.txt
done

a detailed outline of what I did can be found on the following gitissue:

https://github.com/conda/conda/issues/7267

which really isn't anything too fancy except re-install conda from scratch and run the following command:

bash Miniconda3-latest-MacOSX-x86_64.sh

and it installed this version of conda:

❯ conda -V
conda 4.7.12

Example of command causing me the warnings:

conda create -n myenv python=3.6

More errors when I install packages with conda:

Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /Users/brandomiranda/miniconda3/envs/automl

  added / updated specs:
    - jupyterlab


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    jupyter_client-5.3.4       |           py37_0         131 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         131 KB

The following NEW packages will be INSTALLED:

  appnope            conda-forge/osx-64::appnope-0.1.0-py37_1000
  attrs              conda-forge/noarch::attrs-19.3.0-py_0
  backcall           conda-forge/noarch::backcall-0.1.0-py_0
  bleach             conda-forge/noarch::bleach-3.1.0-py_0
  decorator          conda-forge/noarch::decorator-4.4.1-py_0
  defusedxml         conda-forge/noarch::defusedxml-0.6.0-py_0
  entrypoints        conda-forge/osx-64::entrypoints-0.3-py37_1000
  importlib_metadata conda-forge/osx-64::importlib_metadata-1.3.0-py37_0
  ipykernel          conda-forge/osx-64::ipykernel-5.1.3-py37h5ca1d4c_0
  ipython            conda-forge/osx-64::ipython-7.11.1-py37h5ca1d4c_0
  ipython_genutils   conda-forge/noarch::ipython_genutils-0.2.0-py_1
  jedi               conda-forge/osx-64::jedi-0.15.2-py37_0
  jinja2             conda-forge/noarch::jinja2-2.10.3-py_0
  json5              conda-forge/noarch::json5-0.8.5-py_0
  jsonschema         conda-forge/osx-64::jsonschema-3.2.0-py37_0
  jupyter_client     conda-forge/osx-64::jupyter_client-5.3.4-py37_0
  jupyter_core       conda-forge/osx-64::jupyter_core-4.6.1-py37_0
  jupyterlab         conda-forge/noarch::jupyterlab-1.2.4-py_0
  jupyterlab_server  conda-forge/noarch::jupyterlab_server-1.0.6-py_0
  libsodium          conda-forge/osx-64::libsodium-1.0.17-h01d97ff_0
  markupsafe         conda-forge/osx-64::markupsafe-1.1.1-py37h0b31af3_0
  mistune            conda-forge/osx-64::mistune-0.8.4-py37h0b31af3_1000
  more-itertools     conda-forge/noarch::more-itertools-8.0.2-py_0
  nbconvert          conda-forge/osx-64::nbconvert-5.6.1-py37_0
  nbformat           conda-forge/noarch::nbformat-5.0.3-py_0
  notebook           conda-forge/osx-64::notebook-6.0.1-py37_0
  pandoc             conda-forge/osx-64::pandoc-2.9.1.1-0
  pandocfilters      conda-forge/noarch::pandocfilters-1.4.2-py_1
  parso              conda-forge/noarch::parso-0.5.2-py_0
  pexpect            conda-forge/osx-64::pexpect-4.7.0-py37_0
  pickleshare        conda-forge/osx-64::pickleshare-0.7.5-py37_1000
  prometheus_client  conda-forge/noarch::prometheus_client-0.7.1-py_0
  prompt_toolkit     conda-forge/noarch::prompt_toolkit-3.0.2-py_0
  ptyprocess         conda-forge/noarch::ptyprocess-0.6.0-py_1001
  pygments           conda-forge/noarch::pygments-2.5.2-py_0
  pyrsistent         conda-forge/osx-64::pyrsistent-0.15.7-py37h0b31af3_0
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.1-py_0
  pyzmq              pkgs/main/osx-64::pyzmq-18.1.0-py37h0a44026_0
  send2trash         conda-forge/noarch::send2trash-1.5.0-py_0
  terminado          conda-forge/osx-64::terminado-0.8.3-py37_0
  testpath           conda-forge/noarch::testpath-0.4.4-py_0
  tornado            conda-forge/osx-64::tornado-6.0.3-py37h0b31af3_0
  traitlets          conda-forge/osx-64::traitlets-4.3.3-py37_0
  wcwidth            conda-forge/noarch::wcwidth-0.1.8-py_0
  webencodings       conda-forge/noarch::webencodings-0.5.1-py_1
  zeromq             conda-forge/osx-64::zeromq-4.3.2-h6de7cb9_2
  zipp               conda-forge/noarch::zipp-0.6.0-py_0

The following packages will be UPDATED:

  ca-certificates    pkgs/main::ca-certificates-2019.11.27~ --> conda-forge::ca-certificates-2019.11.28-hecc5488_0

The following packages will be SUPERSEDED by a higher-priority channel:

  certifi                                         pkgs/main --> conda-forge
  openssl              pkgs/main::openssl-1.1.1d-h1de35cc_3 --> conda-forge::openssl-1.1.1d-h0b31af3_0



Proceed ([y]/n)? y


Downloading and Extracting Packages
jupyter_client-5.3.4 | 131 KB    | ################################################################################################################################################################# | 100%
Preparing transaction: done
Verifying transaction: | WARNING conda.core.path_actions:verify(963): Unable to create environments file. Path not writable.
  environment location: /Users/brandomiranda/.conda/environments.txt

done
Executing transaction: - WARNING conda.core.envs_manager:register_env(52): Unable to register environment. Path not writable or missing.
  environment location: /Users/brandomiranda/miniconda3/envs/automl
  registry file: /Users/brandomiranda/.conda/environments.txt
done

command that I ran:

(automl) brandomiranda~/automl-meta-learning ❯ conda install -c conda-forge jupyterlab

I tried changing the permission according to the suggested answers, BUT it seems it won't work without sudo. Is it really safe to do sudo here? why isn't it writable to the correct set of users already?

(automl) brandomiranda~/.conda ❯ if [ -w "/Users/brandomiranda/.conda" ]; then echo "WRITABLE"; else echo "NOT WRITABLE"; fi
NOT WRITABLE
(automl) brandomiranda~/.conda ❯ chmod 775 /Users/brandomiranda/.conda
chmod: Unable to change file mode on /Users/brandomiranda/.conda: Operation not permitted

Update after running suggested answers

I've ran the chmod command in sudo. I checked the permissions of that file and I got the following:

(automl-meta-learning) brandomiranda~/automl-meta-learning/automl/automl ❯ ls -lha /Users/brandomiranda/.conda                                                        
total 8
drwxrwxr-x    3 root           staff    96B Jan  5 16:57 .
drwxr-xr-x+ 117 brandomiranda  staff   3.7K Jan 19 17:25 ..
-rw-r--r--    1 root           staff    32B Jan  5 16:57 environments.txt

I checked this because I tried to install conda-build with conda install conda-build command but got the error towards the end:

Preparing transaction: done
Verifying transaction: \ WARNING conda.core.path_actions:verify(963): Unable to create environments file. Path not writable.
  environment location: /Users/brandomiranda/.conda/environments.txt
                                                                                                                                                                                                                                                                       done
Executing transaction: \ WARNING conda.core.envs_manager:register_env(52): Unable to register environment. Path not writable or missing.
  environment location: /Users/brandomiranda/miniconda3/envs/automl-meta-learning
  registry file: /Users/brandomiranda/.conda/environments.txt                                                                                                                                                                                                          done

which seemed weird and that when I notice the environment.txt didn't have the same permissions as the other file/directories. I am tempted to chmod that file too but all this business seems to be putting a bandage on the problem. I feel this shouldn't have happened in the first place so I will ask:

for now I will run:

sudo chmod 775 /Users/brandomiranda/.conda/environments.txt

although, it makes me uneasy that I am having to run sudo for conda related stuff. Anyone know how to do this without requiring sudo or is sudo supposed to be required?

As a side comment, I am glad I never tried installing anything from conda using sudo and only changed the permissions of a few folders/files. That seems much safer than allowing conda to run arbitrary code in sudo (instead here it can run its stuff to a specific location while NOT running in sudo, so I guess changing folder permissions isn't that bad?).

Upvotes: 42

Views: 49923

Answers (6)

AlexW
AlexW

Reputation: 1166

As an alternative solution, I changed the owner of ~/.conda to myself:

sudo chown -R $USER ~/.conda

I think the root cause of the problem (at least in my case) was that ~/.conda was owned by root for some reason. Other solutions suggest making its access more permissive (open writing to the group or even to all) as a workaround. While technically that should work, I think changing the owner (and keeping existing permissions) is a safer approach.

Upvotes: 57

mrajase
mrajase

Reputation: 67

I faced this issue in Windows 10, and couldn't find the answer anywhere.

Turns out this was because .conda/ folder did not exist at my %USERPROFILE% location, which for me happens to be at C:\Users\<username>.

I created the folder using the following command in the cmd.exe

mkdir C:\Users\<username>\.conda\

and now conda does not throw this error anymore.

Upvotes: 0

Jay Prakash Thakur
Jay Prakash Thakur

Reputation: 615

if you are on Mac & have install Anaconda from GUI. try

change the permission of opt/anaconda3/ folder to Read & write.

This solved my problem.

Upvotes: 0

Charlie Parker
Charlie Parker

Reputation: 5111

I ran the top voted answer but because the chmod command did not have the recursive flag it did not work and later gave me problems (because I didn't change the permissions of EVERYTHING inside the conda folder of course):

So change permissions recursively of the directory with:

sudo chmod -R 775 /Users/brandomiranda/.conda

swap /Users/brandomiranda/ for your path to .conda of course.

If you are worried about using sudo I believe its not that bad to have to run it because we are only changing the permissions of a very specific directory (which is much safer than say, running any conda command with sudo!)

The fact is, I don't know why the issue came despite me (I believe) installing conda properly with the conda .sh script as I outlined in the question. Solving that is the real solution I assume but I don't know how to solve that (I guess I could try re-installing yet again...)

Upvotes: 2

chrisckwong821
chrisckwong821

Reputation: 1173

reference: to https://gist.github.com/zoka123/f2b03f19924258d28441fe2d88750145

check if a path is writable:

if [ -w "./.conda" ]; then echo "WRITABLE"; else echo "NOT WRITABLE"; fi

if it is not writable, change writability to anybody:

chmod 775 ./.conda

If you are curious of existing file permission:

ls -lha outputs the set of access right of current locations, where d refers to current directory. Eg: drwxr-xr-x :

each digit refers to right for User, Group and Global respectively. For the above example, rwx means current user can read,write and execute; r-x for both group and global, which means they can read and execute only.

chmod is used with a 3-digit commands, each digit refers to one combination of the read, write, execute access for the above three types of identity.

755 means rwx for current user, and r-x for Group and Global.

You may refer to https://www.linode.com/docs/tools-reference/tools/modify-file-permissions-with-chmod/ for reference.

Upvotes: 16

Matt Shin
Matt Shin

Reputation: 434

To add user write permission to a directory recursively:

chmod -R u+w /Users/brandomiranda/.conda

Upvotes: 3

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