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

Question

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 

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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 

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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 

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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:

• How do we fix this properly?
• How is one suppose to install conda (in the new Catalina OS for Mac using zsh)?
• Regardless of anything, what are the permissions of the /Users/brandomiranda/.conda conda folder suppose to be and should all folders/files have the same permissions?

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?).

Answer 1

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.

Answer 2

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

$ chown -R $USER ~/.conda 

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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.