I have anaconda installed in my computer and after installing Oh my zsh. Conda and python etc. command is not found.
zsh: command not found: conda
How can I fix this? It seems that the solutions I can find on the internet is a bit outdated.
It depends on how you installed it. You'll need to check your PATH variable, and compare against what you had in the original .zshrc file. You can then add it back like so
PATH="<PATH_TO_DIR_CONTAINING_CONDA:$PATH"
I've installed tmux using brew ( arch -x86_64 brew install tmux ) on M1 Mac and since then my terminal is super slow. on lunch, after running commands and it's just incredibly slow.
I tried deleting the package using
brew uninstall pkg
it didn't work. I tried using the following commands as well.
brew remove pkg
brew rmtree tmux
I get "Error: tmux is not currently installed" since I've already uninstalled it..
and when using
sudo find / -name "*tmux*"
I still get many files including tmux.
GIFs showing the situation
any ideas/help on how to solve this?
Ok I have fixed it.
although I didn't know exactly what was the problem but it was something related to oh-my-zsh and to be more specific it was with the current oh-my-zsh theme powerlevel9k after installing tmux.
here is the steps I toke: I tried to change my shell to bin/bash it worked great. Tried a couple more shells and all worked great except zsh. then I tried to change the .oh-my-zsh directory name just for testing purposes and opened zsh, it worked great but of course without oh-my-zsh.
so I went to .zshrc and commented this line.
#ZSH_THEME="powerlevel9k/powerlevel9k"
obviously installing tmux messed things up so I'll need to reinstall the theme or oh-my-zsh all over again.
I previously had Conda running smoothly on Mojave, but I've found that the upgrade to Catalina moves the "anaconda3" folder to your Desktop > Relocated Items > Security > anaconda3. It seems Catalina's security settings may not allow applications to install directly under the user directory anymore.
I tried the suggestion here, written below:
Hi, I might have a solution
Copy the folder anaconda3 located in Relocated Items to /Users/myname/
Open Terminal
Enter: export PATH=''/Users/myname/anaconda3/bin:$PATH"
Enter: conda init zsh
It worked! Good luck!
But this doesn't work for me. After conda init zsh I get:
-bash: /Users/USER/anaconda3/bin/conda: /anaconda3/bin/python: bad interpreter: No such file or directory
How can I get Conda up and running again without losing all my virtual environments? Thanks!
Update
I got Conda to work following #Ted Shaowang's suggestion. This means that conda env list shows all the virtual environments created via Conda.
However I am still experiencing an issue with virtualenv as since I changed the default anaconda3 file locations, python cannot be found.
The python executable located at .virtualenvs/env/bin/python cannot be found. Do I need to make further changes in order for python to work from virtualenv too?
I have the exact same problem and this works for me:
After you move anaconda from "Relocated Items" to ~/anaconda3, edit the first line of ~/anaconda3/bin/conda file from #!/anaconda3/bin/python to #!/Users/USERNAME/anaconda3/bin/python to reflect the change.
I would probably abstain from using the above solution. That ~/anaconda3/bin directory has lots of runnables (not just the conda one) that would need to be altered in this manual way. For example, unless you make the same change you cannot run jupyter notebook either, neither from base nor from other envs you might have.
My tip: Try getting a requirements file for your virtual envs, and do a fresh installation. You could use pipreqs to get the requirements used for individual projects: https://www.idiotinside.com/2015/05/10/python-auto-generate-requirements-txt/
No solution will be completely working without fixing the baked-in hard-coded prefix entries in files. There's a longer description and a recommended fix at https://www.anaconda.com/how-to-restore-anaconda-after-macos-catalina-update/
Technically this is reinstalling anaconda, however, I restored all my conda envs so, hopefully this is an acceptable solution!
Here is how I got it working on Catalina as of a few minutes ago (now using z-shell):
- Verified the existence of "Relocated Items" directory on my desktop and the "anaconda3" directory and its contents inside
- Navigated into the envs directory under "anaconda3" and left the finder window open (see screenshot)
THEN:
opened new Terminal (z-shell)
ran (this installed to /usr/local/anaconda3):
brew cask install anaconda
after installation was successful I opened my ~/.zshrc file (for my z-shell aliases) and added the following line:
export PATH="/usr/local/anaconda3/bin:$PATH"
saved my ~/.zshrc file, then reloaded with:
source ~/.zshrc
to verify conda command works now, I ran:
conda env list
for me, this showed a base env and that was it
then open Finder to the new envs location:
open /usr/local/anaconda3/envs/.
I dragged (moved) all my old envs into the new envs folder, and then ran:
conda env list
And all my old envs are back! :)
updated my PyCharm interpreter / env paths to reflect the new locations of these envs (had to restart PyCharm after, but now it works!)
DONE
Unsure whether this is considered a comment or at least a temporary answer, but I would refrain from attempting to fix any Catalina compatibility issues with Anaconda for now. See this GitHub issue.
I have the same problem, and this work for me :
My solution:
Copy your anaconda3 from Relocated Items folder
Paste in User/YourUserName
Open conda file in anaconda3/bin with the editor and edit the first line #!/anaconda3/bin/python to #!/Users/YourUserName/anaconda3/bin/python
Save it and run conda file
Open Terminal
Run this : export PATH=''/Users/YourUserName/anaconda3/bin:$PATH"
Run conda init zsh
I had incurred the same issue, and the following solution worked for me, and this is the easiest solution:
Instead of messing around copying the anaconda3 file from relocated items into User/USERNAME directory, better would be just to reinstall anaconda navigator's latest version from its official website : https://www.anaconda.com/distribution/#macos
While installation, it will ask you some permissions which are a result of new Apple Security Policies, just grant them, and it works just the way it should after this fresh installation!
This is what worked for me.
These are my header files (Catalina 10.15):
/Library/Developer/CommandLineTools/usr/include/c++/v1/stdio.h
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stdio.h
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/stdio.h
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Kernel.framework/Versions/A/Headers/sys/stdio.h
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/sys/stdio.h
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/stdio.h
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/Kernel.framework/Versions/A/Headers/sys/stdio.h
Run sudo find /Library -name stdio.h to see where yours are located.
Mojave 10.14 header files:
$ sudo find /Library -name stdio.h
/Library/Developer/CommandLineTools/usr/include/c++/v1/stdio.h
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/stdio.h
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/System/Library/Frameworks/Kernel.framework/Versions/A/Headers/sys/stdio.h
As can be seen the SDKs are now split into MACOSX10.14 and 10.15 unlike in Mojave.
TLDR
So, these were my SDK folders on Catalina:
Rename MacOSX.sdk to MacOSX_orig.sdk
Right click on MacOSX10.14.sdk
Duplicate
Rename duplicate folder to MacOSX.sdk
Your folder structure should now look like this:
Like this we are basically using the previous version's OSX sdk as sysroot. Hope this helps.
When I first got my Macbook Pro, I set it up where my home folder was named
/Users/monicaheddneck/
I installed all the software I needed, like python, etc, and went about my business.
Last night, I decided to change the name of my folder to simply
/Users/monica/
and did it this way.
Fine.
Today, I decided to run jupyter notebook for the millionth time, and realized I may have borked all paths for all the libraries I have...and who knows what else.
For example,
conda --version
tells me I don't even have conda installed:
-bash: conda: command not found
My question: is there any way to fix the broken path to conda?
I am using Mac High Sierra, version 10.13.3
When using the conda installer, it asks if you want to add and export line with the path to conda in your bashrc file. My guess is that it wasn't updated when you changed the name of your account.
Have a look at your bashrc (hidden file) which should be in your home and update it as necessary ! The line should look like this:
export PATH="/Users/monicaheddneck/xxxconda/bin:$PATH"
and should be fixed appropriatly:
export PATH="/Users/monica/xxxconda/bin:$PATH"
You will then have to source your new bashrc file or restart a terminal.
I delete the zsh binary from bin folder , so when i try to change my shell i get this :
chsh: WARNING: shell '/bin/zsh' does not exist
I don't know how to reinstall zsh shell and MacOs come with zsh by default.
The easiest thing would be to install zsh using brew (which will install it in /usr/local/bin/zsh) and then symlink it to /bin/zsh.
There are obvious more ways to fix this, but this seems (to me) to be the simplest.
I fixed that problem using mac tools. I invested only about 30 min of my time whith the reinstall option. It's obviously there is a way to generate a zsh binary, but I find easy reinstall the osx due to Osx come by default with the zsh binary and brew install doesn't install the zsh binary. On the other hand, there must a way to install zsh from scratch but I think find the correct way would take more time