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.
Related
I've installed miniconda3 on my raspberry pi 3. I've added the path to the .bashrc which is export PATH="/home/pi/miniconda3/bin:$PATH" at the end of the file. I did not jump many lines, I only started a new one.
But when I write conda in terminal I get the error command not found. Where could I have gone wrong? Was I suppose to add the path in a specific place in the .bashrc ?
Installed version from: http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-armv7l.sh by recommendation of this answer: How to install Anaconda on RaspBerry Pi 3 Model B
When you install Miniconda, by default it will choose "/root/miniconda3" unless you change. Follow the install process again, but when asked about the location, input this "/home/pi/miniconda3/". Copy and paste the path between quotes. After miniconda install, add this: export PATH="/home/pi/miniconda3/bin:$PATH" to .bashrc. After "sudo reboot" you will be able to use conda commands. :)
Sorry if this is a stupid question. I use python/jupyter a lot and it's stopped working after updating from Mac OS High Sierra to Big Sur. I'm trying to figure out why, but I'm not great with command line stuff.
The problem. When I try python3, pip -v, conda, etc. it says "command not found". python still seems to run, but it's 2.7 and I know I had 3 (I probably had a few versions from untidy file systems). I want to avoid reinstalling all my packages and things again, because I know it's still there and I've done this a few times already.
Some clues. I know this OS upgrade moves me from bash to zsh. I've tried just switching back to bash with chsh -s /bin/zsh but it still says command not found. I also noticed the OS update creates a Mac HD (below System/Volumes) within my Mac HD, and in that second one seems to be still all my python3/conda/pip/etc. folders. Not sure if/how this matters. Or if this is just a path issue.
I just want to get Jupyter running again on my Mac without reinstalling all my myriad packages from square one. Any help appreciated!
After extreme toil and research, I finally found something that worked for me.
Find the location of your Anaconda3. For me it was in ~/opt/anaconda3
Open terminal and type source <location of anaconda3>/bin/activate and then in the next line, write conda init zsh
Close your terminal and open it again. You should see a prefix (base) when you open it again.
All in all, for me it was
rko3 ~ % source opt/anaconda3/bin/activate
rko3 ~ % conda init zsh
Let me know if this works for you!
PS. You may be tempted to change $PATH variables. Anaconda advises against that. Use this reference instead that suggests the above. https://docs.anaconda.com/anaconda/install/mac-os/
I've just resolved this exact issue on my machine after upgrading to Big Sur from Mojave.
The issue: MacOS, as of Catalina, no longer lets you use the system root folder. Anaconda used to install in this folder. After upgrading from Mojave to Big Sur, you'll likely find your anaconda3 folder, including all your environments and packages, located here: /System/Volumes/Data/anaconda3.
Here is what to do to fix it:
Open Terminal
Move the anaconda3 folder:
sudo mv /System/Volumes/Data/anaconda3 ~/
Download Anaconda's Conda Prefix Replacement (crp) tool:
curl -L https://repo.anaconda.com/pkgs/misc/cpr-exec/cpr-0.1.1-osx-64.exe -o cpr && chmod +x cpr
Run the CRP tool (this will take a few minutes):
./cpr rehome ~/anaconda3/
Source anacoda3
source ~/anaconda3/bin/activate
Initiate conda
conda init
Quit Terminal and open it again.
Edit: Someone didn't like that I ended this answer with "That's it! Enjoy". In the scenario described, the steps above were indeed all it took to resolve the issue. If you're experiencing the same issue, I hope this helps resolve it, so you can get back to enjoying your updated OS.
Seems like your environement is not activated. Zsh sources ~/.zshrc while bash sources ~/.bashrc.
You can copy lines related to conda from your ~/.bashrc to your ~/.zshrc.
AF
Open the Anaconda navigator and click on the Environments section. There you will see the base (root) and a green triangle next to it.
Click on the triangle and select Open Terminal.
Now, in the terminal you will be already in the necessary directory for anaconda and you can then update any packages.
For example, just by writing conda update --all you can update all packages available for updates.
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.
So I ran into the same problem as this question asker's: https://ask.sagemath.org/question/35132/how-do-i-solve-this-installation-problem/
The solution seems to be effectively to delete the line
export PATH="/home/addem/anaconda3/bin:$PATH"
from the .bashrc file, but then I won't be able to use Anaconda. Is there any way to have access to both softwares on the same computer? This question seems to have been asked in a couple places but never with an answer.
One way to solve this problem would be to install SageMath via Conda.
Install instructions: https://wiki.sagemath.org/Conda
Or, instead of including the line
export PATH="/home/addem/anaconda3/bin:$PATH"
in your .bashrc, you could include this line
alias condapath='export PATH="/home/addem/anaconda3/bin:$PATH"'
and run condapath to change the PATH only when you want to use conda.
Or use an alias to set a conda-less PATH, to run before running Sage.
I have two problems:
Git is not working although it is installed. Mavericks pops up a window and suggests to install Xcode (I don't want to): "The 'git' command requires the command line developer tools. Would you like to install it now?"
Sometimes even basic commands such as "ls" don't work. "-bash: ls: command not found". However, after inserting the command " . /etc/profile" it works for a while.
My ~/.bash_profile:
export PATH=/usr/local/git/bin:$PATH
export PATH=/usr/local/mongodb/bin
### Added by the Heroku Toolbelt
export PATH="/usr/local/heroku/bin:$PATH"
I'm very new to this. Please be aware while helping out.;) Your help is highly appreciated.
Amir
You are overwriting your PATH in this line:
export PATH=/usr/local/mongodb/bin
it should be:
export PATH=/usr/local/mongodb/bin:$PATH
Then if you are using OSX I strongly suggest that you use Homebrew http://brew.sh/ which is a package manager (like linux) for mac.
If you are developing on Mac, the command line tools are (almost) required for C/C++/ObjC dev. You can download them without XCode but it is not recommended. Homebrew will need them to build the software for your platform.
To download them go to https://developer.apple.com/downloads/index.action
Note, you'll need a developer account (it is free)
Once you have installed homebrew it is easy to have access to the latest software e.g:
brew install git
brew install mongodb
etc.
You don't have to manage and download the packages by hand. Very handy !
export PATH=/usr/local/git/bin:$PATH
export PATH=/usr/local/mongodb/bin
That second export overwrites PATH completely and sets it to the mongodb directory only. You need to append (or prepend) to PATH, not overwrite it.
export PATH="/usr/local/git/bin:$PATH"
export PATH="/usr/local/mongodb/bin:$PATH"
...