Troubleshooting

Updating nvim plugins

In nvim, run :Lazy. In the interface, use U to update plugins. Use X to clean up any other plugins. Run :Mason to select language server protocols (more info at mason.nvim).

You can optionally remove your ~/.local/share/nvim directory, which will completely clean out any old plugins; you’ll need to let lazy.nvim reinstall plugins upon next starting nvim.

nvim has light gray text, colorscheme looks broken

Are you using Mac’s built-in Terminal app? Terminal.app does not support true colors, so the true-color default zenburn colorscheme (or any true color colorscheme) will not work.

Run this command to see if your terminal supports true color. If it shows up in red, then it supports true color. If it just looks like regular black text, your terminal does NOT support true color.

printf "\x1b[38;2;255;100;0mTRUECOLOR\x1b[0m\n"

If you are unable to use a terminal emulator like iTerm2, alacritty, kitty, etc, that supports 24-bit colors, then you can use a different color scheme.

You can find an excellent writeup of this at docs for the onedark colorscheme – see the Troubleshooting section.

As a fallback, you can make the following changes in your ./config/nvim/init.lua file. This will turn off termguicolors (the setting in vim that supports true color) and set the colorscheme to onedark, which supports 256- and 16-color-only terminals:

-- vim.cmd("colorscheme zenburn")
vim.cmd("colorscheme onedark")

-- vim.cmd("set termguicolors")
vim.cmd("set notermguicolors")

Comments don’t show up as italic

This is a bit of a rabbit hole, but it’s due to an interaction between terminals and tmux and nvim.

This gist has a nice writeup and description of the fix.

For Alacritty, see this gist, which also includes a setting you need in .config/alacritty/alacritty.yml.

On Mac, you can use ./setup.sh --fix-tmux-terminfo and follow the instructions after running to update your tmux config.

Can’t install conda packages from Bioconda

Bioconda does not yet build packages for Mac ARM chips (Mac M1 or M2). You can install docker and use a container, or wait until Bioconda starts building those packages.

Errors about not finding CC or GCC when opening vim

You may get an error like this when opening nvim:

Error detected while processing BufReadPost Autocommands for "*":
No C compiler found! "cc", "gcc", "clang", "cl", "zig" are not executable.
No C compiler found! "cc", "gcc", "clang", "cl", "zig" are not executable.
....

This happens because nvim is trying to install the treesitter parsers, but that needs a compiler to be available. See treesitter for details on how to address this.