Brew error "No such file or directory - /usr/local/Cellar/pango/1.46.1" on running "brew install brewsci/bio/pymol"

Question

I am trying to install the open-source version of PyMOL on a mac through the Homebrew package manager as recommended on the official website: https://pymolwiki.org/index.php/MAC_Install#Open-Source_PyMOL.

During the installation process, Homebrew upgrades the pango dependency from 1.46.1 to 1.46.2, removes the old version, and then throws an error while checking for it.

Any ideas where this error is coming from? And how to fix it?

Answer 1

I too received the same error: Error: /usr/local/Cellar/libusbmuxd/HEAD-3eb50a0 is not a directory. I received this error after running: ~ brew update ~ brew outdated

Simply run: ~ brew install pango
(Pango is Framework for layout and rendering of i18n text)

Before running upgrade make sure your Apple Command Line tools are updated as well.

Then I was able to run: ~ brew upgrade

and everything updated normally without any error. I did not have to update ruby at all.

Answer 2

Error: No such file or directory - /usr/local/Cellar/pango/1.46.1
$ ruby -v
ruby 2.6.3p62 (2019-04-16 revision 67580) [universal.x86_64-darwin19]

$ brew reinstall pango

$ brew install ruby   
(if you already have an old version, then reinstall it by:)
$ brew reinstall ruby

Then your ruby should be updated to 2.7.2, however, there might exist a configuration problem.

==> Downloading https://homebrew.bintray.com/bottles/ruby-2.7.2.catalina.bottle.
Already downloaded: /Users/lydia/Library/Caches/Homebrew/downloads/00c97dba192e9c242c6bb51b7d0a4a3a9fc77328277e43e49497c64e6450b55d--ruby-2.7.2.catalina.bottle.tar.gz
==> Reinstalling ruby 
==> Pouring ruby-2.7.2.catalina.bottle.tar.gz
==> Caveats
By default, binaries installed by gem will be placed into:
  /usr/local/lib/ruby/gems/2.7.0/bin

You may want to add this to your PATH.

ruby is keg-only, which means it was not symlinked into /usr/local,
because macOS already provides this software and installing another version in
parallel can cause all kinds of trouble.

If you need to have ruby first in your PATH run:
  echo 'export PATH="/usr/local/opt/ruby/bin:$PATH"' >> /Users/lydia/.bash_profile

For compilers to find ruby you may need to set:
  export LDFLAGS="-L/usr/local/opt/ruby/lib"
  export CPPFLAGS="-I/usr/local/opt/ruby/include"

For pkg-config to find ruby you may need to set:
  export PKG_CONFIG_PATH="/usr/local/opt/ruby/lib/pkgconfig"

==> Summary
  /usr/local/Cellar/ruby/2.7.2: 20,156 files, 35.3MB