Recent `anaconda` update broken - fails to upgrade

[cmahnke]

brew config AND brew doctor output OR brew gist-logs <formula> link

$ brew config
HOMEBREW_VERSION: 5.0.10-52-g793daa4
ORIGIN: https://github.com/Homebrew/brew
HEAD: 793daa420769647470a6367161d974c209df052d
Last commit: 72 minutes ago
Branch: main
Core tap JSON: 16 Jan 19:37 UTC
Core cask tap JSON: 16 Jan 19:37 UTC
HOMEBREW_PREFIX: /opt/homebrew
HOMEBREW_CASK_OPTS: []
HOMEBREW_DISPLAY: /private/tmp/com.apple.launchd.yZJrGazl1g/org.xquartz:0
HOMEBREW_DOWNLOAD_CONCURRENCY: 20
HOMEBREW_FORBID_PACKAGES_FROM_PATHS: set
HOMEBREW_MAKE_JOBS: 10
HOMEBREW_SORBET_RUNTIME: set
Homebrew Ruby: 3.4.8 => /opt/homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/bin/ruby
CPU: deca-core 64-bit arm_firestorm_icestorm
Clang: 17.0.0 build 1700
Git: 2.50.1 => /Applications/Xcode.app/Contents/Developer/usr/bin/git
Curl: 8.7.1 => /usr/bin/curl
macOS: 26.2-arm64
CLT: 26.2.0.0.1.1764812424
Xcode: 26.2
Metal Toolchain: N/A
Rosetta 2: false


---

$ brew doctor
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry or file an issue; just ignore this. Thanks!

Warning: Some installed casks are deprecated or disabled.
You should find replacements for the following casks:
  chromium
  codux
  diffmerge
  dupeguru
  electron
  gstreamer-runtime
  ilspy
  imhex
  intellij-idea-ce
  liteide
  macdown
  powershell
  protege
  qlstephen
  quicklook-json
  qview
  seamonkey
  unison-app
  webpquicklook
  wine@staging

Warning: Some installed kegs have no formulae!
This means they were either deleted or installed manually.
You should find replacements for the following formulae:
  dart-sass-embedded

Warning: Some installed formulae are deprecated or disabled.
You should find replacements for the following formulae:
  icu4c@76
  icu4c@77
  openssl@1.1
  postgresql@14
  python@3.9
  six
  zopfli

Warning: Unbrewed dylibs were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae and may need to be deleted.

Unexpected dylibs:
  /usr/local/lib/libuhdr.dylib
  /usr/local/lib/libvips-cpp.42.dylib
  /usr/local/lib/libvips.42.dylib

Warning: Unbrewed header files were found in /usr/local/include.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae and may need to be deleted.

Unexpected header files:
  /usr/local/include/ultrahdr_api.h
  /usr/local/include/vips/*

Warning: Unbrewed '.pc' files were found in /usr/local/lib/pkgconfig.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae and may need to be deleted.

Unexpected '.pc' files:
  /usr/local/lib/pkgconfig/libuhdr.pc
  /usr/local/lib/pkgconfig/vips-cpp.pc
  /usr/local/lib/pkgconfig/vips.pc

Warning: You have unlinked kegs in your Cellar.
Leaving kegs unlinked can lead to build-trouble and cause formulae that depend on
those kegs to fail to run properly once built. Run `brew link` on these:
  parallel
  pycparser

Warning: Homebrew's "sbin" was not found in your PATH but you have installed
formulae that put executables in /opt/homebrew/sbin.
Consider setting your PATH for example like so:
  echo 'export PATH="/opt/homebrew/sbin:$PATH"' >> /Users/cmahnke/.bash_profile

Verification

• My brew doctor output says Your system is ready to brew. and am still able to reproduce my issue.
• I ran brew update and am still able to reproduce my issue.
• I have resolved all warnings from brew doctor and that did not fix my problem.
• I searched for recent similar issues at https://github.com/Homebrew/homebrew-core/issues?q=is%3Aissue and found no duplicates.
• My issue is not about a failure to build a formula from source.

What were you trying to do (and why)?

Just tried to upgrade (using brew upgrade --greedy)

What happened (include all command output)?

Password:
ERROR: File or directory already exists: '/opt/homebrew/anaconda3'
If you want to update an existing installation, use the -u option.
==> Purging files for version 2025.12-2 of Cask anaconda
Error: Failure while executing; `/usr/bin/sudo -E PATH=/opt/homebrew/bin:/opt/homebrew/sbin:/opt/homebrew/Library/Homebrew/shims/shared:/usr/bin:/bin:/usr/sbin:/sbin -- /opt/homebrew/Caskroom/anaconda/2025.12-2/Anaconda3-2025.12-2-MacOSX-arm64.sh -b -p /opt/homebrew/anaconda3` exited with 1. Here's the output:
ERROR: File or directory already exists: '/opt/homebrew/anaconda3'
If you want to update an existing installation, use the -u option.

What did you expect to happen?

Upgrade should work, the main backdraw of the anaconda distribution is it's own packaging, this means that the distro is uninstalled before the error has been hit, which can lead to a broken installation, if it's your default:

 $ pip
-bash: /opt/homebrew/anaconda3/bin/pip: No such file or directory

Step-by-step reproduction instructions (by running brew commands)

Additional comments

Since there is no field for additional comments
I was forced to check "I have resolved all warnings from brew doctor and that did not fix my problem.", but didn't since there is no way this would a broken installer of a package not mentioned, consider to make this optional.
Same applies to "My brew doctor output says Your system is ready to brew. and am still able to reproduce my issue." as you can see above. Again forced to do it, again, make it optional. at least until:

• Homebrew's "sbin" was not found in your PATH but you have installed shouldn't be a warning
• Stop warning about "/usr/local" and stick to /opt/homebrew ;)
  At least both warnings should not lead to the requested message to be not printed

[bevanjkay]

Can you please provide the full output from brew upgrade anaconda, and not just the part after providing your password.
It seems like something must have failed earlier in the process that caused the folder to persist.