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• are reporting a bug others will be able to reproduce and not asking a question. If you're not sure or want to ask a question do so on our Discourse: https://discourse.brew.sh
• ran a brew command and reproduced the problem with multiple formulae? If it's a problem with a single, official formula (not cask) please file this issue at Homebrew/homebrew-core: https://github.com/Homebrew/homebrew-core/issues/new/choose. If it's a brew cask problem please file this issue at https://github.com/Homebrew/homebrew-cask/issues/new/choose. If it's a tap (e.g. Homebrew/homebrew-php) problem please file this issue at the tap.
• ran brew update and can still reproduce the problem?
• ran brew doctor, fixed all issues and can still reproduce the problem?
• ran brew config and brew doctor and included their output with your issue?

What you were trying to do (and why)

Run brew doctor, which I do regularly to make sure everything is happy with the installation.

What happened (include command output)

Brew doctor just recently (within the last couple of days) started complaining about my own software that has been installed into /usr/local/Cellar and brew link'ed.

I would like to emphasize this is not just a fringe weird thing I'm doing, as this procedure is specifically recommended in the official Homebrew FAQ in the part about installing other stuff into /usr/local/Cellar. See this link.

Basically, I take advantage of Homebrew's wonderful linking ability by installing useful things into /usr/local/Cellar, and then brew link those useful things.

> 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 formulae are not readable:
  No available formula with the name "__ncl_ncar"

  No available formula with the name "pdfjam"

  No available formula with the name "__hdfeos"

In this case, there are two things I have installed into /usr/local/Cellar myself in accordance with the Homebrew FAQ. These are the two things starting with the double underscore. It appears the third thing (pdfjam) is no longer a formula, so that's a different issue.

What you expected to happen

I don't think Homebrew needs to produce warnings about non-Homebrew installed software in /usr/local.

Obviously, this isn't a huge problem by any means. It's just that problems reported by brew doctor catch one's eye, and in this case there is no actual problem. There is no formula to read.

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

brew doctor

Additional info:

> brew config
HOMEBREW_VERSION: 2.0.6-93-gde86424
ORIGIN: https://github.com/Homebrew/brew
HEAD: de8642411b4630058f2e9ab93315387343701351
Last commit: 3 hours ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 4050d7cca8036179f372cdb1cb27a0dd388d3c48
Core tap last commit: 80 minutes ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CASK_OPTS: --appdir=/Applications
HOMEBREW_DEV_CMD_RUN: 1
HOMEBREW_DISPLAY: /private/tmp/com.apple.launchd.pCDpeP9Djr/org.macosforge.xquartz:0
HOMEBREW_LOGS: /Users/haynes/Library/Logs/Homebrew
HOMEBREW_NO_INSTALL_CLEANUP: 1
CPU: quad-core 64-bit broadwell
Homebrew Ruby: 2.3.7 => /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/bin/ruby
Clang: 10.0 build 1000
Git: 2.21.0 => /usr/local/bin/git
Curl: 7.54.0 => /usr/bin/curl
Java: 1.8.0_60
macOS: 10.13.6-x86_64
CLT: 10.1.0.0.1.1539992718
Xcode: N/A
XQuartz: 2.7.11 => /opt/X11

brew config
HOMEBREW_VERSION: 2.0.6-93-gde86424
ORIGIN: https://github.com/Homebrew/brew
HEAD: de86424
Last commit: 3 hours ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 4050d7c
Core tap last commit: 80 minutes ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CASK_OPTS: --appdir=/Applications
HOMEBREW_DEV_CMD_RUN: 1
HOMEBREW_DISPLAY: /private/tmp/com.apple.launchd.pCDpeP9Djr/org.macosforge.xquartz:0
HOMEBREW_LOGS: /Users/me/Library/Logs/Homebrew
HOMEBREW_NO_INSTALL_CLEANUP: 1
CPU: quad-core 64-bit broadwell
Homebrew Ruby: 2.3.7 => /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/bin/ruby
Clang: 10.0 build 1000
Git: 2.21.0 => /usr/local/bin/git
Curl: 7.54.0 => /usr/bin/curl
Java: 1.8.0_60
macOS: 10.13.6-x86_64
CLT: 10.1.0.0.1.1539992718
Xcode: N/A
XQuartz: 2.7.11 => /opt/X11