# Recording how I did homebrew doctor
###### tags: `homebrew`

~ ❯❯❯ 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 were deleted!
You should find replacements for the following formulae:
  libmpc@0.8
  mpfr@2
  gmp@4
  cloog@0.15
  ppl@0.11
  pip-list

Warning: Some installed formulae are deprecated or disabled.
You should find replacements for the following formulae:
  protobuf@3.7

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/JPKIPKCS11.dylib
  /usr/local/lib/JPKIPKCS11Auth.dylib
  /usr/local/lib/JPKIPKCS11Sign.dylib
  /usr/local/lib/JPKIServiceAPI.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/python2.7/bsddb3/bsddb.h

Warning: You have unlinked kegs in your Cellar.
Leaving kegs unlinked can lead to build-trouble and cause brews that depend on
those kegs to fail to run properly once built. Run `brew link` on these:
  docker
  mpfr@2
  docker-compose
  python@3.8

Warning: Some installed formulae are not readable:
  mpfr@2: undefined method `undent' for #<String:0x00007fc2a8425cf8>

Warning: You have uncommitted modifications to Homebrew/brew.
If this is a surprise to you, then you should stash these modifications.
Stashing returns Homebrew to a pristine state but can be undone
should you later need to do so for some reason.
  cd /usr/local/Homebrew && git stash && git clean -d -f

Uncommitted files:
  ?? Library/Locks/update
Error: could not get runtime dependencies from /usr/local/opt/libmpc@0.8/.brew/[e-mail]!

---------------

## Deleted formula list
### ppl

~ ❯❯❯ brew info ppl                                                                                                                                                                                 ✘ 1
ppl: stable 1.2 (bottled)
Parma Polyhedra Library: numerical abstractions for analysis, verification
https://bugseng.com/ppl
Not installed
From: https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/ppl.rb
License: GPL-3.0
==> Dependencies
Required: gmp ✔
==> Analytics
install: 81 (30 days), 208 (90 days), 514 (365 days)
install-on-request: 69 (30 days), 156 (90 days), 440 (365 days)
build-error: 0 (30 days)
~ ❯❯❯ brew info ppl@0.11
ppl@0.11: stable 0.11 [keg-only]
Numerical abstractions for analysis, verification
http://bugseng.com/products/ppl/
/usr/local/Cellar/ppl@0.11/0.11_1 (1,401 files, 46.8MB)
  Poured from bottle on 2017-01-05 at 21:38:49
From: /usr/local/opt/ppl@0.11/.brew/[e-mail]
==> Dependencies
Required: gmp@4 ✔
==> Caveats
ppl@0.11 is keg-only, which means it was not symlinked into /usr/local,
because Older version of ppl.

If you need to have ppl@0.11 first in your PATH run:
  echo 'export PATH="/usr/local/opt/ppl@0.11/bin:$PATH"' >> ~/.zshrc

For compilers to find ppl@0.11 you may need to set:
  export LDFLAGS="-L/usr/local/opt/ppl@0.11/lib"
  export CPPFLAGS="-I/usr/local/opt/ppl@0.11/include"

~ ❯❯❯ brew uninstall ppl@0.11
Error: could not get runtime dependencies from /usr/local/opt/libmpc@0.8/.brew/[e-mail]!
Error: Refusing to uninstall /usr/local/Cellar/ppl@0.11/0.11_1
because it is required by cloog@0.15, which is currently installed.
You can override this and force removal with:
  brew uninstall --ignore-dependencies ppl@0.11

### cloog

~ ❯❯❯ brew info cloog@0.15
cloog@0.15: stable 0.15.11 [keg-only]
Generate code for scanning Z-polyhedra
http://repo.or.cz/w/cloog-ppl.git
/usr/local/Cellar/cloog@0.15/0.15.11 (23 files, 491.4KB)
  Poured from bottle on 2017-01-05 at 21:38:51
From: /usr/local/opt/cloog@0.15/.brew/[e-mail]
==> Dependencies
Required: gmp@4 ✔, ppl@0.11 ✔
==> Caveats
cloog@0.15 is keg-only, which means it was not symlinked into /usr/local,
because Older version of cloog.

If you need to have cloog@0.15 first in your PATH run:
  echo 'export PATH="/usr/local/opt/cloog@0.15/bin:$PATH"' >> ~/.zshrc

For compilers to find cloog@0.15 you may need to set:
  export LDFLAGS="-L/usr/local/opt/cloog@0.15/lib"
  export CPPFLAGS="-I/usr/local/opt/cloog@0.15/include"

~ ❯❯❯ brew info cloog
cloog: stable 0.18.4 (bottled)
Generate code for scanning Z-polyhedra
https://www.bastoul.net/cloog/
Not installed
From: https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/cloog.rb
==> Dependencies
Build: pkg-config ✔
Required: gmp ✔
==> Analytics
install: 321 (30 days), 1,045 (90 days), 5,192 (365 days)
install-on-request: 133 (30 days), 291 (90 days), 1,249 (365 days)
build-error: 0 (30 days)

~ ❯❯❯ brew uninstall cloog@0.15
Error: could not get runtime dependencies from /usr/local/opt/libmpc@0.8/.brew/[e-mail]!
Uninstalling /usr/local/Cellar/cloog@0.15/0.15.11... (23 files, 491.4KB)

~ ❯❯❯ brew uninstall ppl@0.11
Error: could not get runtime dependencies from /usr/local/opt/libmpc@0.8/.brew/[e-mail]!
Uninstalling /usr/local/Cellar/ppl@0.11/0.11_1... (1,401 files, 46.8MB)

### gmp

~ ❯❯❯ brew info gmp@4
gmp@4: stable 4.3.2 [keg-only]
GNU multiple precision arithmetic library
http://gmplib.org/
/usr/local/Cellar/gmp@4/4.3.2 (20 files, 2.4MB)
  Poured from bottle on 2017-01-05 at 21:38:33
From: /usr/local/opt/gmp@4/.brew/[e-mail]
==> Caveats
gmp@4 is keg-only, which means it was not symlinked into /usr/local,
because Older version of gmp.

For compilers to find gmp@4 you may need to set:
  export LDFLAGS="-L/usr/local/opt/gmp@4/lib"
  export CPPFLAGS="-I/usr/local/opt/gmp@4/include"

~ ❯❯❯ brew info gmp
gmp: stable 6.2.0 (bottled)
GNU multiple precision arithmetic library
https://gmplib.org/
/usr/local/Cellar/gmp/6.2.0 (20 files, 3.2MB) *
  Poured from bottle on 2020-03-07 at 17:56:17
From: https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/gmp.rb
License: GPL-3.0
==> Analytics
install: 162,011 (30 days), 529,847 (90 days), 1,847,899 (365 days)
install-on-request: 5,408 (30 days), 17,742 (90 days), 66,841 (365 days)
build-error: 0 (30 days)

~ ❯❯❯ brew info mpfr@2                                                                                                                                                                              ✘ 1
Error: mpfr@2: undefined method `undent' for #<String:0x00007fb0ca21d5e0>
~ ❯❯❯ brew info mpfr                                                                                                                                                                                ✘ 1
mpfr: stable 4.0.2 (bottled)
C library for multiple-precision floating-point computations
https://www.mpfr.org/
/usr/local/Cellar/mpfr/4.0.2 (28 files, 4.7MB) *
  Poured from bottle on 2019-06-29 at 15:46:43
From: https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/mpfr.rb
License: GPL-3.0
==> Dependencies
Required: gmp ✔
==> Analytics
install: 48,848 (30 days), 157,993 (90 days), 667,628 (365 days)
install-on-request: 486 (30 days), 1,494 (90 days), 7,273 (365 days)
build-error: 0 (30 days)


~ ❯❯❯ brew uninstall mpfr@2
Error: could not get runtime dependencies from /usr/local/opt/libmpc@0.8/.brew/[e-mail]!
Uninstalling /usr/local/Cellar/mpfr@2/2.4.2... (25 files, 2.7MB)

### pip-list

~ ❯❯❯ brew uninstall pip-list
Error: could not get runtime dependencies from /usr/local/opt/libmpc@0.8/.brew/[e-mail]!
Uninstalling /usr/local/Cellar/pip-list/pypi... (6 files, 1.4KB)

### libmpc

~ ❯❯❯ brew uninstall libmpc@0.8   
Uninstalling /usr/local/Cellar/libmpc@0.8/0.8.1... (12 files, 273.7KB)

## brew cleanup

~ ❯❯❯ 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: 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/JPKIPKCS11.dylib
  /usr/local/lib/JPKIPKCS11Auth.dylib
  /usr/local/lib/JPKIPKCS11Sign.dylib
  /usr/local/lib/JPKIServiceAPI.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/python2.7/bsddb3/bsddb.h

Warning: You have unlinked kegs in your Cellar.
Leaving kegs unlinked can lead to build-trouble and cause brews that depend on
those kegs to fail to run properly once built. Run `brew link` on these:
  docker
  docker-compose
  python@3.8

Warning: You have uncommitted modifications to Homebrew/brew.
If this is a surprise to you, then you should stash these modifications.
Stashing returns Homebrew to a pristine state but can be undone
should you later need to do so for some reason.
  cd /usr/local/Homebrew && git stash && git clean -d -f

Uncommitted files:
  ?? Library/Locks/update

Warning: Broken symlinks were found. Remove them with `brew cleanup`:
  /usr/local/opt/cloog-ppl015
  /usr/local/opt/gmp4
  /usr/local/opt/libmpc08
  /usr/local/opt/mpfr2
  
  
~ ❯❯❯ brew cleanup
Warning: Skipping aws-iam-authenticator: most recent version 0.5.1 not installed
Warning: Skipping bison: most recent version 3.6.4 not installed
Warning: Skipping boost: most recent version 1.72.0_3 not installed
Warning: Skipping c-ares: most recent version 1.16.1 not installed
Warning: Skipping circleci: most recent version 0.1.8764 not installed
Warning: Skipping clang-format: most recent version 10.0.0 not installed
Removing: /Users/yuokada/Library/Caches/Homebrew/clang-format--2019-05-14.mojave.bottle.tar.gz... (1.5MB)
Warning: Skipping cloc: most recent version 1.86 not installed
Warning: Skipping cmake: most recent version 3.17.3 not installed
Removing: /Users/yuokada/Library/Caches/Homebrew/coreutils--8.32.mojave.bottle.tar.gz... (3.8MB)
Removing: /Users/yuokada/Library/Caches/Homebrew/docker--19.03.12.mojave.bottle.tar.gz... (28.2MB)
Warning: Skipping docker-compose: most recent version 1.26.2 not installed
Removing: /Users/yuokada/Library/Caches/Homebrew/docker-compose--1.26.0.mojave.bottle.tar.gz... (3.8MB)
Warning: Skipping weaveworks/tap/eksctl: most recent version 0.24.0 not installed
Removing: /usr/local/Cellar/freetype/2.10.1... (61 files, 2.2MB)
Warning: Skipping fribidi: most recent version 1.0.10 not installed
Removing: /Users/yuokada/Library/Caches/Homebrew/fribidi--1.0.9.mojave.bottle.tar.gz... (128.1KB)
Removing: /Users/yuokada/Library/Caches/Homebrew/git--2.27.0.mojave.bottle.tar.gz... (19.2MB)
Warning: Skipping glib: most recent version 2.64.4 not installed
Removing: /Users/yuokada/Library/Caches/Homebrew/glib--2.64.3.mojave.bottle.tar.gz... (4.6MB)
Removing: /Users/yuokada/Library/Caches/Homebrew/gmp--6.2.0.mojave.bottle.tar.gz... (1022.7KB)
Warning: Skipping gnupg: most recent version 2.2.21 not installed
Removing: /Users/yuokada/Library/Caches/Homebrew/gnupg--2.2.20.mojave.bottle.tar.gz... (4.3MB)
Warning: Skipping google-java-format: most recent version 1.8 not installed
Warning: Skipping grpc: most recent version 1.30.1 not installed
Removing: /Users/yuokada/Library/Caches/Homebrew/guile--3.0.4.mojave.bottle.tar.gz... (11.5MB)
Warning: Skipping heroku/brew/heroku: most recent version 7.42.4 not installed
Removing: /Users/yuokada/Library/Caches/Homebrew/hub--2.14.2.mojave.bottle.tar.gz... (4.8MB)
Removing: /usr/local/Cellar/icu4c/66.1... (258 files, 70.3MB)
Removing: /usr/local/Cellar/krb5/1.18.1... (162 files, 3.8MB)
Warning: Skipping ktlint: most recent version 0.37.2 not installed
Warning: Skipping kubernetes-cli: most recent version 1.18.6 not installed
Warning: Skipping leiningen: most recent version 2.9.4 not installed
Removing: /Users/yuokada/Library/Caches/Homebrew/leiningen--2.9.3.mojave.bottle.tar.gz... (12.6MB)
Warning: Skipping libarchive: most recent version 3.4.3 not installed
Warning: Skipping libav: most recent version 12.3_4 not installed
Warning: Skipping libevent: most recent version 2.1.12 not installed
Warning: Skipping libgcrypt: most recent version 1.8.6 not installed
Removing: /Users/yuokada/Library/Caches/Homebrew/libgcrypt--1.8.5.mojave.bottle.tar.gz... (1MB)
Warning: Skipping libmagic: most recent version 5.39 not installed
Removing: /usr/local/Cellar/libspiro/0.5.20150702... (16 files, 94.9KB)
Removing: /Users/yuokada/Library/Caches/Homebrew/libtasn1--4.16.0.mojave.bottle.tar.gz... (121.9KB)
Removing: /usr/local/Cellar/libtool/2.4.6_1... (70 files, 3.7MB)
Warning: Skipping libvorbis: most recent version 1.3.7 not installed
Removing: /usr/local/Cellar/libyaml/0.2.4... (10 files, 300.6KB)
Removing: /Users/yuokada/Library/Caches/Homebrew/maven--3.6.3.tar.gz... (9MB)
Warning: Skipping mercurial: most recent version 5.4.2 not installed
Removing: /Users/yuokada/Library/Caches/Homebrew/mercurial--5.4.1.mojave.bottle.tar.gz... (2.6MB)
Warning: Skipping minikube: most recent version 1.12.1 not installed
Warning: Skipping mongodb/brew/mongodb-community: most recent version 4.2.8 not installed
Warning: Skipping mosh: most recent version 1.3.2_11 not installed
Warning: Skipping mysql: most recent version 8.0.21 not installed
Warning: Skipping mysql-client: most recent version 8.0.21 not installed
Removing: /Users/yuokada/Library/Caches/Homebrew/mysql-client--8.0.19.mojave.bottle.tar.gz... (42.0MB)
Removing: /Users/yuokada/Library/Caches/Homebrew/ncurses--6.2.mojave.bottle.tar.gz... (2.3MB)
Warning: Skipping node-build: most recent version 4.9.1 not installed
Removing: /Users/yuokada/Library/Caches/Homebrew/nvm--0.35.3.tar.gz... (127.5KB)
Warning: Skipping oniguruma: most recent version 6.9.5-rev1 not installed
Removing: /usr/local/Cellar/openjdk/13.0.2+8_2... (631 files, 314.6MB)
Removing: /Users/yuokada/Library/Caches/Homebrew/openjdk--13.0.2+8_2.mojave.bottle.tar.gz... (189.3MB)
Removing: /usr/local/Cellar/openssl/1.0.2t... (1,795 files, 12.0MB)
Warning: Skipping orc-tools: most recent version 1.6.3 not installed
Removing: /Users/yuokada/Library/Caches/Homebrew/pcre--8.44.mojave.bottle.tar.gz... (1.8MB)
Removing: /usr/local/Cellar/pcre2/10.34... (230 files, 5.9MB)
Warning: Skipping popt: most recent version 1.18 not installed
Warning: Skipping pre-commit: most recent version 2.6.0 not installed
Removing: /Users/yuokada/Library/Caches/Homebrew/pre-commit--2.5.1.mojave.bottle.tar.gz... (7.0MB)
Warning: Skipping protobuf: most recent version 3.12.3 not installed
Warning: Skipping pyenv: most recent version 1.2.19 not installed
Warning: Skipping python@3.8: most recent version 3.8.4 not installed
Removing: /Users/yuokada/Library/Caches/Homebrew/[e-mail]... (15.3MB)
Removing: /Users/yuokada/Library/Caches/Homebrew/readline--8.0.4.mojave.bottle.tar.gz... (517.6KB)
Warning: Skipping ruby-build: most recent version 20200520 not installed
Warning: Skipping rustup-init: most recent version 1.22.1 not installed
Warning: Skipping sphinx-doc: most recent version 3.1.2 not installed
Removing: /Users/yuokada/Library/Caches/Homebrew/sphinx-doc--3.1.1.mojave.bottle.tar.gz... (14.7MB)
Warning: Skipping sqlite: most recent version 3.32.3 not installed
Removing: /Users/yuokada/Library/Caches/Homebrew/sqlite--3.32.1.mojave.bottle.tar.gz... (1.9MB)
Warning: Skipping tmux: most recent version 3.1b not installed
Warning: Skipping uncrustify: most recent version 0.71.0 not installed
Warning: Skipping unrar: most recent version 5.9.4 not installed
Warning: Skipping wxmac: most recent version 3.0.5.1_1 not installed
Warning: Skipping x264: most recent version r3011 not installed
Removing: /Users/yuokada/Library/Caches/Homebrew/zsh--5.8.mojave.bottle.tar.gz... (3.6MB)
Warning: Skipping zsh-completions: most recent version 0.32.0 not installed
Warning: Skipping zstd: most recent version 1.4.5 not installed
Removing: /Users/yuokada/Library/Caches/Homebrew/python--3.7.7.mojave.bottle.tar.gz... (14.9MB)
Removing: /Users/yuokada/Library/Caches/Homebrew/Cask/processing--3.5.4.zip... (124.0MB)
Removing: /Users/yuokada/Library/Caches/Homebrew/Cask/virtualbox--6.1.10,138449.dmg... (117.9MB)
Pruned 5 symbolic links and 3 directories from /usr/local  

## brew link again

~ ❯❯❯ brew link docker docker-compose 
Linking /usr/local/Cellar/docker/19.03.12...
Error: Could not symlink bin/docker
Target /usr/local/bin/docker
already exists. You may want to remove it:
  rm '/usr/local/bin/docker'

To force the link and overwrite all conflicting files:
  brew link --overwrite docker

To list all files that would be deleted:
  brew link --overwrite --dry-run docker
~ ❯❯❯ brew link --overwrite --dry-run docker 
Would remove:
/usr/local/bin/docker
~ ❯❯❯ file /usr/local/bin/docker
/usr/local/bin/docker: Mach-O 64-bit executable x86_64
~ ❯❯❯ brew link --overwrite --dry-run docker-compose
Would remove:
/usr/local/bin/docker-compose
~ ❯❯❯ file /usr/local/bin/docker-compose
/usr/local/bin/docker-compose: Mach-O 64-bit executable x86_64

~ ❯❯❯ brew link --overwrite docker-compose
Linking /usr/local/Cellar/docker-compose/1.26.0... 3 symlinks created

~ ❯❯❯ docker-compose version
docker-compose version 1.26.0, build unknown
docker-py version: 4.2.1
CPython version: 3.8.3
OpenSSL version: OpenSSL 1.1.1g  21 Apr 2020

~ ❯❯❯ docker version
Client: Docker Engine - Community
 Version:           19.03.1
 API version:       1.40
 Go version:        go1.12.5
 Git commit:        74b1e89
 Built:             Thu Jul 25 21:18:17 2019
 OS/Arch:           darwin/amd64
 Experimental:      false

Server: Docker Engine - Community
 Engine:
  Version:          19.03.1
  API version:      1.40 (minimum version 1.12)
  Go version:       go1.12.5
  Git commit:       74b1e89e8a
  Built:            Thu Jul 25 21:27:55 2019
  OS/Arch:          linux/amd64
  Experimental:     false
 containerd:
  Version:          v1.2.6
  GitCommit:        894b81a4b802e4eb2a91d1ce216b8817763c29fb
 runc:
  Version:          1.0.0-rc8
  GitCommit:        425e105d5a03fabd737a126ad93d62a9eeede87f
 docker-init:
  Version:          0.18.0
  GitCommit:        fec3683
  
-------------
~ ❯❯❯ brew link --overwrite docker
Linking /usr/local/Cellar/docker/19.03.12... 10 symlinks created

~ ❯❯❯ docker version
Client: Docker Engine - Community
 Version:           19.03.12
 API version:       1.40
 Go version:        go1.14.4
 Git commit:        48a6621
 Built:             Thu Jun 25 18:52:05 2020
 OS/Arch:           darwin/amd64
 Experimental:      false

Server: Docker Engine - Community
 Engine:
  Version:          19.03.1
  API version:      1.40 (minimum version 1.12)
  Go version:       go1.12.5
  Git commit:       74b1e89e8a
  Built:            Thu Jul 25 21:27:55 2019
  OS/Arch:          linux/amd64
  Experimental:     false
 containerd:
  Version:          v1.2.6
  GitCommit:        894b81a4b802e4eb2a91d1ce216b8817763c29fb
 runc:
  Version:          1.0.0-rc8
  GitCommit:        425e105d5a03fabd737a126ad93d62a9eeede87f
 docker-init:
  Version:          0.18.0
  GitCommit:        fec3683

-------

## 2025-03-14

`aws/tap` has been removed.

❯❯❯ 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: The following formulae have the same name as core formulae:
  aws/tap/eksctl
Some of these can be resolved with:
  brew untap aws/tap

❯❯❯ brew untap aws/tap
Untapping aws/tap...
Untapped 23 formulae (101 files, 1.5MB).

❯❯❯ brew doctor
Your system is ready to brew.