a lot of error after updating to mojave

[Djerbiien]

Please note we will close your issue without comment if you delete, do not read or do not fill out the issue checklist below and provide ALL the requested information. If you repeatedly fail to use the issue template, we will block you from ever submitting issues to Homebrew again.

• 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?

To help us debug your issue please explain:

• What you were trying to do (and why)
  to update homebrew after installing mojave
• What happened (include command output)
  brew update
  Ignoring bigdecimal-1.3.5 because its extensions are not built. Try: gem pristine bigdecimal --version 1.3.5
  Ignoring bigdecimal-1.3.5 because its extensions are not built. Try: gem pristine bigdecimal --version 1.3.5
• What you expected to happen
  brew to update
• Step-by-step reproduction instructions (by running brew commands)

brew config
Ignoring bigdecimal-1.3.5 because its extensions are not built. Try: gem pristine bigdecimal --version 1.3.5
HOMEBREW_VERSION: 1.7.6
ORIGIN: https://github.com/Homebrew/brew
HEAD: f239b7a
Last commit: 3 days ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: fe7334d
Core tap last commit: 89 minutes ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_GIT: git
HOMEBREW_MACOS_VERSION_NUMERIC: 101400
CPU: octa-core 64-bit kabylake
Homebrew Ruby: 2.3.7 => /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/bin/ruby
Clang: 10.0 build 1000
Git: 2.17.1 => /Applications/Xcode.app/Contents/Developer/usr/bin/git
Curl: 7.54.0 => /usr/bin/curl
Java: 10.0.2
macOS: 10.14-x86_64
CLT: N/A
Xcode: 10.0
XQuartz: N/A

brew doctor
Ignoring bigdecimal-1.3.5 because its extensions are not built. Try: gem pristine bigdecimal --version 1.3.5
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 directories do not exist:
/usr/local/sbin

You should create these directories and change their ownership to your account.
sudo mkdir -p /usr/local/sbin
sudo chown -R $(whoami) /usr/local/sbin

[yoavmmn]

+1.
After updating to Mojave I get this when running brew doctor:

Warning: Missing Homebrew/brew git origin remote.

Without a correctly configured origin, Homebrew won't update
properly. You can solve this by adding the Homebrew remote:
  git -C "/usr/local/Homebrew" remote add origin https://github.com/Homebrew/brew.git

Warning: The following directories do not exist:
/usr/local/sbin

You should create these directories and change their ownership to your account.
  sudo mkdir -p /usr/local/sbin
  sudo chown -R $(whoami) /usr/local/sbin

Warning: No developer tools installed.
Install the Command Line Tools:
  xcode-select --install


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/greenlet/greenlet.h
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun

I only tried setting the remote origin of the git repository but I got fatal: remote origin already exists..
Meanwhile I can't upgrade or install any packages(everything worked properly before updating to Mojave).
Hope to get a fix soon :)

My config:

HOMEBREW_VERSION: 1.7.6-6-g899bfbc
ORIGIN: (none)
HEAD: (none)
Last commit: never
Core tap ORIGIN: (none)
Core tap HEAD: (none)
Core tap last commit: never
HOMEBREW_PREFIX: /usr/local
HOMEBREW_DEV_CMD_RUN: 1
CPU: quad-core 64-bit kabylake
Homebrew Ruby: 2.3.7 => /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/bin/ruby
Clang: N/A
Git: 2.19.0 => /usr/local/bin/git
Curl: 7.54.0 => /usr/bin/curl
Java: N/A
macOS: 10.14-x86_64
CLT: N/A
Xcode: N/A
XQuartz: N/A

[rockymadden]

This worked for me: Open Xcode, go to Preferences, go to Locations, update the Command Line Tools in the drop down to Xcode 10.0.

[chuxubank]

try xcode-select --install in Terminal.

[yoavmmn]

try xcode-select --install in Terminal.

Worked for me. Thanks!

[MikeMcQuaid]

Run xcode-select --install, rerun brew doctor and fix any permissions errors using the instructions it gives you.

[FradSer]

xcode-select --install does't work for me. Reinstall ruby doesn't works, too.
Try sudo chown -R $(whoami) /usr/local/lib/ruby/gems/* to fix permissions error, but same problem comes.

[MikeMcQuaid]

@FradSer What is the specific error you're seeing?

[kirkegaard]

I just did a fresh install of Mojave and installed xcode as the first thing. Then installed brew using the installer off brew.sh. brew doctor is telling me that command line tools are outdated and xcode-select --install says command line tools are already installed and that i should use Software Update to install updates. Software Updates says i've got the newest version already. Ive also selected the newest version inside xcode > preferences > locations.

I think the installer might be installing an old version of command line tools which cause some kind of confligt since the installer tried to install command line tools for High Sierra.

birdie:~ christian$ xcode-select -p
/Applications/Xcode.app/Contents/Developer

birdie:~ christian$ xcode-select -v
xcode-select version 2354.

birdie:~ christian$ 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: Your Command Line Tools are too outdated.
Update them from Software Update in the App Store.


Warning: A newer Command Line Tools release is available.
Update them from Software Update in the App Store.

[FradSer]

@MikeMcQuaid My error is:

$ brew update
Ignoring bigdecimal-1.3.2 because its extensions are not built.  Try: gem pristine bigdecimal --version 1.3.2
Ignoring bigdecimal-1.3.2 because its extensions are not built.  Try: gem pristine bigdecimal --version 1.3.2
Already up-to-date.

---

$ brew config
HOMEBREW_VERSION: 1.7.6
ORIGIN: https://github.com/Homebrew/brew
HEAD: f239b7a62790cfb4f33bda9aab7597d43f1b1e3b
Last commit: 4 days ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: ae68a80c0257579b3c109cb56c53c6dcc979d984
Core tap last commit: 4 hours ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_GIT: git
HOMEBREW_MACOS_VERSION_NUMERIC: 101400
CPU: octa-core 64-bit ivybridge
Homebrew Ruby: 2.3.7 => /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/bin/ruby
Clang: 10.0 build 1000
Git: 2.19.0 => /usr/local/bin/git
Curl: 7.54.0 => /usr/bin/curl
Java: 1.8.0_51
macOS: 10.14-x86_64
CLT: 10.0.0.0.1.1535735448
CLT headers: N/A
Xcode: 10.0
XQuartz: N/A

---

Maybe the problem is version of Ruby?

$ ruby -v
ruby 2.5.1p57 (2018-03-29 revision 63029) [x86_64-darwin18]

My Ruby is 2.5.1 which install with Homebrew, not 2.3.7.

---

$ gem pristine --all
Restoring gems to pristine condition...
Restored actionpack-5.2.0
Restored actionpack-5.1.4
Restored actionpack-action_caching-1.2.0
Restored actionview-5.2.0
Restored actionview-5.1.4
Restored active-model-adapter-source-2.1.1
Restored active_model_serializers-0.10.7
Restored activejob-5.2.0
Restored activemodel-5.2.0
Restored activemodel-5.1.4
Restored activemodel-4.0.2
Restored activerecord-5.2.0
Restored activerecord-4.0.2
Restored activerecord-deprecated_finders-1.0.4
Restored activesupport-5.2.0
Restored activesupport-5.1.4
Restored activesupport-4.0.2
Restored addressable-2.5.2
Restored airbrake-7.3.4
Restored airbrake-ruby-2.11.0
Restored annotate-2.7.4
Restored arel-9.0.0
Restored arel-4.0.1
Restored babel-source-5.8.35
Restored babel-transpiler-0.7.0
Restored barber-0.12.0
Restored better_errors-2.4.0
Building native extensions. This could take a while...
Restored bigdecimal-1.3.5
Skipped bigdecimal-1.3.4, it is a default gem
Building native extensions. This could take a while...
Restored binding_of_caller-0.8.0
Restored builder-3.2.3
Restored builder-3.1.4
Restored bundler-1.16.5
Skipped bundler-1.16.1, it is a default gem
Restored case_transform-0.2
Restored celluloid-0.17.3
Restored celluloid-essentials-0.20.5
Restored celluloid-extras-0.20.5
Restored celluloid-fsm-0.20.5
Restored celluloid-pool-0.20.5
Restored celluloid-supervision-0.20.6
IMPORTANT: Remember to use the included executable `certifed-update` regularly to keep your certificate bundle up to date.
Restored certified-1.0.0
Skipped cmath-1.0.0, it is a default gem
Restored coderay-1.1.2
Restored concurrent-ruby-1.0.5
Restored connection_pool-2.2.2
Restored crass-1.0.4
Restored csv-3.0.0
Skipped csv-1.0.0, it is a default gem
Restored daemons-1.2.6
Skipped date-1.0.0, it is a default gem
Skipped dbm-1.0.0, it is a default gem
Building native extensions. This could take a while...
Restored debug_inspector-0.0.3
Restored did_you_mean-1.2.1
Restored did_you_mean-1.2.0
Restored diff-lcs-1.3
Restored email_reply_parser-discourse-0.6
Restored ember-cli-assets-0.0.37
Restored ember-data-source-3.0.2
Restored ember-data-source-2.16.1
Restored ember-es6_template-0.6.0
Restored ember-handlebars-template-0.8.0
Restored ember-rails-0.21.0
Restored ember-source-2.18.2
Restored erubi-1.7.1
Restored erubis-2.7.0
Building native extensions. This could take a while...
Restored etc-1.0.1
Skipped etc-1.0.0, it is a default gem
Restored execjs-2.7.0
Skipped fcntl-1.0.0, it is a default gem
Building native extensions. This could take a while...
Restored ffi-1.9.25
Skipped fiddle-1.0.0, it is a default gem
Restored fileutils-1.1.0
Skipped fileutils-1.0.2, it is a default gem
Restored globalid-0.4.1
Restored handlebars-source-4.0.11
Restored handlebars-source-1.1.2
Building native extensions. This could take a while...
Restored hitimes-1.3.0
Restored i18n-1.0.1
Restored i18n-0.9.3
Skipped io-console-0.4.6, it is a default gem
Skipped ipaddr-1.2.0, it is a default gem
Restored jquery-rails-4.3.3
Skipped json-2.1.0, it is a default gem
Restored jsonapi-renderer-0.2.0
Restored loofah-2.2.2
Restored mail-2.7.0
Restored method_source-0.9.0
Restored mime-types-3.1
Restored mime-types-data-3.2016.0521
Restored mini_mime-1.0.0
Restored mini_portile2-2.3.0
Restored minitest-5.11.3
Restored minitest-5.10.3
Restored minitest-4.7.5
Restored multi_json-1.13.1
Restored net-telnet-0.1.1
Building native extensions. This could take a while...
Restored nokogiri-1.8.4
Building native extensions. This could take a while...
Restored openssl-2.1.1
Skipped openssl-2.1.0, it is a default gem
Restored polyglot-0.3.5
Restored power_assert-1.1.3
Restored power_assert-1.1.1
Skipped psych-3.0.2, it is a default gem
Restored public_suffix-3.0.2
Restored rack-2.0.5
Restored rack-1.5.2
Restored rack-test-1.0.0
Restored rack-test-0.8.2
Restored rails-dom-testing-2.0.3
Restored rails-html-sanitizer-1.0.4
Restored railties-5.2.0
Restored rake-12.3.1
Restored rake-12.3.0
Restored rake-10.1.1
Restored rb-fsevent-0.10.3
Restored rb-inotify-0.9.10
Restored rdoc-6.0.4
Skipped rdoc-6.0.1, it is a default gem
Restored sass-3.5.6
Restored sass-listen-4.0.0
Skipped scanf-1.0.0, it is a default gem
Skipped sdbm-1.0.0, it is a default gem
Restored sprockets-3.7.2
Skipped stringio-0.0.1, it is a default gem
Skipped strscan-1.0.0, it is a default gem
Restored test-unit-3.2.8
Restored test-unit-3.2.7
Restored thor-0.20.0
Restored thread_safe-0.3.6
Restored timers-4.1.2
Restored treetop-1.6.10
Restored tzinfo-1.2.5
Restored tzinfo-0.3.38
Skipped webrick-1.4.2, it is a default gem
Restored xmlrpc-0.3.0
Skipped zlib-1.0.0, it is a default gem

bigdecimal is 1.3.5, not 1.3.2. 😐😐😐

[MikeMcQuaid]

@FradSer None of those errors are from Homebrew.

[FradSer]

@FradSer None of those errors are from Homebrew.

@MikeMcQuaid Get it.

_{Sent with GitHawk}

[FradSer]

@kirkegaard I've uninstall command line tools with sudo rm -rf /Library/Developer/CommandLineTools and reinstall it, still get the the warnings.

$ brew update
Ignoring bigdecimal-1.3.2 because its extensions are not built.  Try: gem pristine bigdecimal --version 1.3.2
Ignoring bigdecimal-1.3.2 because its extensions are not built.  Try: gem pristine bigdecimal --version 1.3.2
Already up-to-date.

I'm also getting this on a secondary install (like not on my main Mac) and have not yet found a solution that worked.

[jonleopard]

This isn't really an issue of Homebrew. Running brew update seems to trigger something that causes the following to display:

$ brew update
Ignoring bigdecimal-1.3.5 because its extensions are not built. Try: gem pristine bigdecimal --version 1.3.5
Ignoring bigdecimal-1.3.5 because its extensions are not built. Try: gem pristine bigdecimal --version 1.3.5

I've tried running the suggested gem pristine bigdecimal --version 1.3.5

$ gem pristine bigdecimal --version 1.3.5
Restoring gems to pristine condition...
Building native extensions. This could take a while...
Restored bigdecimal-1.3.5

After running, I still get the same results.

Has anyone else found a solution for this yet?