brew upgrade failure saying Xcode CLT isn't installed

[ksaro1]

When upgrading brew installed apps I get failure messages telling me that the CLT for Xcode isn't installed, when indeed it is installed.

==> Upgrading imagemagick 7.0.11-0 -> 7.0.11-1
Warning: Building python@3.9 from source:
The bottle needs the Apple Command Line Tools to be installed.
You can install them, if desired, with:
xcode-select --install

brew config returns the following info:
macOS: 11.2.1-x86_64
CLT: N/A
Xcode: 12.4

Yet, I see the following too:
$ xcode-select -p
/Applications/Xcode.app/Contents/Developer
$ xcode-select -v
xcode-select version 2384.

I've also installed Python 3.9.2 directly from the source and I see the following:
$ python3 -V
Python 3.9.2

I also see the following :
$ ls -larth /opt/local/Library/Frameworks/Python.framework/Versions
total 0
lrwxr-xr-x 1 root wheel 59B 11 Sep 11:33 Current -> /opt/local/Library/Frameworks/Python.framework/Versions/3.8
drwxr-xr-x 6 root wheel 192B 11 Sep 11:33 ..
drwxr-xr-x 5 root wheel 160B 11 Sep 11:33 .
drwxr-xr-x 3 root wheel 96B 9 Dec 15:18 3.7
drwxr-xr-x 9 root wheel 288B 30 Dec 10:41 3.8
$ ls -larth /Library/Frameworks/Python.framework/Versions
total 0
lrwxr-xr-x 1 root wheel 3B 25 Feb 10:34 Current -> 3.9
drwxrwxr-x 4 root wheel 128B 25 Feb 10:34 .
drwxrwxr-x 11 root admin 352B 25 Feb 10:34 3.9
drwxr-xr-x 6 root wheel 192B 25 Feb 10:34 ..

Any suggestions on how to upgrade my brew installations now?

 

[mporcheron]

Each and every time I have updated Big Sur, it partially breaks CLT (some things remain, but some libraries disappear, e.g. I can no longer compile C++ code although Clang remains installed). Reinstalling with xcode-select —install fixes it each time

 

[Monotremata]

Same here. I had to reinstall mine the other night just to codesign/dequarantine an app from Github. Somewhere in between one of these updates, it wiped mine out. I think this is the third time Ive reinstalled it since upgrading to Big Sur in November..

 

[EigenTheory]

I am experiencing this same issue. Every time Big Sur updates I have to manually rerun xcode-select --install.

 

[rezwits]

Sometimes, when they upgrade macOS, they throw an Xcode+CLT (before or after the macOS update), but seems like times when they don't do an ABSOLUTE CLT upgrade package, you have to run the --install...now

 

[ksaro1]

BTW - after upgrading to 11.2.3 the CLT tool was missing again, which I re-installed via xcode-select --install. And I see the following:


$ brew config
HOMEBREW_VERSION: 3.0.10
ORIGIN: https://github.com/Homebrew/brew
HEAD: 0ad2564c5f1ddf6f16f707f2861556b80546713c
Last commit: 5 days ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: ddaf8f1295abaa372ebf968ec845982f35703e1e
Core tap last commit: 26 minutes ago
Core tap branch: master
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CASK_OPTS: []
HOMEBREW_DISPLAY: /private/tmp/com.apple.launchd.ZBLJZiyq8c/org.xquartz:0
HOMEBREW_MAKE_JOBS: 4
Homebrew Ruby: 2.6.3 => /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/bin/ruby
CPU: quad-core 64-bit kabylake
Clang: 12.0 build 1200
Git: 2.24.3 => /Applications/Xcode.app/Contents/Developer/usr/bin/git
Curl: 7.64.1 => /usr/bin/curl
macOS: 11.2.3-x86_64
CLT: 12.4.0.0.1.1610135815
Xcode: 12.4
XQuartz: 2.7.11 => /opt/X11

$ port upgrade outdated
:
:
:

--> Fetching archive for pkgconfig
---> Attempting to fetch pkgconfig-0.29.2_0.darwin_20.x86_64.tbz2 from https://mse.uk.packages.macports.org/pkgconfig
---> Attempting to fetch pkgconfig-0.29.2_0.Darwin_20.x86_64.tbz2.rmd160 from https://mse.uk.packages.macports.org/pkgconfig
---> Installing pkgconfig @0.29.2_0
---> Activating pkgconfig @0.29.2_0
---> Cleaning pkgconfig
Warning: The macOS 11.2 SDK does not appear to be installed. Ports may not build correctly.
Warning: You can install it as part of the Xcode Command Line Tools package by running `xcode-select --install'.
---> Computing dependencies for python38
---> Fetching archive for python38
---> Attempting to fetch python38-3.8.9_0.darwin_20.x86_64.tbz2 from https://mse.uk.packages.macports.org/python38
---> Attempting to fetch python38-3.8.9_0.darwin_20.x86_64.tbz2 from https://lil.fr.packages.macports.org/python38
---> Attempting to fetch python38-3.8.9_0.darwin_20.x86_64.tbz2 from https://packages.macports.org/python38
---> Fetching distfiles for python38
---> Attempting to fetch Python-3.8.9.tar.xz from https://www.python.org/ftp/python/3.8.9/
---> Verifying checksums for python38
---> Extracting python38
---> Applying patches to python38
---> Configuring python38
---> Building python38
---> Staging python38 into destroot
---> Installing python38 @3.8.9_0
---> Cleaning python38
Warning: The macOS 11.2 SDK does not appear to be installed. Ports may not build correctly
Warning: You can install it as part of the Xcode Command Line Tools package by running `xcode-select --install'.
---> Computing dependencies for python38
---> Deactivating python38 @3.8.8_1
---> Cleaning python38
---> Activating python38 @3.8.9_0

 

[rezwits]

After installing Big Sur 11.3,
if you proceed to Xcode 12.5,
after that is done,
BEFORE using xcode-select --install
going to Brew and upgrading/updating
go BACK to Software Update and install CLTs
then go back to `brew upgrade`

If not you'll probably get the warning (again)...

 

[Dawn Song]

I've already installed Xcode, and run `sudo xcode-select -s /Applications/Xcode.app`.
Why `brew` requires me to install a standalone command line tools?
It does not make sense.

 

[rezwits]

I've already installed Xcode, and run `sudo xcode-select -s /Applications/Xcode.app`.
Why `brew` requires me to install a standalone command line tools?
It does not make sense.

There is definitely a bug with older installs of Brew(ing)

For instance you could install EVERYTHING CLT related double triple times over, and then you go to "brew" something and the brew or cask will say:

Install CLT from blah blah etc

It's BS just ignore...

Hope this helps...