pyenv configure: error: C compiler cannot create executables

Question

I am trying to install multiple versions of Python on my laptop running MacOS Big Sur v11.1. I initially installed xcode command line tools, homebrew, and python via instructions here

xcode-select --install

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"

brew install python

But later on involuntarily upgraded python to 3.9, and I need to go back to 3.7.9. So I installed pyenv and attempted to install python 3.7.9 per instructions here

brew install pyenv

pyenv install 3.7.9

But I encountered the following error:

/var/folders/8n/ml0qwc091w9bhpszzxy9djl00000gn/T/python-build.20210118111111.56108 /usr/local/Cellar
/var/folders/8n/ml0qwc091w9bhpszzxy9djl00000gn/T/python-build.20210118111111.56108/Python-3.7.9 /var/folders/8n/ml0qwc091w9bhpszzxy9djl00000gn/T/python-build.20210118111111.56108 /usr/local/Cellar
checking build system type... x86_64-apple-darwin20.2.0
checking host system type... x86_64-apple-darwin20.2.0
checking for python3.7... no
checking for python3... python3
checking for --enable-universalsdk... no
checking for --with-universal-archs... no
checking MACHDEP... checking for --without-gcc... no
checking for --with-icc... no
checking for gcc... clang
checking whether the C compiler works... no
configure: error: in `/var/folders/8n/ml0qwc091w9bhpszzxy9djl00000gn/T/python-build.20210118111111.56108/Python-3.7.9':
configure: error: C compiler cannot create executables
See `config.log' for more details
make: *** No targets specified and no makefile found.  Stop.

From other answers online it seems my gcc may be out of date. I checked my gcc version with

[/usr/local/Cellar]$ gcc --version
Configured with: --prefix=/Library/Developer/CommandLineTools/usr
    --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/4.2.1 Apple clang version 11.0.3 (clang-1103.0.32.62) Target: x86_64-apple-darwin20.2.0 Thread model: posix InstalledDir: /Library/Developer/CommandLineTools/usr/bin

Which seems to indicate I am on version 4.2.1. I have not been able to find a way to update it on my own yet, but did brew install gcc which did not resolve the problem. Any help would be much appreciated

EDIT: Seems pyenv is using clang and not gcc. Perhaps xcode-select installed both? clang --version returns:

Apple clang version 11.0.3 (clang-1103.0.32.62)
Target: x86_64-apple-darwin20.2.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

Answer 1

This worked for me: I removed the command line tools as root and reinstalled ...

Your Command Line Tools (CLT) does not support macOS 11. It is either outdated or was modified. Please update your Command Line Tools (CLT) or delete it if no updates are available.

Update them from Software Update in System Preferences or run:

softwareupdate --all --install --force

If that doesn't show you any updates, run:

sudo rm -rf /Library/Developer/CommandLineTools
sudo xcode-select --install

Alternatively, manually download them from:

https://developer.apple.com/download/more/.

Answer 2

I used the following and it worked

CC=gcc pyenv install 3.7.10

Answer 3

Seems there is a problem with Xcode, zlib and compiler options. From brew they made some patches to 3.8.0 python version.

My configuration

$ sw_vers
ProductName:    macOS
ProductVersion: 11.2.3
BuildVersion:   20D91

$ clang --version
Apple clang version 12.0.0 (clang-1200.0.32.29)
Target: x86_64-apple-darwin20.3.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

This worked for me to install 3.8.3 and 3.9.0

# Re-install Xcode
sudo rm -rf /Library/Developer/CommandLineTools
xcode-select --install

# Install zlib and bzip2 using brew
brew reinstall zlib bzip2
 
# Install tcl-tk tkinter
brew install tcl-tk

# Uninstall previous versions from python
pyenv uninstall 3.8.3
pyenv uninstall 3.9.0

# Install python 3.8.3 patched
env \
  PATH="$(brew --prefix tcl-tk)/bin:$PATH" \
  LDFLAGS="-L$(brew --prefix tcl-tk)/lib -L$(brew --prefix zlib)/lib -L$(brew --prefix bzip2)/lib" \
  CPPFLAGS="-I$(brew --prefix tcl-tk)/include -L$(brew --prefix zlib)/include -L$(brew --prefix bzip2)/include" \
  PKG_CONFIG_PATH="$(brew --prefix tcl-tk)/lib/pkgconfig" \
  CFLAGS="-I$(brew --prefix tcl-tk)/include -I$(brew --prefix openssl)/include -I$(brew --prefix bzip2)/include -I$(brew --prefix zlib)/include -I$(brew --prefix readline)/include -I$(xcrun --show-sdk-path)/usr/include" \
  LDFLAGS="-I$(brew --prefix tcl-tk)/lib -L$(brew --prefix openssl)/lib -L$(brew --prefix readline)/lib -L$(brew --prefix zlib)/lib -L$(brew --prefix bzip2)/lib"
  pyenv install --patch 3.8.3 < <(curl -sSL https://github.com/python/cpython/commit/8ea6353.patch\?full_index\=1)
  
env \
  PATH="$(brew --prefix tcl-tk)/bin:$PATH" \
  LDFLAGS="-L$(brew --prefix tcl-tk)/lib -L$(brew --prefix zlib)/lib -L$(brew --prefix bzip2)/lib" \
  CPPFLAGS="-I$(brew --prefix tcl-tk)/include -L$(brew --prefix zlib)/include -L$(brew --prefix bzip2)/include" \
  PKG_CONFIG_PATH="$(brew --prefix tcl-tk)/lib/pkgconfig" \
  CFLAGS="-I$(brew --prefix tcl-tk)/include -I$(brew --prefix openssl)/include -I$(brew --prefix bzip2)/include -I$(brew --prefix zlib)/include -I$(brew --prefix readline)/include -I$(xcrun --show-sdk-path)/usr/include" \
  LDFLAGS="-I$(brew --prefix tcl-tk)/lib -L$(brew --prefix openssl)/lib -L$(brew --prefix readline)/lib -L$(brew --prefix zlib)/lib -L$(brew --prefix bzip2)/lib"
  pyenv install 3.9.0

My sources where I did come up with the solution:

• pyenv configure: error: C compiler cannot create executables
• unable to install python 3.8.0 on macox 11 #1740
• Unable to build Python on macOS Big Sur with Xcode 12 beta #1643

Answer 4

For me it was a problem with the clang compiler that pyenv was trying to use. As I had an active Anaconda version that was set up with pyenv, it tried to use the clang version bundled with Anaconda:

$ clang --version
clang version 10.0.0
Target: x86_64-apple-darwin19.6.0
Thread model: posix
InstalledDir: /Users/myuser/.pyenv/versions/anaconda3-2020.02/bin

With:

pyenv shell system

I was able to use the XCode clang compiler and everything worked all right. I was able to install the new version of Python with a typical:

pyenv install 3.9.5