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Fixing Pyenv Install Errors on Ubuntu

pythonpyenvubuntutroubleshootingbrew

I was trying to install specific version of python and decided to install pyenv for this purpose. After installing pyenv with brew I tried to install python but I started to get errors. I will try to show how I fix them.

System Information

Here's my setup where I encountered this issue:

  • OS: Ubuntu 24.04.3 LTS
  • Pyenv version: 2.6.17
  • Homebrew version: 5.0.7
  • Python version attempting to install: 3.13t

The Problem

I tried to install Python 3.13t (experimental no-GIL version) using pyenv on Ubuntu. Normally I use pyenv in mac and I installed with brew and it was smooth. I did not have any issues.

So I decided to go similar approach in my personal computer and install the pyenv with brew.

First I installed pyenv with :

brew install pyenv

Then tried to install Python 3.13t with pyenv:

pyenv install 3.13t

The installation failed with this error:

/usr/bin/install: cannot stat 'Modules/_decimal.cpython-313-x86_64-linux-gnu.so': No such file or directory
make: *** [Makefile:2309: sharedinstall] Error 1

First Attempt: Following the Documentation

First I quickly checked the pyenv issues page to see if anyone else had the same issue. I found this related issue that suggested unlinking pkg-config.

I ran the unlink command:

brew unlink pkg-config

Second Problem

Now I had another error. This time I was missing libraries like readline, _sqlite3, tkinter, and _lzma. The installation was failing with "no module named _sqlite3" etc.

Second Attempt: Installing Dependencies

When I saw that I was missing libraries, I checked the pyenv build dependencies documentation again.

I tried installing with brew first:

brew install openssl readline sqlite3 xz tcl-tk@8 libb2 zstd zlib pkgconfig

But my issue still wasn't resolved. So I decided to use the standard Ubuntu approach.

I found the Ubuntu section in the documentation and ran:

sudo apt update; sudo apt install make build-essential libssl-dev zlib1g-dev \
libbz2-dev libreadline-dev libsqlite3-dev curl git \
libncursesw5-dev xz-utils tk-dev libxml2-dev libxmlsec1-dev libffi-dev liblzma-dev

After the installation finished, I tried again:

pyenv install 3.13t

This time it worked!

Key Takeaways

I started to feel like brew setup was not good for me. I did not have any issue working with macbook but in ubuntu I might have different setup. So I recommend following standart ubuntu parts from documentation instead of brew.

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