The Mysterious Case of Non-Terminating R Commands: A Deep Dive into R 4.0, Ubuntu 20.04, and Package Management
The world of data analysis and statistical modeling is full of surprises, especially when it comes to package management and library dependencies. In this article, we’ll delve into the complexities of upgrading R from version 3.6 to 4.0, RStudio from version 1.1 to 1.2.5, and Ubuntu from version 18.04 to 20.04. We’ll explore the reasons behind non-terminating commands, particularly with the ivreg function from package AER, and discuss possible solutions.
Understanding Package Management in R
In R, packages are collections of functions, data structures, and other resources that provide specific functionality. When you install a new package, R searches for it on your system’s package repositories, including CRAN (Comprehensive R Archive Network) and local repositories. If the package is not found, R will attempt to download and install it from CRAN.
The Role of libblas.so.3-x86_64-linux-gnu
The libblas library is a crucial component of many mathematical packages in R, including AER. It provides basic linear algebra operations, such as matrix multiplication and inverse computation. When you install AER, R automatically links against the libblas library.
However, when you upgrade to R 4.0, you might encounter issues with libblas.so.3-x86_64-linux-gnu, which is a legacy version of the library. This can happen if your system’s package repositories do not have the latest version of libblas.
The Impact of Ubuntu 20.04 on Package Management
Ubuntu 20.04 has introduced several changes to its package management, including the use of alternative libraries for some packages. For example, the libopenblas-openmp-dev package is now recommended instead of libopenblas-pthread-dev. This change can sometimes cause conflicts with existing packages, leading to non-terminating commands.
The Role of update-alternatives
When you run the command update-alternatives --config libblas.so.3-x86_64-linux-gnu, you’re essentially switching between different versions of the libblas library. This allows you to choose which version to use for your packages.
In this case, selecting /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 (instead of pthread) tells R to use the legacy version of the library instead of the newer pthread-based version.
Installing libopenblas-openmp-dev
After updating the default library for libblas, you need to install the new package, libopenblas-openmp-dev. This will ensure that your system has the necessary libraries for R packages like AER.
Running the command sudo apt install libopenblas-openmp-dev will install the package and its dependencies.
Removing Conflicting Packages
To resolve any conflicts between the old and new packages, you need to remove the conflicting packages. The command sudo apt remove libopenblas-pthread-dev libopenblas0-pthread removes the older versions of the library, which should fix any issues with non-terminating commands.
Example Use Case: Installing AER
To test if the package management changes have resolved the issue, you can try installing AER again. Run the command example('AER'), and it should work fine without throwing any warnings or errors.
However, be aware that some packages might still throw warnings or errors due to missing dependencies or conflicting libraries. In this case, updating your system’s package repositories or running sudo apt update can sometimes resolve the issue.
Conclusion
The upgrade from R 3.6 to 4.0 and Ubuntu 18.04 to 20.04 introduced several changes to package management, including updates to the default library for libblas. This change can sometimes cause non-terminating commands, particularly with packages like AER.
By running the command update-alternatives --config libblas.so.3-x86_64-linux-gnu and selecting the legacy version of the library, you can switch between different versions of libblas. Installing libopenblas-openmp-dev ensures that your system has the necessary libraries for R packages like AER.
Remember to remove any conflicting packages using sudo apt remove libopenblas-pthread-dev libopenblas0-pthread and update your system’s package repositories as needed.
Troubleshooting Tips
- If you’re still experiencing issues with non-terminating commands, try running
sudo apt cleanandsudo apt updateto refresh the package repository. - Check if any packages are missing dependencies or conflicting libraries. You can use tools like
dpkg --list-devicesorapt-cache policyto diagnose issues.
Next Steps
- Familiarize yourself with the updated package management in R 4.0 and Ubuntu 20.04.
- Experiment with different package versions and libraries to understand how they interact with each other.
- Keep your system’s package repositories up-to-date to ensure you have the latest security patches and features.
By following these steps, you’ll be better equipped to handle potential issues with package management in R and Ubuntu. Happy coding!
Last modified on 2024-10-29