Error running Python’s GLMnet implementation `glmnet_py` (missing libgfortran.so.3)

For machine learning tasks with not a lot of instances (n) but a lot of features, the ElasticNet by Zou and Hastie, 2005 in my experience often works well in practice.

Missing libgfortran.so.3

To use the ElasticNet in Python, there are various packages on PiPy. I used glmnet_py/glmnet-py since it is referred to by the glmnet_python wrapper published on GitHub which is in turn linked by the original authors.

However, when I installed glmnet_py from PyPi via “pip install glmnet_py” (as recommended by the documentation), I get an error about a missing library file, namely libgfortran.so.3:

To solve this, I had compile and install glmnet_py manually from the code on GitHub:

This happened to my on a Fedora 29 with Python 3.7.2.

To track this issue, please see here.

Different versions of the same thing

The glmnet_py situation seems to be a little strange at first glance since there are two very similar PiPy repositories, namely glmnet_py and glmnet_python.

However, the latter seems to have been removed since a) its project description also refers to glmnet_py and b) pip seems not to be able to install the latter (at least for me).

Similarly, there are two GitHub repositories: one (by bbalasub1) linked by the original authors and one (by hanfang) that claims to have modified the former. However, the one by hanfang seems outdated. In contrast the one by bbalasub1 has actually seen some updates as of the time of writing this note.

Other ElasticNet implementations in Python

Of course, there are other ElasticNet implementations in Python. I have simply opted for the one above since it seems to be closely related to the original authors as well as the R code used by my colleagues. Here are some other examples of Python implementations:

Hello world!

Welcome to my Blog! This is my first post where I try out some plug-ins before starting to write away.

Crayon Syntax Highlighter

This is Crayon Syntax Highlighter:

 

WP LaTeX

And this is WP LaTeX:
e^{\i \pi} + 1 = 0

BibSonomy/PUMA CSL

I also use BibSonomy, so I tried to install the corresponding plug-in in order to list some publications and research articles.  This turned out to be a little cumbersome since it does not seem to be compatible with PHP7. When I try to activate the plug-in, I get two errors:

The first error we can solve by modifying the file CurlHttpRequestProxy.php , i.e., we replace

by

The second error I was able to “fix” by installing the package php-xml :

After this, the BibSonomy plug-in worked for me.