Admin: Created page with "=Debugging R packages written in C++= Suppose you are faced with an R package, the bulk of which is written in C++. Such a package may be monolithic, and without looking at the C++ code it may be difficult to figure out what’s going on. The R package "specs" (https://github.com/wijler/specs/) is an example of such a package. First, a word of warning: don’t try to compile this code using Visual Studio. You will run into all sorts of compatibility issues with R head..."

2023-12-24T15:22:29Z

Created page with "=Debugging R packages written in C++= Suppose you are faced with an R package, the bulk of which is written in C++. Such a package may be monolithic, and without looking at the C++ code it may be difficult to figure out what’s going on. The R package "specs" (https://github.com/wijler/specs/) is an example of such a package. First, a word of warning: don’t try to compile this code using Visual Studio. You will run into all sorts of compatibility issues with R head..."

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=Debugging R packages written in C++=

Suppose you are faced with an R package, the bulk of which is written in C++. Such a package may be monolithic, and without looking at the C++ code it may be difficult to figure out what’s going on.

The R package "specs" (https://github.com/wijler/specs/) is an example of such a package.

First, a word of warning: don’t try to compile this code using Visual Studio. You will run into all sorts of compatibility issues with R headers and libraries and can potentially waste quite a bit of time. This approach is therefore not recommended.

This is what we are going to do instead. First, we are going to fork the R package, thus obtaining https://github.com/sydx/specs/ (sydx is my GitHub username).

Next, we are going to install this package into R, from GitHub. For this we can either use the R package "pak" or the R package "devtools". We will go for the more standard "devtools".
It turns out it’s not a trivial task to install "devtools" itself, even on a new AWS instance with a clean Ubuntu installation. "devtools" has various prerequisites and we can get stuck at several steps. Let us consider these prerequisites and what can go wrong during their installation.

<pre>
install.packages("openssl")
</pre>

You may get the error message
<pre>
-------------------------- [ERROR MESSAGE] ---------------------------
tools/version.c:1:10: fatal error: openssl/opensslv.h: No such file or directory
1 | #include <openssl/opensslv.h>
| ^~~~~~~~~~~~~~~~~~~~
compilation terminated.
--------------------------------------------------------------------
</pre>
This is solved with
<pre>
sudo apt-get install libssl-dev
</pre>
Next prerequisite:
<pre>
install.packages("curl")
</pre>
You may get the error message
<pre>
-------------------------- [ERROR MESSAGE] ---------------------------
<stdin>:1:10: fatal error: curl/curl.h: No such file or directory
compilation terminated.
--------------------------------------------------------------------
</pre>
This is solved with
<pre>
sudo apt-get install libcurl4-openssl-dev
</pre>
Next prerequisite:
install.packages("usethis")
Next prerequisite:
install.packages("systemfonts")
You may get the error message
<pre>
-------------------------- [ERROR MESSAGE] ---------------------------
<stdin>:1:10: fatal error: fontconfig/fontconfig.h: No such file or directory
compilation terminated.
--------------------------------------------------------------------
</pre>
This is solved with
<pre>
sudo apt-get install libfontconfig1-dev
</pre>
Next prerequisite:
<pre>
install.packages("textshaping")
</pre>
You may get the error message
<pre>
-------------------------- [ERROR MESSAGE] ---------------------------
<stdin>:1:10: fatal error: hb-ft.h: No such file or directory
compilation terminated.
--------------------------------------------------------------------
</pre>
This is solved with
<pre>
sudo apt-get install libharfbuzz-dev
sudo apt-get install libfribidi-dev
</pre>
Next prerequisite:
<pre>
install.packages("ragg")
</pre>
You may run into the error message
<pre>
-------------------------- [ERROR MESSAGE] ---------------------------
<stdin>:1:10: fatal error: ft2build.h: No such file or directory
compilation terminated.
--------------------------------------------------------------------
</pre>
And a few other problems when installing this package. This is solved with
<pre>
sudo apt-get install libfreetype6-dev
sudo apt-get install libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev
</pre>
and then installing a development version of this package from the source code repository using the R package "pak":
<pre>
install.packages("pak")
pak::pak("r-lib/ragg")
</pre>
(In fact, at this point, we could have installed our R package of interest, "specs", using "pak", but we decided to still install it using "devtools".)

Next prerequisites:
<pre>
install.packages("pkgdown")
install.packages("rcmdcheck")
install.packages("rversions")
install.packages("urlchecker")
</pre>
Finally, we can install "devtools" itself:
<pre>
install.packages("devtools")
</pre>
Using "devtools", we install the "specs" package from our forked repository:
<pre>
library("devtools")
devtools::install_github("sydx/specs")
</pre>
We can then load this package and work with it in R as usual:
<pre>
library(specs)
unemployment <- Unempl_GT[,1] #Extract the Dutch unemployment levels (x1,000)
GT <- Unempl_GT[,2:11] #Select the first ten Google Trends
my_specs <- specs(unemployment,GT,p=1) #Estimate specs
my_coefs <- my_specs$gammas #store the coefficients
y_d <- my_specs$y_d #Transformed dependent variable
z_l <- my_specs$v #Transformed independent variables
</pre>
This package does not provide much in terms of diagnostics, so we are going to add some debug output to the package source, which is in C++. First,
<pre>
remove.packages('specs')
</pre>
From shell, we
<pre>
cd ~
mkdir dev
cd dev
git clone git@github.com:sydx/specs.git
</pre>
(Make sure that we have the correct SSH keys on GitHub and on our operating system – see https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent)

Now
<pre>
cd specs/src
</pre>
and
<pre>
vim specs.cpp
</pre>
(Of course, if you prefer emacs, use emacs, etc.) To the top of the file, add
<pre>
#include <iostream>
</pre>
To the beginning of the body of the specs_rcpp function, add
<pre>
std::cout << "In specs_rcpp..." << std::endl;
</pre>
Now
<pre>
git add specs.cpp
git commit -m "Added some debug output."
git push
</pre>
Next time you go back to R
<pre>
library("devtools")
devtools::install_github("sydx/specs")
</pre>
and run the same R code, you will see the newly added debug output:
<pre>
> library(specs)
> unemployment <- Unempl_GT[,1] #Extract the Dutch unemployment levels (x1,000)
GT <- Unempl_GT[,2:11] #Select the first ten Google Trends
my_specs <- specs(unemployment,GT,p=1) #Estimate specs
In specs_rcpp...
</pre>
Now you can use debug output (or indeed attach a debugger, such as gdb) to understand what the package is doing step by step and relate these actions to the corresponding research paper.

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