Running GDB on R Itself
GDB (GNU Debugger) is a powerful tool used for debugging programs written in languages such as C, C++, and Fortran. It can also be used to debug R itself, which is particularly useful if you need to investigate issues within the R interpreter or diagnose problems with compiled R packages.
Here’s a detailed guide on how to use GDB to debug R:
Prerequisites
Before running GDB on R, you need to ensure the following:
- GDB Installation: GDB should be installed on your system. You can install it using your package manager. For example, on Debian-based systems, use sudo apt-get install gdb.
- R with Debug Symbols: R needs to be compiled with debugging symbols. This allows GDB to provide detailed debugging information. Typically, you need to compile R from source with debugging symbols enabled.
Compiling R with Debug Symbols
To enable debugging symbols, you need to compile R from source with the appropriate flags. Here’s how you can do it:
Download R Source Code
Download the Source Code:
Get the latest R source tarball from the CRAN R website.
Extract the Tarball:
tar -xzvf R-<version>.tar.gz cd R-<version>
Configure and Compile R
Configure with Debug Symbols:
Use the –enable-debug flag to include debugging symbols.
./configure --enable-debug
Compile R:
make
Install R (optional):
sudo make install
Running GDB on R
Once R is compiled with debugging symbols, you can start using GDB to debug it.
Start GDB
Launch GDB with R:
Open a terminal and start GDB with the R executable.
gdb R
Set GDB Commands:
At the GDB prompt, you can set breakpoints, run R scripts, and inspect the state of R.
(gdb) break main (gdb) run
Set Breakpoints
Breakpoints allow you to pause execution at specific points in the code.
Set a Breakpoint in R Source Code:
To set a breakpoint in the R source code (e.g., src/main/rmain.c), use:
(gdb) break rmain.c:line_number
Set a Breakpoint in a Function:
To set a breakpoint in a function (e.g., R_eval), use:
(gdb) break R_eval
Running and Debugging
Run R:
Start R within GDB.
(gdb) run
Execute R Commands:
Once R is running, you can execute R commands as usual. You can also set breakpoints and inspect variables within GDB.
Inspect Variables:
To inspect variables, use the print command in GDB.
(gdb) print variable_name
Step Through Code:
Use GDB commands to step through code and observe behavior.
(gdb) next # Step over to the next line (gdb) step # Step into the function (gdb) continue # Continue execution until the next breakpoint
View the Call Stack:
To view the call stack, use:
(gdb) backtrace
Exiting GDB
Exit GDB:
To exit GDB, use:
(gdb) quit
Debugging Specific Scenarios
Debugging R Packages:
If you are developing or troubleshooting an R package, you can use GDB to debug compiled code within the package.
Set Breakpoints in Package Code:
Load your package and set breakpoints in the relevant C or C++ code.
Reproduce the Issue:
Run the R code that triggers the issue and observe behavior in GDB.
Debugging R Internals:
For debugging issues related to R internals or the R interpreter itself:
Investigate R Core Functions:
Set breakpoints in core R functions and inspect how they behave.
Analyze Core Dumps:
If R crashes, analyze core dumps with GDB to diagnose the issue.
Example: Debugging a Simple R Script
Here’s a step-by-step example of how you might debug a simple R script using GDB.
Example R Script
Consider an R script test.R that performs some operations:
# test.R x <- 1:10 y <- x / 0 # This will cause a division by zero print(y)
Start GDB and Set Up Breakpoints
Start GDB with R:
gdb R
Set a Breakpoint in R’s Code:
(gdb) break src/main/eval.c:123 # Example line number where you suspect the issue
Run R and Source the Script:
(gdb) run
(gdb) source("test.R")
Inspecting and Debugging
Inspect Variable Values:
(gdb) print variable_name
Step Through Code:
(gdb) next (gdb) step
Continue Execution:
(gdb) continue
Exit GDB
Exit GDB:
(gdb) quit
Conclusion
Compiling R with Debug Symbols: Ensure R is compiled with debugging symbols to enable detailed debugging.
Using GDB: Launch GDB with the R executable, set breakpoints, run R, and inspect the code and variables.
Debugging Scenarios: Use GDB to troubleshoot R packages, core functions, or R internals. You can debug specific issues by setting breakpoints in relevant code and examining the execution flow.