Debug

R

How to debug an R code

Using assign() in functions

For example, insert the following line to your function

 assign(envir=globalenv(), "GlobalVar", localvar)

Debug lapply()/sapply()

• https://stackoverflow.com/questions/1395622/debugging-lapply-sapply-calls
• https://stat.ethz.ch/R-manual/R-devel/library/utils/html/recover.html. Use options(error=NULL) to turn it off.

Debugging with RStudio

• https://www.rstudio.com/resources/videos/debugging-techniques-in-rstudio/
• https://github.com/ajmcoqui/debuggingRStudio/blob/master/RStudio_Debugging_Cheatsheet.pdf
• https://support.rstudio.com/hc/en-us/articles/205612627-Debugging-with-RStudio

Debug R source code

Build R with debug information

• R -> Build R from its source on Windows
• http://www.stats.uwo.ca/faculty/murdoch/software/debuggingR/ (defunct)
• http://www.stats.uwo.ca/faculty/murdoch/software/debuggingR/gdb.shtml (defunct)
• Build R with debug information (see the discussion here). Cf output messages from running ./configure and make using the default options.

$ ./configure --help
$ ./configure --enable-R-shlib --with-valgrind-instrumentation=2 \
                               --with-system-valgrind-headers \
               CFLAGS='-g -O0 -fPIC' \
               FFLAGS='-g -O0 -fPIC' \
               CXXFLAGS='-g -O0 -fPIC' \
               FCFLAGS='-g -O0 -fPIC' 
$ make -j4
$ sudo make install

• My note of debugging cor() function
• Using gdb to debug R packages with native code (Video) The steps to debug is given below.

# Make sure to create a file <src/Makevars> with something like: CFLAGS=-ggdb -O0
# Or more generally
# CFLAGS=-Wall -Wextra -pedantic -O0 -ggdb
# CXXFLAGS=-Wall -Wextra -pedantic -O0 -ggdb
# FFLAGS=-Wall -Wextra -pedantic -O0 -ggdb

$ tree nidemo
$ R CMD INSTALL nidemo
$ cat bug.R
$ R -f bug.R 
$ R -d gdb
(gdb) r
> library(nidemo)
> Ctrl+C
(gdb) b nid_buggy_freq
(gdb) c  # continue
> buggy_freq("nidemo/DESCRIPTION") # stop at breakpoint 1
(gdb) list
(gdb) n # step through
(gdb) # press RETURN a few times until you see the bug
(gdb) d 1 # delete the first break point
(gdb) b Rf_error # R's C entry point for the error function
(gdb) c
> buggy_freq("nidemo/DESCRIPTION")
(gdb) bt 5 # last 5 stack frames
(gdb) frame 2
(gdb) list
(gdb) p freq_data
(gdb) p ans
(gdb) call Rf_PrintValues(ans)
(gdb) call Rf_PrintValues(fname)
(gdb) q
# Edit buggy.c

$ R CMD INSTALL nidemo # re-install the package
$ R -f bug.R
$ R -d gdb
(gdb) run
> source("bug.R") # error happened
(gdb) bt 5 # show the last 5 frames
(gdb) frame 2
(gdb) list
(gdb) frame 1
(gdb) list
(gdb) p file
(gdb) p fh
(gdb) q
# Edit buggy.c

$ R CMD INSTALL nidemo
$ R -f bug.R

• Compiled code from "R packages" by Hadley Wickham
• Debugging C/C++ code from Bioconductor (case study)
• Same idea for the Rcpp situation. See What are productive ways to debug Rcpp compiled code loaded in R (on OS X Mavericks)?

.Call

• Writing R Extensions manual.
• R’s C interface from Advanced R by Hadley Wickham

Registering native routines

https://cran.rstudio.com/doc/manuals/r-release/R-exts.html#Registering-native-routines

Pay attention to the prefix argument .fixes (eg .fixes = "C_") in useDynLib() function in the NAMESPACE file.

Example of debugging cor() function

Note that R's cor() function called a C function cor().

stats::cor
....
 .Call(C_cor, x, y, na.method, method == "kendall")

A step-by-step screenshot of debugging using the GNU debugger gdb can be found on my Github repository https://github.com/arraytools/r-debug.