Difference between revisions of "Debug"

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[https://www.inwt-statistics.com/read-blog/debugging-in-r.html How to Easily and Efficiently Conquer Errors in Your Code]
 
[https://www.inwt-statistics.com/read-blog/debugging-in-r.html How to Easily and Efficiently Conquer Errors in Your Code]
  
=== debug() and isdebugged() functions ===
+
=== debug(), debugonce() and isdebugged() functions ===
 +
 
 +
=== How to quit debugging ===
 +
press '''Q''' and then ENTER
  
 
=== list or undebug all debugged functions ===
 
=== list or undebug all debugged functions ===

Revision as of 15:13, 9 January 2020

R

How to debug an R code

How to Easily and Efficiently Conquer Errors in Your Code

debug(), debugonce() and isdebugged() functions

How to quit debugging

press Q and then ENTER

list or undebug all debugged functions

https://stackoverflow.com/a/12807637

Using assign() in functions

For example, insert the following line to your function

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

Debug lapply()/sapply()

Debugging with RStudio

Debug R source code

Build R with debug information

$ ./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
# 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

.Call

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.