Debugging Utilities

Several debugging utilities are available for R. They include:

  • traceback
  • browser
  • options(error=recover)
  • options(error=NULL)
  • debug

The Debugging in R page provides an overview of the available resources.

Regular Expressions

R’s regular expression utilities work similar as in other languages. To learn how to use them in R, one can consult the main help page on this topic with ?regexp.

String matching with grep

The grep function can be used for finding patterns in strings, here letter A in vector month.name.

month.name[grep("A", month.name)] 

## [1] "April"  "August"

String substitution with gsub

Example for using regular expressions to substitute a pattern by another one using a back reference. Remember: single escapes \ need to be double escaped \\ in R.

gsub('(i.*a)', 'xxx_\\1', "virginica", perl = TRUE) 

## [1] "vxxx_irginica"

Interpreting a Character String as Expression

Some useful examples

Generates vector of object names in session

mylist <- ls()
mylist[1] 

## [1] "i"

Executes 1st entry as expression

get(mylist[1])

## [1] 150

Alternative approach

eval(parse(text=mylist[1])) 

## [1] 150

Replacement, Split and Paste Functions for Strings

Selected examples

Substitution with back reference which inserts in this example _ character

x <- gsub("(a)","\\1_", month.name[1], perl=T) 
x

## [1] "Ja_nua_ry"

Split string on inserted character from above

strsplit(x,"_")

## [[1]]
## [1] "Ja"  "nua" "ry"

Reverse a character string by splitting first all characters into vector fields

paste(rev(unlist(strsplit(x, NULL))), collapse="") 

## [1] "yr_aun_aJ"

Time, Date and Sleep

Selected examples

Return CPU (and other) times that an expression used (here ls)

system.time(ls()) 

##    user  system elapsed 
##       0       0       0

Return the current system date and time

date() 

## [1] "Wed Apr 13 16:06:06 2016"

Pause execution of R expressions for a given number of seconds (e.g. in loop)

Sys.sleep(1)

Example

Import of Specific File Lines with Regular Expression

The following example demonstrates the retrieval of specific lines from an external file with a regular expression. First, an external file is created with the cat function, all lines of this file are imported into a vector with readLines, the specific elements (lines) are then retieved with the grep function, and the resulting lines are split into vector fields with strsplit.

cat(month.name, file="zzz.txt", sep="\n")
x <- readLines("zzz.txt")
x[1:6] 

## [1] "January"  "February" "March"    "April"    "May"      "June"

x <- x[c(grep("^J", as.character(x), perl = TRUE))]
t(as.data.frame(strsplit(x, "u")))

##                 [,1]  [,2] 
## c..Jan....ary.. "Jan" "ary"
## c..J....ne..    "J"   "ne" 
## c..J....ly..    "J"   "ly"

## Calling External Software

External command-line software can be called with system. The following example calls blastall from R

system("blastall -p blastp -i seq.fasta -d uniprot -o seq.blastp")
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