debug-session

> isIn <- function(x, y) {
+     sel <- match(x, y)
+     y[sel]
+ }
> x <- sample(LETTERS, 5)
> isIn(x, LETTERS)
[1] "Q" "Z" "K" "V" "U"
> 
> x
[1] "Q" "Z" "K" "V" "U"
> isIn(x, LETTERS)
[1] "Q" "Z" "K" "V" "U"
> isIn(c(x, "a"), LETTERS)
[1] "Q" "Z" "K" "V" "U" NA 
> debug(isIn)
> isIn(c(x, "a"), LETTERS)
debugging in: isIn(c(x, "a"), LETTERS)
debug at #1: {
    sel <- match(x, y)
    y[sel]
}
Browse[2]> ls()
[1] "x" "y"
Browse[2]> x
[1] "Q" "Z" "K" "V" "U" "a"
Browse[2]> y
 [1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O" "P" "Q" "R" "S"
[20] "T" "U" "V" "W" "X" "Y" "Z"
Browse[2]> 
debug at #2: sel <- match(x, y)
Browse[2]> ls()
[1] "x" "y"
Browse[2]> 
debug at #3: y[sel]
Browse[2]> ls()
[1] "sel" "x"   "y"  
Browse[2]> sel
[1] 17 26 11 22 21 NA
Browse[2]> y[sel]
[1] "Q" "Z" "K" "V" "U" NA 
Browse[2]> sel[1:5]
[1] 17 26 11 22 21
Browse[2]> sel <- sel[1:5]
Browse[2]> sel
[1] 17 26 11 22 21
Browse[2]> y[sel]
[1] "Q" "Z" "K" "V" "U"
Browse[2]> 
exiting from: isIn(c(x, "a"), LETTERS)
[1] "Q" "Z" "K" "V" "U"
> undeg(isIn)
Error: could not find function "undeg"
> undebug(isIn)
> isIn(c(x, "a"), LETTERS)
[1] "Q" "Z" "K" "V" "U" NA 
> fix(isIn)
Waiting for Emacs...
> isIn
function(x, y) {
    print("hello")
    sel <- match(x, y)
    y[sel]
}
> library("RUnit")
> 
+ + + > x <- sample(LETTERS, 5)
> isIn(x, LETTERS)
[1] "H" "Y" "I" "X" "Z"
> isIn(c(x, "a"), LETTERS)
[1] "H" "Y" "I" "X" "Z" NA 
> 
Error in checkIdentical(x, isIn(c(x, "a"), LETTERS)) (from #4) : FALSE 
> [1] TRUE
> 
> test_isIn()
[1] TRUE
> 
+ + + > x <- sample(LETTERS, 5)
> isIn(x, LETTERS)
[1] "S" "A" "E" "C" "J"
> isIn(c(x, "a"), LETTERS)
[1] "S" "A" "E" "C" "J" NA 
> library("RUnit")
> 
+ + + + > test_isIn()
Error in checkIdentical(x, isIn(c(x, "a"), LETTERS)) (from debug.R!2533YNG#4) : FALSE 
> x
[1] "S" "A" "E" "C" "J"
> isIn(c(x, "a"), LETTERS)
[1] "S" "A" "E" "C" "J" NA 
> 
+ + + > test_isIn()
[1] TRUE
> 
+ + + > isIn(c(x, "a"), LETTERS)
[1] "S" "A" "E" "C" "J" NA 
> traceback()
3: stop(paste(paste(result, collapse = "\n"), msg))
2: checkIdentical(x, isIn(c(x, "a"), LETTERS)) at debug.R!2533YNG#4
1: test_isIn()
> stop("there is an error")
Error: there is an error

> options(error = recover)

+ . + > test_isIn()
Error in checkIdentical(x, isIn(c(x, "a"), LETTERS)) (from debug.R!2533M2e#4) : FALSE 

Enter a frame number, or 0 to exit   

1: test_isIn()
2: debug.R!2533M2e#4: checkIdentical(x, isIn(c(x, "a"), LETTERS))

Selection: 1
Called from: top level 
Browse[1]> ls()
[1] "x"
Browse[1]> x
[1] "A" "B" "Z"
Browse[1]> 

Enter a frame number, or 0 to exit   

1: test_isIn()
2: debug.R!2533M2e#4: checkIdentical(x, isIn(c(x, "a"), LETTERS))

Selection: 0
> options(error = stop)
> test_isIn()
Error in checkIdentical(x, isIn(c(x, "a"), LETTERS)) (from debug.R!2533M2e#4) : FALSE 
Error during wrapup: 
> library("Biobase")
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:stats’:

    xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
    do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
    is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unlist

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> new("ExpressionSet")
ExpressionSet (storageMode: lockedEnvironment)
assayData: 0 features, 0 samples 
  element names: exprs 
protocolData: none
phenoData: none
featureData: none
experimentData: use 'experimentData(object)'
Annotation:  
> validObject(new("ExpressionSet"))
[1] TRUE
> 
> 
> q("no")

Process R finished at Wed Jul 30 16:47:04 2014