Why does my unit test run successfully in the R console but returns an error with "make test"?

Question

I am learning how to develop an R package. Everything goes well, thanks to the R manuals and this wiki for RUnit. More precisely, when I launch my unit tests within a new R console, all tests finish successfully:

#rm(list=ls())
library(RUnit)
testSuite <- defineTestSuite("current", "~/src/mypkg/inst/unitTests/")
isValidTestSuite  # returns TRUE
runTestSuite(testSuite)  # returns Number of errors: 0 and Number of failures: 0

However, when I launch them in a terminal, I got one error (the function in question uses the package GenomicRanges that I installed in "~/src/Rlibs"):

$ make test R_LIBS="~/src/Rlibs/"
...
ERROR in test.MyFunction: Error in match(x, table, nomatch = 0L) :
  'match' requires vector arguments

I don't see what is causing this error. I guess you will need more info about the code and the test, but it's not easy because I don't know how to replicate this error on a small example without making a new package just for this. Maybe some of you will have an idea about this error message and give me some hints?

Edit: to help someone to give me a hint on the error, here is the code I wrote for a dummy package. The aim is to find which items of "p" are included within items of "g".

Here is the test:

test.MyFunction <- function(){
  g <- list(c1=data.frame(name=c("g1","g2"), start=c(11,1111),
                  end=c(500,1500), strand=c("+","+"), stringsAsFactors=FALSE))
  p <- list(c1=data.frame(name=c("p1","p2"), strand=c("+","-"),
                   start=c(11,601), end=c(20, 610), stringsAsFactors=FALSE))
  exp <- list(c1=list(g1=c("p1")))  # item "p1" is included in item "g1"
  obs <- MyFunction(g, p)
  checkEquals(obs, exp)
}

And here is the function itself:

MyFunction <- function(g, p){
  res <- lapply(names(g), function(c.name){
    res.c <- list()
    nb.g <- length(g[[c.name]]$name)

    if(length(.find.package("GenomicRanges", quiet=TRUE)) > 0){
      g.ranges <- GRanges(seqnames=Rle(c(c.name), c(nb.g)),
                            ranges=IRanges(g[[c.name]]$start,
                              g[[c.name]]$end, names=g[[c.name]]$name),
                            strand="*")
      p.ranges <- GRanges(seqnames=Rle(c(c.name), nrow(p[[c.name]])),
                             ranges=IRanges(p[[c.name]]$start,
                               p[[c.name]]$end, names=p[[c.name]]$name),
                             strand=p[[c.name]]$strand)
      for(g.name in names(g.ranges)){
        links <- p.ranges %in% g.ranges[names(g.ranges) == g.name]
        if(sum(links) > 0)
          res.c[[g.name]] <- names(p.ranges)[which(links)]
      }
    } else{
      msg <- "can't find package GenomicRanges"
      stop(msg, call.=FALSE)
    }
    res.c
  })

  names(res) <- names(g)
  return(res)
}

Answer 1

I think this line is your culprit:

links <- p.ranges %in% g.ranges[names(g.ranges) == g.name].

%in% is match, and that is what the error message seems to be reading:

ERROR in test.MyFunction: Error in match(x, table, nomatch = 0L) :
  'match' requires vector arguments

There is something about p.ranges and g.ranges that it doesn't like. I.e., they can't be coerced to vectors OR you're not subsetting properly and the object type is incorrect ([ or [[).