The "==" method that I have defined for my class, MTuples, is breaking the "==" method for signature c("Rle", "vector"). I discovered this when working on something quite unrelated, namely, I couldn't resize IRanges with "fixed = end" when my package was loaded. The attached code highlights the initial problem.

The error message and traceback were a little hairy - could someone please help me figure out what's going wrong?

Thanks,
Pete

------------------------------------------------------------------------------------------------------------------
# Mimics the initial problem
# Fresh R session
library(IRanges)
ir <- IRanges(start = 11, end = rep.int(20, 5))

 # Works when repeatedly called
resize(ir, 1, 'end') # Works
resize(ir, 1, 'end') # Works

# The method definition that breaks things
# I haven't included the MTuples class definition or the .MTuples.compare function 
# But that shouldn't matter in order to highlight the problem, should it?
setMethod("==", c("MTuples", "MTuples"), function(e1, e2) {
  .MTuples.compare(e1, e2) == 0L
})

# No longer works
resize(ir, 1, 'end') 
------------------------------------------------------------------------------------------------------------------


I managed to simplify the reproducible example to the following, but I can't figure out what's going wrong:
------------------------------------------------------------------------------------------------------------------
# A simplified example
# Fresh R session
library(IRanges)
fix <- Rle('end', 10)

# Works when repeatedly called
fix == 'end' # Works
fix == 'end' # Works 

# The method definition that breaks things
# I haven't included the MTuples class definition or the .MTuples.compare function 
# But that shouldn't matter in order to highlight the problem, should it?
setMethod("==", c("MTuples", "MTuples"), function(e1, e2) {
  .MTuples.compare(e1, e2) == 0L
})

# Works the first time, but not the second
fix == 'end' # Works
fix == 'end' # Breaks
------------------------------------------------------------------------------------------------------------------

The same problem occurs if the vector is numeric and not character, e.g. using 7 instead of 'end'.

When this breaks I get the error:
------------------------------------------------------------------------------------------------------------------
Error in Rle(values = callGeneric(runValue(e1)[which1], runValue(e2)[which2]),  : 
  error in evaluating the argument 'values' in selecting a method for function 'Rle': Error in as.character(call[[1L]]) : 
  cannot coerce type 'builtin' to vector of type 'character'
------------------------------------------------------------------------------------------------------------------

My session info is:
------------------------------------------------------------------------------------------------------------------
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods 
[8] base     

other attached packages:
[1] IRanges_1.22.7      BiocGenerics_0.10.0

loaded via a namespace (and not attached):
[1] stats4_3.1.0
------------------------------------------------------------------------------------------------------------------


--------------------------------
Peter Hickey,
PhD Student/Research Assistant,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
Ph: +613 9345 2324

hickey@wehi.edu.au
http://www.wehi.edu.au


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