Thanks for making that change, Hervé. It allows my package to avoid the bug that I reported (tested with GenomicRanges_1.17.17 built from source). However, I can still reproduce the simplified bug using the latest devel versions (see below) but I'm happy that I now no longer get bitten by it.

Thanks,
Pete

------------------------------------------------------------------------------------------------------------------
# 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
------------------------------------------------------------------------------------------------------------------

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   base     

other attached packages:
[1] IRanges_1.99.15     S4Vectors_0.0.7     BiocGenerics_0.11.2

loaded via a namespace (and not attached):
 [1] devtools_1.5   digest_0.6.4   evaluate_0.5.5 httr_0.3       memoise_0.2.1  RCurl_1.95-4.1
 [7] stats4_3.1.0   stringr_0.6.2  tools_3.1.0    whisker_0.3-2
------------------------------------------------------------------------------------------------------------------

On 28/05/2014, at 3:23 AM, Hervé Pagès <hpages@fhcrc.org> wrote:

> Hi Peter,
> 
> On 05/26/2014 04:37 PM, Peter Hickey wrote:
>> Thanks for the suggested work-around, Martin. In order to define the method on the group generic 'Ops' rather than '==' I will need to generalise .MTuples.compare to the 'Arith', 'Compare' and 'Logic' sub-groups listed in ?Ops, won't I? I'll try to implement the comparison methods for MTuples via the 'Ops' group generic but I want to first make sure that I'm not missing out on getting some of these "for free". The rest of this post might be tangential to the issue I first raised, but it also explains why I implemented '==' rather than on the group generic 'Ops'.
>> 
>> The MTuples class extends GRanges:
>> 
>> setClass('MTuples', representation(extraPos = "matrix"), contains = "GRanges", validity = .valid.MTuples)
>> 
>> I defined .MTuples.compare because while MTuples is based on GRanges, the GRanges 'compare' method is inappropriate for MTuples (see https://github.com/PeteHaitch/cometh/blob/8be01b8b37b6288db5493f53188a193a423ab69f/R/methods-MTuples-class.R if interested). Based on reading ?compare, I'd hoped that the binary "parallel" comparison operators (<=, ==, !=, >=, < and >) would work out-of-the-box. But I already found that I needed to include explicit method definitions for '<=' and '=='  because otherwise these (and the other binary comparison operators) would dispatch on the GRanges methods rather than the MTuples methods. This is because the GRanges '==' and '<=' methods are explicitly implemented as:
>> 
>> setMethod("==", signature(e1="GenomicRanges", e2="GenomicRanges"), function(e1, e2) { .GenomicRanges.compare(e1, e2) == 0L })
>> setMethod("<=", signature(e1="GenomicRanges", e2="GenomicRanges"), function(e1, e2) { .GenomicRanges.compare(e1, e2) <= 0L })
>> 
>> I don't understand why these explicit definitions are necessary; the 'compare' method for GRanges is already defined so why don't these work out-of-the-box, which is what I expected based on my reading of ?compare (specifically, point 1 in the Note sub-section).
> 
> You're right, they are not needed. I just removed them from
> GenomicRanges 1.17.17. See if that helps with the original problem
> you reported.
> 
> Cheers,
> H.
> 
> 
>> Because these are explicitly defined, and not simply defined via inheritance, I must also explicitly define '<=' and '==' methods for MTuples (although I do get '>=', '!=', '<' and '>' for free, which is great!). Unfortunately, as you can see, the MTuples '==' method breaks '==' for other signatures. Hope that wasn't too tangential.
>> 
>> Cheers,
>> Pete
>> 
>> 
>> On 27/05/2014, at 2:44 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote:
>> 
>>> On 05/25/2014 09:39 PM, Peter Hickey wrote:
>>>> 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?
>>>> 
>>> 
>>> I don't have an immediate answer. A work-around is to define the method on the group generic 'Ops' rather than '==', though maybe the generalization of .MTuples.compare to other members of the Ops family is not easy?
>>> 
>>> setMethod("Ops", c("MTuples", "MTuples"), function(e1, e2) TRUE)
>>> 
>>> Martin
>>> 
>>>> 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
>>>> 
>>>> 
>>>> ______________________________________________________________________
>>>> The information in this email is confidential and intend...{{dropped:8}}
>>>> 
>>>> _______________________________________________
>>>> Bioc-devel@r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>> 
>>> 
>>> 
>>> --
>>> Computational Biology / Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N.
>>> PO Box 19024 Seattle, WA 98109
>>> 
>>> Location: Arnold Building M1 B861
>>> Phone: (206) 667-2793
>> 
>> --------------------------------
>> 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
>> 
>> ______________________________________________________________________
>> The information in this email is confidential and intend...{{dropped:6}}
>> 
>> _______________________________________________
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> 
> 
> -- 
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
> E-mail: hpages@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319

--------------------------------
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


______________________________________________________________________
The information in this email is confidential and intend...{{dropped:8}}

