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 <[email protected]> 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 <[email protected]> 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
>>>>
>>>> [email protected]
>>>> http://www.wehi.edu.au
>>>>
>>>>
>>>> ______________________________________________________________________
>>>> The information in this email is confidential and intend...{{dropped:8}}
>>>>
>>>> _______________________________________________
>>>> [email protected] 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
>>
>> [email protected]
>> http://www.wehi.edu.au
>>
>> ______________________________________________________________________
>> The information in this email is confidential and intend...{{dropped:6}}
>>
>> _______________________________________________
>> [email protected] 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: [email protected]
> 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
[email protected]
http://www.wehi.edu.au
______________________________________________________________________
The information in this email is confidential and intend...{{dropped:8}}
_______________________________________________
[email protected] mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
