[Bioc-devel] A question on IRanges package

[Martin Morgan]

On 04/03/2014 04:42 PM, Michael Lawrence wrote:
> I'll look at the code. As far as tracking line numbers, no, because the
> code is bundled into a package -- there are no files anymore. In principle,
> that could be improved, but as far as I know, it hasn't been. If you're

I think there's an option, set in .Rprofile or as an environment variable 
described in ?options,

   options(keep.source.pkgs=TRUE)

that annotates the source of installed packages with line numbers, e.g., after 
doing this and then installing GenomicRanges (on my own version)

 > library(GenomicRanges)
 > findOverlaps(GRanges(), GRanges(), type="o")
Error in match.arg(type) :
   'arg' should be one of "any", "start", "end", "within", "equal"
 > traceback()
5: stop(gettextf("'arg' should be one of %s", paste(dQuote(choices),
        collapse = ", ")), domain = NA)
4: match.arg(type) at findOverlaps-methods.R#63
3: .local(query, subject, maxgap, minoverlap, type, select, ...)
2: findOverlaps(GRanges(), GRanges(), type = "o")
1: findOverlaps(GRanges(), GRanges(), type = "o")


I'm not really sure which lines are annotated with source information.

Martin

> trying to figure out dispatch behavior, things like
> selectMethod(findOverlaps, c("GRanges, "GRanges")) and trace(findOverlaps,
> browser, sig=c("GRanges", "GRanges")) are your friend.
>
> Michael
>
>
> On Thu, Apr 3, 2014 at 4:22 PM, Yuan Luo <yuan.hypnos.luo at gmail.com> wrote:
>
>> At the moment I am using the package to tweak some design on interval tree
>> algorithm, and much of my efforts are hack. So does the code suggest to you
>> what I am doing wrong to get the match.arg failing error?
>> Also, when you were developing the package, how do you tell the traceback
>> to show line numbers and file names. My googling seems to suggest it's hard
>> to do so in R, but I figured gurus may see better.
>>
>> Best,
>> Yuan
>>
>>
>> On Thu, Apr 3, 2014 at 6:05 PM, Michael Lawrence <
>> lawrence.michael at gene.com> wrote:
>>
>>> It looks like the only hits this will filter out are cases where the
>>> start of the query (X) is equal to the end of the subject (Y), but it seems
>>> like the "o" operation is different -- it requires that X start before Y
>>> starts and end before Y ends.
>>>
>>> We could add these relations to IRanges, but maybe findOverlaps is not
>>> the right place. Instead, we could have an %o% operator, plus operators for
>>> the rest of the algebra. But maybe it would help to hear your use case.
>>>
>>> Michael
>>>
>>>
>>>
>>> On Thu, Apr 3, 2014 at 1:13 PM, Yuan Luo <yuan.hypnos.luo at gmail.com>wrote:
>>>
>>>> Hi Michael,
>>>> Thanks for your reply! I covered setGeneric as well, attached is the
>>>> modified code.
>>>> My change is pretty simple, I want to support the o relation in Allen's
>>>> Interval algebra (http://en.wikipedia.org/wiki/Allen's_interval_algebra)
>>>> So I added one more filter option
>>>>      } else if (type == "o") {
>>>>          m <- m[start(query)[m[,1L]] < end(subject)[m[,2L]], , drop=FALSE]
>>>>      }
>>>>
>>>>  From the stack trace, I suspect the method
>>>> definition setMethod("findOverlaps", c("RangesList", "IntervalForest"),
>>>> is not called upon, and the error happens before that, but since the
>>>> stack trace doesn't tell me in which file and which line each frame is, I
>>>> am a bit clueless. Is there anyway to reveal that information?
>>>>
>>>> Best,
>>>> Yuan
>>>>
>>>>
>>>> On Thu, Apr 3, 2014 at 3:57 PM, Michael Lawrence <
>>>> lawrence.michael at gene.com> wrote:
>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Thu, Apr 3, 2014 at 11:33 AM, Yuan Luo <yuan.hypnos.luo at gmail.com>wrote:
>>>>>
>>>>>> Hi All,
>>>>>> Sorry for possible spam, but I am trying to customize IRanges package
>>>>>> locally. For what I am doing, I introduced another option to type
>>>>>> parameters to the findOverlaps method. In the file
>>>>>> findOverlaps-methods.R,
>>>>>> I modified every instance of
>>>>>> type = c("any", "start", "end", "within", "equal"),
>>>>>> into
>>>>>> type = c("any", "start", "end", "within", "equal", "o"),
>>>>>>
>>>>>>
>>>>> I'm curious as to what "o" is supposed to do and wonder whether you
>>>>> really need to be making this modification. Tough to help without seeing
>>>>> any of your code. Probably, you just missed one, maybe the generic itself?
>>>>>
>>>>> Michael
>>>>>
>>>>>
>>>>>> But when I call
>>>>>> h = findOverlaps(varanges, rna_tree, type="o")
>>>>>>
>>>>>> I got the error
>>>>>>> h = findOverlaps(varanges, rna_tree, type="o")
>>>>>> Error in match.arg(type) :
>>>>>>    'arg' should be one of "any", "start", "end", "within", "equal"
>>>>>> with the following traceback information
>>>>>>> traceback()
>>>>>> 5: stop(gettextf("'arg' should be one of %s", paste(dQuote(choices),
>>>>>>         collapse = ", ")), domain = NA)
>>>>>> 4: match.arg(type)
>>>>>> 3: .local(query, subject, maxgap, minoverlap, type, select, ...)
>>>>>> 2: findOverlaps(varanges, rna_tree, type = "o")
>>>>>> 1: findOverlaps(varanges, rna_tree, type = "o")
>>>>>>
>>>>>> Is there any place that I missed where there is a default type vector
>>>>>> specification?
>>>>>> Also, how do you guys get R to display filename and line numbers for
>>>>>> the
>>>>>> methods in the traceback stack?
>>>>>>
>>>>>> Best,
>>>>>> Yuan
>>>>>>
>>>>>>          [[alternative HTML version deleted]]
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioc-devel at r-project.org mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>
> 	[[alternative HTML version deleted]]
>
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