If you want to step into the environments where the errors are happening
you want options(error=recover) not traceback. In that case, you can step
into each of the frames.
The .local is actually the body of the method being called though, nothing
to do with an environment.
~G
On Thu, Apr 3, 2014 at 6:17 PM, Yuan Luo <yuan.hypnos....@gmail.com> wrote:
> A side question, in the frame 3, what does .local mean? local environment?
> like if I go into frame 3, I'd be able to print out their values?
>
>
> On Thu, Apr 3, 2014 at 9:10 PM, Yuan Luo <yuan.hypnos....@gmail.com>
> wrote:
>
> > I think that line at 4 points to the generic definition, at least on my
> > machine (and keep source works, thanks!).
> >
> > Just found what was the culprit, there is a wrapper in
> > findOverlaps-GIntervalTree-methods.R#12. After updating that, it works.
> > > traceback()
> > 5: stop(gettextf("'arg' should be one of %s", paste(dQuote(choices),
> > collapse = ", ")), domain = NA)
> > 4: match.arg(type) at findOverlaps-GIntervalTree-methods.R#12
> > 3: .local(query, subject, maxgap, minoverlap, type, select, ...)
> > 2: findOverlaps(varanges, rna_tree, type = "o") at
> > findOverlaps-methods.R#14
> > 1: findOverlaps(varanges, rna_tree, type = "o")
> >
> > Again, thank you both!
> >
> > Best,
> > Yuan
> >
> >
> >
> > On Thu, Apr 3, 2014 at 7:49 PM, Martin Morgan <mtmor...@fhcrc.org>
> wrote:
> >
> >> 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....@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.mich...@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....@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.mich...@gene.com> wrote:
> >>>>>>
> >>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> On Thu, Apr 3, 2014 at 11:33 AM, Yuan Luo <
> yuan.hypnos....@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@r-project.org mailing list
> >>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>>>>>>
> >>>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>
> >>>>
> >>> [[alternative HTML version deleted]]
> >>>
> >>> _______________________________________________
> >>> 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
> >>
> >
> >
>
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>
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