I am having a little trouble with the install on macosx. hints?
Creating a generic function for 'split<-' from package 'base' in package
'IRanges'
Creating a generic function for 'aggregate' from package 'stats' in package
'IRanges'
Error in setMethod("isEmpty", "List", function(x) all(elementLengths(x) ==
:
no existing definition for function 'isEmpty'
Error : unable to load R code in package 'IRanges'
ERROR: lazy loading failed for package 'IRanges'
* removing
'/Users/stvjc/ExternalSoft/R-3-0-patched-dist/R.framework/Versions/3.0/Resources/library/IRanges'
* restoring previous
'/Users/stvjc/ExternalSoft/R-3-0-patched-dist/R.framework/Versions/3.0/Resources/library/IRanges'
Error: Command failed (1)
> sessionInfo()
R version 3.0.0 Patched (2013-04-15 r62585)
Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit)
locale:
[1]
en_US.US-ASCII/en_US.US-ASCII/en_US.US-ASCII/C/en_US.US-ASCII/en_US.US-ASCII
attached base packages:
[1] stats graphics grDevices datasets utils tools methods
[8] base
other attached packages:
[1] devtools_1.2 BiocInstaller_1.11.1 weaver_1.27.0
[4] codetools_0.2-8 digest_0.6.3
loaded via a namespace (and not attached):
[1] evaluate_0.4.3 httr_0.2 memoise_0.1 parallel_3.0.0
RCurl_1.95-4.1
[6] stringr_0.6.2 whisker_0.3-2
On Wed, May 29, 2013 at 5:12 PM, Hector Corrada Bravo <hcorr...@gmail.com>wrote:
> That's great! There's some cleaning up to do there how should we do this
> post-merge?
>
> On Wed, May 29, 2013 at 4:19 PM, Valerie Obenchain <voben...@fhcrc.org>
> wrote:
>
> > Hi Hector, Michael,
> > This sounds great. Bringing these into svn is fine with us. Michael, do
> > you want to merge these in?
> > Val
> > On 05/24/2013 07:30 AM, Hector Corrada Bravo wrote:
> >> Thanks Michael,
> >>
> >> It has made significant difference for our visualization project. I
> would
> >> like to merge this into svn asap. Can I get a ruling from the rest of
> the
> >> core group? Please let me know if/when/how to proceed.
> >>
> >> Cheers,
> >> Hector
> >>
> >>
> >> On Wed, May 22, 2013 at 1:00 PM, Michael Lawrence <
> lawrence.mich...@gene.com
> >>> wrote:
> >>
> >>> *Added bioc-devel; hope you don't mind*
> >>>
> >>> Hector,
> >>>
> >>> This is great stuff. The overall design is on the right track. As you
> >>> said, there's a bit of cleaning to do, but I think we should merge this
> >>> into svn and work the rest out from there. This will really benefit
> >>> performance, especially for visualization. Of course, I can't speak
> for the
> >>> others.
> >>>
> >>> Michael
> >>>
> >>>
> >>>
> >>> On Tue, May 21, 2013 at 11:52 AM, Hector Corrada Bravo <
> >>> hcorr...@umiacs.umd.edu> wrote:
> >>>
> >>>> Since the semester is over I finally finished this...
> >>>>
> >>>> Recall that I wanted a persistent set of IntervalTrees for GRanges
> >>>> objects for repeated querying. (The application is this:
> >>>> http://epiviz.cbcb.umd.edu/help/?page_id=62 which I hope to get out
> >>>> soon). Folding this into IRanges and GenomicRanges would make our life
> >>>> easier come installation time.
> >>>>
> >>>> I've implemented class 'IntervalForest' within IRanges following
> >>>> Michael's suggestion of storing this as an array of rbTree on the C
> side.
> >>>> I've implemented findOverlaps that operates with this array in C.
> There is
> >>>> code duplication in IntervalTree.c that could be reduced but that's
> if this
> >>>> makes it into the package.
> >>>>
> >>>> I've also implemented a 'GIntervalTree' that uses 'IntervalForest'
> >>>> underneath. findOverlaps-GenomicRanges-GIntervalTree-method is
> implemented
> >>>> for this class. I didn't touch the existing
> >>>> findOverlaps-GenomicRanges-GenomicRanges-method.
> >>>>
> >>>> You can pull these here:
> >>>> http://github.com/hcorrada/IRanges
> >>>> http://github.com/hcorrada/GenomicRanges
> >>>>
> >>>> These track the devel branch of the two packages. Let me know the best
> >>>> way to propagate to svn if you guys want this. It needs
> documentation, but
> >>>> I'll add that once implementation is settled.
> >>>>
> >>>> Kasper, I'm not sure if this would help with the 'too many seqlevels'
> >>>> problem but I'd be curious to know if you try it.
> >>>>
> >>>> Cheers,
> >>>> Hector
> >>>>
> >>>
> >>>
> >>
> >> [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> Bioc-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> [[alternative HTML version deleted]]
>
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