Vince,
I updated to current IRanges devel so install should work again.
Hector
On Wed, May 29, 2013 at 5:17 PM, Vincent Carey
<st...@channing.harvard.edu>wrote:
> 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]]
>> >>
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>> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >>
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>
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