yes, the infrastructure is installing now. i'd love to look at epivizr too
but am hitting another snag.
> library(devtools)
> install_github("epivizr", user="hcorrada", subdir="pkg")
Installing github repo(s) epivizr/master from hcorrada
Installing epivizr.zip from
https://github.com/hcorrada/epivizr/archive/master.zip
Error: client error: (406) Not Acceptable
Enter a frame number, or 0 to exit
1: install_github("epivizr", user = "hcorrada", subdir = "pkg")
2: install_url(url, name = paste(repo, ".zip", sep = ""), subdir = subdir,
con
3: mapply(install_url_single, url, name, MoreArgs = list(subdir = subdir,
conf
4: (function (url, name = NULL, subdir = NULL, config = list(), ...)
{
if (
5: stop_for_status(request)
On Thu, May 30, 2013 at 6:49 AM, Hector Corrada Bravo <hcorr...@gmail.com>wrote:
> 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]]
>>> >>
>>> >> _______________________________________________
>>> >> 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
>>>
>>
>>
>
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