Hi Vince (and everyone else),
We put up a preliminary version of the visualization stuff we've been
working on. Please go to http://github.com/epiviz/epivizr. Make sure to
checkout the introductory vignette. Comments and suggestions welcomed.
And now that that's done... Can we proceed on merging the GIntervalTree
stuff to svn?
Thanks!
Hector
On Thu, May 30, 2013 at 8:05 AM, Hector Corrada Bravo <hcorr...@gmail.com>wrote:
> Good. We're putting epivizr up tomorrow, I'll let you know.
> Hector
>
>
> On Thu, May 30, 2013 at 7:53 AM, Vincent Carey <st...@channing.harvard.edu
> > wrote:
>
>> 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
>>>>>
>>>>
>>>>
>>>
>>
>
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
