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
