Hi Valerie (and others),

while installing the new GenomicRanges from SVN, I get this error:

GenomicRanges.so: undefined symbol: IntAE_set_nelt

I installed the newest version of IRanges, where this error appears to be
coming from.  Is this a common problem?  If so, what's the fix?
It has happened before, I'm not sure whether the reason is instability in
SVN or something with my install.

 Thanks,

--t


On Wed, Apr 11, 2012 at 11:44 AM, Valerie Obenchain <vobencha@fhcrc.org>wrote:

> Hi Malcom,
>
> For distanceToNearest() I started with the ranges method in IRanges. Along
> the way I did find that distance,GenomicRanges,**GenomicRanges was not
> handling the situation of '*','-' and '*','+' strand pairs (simply
> returning NA). Now those strand combinations are considered compatible just
> as '-','-' and '+','+' are.
>
> Let me know if you run into problems with the method or have other
> suggestions.
>
> Take care,
> Valerie
>
>
> On 04/11/2012 09:46 AM, Cook, Malcolm wrote:
>
>> thanks Valerie,
>>
>> Did you happen to vet the logic of my implementation, or did you just
>> code it lower level from first principals?
>>
>> Cheers,
>>
>> ~Malcolm
>>
>>  -----Original Message-----
>>> From: Valerie Obenchain [mailto:vobencha@fhcrc.org]
>>> Sent: Wednesday, April 11, 2012 11:13 AM
>>> To: Janet Young
>>> Cc: Cook, Malcolm; bioconductor@r-project.org
>>> Subject: Re: [BioC] distanceToNearest for GRanges?
>>>
>>> This has been added to GenomicRanges 1.9.4. You will also need IRanges
>>> 1.15.2.
>>>
>>> Valerie
>>>
>>>
>>> On 03/27/2012 10:36 AM, Janet Young wrote:
>>>
>>>> Hi,
>>>>
>>>> thank you both - very helpful.
>>>>
>>>> Janet
>>>>
>>>>
>>>>
>>>> On Mar 27, 2012, at 6:35 AM, Valerie Obenchain wrote:
>>>>
>>>>  Hi Janet, Malcom,
>>>>>
>>>>> Yes, we can add distanceToNearest for GRanges. This will probably
>>>>>
>>>> happen after the release (i.e., next week). I'll post back here when
>>> it's
>>> complete.
>>>
>>>> Valerie
>>>>>
>>>>>
>>>>> On 03/26/12 16:26, Cook, Malcolm wrote:
>>>>>
>>>>>> Janet,
>>>>>>
>>>>>> In the mean time....
>>>>>>
>>>>>> distanceToNearest.GRanges<- function
>>>>>>
>>>>> (query,subject=query,...,.AS=**DataFrame) {
>>>
>>>>   ## PURPOSE: an implementation of distanceToNearest for GRanges in
>>>>>>   ## terms of 'nearest' and 'distance' whose return value is shaped
>>>>>>   ## like that of IRange's 'nearest', by default, but you can ask for
>>>>>>   ## the result .AS=data.table or .AS=data.frame if you prefer.
>>>>>>    if(missing(subject)) {
>>>>>>      nearestSubjectIndex<-nearest(**query,...)
>>>>>>    } else {
>>>>>>      nearestSubjectIndex<-nearest(**query,subject,...)
>>>>>>    }
>>>>>>    queryHasNearest<-! is.na(nearestSubjectIndex)
>>>>>>    queryIndex<-which(**queryHasNearest)
>>>>>>    queryHavingNearest<-query[**queryIndex]
>>>>>>    nearestSubjectIndex<-**nearestSubjectIndex[**queryIndex]
>>>>>>    nearestSubject<-subject[**nearestSubjectIndex]
>>>>>>    d<-distance(**queryHavingNearest,**nearestSubject)
>>>>>>    .AS(query=queryIndex
>>>>>>               ,subject=nearestSubjectIndex
>>>>>>               ,distance=d)
>>>>>> }
>>>>>>
>>>>>> You've asked so many questions in this forum whose answer I made use
>>>>>>
>>>>> of that I must owe you this tidbit....
>>>
>>>> Lurkers, and fellow travelers, I welcome corrections and stylistic
>>>>>>
>>>>> suggestions.
>>>
>>>> Cheers,
>>>>>>
>>>>>> Malcolm Cook
>>>>>>
>>>>>>
>>>>>> ______________________________**__________
>>>>>> From: bioconductor-bounces@r-**project.org<bioconductor-bounces@r-project.org>[bioconductor-bounces@r-
>>>>>>
>>>>> project.org] On Behalf Of Janet Young [jayoung@fhcrc.org]
>>>
>>>> Sent: Monday, March 26, 2012 4:42 PM
>>>>>> To: bioconductor@r-project.org
>>>>>> Subject: [BioC] distanceToNearest for GRanges?
>>>>>>
>>>>>> Hi there,
>>>>>>
>>>>>> Any plans to implement distanceToNearest for GRanges objects?   That
>>>>>>
>>>>> would be really useful for me.
>>>
>>>> thanks,
>>>>>>
>>>>>> Janet
>>>>>>
>>>>>>
>>>>>> ------------------------------**------------------------------**
>>>>>> -------
>>>>>>
>>>>>> Dr. Janet Young
>>>>>>
>>>>>> Tapscott and Malik labs
>>>>>>
>>>>>> Fred Hutchinson Cancer Research Center
>>>>>> 1100 Fairview Avenue N., C3-168,
>>>>>> P.O. Box 19024, Seattle, WA 98109-1024, USA.
>>>>>>
>>>>>> tel: (206) 667 1471 fax: (206) 667 6524
>>>>>> email: jayoung  ...at...  fhcrc.org
>>>>>>
>>>>>>
>>>>>> ------------------------------**------------------------------**
>>>>>> -------
>>>>>>
>>>>>> ______________________________**_________________
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>>>>>> Search the archives:
>>>>>>
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>>>
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>>>>>>
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>>>
>>
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-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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