Ok, I will try it out and see how things go. Thanks for the clarification.
On Feb 21, 2013 6:37 PM, "Martin Morgan" <mtmorgan@fhcrc.org> wrote:

> On 02/21/2013 04:43 PM, Ryan C. Thompson wrote:
>
>> Ok, so it looks like this splice graph functionality is currently in
>> limbo. If I wanted to use it right now with the current release of BioC,
>> could I just use the old spliceGraph function from the previous
>> GenomicFeatures version? I figure I could get it working by taking the R
>> files from the old version, prefixing a few things with
>> "GenomicFeatures::", and then sourcing the files.
>>
>
> it would be better to download and install from svn, for your version of
> R, e.g., for Bioc 2.11 / R-2.15.2
>
>  svn co https://hedgehog.fhcrc.org/**bioconductor/branches/RELEASE_**
> 2_11/madman/Rpacks/SpliceGraph<https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/SpliceGraph>
>   R CMD INSTALL SpliceGraph
>
> Martin
>
>
>>
>> On 02/21/2013 03:05 PM, Tim Triche, Jr. wrote:
>>
>>> yes, that
>>>
>>>
>>> On Thu, Feb 21, 2013 at 2:55 PM, Steve Lianoglou
>>> <mailinglist.honeypot@gmail.**com <mailinglist.honeypot@gmail.com>
>>> <mailto:mailinglist.honeypot@**gmail.com<mailinglist.honeypot@gmail.com>>>
>>> wrote:
>>>
>>>      On Thu, Feb 21, 2013 at 5:42 PM, Tim Triche, Jr.
>>>      <tim.triche@gmail.com <mailto:tim.triche@gmail.com>> wrote:
>>>      > the SpliceGraph and SpliceGrapher packages took over that
>>>      functionality
>>>
>>>      Which are presumably only available via svn at the moment?
>>>
>>>      I see that SpliceGraph is in svn and not on the devel package list
>>> --
>>>      I can't find SplieGrapher anywhere, tho.
>>>
>>>      Maybe you mean SplicingGraphs?
>>>
>>>      -steve
>>>
>>>      --
>>>      Steve Lianoglou
>>>      Graduate Student: Computational Systems Biology
>>>       | Memorial Sloan-Kettering Cancer Center
>>>       | Weill Medical College of Cornell University
>>>      Contact Info: http://cbio.mskcc.org/~lianos/**contact<http://cbio.mskcc.org/~lianos/contact>
>>>      <http://cbio.mskcc.org/%**7Elianos/contact<http://cbio.mskcc.org/%7Elianos/contact>
>>> >
>>>
>>>
>>>
>>>
>>> --
>>> /A model is a lie that helps you see the truth./
>>> /
>>> /
>>> Howard Skipper
>>> <http://cancerres.**aacrjournals.org/content/31/9/**1173.full.pdf<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>
>>> >
>>>
>>
>>
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