[BioC] VariantAnnotation development branch issue

[Hamid Bolouri]

Thanks very much for the quick diagnosis & fix Martin. Will do.

Hamid

----- Original Message -----
From: "Martin Morgan" <mtmorgan at fhcrc.org>
To: "Steve Lianoglou" <mailinglist.honeypot at gmail.com>
Cc: "Hamid Bolouri" <hbolouri at fhcrc.org>, bioconductor at r-project.org
Sent: Monday, November 5, 2012 8:30:13 PM
Subject: Re: [BioC] VariantAnnotation development branch issue

On 11/05/2012 07:00 PM, Steve Lianoglou wrote:
> Hi,
>
> On Mon, Nov 5, 2012 at 9:42 PM, Hamid Bolouri <hbolouri at fhcrc.org> wrote:
>> hi : I am finding that the development version of R with VariantAnnotation_1.5.7 runs fine on one PC but not on another with very similar hardware and configuration:
>>
>>> fl <- system.file("extdata", "example.gtf.gz", package="Rsamtools",
>> +                   mustWork=TRUE)
>>> tbx <- TabixFile(fl)
>> Error in eval(expr, envir, enclos) :
>>    no slot of name "generator" for this object of class "refObjectGenerator"
>>>
>>> traceback()
>> 7: eval(expr, envir, enclos)
>> 6: eval(expr, p)
>> 5: eval.parent(substitute(x at generator$name))
>> 4: g$new
>> 3: g$new
>> 2: .RsamtoolsFile(.TabixFile, file, index, yieldSize = yieldSize,
>>         ...)
>> 1: TabixFile(fl)
>>>
>>> sessionInfo()
>> R Under development (unstable) (2012-11-01 r61067)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> Could it be related to this issue?
>
> https://stat.ethz.ch/pipermail/r-devel/2012-October/065109.html
>
> Perhaps the machine that has this working is using a version of
> R-devel from svn that's pre r61035?

Re-installing Rsamtools (and other packages with reference classes) seems to do 
the trick, in a new session

   source("http://bioconductor.org/biocLite.R')
   biocLite('Rsamtools')

and then

   library(Rsamtools)
   example(TabixFile)

Martin

>
> -steve
>


-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

-- 
http://labs.fhcrc.org/bolouri