[BioC] VariantAnnotation development branch issue

[Steve Lianoglou]

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?

-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