[BioC] (no subject)

[Valerie Obenchain]

Hello,

What version of gwascat and rtracklayer are you using? Please provide 
the output of sessionInfo().

I think you have an old version of gwascat. The chr1 data you are trying 
to load doesn't exist in the package in release or devel and has been 
replaced by chr17 data.

The most current vignette for gwascat is located here,

http://bioconductor.org/packages/2.12/bioc/html/gwascat.html

Help with updating R and Bioconductor packages is here,

http://bioconductor.org/install/

Valerie


On 03/22/2013 06:40 AM, Deisy Gysi wrote:
> Hi I'm having some troubles in the importation of an archive .GFF3, i've
> read the Help and the vinhtes so many times, made so many things and still
> don't work!
>
>> gffpath = system.file("gff3/chr1_1_247249719.gff3", package="gwascat")
>> library(rtracklayer)
>> c1 = import(gffpath, asRangedData = FALSE)
> Erro em .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") :
>    solving row 975: range cannot be determined from the supplied arguments
> (too many NAs)
>
>
> Here is part of the database...
> I cannot found the error!!
>
> The first line is the line 975, where R says that there is "too many NAs":
>
> chr1    UCSC    cytoband    7100000    9200000    .    +    .
> Parent=Sequence:Cytoband:1p36.23;Alias=p36.23;Alias=1p36.23;Stain=gpos25
> chr1    UCSC    chromosome    5300000    7100000    .    +    .
> ID=Sequence:Cytoband:1p36.31;Alias=p36.31;Alias=1p36.31;Stain=gneg
> chr1    UCSC    cytoband    5300000    7100000    .    +    .
> Parent=Sequence:Cytoband:1p36.31;Alias=p36.31;Alias=1p36.31;Stain=gneg
> chr1    UCSC    chromosome    2300000    5300000    .    +    .
> ID=Sequence:Cytoband:1p36.32;Alias=p36.32;Alias=1p36.32;Stain=gpos25
> chr1    UCSC    cytoband    2300000    5300000    .    +    .
> Parent=Sequence:Cytoband:1p36.32;Alias=p36.32;Alias=1p36.32;Stain=gpos25
> chr1    UCSC    chromosome    .    2300000    .    +    .
> ID=Sequence:Cytoband:1p36.33;Alias=p36.33;Alias=1p36.33;Stain=gneg
> chr1    UCSC    cytoband    .    2300000    .    +    .
> Parent=Sequence:Cytoband:1p36.33;Alias=p36.33;Alias=1p36.33;Stain=gneg
>
>
> Thanks in advance for help!
>
>
>
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