[Bioc-devel] setdiff error (GenomicRanges)

[Michael Stadler]

Hi Herve,

Yes, same here. I can't reproduce it anymore using the most recent
package version.

Regards,
Michael



On 03.09.2013 23:06, Hervé Pagès wrote:
> Hi Michael,
> 
> I can't reproduce this:
> 
>   > library(GenomicRanges)
>   > chrs <- c(chr1=20, chr2=20)
>   > grA <- GRanges("chr1", IRanges(1,10), strand="*", seqlengths=chrs)
>   > grB <- GRanges("chr2", IRanges(11,15), strand="*", seqlengths=chrs)
>   > setdiff(grA, grB)
>   GRanges with 1 range and 0 metadata columns:
>         seqnames    ranges strand
>            <Rle> <IRanges>  <Rle>
>     [1]     chr1   [1, 10]      *
>     ---
>     seqlengths:
>      chr1 chr2
>        20   20
> 
> Some core packages have been updated since your original post so that
> could explain why the problem is gone now. See my session info below.
> 
> Cheers,
> H.
> 
> 
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
> 
> other attached packages:
> [1] GenomicRanges_1.13.39 XVector_0.1.0         IRanges_1.19.28
> [4] BiocGenerics_0.7.4
> 
> loaded via a namespace (and not attached):
> [1] stats4_3.0.1
> 
> 
> On 08/29/2013 08:48 AM, Michael Stadler wrote:
>> Dear masters of genomic ranges,
>>
>> Since a few days, I am getting an error in Bioc 2.13 when comparing two
>> GRanges objects by setdiff():
>>
>> chrs <- c(chr1=20, chr2=20)
>> grA <- GRanges("chr1", IRanges(1,10), strand="*", seqlengths=chrs)
>> grB <- GRanges("chr2", IRanges(11,15), strand="*", seqlengths=chrs)
>> setdiff(grA, grB)
>>
>> Warning messages:
>> 1: In ans[] <- x :
>>    number of items to replace is not a multiple of replacement length
>> 2: In ans[] <- x :
>>    number of items to replace is not a multiple of replacement length
>> Error in gaps(union(gaps(x, end = seqlengths), y), end = seqlengths) :
>>    error in evaluating the argument 'x' in selecting a method for
>> function 'gaps': Error in union(gaps(x, end = seqlengths), y) :
>>    error in evaluating the argument 'x' in selecting a method for
>> function 'union': Error in Rle(strand(listNameMatrix[2L, ]), k) :
>>    error in evaluating the argument 'values' in selecting a method for
>> function 'Rle': Error in .local(x, ...) : strand values must be in '+'
>> '-' '*'
>>
>> This is in:
>> sessionInfo()
>> R version 3.0.1 (2013-05-16)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>> [1] C
>>
>> attached base packages:
>> [1] parallel  stats     graphics  grDevices utils     datasets  methods
>> [8] base
>>
>> other attached packages:
>> [1] GenomicRanges_1.13.38 XVector_0.1.0         IRanges_1.19.27
>> [4] BiocGenerics_0.7.4    RColorBrewer_1.0-5
>>
>> loaded via a namespace (and not attached):
>> [1] stats4_3.0.1
>>
>>
>> The same code runs fine for Bioc 2.12:
>> chrs <- c(chr1=20, chr2=20)
>> grA <- GRanges("chr1", IRanges(1,10), strand="*", seqlengths=chrs)
>> grB <- GRanges("chr2", IRanges(11,15), strand="*", seqlengths=chrs)
>> setdiff(grA, grB)
>>
>> GRanges with 1 range and 0 metadata columns:
>>        seqnames    ranges strand
>>           <Rle> <IRanges>  <Rle>
>>    [1]     chr1   [1, 10]      *
>>    ---
>>    seqlengths:
>>     chr1 chr2
>>       20   20
>>
>> for:
>> sessionInfo()
>> R version 3.0.1 (2013-05-16)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>> [1] C
>>
>> attached base packages:
>> [1] parallel  stats     graphics  grDevices utils     datasets  methods
>> [8] base
>>
>> other attached packages:
>> [1] GenomicRanges_1.12.4 IRanges_1.18.2       BiocGenerics_0.7.0
>> [4] RColorBrewer_1.0-5
>>
>> loaded via a namespace (and not attached):
>> [1] stats4_3.0.1
>>
>>
>> Would anybody have an idea what could be wrong?
>>
>> Kind regards,
>> Michael
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
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>>
>