[BioC] GenomicRanges:::.filterMatchMatrix blows up nearest()

[Valerie Obenchain]

Thanks for the bug report.  Now fixed in 1.11.6 devel and 1.10.3 in release.

Valerie



On 10/25/2012 12:09 PM, Harris A. Jaffee wrote:
> The statement
>
> 	m[, 1L] <- map[m[, 1L]]
>
> seems pretty likely to cause
>
> 	Error in map[m[, 1L]] : object of type 'closure' is not subsettable
>
> This occurs with nearest(select="all") when there is no overlap.
>
> Slightly sanitized real-life example:
>
>> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
> Loading required package: GenomicFeatures
> Loading required package: BiocGenerics
> ...
>> TT <- transcriptsBy(TxDb.Hsapiens.UCSC.hg19.knownGene, by="gene")
>> tt <- TT[[1]]
>> tt
> GRanges with 2 ranges and 2 metadata columns:
>        seqnames               ranges strand |     tx_id     tx_name
>           <Rle>            <IRanges>  <Rle> | <integer> <character>
>    [1]    chr19 [58858172, 58864865]      - |     68796  uc002qsd.4
>    [2]    chr19 [58859832, 58874214]      - |     68797  uc002qsf.2
>    ---
>    seqlengths:
>                      chr1                  chr2 ...        chrUn_gl000249
>                 249250621             243199373 ...                 38502
>
>> q <- GRanges(IRanges(1,1), seqnames="chr19", strand="*")
>> nearest(q, tt)
> [1] 1
>> nearest(q, tt, select="all")
> Error in map[m[, 1L]] : object of type 'closure' is not subsettable
>
>> sessionInfo()
> R version 2.15.1 Patched (2012-07-01 r59713)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
>   [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
>   [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
>   [7] LC_PAPER=C                     LC_NAME=C
>   [9] LC_ADDRESS=C                   LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base
>
> other attached packages:
> [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0
> [2] GenomicFeatures_1.10.0
> [3] AnnotationDbi_1.20.2
> [4] Biobase_2.18.0
> [5] GenomicRanges_1.10.2
> [6] IRanges_1.16.3
> [7] BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
>   [1] biomaRt_2.14.0     Biostrings_2.26.2  bitops_1.0-4.1     BSgenome_1.26.1
>   [5] DBI_0.2-5          parallel_2.15.1    RCurl_1.95-1.1     Rsamtools_1.10.1
>   [9] RSQLite_0.11.2     rtracklayer_1.18.0 stats4_2.15.1      tools_2.15.1
> [13] XML_3.95-0.1       zlibbioc_1.4.0
>
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