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

[Harris A. Jaffee]

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