There's a problem with the export function in the rtracklayer package, which seems to be influenced by global definitions of con:

> require(rtracklayer)
> export(con="whee.bed", GRanges(1, IRanges(1, 1), score=10)) # works fine.
> con <- rbind(1:5)
> export(con="whee.bed", GRanges(1, IRanges(1, 1), score=10)) # no longer works.
Error in UseMethod("close") :
  no applicable method for 'close' applied to an object of class "c('matrix', 'integer', 'numeric')"

Presumably, this shouldn't be happening.

> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: i686-pc-linux-gnu (32-bit)
Running under: Ubuntu 14.04.3 LTS

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
 [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8   
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base     

other attached packages:
[1] rtracklayer_1.28.8   GenomicRanges_1.20.5 GenomeInfoDb_1.4.2  
[4] IRanges_2.2.7        S4Vectors_0.6.3      BiocGenerics_0.14.0

loaded via a namespace (and not attached):
 [1] XML_3.98-1.3            Rsamtools_1.20.4        Biostrings_2.36.3      
 [4] bitops_1.0-6            GenomicAlignments_1.4.1 futile.options_1.0.0   
 [7] zlibbioc_1.14.0         XVector_0.8.0           futile.logger_1.4.1    
[10] lambda.r_1.1.7          BiocParallel_1.2.20     tools_3.2.1            
[13] RCurl_1.95-4.7        

Yea, this was a bug. Fixed in (upcoming) 1.28.9.