I am using bumphunters' matchGenes function to annotate some genomic data, and am getting this error when some regions cannot be mapped with `nearest`

Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) : 
  subscript contains NAs or out-of-bounds indices

The code I am running is below:

>library(GenomicFeatures)

>library(bumphunter)

>dmrs <- read.csv(path/to/file)

>library(TxDb.Hsapiens.UCSC.hg19.knownGene)

>txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene

>annotations <- annotateTranscripts(txdb)

>matched <- matchGenes(dmrs, annotations)

Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) : 
  subscript contains NAs or out-of-bounds indices
9: stop("subscript contains NAs or out-of-bounds indices")
8: NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append)
7: NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append)
6: normalizeSingleBracketSubscript(i, x)
5: extractROWS(x, i)
4: extractROWS(x, i)
3: subject[i, ]
2: subject[i, ]
1: matchGenes(dmrs, annotations)

The error only occurs when `nearest` fails to map some regions

> map <- nearest(makeGRangesFromDataFrame(dmrs), annotations)

> which(is.na(map))[1:10]
[1]  729 1379 1624 1927 1973 1986 1987 2031 2099 2111

> a <- matchGenes(dmrs[700:725,], annotations)

> b <- matchGenes(dmrs[725:730,], annotations)
Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :
  subscript contains NAs or out-of-bounds indices
9: stop("subscript contains NAs or out-of-bounds indices")
8: NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append)
7: NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append)
6: normalizeSingleBracketSubscript(i, x)
5: extractROWS(x, i)
4: extractROWS(x, i)
3: subject[i, ]
2: subject[i, ]
1: matchGenes(dmrs[725:730, ], annotations)

The error disappears when the first line of the for loop in matchGenes is changed from

 i <- map[ind][j]

to 

i <- map[j] 

dmrs is a dataframe of regions obtained from bumphunterEngine. The first line is

> dmrs[1,]
    chr    start      end      value     area cluster indexStart indexEnd  L clusterL      p.value fwer  p.valueArea fwerArea
1 chr19 48945971 48947362 -0.5952619 19.64364   30722     467311   467396 86       98 1.804523e-06  0.1 1.804523e-06      0.1

(The relevant part of) my session info is:

R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.8 (Final)

other attached packages:
 [1] org.Hs.eg.db_3.2.3                      RSQLite_1.0.0                           DBI_0.3.1                              
 [4] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 bumphunter_1.10.0                       locfit_1.5-9.1                         
 [7] iterators_1.0.8                         foreach_1.4.3                           GenomicFeatures_1.22.13                
[10] AnnotationDbi_1.32.3                    Biobase_2.30.0                          GenomicRanges_1.22.4                   
[13] GenomeInfoDb_1.6.3                      IRanges_2.4.8                           S4Vectors_0.8.11                       
[16] BiocGenerics_0.16.1