There appears to be a bug in pairwiseAlignment() in which an error is thrown when when a substitution matrix is specified, but all strings are empty. Is this intended?

A minimal reproducible test is as follows:

> pairwiseAlignment(c(""), c(""), substitutionMatrix=nucleotideSubstitutionMatrix())

Error in buildLookupTable(alphabetToCodes[availableLetters], 0:(length(availableLetters) -  : 
  'vals' must be a vector of the length of 'keys'
> traceback()
7: stop("'vals' must be a vector of the length of 'keys'")
6: buildLookupTable(alphabetToCodes[availableLetters], 0:(length(availableLetters) - 
       1))
5: XStringSet.pairwiseAlignment(pattern = pattern, subject = subject, 
       type = type, substitutionMatrix = substitutionMatrix, gapOpening = gapOpening, 
       gapExtension = gapExtension, scoreOnly = scoreOnly)
4: mpi.XStringSet.pairwiseAlignment(pattern, subject, type = type, 
       substitutionMatrix = substitutionMatrix, gapOpening = gapOpening, 
       gapExtension = gapExtension, scoreOnly = scoreOnly)
3: .local(pattern, subject, ...)
2: pairwiseAlignment(c(""), c(""), substitutionMatrix = nucleotideSubstitutionMatrix())
1: pairwiseAlignment(c(""), c(""), substitutionMatrix = nucleotideSubstitutionMatrix())
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252    LC_MONETARY=English_Australia.1252 LC_NUMERIC=C                       LC_TIME=English_Australia.1252    

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

other attached packages:
 [1] StructuralVariantAnnotation_0.1 stringr_1.0.0                   DECIPHER_1.16.1                 RSQLite_1.0.0                   DBI_0.3.1                      
 [6] BiocInstaller_1.20.1            profvis_0.1.6                   lineprof_0.1.9001               ggplot2_2.1.0                   VariantAnnotation_1.16.4       
[11] Rsamtools_1.22.0                Biostrings_2.38.4               XVector_0.10.0                  SummarizedExperiment_1.0.2      Biobase_2.30.0                 
[16] GenomicRanges_1.22.4            GenomeInfoDb_1.6.3              IRanges_2.4.8                   S4Vectors_0.8.11                BiocGenerics_0.16.1            
[21] assertthat_0.1                  roxygen2_5.0.1                  testthat_0.11.0                 devtools_1.10.0                

loaded via a namespace (and not attached):
 [1] colorspace_1.2-6                  BSgenome.Hsapiens.UCSC.hg19_1.4.0 htmltools_0.3                     rtracklayer_1.30.3                yaml_2.1.13                      
 [6] GenomicFeatures_1.22.13           XML_3.98-1.4                      withr_1.0.1                       BiocParallel_1.4.3                lambda.r_1.1.7                   
[11] plyr_1.8.3                        zlibbioc_1.16.0                   munsell_0.4.3                     gtable_0.2.0                      futile.logger_1.4.1              
[16] htmlwidgets_0.6                   memoise_1.0.0                     labeling_0.3                      biomaRt_2.26.1                    curl_0.9.6                       
[21] AnnotationDbi_1.32.3              Rcpp_0.12.3                       scales_0.4.0                      BSgenome_1.38.0                   jsonlite_0.9.19                  
[26] digest_0.6.9                      stringi_1.0-1                     grid_3.2.2                        tools_3.2.2                       bitops_1.0-6                     
[31] magrittr_1.5                      RCurl_1.95-4.8                    futile.options_1.0.0              crayon_1.3.1                      MASS_7.3-45                      
[36] httr_1.1.0                        R6_2.1.2                          GenomicAlignments_1.6.3           git2r_0.14.0