I ran the following example from page 6 of the PairwiseAlignment documentation (https://bioconductor.org/packages/release/bioc/vignettes/Biostrings/inst/doc/PairwiseAlignments.pdf):

> submat <- matrix(-1, nrow = 26, ncol = 26, dimnames = list(letters, letters))
> diag(submat) <- 0
> psa2 <- pairwiseAlignment(pattern = c("succeed", "precede"), subject = "supersede", substitutionMatrix = submat, gapOpening = 0, gapExtension = 1)
> score(psa2)
Error in UseMethod("score") :
  no applicable method for 'score' applied to an object of class "c('PairwiseAlignmentsSingleSubject', 'PairwiseAlignments')"
> traceback()
1: score(psa2)

The expected output according to the manual is:

> score(psa2) [1] -5 -5

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] seqinr_3.1-3        ade4_1.7-4          ggplot2_2.1.0       Biostrings_2.38.4  
[5] XVector_0.10.0      IRanges_2.4.8       S4Vectors_0.8.11    BiocGenerics_0.16.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.4      grid_3.2.2       plyr_1.8.3       gtable_0.2.0     scales_0.4.0    
 [6] zlibbioc_1.16.0  labeling_0.3     tools_3.2.2      munsell_0.4.3    colorspace_1.2-6

I've just downloaded this package using:

source("https://bioconductor.org/biocLite.R")
biocLite("Biostrings")

Thank you!

Hello,

The attached package seqinr also has score() which is masks the Biostrings score().  If you change 

score(psa2)

to 

Biostrings::score(psa2)

you should get the result expected.  Another solution would be to not load seqinr in the same session as Biostrings.