In the function GetReadCountFromBAM, sl corresponds to the lengths of the chromosomes. At some point there is a line:

sl <- as.integer(unique(sl))

So if two or more chromosomes have the same length this vector will be shorter than the sn vector which holds the names of the chromosomes. Although uncommon, it happens if the reference genome contains the ERCC spike-ins for instance.

Thanks

sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Buildroot 2014.02

Matrix products: default
BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.9.so

locale:
[1] C

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

other attached packages:
[1] Rsamtools_2.4.0      Biostrings_2.56.0    XVector_0.28.0      
[4] cn.mops_1.34.0       GenomicRanges_1.40.0 GenomeInfoDb_1.24.0 
[7] IRanges_2.22.1       S4Vectors_0.26.0     BiocGenerics_0.34.0 

loaded via a namespace (and not attached):
 [1] crayon_1.3.4           bitops_1.0-6           exomeCopy_1.34.0      
 [4] zlibbioc_1.34.0        BiocParallel_1.22.0    tools_4.0.0           
 [7] Biobase_2.48.0         RCurl_1.98-1.2         compiler_4.0.0        
[10] GenomeInfoDbData_1.2.3