> library(msa)
> library(Biostrings)
> 
> x="ATGC"
> y="ATGA"
> z=msa(c(x,y), type="dna")
use default substitution matrix
Error in .Primitive("c")(<s4 object="" of="" class="" "iranges"="">) : 
  could not find symbol "recursive" in environment of the generic function
> devtools::session_info()
Session info -------------------------------------------------------------------
 setting  value                       
 version  R version 3.3.3 (2017-03-06)
 system   x86_64, darwin16.4.0        
 ui       unknown                     
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       America/Detroit             
 date     2017-03-10                  

Packages -----------------------------------------------------------------------
 package       * version date       source        
 ape             4.1     2017-02-14 CRAN (R 3.3.2)
 BiocGenerics  * 0.20.0  2017-02-09 Bioconductor  
 BiocInstaller * 1.24.0  2017-02-09 Bioconductor  
 Biostrings    * 2.42.1  2017-02-09 Bioconductor  
 devtools        1.12.0  2016-12-05 CRAN (R 3.3.2)
 digest          0.6.12  2017-01-27 CRAN (R 3.3.2)
 htmltools       0.3.5   2016-03-21 CRAN (R 3.3.2)
 htmlwidgets     0.8     2016-11-09 CRAN (R 3.3.2)
 IRanges       * 2.8.1   2017-02-09 Bioconductor  
 lattice         0.20-34 2016-09-06 CRAN (R 3.3.3)
 memoise         1.0.0   2016-01-29 CRAN (R 3.3.2)
 msa           * 1.6.0   2017-03-10 Bioconductor  
 msaR            0.2.0   2017-02-24 CRAN (R 3.3.3)
 nlme            3.1-131 2017-02-06 CRAN (R 3.3.3)
 Rcpp            0.12.9  2017-01-14 CRAN (R 3.3.2)
 S4Vectors     * 0.12.1  2017-02-09 Bioconductor  
 withr           1.0.2   2016-06-20 CRAN (R 3.3.2)
 XVector       * 0.14.0  2017-02-09 Bioconductor  
 zlibbioc        1.20.0  2017-02-09 Bioconductor  

See here A: Combining RangedData objects is broken (IRanges 2.8.1 with R version 3.3.3 RC) for a similar problem -- reinstall your Bioconductor packages.