Well, as obvious from your
sessionInfo() results, you are using R 3.2.4 which is more than two years old. Since Bioconductor binds releases to the latest R version, you only have Bioconductor 3.3, which includes '
msa' version 1.2.1. The
msaConvert() function has been introduced in '
msa' version 1.3.3. In order to use
msaConvert(), you need to install a newer version of R (ideally R 3.5.0 or 3.5.1), otherwise you will not have access to the latest features.