I am trying to run use DESeqDataSetFromHTSeq to generate the count matrix, but I get the error that this function is not found.  

This usually means that you haven't loaded the package that contains the function. But using the Bioconductor code search, and looking at the pdf help for both DESeq and DESeq2 indicates that this function doesn't actually exist in any Bioconductor package.

Also please note that it would have been helpful for you to say what package you are attempting to use. And using a tag of 'software error' is not useful, because that's not inherently meaningful and almost surely inaccurate.