How to obtain amino acid context at a given position I'm trying to find the amino acid context around a particular position in a protein (5 aa amino acid window on each side).

I used to have some code that works and then biomaRt stopped working. I think some of these issues would be fixed in later versions of biomaRt, but I would have to install a new version of R, which would require me to install a new version of my OS.

require('biomaRt')
require('Biostrings')
hs_ensembl_mart = 
useMart(biomart="ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl")

gene_names=c('KRAS')
aa_affected_loc=12

biomart_query_results=getBM(attributes=c('hgnc_symbol', 'entrezgene','coding'), 
  filters = 'hgnc_symbol', 
  values = gene_names, 
  mart = hs_ensembl_mart)

preceding_peptide= substr(as.character(translate(DNAString(biomart_query_results[1,'coding']))),aa_affected_loc-5,aa_affected_loc-1)

trailing_peptide= substr(as.character(translate(DNAString(biomart_query_results[1,'coding']))),aa_affected_loc+1,aa_affected_loc+5)


Does anyone have a workaround for this?
It turned out that I needed to reinstall OSX to upgrade my R version and biomaRt install.