R/extern.R

In micropan: Microbial Pan-Genome Analysis

## Non-exported function to gracefully fail when external dependencies are missing.
available.external <- function(what){
  if(what == "hmmer"){
    chr <- NULL
    try(chr <- system('hmmscan -h', intern = TRUE), silent = TRUE)
    if(is.null(chr)){
      stop(paste('hmmer was not found by R.',
                 'Please install hmmer from: http://hmmer.org/download.html',
                 'After installation, re-start R and make sure the hmmer softwares can be run from R by',
                 'the command \'system("hmmscan -h")\'.', sep = '\n'))
      return(FALSE)
    } else {
      return(TRUE)
    }
  } else if(what == "blast+"){
    chr <- NULL
    try(chr <- system('makeblastdb -help', intern = TRUE), silent = TRUE)
    if(is.null(chr)){
      stop(paste('blast+ was not found by R.',
                 'Please install blast+ from: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/',
                 'After installation, re-start R and make sure the blast+ softwares can be run from R by',
                 'the command \'system("makeblastdb -help")\'.', sep = '\n'))
      return(FALSE)
    } else {
      return(TRUE)
    }
  }
}