Nothing
downloadFMA <- function(filename = "fma15command.exe"){
# Downloads program from GitHub
# Only works on Linux
if (!Sys.info()['sysname']=='Linux'){
stop('This function only works on Linux and requires git')
}
windows_dirname <- paste("Z:", gsub('/', '\\\\', tempdir()),
'\\fma\\', sep='')
directory <- paste(tempdir(), '/fma/', sep='')
options(CALIBERfma_command=paste("wine ", directory,
filename, sep=''))
# Set up temporary folders, download Git repositories,
# and move relevant files to tempdir/fma
message('Pulling FMA from GitHub repositories into a temporary folder')
unlink(paste(tempdir(), '/fma', sep=''), recursive = TRUE)
system(paste('cd', tempdir(), '; mkdir fma; cd fma; mkdir lookups;',
'mkdir program; cd lookups; git init;',
'git pull https://github.com/anoopshah/freetext-matching-algorithm-lookups.git;',
'mv * ../; cd ../program; git init;',
'git pull https://github.com/anoopshah/freetext-matching-algorithm.git;',
'mv binaries/* ../'))
# R version of path to FMA lookups
options(CALIBERfma_dir_R = directory)
options(CALIBERfma_dir_win = windows_dirname)
cat('\nFiles downloaded from GitHub to', directory,
'and CALIBERfma options set.\n')
cat('\nCALIBERfma_dir_R =', getOption('CALIBERfma_dir_R'))
cat('\nCALIBERfma_dir_win =', getOption('CALIBERfma_dir_win'))
cat('\nCALIBERfma_command =', getOption('CALIBERfma_command'))
cat('\n\nNow you can use the program by calling doAnalysis()\n')
}
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