Commit 3d56e9f9 authored by Holger Brandl's avatar Holger Brandl
Browse files

clarified additional arguments

parent 872cbe33
......@@ -163,7 +163,7 @@ replaceNA <- function(x, withValue) { x[is.na(x)] <- withValue; x }
## related: http://cran.r-project.org/web/packages/R.cache/R.cache.pdf
cache_it <- function(expr, cacheName=paste0("cache_", substr(digest(expr), 1,6))){
cache_it <- function(expr, cacheName=paste0("cache_", substr(digest::digest(expr), 1,6))){
cacheFile <- paste0(".", cacheName, ".RData")
if(file.exists(cacheFile)){
......
......@@ -15,7 +15,7 @@ suppressMessages(library(docopt))
# retrieve and parse the command-line arguments
doc <- '
Use knitr to spin R documents
Usage: spin.R [options] <r_script> [<script_args>...]
Usage: spin.R [options] <r_script> [<quoted_script_args>]
Options:
-c Cache results
......@@ -26,6 +26,7 @@ Options:
'
#!docopt(doc, "-w test a b c ")$keep
#docopt(doc, "-w test a b c ")$"-w"
#docopt(doc, "$DGE_HOME/dge_analysis.R \"--undirected --qcutoff 0.05 --minfpkm 2 ..\"")
spin_opts <- docopt(doc)
#print(spin_opts)
......@@ -51,7 +52,7 @@ options(width=150)
#https://groups.google.com/forum/#!topic/knitr/ojcnq5Nm298
## better table css: http://www.stat.ubc.ca/~jenny/STAT545A/topic10_tablesCSS.html
commandArgs <- function(trailingOnly = FALSE){ return(as.character(spin_opts$script_args)) }
commandArgs <- function(trailingOnly = FALSE){ return(as.character(spin_opts$quoted_script_args)) }
#print("trimmed args are")
#print(commandArgs())
#print("end args")
......
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