inst/testScripts/testAll.R

In HenrikBengtsson/aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

#!/usr/bin/env Rscript

if (interactive()) {
  savehistory()
} else {
  # GLAD v1.12.0 depends on the 'tcltk' package, but that
  # cannot be loaded if there is no display.  A workaround
  # is to fake that the 'tcltk' package is loaded:
  attach(list(), name="package:tcltk")
}
library(aroma.affymetrix)
#source("init.R")

# Use special file cache for testing
options("R.cache::rootPath"="~/.Rcache,scratch")
options("R.cache::touchOnLoad"=TRUE)


args <- commandArgs(asValues=TRUE, excludeReserved=TRUE, excludeEnvVars=TRUE)
print(args)

if (isTRUE(args$devel)) {
  setOption(aromaSettings, "devel/dropRootPathTags", TRUE)
}
print(getOption(aromaSettings, "devel/dropRootPathTags"))


paths <- c()
allPaths <- c("testScripts/replication/chipTypes", 
              "testScripts/system/chipTypes")
for (path in allPaths) {
  path <- Arguments$getReadablePath(path, mustExist=TRUE)
  paths0 <- list.files(path=path, full.names=TRUE)
  paths <- c(paths, paths0)
}

..pathnames <- lapply(paths, FUN=list.files, pattern="[.]R$", full.names=TRUE)
names(..pathnames) <- basename(paths)
#..pathnames <- ..pathnames[names(..pathnames)]

..chipTypes <- c("Mapping10K_Xba142",
                 "Test3",
                 "HG-U133_Plus_2",
                 "Mapping50K_Hind240",
                 "Hs_PromPR_v02",
                 "Mapping250K_Nsp",
                 "Mapping250K_Sty",
                 "HuEx-1_0-st-v2",
                 "GenomeWideSNP_5",
                 "GenomeWideSNP_6",
                 "Cytogenetics_Array",
                 "MOUSEDIVm520650")


if (!is.null(args$chipTypes)) {
  cat("User-specified chip types:\n")
  ..chipTypes <- trim(unlist(strsplit(args$chipTypes, split="")))
  print(..chipTypes)
}

if (isTRUE(args$reverse)) {
  cat("Reversing chip types:\n")
  ..chipTypes <- rev(..chipTypes)
  print(..chipTypes)
}

if (isTRUE(args$shuffle)) {
  cat("Reshuffling chip types:\n")
  ..chipTypes <- sample(..chipTypes)
  print(..chipTypes)
}

cat("Processing chip types:\n")
print(..chipTypes)


for (..chipType in ..chipTypes) {
  keep <- (names(..pathnames) == ..chipType)
  ..pathnamesT <- unlist(..pathnames[keep], use.names=FALSE)
  cat("PATHNAMES CHIPTYPE: \n")
  print(..pathnamesT)
  for (pathname in ..pathnamesT) {
    if (regexpr("hetero", pathname) != -1)
      next
    if (regexpr("expectile", pathname) != -1)
      next

    cat("** PATHNAME: ", pathname, "\n", sep="")
    tryCatch({
      source(pathname, echo=TRUE)
      cat("** PATHNAME DONE: ", pathname, "\n", sep="")
    }, error = function(ex) {
      cat("************************************************\n")
      cat("** ", rep(c(" ER", "ROR "), times=6), " **\n", sep="")
      print(ex)
      print(sessionInfo())
      cat("************************************************\n")
      cat("** PATHNAME FAILED: ", pathname, "\n", sep="")
    })
    
    rm(list=setdiff(ls(), c("..chipType", "..chipTypes", 
                    "pathname", "..pathnames", "..pathnamesT")))
    gc()
  }
}