R version 4.5.0 RC (2025-04-04 r88112 ucrt) -- "How About a Twenty-Six"
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> library("aroma.apd")
Loading required package: affxparser
aroma.apd v0.7.1 successfully loaded. See ?aroma.apd for help.
> library("R.utils") # Arguments
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.8.2 (2022-06-13 22:00:14 UTC) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.27.0 (2024-11-01 18:00:02 UTC) successfully loaded. See ?R.oo for help.

Attaching package: 'R.oo'

The following object is masked from 'package:R.methodsS3':

    throw

The following objects are masked from 'package:methods':

    getClasses, getMethods

The following objects are masked from 'package:base':

    attach, detach, load, save

R.utils v2.13.0 (2025-02-24 21:20:02 UTC) successfully loaded. See ?R.utils for help.

Attaching package: 'R.utils'

The following object is masked from 'package:affxparser':

    findFiles

The following object is masked from 'package:utils':

    timestamp

The following objects are masked from 'package:base':

    cat, commandArgs, getOption, isOpen, nullfile, parse, use, warnings

> 
> verbose <- Arguments$getVerbose(TRUE)
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # 1. Scan for existing CEL files
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # a) Scan current directory for CEL files
> files <- list.files(pattern="[.](cel|CEL)$")
> files <- files[!file.info(files)$isdir]
> 
> if (length(files) > 0 && require("affxparser")) {
+   # b) Corresponding APD filenames
+   celNames <- files
+   apdNames <- gsub(pattern, ".apd", files)
+ 
+   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+   # 1. Copy the probe intensities from a CEL to an APD file
+   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+   for (kk in 1) {
+     verbose && enter(verbose, "Reading CEL file #", kk)
+     cel <- readCel(celNames[kk])
+     verbose && exit(verbose)
+ 
+     if (!file.exists(apdNames[kk])) {
+       verbose && enter(verbose, "Creating APD file #", kk)
+       chipType <- cel$header$chiptype
+       writeApd(apdNames[kk], data=cel$intensities, chipType=chipType)
+       verbose && exit(verbose)
+     }
+ 
+     verbose && enter(verbose, "Verifying APD file #", kk)
+     apd <- readApd(apdNames[kk])
+     verbose && exit(verbose)
+     stopifnot(identical(apd$intensities, cel$intensities))
+   }
+ 
+ 
+   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+   # 2. Read a subset of the units
+   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+   units <- c(1, 20:205)
+   cel <- readCelUnits(celNames[1], units=units)
+   apd <- readApdUnits(apdNames[1], units=units)
+   stopifnot(identical(apd, cel))
+ 
+ 
+   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+   # 3. The same, but stratified on PMs and MMs
+   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+   apd <- readApdUnits(apdNames[1], units=units, stratifyBy="pmmm",
+                                                 addDimnames=TRUE)
+ } # if (length(files) > 0)
> 
> proc.time()
   user  system elapsed 
   0.18    0.07    0.25