R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(ddCt)
> 
> test_check("ddCt")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
   1.21    0.15    1.35 

R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(ddCt)
> 
> test_check("ddCt")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
   1.40    0.15    1.54 

R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> ################################################################################
> ##
> ## This software is created by Molecular Genom Analysis Group
> ## Department of German Cancer Research Center in Heidelberg
> ##
> ##
> ##  unit.R
> ##  Created on: Oct 23, 2008
> ##      Author: Rudolf Biczok <r.biczok@dkfz-heidelberg.de>
> ##      Description: RUnit test suit for ddCt classes
> ##
> ################################################################################
> 
> pkg <- "ddCt"
> unit.path <- file.path(getwd(), "units")
> 
> unitMode <- function() {
+   if(Sys.getenv("R_DEVELOP_MODE") == "TRUE")
+     return("unit")
+   else
+     return("normal")
+ }
> 
> normalTest <- function() {
+   testFile <- system.file("./extdata/Experiment2.txt", package=pkg)
+   
+   ## Basic SDMFrame
+   sdm <- SDMFrame(testFile)
+   
+   ## ddCt
+   x <- ddCtExpression(sdm,
+                   calibrationSample="Sample3",
+                   housekeepingGenes="Gene2")
+   
+   ## coerece as data frame
+   y1 <- as(x, "data.frame")
+   y2 <- elist(x)
+   stopifnot(all.equal(y1,y2))
+   
+   ## visualization
+   errBarchart(x)
+ }
> 
> 
> ## --- Setup ---
> 
> library(package=pkg, character.only=TRUE)
> 
> # put this in an enclosure so we can return early
> (function() {
+     if(unitMode() != "unit") {
+         normalTest()
+         return()
+     }
+ 
+     if(!require("RUnit", quietly=TRUE)) {
+         stop("cannot run unit tests -- package RUnit is not available")
+     }
+ 
+     ## --- Testing ---
+     cat("------------------- BEGIN UNIT TESTS ----------------------\n\n")
+ 
+     ## --- Setup test suit ---
+     testSuite <- defineTestSuite(name=paste(pkg, "unit testing"), dirs=unit.path)
+     tests <- runTestSuite(testSuite)
+ 
+     ## --- Setup report directory ---
+     pathReport <- file.path(getwd(),"report")
+     if (!file.exists(pathReport)) {
+         dir.create(pathReport)
+     }
+ 
+     ## --- Reporting ---
+     cat("------------------- UNIT TEST SUMMARY ---------------------\n\n")
+ 
+     printTextProtocol(tests, showDetails=FALSE)
+     printTextProtocol(tests, showDetails=FALSE,
+                       fileName=file.path(pathReport, "summary.txt"))
+     printTextProtocol(tests, showDetails=TRUE,
+                       fileName=file.path(pathReport, "summary-detail.txt"))
+     printHTMLProtocol(tests,
+                       fileName=file.path(pathReport, "summary.html"))
+ 
+     errors <- getErrors(tests)
+     if(errors$nFail > 0 | errors$nErr > 0) {
+         warning(paste("\n\nunit testing failed (#unit failures: ", errors$nFail,
+                       ", #R errors: ",  errors$nErr, ")\n\n", sep=""))
+     }
+ 
+     cat("------------------- END OF UNIT TESTING -------------------\n\n")
+ })()
NULL
> 
> proc.time()
   user  system elapsed 
   1.07    0.06    1.14 

R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> ################################################################################
> ##
> ## This software is created by Molecular Genom Analysis Group
> ## Department of German Cancer Research Center in Heidelberg
> ##
> ##
> ##  unit.R
> ##  Created on: Oct 23, 2008
> ##      Author: Rudolf Biczok <r.biczok@dkfz-heidelberg.de>
> ##      Description: RUnit test suit for ddCt classes
> ##
> ################################################################################
> 
> pkg <- "ddCt"
> unit.path <- file.path(getwd(), "units")
> 
> unitMode <- function() {
+   if(Sys.getenv("R_DEVELOP_MODE") == "TRUE")
+     return("unit")
+   else
+     return("normal")
+ }
> 
> normalTest <- function() {
+   testFile <- system.file("./extdata/Experiment2.txt", package=pkg)
+   
+   ## Basic SDMFrame
+   sdm <- SDMFrame(testFile)
+   
+   ## ddCt
+   x <- ddCtExpression(sdm,
+                   calibrationSample="Sample3",
+                   housekeepingGenes="Gene2")
+   
+   ## coerece as data frame
+   y1 <- as(x, "data.frame")
+   y2 <- elist(x)
+   stopifnot(all.equal(y1,y2))
+   
+   ## visualization
+   errBarchart(x)
+ }
> 
> 
> ## --- Setup ---
> 
> library(package=pkg, character.only=TRUE)
> 
> # put this in an enclosure so we can return early
> (function() {
+     if(unitMode() != "unit") {
+         normalTest()
+         return()
+     }
+ 
+     if(!require("RUnit", quietly=TRUE)) {
+         stop("cannot run unit tests -- package RUnit is not available")
+     }
+ 
+     ## --- Testing ---
+     cat("------------------- BEGIN UNIT TESTS ----------------------\n\n")
+ 
+     ## --- Setup test suit ---
+     testSuite <- defineTestSuite(name=paste(pkg, "unit testing"), dirs=unit.path)
+     tests <- runTestSuite(testSuite)
+ 
+     ## --- Setup report directory ---
+     pathReport <- file.path(getwd(),"report")
+     if (!file.exists(pathReport)) {
+         dir.create(pathReport)
+     }
+ 
+     ## --- Reporting ---
+     cat("------------------- UNIT TEST SUMMARY ---------------------\n\n")
+ 
+     printTextProtocol(tests, showDetails=FALSE)
+     printTextProtocol(tests, showDetails=FALSE,
+                       fileName=file.path(pathReport, "summary.txt"))
+     printTextProtocol(tests, showDetails=TRUE,
+                       fileName=file.path(pathReport, "summary-detail.txt"))
+     printHTMLProtocol(tests,
+                       fileName=file.path(pathReport, "summary.html"))
+ 
+     errors <- getErrors(tests)
+     if(errors$nFail > 0 | errors$nErr > 0) {
+         warning(paste("\n\nunit testing failed (#unit failures: ", errors$nFail,
+                       ", #R errors: ",  errors$nErr, ")\n\n", sep=""))
+     }
+ 
+     cat("------------------- END OF UNIT TESTING -------------------\n\n")
+ })()
NULL
> 
> proc.time()
   user  system elapsed 
   1.09    0.07    1.15