Package: ddCt

Version: 1.38.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ddCt.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ddCt_1.38.0.tar.gz

StartedAt: 2019-04-15 23:19:28 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:20:04 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 35.6 seconds

RetCode: 0

Status:  OK

CheckDir: ddCt.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ddCt.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ddCt_1.38.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/ddCt.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ddCt/DESCRIPTION’ ... OK
* this is package ‘ddCt’ version ‘1.38.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ddCt’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
barploterrbar: no visible global function definition for ‘par’
barploterrbar: no visible global function definition for ‘layout’
barploterrbar: no visible global function definition for ‘barplot’
barploterrbar: no visible global function definition for ‘segments’
barploterrbar: no visible global function definition for ‘plot’
ddCtErrBarchart: no visible global function definition for ‘as.formula’
ddCtReport: no visible global function definition for ‘write.table’
na.mad: no visible global function definition for ‘mad’
na.median: no visible global function definition for ‘median’
na.sd: no visible global function definition for ‘sd’
replaceNames: no visible global function definition for ‘na.omit’
ddCtWithEExec,InputFrame: no visible global function definition for
  ‘deriv’
ddCtWithEExec,InputFrame: no visible global function definition for
  ‘as.formula’
elistWrite,ddCtExpression-character: no visible global function
  definition for ‘write.table’
readRawData,QuantStudioReader-character: no visible global function
  definition for ‘read.table’
readRawData,SDMReader-character: no visible global function definition
  for ‘read.table’
readRawData,TSVReader-character: no visible global function definition
  for ‘read.table’
Undefined global functions or variables:
  as.formula barplot deriv layout mad median na.omit par plot
  read.table sd segments write.table
Consider adding
  importFrom("graphics", "barplot", "layout", "par", "plot", "segments")
  importFrom("stats", "as.formula", "deriv", "mad", "median", "na.omit",
             "sd")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘unit.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/ddCt.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL ddCt
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘ddCt’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ddCt)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  1.196   0.060   1.288 

name	user	system	elapsed
InputFrame	0.012	0.000	0.011
InputReader-class	0.000	0.004	0.001
QuantStudioFrame	0.176	0.024	0.201
SDMFrame-class	0.028	0.008	0.065
SDMFrame	0.012	0.000	0.010
barploterrbar	0.008	0.000	0.007
ddCtExpression-class	0.116	0.008	0.123
ddCtExpression-methods	0.112	0.000	0.115
elistWrite-methods	0.048	0.000	0.051
errBarchartParameter-class	0.004	0.000	0.000
getDir	0	0	0
replaceVectorByEquality	0	0	0