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CHECK report for ddCt on merida2

This page was generated on 2018-10-17 08:48:14 -0400 (Wed, 17 Oct 2018).

Package 351/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ddCt 1.36.0
Jitao David Zhang
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/ddCt
Branch: RELEASE_3_7
Last Commit: d642659
Last Changed Date: 2018-04-30 10:35:11 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ddCt
Version: 1.36.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ddCt.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ddCt_1.36.0.tar.gz
StartedAt: 2018-10-16 20:48:40 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:49:21 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 41.2 seconds
RetCode: 0
Status:  OK 
CheckDir: ddCt.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ddCt.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ddCt_1.36.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/ddCt.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ddCt/DESCRIPTION’ ... OK
* this is package ‘ddCt’ version ‘1.36.0’
* 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 sizes of PDF files under ‘inst/doc’ ... 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
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/ddCt.Rcheck/00check.log’
for details.



Installation output

ddCt.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ddCt
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/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)

Tests output

ddCt.Rcheck/tests/unit.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 
  1.171   0.111   1.259 

Example timings

ddCt.Rcheck/ddCt-Ex.timings

nameusersystemelapsed
InputFrame0.0120.0020.014
InputReader-class0.0030.0010.003
QuantStudioFrame0.1820.0330.220
SDMFrame-class0.0390.0060.045
SDMFrame0.0150.0020.017
barploterrbar0.0070.0010.008
ddCtExpression-class0.1230.0030.128
ddCtExpression-methods0.1130.0010.115
elistWrite-methods0.0540.0010.055
errBarchartParameter-class0.0010.0000.001
getDir0.0010.0000.002
replaceVectorByEquality0.0020.0010.002