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CHECK report for ddCt on tokay1

This page was generated on 2019-04-13 11:21:01 -0400 (Sat, 13 Apr 2019).

Package 374/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ddCt 1.38.0
Jitao David Zhang
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/ddCt
Branch: RELEASE_3_8
Last Commit: e42a7c5
Last Changed Date: 2018-10-30 11:41:45 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ddCt
Version: 1.38.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ddCt.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings ddCt_1.38.0.tar.gz
StartedAt: 2019-04-13 01:39:00 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:40:46 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 106.4 seconds
RetCode: 0
Status:  OK  
CheckDir: ddCt.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ddCt.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings ddCt_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/ddCt.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'unit.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/ddCt.Rcheck/00check.log'
for details.



Installation output

ddCt.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/ddCt_1.38.0.tar.gz && rm -rf ddCt.buildbin-libdir && mkdir ddCt.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ddCt.buildbin-libdir ddCt_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL ddCt_1.38.0.zip && rm ddCt_1.38.0.tar.gz ddCt_1.38.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  193k  100  193k    0     0  3129k      0 --:--:-- --:--:-- --:--:-- 3328k

install for i386

* installing *source* package 'ddCt' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ddCt'
    finding HTML links ... done
    InputFrame                              html  
    InputReader-class                       html  
    QuantStudioFrame                        html  
    SDMFrame-class                          html  
    SDMFrame                                html  
    barploterrbar                           html  
    ddCtAbsolute                            html  
    finding level-2 HTML links ... done

    ddCtExpression-class                    html  
    ddCtExpression-methods                  html  
    elistWrite-methods                      html  
    errBarchart-methods                     html  
    errBarchartParameter-class              html  
    getDir                                  html  
    removeNTC-methods                       html  
    replaceVectorByEquality                 html  
    write.htmltable                         html  
    writeSimpleTabCsv                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'ddCt' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ddCt' as ddCt_1.38.0.zip
* DONE (ddCt)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'ddCt' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

ddCt.Rcheck/tests_i386/unit.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 
   0.98    0.03    1.00 

ddCt.Rcheck/tests_x64/unit.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 
   0.82    0.12    0.93 

Example timings

ddCt.Rcheck/examples_i386/ddCt-Ex.timings

nameusersystemelapsed
InputFrame0.020.000.02
InputReader-class000
QuantStudioFrame0.090.010.41
SDMFrame-class0.030.000.03
SDMFrame0.000.020.01
barploterrbar000
ddCtExpression-class0.080.000.08
ddCtExpression-methods0.060.000.06
elistWrite-methods0.030.000.04
errBarchartParameter-class000
getDir000
replaceVectorByEquality000

ddCt.Rcheck/examples_x64/ddCt-Ex.timings

nameusersystemelapsed
InputFrame0.020.000.02
InputReader-class000
QuantStudioFrame0.120.000.13
SDMFrame-class0.020.000.01
SDMFrame000
barploterrbar0.000.020.02
ddCtExpression-class0.080.000.07
ddCtExpression-methods0.060.000.07
elistWrite-methods0.030.000.03
errBarchartParameter-class000
getDir000
replaceVectorByEquality000