Package: HTqPCR

Version: 1.34.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HTqPCR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings HTqPCR_1.34.0.tar.gz

StartedAt: 2018-10-17 02:42:31 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 02:43:55 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 84.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: HTqPCR.Rcheck

Warnings: 1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HTqPCR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings HTqPCR_1.34.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/HTqPCR.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HTqPCR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HTqPCR' version '1.34.0'
* 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 whether package 'HTqPCR' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpkbut7Y/R.INSTALL187071b36334/HTqPCR/man/limmaCtData.Rd:29: file link 'duplicateCorrelation' in package 'limma' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/HTqPCR.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'Biobase' 'limma' 'RColorBrewer'
A package should be listed in only one of these fields.
* 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
heatmapSig: warning in heatmap.2(data, trace = "none", density.info =
  "none", col = col, distfun = d, breaks = b, mar = mar, ...): partial
  argument match of 'mar' to 'margins'
limmaCtData: warning in topTable(fit2, sort = "none", n = nrow(fit2)):
  partial argument match of 'n' to 'number'
limmaCtData: warning in topTable(fit2, sort = "none", n = nrow(fit2)):
  partial argument match of 'sort' to 'sort.by'
plotCtCor: warning in heatmap.2(x, col = col, breaks = b, scale =
  "none", dendrogram = "row", trace = "none", main = main, density.info
  = "none", mar = mar, ...): partial argument match of 'mar' to
  'margins'
plotCtHeatmap: warning in heatmap.2(data, trace = "none", density.info
  = "none", main = main, col = col, distfun = d, breaks = breaks, mar =
  mar, ...): partial argument match of 'mar' to 'margins'
plotCtOverview: warning in plotCI(x = x.pos + i - 1, y = M[i, ], uiw =
  SD[i, ], add = TRUE, gap = 0, pch = 20, xpd = TRUE, sfra = 0.001):
  partial argument match of 'sfra' to 'sfrac'
plotCtOverview: warning in plotCI(x = x.pos + i - 1, y = M[i, ], uiw =
  SD.ratio[i, ], add = TRUE, gap = 0, pch = 20, xpd = TRUE, sfra =
  0.001): partial argument match of 'sfra' to 'sfrac'
.readCtBioMark: no visible global function definition for 'read.csv'
.readCtCFX: no visible global function definition for 'read.csv'
.readCtOpenArray: no visible global function definition for 'read.csv'
cbind.qPCRset: no visible global function definition for 'phenoData<-'
cbind.qPCRset: no visible global function definition for
  'AnnotatedDataFrame'
cbind.qPCRset: no visible global function definition for 'pData'
cbind.qPCRset: no visible global function definition for
  'capture.output'
changeCtLayout: no visible global function definition for
  'featureData<-'
changeCtLayout: no visible global function definition for 'featureData'
changeCtLayout: no visible global function definition for 'phenoData<-'
changeCtLayout: no visible global function definition for
  'capture.output'
filterCategory: no visible global function definition for
  'capture.output'
filterCtData: no visible binding for global variable 'IQR'
filterCtData: no visible global function definition for
  'capture.output'
mannwhitneyCtData : <anonymous>: no visible global function definition
  for 'wilcox.test'
normalizeCtData: no visible global function definition for
  'capture.output'
rbind.qPCRset: no visible global function definition for
  'featureData<-'
rbind.qPCRset: no visible global function definition for
  'AnnotatedDataFrame'
rbind.qPCRset: no visible global function definition for 'fData'
rbind.qPCRset: no visible global function definition for
  'capture.output'
readCtData: no visible global function definition for
  'AnnotatedDataFrame'
readCtData: no visible global function definition for 'capture.output'
setCategory: no visible global function definition for 'capture.output'
[,qPCRset: no visible global function definition for 'phenoData<-'
[,qPCRset: no visible global function definition for 'phenoData'
exprs,qPCRset: no visible global function definition for
  'assayDataElement'
exprs<-,qPCRset-ANY: no visible global function definition for
  'assayDataElementReplace'
featureCategory,qPCRset: no visible global function definition for
  'assayDataElement'
featureCategory<-,qPCRset: no visible global function definition for
  'assayDataElementReplace'
featureClass,qPCRset: no visible global function definition for 'fData'
featureClass<-,qPCRset: no visible global function definition for
  'fData'
featureClass<-,qPCRset: no visible global function definition for
  'fData<-'
featureNames,qPCRset: no visible global function definition for 'fData'
featureNames<-,qPCRset-character: no visible global function definition
  for 'fData'
featureNames<-,qPCRset-character: no visible global function definition
  for 'fData<-'
featurePos,qPCRset: no visible global function definition for 'fData'
featurePos<-,qPCRset: no visible global function definition for 'fData'
featurePos<-,qPCRset: no visible global function definition for
  'fData<-'
featureType,qPCRset: no visible global function definition for 'fData'
featureType<-,qPCRset: no visible global function definition for
  'fData'
featureType<-,qPCRset: no visible global function definition for
  'fData<-'
flag,qPCRset: no visible global function definition for
  'assayDataElement'
flag<-,qPCRset: no visible global function definition for
  'assayDataElementReplace'
Undefined global functions or variables:
  AnnotatedDataFrame IQR assayDataElement assayDataElementReplace
  capture.output fData fData<- featureData featureData<- pData
  phenoData phenoData<- read.csv wilcox.test
Consider adding
  importFrom("stats", "IQR", "wilcox.test")
  importFrom("utils", "capture.output", "read.csv")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: cbind.Rd:35-36: Dropping empty section \examples
prepare_Rd: heatmapSig.Rd:31-32: Dropping empty section \examples
prepare_Rd: mannwhitneyCtData.Rd:52-62: Dropping empty section \examples
prepare_Rd: plotCtRQ.Rd:46-48: Dropping empty section \examples
prepare_Rd: plotCtSignificance.Rd:46-47: Dropping empty section \examples
prepare_Rd: ttestCtData.Rd:49-50: Dropping empty section \examples
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 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 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/HTqPCR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/HTqPCR_1.34.0.tar.gz && rm -rf HTqPCR.buildbin-libdir && mkdir HTqPCR.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HTqPCR.buildbin-libdir HTqPCR_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL HTqPCR_1.34.0.zip && rm HTqPCR_1.34.0.tar.gz HTqPCR_1.34.0.zip
###
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install for i386

* installing *source* package 'HTqPCR' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'HTqPCR'
    finding HTML links ... done
    HTqPCR-package                          html  
    cbind                                   html  
    changeCtLayout                          html  
    clusterCt                               html  
    filterCategory                          html  
    filterCtData                            html  
    heatmapSig                              html  
    limmaCtData                             html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpkbut7Y/R.INSTALL187071b36334/HTqPCR/man/limmaCtData.Rd:29: file link 'duplicateCorrelation' in package 'limma' does not exist and so has been treated as a topic
    mannwhitneyCtData                       html  
    normalizeCtData                         html  
    plotCVBoxes                             html  
    plotCtArray                             html  
    plotCtBoxes                             html  
    plotCtCard                              html  
    plotCtCategory                          html  
    plotCtCor                               html  
    plotCtDensity                           html  
    plotCtHeatmap                           html  
    plotCtHistogram                         html  
    plotCtOverview                          html  
    plotCtPCA                               html  
    plotCtPairs                             html  
    plotCtRQ                                html  
    plotCtReps                              html  
    plotCtScatter                           html  
    plotCtSignificance                      html  
    plotCtVariation                         html  
    plotGenes                               html  
    qPCRpros                                html  
    qPCRraw                                 html  
    qPCRset-class                           html  
    finding level-2 HTML links ... done

    readCtData                              html  
    setCategory                             html  
    ttestCtData                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'HTqPCR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HTqPCR' as HTqPCR_1.34.0.zip
* DONE (HTqPCR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'HTqPCR' successfully unpacked and MD5 sums checked
In R CMD INSTALL