Package: HTqPCR

Version: 1.37.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:HTqPCR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings HTqPCR_1.37.0.tar.gz

StartedAt: 2019-04-09 01:15:55 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:16:48 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 52.6 seconds

RetCode: 0

Status:  OK

CheckDir: HTqPCR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:HTqPCR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings HTqPCR_1.37.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/HTqPCR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HTqPCR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTqPCR’ version ‘1.37.0’
* 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 ‘HTqPCR’ can be installed ... OK
* 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
* 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 ... 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/HTqPCR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL HTqPCR
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘HTqPCR’ ...
** using staged installation
** R
** data
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HTqPCR)

name	user	system	elapsed
changeCtLayout	0.148	0.000	0.149
clusterCt	0.064	0.016	0.080
filterCategory	0.047	0.000	0.047
filterCtData	0.403	0.000	0.403
limmaCtData	0.090	0.000	0.101
normalizeCtData	0.369	0.004	0.374
plotCVBoxes	0.163	0.004	0.166
plotCtArray	0.099	0.007	0.680
plotCtBoxes	0.043	0.001	0.043
plotCtCard	0.054	0.000	0.054
plotCtCategory	0.734	0.008	0.742
plotCtCor	0.067	0.000	0.066
plotCtDensity	0.038	0.000	0.037
plotCtHeatmap	1.527	0.004	1.530
plotCtHistogram	0.013	0.000	0.013
plotCtOverview	0.051	0.000	0.052
plotCtPCA	0.022	0.000	0.023
plotCtPairs	0.373	0.003	0.377
plotCtReps	0.086	0.000	0.087
plotCtScatter	0.015	0.000	0.016
plotCtVariation	0.235	0.004	0.238
plotGenes	0.014	0.000	0.014
qPCRpros	0.005	0.000	0.005
qPCRraw	0.005	0.000	0.005
qPCRset-class	0.058	0.000	0.058
readCtData	0.091	0.000	1.245
setCategory	0.04	0.00	0.04