BioC 3.5: CHECK report for HTqPCR on veracruz2

Package: HTqPCR

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HTqPCR_1.30.0.tar.gz

StartedAt: 2017-10-18 04:52:04 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 04:53:07 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 63.4 seconds

RetCode: 0

Status:  OK

CheckDir: HTqPCR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HTqPCR_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/HTqPCR.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.30.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/HTqPCR.Rcheck/00check.log’
for details.

* installing *source* package ‘HTqPCR’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (HTqPCR)

name	user	system	elapsed
changeCtLayout	0.332	0.008	0.345
clusterCt	0.893	0.017	0.946
filterCategory	0.077	0.003	0.082
filterCtData	0.462	0.005	0.481
limmaCtData	0.273	0.004	0.283
normalizeCtData	0.441	0.013	0.469
plotCVBoxes	0.139	0.004	0.149
plotCtArray	0.158	0.003	0.167
plotCtBoxes	0.077	0.002	0.083
plotCtCard	0.143	0.004	0.155
plotCtCategory	0.692	0.010	0.721
plotCtCor	0.836	0.010	0.864
plotCtDensity	0.030	0.004	0.035
plotCtHeatmap	1.413	0.012	1.475
plotCtHistogram	0.015	0.002	0.018
plotCtOverview	0.241	0.004	0.255
plotCtPCA	0.068	0.002	0.074
plotCtPairs	0.376	0.010	0.398
plotCtReps	0.118	0.004	0.125
plotCtScatter	0.064	0.003	0.070
plotCtVariation	0.430	0.007	0.453
plotGenes	0.057	0.003	0.063
qPCRpros	0.004	0.000	0.005
qPCRraw	0.004	0.001	0.008
qPCRset-class	0.116	0.004	0.122
readCtData	0.234	0.002	0.249
setCategory	0.134	0.002	0.137