BioC 3.3: CHECK report for HTqPCR on oaxaca

Package: HTqPCR

Version: 1.26.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HTqPCR_1.26.0.tar.gz

StartedAt: 2016-10-13 02:45:26 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 02:47:11 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 105.5 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_1.26.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/HTqPCR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.26.0’
* 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 ‘featureData<-’
[,qPCRset: no visible global function definition for ‘featureData’
[,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 ... 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 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-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
HTqPCR-package	2.415	0.026	2.524
cbind	0.076	0.003	0.078
changeCtLayout	0.094	0.002	0.095
clusterCt	0.147	0.008	0.157
filterCategory	0.082	0.001	0.084
filterCtData	0.153	0.007	0.162
heatmapSig	1.051	0.009	1.062
limmaCtData	0.538	0.004	0.543
mannwhitneyCtData	0.875	0.003	0.880
normalizeCtData	0.299	0.013	0.317
plotCVBoxes	0.143	0.004	0.156
plotCtArray	0.117	0.003	0.120
plotCtBoxes	0.046	0.002	0.056
plotCtCard	0.046	0.005	0.053
plotCtCategory	0.594	0.005	0.600
plotCtCor	0.050	0.003	0.053
plotCtDensity	0.035	0.003	0.039
plotCtHeatmap	1.907	0.010	2.231
plotCtHistogram	0.017	0.002	0.020
plotCtOverview	0.096	0.004	0.101
plotCtPCA	0.038	0.003	0.071
plotCtPairs	0.547	0.010	0.560
plotCtRQ	0.261	0.004	0.281
plotCtReps	0.095	0.003	0.099
plotCtScatter	0.024	0.003	0.044
plotCtSignificance	0.310	0.003	0.315
plotCtVariation	0.490	0.007	0.508
plotGenes	0.022	0.002	0.026
qPCRpros	0.006	0.001	0.007
qPCRraw	0.006	0.001	0.007
qPCRset-class	0.061	0.003	0.064
readCtData	0.170	0.002	0.173
setCategory	3.332	0.032	3.370
ttestCtData	0.713	0.002	0.718