BioC 3.1: CHECK report for HTqPCR on petty

Package: HTqPCR

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HTqPCR_1.22.0.tar.gz

StartedAt: 2015-10-08 23:42:58 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:44:42 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 104.3 seconds

RetCode: 0

Status:  OK

CheckDir: HTqPCR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HTqPCR_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/HTqPCR.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.22.0’
* 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 ... [6s/7s] 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'
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’
changeCtLayout: no visible global function definition for
  ‘featureData<-’
changeCtLayout: no visible global function definition for ‘featureData’
changeCtLayout: no visible global function definition for ‘phenoData<-’
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’
readCtData: no visible global function definition for
  ‘AnnotatedDataFrame’
[,qPCRset : .local: no visible global function definition for
  ‘featureData<-’
[,qPCRset : .local: no visible global function definition for
  ‘featureData’
[,qPCRset : .local: no visible global function definition for
  ‘phenoData<-’
[,qPCRset : .local: 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 : .local: no visible global function
  definition for ‘assayDataElementReplace’
featureClass,qPCRset: no visible global function definition for ‘fData’
featureClass<-,qPCRset : .local: no visible global function definition
  for ‘fData’
featureClass<-,qPCRset : .local: 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 : .local: no visible global function definition
  for ‘fData’
featurePos<-,qPCRset : .local: no visible global function definition
  for ‘fData<-’
featureType,qPCRset: no visible global function definition for ‘fData’
featureType<-,qPCRset : .local: no visible global function definition
  for ‘fData’
featureType<-,qPCRset : .local: no visible global function definition
  for ‘fData<-’
flag,qPCRset: no visible global function definition for
  ‘assayDataElement’
flag<-,qPCRset : .local: no visible global function definition for
  ‘assayDataElementReplace’
* 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 ... [24s/27s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
setCategory 5.176  0.034   5.218
* 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-3.1-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	3.121	0.033	3.279
cbind	0.124	0.004	0.129
changeCtLayout	0.171	0.002	0.172
clusterCt	0.244	0.012	1.546
filterCategory	0.121	0.001	0.123
filterCtData	0.209	0.015	0.225
heatmapSig	1.377	0.008	1.431
limmaCtData	0.773	0.006	0.780
mannwhitneyCtData	1.413	0.004	1.418
normalizeCtData	0.424	0.017	0.863
plotCVBoxes	0.214	0.004	0.277
plotCtArray	0.116	0.003	0.186
plotCtBoxes	0.060	0.003	0.167
plotCtCard	0.076	0.005	0.149
plotCtCategory	0.943	0.009	1.165
plotCtCor	0.061	0.002	0.064
plotCtDensity	0.046	0.003	0.059
plotCtHeatmap	2.537	0.015	2.971
plotCtHistogram	0.023	0.002	0.047
plotCtOverview	0.142	0.005	0.148
plotCtPCA	0.051	0.003	0.055
plotCtPairs	0.730	0.010	0.753
plotCtRQ	0.415	0.005	0.423
plotCtReps	0.138	0.005	0.143
plotCtScatter	0.032	0.003	0.042
plotCtSignificance	0.491	0.005	0.496
plotCtVariation	0.749	0.012	0.768
plotGenes	0.035	0.003	0.042
qPCRpros	0.007	0.000	0.008
qPCRraw	0.007	0.000	0.007
qPCRset-class	0.103	0.004	0.108
readCtData	0.194	0.003	0.198
setCategory	5.176	0.034	5.218
ttestCtData	0.997	0.002	1.000